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The prediction of protein–ligand interactions and their corresponding binding free energy is a challenging task in structure-based drug design and related applications. Docking and scoring is broadly used to propose the binding mode and underlying interactions as well as to provide a measure for ligand affinity or differentiate between active and inactive ligands. Various studies have revealed that most docking software packages reliably predict the binding mode, although scoring remains a challenge. Here, a diverse benchmark data set of 99 matched molecular pairs (3D-MMPs) with experimentally determined X-ray structures and corresponding binding affinities is introduced. This data set was used to study the predictive power of 13 commonly used scoring functions to demonstrate the applicability of the 3D-MMP data set as a valuable tool for benchmarking scoring functions.
Background: Immigration has a strong impact on the development of health systems, medicine and science worldwide. Therefore, this article provides a descriptive study on the overall research output.
Methods: Utilizing the scientific database Web of Science, data research was performed. The gathered bibliometric data was analyzed using the established platform NewQIS, a benchmarking system to visualize research quantity and quality indices.
Findings: Between 1900 and 2016 a total of 6763 articles on immigration were retrieved and analyzed. 86 different countries participated in the publications. Quantitatively the United States followed by Canada and Spain were prominent regarding the article numbers. On comparing by additionally taking the population size into account, Israel followed by Sweden and Norway showed the highest performance. The main releasing journals are the Public Health Reports, the Journal of Immigrant and Minority Health and Social Science & Medicine. Over the decades, an increasing number of Public, Environmental & Occupational Health articles can be recognized which finally forms the mainly used subject area.
Conclusion: Considerably increasing scientific work on immigration cannot only be explained by the general increase of scientific work but is also owed to the latest development with increased mobility, worldwide crises and the need of flight and migration. Especially countries with a good economic situation are highly affected by immigrants and prominent in their publication output on immigration, since the countries’ publication effort is connected with the appointed expenditures for research and development. Remarkable numbers of immigrants throughout Europe compel medical professionals to consider neglected diseases, requires the public health system to restructure itself and finally promotes science.
The HCV NS5A protein plays multiple roles during viral replication, including viral genome replication and virus particle assembly. The crystal structures of the NS5A N-terminal domain indicated the potential existence of the NS5A dimers formed via at least two or more distinct dimeric interfaces. However, it is unknown whether these different forms of NS5A dimers are involved in its numerous functions. To address this question, we mutated the residues lining the two different NS5A dimer interfaces and determined their effects on NS5A self-interaction, NS5A-cyclophilin A (CypA) interaction, HCV RNA replication and infectious virus production. We found that the mutations targeting either of two dimeric interfaces disrupted the NS5A self-interaction in cells. The NS5A dimer-interrupting mutations also inhibited both viral RNA replication and infectious virus production with some genotypic differences. We also determined that reduced NS5A self-interaction was associated with altered NS5A-CypA interaction, NS5A hyperphosphorylation and NS5A subcellular localization, providing the mechanistic bases for the role of NS5A self-interaction in multiple steps of HCV replication. The NS5A oligomers formed via different interfaces are likely its functional form, since the residues at two different dimeric interfaces played similar roles in different aspects of NS5A functions and, consequently, HCV replication. In conclusion, this study provides novel insight into the functional significance of NS5A self-interaction in different steps of the HCV replication, potentially, in the form of oligomers formed via multiple dimeric interfaces.
The NF-κB-like velvet domain protein VosA (viability of spores) binds to more than 1,500 promoter sequences in the filamentous fungus Aspergillus nidulans. VosA inhibits premature induction of the developmental activator gene brlA, which promotes asexual spore formation in response to environmental cues as light. VosA represses a novel genetic network controlled by the sclB gene. Bfunction is antagonistic to VosA, because it induces the expression of early activator genes of asexual differentiation as flbC and flbD as well as brlA. The SclB controlled network promotes asexual development and spore viability, but is independent of the fungal light control. SclB interactions with the RcoA transcriptional repressor subunit suggest additional inhibitory functions on transcription. SclB links asexual spore formation to the synthesis of secondary metabolites including emericellamides, austinol as well as dehydroaustinol and activates the oxidative stress response of the fungus. The fungal VosA-SclB regulatory system of transcription includes a VosA control of the sclB promoter, common and opposite VosA and SclB control functions of fungal development and several additional regulatory genes. The relationship between VosA and SclB illustrates the presence of a convoluted surveillance apparatus of transcriptional control, which is required for accurate fungal development and the linkage to the appropriate secondary metabolism.
