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2.1. Background & purpose The recent introduction of new technical innovations such as CT perfusion (CTP) and dual energy CT (DECT) increases the diagnostic abilities of CT for imaging of the head and neck (H&N). The aim of this work was to evaluate the role of CTP and DECT in head and neck imaging. The first part tests whether CTP can differentiate between malignant H&N tumors and surrounding muscle, and discusses the impact of arterial input selection and tumor region of interest (ROI) on CTP of H&N cancer. The second part of the study evaluates radiation dose and image quality of DECT of the H&N. Finally the use of DE derived weighted averaging to improve lesion delineation and image quality is discussed. 2.2. Patients and methods CT perfusion Retrospective analysis of CTP was done for a total number of 55 cases of H&N tumors. Perfusion parameters were calculated for 33 cases of squamous cell carcinoma (SCC) and compared to those of muscles. CTP parameters of 50 cases of H&N tumors calculated using different arterial input functions were compared. CTP was calculated for 28 SCC cases using the single dynamic CT section that shows maximal tumor dimension compared to using average values obtained from all tumor-containing dynamic CT sections. Dual energy CT of head and neck This prospective part of the study was further divided into 2 parts. In the first part 32 consecutive patients underwent DECT of the H&N and were compared to a standard single energy CT (SE) control group. Radiation doses were compared. Weighted-average images from raw data of the 2 DE tubes (weighting factor 0.3 from 80 kVp and 0.7 from 140 KVp) were compared to SE images. Image noise was compared at 5 anatomic levels. Two blinded readers compared subjective overall image quality on a 5-point grading scale. In the second part 35 proved SCC cases underwent DECT of the neck. Pure 140 kVp and 80 kVp image datasets as well as weighted-average images from raw data of the 2 DE tubes at weighting factors 0.3, 0.6, 0.8 (30%, 60% and 80% from 80 kVp raw data respectively) were reconstructed. Objective image noise, contrast to noise ratio (CNR) and subjective image quality were compared between the 5 image datasets. Results CT perfusion Tumor perfusion parameters were significantly higher than those of muscle (p <0.05). Significant high correlation with no significant differences between the means (p >0.05) were observed between perfusion parameters obtained using internal carotid artery (ICA) versus external carotid artery (ECA) and ipsilateral versus contralateral ICA. High correlation was observed between perfusion parameters calculated using one section with maximal tumor dimension and the average of multiple sections. Differences between the means were non significant, p values>0.05. The 95% limits of agreement between repeated measurements using average of multiple sections were slightly narrower for blood volume and permeability than those of repeated measurements using one section. Dual energy CT of head and neck CTDIvol was 12% lower with DE than SECT (p<0.0001). There were no significant differences in objective noise between DECT and SECT at any of the anatomic levels (p >0.05). There were no significant differences between DE- and SECT in attenuation measurements, all p values >0.05. No significant differences in subjective image quality scores were observed between DE- and SECT at any of the 5 anatomic levels (p >0.05). At weighting factor 0.6 the lesion CNR was significantly higher than at weighting factor 0.3 and at pure 140 kVp image dataset (p< 0.0001); while non significantly lower than at weighting factor 0.8 and pure 80 kVp (p=1.00). The 0.6 weighting factor was rated the best at subjective image quality and lesion delineation. 2.4. Conclusion In conclusion; this study demonstrated the ability of CTP to differentiate SCC from surrounding muscle tissue. The choice of arterial input selection has no significant impact on quantitative CTP of H&N tumors. CTP of SCC calculated from one section with maximal tumor dimensions and the average values from multiple sections are not significantly different. The second part of the study showed that DE scanning can be routinely used for H&N imaging; preserving high diagnostic image quality even when the radiation dose was lowered by 12%. Average weighting of DE raw data, with a weighting factor 0.6, results in significant improvement in both tumor delineation and image quality.
This study comprises a survey on ecology, morphology and taxonomy of parasitic fungi infecting Pteridophytes and Orchidaceae found by the author on several field trips to Western Panama as part of the project plant parasitic micro-fungi of Western Panama (ppMP). In Panama, approximately 9500 species of vascular plants are found. Of these, Orchidaceae are with ca. 1150 (ca. 12%) species by far the most speciose family. The Pteridophytes in Panama comprise ca. 940 species in 31 families. Most fungal pathogens on Orchidaceae in tropical regions were described from plants in culture or from material intercepted at borders by plant quarantine services and not from their natural habitats. Therefore, little is known about distribution and ecology of these pathogens in their natural range. The author determined and classified several hundred Orchidaceae-species and Pteridophytes at the sites selected in the context of the project. This work facilitated the identification of many host plants (at least to genus-level) even in sterile condition in the field. About 65 species of Pucciniales are known to infest Orchidaceae and ca. 38% of them are described from tropical America. All available types of Pucciniales on Orchidaceae in tropical America were studied and compared with 91 specimens of rust fungi on orchids collected by the author in Panama. Several hundred additional specimens housed in the BPI, almost all intercepted from plant quarantine services, were used for comparison. As result of this work, it is suggested to combine Uromyces stenorrhynchi Henn. to Sphenospora and, as this is the oldest epithet, to synonymize S. kevorkianii Linder, S. mera Cumm. and S. saphena Cumm. with it. Further, it could be demonstrated that Uredo aurantiaca Montemartini, U. cyrtopodii Syd. & P. Syd., U. epidendri Henn., U. guacae Mayor, U. gynandrearum Corda, U. lynchii (Berk.) Plowr., U. neopustulata Cumm. (≡U. pustulata Henn.), U. nigropuncta Henn., U. oncidii Henn., U. ornithidii F. Kern., Cif. & Thurst., and presumably U. scabies Cke., are anamorphs of this variable species. U. gynandrearum is the oldest anamorph-name for all these taxa. Therefore, it can be established that this rust infects more than 80 species of Orchidaceae in three subfamilies. In total, the anamorph of this species was collected by the author on 17 different species of Orchidaceae in Panama which, apart from one species, are all new hosts to science. The molecular data obtained by the author confirm this view, although more data, especially from material from the whole range of distribution of U. gynandrearum, are necessary. Puccinia spiranthicola Cumm. was found to be a synonym of P. cinnamomea Diet. & Holw. and was found by the author on three different Orchidaceae in two subfamilies. Uredo pleurothallidis Keissl. is now considered a synonym of U. wittmackiana Henn. and the latter as the anamorph of Puccinia oncidii Cumm. In the anamorph genus Uredo, a new species was found infecting at least five different species of Sobralia and Elleanthus (Sobraliinae) at different localities. Molecular data indicate it to be related to the currently polyphyletic Phakopsoraceae. For the rusts with suprastomatal sori on Orchidaceae, now separated from Hemileia and placed in the genus Desmosorus (nom. inval.), the current concept with only one taxon is rejected and the establishment of three subspecies is suggested. The complicated taxonomy is discussed and makes it necessary to validate the genus-name and make a new combination. Another Hemileia-anamorph species was found by the author and is considered to be new to science. This is the first species of this alliance in America on Orchidaceae. Molecular data obtained by the author confirm the separation of Desmosorus from Hemileia and the position of the new species. For rusts on Pteridophytes, a new species of Milesia, (teleomorph: Milesina) and a new anamorphic species of Uredinopsis was found, both on hosts hitherto not known. In Calidion, the presumable anamorph-genus of Uncol, the species C. cf. cenicafeae Salazar & Buriticá was found on several new hosts. Further, the teleomorph was found. Morphologically, this teleomorph did not agree with the description of Uncol by the author of the genus, although the anamorph characteristics left no doubt that it is Calidion. Apparently, the description of Uncol is inadequate, but cannot be improved, as the type is unavailable. Molecular data obtained by the author show this species to be closest to Desmosorus. For Uredo superficialis Speg., the anamorph of Desmella, nine new hosts in eight different fern families were found by the author and the collaborators of the ppMP-project. Ecological data indicate that this species includes different host specific races, which, however could not be distinguished morphologically. For all these rusts, a thorough discussion of the ecology in their habitats is given. In total, 21 LSU rDNA sequences from 6 different rust species on Orchidaceae and Pteridophytes were obtained and analyzed with the Maximum Parsimony and Minimum Evolution method. Here, the position of several groups could be confirmed, and some anamorphs could be assigned to different teleomorphic relationships. Within the Ascomycota and their anamorphs, several hitherto unknown species and species not known from these hosts or not known from Panama were found and analyzed. On Orchidaceae, the following fungi belonging to the Ascomycota are described, illustrated and discussed: In the Phyllachorales, a hitherto not known Phyllachora sp. was found on Oncidium warszewiczii Rchb. f. and was compared with the other species of this order currently known from Orchidaceae. In the Asterinaceae s. l. Lembosia cf. epidendri Meir. Silva & O. R. Pereia was found on Maxillaria crassifolia (Lindl.) Rchb. f., which is a new host and new host alliance for this fungus hitherto only known from Brazil. The fungus is described and compared with all species of Asterinaceae currently known on Orchidaceae. In the Meliolaceae, Meliola orchidacearum Cif. was found on Camaridium biolleyi (Schltr.) Schltr. and an Epidendrum sp. which are new hosts and new host alliances of this fungus which was hitherto only known from the Caribbean Islands. It is described, illustrated and compared with the type. In the Glomerellaceae, Glomerella cingulata and its anamorph Colletotrichum gloeosporioides were found on several hosts. The species is illustrated, described and compared with data from literature. In the anamorphic Mycosphaerellaceae, Pseudocercospora odontoglossii (Prill. & Delacr.) U. Braun, a species currently only known from culture, was found on the new host Pleurothallis imraei Lindl. It is illustrated, described and compared with data from literature. On ferns, the following other fungi are described, illustrated and discussed: A conspicuous undescribed form of Polycyclus was found by the author on Elaphoglossum ciliatum (C. Presl.) T. Moore (Dryopteridaceae) and Serpocaulon loriceum (L.) A. R. Sm. (Polypodiaceae). A conspectus of Parmulariaceae infecting ferns is given and demonstrated that Polycyclina should be synonymized under Polycyclus. Summing up, it can be assessed, especially for the Pucciniales, that the most speciose plant family in Panama carries remarkable few species of specific parasites, and that many of them seem to be distributed over a wide range of species which often are not closely related. One reason amongst others seems to be that parasites need a minimum density of host plants in a habitat to survive. As orchid species often occur with only few (and often small) individual plants at a given locality, the probability for a specific pathogen to infect a plant gets too low, hence high diversity by low abundance of hosts might be an impediment for specific pathogens. In this case, unspecific parasites, or such which are infecting larger alliances, are in advantage. Other reasons could be specific traits of orchids, like succulence and mycotrophy which might hamper fungal infections.
Forty two samples of the Late Eocene Kiliran oil shale, Central Sumatra Basin, Indonesia were collected from a 102 m long drill core. The oil shale core represents the deposition time of about 240.000 years. Palynofacies and geochemical analyses have been carried out to reconstruct the paleoenvironmental conditions and paleoecology during deposition of the oil shale. Amorphous organic matter (AOM) is very abundant (>76%). B. braunii palynomorphs are present (3-16%) as the only autochtonous structured organic matter and generally more abundant in the middle part of the profile. The stable carbon isotopic composition of bulk organic matter (13C) varies from -27.0 to -30.5‰ and is generally more depleted in the middle part of the profile. The ratio of total organic carbon to sulfur (TOC/S), used as salinity indicator, ranges from 2.5 to 15.8 and shows variations along the profile. Slightly less saline environments are observed in the middle part of the profile. Fungal remains are generally present only in this part with a distinct peak of abundance. The presence of fungal remains is regarded as an indication for a relatively warmer climate during deposition of the middle part of the profile. The warmer climate is thought to influence the establishment of a thermocline, limiting the supply of recycled nutrients to epilimnion. Consequently, the primary productivity in the Kiliran lake decreased during deposition of the middle part of the profile as indicated by the relatively depleted 13C values and the blooming of B. braunii. The chemocline was also shoaling during the deposition according to the higher abundance of total isorenieratane and its derivatives originated from green sulfur bacteria dwelling in the photic zone euxinia. The warmer climate is also thought to influence the slightly decrease of water salinity during deposition of the middle part of the profile. The occurrence of B. braunii in Kiliran lake is also recognized from organic geochemical data. The distribution of n-alkanes is characterized by the unusual high amount of C27 n-alkane relative to the other long-chain n-alkanes. The concentrations of C27 n-alkane vary from 30.1 to 393.7 μg/g TOC and are generally in parallel with the abundances of B. braunii palynomorphs along the profile. The 13C values of this compound are about -31‰ and up to 2‰ enriched relative to those of the adjacent long-chain n-alkanes. B. braunii race A can thus be regarded as the significant biological source of the C27 n-alkane. Lower amounts of lycopane are observed in many oil shale samples (0 to 54.7 μg/g TOC). The 13C value of this compound is 17.2‰. This strong enrichment of 13C suggests that the lycopane was derived from B. braunii race L. The concentrations of lycopane develop generally in opposite with those of C27 μalkane. It is likely that both B. braunii races bloomed in alternation in the lake, probably due to changes on specific water chemistry. Norneohop-13(18)-ene and neohop-13(18)-ene derived from methanotrophic bacteria are the dominant hopanoid hydrocarbons. The sum of their concentrations varies from 40.6 to 360.0 μg/g TOC. The 13C of these compounds are extremely depleted (-45.2 to -50.2‰). The occurrence of abundant bacteria including methanotrophic bacteria was responsible for the recycling of carbon below the chemocline of the lake. The effect of the recycling of carbon is observed by the presence of a concomitant depletion (about 7-9‰) in 13C of some specific biomarkers derived from organisms dwelling in the whole phototrophic zone. 4-Methylsterane and 4-methyldiasterene homologues occur in the oil shale as the predominant biomarkers. The sum of the concentrations of all homologues are about 40.3-1,009.2 μg/g TOC with generally higher values in the uppermost and lower parts of the profile. Calcium (Ca) accounts as the predominant element in the oil shale, ranging from 5.0 to 16.7%. This element shows generally parallel variation with the 4-methylsterane and 4-methyldiasterene homologues along the profile. This suggests that these compounds were derived from biological sources favoring more alkaline and more trophic environments. On the other hand, these compounds were less abundant in the middle part of the profile which is consistent with less alkaline and less trophic environments promoting B. braunii to bloom. Alternation between Dinoflagellates and B. braunii in ancient lacustrine environments due to water chemistry changes have been known from previous studies. In the present case, distinct alternation between B. braunii abundances and concentrations of 4-methylsterane and 4-methyldiasterene homologues along the studied oil shale profile suggest a hypothesis that these compounds were derived from freshwater Dinoflagellates although dinosterane is not present in the sediment extracts. Water alkalinity and trophic level changes were most likely responsible for the alternation of Dinoflagellates and B. braunii blooming.
