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In this paper we present a new approach to deterministic modelling of COVID-19 epidemic. Our model dynamics is expressed by a single prognostic variable which satisfies an integro-differential equation. All unknown parameters are described with a single, time-dependent variable R(t). We show that our model has similarities to classic compartmental models, such as SIR, and that the variable R(t) can be interpreted as a generalized effective reproduction number. The advantages of our approach are the simplicity of having only one equation, the numerical stability due to an integral formulation and the reliability since the model is formulated in terms of the most trustable statistical data variable: the number of cumulative diagnosed positive cases of COVID-19. Once this dynamic variable is calculated, other non-dynamic variables, such as the number of heavy cases (hospital beds), the number of intensive-care cases (ICUs) and the fatalities, can be derived from it using a similarly stable, integral approach. The formulation with a single equation allows us to calculate from real data the values of the sample effective reproduction number, which can then be fitted. Extrapolated values of R(t) can be used in the model to make reliable forecasts, though under the assumption that measures for reducing infections are maintained. We have applied our model to more than 15 countries and the ongoing results are available on a web-based platform [1]. In this paper, we focus on the data for two exemplary countries, Italy and Germany, and show that the model is capable of reproducing the course of the epidemic in the past and forecasting its course for a period of four to five weeks with a reasonable numerical stability.
Weigel, Robert ; Irl, Severin ; Treydte, Kerstin ; Beierkuhnlein, Carl ; Berels, Johanna ; Field, Richard ; Miranda, José Carlos ; Steinbauer, Alana ; Steinbauer, Manuel ; Jentsch, Anke
Climatic seasonality drives ecosystem processes (e.g. productivity) and influences plant species distribution. However, it is poorly understood how different aspects of seasonality (especially regarding temperature and precipitation) affect growth continuity of trees in climates with low seasonality because seasonality is often only crudely measured. On islands, exceptionally wide elevational species distribution ranges allow the use of tree rings to identify how growth continuity and climate–growth relationships change with elevation. Here, we present a novel dendroecological method to measure stem growth continuity based on annual density fluctuations (ADFs) in tree rings of Pinus canariensis to indicate low climatic seasonality. The species ranges from 300 to >2000 m a.s.l. on the trade wind-influenced island of La Palma (Canary Islands), where we measured three decades of tree-ring data of 100 individuals distributed over 10 sites along the entire elevational range. The successfully implemented ADF approach revealed a major shift of stem growth continuity across the elevational gradient. In a remarkably clear pattern, stem growth continuity (percentage of ADFs) showed a hump-shaped relationship with elevation reaching a maximum at around 1000 m a.s.l. Low- to mid-elevation tree growth was positively correlated with the Palmer Drought Severity Index (PDSI; indicating aridity) and sea surface temperature (indicating trade wind-influenced moderation of water supply), while high-elevation tree growth was positively correlated with winter temperature (indicating a cold-induced dormancy period). We conclude that ADFs are a useful method to measure stem growth continuity in low-seasonality climates. Growth of P. canariensis on the Canary Islands is more frequently interrupted by winter cold at high elevations and by summer drought at low elevations than in the trade wind-influenced mid elevations, where growth sometimes continues throughout the year. Climate change-associated alterations in trade wind cloud formation might cause non-analogue growth limitations for many unique island species.
Beller, Jacob Daniel ; Fransen, Christoph ; Kotila, Jenni ; Möller, Oliver ; Pietralla, Norbert ; Romig, Christopher ; Savran, Deniz ; Scheck, Marcus ; Werner, Volker ; Zilges, Andreas ; Zweidinger, Markus
The transitional nucleus 154Gd was investigated using a combination of a photon scattering experiment and a γγ-coincidence study following the β decay of 154Tb. A novel decay channel from the scissors mode to the band head of the β-band was observed. Its transition strength B(M1; 1sc+ → 0β+) was determined. An IBM-2 calculation reveals a correlation of this decay channel and the shape phase transition between spherical and deformed nuclei.
Shin, Saeam ; Kim, Juwon ; Kim-Wanner, Soo-Zin ; Bönig, Halvard-Björn ; Cho, Sung Ran ; Kim, Sinyoung ; Choi, Jong Rak ; Lee, Kyung-A
Mobilization of hematopoietic stem cells (HSCs) from the bone marrow to the peripheral blood is a complex mechanism that involves adhesive and chemotactic interactions of HSCs as well as their bone marrow microenvironment. In addition to a number of non-genetic factors, genetic susceptibilities also contribute to the mobilization outcome. Identification of genetic factors associated with HSC yield is important to better understand the mechanism behind HSC mobilization. In the present study, we enrolled 148 Korean participants (56 healthy donors and 92 patients) undergoing HSC mobilization for allogeneic or autologous HSC transplantation. Among a total of 53 polymorphisms in 33 candidate genes, one polymorphism (rs11264422) in relaxin/insulin-like family peptide receptor 4 (RXFP4) gene was significantly associated with a higher HSC yield after mobilization in Koreans. However, in a set of 101 Europeans, no association was found between circulating CD34+ cell counts and rs11264422 genotype. Therefore, we suggest that the ethnic differences in subjects’ genetic background may be related to HSC mobilization. In conclusion, the relaxin—relaxin receptor axis may play an important role in HSC mobilization. We believe that the results of the current study could provide new insights for therapies that use relaxin and HSC populations, as well as a better understanding of HSC regulation and mobilization at the molecular level.
Hahn, Tim ; Marquand, Andre F. ; Plichta, Michael M. ; Ehlis, Ann-Christine ; Schecklmann, Martin ; Dresler, Thomas ; Jarczok, Tomasz Antoni ; Eirich, Elisa ; Leonhard, Christine ; Reif, Andreas ; Lesch, Klaus-Peter J. ; Brammer, Michael J. ; Mourão-Miranda, Janaina ; Fallgatter, Andreas Jochen
Pattern recognition approaches to the analysis of neuroimaging data have brought new applications such as the classification of patients and healthy controls within reach. In our view, the reliance on expensive neuroimaging techniques which are not well tolerated by many patient groups and the inability of most current biomarker algorithms to accommodate information about prior class frequencies (such as a disorder's prevalence in the general population) are key factors limiting practical application. To overcome both limitations, we propose a probabilistic pattern recognition approach based on cheap and easy-to-use multi-channel near-infrared spectroscopy (fNIRS) measurements. We show the validity of our method by applying it to data from healthy controls (n = 14) enabling differentiation between the conditions of a visual checkerboard task. Second, we show that high-accuracy single subject classification of patients with schizophrenia (n = 40) and healthy controls (n = 40) is possible based on temporal patterns of fNIRS data measured during a working memory task. For classification, we integrate spatial and temporal information at each channel to estimate overall classification accuracy. This yields an overall accuracy of 76% which is comparable to the highest ever achieved in biomarker-based classification of patients with schizophrenia. In summary, the proposed algorithm in combination with fNIRS measurements enables the analysis of sub-second, multivariate temporal patterns of BOLD responses and high-accuracy predictions based on low-cost, easy-to-use fNIRS patterns. In addition, our approach can easily compensate for variable class priors, which is highly advantageous in making predictions in a wide range of clinical neuroimaging applications. Hum Brain Mapp, 2013. © 2012 Wiley Periodicals, Inc.