This thesis investigates whether professionals on the global financial markets, such as investment bankers, traders, and analysts, form a global social class.
Over recent decades, rising inequality has reinvigorated interest in issues of class. Despite the experience of world-wide economic crises demonstrating the global reach of the contemporary economy, the research areas of globalisation and class remain surprisingly disengaged from each other. Especially the question of global class formation remains underexplored.
The first part of this thesis examines why the issue of globalisation remains a niche within research on class. Therefore, the theoretical foundations of the dominant approaches to class are investigated, identifying the causes for the implicit “methodological nationalism” of modern mainstream class analysis in the underlying theories of the economy and social action. Vice-versa, an examination of globalisation theory shows that similar obstacles persist in the theoretical reasoning on inequality from a global perspective, precluding a conceptualisation of global class formation. In dialogue with the few existing approaches to conceptualize class on a global level, a framework for the study of global class formation based on Pierre Bourdieu’s notion of social fields is developed.
In part two of the thesis this framework is employed to examine empirically, whether the global field of finance is currently the source for the formation of a global financial class. The field of finance as the most globalised economic sector is a paradigmatic case for studying the formation of a global class. An interview study on the career trajectories of financial professionals from Frankfurt and Sydney uncovers that despite the legacy of national economic specificities on the institutional level, financial actors draw in their social praxis on global forms of social, cultural, and economic capital and have developed a common culture, worldview, praxis, and habitus, delineating the formation of a global financial class.
Five new species belonging to Hermatomyces (Hermatomycetaceae, Pleosporales) are described based on morphological investigations of specimens collected on rotten twigs and stems of various plants in Panama as well as phylogenetic analyses of sequence data of nuclear ribosomal and protein coding genes (EF1-α, RPB2, β-TUB). The new species are described as: Hermatomyces bifurcatus, H. constrictus, H. megasporus, H. sphaericoides, and H. verrucosus spp. nov. Previously described species such as H. sphaericus and H. tucumanensis were identified among the studied specimens. The new combination, H. reticulatus, is made for Subicularium reticulatum based on examination of the holotype and fresh collections. Hermatomyces subiculosus, originally described from Thailand, is reduced to synonymy with H. reticulatus; H. tectonae is synonymized under H. sphaericus based on morphological and molecular evidence; and H. chiangmaiensis and H. thailandicus are considered later synonyms of H. krabiensis and H. indicus, respectively. The type material of Scyphostroma mirum was found to be conspecific with H. tucumanensis and, therefore, the generic name Hermatomyces should be conserved or protected against the older name Scyphostroma and the binomial H. tucumanensis against S. mirum. Sixteen species of Hermatomyces are recognized, their distinctive characteristics are highlighted in line drawings and a key is provided for their identification. The peculiar morphology and consistent phylogeny of new and previously known Hermatomyces species supports the recognition of the recently introduced monotypic family Hermatomycetaceae as a well delimited monophyletic taxon within the order Pleosporales.