Introduction: Evidence from a number of open-label, uncontrolled studies has suggested that rituximab may benefit patients with autoimmune diseases who are refractory to standard-of-care. The objective of this study was to evaluate the safety and clinical outcomes of rituximab in several standard-of-care-refractory autoimmune diseases (within rheumatology, nephrology, dermatology and neurology) other than rheumatoid arthritis or non-Hodgkin's lymphoma in a real-life clinical setting.
Methods: Patients who received rituximab having shown an inadequate response to standard-of-care had their safety and clinical outcomes data retrospectively analysed as part of the German Registry of Autoimmune Diseases. The main outcome measures were safety and clinical response, as judged at the discretion of the investigators.
Results: A total of 370 patients (299 patient-years) with various autoimmune diseases (23.0% with systemic lupus erythematosus, 15.7% antineutrophil cytoplasmic antibody-associated granulomatous vasculitides, 15.1% multiple sclerosis and 10.0% pemphigus) from 42 centres received a mean dose of 2,440 mg of rituximab over a median (range) of 194 (180 to 1,407) days. The overall rate of serious infections was 5.3 per 100 patient-years during rituximab therapy. Opportunistic infections were infrequent across the whole study population, and mostly occurred in patients with systemic lupus erythematosus. There were 11 deaths (3.0% of patients) after rituximab treatment (mean 11.6 months after first infusion, range 0.8 to 31.3 months), with most of the deaths caused by infections. Overall (n = 293), 13.3% of patients showed no response, 45.1% showed a partial response and 41.6% showed a complete response. Responses were also reflected by reduced use of glucocorticoids and various immunosuppressives during rituximab therapy and follow-up compared with before rituximab. Rituximab generally had a positive effect on patient well-being (physician's visual analogue scale; mean improvement from baseline of 12.1 mm).
Conclusions: Data from this registry indicate that rituximab is a commonly employed, well-tolerated therapy with potential beneficial effects in standard of care-refractory autoimmune diseases, and support the results from other open-label, uncontrolled studies.
Background: The zinc finger transcription factor Egr-1 (Early growth response 1) is central to several growth factors and represents an important activator of target genes not only involved in physiological processes like embryogenesis and neonatal development, but also in a variety of pathophysiological processes, for example atherosclerosis or cancer. Current options to investigate its transcription and activation in vivo are end-point measurements that do not provide insights into dynamic changes in the living organism. Results: We developed a transgenic mouse (Egr-1-luc) in which the luciferase reporter gene is under the control of the murine Egr-1 promoter providing a versatile tool to study the time course of Egr-1 activation in vivo. In neonatal mice, bioluminescence imaging revealed a high Egr-1 promoter activity reaching basal levels three weeks after birth with activity at snout, ears and paws. Using a model of partial hepatectomy we could show that Egr-1 promoter activity and Egr-1 mRNA levels were increased in the regenerating liver. In a model of wound healing, we demonstrated that Egr-1 promoter activity was upregulated at the site of injury. Conclusion: Taken together, we have developed a transgenic mouse model that allows real time in vivo imaging of the Egr-1 promoter activity. The ability to monitor and quantify Egr-1 activity in the living organism may facilitate a better understanding of Egr-1 function in vivo. Additional File 1: BLI of adult Egr-1-luc mice with opened body cavity. Transgenic Egr-1-luc mice (one month old) received 6 mg luciferin in 100 μl PBS by intraperitoneal injection. Ten minutes thereafter the animal was killed by cervical dislocation, the body cavity opened immediately, skin from the ventral side partially removed and BLI measurement was carried out (10 min signal collection, setting 'high resolution'). A representative animal is shown with similar amplification setting as in Figure 2A.
Background: Factors and processes shaping the population structure and spatial distribution of genetic diversity across a species' distribution range are important in determining the range limits. We comprehensively analysed the influence of recurrent and historic factors and processes on the population genetic structure, mating system and the distribution of genetic variability of the pulmonate freshwater snail Radix balthica. This analysis was based on microsatellite variation and mitochondrial haplotypes using Generalised Linear Statistical Modelling in a Model Selection framework. Results: Populations of R. balthica were found throughout North-Western Europe with range margins marked either by dispersal barriers or the presence of other Radix taxa. Overall, the population structure was characterised by distance independent passive dispersal mainly along a Southwest-Northeast axis, the absence of isolation-by-distance together with rather isolated and genetically depauperated populations compared to the variation present in the entire species due to strong local drift. A recent, climate driven range expansion explained most of the variance in genetic variation, reducing at least temporarily the genetic variability in this area. Other factors such as geographic marginality and dispersal barriers play only a minor role. Conclusions: To our knowledge, such a population structure has rarely been reported before. It might nevertheless be typical for passively dispersed, patchily distributed taxa (e.g. freshwater invertebrates). The strong local drift implied in such a structure is expected to erode genetic variation at both neutral and coding loci and thus probably diminish evolutionary potential. This study shows that the analysis of multiple factors is crucial for the inference of the processes shaping the distribution of genetic variation throughout species ranges. Additional files Additional file 1: Distribution of Radix taxa. Spatial distribution of the Radix MOTU as defined in Pfenninger et al. 2006 plus an additional, newly discovered taxon. This map is the basis for the inference of the species range of R. balthica. Additional file 2: Sampling site table and spatial distribution of diversity indices, selfing estimates and inferred population bottlenecks for R. balthica. Table of sampling site code, geographical position in decimal degrees latitude and longitude, number of individuals analysed with microsatellites (Nnuc), expected heterozygosity (HE) and standard deviation across loci, mean rarefied number of alleles per microsatellite locus (A) and their standard deviation, number of individuals analysed for mitochondrial variation (Nmt), rarefied number of mitochondrial COI haplotypes (Hmt), number of individuals measured for body size (Nsize). Figures A1 - A3 show a graphical representation of the spatial distribution of He, Hmt and, s, respectively. Additional file 3: Assessment of environmental marginality. PCA (principle component analysis) on 35 climatic parameters for the period from 1960 - 2000 from publicly availableWorldClim data. Additional file 4: Inference of a recent climate driven range expansion in R. balthica. Analysis of the freshwater benthos long term monitoring data of the Swedish national monitoring databases at the Swedish University of Agricultural Sciences SLU with canonical correspondence analysis.
Background: Asthma is increasing worldwide and results from a complex immunological interaction between genetic susceptibility and environmental factors. Autovaccination with E. coli induces a strong TH-1 immune response, thus offering an option for the treatment of allergic diseases. Methods: Prospective open trial on safety, tolerability, and impact on allergic inflammation of an autologous E.coli autovaccine in intermittent or mild persistent house dust mite asthma. Determination of exhaled nitric monoxide (eNO) before and after bronchial mite challenge initially and after nine months of autovaccination. Results: Median eNO increase after autovaccination was significantly smaller (from 27.3 to 33.8 ppb; p=0.334) compared to initial values (from 32.6 to 42.2 ppb; p=0.046) (p=0.034). In nine subjects and a total of 306 injections, we observed 101 episodes of local erythema (33.3%; median of maximal diameter 2.5 cm), 95 episodes of local swelling (31.1%; median of maximal diameter 3 cm), and 27 episodes of local pain (8.8%). Four subjects reported itching at the injection site with a total of 30 episodes (9.8%). We observed no serious adverse events. All organ functions (inclusive electrocardiogramm) and laboratory testing of the blood (clinical chemistry, hematology) and the urine (screening test, B-microglobuline) were within normal limits. Vital signs undulated within the physiological variability. Conclusion: The administration of autologous autovacine for the treatment of house dust mite asthma resulted in a reduction of the eNO increase upon bronchial mite challenge. In nine subjects and 306 injections, only a few mild local reactions and no systemic severe adverse events were observed. EudraCT Nr. 2005-005534-12 ClinicalTrials.gov ID NCT00677209
Background: Care management programmes are an effective approach to care for high risk patients with complex care needs resulting from multiple co-occurring medical and non-medical conditions. These patients are likely to be hospitalized for a potentially "avoidable" cause. Nurse-led care management programmes for high risk elderly patients showed promising results. Care management programmes based on health care assistants (HCAs) targeting adult patients with a high risk of hospitalisation may be an innovative approach to deliver cost-efficient intensified care to patients most in need. Methods: PraCMan is a cluster randomized controlled trial with primary care practices as unit of randomisation. The study evaluates a complex primary care practice-based care management of patients at high risk for future hospitalizations. Eligible patients either suffer from type 2 diabetes mellitus, chronic obstructive pulmonary disease, chronic heart failure or any combination. Patients with a high likelihood of hospitalization within the following 12 months (based on insurance data) will be included in the trial. During 12 months of intervention patients of the care management group receive comprehensive assessment of medical and non-medical needs and resources as well as regular structured monitoring of symptoms. Assessment and monitoring will be performed by trained HCAs from the participating practices. Additionally, patients will receive written information, symptom diaries, action plans and a medication plan to improve self-management capabilities. This intervention is addition to usual care. Patients from the control group receive usual care. Primary outcome is the number of all-cause hospitalizations at 12 months follow-up, assessed by insurance claims data. Secondary outcomes are health-related quality of life (SF12, EQ5D), quality of chronic illness care (PACIC), health care utilisation and costs, medication adherence (MARS), depression status and severity (PHQ-9), self-management capabilities and clinical parameters. Data collection will be performed at baseline, 12 and 24 months (12 months post-intervention). Discussion: Practice-based care management for high risk individuals involving trained HCAs appears to be a promising approach to face the needs of an aging population with increasing care demands. Trial registration: Current Controlled Trials ISRCTN56104508
Background: The automation of objectively selecting amino acid residue ranges for structure superpositions is important for meaningful and consistent protein structure analyses. So far there is no widely-used standard for choosing these residue ranges for experimentally determined protein structures, where the manual selection of residue ranges or the use of suboptimal criteria remain commonplace. Results: We present an automated and objective method for finding amino acid residue ranges for the superposition and analysis of protein structures, in particular for structure bundles resulting from NMR structure calculations. The method is implemented in an algorithm, CYRANGE, that yields, without protein-specific parameter adjustment, appropriate residue ranges in most commonly occurring situations, including low-precision structure bundles, multi-domain proteins, symmetric multimers, and protein complexes. Residue ranges are chosen to comprise as many residues of a protein domain that increasing their number would lead to a steep rise in the RMSD value. Residue ranges are determined by first clustering residues into domains based on the distance variance matrix, and then refining for each domain the initial choice of residues by excluding residues one by one until the relative decrease of the RMSD value becomes insignificant. A penalty for the opening of gaps favours contiguous residue ranges in order to obtain a result that is as simple as possible, but not simpler. Results are given for a set of 37 proteins and compared with those of commonly used protein structure validation packages. We also provide residue ranges for 6351 NMR structures in the Protein Data Bank. Conclusions: The CYRANGE method is capable of automatically determining residue ranges for the superposition of protein structure bundles for a large variety of protein structures. The method correctly identifies ordered regions. Global structure superpositions based on the CYRANGE residue ranges allow a clear presentation of the structure, and unnecessary small gaps within the selected ranges are absent. In the majority of cases, the residue ranges from CYRANGE contain fewer gaps and cover considerably larger parts of the sequence than those from other methods without significantly increasing the RMSD values. CYRANGE thus provides an objective and automatic method for standardizing the choice of residue ranges for the superposition of protein structures. Additional files Additional file 1: Dependence of Q on the order parameter rank. The quantity Qi is plotted against the order parameter rank i for 9 different protein structure bundles. Additional file 2: Dependence of P on the clustering stage. The quantity Pi is plotted against the clustering stage i for 9 different protein structure bundles. Additional file 3: Dependence of CYRANGE results on the minimal cluster size parameter my. The sequence coverage (red) and RMSD (blue) of the residue ranges determined by CYRANGE were plotted as a function of my for 9 different protein structure bundles. The dotted vertical line indicates the default value, my = 8. Where CYRANGE found two domains, the RMSD values of the individual domains are shown in light and dark blue. Additional file 4: Dependence of CYRANGE results on the domain boundary extension parameter m. See Additional File 3 for details. Additional file 5: Dependence of CYRANGE results on the minimal gap width g. See Additional File 3 for details. Additional file 6: Dependence of CYRANGE results on the relative RMSD decrease parameter delta. See Additional File 3 for details. Additional file 7: Dependence of CYRANGE results on the absolute RMSD decrease parameter delta abs. See Additional File 3 for details. Additional file 8: Dependence of CYRANGE results on the gap penalty parameter gamma. See Additional File 3 for details. Additional file 9: Correlation between the sequence coverage from CYRANGE, FindCore and PSVS, and the GDT total score, GDT_TS. Each data point represents a protein shown in Figures 3 and 4. The coverage is the percentage of amino acid residues included in the residue ranges found by the different methods. The GDT_TS value is defined by GDT_TS = (P1 + P2 + P4 + P8)/4, where Pd is the fraction of residues that can be superimposed under a distance cutoff of d Å. Additional file 10: Correlation between the RMSD value for the residue ranges from CYRANGE, FindCore and PSVS, and the GDT total score, GDT_TS. Each data point represents one protein domain. See Additional File 9 for details.