A novel approach to measure brain-to-brain spatial and temporal alignment during positive empathy
(2022)
Toppi, Jlenia ; Siniatchkin, Michael ; Vogel, Pascal ; Freitag, Christine M. ; Astolfi, Laura ; Ciaramidaro, Angela
Empathy is defined as the ability to vicariously experience others’ suffering (vicarious pain) or feeling their joy (vicarious reward). While most neuroimaging studies have focused on vicarious pain and describe similar neural responses during the observed and the personal negative affective involvement, only initial evidence has been reported for the neural responses to others’ rewards and positive empathy. Here, we propose a novel approach, based on the simultaneous recording of multi-subject EEG signals and exploiting the wavelet coherence decomposition to measure the temporal alignment between ERPs in a dyad of interacting subjects. We used the Third-Party Punishment (TPP) paradigm to elicit the personal and vicarious experiences. During a positive experience, we observed the simultaneous presence in both agents of the Late Positive Potential (LPP), an ERP component related to emotion processing, as well as the existence of an inter-subject ERPs synchronization in the related time window. Moreover, the amplitude of the LPP synchronization was modulated by the presence of a human-agent. Finally, the localized brain circuits subtending the ERP-synchronization correspond to key-regions of personal and vicarious reward. Our findings suggest that the temporal and spatial ERPs alignment might be a novel and direct proxy measure of empathy.
Casey, Jillian P. ; Magalhães, Tiago R. ; Conroy, Judith M. ; Regan, Regina ; Shah, Naisha ; Anney, Richard ; Shields, Denis C. ; Abrahams, Brett S. ; Almeida, Joana ; Bacchelli, Elena ; Bailey, Anthony J. ; Baird, Gillian ; Battaglia, Agatino ; Berney, Tom ; Bolshakova, Nadia ; Bolton, Patrick F. ; Bourgeron, Thomas ; Brennan, Sean ; Cali, Phil ; Correia, Catarina ; Corsello, Christina ; Coutanche, Marc ; Dawson, Geraldine ; Jonge, Maretha de ; Delorme, Richard ; Duketis, Eftichia ; Duque, Frederico ; Estes, Annette ; Farrar, Penny ; Fernandez, Bridget A. ; Folstein, Susan E. ; Foley, Suzanne ; Fombonne, Eric ; Freitag, Christine M. ; Gilbert, John ; Gillberg, Christopher ; Glessner, Joseph T. ; Green, Jonathan ; Guter, Stephen J. ; Hakonarson, Hakon ; Holt, Richard ; Hughes, Gillian ; Hus, Vanessa ; Igliozzi, Roberta ; Kim, Cecilia ; Klauck, Sabine M. ; Kolevzon, Alexander ; Lamb, Janine A. ; Leboyer, Marion ; Le Couteur, Ann ; Leventhal, Bennett L. ; Lord, Catherine ; Lund, Sabata C. ; Maestrini, Elena ; Mantoulan, Carine ; Marshall, Christian R. ; McConachie, Helen ; McDougle, Christopher J. ; McGrath, Jane ; McMahon, William M. ; Merikangas, Alison ; Miller, Judith ; Minopoli, Fiorella ; Mirza, Ghazala K. ; Munson, Jeff ; Nelson, Stanley F. ; Nygren, Gudrun ; Oliveira, Guiomar ; Pagnamenta, Alistair T. ; Papanikolaou, Katerina ; Parr, Jeremy R. ; Parrini, Barbara ; Pickles, Andrew ; Pinto, Dalila ; Piven, Joseph ; Posey, David J. ; Poustka, Annemarie ; Poustka, Fritz ; Ragoussis, Jiannis ; Roge, Bernadette ; Rutter, Michael L. ; Sequeira, Ana F. ; Soorya, Latha ; Sousa, Inês ; Sykes, Nuala ; Stoppioni, Vera ; Tancredi, Raffaella ; Tauber, Maïté ; Thompson, Ann P. ; Thomson, Susanne ; Tsiantis, John ; Engeland, Herman van ; Vincent, John B. ; Volkmar, Fred ; Vorstman, Jacob A. S. ; Wallace, Simon ; Wang, Kai ; Wassink, Thomas H. ; White, Kathy ; Wing, Kirsty ; Wittemeyer, Kerstin ; Yaspan, Brian L. ; Zwaigenbaum, Lonnie ; Betancur, Catalina ; Buxbaum, Joseph D. ; Cantor, Rita M. ; Cook, Edwin H. ; Coon, Hilary ; Cuccaro, Michael L. ; Geschwind, Daniel H. ; Haines, Jonathan L. ; Hallmayer, Joachim ; Monaco, Anthony P. ; Nurnberger, John I. ; Pericak-Vance, Margaret Ann ; Schellenberg, Gerard D. ; Scherer, Stephen W. ; Sutcliffe, James S. ; Szatmari, Peter ; Vieland, Veronica J. ; Wijsman, Ellen M. ; Green, Andrew ; Gill, Michael ; Gallagher, Louise ; Vicente, Astrid M. ; Ennis, Sean
Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.
Patil, Shivaprasad ; Linge, Annett ; Hiepe, Hannah ; Grosser, Marianne ; Lohaus, Fabian ; Gudziol, Volker ; Kemper, Max ; Nowak, Alexander ; Haim, Dominik ; Tinhofer, Ingeborg ; Budach, Volker ; Guberina, Maja ; Stuschke, Martin ; Balermpas, Panagiotis ; Müller-von der Grün, Jens ; Schäfer, Henning Sebastian ; Grosu, Anca-Ligia ; Abdollahi, Amir ; Debus, Jürgen ; Ganswindt, Ute ; Belka, Claus ; Pigorsch, Steffi Ulrike ; Combs, Stephanie ; Böke, Simon ; Zips, Daniel ; Jöhrens, Korinna ; Baretton, Gustavo Bruno ; Baumann, Michael ; Krause, Mechthild ; Löck, Steffen
(1) Background: Patients with locally advanced head and neck squamous cell carcinoma (HNSCC) who are biologically at high risk for the development of loco–regional recurrences after postoperative radiotherapy (PORT) but at intermediate risk according to clinical risk factors may benefit from additional concurrent chemotherapy. In this matched-pair study, we aimed to identify a corresponding predictive gene signature. (2) Methods: Gene expression analysis was performed on a multicenter retrospective cohort of 221 patients that were treated with postoperative radiochemotherapy (PORT-C) and 283 patients who were treated with PORT alone. Propensity score analysis was used to identify matched patient pairs from both cohorts. From differential gene expression analysis and Cox regression, a predictive gene signature was identified. (3) Results: 108 matched patient pairs were selected. We identified a 2-metagene signature that stratified patients into risk groups in both cohorts. The comparison of the high-risk patients between the two types of treatment showed higher loco–regional control (LRC) after treatment with PORT-C (p < 0.001), which was confirmed by a significant interaction term in Cox regression (p = 0.027), i.e., the 2-metagene signature was indicative for the type of treatment. (4) Conclusion: We have identified a novel gene signature that may be helpful to identify patients with high-risk HNSCC amongst those at intermediate clinical risk treated with PORT, who may benefit from additional concurrent chemotherapy.
This paper presents a comprehensive extension of pricing two-dimensional derivatives depending on two barrier constraints. We assume randomness on the covariance matrix as a way of generalizing. We analyse common barrier derivatives, enabling us to study parameter uncertainty and the risk related to the estimation procedure (estimation risk). In particular, we use the distribution of empirical parameters from IBM and EURO STOXX50. The evidence suggests that estimation risk should not be neglected in the context of multidimensional barrier derivatives, as it could cause price differences of up to 70%.
This article shows that there exist two particular linear orders such that first-order logic with these two linear orders has the same expressive power as first-order logic with the Bit-predicate FO(Bit). As a corollary we obtain that there also exists a built-in permutation such that first-order logic with a linear order and this permutation is as expressive as FO(Bit).
Arrieta, Antonio C. ; Sung, Lillian ; Bradley, John S. ; Zwaan, C. Michel ; Gates, Davis ; Waskin, Hetty ; Carmelitano, Patricia ; Groll, Andreas Hermann ; Lehrnbecher, Thomas ; Mangin, Eric ; Joshi, Amita ; Kartsonis, Nicholas A. ; Walsh, Thomas J. ; Paschke, Amanda
Background: Posaconazole (POS) is a potent triazole antifungal agent approved in adults for treatment and prophylaxis of invasive fungal infections (IFIs). The objectives of this study were to evaluate the pharmacokinetics (PK), safety, and tolerability of POS oral suspension in pediatric subjects with neutropenia.