Leaf-stripe smuts on grasses are a highly polyphyletic group within Ustilaginomycotina, occurring in three genera, Tilletia, Urocystis, and Ustilago. Currently more than 12 Ustilago species inciting stripe smuts are recognised. The majority belong to the Ustilago striiformis-complex, with about 30 different taxa described from 165 different plant species. This study aims to assess whether host distinct-lineages can be observed amongst the Ustilago leaf-stripe smuts using nine different loci on a representative set. Phylogenetic reconstructions supported the monophyly of the Ustilago striiformis-complex that causes leaf-stripe and the polyphyly of other leaf-stripe smuts within Ustilago. Furthermore, smut specimens from the same host genus generally clustered together in well-supported clades that often had available species names for these lineages. In addition to already-named lineages, three new lineages were observed, and described as new species on the basis of host specificity and molecular differences: namely Ustilago jagei sp. nov. on Agrostis stolonifera, U. kummeri sp. nov. on Bromus inermis, and U. neocopinata sp. nov. on Dactylis glomerata.
Background: Recent epidemics have entailed global discussions on revamping epidemic control and prevention approaches. A general consensus is that all sources of data should be embraced to improve epidemic preparedness. As a disease transmission is inherently governed by individual-level responses, pathogen dynamics within infected hosts posit high potentials to inform population-level phenomena. We propose a multiscale approach showing that individual dynamics were able to reproduce population-level observations.
Methods: Using experimental data, we formulated mathematical models of pathogen infection dynamics from which we simulated mechanistically its transmission parameters. The models were then embedded in our implementation of an age-specific contact network that allows to express individual differences relevant to the transmission processes. This approach is illustrated with an example of Ebola virus (EBOV).
Results: The results showed that a within-host infection model can reproduce EBOV’s transmission parameters obtained from population data. At the same time, population age-structure, contact distribution and patterns can be expressed using network generating algorithm. This framework opens a vast opportunity to investigate individual roles of factors involved in the epidemic processes. Estimating EBOV’s reproduction number revealed a heterogeneous pattern among age-groups, prompting cautions on estimates unadjusted for contact pattern. Assessments of mass vaccination strategies showed that vaccination conducted in a time window from five months before to one week after the start of an epidemic appeared to strongly reduce epidemic size. Noticeably, compared to a non-intervention scenario, a low critical vaccination coverage of 33% cannot ensure epidemic extinction but could reduce the number of cases by ten to hundred times as well as lessen the case-fatality rate.
Conclusions: Experimental data on the within-host infection have been able to capture upfront key transmission parameters of a pathogen; the applications of this approach will give us more time to prepare for potential epidemics. The population of interest in epidemic assessments could be modelled with an age-specific contact network without exhaustive amount of data. Further assessments and adaptations for different pathogens and scenarios to explore multilevel aspects in infectious diseases epidemics are underway.
In several tumor entities, transketolase-like protein 1 (TKTL1) has been suggested to promote the nonoxidative part of the pentose phosphate pathway (PPP) and thereby to contribute to a malignant phenotype. However, its role in glioma biology has only been sparsely documented. In the present in vitro study using LNT-229 glioma cells, we analyzed the impact of TKTL1 gene suppression on basic metabolic parameters and on survival following oxygen restriction and ionizing radiation. TKTL1 was induced by hypoxia and by hypoxia-inducible factor-1α (HIF-1α). Knockdown of TKTL1 via shRNA increased the cells’ demand for glucose, decreased flux through the PPP and promoted cell death under hypoxic conditions. Following irradiation, suppression of TKTL1 expression resulted in elevated levels of reactive oxygen species (ROS) and reduced clonogenic survival. In summary, our results indicate a role of TKTL1 in the adaptation of tumor cells to oxygen deprivation and in the acquisition of radioresistance. Further studies are necessary to examine whether strategies that antagonize TKTL1 function will be able to restore the sensitivity of glioma cells towards irradiation and antiangiogenic therapies in the more complex in vivo environment.
Cardiac sarcoidosis is a rare immunologic disease causing heart involvement in 5% of patients. Cardiac sarcoidosis may manifest clinically as a cardiomyopathy with impaired left ventricular (LV) function or as tachyarrhythmias or bradyarrhythmias. On autopsy, cardiac granulomas can be found in approximately 25% of patients. The most common location for granulomas and scars is the LV free wall, followed by the intraventricular septum, often with involvement of the conduction system. ...