Background: Dispersal rates, i.e. the effective number of dispersing individuals per unit time, are the product of dispersal capacity, i.e. a species physiological potential for dispersal, dispersal behaviour, i.e. the decision to leave a habitat patch in favour of another, and connectivity of occupied habitat. Dispersal of species that are highly specialised to a certain habitat is thus strongly limited by habitat availability. Additionally, species inhabiting very stable environments may adopt a sedentary life-style. Both factors should lead to strong genetic differentiation in highly specialised species inhabiting stable environments. These two factors apply to our model species Rhyacophila pubescens a highly specialised freshwater insect that occurs in tufa springs, a very stable habitat. Results: We examined the genetic population structure and phylogeography using range-wide mtCOI sequence and AFLP data from 333 individuals of R. pubescens. We inferred the location of Pleistocene refugia and postglacial colonisation routes of R. pubescens, and examined ongoing local differentiation. Our results indicate intraregional differentiation with a high number of locally endemic haplotypes, that we attributed to habitat specificity and low dispersal rates of R. pubescens. We observed high levels of genetic diversity south of the Alps and genetic impoverishment north of the Alps. Estimates of migrants placed the refugium and the source of the colonisation in the Dauphine Alps (SW Alps). Conclusions: This is the first example of an aquatic insect with a colonisation route along the western margin of the Alps to the Central European highlands. The study also shows that specialisation to a stable environment may have promoted a behavioural shift to decreased dispersal rates, leading to stronger local population differentiation than in less specialised aquatic insects. Alternatively, the occurrence of highly specialised tufa spring habitats may have been more widespread in the past, leading to range regression and fragmentation among present day R. pubescens populations.
Background: Natural history museums receive a rapidly growing number of requests for tissue samples from preserved specimens for DNA-based studies. Traditionally, dried vertebrate specimens were treated with arsenic because of its toxicity and insect-repellent effect. Arsenic has negative effects on in vivo DNA repair enzymes and consequently may inhibit PCR performance. In bird collections, foot pad samples are often requested since the feet were not regularly treated with arsenic and because they are assumed to provide substantial amounts of DNA. However, the actual influence of arsenic on DNA analyses has never been tested. Findings: PCR success of both foot pad and body skin samples was significantly lower in arsenic-treated samples. In general, foot pads performed better than body skin samples. Moreover, PCR success depends on collection date in which younger samples yielded better results. While the addition of arsenic solution to the PCR mixture had a clear negative effect on PCR performance after the threshold of 5.4 μg/μl, such high doses of arsenic are highly unlikely to occur in dried zoological specimens. Conclusions: While lower PCR success in older samples might be due to age effects and/or DNA damage through arsenic treatment, our results show no inhibiting effect on DNA polymerase. We assume that DNA degradation proceeds more rapidly in thin tissue layers with low cell numbers that are susceptible to external abiotic influences. In contrast, in thicker parts of a specimen, such as foot pads, the outermost horny skin may act as an additional barrier. Since foot pads often performed better than body skin samples, the intention to preserve morphologically important structures of a specimen still conflicts with the aim to obtain optimal PCR success. Thus, body skin samples from recently collected specimens should be considered as alternative sources of DNA.
Background: Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes. Results: A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads with median read length of 61 bases. The assemblies generated by VELVET, OASES, and SeqMan NGEN differed in the total number of contigs, contig length, the number and quality of gene hits obtained by BLAST searches against various databases, and contig performance in the mt genome comparison. While VELVET produced the highest overall number of contigs, a large fraction of these were of small size (< 200bp), and gave redundant hits in BLAST searches and the mt genome alignment. The best overall contig performance resulted from the NGEN assembly. It produced the second largest number of contigs, which on average were comparable to the OASES contigs but gave the highest number of gene hits in two out of four BLAST searches against different reference databases. A subsequent meta-assembly of the four contig sets resulted in larger contigs, less redundancy and a higher number of BLAST hits. Conclusion: Our results document the first de novo transcriptome assembly of a non-model species using Illumina sequencing data. We show that de novo transcriptome assembly using this approach yields results useful for downstream applications, in particular if a meta-assembly of contig sets is used to increase contig quality. These results highlight the ongoing need for improvements in assembly methodology. Keywords: next generation sequencing; short read assembly; Mollusca
Background: The ventral midbrain contains a diverse array of neurons, including dopaminergic neurons of the ventral tegmental area (VTA) and substantia nigra (SN) and neurons of the red nucleus (RN). Dopaminergic and RN neurons have been shown to arise from ventral mesencephalic precursors that express Sonic Hedgehog (Shh). However, Shh expression, which is initially confined to the mesencephalic ventral midline, expands laterally and is then downregulated in the ventral midline. In contrast, expression of the Hedgehog target gene Gli1 initiates in the ventral midline prior to Shh expression, but after the onset of Shh expression it is expressed in precursors lateral to Shh-positive cells. Given these dynamic gene expression patterns, Shh and Gli1 expression could delineate different progenitor populations at distinct embryonic time points. Results: We employed genetic inducible fate mapping (GIFM) to investigate whether precursors that express Shh (Shh-GIFM) or transduce Shh signaling (Gli1-GIFM) at different time points give rise to different ventral midbrain cell types. We find that precursors restricted to the ventral midline are labeled at embryonic day (E)7.5 with Gli1-GIFM, and with Shh-GIFM at E8.5. These precursors give rise to all subtypes of midbrain dopaminergic neurons and the anterior RN. A broader domain of progenitors that includes the ventral midline is marked with Gli1-GIFM at E8.5 and with Shh-GIFM at E9.5; these fate-mapped cells also contribute to all midbrain dopaminergic subtypes and to the entire RN. In contrast, a lateral progenitor domain that is labeled with Gli1-GIFM at E9.5 and with Shh-GIFM at E11.5 has a markedly reduced potential to give rise to the RN and to SN dopaminergic neurons, and preferentially gives rise to the ventral-medial VTA. In addition, cells derived from Shh- and Gli1-expressing progenitors located outside of the ventral midline give rise to astrocytes. Conclusions: We define a ventral midbrain precursor map based on the timing of Gli1 and Shh expression, and suggest that the diversity of midbrain dopaminergic neurons is at least partially determined during their precursor stage when their medial-lateral position, differential gene expression and the time when they leave the ventricular zone influence their fate decisions.
Background: Parkinson's disease (PD) is a slowly progressive neurodegenerative disorder which affects widespread areas of the brainstem, basal ganglia and cerebral cortex. A number of proteins are known to accumulate in parkinsonian brains including ubiquitin and alpha-synuclein. Prion diseases are sporadic, genetic or infectious disorders with various clinical and histopathological features caused by prion proteins as infectious proteinaceous particles transmitting a misfolded protein configuration through brain tissue. The most important form is Creutzfeldt-Jakob disease which is associated with a self-propagating pathological precursor form of the prion protein that is physiologically widely distributed in the central nervous system. Discussion: It has recently been found that alpha-synuclein may behave similarly to the prion precursor and propagate between cells. The post-mortem proof of alpha-synuclein containing Lewy bodies in embryonic dopamine cells transplants in PD patient suggests that the misfolded protein might be transmitted from the diseased host to donor neurons reminiscent of prion behavior. The involvement of the basal ganglia and brainstem in the degenerative process are other congruencies between Parkinson's and Creutzfeldt-Jakob disease. However, a number of issues advise caution before categorizing Parkinson's disease as a prion disorder, because clinical appearance, brain imaging, cerebrospinal fluid and neuropathological findings exhibit fundamental differences between both disease entities. Most of all, infectiousness, a crucial hallmark of prion diseases, has never been observed in PD so far. Moreover, the cellular propagation of the prion protein has not been clearly defined and it is, therefore, difficult to assess the molecular similarities between the two disease entities. Summary: At the current state of knowledge, the molecular pathways of transmissible pathogenic proteins are not yet fully understood. Their exact involvement in the pathophysiology of prion disorders and neurodegenerative diseases has to be further investigated in order to elucidate a possible overlap between both disease categories that are currently regarded as distinct entities.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. In statistical spike train analysis, stochastic point process models usually assume stationarity, in particular that the underlying spike train shows a constant firing rate (e.g. [1]). However, such models can lead to misinterpretation of the associated tests if the assumption of rate stationarity is not met (e.g. [2]). Therefore, the analysis of nonstationary data requires that rate changes can be located as precisely as possible. However, present statistical methods focus on rejecting the null hypothesis of stationarity without explicitly locating the change point(s) (e.g. [3]). We propose a test for stationarity of a given spike train that can also be used to estimate the change points in the firing rate. Assuming a Poisson process with piecewise constant firing rate, we propose a Step-Filter-Test (SFT) which can work simultaneously in different time scales, accounting for the high variety of firing patterns in experimental spike trains. Formally, we compare the numbers N1=N1(t,h) and N2=N2(t,h) of spikes in the time intervals (t-h,t] and (h,t+h]. By varying t within a fine time lattice and simultaneously varying the interval length h, we obtain a multivariate statistic D(h,t):=(N1-N2)/V(N1+N2), for which we prove asymptotic multivariate normality under homogeneity. From this a practical, graphical device to spot changes of the firing rate is constructed. Our graphical representation of D(h,t) (Figure 1A) visualizes the changes in the firing rate. For the statistical test, a threshold K is chosen such that under homogeneity, |D(h,t)|<K holds for all investigated h and t with probability 0.95. This threshold can indicate potential change points in order to estimate the inhomogeneous rate profile (Figure 1B). The SFT is applied to a sample data set of spontaneous single unit activity recorded from the substantia nigra of anesthetized mice. In this data set, multiple rate changes are identified which agree closely with visual inspection. In contrast to approaches choosing one fixed kernel width [4], our method has advantages in the flexibility of h.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. One of the central questions in neuroscience is how neural activity is organized across different spatial and temporal scales. As larger populations oscillate and synchronize at lower frequencies and smaller ensembles are active at higher frequencies, a cross-frequency coupling would facilitate flexible coordination of neural activity simultaneously in time and space. Although various experiments have revealed amplitude-to-amplitude and phase-to-phase coupling, the most common and most celebrated result is that the phase of the lower frequency component modulates the amplitude of the higher frequency component. Over the recent 5 years the amount of experimental works finding such phase-amplitude coupling in LFP, ECoG, EEG and MEG has been tremendous (summarized in [1]). We suggest that although the mechanism of cross-frequency-coupling (CFC) is theoretically very tempting, the current analysis methods might overestimate any physiological CFC actually evident in the signals of LFP, ECoG, EEG and MEG. In particular, we point out three conceptual problems in assessing the components and their correlations of a time series. Although we focus on phase-amplitude coupling, most of our argument is relevant for any type of coupling. 1) The first conceptual problem is related to isolating physiological frequency components of the recorded signal. The key point is to notice that there are many different mathematical representations for a time series but the physical interpretation we make out of them is dependent on the choice of the components to be analyzed. In particular, when one isolates the components by Fourier-representation based filtering, it is the width of the filtering bands what defines what we consider as our components and how their power or group phase change in time. We will discuss clear cut examples where the interpretation of the existence of CFC depends on the width of the filtering process. 2) A second problem deals with the origin of spectral correlations as detected by current cross-frequency analysis. It is known that non-stationarities are associated with spectral correlations in the Fourier space. Therefore, there are two possibilities regarding the interpretation of any observed CFC. One scenario is that basic neuronal mechanisms indeed generate an interaction across different time scales (or frequencies) resulting in processes with non-stationary features. The other and problematic possibility is that unspecific non-stationarities can also be associated with spectral correlations which in turn will be detected by cross frequency measures even if physiologically there is no causal interaction between the frequencies. 3) We discuss on the role of non-linearities as generators of cross frequency interactions. As an example we performed a phase-amplitude coupling analysis of two nonlinearly related signals: atmospheric noise and the square of it (Figure 1) observing an enhancement of phase-amplitude coupling in the second signal while no pattern is observed in the first. Finally, we discuss some minimal conditions need to be tested to solve some of the ambiguities here noted. In summary, we simply want to point out that finding a significant cross frequency pattern does not always have to imply that there indeed is physiological cross frequency interaction in the brain.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. To truly appreciate the myriad of events which relate synaptic function and vesicle dynamics, simulations should be done in a spatially realistic environment. This holds true in particular in order to explain the rather astonishing motor patterns presented here which we observed within in vivo recordings which underlie peristaltic contractions at a well characterized synapse, the neuromuscular junction (NMJ) of the Drosophila larva. To this end, we have employed a reductionist approach and generated three dimensional models of single presynaptic boutons at the Drosophila larval NMJ. Vesicle dynamics are described by diffusion-like partial differential equations which are solved numerically on unstructured grids using the uG platform. In our model we varied parameters such as bouton-size, vesicle output probability (Po), stimulation frequency and number of synapses, to observe how altering these parameters effected bouton function. Hence we demonstrate that the morphologic and physiologic specialization maybe a convergent evolutionary adaptation to regulate the trade off between sustained, low output, and short term, high output, synaptic signals. There seems to be a biologically meaningful explanation for the co-existence of the two different bouton types as previously observed at the NMJ (characterized especially by the relation between size and Po),the assigning of two different tasks with respect to short- and long-time behaviour could allow for an optimized interplay of different synapse types. As a side product, we demonstrate how advanced methods from numerical mathematics could help in future to resolve also other difficult experimental neurobiological issues.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. Parallel multiunit recordings from V1 in anesthetized cat were collected during the presentation of random sequences of drifting sinusoidal gratings at 12 fixed orientations while gamma oscillations were present. In agreement with the seminal work [1], most units were orientation selective to varying degrees and synchronization was evident in spike train crosscorrelograms computed between units with similar preferred orientations, particularly during the presentation of optimal stimuli. Interestingly, a subset of units, which we refer to as synchronization hubs, were additionally found to synchronize with units having differing preferred orientations which was consistent with a previous study [2]. Moreover, oscillatory patterning in spike train autocorrelograms was also found to be strongest in units denoted as synchronization hubs, and synchronization hubs also tended to have narrower tuning curves relative to other units. We used simplified computational models of small networks of V1 neurons to demonstrate that neurons subject to a sufficiently strong level of inhibitory input can function as synchronization hubs. Neurons were endowed either with integrate-and-fire or conductance-based dynamics and each neuron received a combination of excitatory (AMPA) synaptic inputs that were Poisson-distributed and inhibitory (GABA) inputs that were coherent at a gamma-frequency range. If the strength of rhythmic inhibition was increased for a subset of neurons in the network, and excitation was increased simultaneously to maintain a fixed firing rate, then these neurons produced stronger oscillatory patterning in their discharge probabilities. The oscillations in turn synchronized these neurons with other neurons in the network. Importantly, the strength of synchronization increased with neurons of differing orientation preferences even though no direct synaptic coupling existed between the hubs and the other neurons. Enhanced levels of inhibition account for the emergence of synchronization hubs in the following way: Inhibitory inputs exhibiting a gamma rhythm determine a time window within which a cell is likely to discharge. Increased levels of inhibition narrow down this window further simultaneously leading to (i) even stronger oscillatory patterning of the neuron's activity and (ii) enhanced synchronization with other neurons. This enables synchronization even between cells with differing orientation preferences. Additionally, the same increased levels of inhibition may be responsible for the narrow tuning curves of hub neurons. In conclusion, synchronization hubs may be the cells that interact most strongly with the network of inhibitory interneurons during gamma oscillations in primary visual cortex.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. Background: Oscillatory activity in high-beta and gamma bands (20-80Hz) is known to play an important role in cortical processing being linked to cognitive processes and behavior. Beta/gamma oscillations are thought to emerge in local cortical circuits via two mechanisms: the interaction between excitatory principal cells and inhibitory interneurons – the pyramidal-interneuron gamma (PING) [1], and in networks of coupled inhibitory interneurons under tonic excitation – the interneuronal gamma (ING) [2]. Experimental evidence underlines the important role of inhibitory interneurons and especially of the fast spiking (FS) interneurons [3,4]. We show in simulation that an important property of FS neurons, namely the membrane resonance (frequency preference), represents an additional mechanism – the resonance induced gamma (RING), i.e. modulation of oscillatory discharge by resonance. RING promotes frequency stability and enables oscillations in purely excitatory networks. Methods: Local circuits were modeled with small world networks of 80% excitatory and 20% inhibitory neuron populations interconnected in small-world topology by realistic conductance-based synapses. Neuron populations were leaky integrate and fire (LIF) or Izhikevich resonator (RES) neurons. We also tested networks of purely inhibitory and purely excitatory RES neurons. Networks were stimulated with miniature postsynaptic potentials (MINIs) [5] and with low frequency sinusoidal (0.5 Hz) input that mimics the effect of gratings passing trough the visual field. The activity was calibrated to match recordings from cat visual cortex (firing rate, oscillatory activity). Results: Sinusoidal input modulates network oscillation frequency. This effect is most prominent in IF excitatory and IF inhibitory (IF-IF) networks and less prominent (about 4 times) in IF-RES or RES-IF networks where frequency remains relatively stable. The most stable frequency was observed in networks of pure resonators (RES-RES, None-RES, RES-None). Interestingly, purely excitatory RES networks (RES-None) were also able to exhibit oscillations through RING. By contrast purely excitatory or inhibitory IF networks (IF-None, None-IF) were not able to express oscillations under these conditions, matching experimental parameters. Conclusions: In both PING and ING, adding membrane resonance to principal cells or inhibitory interneurons stabilizes network oscillation frequency via the RING mechanism. Notably, in networks of purely excitatory networks, where ING and PING are not defined, oscillations can emerge via the RING mechanism if membrane resonance is expressed. Thus, RING appears as a potentially important mechanism for promoting stable network oscillations.
