bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning of the riceXo1resistance gene and interaction of the Xo1 protein with the defense-suppressingXanthomonaseffector Tal2h
Authors: Read Andrew C. , Hutin Mathilde , Moscou Matthew J. , Rinaldi Fabio C. , Bogdanove Adam J. 
Published: May 2020

AbstractTheXo1locus in the heirloom rice variety Carolina Gold Select confers resistance to bacterial leaf streak and bacterial blight, caused byXanthomonas oryzaepvs. oryzicola and oryzae, respectively. Resistance is triggered by pathogen-delivered transcription activator-like effectors (TALEs) independent of their ability to activate transcription, and is suppressed by variants called truncTALEs common among Asian strains. By transformation of the susceptible variety Nipponbare, we show that one of 14 nucleotide-binding, leucine-rich repeat (NLR) protein genes at the locus, with a zfBED domain, is theXo1gene. Analyses of published transcriptomes revealed that theXo1-mediated response is similar to those of NLR resistance genesPiaandRxo1and distinct from that associated with induction of the executor resistance geneXa23, and that a truncTALE dampens or abolishes activation of defense-associated genes byXo1. InNicotiana benthamianaleaves, fluorescently-tagged Xo1 protein, like TALEs and truncTALEs, localized to the nucleus. And, endogenous Xo1 specifically co-immunoprecipitated from rice leaves with a pathogen-delivered, epitope-tagged truncTALE. These observations suggest that suppression of Xo1-function by truncTALEs occurs through direct or indirect physical interaction. They further suggest that effector co-immunoprecipitation may be effective for identifying or characterizing other resistance genes.
Deciphering trophic interactions in a mid-Cambrian assemblage
Authors: Swain Anshuman , Devereux Matthew , Fagan William F 
Published: May 2020

AbstractThe Cambrian Period (541-485 Mya) represents a major stage in the development of metazoan-dominated assemblages with complex community structure and species interactions. Exceptionally preserved fossil sites have allowed specimen-based identification of putative trophic interactions to which network analyses have been applied. However, network analyses of the fossil record suffer from incomplete and indirect data, time averaging that obscures species coexistence, and biases in preservation. Here, we present a novel high-resolution fossil dataset from the Raymond Quarry (RQ) member of the mid-Cambrian Burgess Shale (7549 specimens, 61 taxa, ~510 Mya) affording new perspectives on these challenging issues. Further, we formulate a new measure of ‘preservation bias’ that aids identification of those assemblage subsets to which network analyses can be reliably applied. For sections with sufficiently low bias, abundance correlation network analyses predicted longitudinally consistent trophic and competitive interactions. Our correlation network analyses predicted previously postulated trophic interactions with 83.5% accuracy and demonstrated a shift from specialist interaction-dominated assemblages to ones dominated by generalist and competitive interactions. This approach provides a robust, taphonomically corrected framework to explore and predict in detail the existence and ecological character of putative interactions in fossil datasets, offering new windows on ancient food-webs.Significance StatementUnderstanding interactions in paleo-ecosystems has been a difficult task due to biases in collection and preservation of taxa, as well as low time resolution of data. In this work, we use network science tools and a fine scale dataset from the Cambrian period to explore: (i) preservation bias due to ecological/physical characteristics of taxa; (ii) evidence that the magnitude and sign of pairwise abundance correlations between two fossil taxa yields information concerning the ecological character about the interaction. All results in our work derive from using complex system approaches to analyze abundance data, without assuming any prior knowledge about species interactions – thereby providing a novel general framework to assess and explore fossil datasets.
Neuronal resonance can be generated independently at distinct levels of organization
Authors: Stark Eran , Rotstein Horacio G. 
Published: May 2020

