bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of wastewater pooled surveillance of SARS-CoV-2 from congregate living settings
Authors: Colosi Lisa M. , Barry Katie E. , Kotay Shireen M. , Porter Michael D. , Poulter Melinda D. , Ratliff Cameron , Simmons William , Steinberg Limor I. , Wilson D. Derek , Morse Rena , Zmick Paul , Mathers Amy J. 
Published: October 2020

AbstractWastewater-based monitoring for SARS-CoV-2 holds promise as tool to inform public health-decision making. Testing at individual building-level could be an efficient, passive means of preventing early detection of new cases in congregate living settings, but this approach has not been validated. Sample collection protocols were developed and refined during preliminary sampling from a hospital and a local municipal wastewater treatment plant. Molecular diagnostic methods were compared side-by-side to assess feasibility, performance and sensitivity. Optimized sample collection and processing protocols were then used to monitor two occupied dormitory complexes (n=105 and 66) over eight weeks. Wastewater results were validated using known case counts from external clinical testing of building occupants. Results confirm that ultracentrifugation from a 24 hour composite collection had a sensitivity of 95% and a specificity of 100%. However, if the detection of convalescent shedding is considered a false positive then the sensitivity would be 95.2% but the specificity would drop to 52%. We determined a highly sensitive method for detecting SARS-CoV-2 shedding in building wastewater however our methods could not distinguish new infectious cases from persistent convalescent shedding of SARS-CoV-2 RNA. Future work must focus on methods to distinguish new infections from convalescent shedding to widely deploy this promising wastewater surveillance tool.
Quality assessment of studies included in Cochrane oral health systematic reviews
Authors: Sofi-Mahmudi Ahmad , Iranparvar Pouria , Shakiba Maryam , Shamsoddin Erfan , Mohammad-Rahimi Hossein , Naseri Sadaf , Motie Parisa , Mesgarpour Bita 
Published: October 2020

AbstractObjectivesThe Risk of Bias (RoB) and other characteristics of randomized clinical trials included in Cochrane oral health systematic reviews were assessed.Study Design and SettingsAll the trials included in Cochrane oral health systematic reviews were examined. The RoB was evaluated for all the included clinical trials according to the Cochrane review standards. The Overall Risk of Bias (ORoB) was defined in this study based on the criteria for determining the overall bias in Cochrane’s RoB tool-v2. Descriptive analyses were carried out to determine the frequency of each intended variable.ResultsA total of 2565 studies were included in our analysis. The majority of the studies (n=1600) had sample sizes of 50 or higher. As for blinding, 907 studies were labelled as double-blind. Performance bias showed the highest rate of high risk (31.4%). Almost half of the studies had a high ORoB compared to 11.1% with low ORoB. The studies that used placebos had higher low ORoB (14.8% vs. 10.7%). The double-blind studies had the highest low ORoB (23.6%). The studies with a cross-over design had the highest low ORoB (28.8%).ConclusionOverall, the RoB for the studies on dentistry and oral health in Cochrane reviews was deemed high.
Micro topographical instruction of bacterial attachment, biofilm formation andin vivohost response
Authors: Romero Manuel , Luckett Jeni , Figueredo Grazziela P. , Carabelli Alessandro M. , Scurr David , Hook Andrew L. , Dubern Jean-Frédéric , Ison Elizabeth , Kammerling Lisa , da Silva Ana C. , Xue Xuan , Blackburn Chester , Carlier Aurélie , Vasilevich Aliaksei , Sudarsanam Phani , Vermeulen Steven , Winkler David , Ghaemmaghami Amir M , de Boer Jan , Williams Paul , Alexander Morgan R 
Published: October 2020