TRENTOOL : an open source toolbox to estimate neural directed interactions with transfer entropy
(2011)
To investigate directed interactions in neural networks we often use Norbert Wiener's famous definition of observational causality. Wiener’s definition states that an improvement of the prediction of the future of a time series X from its own past by the incorporation of information from the past of a second time series Y is seen as an indication of a causal interaction from Y to X. Early implementations of Wiener's principle – such as Granger causality – modelled interacting systems by linear autoregressive processes and the interactions themselves were also assumed to be linear. However, in complex systems – such as the brain – nonlinear behaviour of its parts and nonlinear interactions between them have to be expected. In fact nonlinear power-to-power or phase-to-power interactions between frequencies are reported frequently. To cover all types of non-linear interactions in the brain, and thereby to fully chart the neural networks of interest, it is useful to implement Wiener's principle in a way that is free of a model of the interaction [1]. Indeed, it is possible to reformulate Wiener's principle based on information theoretic quantities to obtain the desired model-freeness. The resulting measure was originally formulated by Schreiber [2] and termed transfer entropy (TE). Shortly after its publication transfer entropy found applications to neurophysiological data. With the introduction of new, data efficient estimators (e.g. [3]) TE has experienced a rapid surge of interest (e.g. [4]). Applications of TE in neuroscience range from recordings in cultured neuronal populations to functional magnetic resonanace imaging (fMRI) signals. Despite widespread interest in TE, no publicly available toolbox exists that guides the user through the difficulties of this powerful technique. TRENTOOL (the TRansfer ENtropy TOOLbox) fills this gap for the neurosciences by bundling data efficient estimation algorithms with the necessary parameter estimation routines and nonparametric statistical testing procedures for comparison to surrogate data or between experimental conditions. TRENTOOL is an open source MATLAB toolbox based on the Fieldtrip data format. ...
Background: In many species males face a higher predation risk than females because males display elaborate traits that evolved under sexual selection, which may attract not only females but also predators. Females are, therefore, predicted to avoid such conspicuous males under predation risk. The present study was designed to investigate predator-induced changes of female mating preferences in Atlantic mollies (Poecilia mexicana). Males of this species show a pronounced polymorphism in body size and coloration, and females prefer large, colorful males in the absence of predators. Results: In dichotomous choice tests predator-naïve (lab-reared) females altered their initial preference for larger males in the presence of the cichlid Cichlasoma salvini, a natural predator of P. mexicana, and preferred small males instead. This effect was considerably weaker when females were confronted visually with the non-piscivorous cichlid Vieja bifasciata or the introduced non-piscivorous Nile tilapia (Oreochromis niloticus). In contrast, predator experienced (wild-caught) females did not respond to the same extent to the presence of a predator, most likely due to a learned ability to evaluate their predators' motivation to prey. Conclusions: Our study highlights that (a) predatory fish can have a profound influence on the expression of mating preferences of their prey (thus potentially affecting the strength of sexual selection), and females may alter their mate choice behavior strategically to reduce their own exposure to predators. (b) Prey species can evolve visual predator recognition mechanisms and alter their mate choice only when a natural predator is present. (c) Finally, experiential effects can play an important role, and prey species may learn to evaluate the motivational state of their predators. Keywords: Sexual selection; female choice; non-independent mate choice; predator recognition; Poecilia mexicana
As a part of this thesis, a Monte Carlo-based code has been developed capable of simulating the transition of proton beam properties to neutron beam properties as it occurs in the Li-7(p, n)Be-7 reaction. It is able to reproduce not only the angle-integrated energy distributions but it is also capable of predicting the angle-dependent neutron spectra as measured at Forschungszentrum Karlsruhe (Karlsruhe, Germany) and Physikalisch-Technische Bundesanstalt (Braunschweig, Germany). Since the code retains all three spatial dimensions as well as all three velocity dimensions, it provides very detailed information on the neutron beam. The resulting data can aid in many different aspects, for example it can be used in shielding construction, or for lithium target design. In this work, the code is used to predict the neutron beam properties expected at the Frankfurt Neutron Source at Stern-Gerlach-Zentrum (FRANZ) facility. For different proton beam energies, the neutron distribution in x/p_x, y/p_y, and z/p_z is shown as well as a Mollweide projection, which illustrates the kinematic collimation effect that limits the neutron cone opening angle to less than 180 degree.
Die Familie der Proteorhodopsine (PR) besteht aus Hunderten von PR Molekülen, die unter Lichteinwirkung Protonen pumpen und somit eine bedeutende Rolle für die Energiegewinnung spielen könnten. Da der pKa Wert des Proton Akzeptors der Schiff‘schen Base (SB) (~7.2) dem pH Wertes der Ozeane (~7.9) ähnelt, wird auch über eine regulatorische Funktion spekuliert. Wird in Erwägung gezogen, dass 24 000 PR Moleküle pro SAR86 Zelle vorhanden sind (Beja et al. 2001) und dass 13% der Bakterien der Meeresoberfläche PR besitzen (Sabehi et al. 2005) liefert dieses Protein wahrscheinlich einen bedeutenden Energiebeitrag neben der Photosynthese. Einblicke in den Mechanismus der Energieumwandlung erfordern sowohl die Untersuchung des Chromophores, welches die Lichtenergie absorbiert als auch der Struktur des Apoproteins, das durch die Generierung eines Protonengradienten zur Energiegewinnung beiträgt. Der Fokus der Doktorarbeit liegt auf dem Chromophor und seiner Umgebung. Eine erste Charakterisierung der SB und des Retinals erfolgt durch UV/VIS und NMR Messungen (Pfleger et al. 2008). Die 13C chemische Verschiebungen von 10,11-13C2 Retinal und die 15N chemische Verschiebung der protonierten SB, gebildet durch K231, zeigt eindeutig, dass im Grundzustand nur eine Konformation der Retinals, all-trans, vorliegt. Die 15N chemische Verschiebung weist außerdem auf eine starke Wechselwirkung der SB mit ihren Gegenionen hin. Desweiteren kann durch Messungen der 15N chemischen Verschiebung der SB bei verschiedenen pH Werten der pKa Wert der SB abgeschätzt werden, auf ~12. Diese Stabilisierung der positiv geladenen protonierten Form der SB weist auf die Existenz eines Wasserclusters hin, das durch die hohe Dielektrizitätskonstante die protonierte Form der SB stabilisieren könnte. Um zu überprüfen, ob Wasser an der SB gebunden ist, wird ein sogenanntes 15N-1H HETCOR Experiment durchgeführt. Der Bereich der 15N chemischen Verschiebung der SB korreliert mit einer Protonenresonanz bei ~5 ppm, welche im Bereich einer Wasserresonanz liegt und die durch D2O austauschbar ist. Dies indiziert eine wichtige Bedeutung von Wasser in der Nähe der SB für die Funktion von PR. Der Einfluss von Mutationen des Histidins H75 und des Aspartats D97 auf die 15N chemische Verschiebung der SB sowie die Auswirkung von Histidinmutationen auf das Chromophor deuten eine direkte Wechselwirkung von Aspartat 97 und der SB an, nicht aber eine direkte Wechselwirkung von H75 und der SB. Neben dem Chromophor ist außerdem das Signalpeptid Gegenstand der Untersuchung der Doktorarbeit. Motivation für die Untersuchung war die Inhomogenität der Proben, die im Zusammenhang mit ungleich prozessiertem PR stehen könnten. Ein zweiter Teil beschäftigt sich mit neuen Konzepten der Datenaufnahme, da das S/R in der Festkörper NMR ein limitierender Faktor darstellt. Diese beinhalten Verstärkung der Relaxation (RELOAD) sowie die Refokussierung von T2 bei Verwendung eines Prozessierungsschrittes, der „half echo alternating transformation“ (HEAT).
In mitochondrial respiration, the soluble protein cytochrome c accepts an electron from the membrane bound cytochrome bc1. The interaction between cytochrome bc1 and cytochrome c is highly transient in nature, enabling turnover numbers greater than 160 s-1. Yeast cytochrome bc1 has been successfully crystallised with bound cytochrome c with the help of an antibody fragment (Lange and Hunte 2002; Solmaz and Hunte 2008). In all crystal structures of the complex, the homodimeric cytochrome bc1 binds only one cytochrome c, with the binding site located on subunit cytochrome c1. Univalent cytochrome c binding is correlated with conformational changes of the Rieske protein head domain and subunit QCR6p. The interface of the complex is small. The haem moieties are centrally located in a mainly non-polar contact site that includes a cation–! interaction and is surrounded by complementary charged residues. The crystal structure is in agreement with the general architecture of the interfaces of transient redox complexes and also reveals several interesting features unique to the cytochrome bc1. On the basis of the crystal structures, an extensive thermodynamic and kinetic characterisation of the interaction was carried out in this work to challenge the static snapshot of the bound proteins in the crystal structure as the relevant physiological electron transfer. The thermodynamic parameters of the interaction between the redox partners were determined using isothermal titration calorimetry (ITC). The association constant for cytochrome bc1 and cytochrome c in oxidised state under physiological ionic strength of 120 mM at 25 °C, was determined to be 5 " 103 M-1 by direct ITC titration. So, the partners interact with an affinity of 200 #M. In spite of the low affinity the complex has a life time ($ = 1/koff) of 5 #second, sufficiently long to enable the theoretically calculated electron transfer rates of 1.0 " 106 to 2.6 " 107 s%1 with a lifetime ($ = 1/rate) of 1-0.04 μseconds and experimentally determined rate of 7.7 " 104 s%1 with a lifetime of 13 μseconds. The low affinity makes it difficult to ascertain the stoichiometry of binding. The enthalpy of the interaction is endothermic, which is consistent with the nature of an interface where hydrophobic interactions are dominant. The enthalpy and entropy is 3.6 kJmol-1 and 83 kJmol-1K-1, respectively. The importance of key interface residues was also investigated. The role of the interface residue G89 of cytochrome c which might have a role in the dissociation of the complex has been probed by site-directed mutagenesis. The interface contains a cation-! interaction between F230 of cytochrome bc1 and R19 of cytochrome c, which is thought to provide the specificity to the interaction between the otherwise promiscuous partners. To analyse the role of this interaction pair in electron transfer, F230L and F230W mutants were used to measure direct electron transfer rates by flash photolysis and steady state kinetics. The findings indicate that another ! system can work as functional substitution of F230, while deleting the ! system has a deleterious effect on the complex formation. The inability of F230L to achieve the transient and steady state turnover rates as wild type protein indicates a scenario where the variant achieves an altered bound state with inefficient electron transfer pathways and higher edge-to-edge distance. The role of supernumerary subunit QCR6p in complex formation was investigated by steady state kinetics measurements. Subunit QCR6p does not interact directly with cytochrome c but is positioned in such a way that it could electrostatically steer cytochrome c in a reactive ensemble. The highly acidic and disordered N-terminus of QCR6p could interact with a patch of conserved lysine residues on cytochrome c. The role of subunit QCR6p has been assessed using QCR6p deleted cytochrome bc1 and a lysine variant of cytochrome c. The results show that QCR6p not only affects the kinetics of the interaction but is also important for the stability of cytochrome bc1. The kinetic and thermodynamic data obtained during this study provide evidence for the functional importance of non-catalytic cytochrome bc1 subunit QCR6p, show that the entropy driven interaction is indeed of low affinity and highly transient in nature and indicate that the interface is well suited to ensure the high turnover of the electron transfer chain where cytochrome c interacts with multiple partners using overlapping interfaces. The suggested role of the cation-! interaction as a highly specific interaction has been validated.