ABSTRACTNeuronal resonance is defined as maximal amplification of the response of a system to a periodic input at a finite non-zero input frequency band. Resonance has been observed experimentally in the nervous system at the level of membrane potentials, spike times, post-synaptic potentials, and neuronal networks. It is often assumed that resonance at one level of organization endows resonance at another level, but how the various forms of neuronal resonances interact is unknown. Here we show that a direct link of the frequency response properties across neuronal levels of organization is not necessary. Using detailed biophysical modeling combined with numerical simulations, extracellular recordings, and optogenetic manipulations from behaving mice, we show how low-pass filtering, high-pass filtering, and amplification mechanisms can generate resonance at a single level of organization. Subthreshold resonance, synaptic resonance, and spiking resonance can each occur in the lack of resonance at any other level of organization. In contrast, frequencydependent mechanisms at several levels of organization are required to generate the more complex phenomenon of network resonance. Together, these results show that multiple independent mechanisms can generate resonance in neuronal systems.
Identifying non-identical-by-descent rare variants in population-scale whole genome sequencing data
Authors: Johnson Kelsey E. , Voight Benjamin F. 
Published: May 2020

AbstractThe site frequency spectrum in human populations is not accurately modeled by an infinite sites model, which assumes that all mutations are unique. Despite the pervasiveness of recurrent mutations, we lack computational methods to identify these events at specific sites in population sequencing data. Rare alleles that are identical-by-descent (IBD) are expected to segregate on a long, shared haplotype background that descends from a common ancestor. However, alleles introduced by recurrent mutation or by non-crossover gene conversions are identical-by-state and will have a shorter expected shared haplotype background. We hypothesized that the expected difference in shared haplotype background length can distinguish IBD and non-IBD variants in population sequencing data without pedigree information. We implemented a Bayesian hierarchical model and used Gibbs sampling to estimate the posterior probability of IBD state for rare variants, using simulations to demonstrate that our approach accurately distinguishes rare IBD and non-IBD variants. Applying our method to whole genome sequencing data from 3,621 individuals in the UK10K consortium, we found that non-IBD variants correlated with higher local mutation rates and genomic features like replication timing. Using a heuristic to categorize non-IBD variants as gene conversions or recurrent mutations, we found that potential gene conversions had expected properties such as enriched local GC content. By identifying recurrent mutations, we can better understand the spectrum of recent mutations in human populations, a source of genetic variation driving evolution and a key factor in understanding recent demographic history.
A pilot study to investigate the fecal dissemination of SARS-CoV-2 virus genome in COVID-19 patients in Odisha, India
Authors: Senapati Shantibhusan , Kshatri Jaya Singh , Prasad Punit , Turuk Jyotirmayee , Pati Sanghamitra , Parida Ajay 
Published: May 2020

AbstractIn infectious diseases, the routes of transmission play major roles in determining the rate and extent of disease spread. Though fomites and aerosol droplets are major sources of SARS-CoV-2 human to human transmission, studies have also reported possible involvement of other routes of transmission like fecal-oral. Multiple studies around the world have reported shedding of the SARS-CoV-2 viral genome in certain COVID-19 patient fecal samples. Hence, the major objective of this study was to get the experimental evidence whether in Indian COVID-19 patients fecal dissemination of the SARS-CoV-2 genome occurs or not. Information obtained from twelve number of patients from a COVID-19 hospital of Odisha has demonstrated that both symptomatic and asymptomatic Indian patients could be positive for the SARS-CoV-2 genome in their fecal component. The findings have also established a protocol to collect and extract viral RNA for SARS-CoV-2 detection in fecal samples. Together, the study supports the hypothesis of possible fecal-oral transmission of SARS-CoV-2 virus and provides a rationale to extend this study in a larger cohort of patient samples and correlate the significance of the SARS-CoV-2 virus genome detection in fecal samples with disease severity and transmission.
Wading through Molasses: A qualitative examination of the experiences, perceptions, attitudes, and knowledge of Australian medical practitioners regarding medical billing
Authors: Faux Margaret , Adams Jon , Dahiya Simran , Wardle Jon 
Published: May 2020