Temperature- and field-dependent 1H-, 19F-, and 79,81Br-NMR measurements together with zero - field 79,81Br-NQR measurements on polycrystalline samples of barlowite, Cu4(OH)6FBr are conducted to study the magnetism and possible structural distortions on a microscopic level. The temperature dependence of the 79,81Br-NMR spin-lattice relaxation rates 1/T1 indicate a phase transition at TN ≃ 15 K which is of magnetic origin, but with an unusually weak slowing down of fluctuations below TN. Moreover, 1/T1T scales linear with the bulk susceptibility which indicates persisting spin fluctuations down to 2 K. Quadupolare resonance (NQR) studies reveal a pair of zero-field NQR- lines associated with the two isotopes of Br with the nuclear spins of I = 3/2. Quadrupole coupling constants of vQ ≃ 28.5 MHz and 24.7 MHz for 79Br- and 81Br-nuclei are determined from Br-NMR and the asymmetry parameter of the electric field gradient was estimated to η ≃ 0.2. The Br-NQR lines are consistent with our findings from Br-NMR and they are relatively broad, even above TN. This broadening and the relative large η value suggests a symmetry reduction at the Br- site reflecting the presence of a local distortion in the lattice. Our density-functional calculations show that the displacements of Cu2 atoms located between the kagome planes do not account for this relatively large η. On the other hand, full structural relaxation, including the deformation of kagome planes, leads to a better agreement with the experiment.
Exploring the ability of acoustic infant cry analysis for discriminating developmental pathologies
(2018)
This thesis aims at exploring the ability of acoustic infant cry analysis for discriminating developmental pathologies. Cries of healthy infants as well as cries of infants suffering from cleft lip and palate, hearing impairment, laryngomalacia, asphyxia and brain damage were recorded and acoustically analyzed. The acoustic properties of the infant cries were identified and tested on their suitability to predict the health state of the infants in an reliable, valid and objective way.
To test the reliability of infant cry analysis, Krippendorff’s Alpha coefficient was calculated to test how homogeneous cries of healthy infants as well as cries of infants suffering from various pathologies are.
To asses if valid methods exist for classifying infant cries, different approaches that can be used to differentiate between the groups and to predict the health state of the infants — e.g., analysis of variances, supervised-learning models and auditory discrimination by human listeners — were tested on their validity.
The objectivity of computer-based and human-based classification approaches was explored and techniques to enhance the objectivity for both approaches are proposed.
Computer-based approaches are more objective and reached higher sensitivity and specificity values in their classification to predict the health state of the infants. Especially C5.0 decision trees reached high and therefore promising classification results, even though infant cries have a great statistical spread and can be seen as very heterogeneous and are therefore not very reliable in general.
Tubulogenesis is essential for the formation and function of internal organs. One such organ is the trachea, which allows gas exchange between the external environment and the lungs. However, the cellular and molecular mechanisms underlying tracheal tube development remain poorly understood. Here, we show that the potassium channel KCNJ13 is a critical modulator of tracheal tubulogenesis. We identify Kcnj13 in an ethylnitrosourea forward genetic screen for regulators of mouse respiratory organ development. Kcnj13 mutants exhibit a shorter trachea as well as defective smooth muscle (SM) cell alignment and polarity. KCNJ13 is essential to maintain ion homeostasis in tracheal SM cells, which is required for actin polymerization. This process appears to be mediated, at least in part, through activation of the actin regulator AKT, as pharmacological increase of AKT phosphorylation ameliorates the Kcnj13-mutant trachea phenotypes. These results provide insight into the role of ion homeostasis in cytoskeletal organization during tubulogenesis.
Background: Most smokers start smoking during their early adolescence, often with the idea that smoking is glamorous. Interventions that harness the broad availability of mobile phones as well as adolescents' interest in their appearance may be a novel way to improve school-based prevention. A recent study conducted in Germany showed promising results. However, the transfer to other cultural contexts, effects on different genders, and implementability remains unknown.