This thesis is based on the following publications (in chronological order): 1. Biegel, E., S. Schmidt & V. Müller (2009) Genetic, immunological and biochemical evidence for a Rnf complex in the acetogen Acetobacterium woodii. Environ. Microbiol. 11: 1438-1443. My contribution: Amplification, sequence determination and analysis of Rnf homologues, enrichment of the Rnf complex 2. Biegel, E. & V. Müller (2010) Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase. Proc. Nat. Acad. Sci. U. S. A. 107: 18138-18142. My contribution: I designed and performed all experiments shown and interpreted the data. 3. Biegel, E., S. Schmidt, J. Gonzáles & V. Müller (2010) Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes. Cell. Mol. Life Sci., in press. DOI: 10.1007/s00018-010-0555-8. My contribution: I was involved in writing all chapters except chapters: „phylogenetic analyses of rnf genes“ and „distribution of rnf genes“. 4. Biegel, E. & V. Müller (2010) A Na+-translocating pyrophosphatase in the acetogenic bacterium Acetobacterium woodii. J. Biol. Chem., in press. DOI: 10.1074/jbc.M110.192823. My contribution: I designed and performed all experiments shown and interpreted the data.
The molecular conformation of the title compound, C18H18N2O3S, is stabilized by an intramolecular N—H ... O hydrogen bond. The crystal packing shows centrosymmetric dimers connected by N—H ... S hydrogen bonds. The terminal ethoxy substituents are statistically disordered [occupancy ratio 0.527 (5):0.473 (5)].
The title compound, C20H22O4S2, was synthesized by the reaction of 1,4-dibromobutene with methyl thiosalicylate. The aliphatic segment of this ligand is in an all-trans conformation. The bridging chain, –S-(CH2)4-S–, is almost planar (r.m.s. deviation for all non-H atoms: 0.056 Å) and its mean plane forms dihedral angles of 16.60 (7) and 5.80 (2)° with the aromatic rings. In the crystal, the molecules are linked by weak C—H ... O interactions into chains with graph-set notation C(14) along [0 0 1]. The crystal studied was a racemic twin, the ratio of the twin components being 0.27 (9):0.73 (9).
The title compound, C14H11NO4, crystallizes with two molecules in the asymmetric unit. The major conformational difference between these two molecules is the dihedral angle between the aromatic rings, namely 36.99 (5) and 55.04 (5)°. The nitro groups are coplanar with the phenyl rings to which they are attached, the O—N—C—C torsion angles being -1.9 (3) and 1.0 (3)° in the two molecules.
The 3,5-methoxy groups in the title compound, C16H23NO4, are almost coplanar with the aromatic ring, whereas the 4-methoxy group is bent out of this plane. The three CH3—O—C—C torsion angles are -1.51 (18), 0.73 (19) and 75.33 (15)°. The cyclohexane ring adopts a chair conformation. In the crystal, molecules are connected by intermolecular N—H ... O hydrogen bonds into chains running along the b axis.
The title compound. C15H14N2O4, (I), has a gauche–gauche (O/C/C/C—O/C/C/C or GG) conformation and is a positional isomer of propane-1,3-diyl bis(pyridine-3-carboxylate), (II). The molecule of (I) lies on a twofold rotation axis, which passes through the central C atom of the aliphatic chain, giving one half-molecule per asymmetric unit. There is excellent agreement of the geometric parameters of (I) and (II). The most obvious differences between them are the O/C/C/C—O/C/C/C torsion angles [56.6 (2)° in (I) and 174.0 (3)/70.2 (3)° in (II) for GG and TG conformations, respectively] and the dihedral angle between the planes of the aromatic rings [80.3 (10)° in (I) and 76.5 (3)° in (II)]. The crystal structure is stabilized by weak C—H ... N and C—H ... O hydrogen bonding.
4-Nitrophenyl 1-naphthoate
(2010)
In the title compound, C17H11NO4, the dihedral angle between the two benzene rings is 8.66 (3)°. The nitro group is twisted by 4.51 (9)° out of the plane of the aromatic ring to which it is attached. The presence of intermolecular C—H ... O contacts in the crystal structure leads to the formation of chains along the c axis.
The title compound, C6H5NO2·C6H6O2, crystallizes with one pyridinium-2-carboxylate zwitterion and one molecule of benzene-1,2-diol in the asymmetric unit. The crystal structure is characterized by alternating molecules forming zigzag chains running along the a axis: the molecules are connected by O—H ... O and N—H ... (O,O) hydrogen bonds.
Crystals of the title compound, C12H8N2·C7H8O2, were obtained during cocrystallization experiments of a compound with two hydrogen-bond donors (2-hydroxybenzyl alcohol) with another compound containing two hydrogen-bond acceptors (phenanthroline). Unexpectedly, the two molecules do not form dimers with two O—H ... N hydrogen bonds connecting the two molecules. However, one of the hydroxy groups forms a bifurcated hydrogen bond to both phenanthroline N atoms, whereas the other hydroxy group forms an O—H ... O hydrogen bond to a symmetry-equivalent 2-hydroxybenzyl alcohol molecule. In addition, the crystal packing is stabilized by Pi – Pi interactions between the two phenanthroline ring systems, with a centroid–centroid distance of 3.570 Å.
In the crystal of the title compound [systematic name: 2-(3,5-diamino-6-chloropyrazin-2-ylcarbonyl)guanidinium chloride methanol disolvate], C6H9ClN7O+·Cl-·2CH3OH , the components are connected by N—H ... N, N—H ... Cl, N—H ... O, O—H ... Cl and O—H ... O hydrogen bonds into a three-dimensional network. The dihedral angle between the aromatic ring and the guanidine residue is 6.0 (2)°.
In contrast to the previous structure determinations of the title structure, (NH4)2[MoS4], the present determination at 173 K localized the positions of the H atoms. The title structure belongs to the beta-K2SO4 family and all the ions are located on crystallographic mirror planes. The ions are held together by N—H ... S hydrogen bonds (some of which are bifurcated), forming a three-dimensional network. One of the N atoms has nine contacts to the S atoms shorter than 4 Å, and the other has ten.
The title compound (also know as azorellanone), C20H32O2, is built up from three fused carbocycles, one five-membered ring and two six-membered rings. The five membered-ring has an envelope conformation, whereas the six-membered rings have a distorted half-chair and a twist–boat conformation. In the crystal, molecules are linked by O—H ... O interactions into zigzag chains with graph-set notation C(8) along [010]. The absolute configuration was assigned on the basis of earlier chemical studies.
The dihydropyrimidine ring of the title compound, C13H15ClN2S, adopts an envelope conformation with five almost coplanar atoms (r.m.s. deviation = 0.054 Å) and the C atom bearing the two methyl substituents deviating from this plane by 0.441 (2) Å. The best plane through the five almost coplanar atoms forms a dihedral angle of 89.56 (5)° with the benzene ring. The crystal packing is characterized by centrosymmetric dimers connected by pairs of N—H ... S hydrogen bonds.
9-Bromo-9-borafluorene
(2010)
The title compound, C12H8BBr, crystallizes with three essentially planar molecules (r.m.s. deviations = 0.018, 0.020 and 0.021Å) in the asymmetric unit: since the title compound is rigid, there are no conformational differences between these three molecules. The crystal packing resembles a herringbone pattern.
The title compound, C22H28N2O6, crystallizes with four half-molecules in the asymmetric unit: each molecule is located about a crystallographic inversion centre. The central methylene groups of two molecules are disordered over two sets of equally occupied sites. The crystal packing is characterized by sheets of molecules parallel to (114).
In the title compound, C27H19N3O4, the phenol and pyrazole rings are almost coplanar [dihedral angle = 0.95 (12)°] due to an intramolecular O—H ... N hydrogen bond, whereas the phenyl ring is tilted by 40.81 (7)° with respect to the plane of the pyrazole ring. The aromatic ring with a nitrophenoxy substituent makes a dihedral angle of 54.10 (7)° with the pyrazole ring.
The title compound, C8H11FN5 +·Cl-, crystallized with a monoprotonated 1-(4-fluorophenyl)biguanidinium cation and a chloride anion in the asymmetric unit. The biguanidium group is not planar [dihedral angle between the two CN3 groups = 52.0 (1)°] and is rotated with respect to the phenyl group [tau = 54.3 (3)°]. In the crystal, N—H ... N hydrogen-bonded centrosymmetric dimers are connected into ribbons, which are further stabilized by N—H ... Cl interactions, forming a three-dimensional hydrogen-bonded network.
The title compound, [Na(CF3O3S)(C12H24O6)], features a sodium cation that is coordinated by eight O atoms in an irregular hexagonal bipyramidal environment. The equatorial positions are occupied by the six O atoms of an 18-crown-6 ether ring. In the axial positions, there is one O atom of a trifluoromethanesulfonate anion and an ether O atom of a symmetry-equivalent crown ether ring. In this way, centrosymmetric dimers are formed.
The asymmetric unit of the title compound, [K(C5HF6N2)(H2O)2]n, is composed of two 3,5-bis(trifluoromethyl)pyrazolide anions, two potassium cations and four water molecules. The water molecules and 3,5-bis(trifluoromethyl)pyrazolide anions act as bridges between the potassium cations. Each potassium cation is surrounded by four O atoms [K—O = 2.705 (3)–2.767 (3) Å] and four F atoms [K—F = 2.870 (7)–3.215 (13) Å]. The water molecules and the 3,5-bis(trifluoromethyl)pyrazolide anions are connected by O—H ... N hydrogen bonds, forming layers in the ab plane. All –CF3 groups show rotational disorder between two orientations each.
The two rings in the title compound, C11H12N2O4S, are roughly coplanar [dihedral angle = 6.77 (8)°]. Whereas the two outer methyl groups of the three methoxy groups are almost coplanar with the aromatic ring to which they are attached [C—C—O—C torsion angles = 8.5 (3) and -8.3 (3)°], the methyl group of the central methoxy substituent is not [C—C—C—C = -78.4 (3)°]. The crystal packing is stabilized by N—H ... O hydrogen bonding.
In the title compound, C11H11N3O2, the dihedral angle between the central ethanone fragment and the 4-methoxyphenyl group is 2.9 (2)°, while that between the ethanone fragment and the triazole ring is 83.4 (2)°. The dihedral angle between the planes of the triazole and benzene rings is 81.7 (1)°. The 4-methoxyphenyl group is cis with respect to the ethanone fragment O atom across the exocyclic C—C bond. In the crystal, molecules are linked by C—H ... N interactions into C(9) chains along [001].
The central structural element of the title compound, C24H29NO2, is a carbazole unit substituted with two acetyl residues and an octyl chain. The acetyl residues are nearly coplanar [dihedral angles = 5.37 (14) and 1.0 (3)°] with the carbazole unit which is essentially planar (r.m.s. deviation for all non-H atoms = 0.025 Å). The octyl chain adopts an all-trans conformation. The crystal packing is stabilized by C—H ... O hydrogen bonds.
17-Acetoxymulinic acid
(2010)
The title compound, [systematic name: 5a-acetoxymethyl-3-isopropyl-8-methyl-1,2,3,3a,4,5,5a,6,7,10,10a,10b-dodecahydro-7,10-endo-epidioxycyclohepta[e]indene-3a-carboxylic acid], C22H32O6 (I), is closely related to methyl 5a-acetoxymethyl-3-isopropyl-8-methyl-1,2,3,3a,4,5,5a,6,7,10,10a,10b-dodecahydro-7,10-endo-epidioxycyclohepta[e]indene-3a-carboxylate, (II) [Brito et al., (2008 [triangle]). Acta Cryst. E64, o1209]. There are two molecules in the asymmetric unit, which are linked by two strong intramolecular O—H ... O hydrogen bonds with graph-set motif R 2 2(8). In both (I) and (II), the conformation of the three fused rings are almost identical. The five-membered ring has an envelope conformation, the six-membered ring has a chair conformation and the seven-membered ring has a boat conformation. The most obvious differences between the two compounds is the observed disorder of the acetoxymethyl fragments in both molecules of the asymmetric unit of (I). This disorder is not observed in (II). The crystal structure and the molecular conformation is stabilized by intermolecular C—H ... O hydrogen bonds. The ability to form hydrogen bonds is different in the two compounds. The crystal studied was a non-merohedral twin, the ratio of the twin components being 0.28 (1):0.72 (1)
In the title compound, C4H7N3O·C2H6OS, creatinine [2-amino-1-methyl-1H-imidazol-4(5H)one] exists in the amine form. The ring is planar (r.m.s. deviation for all non-H atoms = 0.017 Å). In the crystal, two creatinine molecules form centrosymmetric hydrogen-bonded dimers linked by pairs of N—H[cdots, three dots, centered]N hydrogen bonds. In addition, creatinine is linked to a dimethyl sulfoxide molecule by an N—H[cdots, three dots, centered]O interaction. The packing shows layers parallel to (120).
The title compound, [Li3(C4F9O)3(C3H6O)3], features an open Li/O cube with an Li ion missing at one corner. Three of the four bridging O atoms of the cube carry a fluorinated tert-butyl residue, whereas the fourth is part of an acetone molecule. Two of the Li atoms are further bonded to a non-bridging acetone molecule. Two of the lithium ion coordination geometries are very distorted LiO4 tetrahedra; the third could be described as a very distorted LiO3 T-shape with two distant F-atom neighbours. The Li[cdots, three dots, centered]Li contact distances for the three-coordinate Li+ ion [2.608 (14) and 2.631 (12) Å] are much shorter that the contact distance [2.940 (13) Å] between the tetrahedrally coordinated species.
The title compound, [Tl4(C4H9O)4], featuring a (Tl—O)4 cube, crystallizes with a quarter-molecule (located on a special position of site symmetry An external file that holds a picture, illustration, etc. Object name is e-66-m1621-efi1.jpg..) and a half-molecule (located on a special position of site symmetry 23.) in the asymmetric unit. The Tl—O bond distances range from 2.463 (12) to 2.506 (12) Å. All O—Tl—O bond angles are smaller than 90° whereas the Tl—O—Tl angles are wider than a rectangular angle.
In the crystal of the title compound, C8H8ClN3S, molecules are connected by N—H[cdots, three dots, centered]S hydrogen bonds into strips parallel to the (112) planes and running along [110]. One of the amino H atoms is not involved in a classical hydrogen bond. In addition, there is a rather short intermolecular Cl ... S distance of 3.3814 (5) Å.