AbstractBackgroundMedical billing errors and fraud have been described as one of the last “great unreduced healthcare costs,” with some commentators suggesting measurable average losses from this phenomenon are 7% of total health expenditure. In Australia, it has been estimated that leakage from Medicare caused by non-compliant medical billing may be 10-15% of the scheme’s total cost. Despite a growing body of international research, mostly from the U.S, suggesting that rather than deliberately abusing the health financing systems they operate within, medical practitioners may be struggling to understand complex and highly interpretive medical billing rules, there is a lack of research in this area in Australia. The aim of this study was to address this research gap by examining the experiences of medical practitioners through the first qualitative study undertaken in Australia, which may have relevance in multiple jurisdictions.MethodThis study interviewed 27 specialist and general medical practitioners who claim Medicare reimbursements in their daily practice. Interviews were recorded, transcribed, and analysed using thematic analysis.ResultsThe qualitative data revealed five themes including inadequate induction, poor legal literacy, absence of reliable advice and support, fear and deference, and unmet opportunities for improvement.ConclusionThe qualitative data presented in this study suggest Australian medical practitioners are ill-equipped to manage their Medicare compliance obligations, have low levels of legal literacy and desire education, clarity and certainty around complex billing standards and rules. Non-compliant medical billing under Australia’s Medicare scheme is a nuanced phenomenon that may be far more complex than previously thought and learnings from this study may offer important insights for other countries seeking solutions to the phenomenon of health system leakage. Strategies to address the barriers and deficiencies identified by participants in this study will require a multi-pronged approach. The data suggest that the current punitive system of ensuring compliance by Australian medical practitioners is not fit for purpose.
Forecasting the Spread of COVID-19 under Different Reopening Strategies
Authors: Liu Meng , Thomadsen Raphael , Yao Song 
Published: May 2020

ABSTRACTWe combine COVID-19 case data with mobility data to estimate a modified susceptible-infected-recovered (SIR) model in the United States. In contrast to a standard SIR model, we find that the incidence of COVID-19 spread is concave in the number of infectious individuals, as would be expected if people have inter-related social networks. This concave shape has a significant impact on forecasted COVID-19 cases. In particular, our model forecasts that the number of COVID-19 cases would only have an exponential growth for a brief period at the beginning of the contagion event or right after a reopening, but would quickly settle into a prolonged period of time with stable, slightly declining levels of disease spread. This pattern is consistent with observed levels of COVID-19 cases in the US, but inconsistent with standard SIR modeling. We forecast rates of new cases for COVID-19 under different social distancing norms and find that if social distancing is eliminated there will be a massive increase in the cases of COVID-19.
Multicellular rosettes organize neuropil formation
Authors: Brittin Christopher A. , Santella Anthony , Barnes Kristopher , Moyle Mark W. , Fan Li , Christensen Ryan , Kolotuev Irina , Mohler William A. , Shroff Hari , Colón-Ramos Daniel A. , Bao Zhirong 
Published: May 2020

SummaryNeuropils are compartments in the nervous system containing dense networks of neurites and synapses which function as information processing centers. Neuropil formation requires structural and functional organization at and across different scales, achieving single-axon precision for circuits that carry out the core functions while simultaneously accommodating variability among individuals [1; 2; 3; 4]. How these organizational features emerge over development is poorly understood. The nerve ring is the primary neuropil inC. elegans, and its structure is thoroughly mapped [5; 6]. We show that prior to axon outgrowth, nerve ring neurons form a ring of multicellular rosettes with surrounding cells to organize the stratified nerve ring structure [7; 8]. Axon bundles which correspond to future nerve ring strata grow from rosette centers, travel along the ring on “bridge” cells that are simultaneously engaged in adjacent rosettes, and assemble into a topographic scaffold of the nerve ring. SAX-3/Robo is required for proper rosette formation and outgrowth from the center. Furthermore, axon contact sites that form early in development are more conserved than the later ones, indicating a temporal component in neuropil structural variability. Our results reveal an unexpected and critical role of collective cell behaviors prior to innervation to pattern a complex neuropil and orchestrate its formation across scales.
Burkholderia thailandensismethylated hydroxy-alkylquinolines: biosynthesis and antimicrobial activity in co-cultures
Authors: Klaus Jennifer R , Majerczyk Charlotte , Moon Stephanie , Epplera Natalie A. , Smith Sierra , Tuma Emily , Groleau Marie-Christine , Asfahl Kyle L. , Smalley Nicole E. , Hayden Hillary S. , Piochon Marianne , Ball Patrick , Dandekar Ajai A. , Gauthier Charles , Déziel Eric , Chandler Josephine R. 
Published: May 2020