ABSTRACTBio-instructive materials that prevent bacterial biofilm formation and drive an appropriate host immune response have the potential to significantly reduce the burden of medical device-associated infections. Since bacterial surface attachment is known to be sensitive to surface topography, we experimentally survey 2,176 combinatorially generated shapes using an unbiased high-throughput micro topographical screen on polystyrene. This identifies topographies that reduce colonizationin vitroby up to 15-fold compared with a flat surface for both motile and non-motile bacterial pathogens. Equivalent reductions are achieved on polyurethane, a polymer commonly used in medical devices. Using machine learning methods, a set of design rules based on generalisable descriptors is established for predicting bacteria-resistant micro topographies. In a murine foreign body infection model, anti-attachment topographies are shown to be refractory toP. aeruginosaand to recruit a productive host response, highlighting the potential of simple topographical patterning of non-eluting implants for preventing medical device associated infections.
Comprehensive identification of somatic nucleotide variants in human brain tissue
Authors: Wang Yifan , Bae Taejeong , Thorpe Jeremy , Sherman Maxwell A. , Jones Attila G. , Cho Sean , Daily Kenneth , Dou Yanmei , Ganz Javier , Galor Alon , Lobon Irene , Pattni Reenal , Rosenbluh Chaggai , Tomasi Simone , Tomasini Livia , Yang Xiaoxu , Zhou Bo , Akbarian Schahram , Ball Laurel L. , Bizzotto Sara , Emery Sarah B. , Doan Ryan , Fasching Liana , Jang Yeongjun , Juan David , Lizano Esther , Moldovan John B. , Narurkar Rujuta , Oetjens Matthew T. , Sekar Shobana , Shin Joo Heon , Soriano Eduardo , Straub Richard E. , Zhou Weichen , Chess Andrew , Gleeson Joseph G. , Marquès-Bonet Tomas , Park Peter J. , Peters Mette A. , Pevsner Jonathan , Walsh Christopher A. , Weinberger Daniel R. ,   Brain Somatic Mosaicism Network, Vaccarino Flora M. , Moran John V. , Urban Alexander E. , Kidd Jeffrey M. , Mills Ryan E. , Abyzov Alexej 
Published: October 2020

AbstractPost-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. Here, the Brain Somatic Mosaicism Network conducted a coordinated, multi-institutional study to: (i) examine the ability of existing methods to detect simulated somatic single nucleotide variants (SNVs) in DNA mixing experiments; (ii) generate multiple replicates of whole genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual; (iii) devise strategies to discover somatic SNVs; and (iv) apply various approaches to validate somatic SNVs. These efforts led to the identification of 43bona fidesomatic SNVs that ranged in variant allele fractions from ~0.005 to ~0.28. Guided by these results, we devised best practices for calling mosaic SNVs from 250X whole genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrated that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. Thus, this study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.
Culture influences audiovisual emotion perception in early sensory areas
Authors: Tanaka Akihiro , Takagi Sachiko , Harada Tokiko , Huis In ’t Veld Elisabeth , de Gelder Beatrice , Hamano Yuki , Tabei Ken-ichi , Sadato Norihiro 
Published: October 2020

AbstractEmotion perception from facial and vocal expressions is a multisensory process critical for human social interaction. When asked to judge emotions by attending to either face or voice, the accuracy was higher when facial expressions are congruent with vocal expressions than when they are incongruent. This congruency effect was shown to be affected by cultural background. Here we conducted functional MRI alongside a multisensory emotion perception task involving Japanese and Dutch participants. They were presented with movies in which congruent or incongruent emotions were expressed through faces and voices. The participants were asked to judge the emotion of either the face or the voice. Consistent with previous studies, behavioral results showed an interaction between group and task. fMRI results revealed that during voice-based judgement, congruency effects of the primary visual cortex, by means of the task related activity of congruent stimuli subtracted by that of incongruent stimuli, were more prominent in the Dutch group than in Japanese group. Finally, behavioral and neural congruency effects of the primary visual cortex were positively correlated only in the Dutch group. Taken together, our results show that culture affects the activities of early sensory areas in multisensory perception from facial and vocal expressions.
BAli-Phy version 3: Model-based co-estimation of Alignment and Phylogeny
Authors: Redelings Benjamin D. 
Published: October 2020

AbstractSummaryWe describe improvements to BAli-Phy, a Markov chain Monte Carlo (MCMC) program that jointly estimates phylogeny, alignment, and other parameters from unaligned sequence data. Version 3 is substantially faster for large trees, and implements covarion models, RNA stem models, and other new models. It implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously.AvailabilitySoftware is available for download athttp://www.bali-phy.org. C++source code is freely available on Github under the GPL2 License.Contactbenjamin.redelings@gmail.com
Features of Functional Human Genes
Authors: Cooper Helena B. , Gardner Paul P. 
Published: October 2020