In the title compound, C15H14N2O4, (I), the molecule lies on a twofold rotation axis which passes through the central C atom of the aliphatic chain, giving one half-molecule per asymmetric unit. The structure is a monoclinic polymorph of the triclinic structure previously reported [Brito, Vallejos, Bolte & López-Rodríguez (2010). Acta Cryst. E66, o792], (II). The most obvious difference between them is the O/C/C/C—O/C/C/C torsion angle [58.2 (7)° in (I) and 173.4 (3)/70.2 (3)° in (II) for GG and TG conformations, respectively]. Another important difference is observed in the dihedral angle between the planes of the aromatic rings [86.49 (7)° for (I) and 76.4 (3)° for (II)]. The crystal structure features a weak pi–pi interaction [centroid–centroid distance = 4.1397 (10)Å]; this latter kind of interaction is not evident in the triclinic polymorph.
The title compound, C15H25N5, is an aminalization product between 2,6-diacetylpyridine and 1,3-diaminopropane. It crystallizes with two independent molecules in the asymmetric unit with different conformations. In the first molecule, the methyl groups are cis oriented with respect to the pyridine ring [N—C—C—C torsion angles = 72.5 (1) and 80.3 (1)°], while they are trans oriented in the second molecule [N—C—C—C torsion angles = 82.6 (1) and -90.8 (1)°]. Each of the two molecules forms centrosymmetric dimers held together by N—H[cdots, three dots, centered]N hydrogen bonds, thus forming R 2 2(16) rings. The two dimers are interlinked by additional N—H[cdots, three dots, centered]N bonds into R 4 4(14) rings, building chains along the a axis. These patterns influence the orientation (either equatorial or axial) of the N—H bonds.
Neanderthal diets are reported to be based mainly on the consumption of large and medium sized herbivores, while the exploitation of other food types including plants has also been demonstrated. Though some studies conclude that early Homo sapiens were active hunters, the analyses of faunal assemblages, stone tool technologies and stable isotopic studies indicate that they exploited broader dietary resources than Neanderthals. Whereas previous studies assume taxon-specific dietary specializations, we suggest here that the diet of both Neanderthals and early Homo sapiens is determined by ecological conditions. We analyzed molar wear patterns using occlusal fingerprint analysis derived from optical 3D topometry. Molar macrowear accumulates during the lifespan of an individual and thus reflects diet over long periods. Neanderthal and early Homo sapiens maxillary molar macrowear indicates strong eco-geographic dietary variation independent of taxonomic affinities. Based on comparisons with modern hunter-gatherer populations with known diets, Neanderthals as well as early Homo sapiens show high dietary variability in Mediterranean evergreen habitats but a more restricted diet in upper latitude steppe/coniferous forest environments, suggesting a significant consumption of high protein meat resources.
Carbon-13 and oxygen-18 abundances were measured in large mammal skeletal remains (tooth enamel, dentine and bone) from the Chiwondo Beds in Malawi, which were dated by biostratigraphic correlation to ca. 2.5 million years ago. The biologic isotopic patterns, in particular the difference in carbon-13 abundances between grazers and browsers and the difference in oxygen-18 abundances between semi-aquatic and terrestrial herbivores, were preserved in enamel, but not in dentine and bone. The isotopic results obtained from the skeletal remains from the Chiwondo Beds indicate a dominance of savannah habitats with some trees and shrubs. This environment was more arid than the contemporaneous Ndolanya Beds in Tanzania. The present study confirms that robust australopithecines were able to live in relatively arid environments and were not confined to more mesic environments elsewhere in southern Africa.
Communication in the Web 2.0 context mainly works through images. The online video platform YouTube uses this form of visual communication and makes art forms of Western societies visible through their online videos. YouTube, as cultural reservoir and visual archive of moving images, accommodates the whole range of visualising creative processes – from artistic finger exercises to fine arts. A general characteristic of YouTube is the publishing of small everyday gestures of the ‘big ones’ (politicians, stars), like small incidents and their clumsiness in everyday actions, e.g. Beyonce´s fall from the stage or Tom Cruise’s demonic pro-scientology interview. Through their viral distribution on different platforms, these incidents will never be covered up or disappear from the public view. At the same time big gestures and star images are replicated and sometimes reinterpreted by the ‘small people’ who present themselves in the poses and attitudes of the stars. Generally, a coexistence of different perspectives is possible. YouTube allows polysemic and polyvalent views on the everyday and media phenomena. This article relies on YouTube research 2 that started in 2006 at the New Media Department of the Goethe University of Frankfurt. The results of the research have already presented representative forms and basic patterns, that is to say, categories for the clips appearing here. These kinds of clips, recurring in the observation period, have an impact on the basic representation of art or artistic expression within moving images on this platform. Methodologically the focus leads to the investigation (which has to be adequate to the specifics of the medium, or ‘media adequate’) of new visual structures and forms which can create – consciously or unconsciously – an art form. After focusing on the media structures, it will be discussed whether any and, if so, which ‘authentic’ new forms were developed solely on YouTube and whether these forms are innovative and can be characterised as avant-garde. This article first takes a small step in evaluating how to get from a general communication through means of visuality in web 2.0, an often endless chatty cheesy visual noise 3 – to the special quality of a consciously created aesthetic. From where do innovative aesthetic forms emerge, related to their media structures? 4 Are they the products of ‘media amateurs’ 5 or do we have to find new specifications and descriptions for the producers? The definition of a ‘media amateur’ describes technically interested private individuals who acquire and develop technology before commercial use of the technology is even recognisable. Just as artists are developing their own techniques, according to Dieter Daniels, media amateurs are autodidacts who invent techniques, rather than just acquire knowledge about them (see for example the demo scene, the machinima, brickfilm producers as well as many areas of computer gaming in general 6). The media amateur directly intervenes in the production processes of the medium and does not just simply use the medium. What is fascinating is the media amateur’s process of self education – not the result – and the direct impact on the internal structure and the control of the medium. 7 Media amateurs open a previously culturally unformed space of experience. This only partially applies to most of the YouTube clips in the realms of the visual arts; it is here most important to look at the visual content. This article discusses all these concepts and introduces new descriptions for the different forms of production: the technically oriented media master, the do-it-yourselfer, the tinkerer, the amateur handicraftsman and the inventor. It outlines a basic research project on ‘visual media culture’ (a triangulation of research on media structure and iconography) of the presented online video platform. It is a product of the analysis of clips focusing on the media structure, analyzing the creative handling of images and the deviations and differences of pre-set media formats and stereotypes.
The Video Vortex Reader is the first collection of critical texts to deal with the rapidly emerging world of online video – from its explosive rise in 2005 with YouTube, to its future as a significant form of personal media. After years of talk about digital convergence and crossmedia platforms we now witness the merger of the Internet and television at a pace no-one predicted. These contributions from scholars, artists and curators evolved from the first two Video Vortex conferences in Brussels and Amsterdam in 2007 which focused on responses to YouTube, and address key issues around independent production and distribution of online video content. What does this new distribution platform mean for artists and activists? What are the alternatives?
A thick Middle and Late Pleistocene loess/palaeosol sequence is exposed at the gravel quarry Gaul located east of Weilbach in the southern foreland of the Taunus Mountains. The loess/palaeosol sequence correlates to the last three glacial cycles. Seven samples were dated by luminescence methods using an elevated temperature IRSL (post-IR IRSL) protocol for polymineral fine-grains to determine the deposition age of the sediment and to set up a more reliable chronological framework for these deposits. The fading corrected IR50 and the pIRIR225 age estimates show a good agreement for almost all samples. The fading corrected IRSL ages range from 23.7 ± 1.6 ka to >350 ka indicating that the oldest loess was deposited during marine isotope stage (MIS) 10 or earlier and that the humic-rich horizon (Weilbacher Humuszone) was developed during the late phase of MIS 7. Loess taken above the fCc horizon most likely accumulated during MIS 6 indicating that the remains of the palaeosol are not belonging to the last interglacial soil. The two uppermost samples indicate that the youngest loess accumulated during MIS 2 (Upper Würmian). Age estimates for the loess-palaeosol sequence of the gravel quarry Gaul/Weilbach could be obtained up to ~350 ka using the pIRIR225 from feldspar. Keywords: loess, luminescence dating, IRSL, fading, Weilbach, chronostratigraphy
Editorial: Jürgen Stark : The ECB's Chief Economist about inflation targeting, liquidity support and the sovereign debt crisis Research Finance: Yulia Plyakha, Raman Uppal, Grigory Vilkov : "Why Does the Equally Weighted Portfolio Outperform the Value and Price Weighted Portfolios?" Research Law: Manfred Wandt : "Legal Objectives of the Solvency II Framework Directive" Research E-Finance: Roman Beck, Timm Pintner, Martin Wolf : "Individual Mindfulness to Mitigate Information Overload within Financial Organizations" Policy Platform: Peter Gomber, Björn Arndt, Marco Lutat, Tim Uhle : "Regulation of High-Frequency Trading – A European Perspective" Interview: Norbert Walter : "The Risko of Compromising on Price Stability Must not be Taken"
Effort estimates are of utmost economic importance in software development projects. Estimates bridge the gap between managers and the invisible and almost artistic domain of developers. They give a means to managers to track and control projects. Consequently, numerous estimation approaches have been developed over the past decades, starting with Allan Albrecht's Function Point Analysis in the late 1970s. However, this work neither tries to develop just another estimation approach, nor focuses on improving accuracy of existing techniques. Instead of characterizing software development as a technological problem, this work understands software development as a sociological challenge. Consequently, this work focuses on the question, what happens when developers are confronted with estimates representing the major instrument of management control? Do estimates influence developers, or are they unaffected? Is it irrational to expect that developers start to communicate and discuss estimates, conform to them, work strategically, hide progress or delay? This study shows that it is inappropriate to assume an independency of estimated and actual development effort. A theory is developed and tested, that explains how developers and managers influence the relationship between estimated and actual development effort. The theory therefore elaborates the phenomenon of estimation fulfillment.
In der vorliegenden Arbeit konzentrierte ich mich auf mediterrane wirbellose Tierarten, welche sich als Konsequenz ihrer Lebensweise nur schlecht ausbreiten können. Nichtsdestotrotz haben es Süßwasserkrabben der Gattung Potamon und Landschnecken der Gattung Tudorella geschafft, große Gebiete zu besiedeln, die heute durch das Mittelmeer getrennt sind. Für beide Gruppen wurde spekuliert, dass Menschen an ihrer Ausbreitung beteiligt waren. Es war mein Ziel die biogeographischen Muster dieser beiden Gattungen zu analysieren und abzuschätzen, ob Menschen tatsächlich Vektoren ihrer Ausbreitung waren. Meine Analysen fanden auf drei Ebenen statt: Taxonomie, Gattung und Art.
The analysis of biomolecular macrocomplexes requires certain preconditions to be fulfilled. The preparation of biomolecular samples usually results in low yields. Due to this constraint of low availability any method should provide a sufficient sensitivity to cope with typical sample amounts. Biomolecules also often show a reduced stability, i.e. a propensity for fragmentation upon ionisation, which requires reasonable soft methods for the investigation. Furthermore macromolecular complexes usually are composed by means of non-covalent interactions presenting additional demands on the softness. This holds true for specific complexes like protein-ligand or DNA double strand binding. For the formation of non-covalent, specific complexes the biomolecules’ native structure and environment are a basic prerequisite and hence crucial. Therefore it is desirable during analysis to keep the biomolecules in a native environment to preserve their structure and weak interactions. One suitable method for analysing biomolecules is mass spectrometry. Mass spectrometry is capable of high throughput screening as well as determining masses with high accuracy and high sensitivity. Especially since the availability of MALDI-MS and ESI-MS mass spectrometry evolved to a versatile tool to investigate biomolecular complexes. Both, MALDI- and ESI-MS are sufficiently soft methods to observe fragile biomolecules. Yet both methods have their advantages and disadvantages. During the recent years an alternative mass spectrometric approach has been developed in our group, termed LILBID-MS (Laser Induced Liquid Bead Ionisation/Desorption). In LILBID microdroplets of aqueous solution containing buffer, salt and further additives among the analyte molecules are injected into vacuum and irradiated one-by-one by mid-IR laser pulses. The absorption of the energy by the water leads to a rapid ablation of the preformed analyte ions. LILBID is highly tolerant for the addition of salts and detergents allowing to study biomolecular complexes in a native environment. As LILBID-MS is soft enough to avoid fragmentation, specific non-covalent complexes can be analysed directly from their native environment by this method. In addition dissociation can be induced on demand by increasing the laser intensity which allows for the study of subunit compositions. A further prominent property of LILBID is the possibility to study hydrophobic membrane proteins due to the tolerated use of detergents. During the course of this work, several instrumental improvements mostly concerning ion focussing and beam steering were introduced. Together with refinements of different modes of measurement the result is a significantly improved signal-to-noise ratio as well as a further improvement in sensitivity. In addition the accessible m/z range for a given flight time has been vastly increased. The new possibilities that LILBID now offers for the study of biomolecular complexes were investigated. The ability to detect specific binding in LILBID-MS was investigated by means of nucleic acids and their interaction with proteins. It could be shown that the stability of a 16bp dsDNA corresponds to that in solution phase regarding the dependency on concentration and type of the salts used. In addition a competitive experiment with the well-known transcription factor p50 was used to demonstrate the detection of sequence-specific binding with LILBID. The improved sensitivity allowed to detect single stranded DNA at nanomolar concentrations and even the 2686bp plasmid pUC19 could be easily detected without fragmentation using a concentration of only 80nM. In case of the transcription factor p63 the mass spectrometric analysis could help to identify a new model of activation and inhibition. For the first time known quarternary structures of membrane proteins like the light-driven proton pump bacteriorhodopsin and the potassium channel KcsA could be detected with mass spectrometry. For the light-driven proton pump proteorhodopsin the type and the concentration of the used detergents significantly influenced the stability of this protein as well as the preferred quarternary structure.