Objective: In this observational study, we aimed to test the perception and implementability of facial-aging apps to prevent smoking in secondary schools in Brazil in accordance with the theory of planned behavior and with respect to different genders.
Methods: We used a free facial-aging mobile phone app ("Smokerface") in three Brazilian secondary schools via a novel method called mirroring. The students’ altered three-dimensional selfies on mobile phones or tablets and images were "mirrored" via a projector in front of their whole grade. Using an anonymous questionnaire, we then measured on a 5-point Likert scale the perceptions of the intervention among 306 Brazilian secondary school students of both genders in the seventh grade (average age 12.97 years). A second questionnaire captured perceptions of medical students who conducted the intervention and its conduction per protocol.
Results: The majority of students perceived the intervention as fun (304/306, 99.3%), claimed the intervention motivated them not to smoke (289/306, 94.4%), and stated that they learned new benefits of not smoking (300/306, 98.0%). Only a minority of students disagreed or fully disagreed that they learned new benefits of nonsmoking (4/306, 1.3%) or that they themselves were motivated not to smoke (5/306, 1.6%). All of the protocol was delivered by volunteer medical students.
Conclusions: Our data indicate the potential for facial-aging interventions to reduce smoking prevalence in Brazilian secondary schools in accordance with the theory of planned behavior. Volunteer medical students enjoyed the intervention and are capable of complete implementation per protocol.
The identification of inhibitors of eukaryotic protein biosynthesis, which are targeting single translation factors, is highly demanded. Here we report on a small molecule inhibitor, gephyronic acid, isolated from the myxobacterium Archangium gephyra that inhibits growth of transformed mammalian cell lines in the nM range. In direct comparison, primary human fibroblasts were shown to be less sensitive to toxic effects of gephyronic acid than cancer-derived cells. Gephyronic acid is targeting the protein translation system. Experiments with IRES dual luciferase reporter assays identified it as an inhibitor of the translation initiation. DARTs approaches, co-localization studies and pull-down assays indicate that the binding partner could be the eukaryotic initiation factor 2 subunit alpha (eIF2α). Gephyronic acid seems to have a different mode of action than the structurally related polyketides tedanolide, myriaporone, and pederin and is a valuable tool for investigating the eukaryotic translation system. Because cancer derived cells were found to be especially sensitive, gephyronic acid could potentially find use as a drug candidate.
TEMPO spin labels protected with 2-nitrobenzyloxymethyl groups were attached to the amino residues of three different nucleosides: deoxycytidine, deoxyadenosine, and adenosine. The corresponding phosphoramidites could be incorporated by unmodified standard procedures into four different self-complementary DNA and two RNA oligonucleotides. After photochemical removal of the protective group, elimination of formic aldehyde and spontaneous air oxidation, the nitroxide radicals were regenerated in high yield. The resulting spin-labeled palindromic duplexes could be directly investigated by PELDOR spectroscopy without further purification steps. Spin–spin distances measured by PELDOR correspond well to the values obtained from molecular models.
The thesis deals with the analysis and modeling of point processes emerging from different experiments in neuroscience. In particular, the description and detection of different types of variability changes in point processes is of interest.
A non-stationary rate or variance of life times is a well-known problem in the description of point processes like neuronal spike trains and can affect the results of further analyses requiring stationarity. Moreover, non-stationary parameters might also contain important information themselves. The goal of the first part of the thesis is the (further) development of a technique to detect both rate and variance changes that may occur in multiple time scales separately or simultaneously. A two-step procedure building on the multiple filter test (Messer et al., 2014) is used that first tests the null hypothesis of rate homogeneity allowing for an inhomogeneous variance and that estimates change points in the rate if the null hypothesis is rejected. In the second step, the null hypothesis of variance homogeneity is tested and variance change points are estimated. Rate change points are used as input. The main idea is the comparison of estimated variances in adjacent windows of different sizes sliding over the process. To determine the rejection threshold functionals of the Brownian motion are identified as limit processes under the null of variance homogeneity. The non-parametric procedure is not restricted to the case of at most one change point. It is shown in simulation studies that the corresponding test keeps the asymptotic significance level for a wide range of parameters and that the test power is remarkable. The practical applicability of the procedure is underlined by the analysis of neuronal spike trains.