Methods: This was a prospective, multicenter, sequential dose-escalation study. Enrolled subjects were divided into 3 age groups: AG1, 7 to <18 years; AG2, 2 to <7 years; and AG3, 3 months to <2 years. AG1 and AG2 were divided into 3 dosage cohorts: DC1, 12 mg/kg/day divided twice daily (BID); DC2, 18 mg/kg/day BID; and DC3, 18 mg/kg/day divided thrice daily (TID). AG3 was also divided into DC1 and DC2; however, no subjects were enrolled in DC2. Subjects received 7–28 days of POS oral suspension. PK samples were collected at predefined time points. The POS PK target was predefined as ~90% of subjects with Cavg (AUC /dosing interval) between 500 and 2500 ng/mL, with an anticipated mean steady state Cavg exposure of ~1200 ng/mL.
Results: The percentage of subjects meeting the PK target was <90% across all age groups and dosage cohorts (range: 31% to 80%). The percentage of subjects that achieved the Cavg target of 500 to 2500 ng/mL on Day 7 ranged from 31% to 80%, with the lowest proportion in subjects 2 to <7 years receiving 12 mg/kg/day BID (AG2/DC1) and the highest proportion in subjects 7 to <18 years receiving 18 mg/kg/day TID (AG1/DC3). At all three dose levels (12 mg/kg/day BID, 18 mg/kg/day BID and 18 mg/kg/day TID), subjects in AG1 (7 to <18 years old) had higher mean PK exposures at steady state than those in AG2. High variability in exposures was observed in all groups. POS oral suspension was generally well tolerated and most of the reported adverse events were related to the subjects’ underlying diseases.
Conclusion: The POS PK target of 90% of subjects with Cavg between 500 and 2500 ng/mL was not achieved in any of the age groups across the different dosage cohorts. New formulations of the molecule with a greater potential to achieve the established PK target are currently under investigation.
Trial registration: ClinicalTrials.gov identifier: NCT01716234
Motivation: Calculating the magnitude of treatment effects or of differences between two groups is a common task in quantitative science. Standard effect size measures based on differences, such as the commonly used Cohen's, fail to capture the treatment-related effects on the data if the effects were not reflected by the central tendency. The present work aims at (i) developing a non-parametric alternative to Cohen’s d, which (ii) circumvents some of its numerical limitations and (iii) involves obvious changes in the data that do not affect the group means and are therefore not captured by Cohen’s d.
Results: We propose "Impact” as a novel non-parametric measure of effect size obtained as the sum of two separate components and includes (i) a difference-based effect size measure implemented as the change in the central tendency of the group-specific data normalized to pooled variability and (ii) a data distribution shape-based effect size measure implemented as the difference in probability density of the group-specific data. Results obtained on artificial and empirical data showed that “Impact”is superior to Cohen's d by its additional second component in detecting clearly visible effects not reflected in central tendencies. The proposed effect size measure is invariant to the scaling of the data, reflects changes in the central tendency in cases where differences in the shape of probability distributions between subgroups are negligible, but captures changes in probability distributions as effects and is numerically stable even if the variances of the data set or its subgroups disappear.
Conclusions: The proposed effect size measure shares the ability to observe such an effect with machine learning algorithms. Therefore, the proposed effect size measure is particularly well suited for data science and artificial intelligence-based knowledge discovery from big and heterogeneous data.
Large, Martin ; Reichert, Sebastian ; Hehlgans, Stephanie ; Fournier, Claudia ; Rödel, Claus ; Rödel, Franz
Background: A discontinuous dose response relationship is a major characteristic of the anti-inflammatory effects of low-dose X-irradiation therapy. Although recent data indicate an involvement of a variety of molecular mechanisms in these characteristics, the impact of reactive oxygen species (ROS) production to give rise or contribute to these phenomena in endothelial cells (EC) remains elusive.
Material and methods: HUVEC derived immortalized EA.hy926 cells were stimulated by tumor necrosis factor-α (TNF-α, 20 ng/ml) 4 h before irradiation with doses ranging from 0.3 to 1 Gy. To analyse DNA repair capacity, phospho-histone H2AX foci were assayed at 1 h, 4 h and 24 h after irradiation. ROS production and superoxide dismutase (SOD) activity were analysed by fluorometric 2',7'-dichlorodihydrofluorescein-diacetate (H2DCFDA) and colorimetric assays. A functional impact of ROS on γH2AX production was analysed by treatment with the scavenger N-acetyl-L-cysteine (NAC).
Results: Irrespective of stimulation by TNF-α, EA.hy926 cells revealed a linear dose response characteristic of γH2AX foci detection at 1 h and 4 h after irradiation. By contrast, we observed a discontinuity in residual γH2AX foci detection at 24 h after irradiation with locally elevated values following a 0.5 Gy exposure that was abolished by inhibition of ROS by NAC. Moreover, SOD protein expression was significantly decreased at doses of 0.5 Gy and 0.7 Gy concomitant with a reduced SOD activity.
Conclusion: These data implicate a non-linear regulation of ROS production and SOD activity in EA.hy926 EC following irradiation with doses < 1 Gy that may contribute to a discontinuous dose-response relationship of residual γH2AX foci detection.
A non-fundamentalist return to origin: the new Islamic reformers’ methodology of (re)interpretation
(2020)
Focusing on some contemporary Islamic reformers’ solutions, in particular, Abolkarim Soroush, Mohsen Kadivar, and Fazlur Rahman, to concrete issues in Muslim societies, this article examines two different methodological strategies of alternative readings of the Sunna: an archeological one and a genealogical one. In the archeological perspective, the holy text has been considered as a repository of answers to all sorts of questions. Through a pathological analysis, this view suggests solutions to correct distortions and looks for new windows seeking an original interpretation of the Qur’an. The genealogical view, on the other hand, puts aside this pathology and instead insists on the idea of the contingency of any interpretation. Regardless of accuracy and validity, according to the genealogical view, all interpretations have addressed temporal and contextual questions. What is important in this perspective is not returning to an original source for finding the exact message of Allah, or correcting previous interpretations, but recurrently referring to an open-ended text in order to explore the futures of the Qur’an.
In this article we use techniques from tropical and logarithmic geometry to construct a non-Archimedean analogue of Teichmüller space T¯g whose points are pairs consisting of a stable projective curve over a non-Archimedean field and a Teichmüller marking of the topological fundamental group of its Berkovich analytification. This construction is closely related to and inspired by the classical construction of a non-Archimedean Schottky space for Mumford curves by Gerritzen and Herrlich. We argue that the skeleton of non-Archimedean Teichmüller space is precisely the tropical Teichmüller space introduced by Chan–Melo–Viviani as a simplicial completion of Culler–Vogtmann Outer space. As a consequence, Outer space turns out to be a strong deformation retract of the locus of smooth Mumford curves in T¯g.