ABSTRACTThe bacteriumBurkholderia thailandensisproduces an arsenal of secondary metabolites that have diverse structures and roles in the ecology of this soil-dwelling bacterium. In liquid co-culture experiments,B. thailandensissecretes an antimicrobial that nearly eliminates another soil bacterium,Bacillus subtilis. To identify the antimicrobial, we used a transposon mutagenesis approach. This screen identified antimicrobial-defective mutants with insertions in thehmqA, hmqCandhmqFgenes involved in biosynthesis of a family of 2-alkyl-4(1H)-quinolones called 4-hydroxy-3-methyl-2-alkenylquinolines (HMAQs), which are closely related to thePseudomonas aeruginosa4-hydroxy-2-alkylquinolines (HAQs). Insertions also occurred in the previously uncharacterized gene BTH_II1576. Results confirm that BTH_II1576 is involved in generatingN-oxide derivatives of HMAQs (HMAQ-NO) inB. thailandensisand that HMAQ-NOs are sufficient to eliminateB. subtilisin co-cultures. Moreover, synthetic HMAQ-NO is ∼50-fold more active than HMAQ. Both the methyl group and the length of the carbon side chain account for high activity of HMAQ-NO againstB. subtilis. The results provide new information on the biosynthesis and activities of HMAQs and reveal new insight into how these molecules might be important for the ecology ofB. thailandensis.IMPORTANCEThe soil bacteriumBurkholderia thailandensisproduces 2-alkyl-4(1H)-quinolones, mostly methylated 4-hydroxy-alkenylquinolines, a family of relatively unstudied metabolites similar to molecules also synthesized byPseudomonas aeruginosa. Several of the methylated 4-hydroxy-alkenylquinolines have antimicrobial activity against other species. We show thatN-oxidated methyl-alkenylquinolines are particularly antimicrobial and sufficient to killBacillus subtilisin co-cultures. We confirmed their biosynthesis requires the previously unstudied protein HmqL. These results provide new information about the biology of 2-alkyl-4(1H)-quinolones, particularly the methylated 4-hydroxy-alkenylquinolines, which are unique toB. thailandensis. This study also has importance for understandingB. thailandensissecondary metabolites and has implications for potential therapeutic development.
Fecal microbiota transplantation efficacy for Clostridium difficile infection: A trans-kingdom battle between donor and recipient gut microbiomes
Authors: Kazemian Negin , Ramezankhani Milad , Sehgal Aarushi , Khalid Faizan Muhammad , Kalkhoran Amir Hossein Zeinali , Narayan Apurva , Wong Gane Ka-Shu , Kao Dina , Pakpour Sepideh 
Published: May 2020

AbstractFundamental restoration ecology and community ecology theories can help us better understand the underlying mechanisms of fecal microbiota transplantation (FMT) and to better design future microbial therapeutics for recurrent Clostridium difficile infections (rCDI) and other dysbiosis-related conditions. In a single cohort study, stool samples were collected from donors and rCDI patients one week prior to FMT (pre-FMT) as well as from patients one week following FMT (post-FMT). Using metagenomic sequencing and machine learning methods, our results suggested that the FMT outcome is not only dependent on the ecological structure of the recipients, but also the interactions between the donor and recipient microbiomes, both at the taxonomical and functional levels. Importantly, we observed that the presence of specific bacteria in donors (Clostridiodes spp., Desulfovibrio spp., Odoribacter spp. and Oscillibacter spp.) and the absence of specific fungi (Yarrowia spp.) and bacteria (Wigglesworthia spp.) in recipients prior to FMT could accurately predict FMT success. Our results also suggested a series of interlocked mechanisms for FMT success, including the repair of the disturbed gut microbial ecosystem by transient colonization of nexus species followed by secondary succession of bile acid metabolizers, sporulators, and short chain fatty acid producers. Therefore, a better understanding of such mechanisms can be fundamental key elements to develop adaptive, personalized microbial-based strategies for the restoration of the gut ecosystem.ImportanceThere have been a number of studies focusing on understanding the underlying mechanisms in FMT treatment, which can accordingly be used for the optimization of future treatments. However, the current scientific lens has mainly had a uni-kingdom major focus on bacteria, leading to the proposition of the existence of FMT “super-donors”. On the contrary, our preliminary study here suggests that FMT is not necessarily a ‘one stool fits all’ approach and that donor-recipient cross-kingdom microbiota interactions, along with their short-term fluctuations in the gut, bring profound implications in FMT success. The results also conceptualize a series of interlocked mechanisms for FMT success, including first repairing the disturbed gut microbial ecosystem by transient species, followed by secondary succession of indigenous or exogenous bile acid metabolizers, sporulators, and short chain fatty acid producers.
Evaluation of Rural Public Libraries to Address Telemedicine Inequities
Authors: DeGuzman Pamela B. , Siegfried Zack , Leimkuhler Megan E. 
Published: May 2020