In nature, society and technology many disordered systems exist, that show emergent behaviour, where the interactions of numerous microscopic agents result in macroscopic, systemic properties, that may not be present on the microscopic scale. Examples include phase transitions in magnetism and percolation, for example in porous unordered media, biological, and social systems. Also technological systems that are explicitly designed to function without central control instances, like their prime example the Internet, or virtual networks, like the World Wide Web, which is defined by the hyperlinks from one web page to another, exhibit emergent properties. The study of the common network characteristics found in previously seemingly unrelated fields of science and the urge to explain their emergence, form a scientific field in its own right, the science of complex networks. In this field, methodologies from physics, leading to simplification and generalization by abstraction, help to shift the focus from the implementation's details on the microscopic level to the macroscopic, coarse grained system level. By describing the macroscopic properties that emerge from microscopic interactions, statistical physics, in particular stochastic and computational methods, has proven to be a valuable tool in the investigation of such systems. The mathematical framework for the description of networks is graph theory, in hindsight founded by Euler in 1736 and an active area of research since then. In recent years, applied graph theory flourished through the advent of large scale data sets, made accessible by the use of computers. A paradigm for microscopic interactions among entities that locally optimize their behaviour to increase their own benefit is game theory, the mathematical framework of decision finding. With first applications in economics e.g. Neumann (1944), game theory is an approved field of mathematics. However, game theoretic behaviour is also found in natural systems, e.g. populations of the bacterium Escherichia coli, as described by Kerr (2002). In the present work, a combination of graph theory and game theory is used to model the interactions of selfish agents that form networks. Following brief introductions to graph theory and game theory, the present work approaches the interplay of local self-organizing rules with network properties and topology from three perspectives. To investigate the dynamics of topology reshaping, coupling of the so called iterated prisoners' dilemma (IPD) to the network structure is proposed and studied in Chapter 4. In dependence of a free parameter in the payoff matrix, the reorganization dynamics result in various emergent network structures. The resulting topologies exhibit an increase in performance, measured by a variance of closeness, of a factor 1.2 to 1.9, depending in the chosen free parameter. Presented in Chapter 5, the second approach puts the focus on a static network structure and studies the cooperativity of the system, measured by the fixation probability. Heterogeneous strategies to distribute incentives for cooperation among the players are proposed. These strategies allow to enhance the cooperative behaviour, while requiring fewer total investments. Putting the emphasis on communication networks in Chapters 6 and 7, the third approach investigates the use of routing metrics to increase the performance of data packet transport networks. Algorithms for the iterative determination of such metrics are demonstrated and investigated. The most successful of these algorithms, the hybrid metric, is able to increase the throughput capacity of a network by a factor of 7. During the investigation of the iterative weight assignments a simple, static weight assignment, the so called logKiKj metric, is found. In contrast to the algorithmic metrics, it results in vanishing computational costs, yet it is able to increase the performance by a factor of 5.
Suicide genes have been broadly used in gene therapy. They can serve as safety tools for conditional elimination of infused cells or for directed tumor therapy. To date, the Herpes simplex virus thymidine kinase/ ganciclovir (HSVtk/GCV) system is the most prominent and the most widely used suicidegene/prodrug combination. Despite its promising performance, the system displays limitations, which include relatively slow killing kinetics and toxicity of the prodrug GCV. Consequently, several groups have either developed new suicide-gene/prodrug combinations or attempted to improve the established HSVtk/GCV suicide system. The present study also aimed towards optimization of the HSVtk/GCV system. To do so, a novel, codon-optimized point mutant (A168H) of HSVtk was developed. The novel mutant was named TK.007. It was extensively tested for its efficiency in two relevant settings: (1) control of severe graft-versus-host disease (GvHD) after adoptive immunotherapy with Tlymphocytes, and (2) direct elimination of targeted tumor cells. TK.007 was compared to the broadly used wild-type, splice-corrected scHSVtk and to a codon-optimized HSVtk (coHSVtk) not bearing the above point mutation. (1) For experiments related to the adoptive immunotherapy approach, HSVtkvariants were expressed from a γ-retroviral MP71 vector as a fusion construct with the selection and marker gene tCD34. Expression levels for TK.007 in transduced lymphoid and myeloid cell lines were significantly higher at initial transduction and over a 12 week period compared to the commonly used scHSVtk and coHSVtk indicating reduced toxicity of TK.007. Killing kinetics of transduced cell lines (PM1 and K562) and primary human T cells were significantly faster for TK.007 in comparison to scHSVtk and coHSVtk in vitro. In vivo-functionality of TK.007 was assessed in an allogeneic transplantation model. T cells derived from C57BL/6J.Ly5.1 donor mice were transduced with MP71 vectors expressing scHSVtk or TK.007. Transduced cells were selected and transplanted into Balb/c Rag2-/- γ-/- immune-deficient recipient mice. Acute, severe GvHD occurred and was effectively abrogated in all mice transplanted with TK.007- transduced T cells, and in five out of six mice transplanted with scHSVtk-transduced cells. In a slightly modified quantitative allogeneic transplantation mouse model, significantly faster and more efficient in vivo killing was demonstrated for TK.007 as compared to scHSVtk, especially at low doses of GCV. (2) In order to assess TK.007 functionality in cells derived from solid tumors, HSVtk-variants were expressed from lentiviral gene ontology (LeGO) vectors in combination with an eGFP/neo-opt selection cassette. Transduced and selected tumor cell lines that derived from several tissues were eliminated at significantly lower GCV doses and to higher extents when transduced with TK.007 compared to scHSVtk. Moreover, a significantly stronger bystander effect of TK.007 was demonstrated. The superior in vitro efficiency of TK.007 was confirmed in an in vivo subcutaneous xenograft mouse model for glioblastoma in NOD/SCID mice. Mice transplanted with TK.007 transduced cells stayed tumor-free after treatment with different GCV-doses. On the contrary, mice of the scHSVtk group either demonstrated only transiently reduced tumor growth in the low-dose GCV group (10 mg/kg) compared to the control groups or suffered from relatively fast relapses after initial tumor shrinking in the standarddose (50 mg/kg) GCV group. As a result, all mice in the scHSVtk group died from vigorous tumor growth. In summary, in two different applications for suicide gene therapy the present study has demonstrated superior functional performance of the novel suicide gene TK.007 as compared to the broadly used wild-type scHSVtk. Differences became particularly pronounced at low doses of GCV. It can be concluded that the new TK.007-gene represents a promising alternative to the commonly used scHSVtk for gene therapeutic applications.
The aim of this work is to develop an effective equation of state for QCD, having the correct asymptotic degrees of freedom, to be used as input for dynamical studies of heavy ion collisions. We present an approach for modeling an EoS that respects the symmetries underlying QCD, and includes the correct asymptotic degrees of freedom, i.e. quarks and gluons at high temperature and hadrons in the low-temperature limit. We achieve this by including quarks degrees of freedom and the thermal contribution of the Polyakov loop in a hadronic chiral sigma-omega model. The hadronic part of the model is a nonlinear realization of an sigma-omega model. As the fundamental symmetries of QCD should also be present in its hadronic states such an approach is widely used to describe hadron properties below and around Tc. The quarks are introduced as thermal quasi particles, coupling to the Polyakov loop, while the dynamics of the Polyakov loop are controlled by a potential term which is fitted to reproduce pure gauge lattice data. In this model the sigma field serves a the order parameter for chiral restoration and the Polyakov loop as order parameter for deconfinement. The hadrons are suppressed at high densities by excluded volume corrections. As a next step, we introduce our new HQ model equation of state in a microscopic+macroscopic hybrid approach to heavy ion collisions. This hybrid approach is based on the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) transport approach with an intermediate hydrodynamical evolution for the hot and dense stage of the collision. The present implementation allows to compare pure microscopic transport calculations with hydrodynamic calculations using exactly the same initial conditions and freeze-out procedure. The effects of the change in the underlying dynamics - ideal fluid dynamics vs. non-equilibrium transport theory - are explored. The final pion and proton multiplicities are lower in the hybrid model calculation due to the isentropic hydrodynamic expansion while the yields for strange particles are enhanced due to the local equilibrium in the hydrodynamic evolution. The elliptic and directed flow are shown to be not sensitive to changes in the EoS while the smaller mean free path in the hydrodynamic evolution reflects directly in higher flow results which are consistent with the experimental data. This finding indicates qualitatively that physical mechanisms like viscosity and other non equilibrium effects play an essentially more important role than the EoS when bulk observables like flow are investigated. In the last chapter, results for the thermal production of MEMOs in nucleus-nucleus collisions from a combined micro+macro approach are presented. Multiplicities, rapidity and transverse momentum spectra are predicted for Pb+Pb interaction at different beam energies. The presented excitation functions for various MEMO multiplicities show a clear maximum at the upper FAIR energy regime making this facility the ideal place to study the production of these exotic forms of multistrange objects.
In human neuroscientific research, there has been an increasing interest in how the brain computes the value of an anticipated outcome. However, evidence is still missing about which valuation related brain regions are modulated by the proximity to an expected goal and the previously invested effort to reach a goal. The aim of this dissertation is to investigate the effects of goal proximity and invested effort on valuation related regions in the human brain. We addressed this question in two fMRI studies by integrating a commonly used reward anticipation task in differential versions of a Multitrial Reward Schedule Paradigm. In both experiments, subjects had to perform consecutive reward anticipation tasks under two different reward contingencies: in the delayed condition, participants received a monetary reward only after successful completion of multiple consecutive trials. In the immediate condition, money was earned after every successful trial. In the first study, we could demonstrate that the rostral cingulate zone of the posterior medial frontal cortex signals action value contingent to goal proximity, thereby replicating neurophysiological findings about goal proximity signals in a homologous region in non-human primates. The findings of the second study imply that brain regions associated with general cognitive control processes are modulated by previous effort investment. Furthermore, we found the posterior lateral prefrontal cortex and the orbitofrontal cortex to be involved in coding for the effort-based context of a situation. In sum, these results extend the role of the human rostral cingulate zone in outcome evaluation to the continuous updating of action values over a course of action steps based on the proximity to the expected reward. Furthermore, we tentatively suggest that previous effort investment invokes processes under the control of the executive system, and that posterior lateral prefrontal cortex and the orbitofrontal cortex are involved in an effort-based context representation that can be used for outcome evaluation that is dependent on the characteristics of the current situation.
The focus of the discussion at the conference on September 23, 2004 was on the long-term impact on capital markets and pension systems. The speakers tried to identify the direction and magnitude of potential changes as well as the likelihood of an eventual asset meltdown. The conference's objective was to combine insights from academia with those from the financial community in order to provide a more comprehensive outlook on capital market developments. Conference Reader Nr. 2005/01
Conference Reader zur gemeinsam von Athansios Orphanides (Federal Reserve Board, Washington D.C.), John C. Williams (Federal Reserve Bank of San Francisco), Heinz Hermann (Deutsche Bundesbank), und Volker Wieland (Center for Financial Studies and Goethe University Frankfurt) organisierten Konferenz, die vom 30. - 31. August, 2003 in Eltville stattgefunden hat. Inhaltsverzeichnis: * Volker Wieland (Director Center for Financial Studies): Foreword * Hans Georg Fabritius (Member of the Executive Board of the Deutsche Bundesbank): Opening Remarks * Charles Goodhart (Norman Sosnow Professor of Banking and Finance at the London School of Economics and External Member of the Bank of England's Monetary Policy Commitee): After Dinner Speech * Paper Abstracts * List of Participants
Over the last years there has been an increasing interest in the involvement of the MVA-pathway and of members of the small GTPases, in the development and progression of AD. Earlier investigations mainly focused on the role of cholesterol in disease pathology. This research was supported by retrospective cohort studies, initially showing beneficial effects of the long-term intake of cholesterol lowering statins, on the incidence of the development of sporadic AD. However, in more recent literature increasing attention has been paid to the isoprenoids, FPP and GGPP, due to their crucial role in the post-translational modifications of members of the superfamily of small GTPases. In AD, these proteins were amongst others shown to be involved in mechanisms affecting APP processing, ROS generation and synaptic plasticity. A major factor impeding the clarification of the role of the MVA-pathway intermediates in these mechanisms was the lack of a sensitive and accurate method to determine FPP and GGPP levels in brain tissue. Hence, a state of the art HPLC-FLD method for the quantification of the isoprenoids FPP and GGPP in brain tissue was successfully developed. After the introduction of a double clean-up step from complex brain matrix samples and the synthesis of an appropriate IS (DNP), the method was fully validated according to the latest FDA guideline for bioanalytical method validation. Furthermore, this method was transferred to a faster and more sensitive, state of the art UHPLC-MS/MS application. Additionally, the method was shown to be applicable for mouse brain tissue and data was generated from an in vivo mouse simvastatin study and for different mouse models. According to the aims of the thesis, the current work describes for the first time absolute isoprenoid concentrations in human frontal cortex white and grey matter. Furthermore, this is the first report of isoprenoid levels in the frontal cortex of human AD brains. Further results were shown from mouse brains originating from different mouse models, including the Thy-1 APP mouse model mimicking AD pathology in terms of Aβ formation or C57Bl/6 mice at different ages. AD prevalence can be clearly correlated with increasing age. Therefore, three different generations of mice were investigated. The study demonstrated constant isoprenoid and cholesterol levels in the first half of their life followed by a significant increase of FPP and GGPP in the second half (between 12 and 24 month of age). Cholesterol levels were also elevated in the aged group, but again the effect was less pronounced than shown for the isoprenoids. These results lead to the tentative conclusion that cerebral isoprenoid levels are elevated during aging and that this accumulation is amplified during AD leading to accelerated neuronal dysfunction. In a different mouse study, using the C57Bl/6 mice, in vivo drug intervention with the HMG-CoA reductase inhibitor simvastatin revealed strong inhibition of the rate limiting step of the mevalonate/isoprenoid/cholesterol pathway and resulted in the first report of significantly reduced FPP and GGPP levels in brain tissue of statin treated mice. These results open for the first time the possibility to monitor drug effects on cerebral isoprenoid levels and correlate these data with a modulation of APP processing, which was shown by our group in previous studies. Interestingly, apart from the isoprenoid reduction following statin treatment the reduction of brain cholesterol was also significant but to a lesser extent. These findings support the notion that isoprenoid levels are more susceptible to statin treatment than cholesterol levels. Furthermore, this suggests a strong cellular dependence on FPP and GGPP, as the pool seems to be easily depleted, which finally could lead to cell death. The first investigations of farnesylated Ras and geranylgeranylated Rac protein levels by means of immuno-blotting, substantiated the notion of a decreased abundance of prenylated small GTPases under statin influence as a consequence of reduced isoprenoid levels. These findings demonstrate for the first time a correlation of FPP and GGPP levels with the abundance of small GTPases. These findings together with the results from the AD study prove that isoprenoid levels are not strictly subject to the same regulation as cholesterol levels. To further understand the physiological regulation in the cell, in vitro experiments with different inhibitors of the mevalonate/isoprenoid/cholesterol pathway were conducted. These results confirmed the isoprenoid and cholesterol reducing effects of statin treatment as observed in the aforementioned in vivo mouse study. Interestingly, cholesterol synthesis inhibition targeted after FPP as the branch point, led to significantly elevated FPP levels. FTase inhibition led to significantly reduced FPP levels, whereas inhibition of the GGTase I did not show a significant change of either isoprenoid levels.