AbstractProteins and non-coding RNAs are functional products of the genome that carry out the bulk of crucial cellular processes. With recent technological advances, researchers can sequence genomes in the thousands as well as probe for specific genomic activities of multiple species and conditions. These studies have identified thousands of potential proteins, RNAs and associated activities, however there are conflicting conclusions on the functional implications depending upon the burden of evidence researchers use, leading to diverse interpretations of which regions of the genome are “functional”. Here we investigate the association between gene functionality and genomic features, by comparing established functional protein-coding and non-coding genes to non-genic regions of the genome. We find that the strongest and most consistent association between functional genes and any genomic feature is evolutionary conservation and transcriptional activity. Other strongly associated features include sequence alignment statistics, such as maximum between-site covariation. We have also identified some concerns with 1,000 Genomes Project and Genome Aggregation Database SNP densities, as short non-coding RNAs tend to have greater than expected SNP densities. Our results demonstrate the importance of evolutionary conservation and transcription for sequence functionality, which should both be taken into consideration when differentiating between functional sequences and noise.
Dynamic binning peak detection and assessment of various lipidomics liquid chromatography-mass spectrometry pre-processing platforms
Authors: Feng Xiaodong , Zhang Wenxuan , Kuipers Folkert , Kema Ido , Barcaru Andrei , Horvatovich Péter 
Published: October 2020

ABSTRACTLiquid chromatography-mass spectrometry (LC-MS) based lipidomics generate a large dataset, which requires high-performance data pre-processing tools for their interpretation such as XCMS, mzMine and Progenesis. These pre-processing tools rely heavily on accurate peak detection, which depends on setting the peak detection mass tolerance (PDMT) properly. The PDMT is usually set with a fixed value in either ppm or Da units. However, this fixed value may result in duplicates or missed peak detection. Therefore, we developed the dynamic binning method for accurate peak detection, which takes into account the peak broadening described by well-known physics laws of ion separation and set dynamically the value of PDMT as a function of m/z. Namely, in our method, the PDMT is proportional tofor FTICR, tofor Orbitrap, tom/zfor Q-TOF and is a constant for Quadrupole mass analyzer, respectively. The dynamic binning method was implemented in XCMS [1,2] and the adopted source code is available in the Appendix. Our further goal was to compare the performance of different lipidomics pre-processing tools to find differential compounds. We have generated set samples with 43 lipids internal standards differentially spiked to aliquots of one human plasma lipid sample using Orbitrap LC-MS/MS. The performance of the various pipelines using aligned parameter sets was quantified by a quality score system which reflects the ability of a pre-processing pipeline to detect differential peaks spiked at various concentration levels. The quality score indicates that the dynamic binning method improves the performance of XCMS (maximum p-value 9.8·10−3of two-sample Wilcoxon test). The modified XCMS software was further compared with mzMine and Progenesis. The results showed that modified XCMS and Progenesis had a similarly good performance in the aspect of finding differential compounds. In addition, Progenesis shows lower variability as indicated by lower CVs, followed by XCMS and mzMine. The lower variability of Progenesis improve the quantification, however, provide an incorrect quantification abundance order of spiked-in internal standards.
A 180 My-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes
Authors: Kuhl Heiner , Guiguen Yann , Höhne Christin , Kreuz Eva , Du Kang , Klopp Christophe , Lopez-Roques Céline , Yebra-Pimentel Elena Santidrian , Ciorpac Mitica , Gessner Jörn , Holostenco Daniela , Kleiner Wibke , Kohlmann Klaus , Lamatsch Dunja K. , Prokopov Dmitry , Bestin Anastasia , Bonpunt Emmanuel , Debeuf Bastien , Haffray Pierrick , Morvezen Romain , Patrice Pierre , Suciu Radu , Dirks Ron , Wuertz Sven , Kloas Werner , Schartl Manfred , Stöck Matthias 
Published: October 2020

SummarySeveral hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified a ~16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchusvs.A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 My of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives.
A General Birth-Death-Sampling Model for Epidemiology and Macroevolution
Authors: MacPherson Ailene , Louca Stilianos , McLaughlin Angela , Joy Jeffrey B. , Pennell Matthew W. 
Published: October 2020