We solved the crystal structure of a novel type of c-ring isolated from Bacillus pseudofirmus OF4 at 2.5 Å, revealing a cylinder with a tridecameric stoichiometry, a central pore, and an overall shape that is distinct from those reported thus far. Within the groove of two neighboring c-subunits, the conserved glutamate of the outer helix shares the proton with a bound water molecule which itself is coordinated by three other amino acids of outer helices. Although none of the inner helices contributes to ion binding and the glutamate has no other hydrogen bonding partner than the water oxygen, the site remains in a stable, ion-locked conformation that represents the functional state present at the c-ring/membrane interface during rotation. This structure reveals a new, third type of ion coordination in ATP synthases. It appears in the ion binding site of an alkaliphile in which it represents a finely tuned adaptation of the proton affinity during the reaction cycle. Formal Correction: This article has been formally corrected to address the following errors. 1. The images for Figures S2 and S3 were incorrectly switched. The image that appears as Figure S2 should be Figure S3, and the image that appears as Figure S3 should be Figure S2. The figure legends appear in the correct order. Please view the correct... (read formal correction) 2. The images for Figures S2 and S3 were incorrectly switched. The image that appears as Figure S2 should be Figure S3, and the image that appears as Figure S3 should be Figure S2. The figure legends appear in the correct order. Please view the correct... (read formal correction)
A new type of Na+-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif
(2013)
Schulz, Sarah ; Iglesias-Cans, Marina ; Krah, Alexander ; Yildiz, Özkan ; Leone, Vanessa ; Matthies, Doreen ; M. Cook, Gregory ; Faraldo-Gómez, José D. ; Meier, Thomas Kurt
Abstract: The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a transmembrane gradient of Na+. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F1Fo-ATP synthase with a novel Na+ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na+ specificity in physiological settings. Consistently, activity measurements showed Na+ stimulation of the enzyme, either membrane-embedded or isolated, and ATP synthesis was sensitive to the Na+ ionophore monensin. Furthermore, Na+ has a protective effect against inhibitors targeting the ion-binding sites, both in the complete ATP synthase and the isolated c-ring. Definitive evidence of Na+ coupling is provided by two identical crystal structures of the c11 ring, solved by X-ray crystallography at 2.2 and 2.6 Å resolution, at pH 5.3 and 8.7, respectively. Na+ ions occupy all binding sites, each coordinated by four amino acids and a water molecule. Intriguingly, two carboxylates instead of one mediate ion binding. Simulations and experiments demonstrate that this motif implies that a proton is concurrently bound to all sites, although Na+ alone drives the rotary mechanism. The structure thus reveals a new mode of ion coupling in ATP synthases and provides a basis for drug-design efforts against this opportunistic pathogen.
Author Summary: Essential cellular processes such as biosynthesis, transport, and motility are sustained by the energy released in the hydrolysis of ATP, the universal energy carrier in living cells. Most ATP in the cell is produced by a membrane-bound enzyme, the ATP synthase, through a rotary mechanism that is coupled to the translocation of ions across the membrane. The majority of ATP synthases are energized by transmembrane electrochemical gradients of protons (proton-motive force), but a number of organisms, including some important human pathogens, use gradients of sodium ions instead (sodium-motive force). The ion specificity of ATP synthases is determined by a membrane-embedded sub-complex, the c-ring, which is the smallest known biological rotor. The functional mechanism of the rotor ring and its variations among different organisms are of wide interest, because of this enzyme's impact on metabolism and disease, and because of its potential for nanotechnology applications. Here, we characterize a previously unrecognized type of Na+-driven ATP synthase from the opportunistic human pathogen Fusobacterium nucleatum, which is implicated in periodontal diseases. We analyzed this ATP synthase and its rotor ring through a multi-disciplinary approach, combining cell-growth and biochemical assays, X-ray crystallography and computer-simulation methods. Two crystal structures of the membrane rotor were solved, at low and high pH, revealing an atypical ion-recognition motif mediated by two carboxylate side-chains. This motif is shared by other human pathogens, such as Mycobacterium tuberculosis or Streptococcus pneumonia, whose ATP synthases are targets of novel antibiotic drugs. The implications of this ion-recognition mode on the mechanism of the ATP synthase and the cellular bioenergetics of F. nucleatum were thus examined. Our results provide the basis for future pharmacological efforts against this important pathogen.
The fractional release factor (FRF) gives information on the amount of a halocarbon that is released at some point into the stratosphere from its source form to the inorganic form, which can harm the ozone layer through catalytic reactions. The quantity is of major importance because it directly affects the calculation of the ozone depletion potential (ODP). In this context time-independent values are needed which, in particular, should be independent of the trends in the tropospheric mixing ratios (tropospheric trends) of the respective halogenated trace gases. For a given atmospheric situation, such FRF values would represent a molecular property.
We analysed the temporal evolution of FRF from ECHAM/MESSy Atmospheric Chemistry (EMAC) model simulations for several halocarbons and nitrous oxide between 1965 and 2011 on different mean age levels and found that the widely used formulation of FRF yields highly time-dependent values. We show that this is caused by the way that the tropospheric trend is handled in the widely used calculation method of FRF.
Taking into account chemical loss in the calculation of stratospheric mixing ratios reduces the time dependence in FRFs. Therefore we implemented a loss term in the formulation of the FRF and applied the parameterization of a mean arrival time to our data set.
We find that the time dependence in the FRF can almost be compensated for by applying a new trend correction in the calculation of the FRF. We suggest that this new method should be used to calculate time-independent FRFs, which can then be used e.g. for the calculation of ODP.
The fractional release factor (FRF) gives information on the amount of a halocarbon that is released at some point in the stratosphere from its source form to the inorganic form, which can harm the ozone layer through catalytic reactions. The quantity is of major importance because it directly affects the calculation of the Ozone Depletion Potential (ODP). To apply FRF in this context, steady-state values are needed, thus representing a molecular property for a given atmospheric situation. In particular, these values should be independent of the tropospheric trends of the respective halogenated trace gases.
We analyzed the temporal evolution of FRF from ECHAM/MESSy Atmospheric Chemistry (EMAC) model simulations for several halocarbons and nitrous oxide between 1965–2011 on different mean age levels and found that the current formulation of FRF yields highly time-dependent values. We show that this is caused by the way that the tropospheric trend is handled in the current calculation method of FRF.
Taking into account chemical loss in the calculation of stratospheric mixing ratios reduces the time-dependence in correlations of different tracers. Therefore we implemented a loss term in the formulation of FRF and applied the parameterization of a "mean arrival time" to our data set.
We find that the time-dependence in FRF can almost be compensated by applying a new trend correction in the calculation of FRF. We suggest that this new method should be used to calculate time-independent FRF, which can then be used e.g. for the calculation of ODP
A new species of the basal araneomorph spider genus Ectatosticta (Araneae, Hypochilidae) from China
(2009)
The hypochilid spider Ectatosticta davidi (Simon) is redescribed on the basis of adults from Mt. Taibaishan in Shaanxi Province, China; the specimens from Qinghai Province previously identified as E. davidi by most modern authors belong to a new species described as E. deltshevi. Keywords: Araneae, Araneomorphae, Hypochilidae, Ectatosticta, China
Modeling long-term neuronal dynamics may require running long-lasting simulations. Such simulations are computationally expensive, and therefore it is advantageous to use simplified models that sufficiently reproduce the real neuronal properties. Reducing the complexity of the neuronal dendritic tree is one option. Therefore, we have developed a new reduced-morphology model of the rat CA1 pyramidal cell which retains major dendritic branch classes. To validate our model with experimental data, we used HippoUnit, a recently established standardized test suite for CA1 pyramidal cell models. The HippoUnit allowed us to systematically evaluate the somatic and dendritic properties of the model and compare them to models publicly available in the ModelDB database. Our model reproduced (1) somatic spiking properties, (2) somatic depolarization block, (3) EPSP attenuation, (4) action potential backpropagation, and (5) synaptic integration at oblique dendrites of CA1 neurons. The overall performance of the model in these tests achieved higher biological accuracy compared to other tested models. We conclude that, due to its realistic biophysics and low morphological complexity, our model captures key physiological features of CA1 pyramidal neurons and shortens computational time, respectively. Thus, the validated reduced-morphology model can be used for computationally demanding simulations as a substitute for more complex models.
A new pseudopolymorph of perchlorinated neopentasilane: the benzene monosolvate Si(SiCl3)4·C6H6
(2020)
A new pseudopolymorph of dodecachloropentasilane, namely a benzene monosolvate, Si5Cl12·C6H6, is described. There are two half molecules of each kind in the asymmetric unit. Both Si5Cl12 molecules are completed by crystallographic twofold symmetry. One of the benzene molecules is located on a twofold rotation axis with two C—H groups located on this rotation axis. The second benzene molecule has all atoms on a general position: it is disordered over two equally occupied orientations. No directional interactions beyond normal van der Waals contacts occur in the crystal.