In the work presented herein the microscopic transport model BAMPS (Boltzmann Approach to Multi-Parton Scatterings) is applied to simulate the time evolution of the hot partonic medium that is created in Au+Au collisions at the Relativistic Heavy Ion Collider (RHIC) and in Pb+Pb collisions at the recently started Large Hadron Collider (LHC). The study is especially focused on the investigation of the nuclear modification factor R_{AA}, that quantifies the suppression of particle yields at large transverse momentum with respect to a scaled proton+proton reference, and the simultaneous description of the collective properties of the medium in terms of the elliptic flow v_{2} within a common framework.
One of the key functions of blood vessels is to transport nutrients and oxygen to distant tissues and organs in the body. When blood supply is insufficient, new vessels form to meet the metabolic tissue demands and to re-establish cellular homeostasis. Expansion of the vascular network through sprouting angiogenesis requires the specification of ECs into leading (sprouting) tip and following (non-sprouting) stalk cells. Attracted by guidance cues tip cells dynamically extend and retract filopodia to navigate the nascent vessel sprout, whereas trailing stalk cells proliferate to form the extending vascular tube. All of these processes are under the control of environmental signals (e.g. hypoxia, metabolism) and numerous cytokines and peptide growth factors. The Dll4/Notch pathway coordinates several critical steps of angiogenic blood vessel growth. Even subtle alterations in Notch activity can profoundly influence endothelial cell behavior and blood vessel formation, yet little is known about the intrinsic regulation and dynamics of Notch signaling in endothelial cells. In addition, it remains an open question, how different growth factor signals impinging on sprouting ECs are coordinated with local environmental cues originating from nutrient-deprived, hypoxic tissue to achieve a balanced endothelial cell response. Acetylation of lysines is a critical posttranslational modification of histones, which acts as an important regulatory mechanism to control chromatin structure and gene transcription. In addition to histones, several non-histone proteins are targeted for acetylation reversible acetylation is emerging as a fundamental regulatory mechanism to control protein function, interaction and stability. Previous studies from our group identified the NAD+-dependent deacetylase SIRT1 as a key regulator of blood vessel growth controlling endothelial angiogenic responses. These studies revealed that SIRT1 is highly expressed in the vascular endothelium during blood vessel development, where it controls the angiogenic activity of endothelial cells. Moreover, in this work SIRT1 has been shown to control the activity of key regulators of cardiovascular homeostasis such as eNOS, Foxo1 and p53. The present study describes that SIRT1 antagonizes Notch signaling by deacetylating the Notch intracellular domain (NICD). We showed that loss of SIRT1 enhances DLL4-induced endothelial Notch responses as assessed by different luciferase responsive elements as well as transcriptional analysis of Notch endogenous target genes activation. Conversely, SIRT1 gain of function by overexpression of pharmacological activation decreases induction of Notch targets in response to DLL4 stimulation. We also showed that the NICD can be directly acetylated by PC AF and p300 and that SIRT1 promotes deacetylation of NICD. We have identified 14 lysines that are targeted for acetylation and their mutation abolishes the effects of SIRT1 of Notch responses. Furthermore, over-expression or activation of SIRT1 significantly reduces the levels of NICD protein. Moreover, SIRT1-mediated NICD degradation can be reversed by blockade of the proteasome suggesting a mechanism resulting from ubiquitin-mediated proteolysis. Indeed, we have shown that SIRT1 knockdown or pharmacological inhibition decreased NICD ubiquitination. We propose a novel molecular mechanism of modulation of the amplitude and duration of Notch responses in which acetylation increases NICD stability and therefore permanence at the promoters, while SIRT1, by inducing NICD degradation through its deacetylation, shortens Notch responses. In order to evaluate the physiological relevance of our findings we used different models in which the Notch functions during blood vessel formation have been extensively characterized. First, retinal angiogenesis in mice lacking SIRT1 activity shows decreased branching and reduced endothelial proliferation, similar to what happens after Notch gain of function mutations. ECs from these mice exhibit increased expression of Notch target genes. Second, these results were reproducible during intersomitic vessel growth in sirt1-deficient zebrafish. In both models, the defects could be partially rescued by inhibition of Notch activation. Third, we used an in vitro model of vessel sprouting from differentiating embryonic bodies in response to VEGF in a collagen matrix. Our results showed that Sirt1-deficient cells shows impaired sprouting which correlated with increased NICD levels. In addition, when in competition with wild-type cells in this assay, Sirt1-deficient cells are more prone to occupy the stalk cell position. Taken together, our study identifies reversible acetylation of NICD as a novel molecular mechanism to adapt the dynamics of Notch signaling and suggest that SIRT1 acts as a rheostat to fine-tune endothelial Notch responses. The NAD+-dependent feature of SIRT1 activity possibly links endothelial Notch responses to environmental cues and metabolic changes during nutrient deprivation in ischemic environments or upon other cellular stresses.
This dissertation contains three essays on monetary policy, dynamics of the interest rates and spillovers across economies. In the first essay I examine the effects of monetary policy and its interaction with financial regulation within a micro-founded macroeconometric framework for a closed economy with a heterogeneous banking system, facing a period of low interest rates. I analyse the interplay between monetary policy and banking regulation and study the role of agents’ expectations for the effectiveness of unconventional monetary policy tools. In the next essay, I argue that openness is crucial for understanding the dynamics of the term structure. In an empirical application, I show that my model of the term structure fits well the yield curve in-sample and has a sound ability to forecast interest rates out-of-sample. The model accounts for the expectations hypothesis, replicates the forward premium anomaly and reconciles the uncovered interest rate parity implications. The last essay is concerned with the dynamics of co-movement among macroeconomic aggregates and the degree of convergence or decoupling amongst economies. The model includes measures of financial and trade-based interdependencies and incorporates feedback between macroeconomic variables and time-varying weights. The findings point at the importance of asset price movements and financial linkages.
Organische Materialien haben bis zur Mitte des 20. Jahrhunderts hinsichtlich ihrer elektronischen Eigenschaften keine besondere Aufmerksamkeit auf sich gezogen. Größeres Interesse an diesen Materialien entstand erst durch die Entdeckung einer ungewöhnlich hohen elektrischen Leitfähigkeit des organischen Perylen-Bromin Ladungstransfer-Komplexes durch Inokuchi et al. im Jahr 1954. Diese neue Klasse von Materialien besteht typischerweise aus Donor- und Akzeptor-Molekülen, die in einer bestimmten Stöchiometrie aneinander gebunden sind. Elektrische Ladung wird zwischen den Donor- und Akzeptor-Molekülen transferiert. Um diesen Prozess zu beschreiben, entwickelte Robert Mulliken in den 60er Jahren ein theoretisches Gerüst. Abhängig von der Anordnung der Moleküle und transferierten elektrischen Ladung kann der Ladungstransfer-Komplex (oder Salz) ein Isolator, ein Halbleiter, ein Metall oder sogar ein Supraleiter sein. Noch mehr Aufmerksamkeit erhielten Ladungstransfer-Materialien mit der Entdeckung des ersten quasi-eindimensionalen organischen Metalls TTF-TCNQ (tetrathiafulvalene-tetracyanoquinodimethane) im Jahr 1973. ...
This dissertation connects two independent fields of theoretical neuroscience: on the one hand, the self-organization of topographic connectivity patterns, and on the other hand, invariant object recognition, that is the recognition of objects independently of their various possible retinal representations (for example due to translations or scalings). The topographic representation is used in the presented approach, as a coordinate system, which then allows for the implementation of invariance transformations. Hence this study shows, that it is possible that the brain self-organizes before birth, so that it is able to invariantly recognize objects immediately after birth. Besides the core hypothesis that links prenatal work with object recognition, advancements in both fields themselves are also presented. In the beginning of the thesis, a novel analytically solvable probabilistic generative model for topographic maps is introduced. And at the end of the thesis, a model that integrates classical feature-based ideas with the normalization-based approach is presented. This bilinear model makes use of sparseness as well as slowness to implement "optimal" topographic representations. It is therefore a good candidate for hierarchical processing in the brain and for future research.
We present simulations with the Chemical Lagrangian Model of the Stratosphere (CLaMS) for the Arctic winter 2002/2003. We integrated a Lagrangian denitrification scheme into the three-dimensional version of CLaMS that calculates the growth and sedimentation of nitric acid trihydrate (NAT) particles along individual particle trajectories. From those, we derive the HNO3 downward flux resulting from different particle nucleation assumptions. The simulation results show a clear vertical redistribution of total inorganic nitrogen ( ), with a maximum vortex average permanent removal of over 5ppb in late December between 500 and 550K and a corresponding increase of of over 2ppb below about 450K. The simulated vertical redistribution of is compared with balloon observations by MkIV and in-situ observations from the high altitude aircraft Geophysica. Assuming a globally uniform NAT particle nucleation rate of 7.8x10-6cm-3h-1 in the model, the observed denitrification is well reproduced.
In the investigated winter 2002/2003, the denitrification has only moderate impact (≤14%) on the simulated vortex average ozone loss of about 1.1ppm near the 460K level. At higher altitudes, above 600K potential temperature, the simulations show significant ozone depletion through -catalytic cycles due to the unusual early exposure of vortex air to sunlight.
Background: The aim of this study was to develop a child-specific classification system for long bone fractures and to examine its reliability and validity on the basis of a prospective multicentre study. Methods: Using the sequentially developed classification system, three samples of between 30 and 185 paediatric limb fractures from a pool of 2308 fractures documented in two multicenter studies were analysed in a blinded fashion by eight orthopaedic surgeons, on a total of 5 occasions. Intra- and interobserver reliability and accuracy were calculated. Results: The reliability improved with successive simplification of the classification. The final version resulted in an overall interobserver agreement of kappa=0.71 with no significant difference between experienced and less experienced raters. Conclusions: In conclusion, the evaluation of the newly proposed classification system resulted in a reliable and routinely applicable system, for which training in its proper use may further improve the reliability. It can be recommended as a useful tool for clinical practice and offers the option for developing treatment recommendations and outcome predictions in the future.
Dynamics of relativistic heavy-ion collisions is investigated on the basis of a simple (1+1)-dimensional hydrodynamical model in light-cone coordinates. The main emphasis is put on studying sensitivity of the dynamics and observables to the equation of state and initial conditions. Low sensitivity of pion rapidity spectra to the presence of the phase transition is demonstrated, and some inconsistencies of the equilibrium scenario are pointed out. Possible non-equilibrium effects are discussed, in particular, a possibility of an explosive disintegration of the deconfined phase into quark-gluon droplets. Simple estimates show that the characteristic droplet size should decrease with increasing the collective expansion rate. These droplets will hadronize individually by emitting hadrons from the surface. This scenario should reveal itself by strong non-statistical fluctuations of observables. Critical Point and Onset of Deconfinement 4th International Workshop July 9-13 2007 GSI Darmstadt,Germany
Event-by-event multiplicity fluctuations in nucleus-nucleus collisions from low SPS up to RHIC energies have been studied within the HSD transport approach. Fluctuations of baryonic number and electric charge also have been explored for Pb+Pb collisions at SPS energies in comparison to the experimental data from NA49. We find a dominant role of the fluctuations in the nucleon participant number for the final hadron multiplicity fluctuations and a strong influence of the experimental acceptance on the final results. Critical Point and Onset of Deconfinement - 4th International Workshop July 9 - 13, 2007 Darmstadt, Germany
Statistical physics of power flows on networks with a high share of fluctuating renewable generation
(2010)
Renewable energy sources will play an important role in future generation of electrical energy. This is due to the fact that fossil fuel reserves are limited and because of the waste caused by conventional electricity generation. The most important sources of renewable energy, wind and solar irradiation, exhibit strong temporal fluctuations. This poses new problems for the security of supply. Further, the power flows become a stochastic character so that new methods are required to predict flows within an electrical grid. The main focus of this work is the description of power flows in a electrical transmission network with a high share of renewable generation of electrical energy. To define an appropriate model, it is important to understand the general set-up of a stable system with fluctuating generation. Therefore, generation time series of solar and wind power are compared to load time series for whole Europe and the required balancing or storage capacities analyzed. With these insights, a simple model is proposed to study the power flows. An approximation to the full power flow equations is used and evaluated with Monte-Carlo simulations. Further, approximations to the distributions of power flows along the links are analytically derived. Finally, the results are compared to the power flows calculated from the generation and load data.
Nanggroe Aceh Darussalam is a multicultural province within a multicultural state. Hence, its political leaders not only face the need to integrate ethnic and cultural diversity into a regional framework, but also have to define Aceh’s role within the Indonesian nation. During its violent past which was characterized by exploitation and military oppression, there were good reasons to emphasize sameness over diversity and to build up the consciousness of a unified Acehnese identity. From both an emic and an etic perspective, it is today widely accepted that there is such a thing as a homogeneous Acehnese culture which is rooted in a glorious, though troublesome, history of repression and rebellion and shaped by a strong Islamic piety. Even if it is true that Acehnese history has created a strong regional identity, it must not be forgotten that people living in this area belong to various ethnic and cultural groups and that they represent a rich variety of different cultures rather than simply a single homogeneous culture. As a matter of fact, the practises and discourses of Islam here also vary depending on the cultural background of the people. As elsewhere in Indonesia and beyond, world religions have to adapt to local customs, have to be appropriated by the local people, and have to be indigenized. This is the reason why adat still continues to play a role in every local context, even if it has been treated with suspicion in many parts of Indonesia since the Dutch colonial administration began using it as a counterforce against Islam in order to implement their divide-and-rule strategy. With this article, I wish to shed some light on the complexities of Acehnese culture, as it encompasses numerous very distinct local cultures and this reflects on the general significance of culture for the construction and reconstruction of post-tsunami Aceh.