Point processes resulting from experiments on bistable perception are analyzed in the second part of the thesis. Visual illusions allowing for than more possible perception lead to unpredictable changes of perception. In the thesis data from (Schmack et al., 2015) are used. A rotating sphere with switching perceived rotation direction was presented to the participants of the study. The stimulus was presented continuously and intermittently, i.e., with short periods of „blank display“ between the presentation periods. There are remarkable differences in the response patterns between the two types of presentation. During continuous presentation the distribution of dominance times, i.e., the intervals of constant perception, is a right-skewed and unimodal distribution with a mean of about five seconds. In contrast, during intermittent presentation one observes very long, stable dominance times of more than one minute interchanging with very short, unstable dominance times of less than five seconds, i.e., an increase of variability.
The main goal of the second part is to develop a model for the response patterns to bistable perception that builds a bridge between empirical data analysis and mechanistic modeling. Thus, the model should be able to describe both the response patterns to continuous presentation and to intermittent presentation. Moreover, the model should be fittable to typically short experimental data, and the model should allow for neuronal correlates. Current approaches often use detailed assumptions and large parameter sets, which complicate parameter estimation.
First, a Hidden Markov Model is applied. Second, to allow for neuronal correlates, a Hierarchical Brownian Model (HBM) is introduced, where perception is modeled by the competition of two neuronal populations. The activity difference between these two populations is described by a Brownian motion with drift fluctuating between two borders, where each first hitting time causes a perceptual change. To model the response patterns to intermittent presentation a second layer with competing neuronal populations (coding a stable and an unstable state) is assumed. Again, the data are described very well, and the hypothesis that the relative time in the stable state is identical in a group of patients with schizophrenia and a control group is rejected. To sum up, the HBM intends to link empirical data analysis and mechanistic modeling and provides interesting new hypotheses on potential neuronal mechanisms of cognitive phenomena.
Hippodamia variegata (Goeze) (Coleoptera: Coccinellidae), a Palearctic lady beetle that has become established in North America, is reported for the first time from the state of Iowa, U.S.A. The earliest specimen of H. variegata from Iowa was collected in 2009, with two subsequent specimens in 2012. Collection records of an advancing, non-native species like H. variegata are important for determining comparative rates of geographic spread across various regions and understanding its invasion dynamics.
Based on morphological features of the adult female, the Brazilian soft scale, Mesolecanium ferum Hempel, 1920 (= Toumeyella ferum) (Hemiptera: Coccomorpha: Coccidae) is transferred to the genus Neotoumeyella Kondo and Williams, 2009, as Neotoumeyella ferum (Hempel), comb. nov. The genus Neotoumeyella is rediagnosed in order to accommodate the unique features of M. ferum and an updated key to the six species of the genus is provided. An English translation of the Spanish redescription of M. ferum (as T. ferum) by Granara de Willink (2012) is also provided, with the author’s comments and interpretations.
A combination of five characters supports the arrangement of three species in the Anthocharis sara complex (Lepidoptera: Pieridae: Pierinae: Anthocharidini) consisting of Anthocharis sara Lucas, 1852 (Sara orangetip), Anthocharis thoosa Scudder, 1878 (southwestern orangetip), and Anthocharis julia W.H. Edwards, 1872 (Julia orangetip). These five characters include adult phenotypes, fifth instar larval coloration, pupal cone curvature and color, number of overwintering cycles, and interspecific contact zone behavior. This taxonomic treatment is generated from extensive life history studies from 12 western U.S. states through most of the sara complex distribution.