Leppik, Liudmila ; Gempp, Anna ; Kuçi, Zyrafete ; Kuçi, Selim ; Bader, Peter ; Bönig, Halvard ; Marzi, Ingo ; Henrich, Dirk
The clinical breakthrough of bone tissue engineering (BTE) depends on the ability to provide patients routinely with BTE products of consistent pharmacological quality. The bottleneck of this approach is the availability of stem cells. To avoid this, we suggest immobilization of random-donor-derived heterologous osteoinductive MSCs onto osteoconductive matrices. Such BTE products could then be frozen and, after thawing, could be released as ready-to-use products for permanent implantation during surgery. For this purpose, we developed a simple protocol for cryopreservation of BTE constructs and evaluated the effects of this procedure on human MSC (hMSCs) metabolic and osteogenic activity in vitro. Our findings show that hMSCs can be freeze-thawed on a β-TCP scaffold through a technically simple procedure. Treated cells sustained their metabolic activity and showed favorable osteogenic potential. Mechanistically, HIF1α and YBX1 genes were activated after freeze-thawing, and supposed to be linked to enhanced osteogenesis. However, the detailed mechanisms as to how the cryopreservation procedure beneficially affects the osteogenic potential of hMSCs remains to be evaluated. Additionally, we demonstrated that our BTE products could be stored for 3 days on dry ice; this could facilitate the supply chain management of cryopreserved BTE constructs from the site of manufacture to the operating room.
Linder, Benedikt ; Köhler, Leonhard H. F. ; Reisbeck, Lisa ; Menger, Dominic ; Subramaniam, Dharmalingam ; Herold-Mende, Christel ; Anant, Shrikant ; Schobert, Rainer ; Biersack, Bernhard ; Kögel, Donat
A new and readily available pentafluorothiophenyl-substituted N-methyl-piperidone curcuminoid 1a was prepared and investigated for its anti-proliferative, pro-apoptotic and cancer stem cell-differentiating activities against a panel of human tumor cell lines derived from various tumor entities. The compound 1a was highly anti-proliferative and reached IC50 values in the nanomolar concentration range. 1a was superior to the known anti-tumorally active curcuminoid EF24 (2) and its known N-ethyl-piperidone analog 1b in all tested tumor cell lines. Furthermore, 1a induced a noticeable increase of intracellular reactive oxygen species in HT-29 colon adenocarcinoma cells, which possibly leads to a distinct increase in sub-G1 cells, as assessed by cell cycle analysis. A considerable activation of the executioner-caspases 3 and 7 as well as nuclei fragmentation, cell rounding, and membrane protrusions suggest the triggering of an apoptotic mechanism. Yet another effect was the re-organization of the actin cytoskeleton shown by the formation of stress fibers and actin aggregation. 1a also caused cell death in the adherently cultured glioblastoma cell lines U251 and Mz54. We furthermore observed that 1a strongly suppressed the stem cell properties of glioma stem-like cell lines including one primary line, highlighting the potential therapeutic relevance of this new compound.
Bonn, Boris ; Boy, Michael ; Kulmala, Markku ; Groth, Angela ; Trawny, Katrin ; Borchert, Sebastian ; Jacobi, Stefan
Atmospheric new particle formation is a general phenomenon observed over coniferous forests. So far nucleation is either parameterised as a function of gaseous sulphuric acid concentration only, which is unable to explain the observed seasonality of nucleation events at different measurement sites, or as a function of sulphuric acid and organic molecules. Here we introduce different nucleation parameters based on the interaction of sulphuric acid and terpene oxidation products and elucidate the individual importance. They include basic trace gas and meteorological measurements such as ozone and water vapour concentrations, temperature (for terpene emission) and UV B radiation as a proxy for OH radical formation. We apply these new parameters to field studies conducted at conducted at Finnish and German measurement sites and compare these to nucleation observations on a daily and annual scale. General agreement was found, although the specific compounds responsible for the nucleation process remain speculative. This can be interpreted as follows: During cooler seasons the emission of biogenic terpenes and the OH availability limits the new particle formation while towards warmer seasons the ratio of ozone and water vapour concentration seems to dominate the general behaviour. Therefore, organics seem to support ambient nucleation besides sulphuric acid or an OH-related compound. Using these nucleation parameters to extrapolate the current conditions to prognosed future concentrations of ozone, water vapour and organic concentrations leads to a significant potential increase in the nucleation event number.
The application of the EU Commission’s Rule of Law Framework in the current Polish case is a step in the right direction. It seems a good instance to develop the Framework as an EU mechanism to protect European constitutional values in a European legal space which is rife with constitutional crises, but short of instruments to address them. Its pertinence appears even more clearly in comparison to the Council’s (in)activity under its own rule-of-law mechanism, hastily put forward after the Commission’s Framework. The activation of the Framework has shown its potential to mobilize European public opinion and orient public discourses to the current condition of EU values
A non-radioactive cell-free assay was developed to quantitatively determine inhibition of plant-type phytoene desaturase by bleaching herbicides. An active desaturase was prepared from an appropriately cloned E. coli transformant. Another E. coli transformant was used to produce the required phytoene. Phytofluene and t-carotene, the products of the desaturase reaction, were either determined by HPLC or optical absorption spectra. Enzyme kinetics and inhibition data for the bleaching tetrazole herbicide WL110547 are presented as an example.
Stein, Harald ; Bob, Roshanak ; Dürkop, Horst ; Erck, Christian ; Kämpfe, Dietrich ; Kvasnicka, Hans Michael ; Martens, Henrik ; Roth, Andreas ; Streubel, Anna
Recent advances in the diagnostic of myeloproliferative neoplasms (MPNs) discovered CALRETICULIN (CALR) mutations as a major driver in these disorders. In contrast to JAK2 mutations being mainly associated with polycythaemia vera, CALR mutations are only associated with primary myelofibrosis (PMF) and essential thrombocythaemia (ET). CALR mutations are present in the majority of PMF and ET patients lacking JAK2 and MPL mutations. As these CALR mutations are absent from reactive bone marrow (BM) lesions their presence indicates ET or PMF. So far these mutations are detectable only by molecular assays. Their molecular detection is cumbersome because of the great CALR mutation heterogeneity. Therefore, the availability of a simple assay would be of great help. All CALR mutations reported lead to a frameshift generating a new 36 amino-acid C-terminus. We generated a monoclonal antibody (CAL2) to this C-neoterminus by immunizing mice with a representative peptide and compared its performance with Sanger sequencing data in 173 MPNs and other BM diseases. There was a 100% correlation between the molecular and the CAL2 immunohistochemical (IHC) assays. Thus, the detection of CALR mutations by the CAL2 IHC is a specific, sensitive, rapid, simple and low-cost method.
Obligate endoparasitic oomycetes are known to ubiquitously occur in marine and freshwater diatoms, but their diversity is still largely unexplored. Many of these parasitoids are members of the early-diverging oomycete lineages (Miracula, Diatomophthora), others are within the Leptomitales of the Saprolegniomycetes (Ectrogella, Lagenisma) and some have been described in the Peronosporomycetes (Aphanomycopsis, Lagenidium). Even though some species have been recently described and two new genera were introduced (Miracula and Diatomophthora), the phylogeny and taxonomy of most of these organisms remain unresolved. This is contrasted by the high number of sequences from unclassified species, as recently revealed from environmental sequencing, suggesting the presence of several undiscovered species. In this study, a new species of Miracula is reported from a marine centric diatom (Minidiscus sp.) isolated from Skagaströnd harbor in Northwest Iceland. The morphology and life cycle traits of this novel oomycete parasite are described herein, and its taxonomic placement within the genus Miracula is confirmed by molecular phylogeny. As it cannot be assigned to any previously described species, it is introduced as Miracula islandica in this study. The genus Miracula thus contains three described holocarpic species (M. helgolandica, M. islandica, M. moenusica) to which likely additional species will need to be added in the future, considering the presence of several lineages known only from environmental sequencing that clustered within the Miracula clade.