AbstractIntroductionIn the United States, access to home-based telemedicine is inequitably distributed due to the limited reach of fixed broadband in rural areas. Public libraries typically offer patrons free access to broadband. Libraries, particularly those in rural regions, need to be evaluated as a site for patients to connect to a health care provider over a video visit. The purpose of this research was to evaluate the technological readiness of public libraries to provide telemedicine support and to determine differences in readiness between rural and urban public libraries.MethodsWe distributed a survey to members of the Virginia Library Association to evaluate technological readiness of Virginia public libraries to support telemedicine use in their facilities. The survey evaluated each library’s availability and speed of fixed broadband internet access, physical equipment, and private space.ResultsRespondents from 39 libraries completed the survey, approximately one-third of which were in rural or small urban areas. All respondents reported fixed broadband, at least four computers, and available staff to assist who technology in their libraries. Eighty-five percent of surveyed libraries reported sufficient broadband speed and a private room available to patrons. There were no significant differences between rural and urban status for any of the library characteristics.DiscussionPublic libraries in Virginia are technologically ready to support patrons connecting to health care providers over telemedicine. Systematic guidelines for library-practice collaborations are needed to support implementation across geographic and socioeconomically diverse areas.
TractLearn: a geodesic learning framework for quantitative analysis of brain bundles
Authors: Attyé Arnaud , Renard Félix , Baciu Monica , Roger Elise , Lamalle Laurent , Dehail Patrick , Cassoudesalle Hélène , Calamante Fernando 
Published: May 2020

ABSTRACTDeep learning-based convolutional neural networks have recently proved their efficiency in providing fast segmentation of major brain fascicles structures, based on diffusion-weighted imaging. The quantitative analysis of brain fascicles then relies on metrics either coming from the tractography process itself or from each voxel along the bundle.Statistical detection of abnormal voxels in the context of disease usually relies on univariate and multivariate statistics models, such as the General Linear Model (GLM). Yet in the case of high-dimensional low sample size data, the GLM often implies high standard deviation range in controls due to anatomical variability, despite the commonly used smoothing process. This can lead to difficulties to detect subtle quantitative alterations from a brain bundle at the voxel scale.Here we introduce TractLearn, a unified framework for brain fascicles quantitative analyses by using geodesic learning as a data-driven learning task. TractLearn allows a mapping between the image high-dimensional domain and the reduced latent space of brain fascicles using a Riemannian approach.We illustrate the robustness of this method on a healthy population with test-retest acquisition of multi-shell diffusion MRI data, demonstrating that it is possible to separately study the global effect due to different MRI sessions from the effect of local bundle alterations. We have then tested the efficiency of our algorithm on a sample of 5 age-matched subjects referred with mild traumatic brain injury.Our contributions are to propose an algorithm based on:1/ A manifold approach to capture controls variability as standard reference instead of an atlas approach based on a Euclidean mean2/ The ability to detect global variation of voxels quantitative values, which means that all the voxels interaction in a structure are considered rather than analyzing each voxel independently.With this regard, TractLearn is a ready-to-use algorithm for precision medicine.KEY POINTWe provide a statistical test taking into account the interaction between voxelsWe propose to use a Riemaniann manifold as reference instead of a Euclidean meanWe demonstrate the usefulness and reliability of the track-weighted contrast