AbstractBirth-death stochastic processes are the foundation of many phylogenetic models and are widely used to make inferences about epidemiological and macroevolutionary dynamics. There are a large number of birth-death model variants that have been developed; these impose different assumptions about the temporal dynamics of the parameters and about the sampling process. As each of these variants was individually derived, it has been difficult to understand the relationships between them as well as their precise biological and mathematical assumptions. Without a common mathematical foundation, deriving new models is non-trivial. Here we unify these models into a single framework, prove that many previously developed epidemiological and macroevolutionary models are all special cases of a more general model, and illustrate the connections between these variants. This framework centers around a technique for deriving likelihood functions for arbitrarily complex birth-death(-sampling) models that will allow researchers to explore a wider array of scenarios than was previously possible. We then use this frame-work to derive general model likelihoods for both the “single-type” case in which all lineages diversify according to the same process and the “multi-type” case, where there is variation in the process among lineages. By re-deriving existing single-type birth-death sampling models we clarify and synthesize the range of explicit and implicit assumptions made by these models.
GlycoPathDB: A database of monosaccharide biosynthesis pathways
Authors: Srivastava Jaya , Sunthar P. , Balaji Petety V. 
Published: October 2020

AbstractA distinctive feature of glycans vis-à-vis proteins and nucleic acids is its structural complexity which arises from the huge repertoire of monosaccharides, isomeric linkages and branching. Around 70 monosaccharides have so far been discovered in natural glycans and the pathway for the biosynthesis of 57 of these have been experimentally characterized. However, there is no common platform with a comprehensive information of monosaccharide pathways and enzymes. We have gathered 542 experimentally characterized enzymes of these pathways from literature and set up a first of its kind database called GlycoPathDB (http://www.bio.iitb.ac.in/glycopathdb/). Annotations such as the reaction catalysed, substrate specificity, biosynthesis pathway and PubMed IDs are provided for all the enzymes in the database. Sequence homologs of the experimentally characterized enzymes found in nearly 13,000 completely sequenced genomes from Bacteria and Archaea have also been included in the database. This platform will help in deduction of evolutionary relationships among enzymes such as aminotransferases, nucleotidyltransferases, acetyltransferases and SDR family enzymes. It can also facilitate experimental studies such as direct enzyme assays to validate putative annotations, establish structure-function relationship, expression profiling to determine the function, determine the phenotypic consequences of gene knock-out/knock-in and complementation studies.
VOLTAGE-GATED POTASSIUM CHANNELS CONTROL THE GAIN OF ROD-DRIVEN LIGHT RESPONSES IN MIXED-INPUT ON BIPOLAR CELLS
Authors: Joselevitch Christina , Klooster Jan , Kamermans Maarten 
Published: October 2020

AbstractTo achieve high sensitivity at scotopic levels, vision sacrifices spatial and temporal resolution. The detection of dim light, however, depends crucially on the ability of the visual system to speed up rod signals as they advance towards the brain. At higher light levels, gain control mechanisms are necessary to prevent premature saturation of second-order neurons. We investigated how goldfish mixed-input ON bipolar cells (ON mBCs) manage to partially compensate for the intrinsically slow kinetics of rod signals in the dark-adapted state, and at the same time control the gain of rod signals. Rod-driven responses of axotomized ON mBCs become faster and more transient than those of rod horizontal cells as stimulus intensity increases. This transientness has a voltage-dependency consistent with the activation of a voltage-gated K+conductance. Simulations with NEURON indicate that the voltage-gated K+channels responsible for speeding up responses are concentrated at the distal tips of the bipolar cell dendrites, close to the glutamate receptors. These channels act as a gain control mechanism, by shunting the effect of tonically hyperpolarized rods onto the ON mBC. Further activation of K+channels accelerates the ON mBC response by decreasing the membrane time constant as light levels increase. Therefore, the presence of voltage-gated K+channels at the dendritic tips of ON mBCs extends the dynamic range of these neurons, and at the same time generates a transient signal already at the first visual synapse.Key Points SummaryHere we show that voltage-gated potassium channels can adjust the gain of the rod input to mixed-input ON bipolar cells and generate a transient signal already at the first visual synapse.These channels are activated during the light-induced depolarization, making bipolar cell light responses smaller, faster, and more transient, effects that can be abolished by the K+channel blocker TEA.Mathematical simulations suggest that these channels are concentrated at the bipolar cell dendritic tips, close to the site of rod input.This kind of gain control happens at all levels in the retina and is especially important for cells that receive mixed input from rods and cones, in order to prevent premature saturation with increasing light levels and remove the temporal redundancy of the photoreceptor signal.