Solé, Floréal ; Amson, Eli ; Borths, Matthew ; Vidalenc, Dominique ; Morlo, Michael ; Bastl, Katharina
We describe a new large-sized species of hypercarnivorous hyainailourine–Kerberos langebadreae gen. & sp. nov.–from the Bartonian (MP16) locality of Montespieu (Tarn, France). These specimens consist of a skull, two hemimandibles and several hind limb elements (fibula, astragalus, calcaneum, metatarsals, and phalanges). Size estimates suggest K. langebadreae may have weighed up to 140 kg, revealing this species as the largest carnivorous mammal in Europe at that time. Besides its very large size, K. langebadreae possesses an interesting combination of primitive and derived features. The distinctive skull morphology of K. langebadreae reflects a powerful bite force. The postcranial elements, which are rarely associated with hyainailourine specimens, indicate an animal capable of a plantigrade stance and adapted for terrestrial locomotion. We performed the first phylogenetic analysis of hyainailourines to determine the systematic position of K. langebadreae and to understand the evolution of the group that includes other massive carnivores. The analysis demonstrates that Hemipsalodon, a North American taxon, is a hyainailourine and is closely related to European Paroxyaena. Based on this analysis we hypothesize the biogeographic history of the Hyainailourinae. The group appeared in Africa with a first migration to Europe during the Bartonian that likely included the ancestors of Kerberos, Paroxyaena and Hemipsalodon, which further dispersed into North America at this time. We propose that the hyainailourines dispersed into Europe also during the Priabonian. These migrants have no ecological equivalent in Europe during these intervals and likely did not conflict with the endemic hyaenodont proviverrines. The discovery of K. langebadreae shows that large body size appears early in the evolution of hyainailourines. Surprisingly, the late Miocene Hyainailouros shares a more recent common ancestor with small-bodied hyainailourines (below 15 kg). Finally, our study supports a close relationship between the Hyainailourinae and Apterodontinae and we propose the new clade: Hyainailouridae.
Detailed information on species temperature preferences are needed to measure the effects of global warming on species and communities in European rivers. However, information currently available in the literature on taxon-specific temperature preferences or temperature tolerances is very heterogeneous and therefore not well suited for forecasting purposes. To close this gap, we derived so-called ’central temperature tendencies’ (CTTt values) for benthic invertebrate species. For this end, 547 species and temperature data from regional monitoring programmes in Germany collected at 4249 sites were analysed. Due to the vulnerability of species to high
temperatures, CTTt values were calculated for mean summer temperatures, following a robust approach of calculating a weighted average based on temperature classes. Derived CTTt values correspond well to species temperature preferences as reported in literature as long as the latter were homogeneous in terms of how they were derived and which temperature reference was at focus. Based on taxon-specific CTTt values, a community value, CTTCom, was calculated for each benthic invertebrate sample. CTTCom values were validated by correlation with mean summer water temperatures. As the slope a of the linear regression model between CTTCom values and measured summer temperatures was comparatively low (a = 0.49), a correction function was derived in order to optimise the relation between both. This was crucial, because it is assumed that although CTTt was derived solely from taxa abundances within summer temperature classes, CTTCom not only reflects the effect of (summer) water temperature itself, but also corresponds to a temperature equivalent value, which describes the overall quality of all respiration-relevant aquatic summer habitat conditions that determine the metabolism of respective benthic invertebrates. By comparing this equivalent value with water temperatures measured in the year previous of sampling, statements can be made about the influence of flow conditions and other factors determining oxygen availability.
Thus, CTTCom reflects the mean aerobic scope of the overall benthic invertebrate fauna: the better the respiration conditions for rheophilic species with high oxygen demand, the larger the aerobic scope and the lower CTTCom.
The approach taken in our study is promising and provides a tool to track and even project past, present, and future impacts of global warming on benthic invertebrates in rivers based on measured values of respiratory relevant environmental variables. We encourage all stakeholders in the field of freshwater ecology to test this
Yoshida, Ken ; Kotsuma, Tadayuki ; Akiyama, Hironori ; Yamazaki, Hideya ; Takenaka, Tadashi ; Masui, Koji ; Tsujimoto, Yutaka ; Murakami, Naoya ; Uesugi, Yasuo ; Shimbo, Taiju ; Yoshikawa, Nobuhiko ; Yoshioka, Hiroto ; Nakata, Mio ; Arika, Takumi ; Takaoka, Yuji ; Tanaka, Eiichi ; Tselis, Nikolaos
Purpose: Tongue edema is a potential cause of treatment target underdosage in high-dose-rate interstitial brachytherapy (HDR-ISBT) of mobile tongue cancer. To prevent such edema-associated alteration of dosimetry, we developed a special silicon device. In this report we communicate our initial experience with two mobile tongue cancer patients whom we treated using this new device.
Material and methods: The device consists of silicone tubes with a fixed width and scalable length depending on tongue size. These tubes are lined and fixed like a palisade, allowing the device to be used also as a template. The device is placed next to the lateral border of the tongue and on the floor of the mouth. In addition, a vinyl template can be placed on the dorsal tongue surface with both devices combined for implantation guidance. Between June and August 2012, two patients with locally confined tongue cancer were treated.
Results: Between June and August 2012, two mobile tongue cancer patients classified as cT2N0M0 were treated with HDR-ISBT using the silicone device. They underwent ISBT as monotherapy with fractional doses of 6.0 Gy up to a total physical dose of 54.0 Gy. The D90 (CTV) values of both patients were 6.3 Gy and 6.6 Gy and the D2cc (mandible) values were 3.4 Gy and 2.6 Gy, respectively. At present, both patients remain without local disease recurrence at 60 and 56 months after ISBT, respectively.
Conclusions: The described silicone device has the potential to prevent underdosage to the treatment target related to tongue edema. It has been shown to be safe and easy to implement.
We describe the frog species Diasporus citrinobapheussp. n. from the Cordillera Central of western Panama. The new species differs from all other species in its genus in coloration, disk cover and disk pad shape, skin texture, advertisement call, and size. It is most similar to Diasporus tigrillo, from which it differs in dorsal skin texture, relative tibia length, number of vomerine teeth, ventral coloration, dorsal markings, and relative tympanum size, and to Diasporus gularis, from which it can be distinguished by the lack of membranes between the toes, adult size, posterior thigh coloration, and position of the choanae. We provide data on morpho- logy, vocalization, and distribution of the new species, as well as brief information on its natural history.
Yver, Camille E. ; Pison, Isabelle C. ; Fortems-Cheiney, Audrey ; Schmidt, Martina ; Chevallier, Frédéric ; Ramonet, Michel ; Jordan, Armin ; Søvde, Ole Amund ; Engel, Andreas ; Fisher, Rebecca E. ; Lowry, David ; Nisbet, Euan G. ; Levin, Ingeborg ; Hammer, Samuel ; Necki, Jaroslaw ; Bartyzel, Jakub ; Reimann, Stefan ; Vollmer, Martin ; Steinbacher, Martin ; Aalto, Tuula ; Maione, Michela ; Arduini, Jgor ; O'Doherty, Simon ; Grant, Aoife ; Sturges, William T. ; Forster, Grant L. ; Lunder, Chris Rene ; Privalov, Viacheslav I. ; Paramonova, Nina N.
This paper presents an analysis of the recent tropospheric molecular hydrogen (H2) budget with a particular focus on soil uptake and surface emissions. A variational inversion scheme is combined with observations from the RAMCES and EUROHYDROS atmospheric networks, which include continuous measurements performed between mid-2006 and mid-2009. Net H2 surface flux, soil uptake distinct from surface emissions and finally, soil uptake, biomass burning, anthropogenic emissions and N2 fixation-related emissions separately were inverted in several scenarios. The various inversions generate an estimate for each term of the H2 budget. The net H2 flux per region (High Northern Hemisphere, Tropics and High Southern Hemisphere) varies between −8 and 8 Tg yr−1. The best inversion in terms of fit to the observations combines updated prior surface emissions and a soil deposition velocity map that is based on soil uptake measurements. Our estimate of global H2 soil uptake is −59 ± 4.0 Tg yr−1. Forty per cent of this uptake is located in the High Northern Hemisphere and 55% is located in the Tropics. In terms of surface emissions, seasonality is mainly driven by biomass burning emissions. The inferred European anthropogenic emissions are consistent with independent H2 emissions estimated using a H2/CO mass ratio of 0.034 and CO emissions considering their respective uncertainties. To constrain a more robust partition of H2 sources and sinks would need additional constraints, such as isotopic measurements.
Pison, Isabelle C. ; Fortems-Cheiney, Audrey ; Schmidt, Martina ; Chevallier, Frédéric ; Ramonet, Michel ; Jordan, Armin ; Søvde, Ole Amund ; Engel, Andreas ; Fisher, Rebecca E. ; Lowry, David ; Nisbet, Euan G. ; Levin, Ingeborg ; Hammer, Samuel ; Necki, Jaroslaw ; Bartyzel, J. ; Reimann, Stefan ; Vollmer, Martin K. ; Steinbacher, Martin ; Aalto, Tuula ; Maione, Michela ; Arduini, Jgor ; O'Doherty, Simon ; Grant, Aoife ; Sturges, William T. ; Forster, Grant L. ; Lunder, Chris Rene ; Privalov, Viacheslav I. ; Paramonova, Nina N. ; Werner, A. ; Bousquet, Philippe
This paper presents an analysis of the recent tropospheric molecular hydrogen (H2) budget with a particular focus on soil uptake and European surface emissions. A variational inversion scheme is combined with observations from the RAMCES and EUROHYDROS atmospheric networks, which include continuous measurements performed between mid-2006 and mid-2009. Net H2 surface flux, then deposition velocity and surface emissions and finally, deposition velocity, biomass burning, anthropogenic and N2 fixation-related emissions were simultaneously inverted in several scenarios. These scenarios have focused on the sensibility of the soil uptake value to different spatio-temporal distributions. The range of variations of these diverse inversion sets generate an estimate of the uncertainty for each term of the H2 budget. The net H2 flux per region (High Northern Hemisphere, Tropics and High Southern Hemisphere) varies between −8 and +8 Tg yr−1. The best inversion in terms of fit to the observations combines updated prior surface emissions and a soil deposition velocity map that is based on bottom-up and top-down estimations. Our estimate of global H2 soil uptake is −59±9 Tg yr−1. Forty per cent of this uptake is located in the High Northern Hemisphere and 55% is located in the Tropics. In terms of surface emissions, seasonality is mainly driven by biomass burning emissions. The inferred European anthropogenic emissions are consistent with independent H2 emissions estimated using a H2/CO mass ratio of 0.034 and CO emissions within the range of their respective uncertainties. Additional constraints, such as isotopic measurements would be needed to infer a more robust partition of H2 sources and sinks.
Zomot, Elia ; Yardeni, Eliane Hadas ; Vargiu, Attilio Vittorio ; Tam, Heng Keat ; Malloci, Giuliano ; Ramaswamy, Venkata Krishnan ; Perach, Michal ; Ruggerone, Paolo ; Pos, Klaas Martinus ; Bibi, Eitan
Secondary multidrug (Mdr) transporters utilize ion concentration gradients to actively remove antibiotics and other toxic compounds from cells. The model Mdr transporter MdfA from Escherichia coli exchanges dissimilar drugs for protons. The transporter should open at the cytoplasmic side to enable access of drugs into the Mdr recognition pocket. Here we show that the cytoplasmic rim around the Mdr recognition pocket represents a previously overlooked important regulatory determinant in MdfA. We demonstrate that increasing the positive charge of the electrically asymmetric rim dramatically inhibits MdfA activity and sometimes even leads to influx of planar, positively charged compounds, resulting in drug sensitivity. Our results suggest that unlike the mutants with the electrically modified rim, the membrane-embedded wild-type MdfA exhibits a significant probability of an inward-closed conformation, which is further increased by drug binding. Since MdfA binds drugs from its inward-facing environment, these results are intriguing and raise the possibility that the transporter has a sensitive, drug-induced conformational switch, which favors an inward-closed state.
Alber, Thomas ; Bartke, Jerzy ; Białkowska, Helena ; Bloomer, Matthew A. ; Bock, Rudolf ; Braithwaite, Wilfred J. ; Brinkmann, Dittmar ; Brockmann, Robert ; Bunčić, Predrag ; Chan, Phaikying ; Chase, S. I. ; Cramer, Pauline B. ; Cramer, John G. ; Derado, Ivan ; Eberlein, Björn ; Eckardt, Volker ; Eschke, Jürgen ; Ferenc, Daniel ; Fleischmann, B. ; Foka, Panagiota ; Freund, Peter ; Fuchs, Michael ; Gładysz-Dziaduś, Ewa ; Harris, John W. ; Hoffmann, Matthias ; Jacobs, Peter Martin ; Kabana, Sonia ; Kadija, Krešo ; Kosiec, Jacek ; Kowalski, Marek ; Lahanas, Michael ; Lee, Jae-Yun ; Ljubicic, Ante Jr. ; Margetis, Spyridon ; Mitchell, Jeffery Thomas ; Morse, Richard J. ; Nappi, Eugenio ; Odyniec, Grazyna Janina ; Paic, Guy ; Panagiotou, Apostolos D. ; Petridis, Athanasios ; Piper, Andreas ; Posa, Francesco ; Poskanzer, Arthur M. ; Pugh, Howel G. ; Rai, Gulshan ; Rauch, Wolfgang Hans ; Renfordt, Rainer Arno Ernst ; Retyk, Waldemar ; Roland, Gunther ; Rothard, Hermann ; Runge, Kay ; Sandoval, Andres ; Schambach, Joachim ; Schmitz, Norbert ; Schmoetten, Emile ; Schneider, Ingo ; Sendelbach, Ralf ; Seyboth, Peter ; Seyerlein, Jürgen ; Skrzypczak, Ewa ; Stefansky, Piotr ; Teitelbaum, Lawrence Paul ; Tonse, Shaheen ; Trainor, Thomas A. ; Vasileiadis, Georgios ; Vassiliou, Maria ; Wenig, Siegfried ; Wensveen, Martinus ; Wosiek, Barbara
We present the measured correlation functions for pi+ pi-, pi- pi- and pi+ pi+ pairs in central S+Ag collisions at 200 GeV per nucleon. The Gamov function, which has been traditionally used to correct the correlation functions of charged pions for the Coulomb interaction, is found to be inconsistent with all measured correlation functions. Certain problems which have been dominating the systematic uncertainty of the correlation analysis are related to this inconsistency. It is demonstrated that a new Coulomb correction method, based exclusively on the measured correlation function for pi+ pi- pairs, may solve the problem.
Schmitt, Imke ; Otte, Jürgen ; Parnmen, Sittiporn ; Sadowska-Deś, Anna ; Lücking, Robert ; Lumbsch, Helge Thorsten
The lichen-forming genus Pertusaria under its current circumscription is polyphyletic and its phylogenetic affiliations are uncertain. Here we study the species of the genera Pertusaria and Varicellaria which containlecanoric acid as major constituent, have disciform apothecia, strongly amyloid asci, non-amyloid hymenial gel, 1-2-spored asci, and 1- or 2-celled ascospores with thick, 1-layered walls. We infer phylogenetic relationships using maximum likelihood and Bayesian analyses based on four molecular loci (mtSSU, nuLSU rDNA, and the protein-coding, nuclear RPB1 and MCM7 genes). Our results show that the lecanoric acid-containing species form a well-supported, monophyletic group, which is only distantly related to Pertusaria s.str. The phylogenetic position of this clade is unclear, but placement in Pertusaria s.str. is rejected using alternative hypothesis testing. The circumscription of the genus Varicellaria is enlarged to also include species with non-septate ascospores. Seven species are accepted in the genus: Varicellaria culbersonii (Vězda) Schmitt & Lumbsch, comb. nov., Varicellaria hemisphaerica (Flörke) Schmitt & Lumbsch, comb. nov., Varicellaria kasandjeffii (Szatala) Schmitt & Lumbsch, comb. nov., Varicellaria lactea (L.) Schmitt & Lumbsch, comb. nov., Varicellaria philippina (Vain.) Schmitt & Lumbsch, comb. nov., Varicellaria rhodocarpa (Körb.) Th. Fr., and Varicellaria velata (Turner) Schmitt & Lumbsch, comb. nov. A key to the species of Varicellaria is provided.
A detailed analysis of the chemical constituents of a Caribbean specimen of Aiolochroia crassa was performed. Five brominated products (1 -5) were isolated and one of these was a new bromotyrosine metabolite. The structure of the new compound 1 has been established from spectral studies. Compounds 1 and 2, which are the major brominated metabolites and have not been previously identified in any Aiolochroia species, could be usefully employed as chemotaxonomic markers.
Relying on the theory of Saward (2010) and Disch (2015), we study political representation through the lens of representative claim-making. We identify a gap between the theoretical concept of claim-making and the empirical (quantitative) assessment of representative claims made in the real world’s representative contexts. Therefore, we develop a new approach to map and quantify representative claims in order to subsequently measure the reception and validation of the claims by the audience. To test our method, we analyse all the debates of the German parliament concerned with the introduction of the gender quota in German supervisory boards from 2013 to 2017 in a two-step process. At first, we assess which constituencies the MPs claim to represent and how they justify their stance. Drawing on multiple correspondence analysis, we identify different claim patterns. Second, making use of natural language processing techniques and logistic regression on social media data, we measure if and how the asserted claims in the parliamentary debates are received and validated by the respective audience. We come to the conclusion that the constituency as ultimate judge of legitimacy has not been comprehensively conceptualized yet.
2004 erschütterten Terroranschläge in London und Madrid die Welt. Die Reaktion der EU/EG im seinerzeit schnellsten Gesetzgebungsverfahren seit Bestehen: Verabschiedung der Vorratsdatenspeicherungsrichtlinie. 2009 sah der EuGH die Richtlinie trotzdem als Binnenmarktregelung an, mit der Harmonisierung auf dem Informationsmarkt herbeigeführt werden sollte. Äußerungen zum Inhalt – quasi als obiter dictum möglich gewesen – versagte er sich. 2010 beurteilte dann das BVerfG die bundesdeutsche Umsetzung, aber – ganz dem Verhältnis von EuGH und BVerfG entsprechend – nur den die europäischen Mindestvorgaben überschießenden Teil. Dieses Gesetz hatte national schon für reichlich Sprengstoff im Rechtsstaat gesorgt und u.a. den Rücktritt der beharrlich widersetzlichen Justizministerin bewirkt. ...
López Jury, Luciana ; García Rosales, Francisco ; González Palomares, Eugenia ; Wetekam, Johannes ; Pasek, Michael ; Hechavarria, Julio C.
Substantial progress in the field of neuroscience has been made from anaesthetized preparations. Ketamine is one of the most used drugs in electrophysiology studies, but how ketamine affects neuronal responses is poorly understood. Here, we used in vivo electrophysiology and computational modelling to study how the auditory cortex of bats responds to vocalisations under anaesthesia and in wakefulness. In wakefulness, acoustic context increases neuronal discrimination of natural sounds. Neuron models predicted that ketamine affects the contextual discrimination of sounds regardless of the type of context heard by the animals (echolocation or communication sounds). However, empirical evidence showed that the predicted effect of ketamine occurs only if the acoustic context consists of low-pitched sounds (e.g., communication calls in bats). Using the empirical data, we updated the naïve models to show that differential effects of ketamine on cortical responses can be mediated by unbalanced changes in the firing rate of feedforward inputs to cortex, and changes in the depression of thalamo-cortical synaptic receptors. Combined, our findings obtained in vivo and in silico reveal the effects and mechanisms by which ketamine affects cortical responses to vocalisations.
In contrast to the symbolic approach, neural networks seldom are designed to explain what they have learned. This is a major obstacle for its use in everyday life. With the appearance of neuro-fuzzy systems which use vague, human-like categories the situation has changed. Based on the well-known mechanisms of learning for RBF networks, a special neuro-fuzzy interface is proposed in this paper. It is especially useful in medical applications, using the notation and habits of physicians and other medically trained people. As an example, a liver disease diagnosis system is presented.
With every glimpse of our eyes, we sample only a small and incomplete fragment of the visual world, which needs to be contextualized and integrated into a coherent scene representation. Here we show that the visual system achieves this contextualization by exploiting spatial schemata, that is our knowledge about the composition of natural scenes. We measured fMRI and EEG responses to incomplete scene fragments and used representational similarity analysis to reconstruct their cortical representations in space and time. We observed a sorting of representations according to the fragments' place within the scene schema, which occurred during perceptual analysis in the occipital place area and within the first 200 ms of vision. This schema-based coding operates flexibly across visual features (as measured by a deep neural network model) and different types of environments (indoor and outdoor scenes). This flexibility highlights the mechanism's ability to efficiently organize incoming information under dynamic real-world conditions.
Sayin, Sercan ; De Backer, Jean-Francois ; Siju, Kunhi Purayil ; Wosniack, Marina Elaine ; Lewis, Laurence P. ; Frisch, Lisa-Marie ; Gansen, Benedikt ; Schlegel, Philipp ; Edmondson-Stait, Amelia ; Sharifi, Nadiya ; Fisher, Corey B. ; Calle-Schuler, Steven A. ; Lauritzen, J. Scott ; Bock, Davi D. ; Costa, Marta ; Jefferis, Gregory S. X. E. ; Gjorgjieva, Julijana ; Grunwald Kadow, Ilona
In pursuit of food, hungry animals mobilize significant energy resources and overcome exhaustion and fear. How need and motivation control the decision to continue or change behavior is not understood. Using a single fly treadmill, we show that hungry flies persistently track a food odor and increase their effort over repeated trials in the absence of reward suggesting that need dominates negative experience. We further show that odor tracking is regulated by two mushroom body output neurons (MBONs) connecting the MB to the lateral horn. These MBONs, together with dopaminergic neurons and Dop1R2 signaling, control behavioral persistence. Conversely, an octopaminergic neuron, VPM4, which directly innervates one of the MBONs, acts as a brake on odor tracking by connecting feeding and olfaction. Together, our data suggest a function for the MB in internal state-dependent expression of behavior that can be suppressed by external inputs conveying a competing behavioral drive.
Research on Podospora anserina unraveled a network of molecular pathways affecting biological aging. In particular, a number of pathways active in the control of mitochondria were identified on different levels. A long-known key process active during aging of P. anserina is the age- related reorganization of the mitochondrial DNA (mtDNA). Mechanisms involved in the stabilization of the mtDNA lead to lifespan extension. Another critical issue is to balance mitochondrial levels of reactive oxygen species (ROS). This is important because ROS are essential signaling molecules, but at increased levels cause molecular damage. At a higher level of the network, mechanisms are active in the repair of damaged compounds. However, if damage passes critical limits, the corresponding pathways are overwhelmed and impaired molecules as well as those present in excess are degraded by specific enzymes or via different forms of autophagy. Subsequently, degraded units need to be replaced by novel functional ones. The corresponding processes are dependent on the availability of intact genetic information. Although a number of different pathways involved in the control of cellular homeostasis were uncovered in the past, certainly many more exist. In addition, the signaling pathways involved in the control and coordination of the underlying pathways are only initially understood. In some cases, like the induction of autophagy, ROS are active. Additionally, sensing and signaling the energetic status of the organism plays a key role. The precise mechanisms involved are elusive and remain to be elucidated.