bluuebunny/crossref_metadata_2025_split huggingface dataset:
A2G2: A Python wrapper to perform very large alignments in semi-conserved regions
Authors: Hleap Jose Sergio , Cristescu Melania E. , Steinke Dirk 
Published: May 2020

AbstractSummaryAmplicons to Global Gene (A2G2) is a Python wrapper that uses MAFFT and an “Amplicon to Gene” strategy to align very large numbers of sequences while improving alignment accuracy. It is specially developed to deal with conserved genes, where traditional aligners introduce a significant amount of gaps.A2G2leverages theadd sequencesoption of MAFFT to align the sequences to a global reference gene and a local reference region. Both of these references can be consensus sequences of trusted sources. Efficient parallelization of these tasks allowsA2G2to align a very large number of sequences (> 500K) in a reasonable amount of time.A2G2can be imported in Python for easier integration with other software, or can be run via command line.AvailabilityA2G2is implemented in Python 3 (3.6) and depends on MAFFT availability. Other package requirements can be found in the requirements.txt file athttps://github.com/jshleap/A2G.A2G2is also available via PyPi (https://pypi.org/project/A2G). It is licensed under the LGPLv3.Supplementary informationSupplementary material is available at github as jupyter notebook.
smORFer: a modular algorithm to detect small ORFs in prokaryotes
Authors: Bartholomäus Alexander , Kolte Baban , Mustafayeva Ayten , Goebel Ingrid , Fuchs Stephan , Engelmann Susanne , Ignatova Zoya 
Published: May 2020

ABSTRACTEmerging evidence places small proteins (≤ 50 amino acids) more centrally in physiological processes. Yet, the identification of functional small proteins and the systematic genome annotation of their cognate small open reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Multiple identifiers of ORFs that use 3-nt periodicity in Ribo-Seq data sets have been successful in eukaryotic smORF annotation. Yet, they have difficulties evaluating prokaryotic genomes due to the unique architecture of prokaryotic genomes (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.). Here, we present our new algorithm, smORFer, which performs with high accuracy in prokaryotic organisms in detecting smORFs. The unique feature of smORFer is that it uses integrated approach and considers structural features of the genetic sequence along with in-register translation and uses Fourier transform to convert these parameters into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way and dependent on the data available for a particular organism allows using different modules for smORF search.
KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities
Authors: Balaji Advait , Sapoval Nicolae , Seto Charlie , Elworth R.A. Leo , Nute Michael G. , Savidge Tor , Segarra Santiago , Treangen Todd J. 
Published: May 2020

AbstractCharacterizing metagenomic samples via kmer-based, database-dependent taxonomic classification methods has provided crucial insight into underlying host-associated microbiome dynamics. However, novel approaches are needed that are able to track microbial community dynamics within metagenomes to elucidate genome flux in response to perturbations and disease states. Here we describe KOMB, a novel approach for tracking homologous regions within microbiomes. KOMB utilizes K-core graph decomposition on metagenome assembly graphs to identify repetitive and homologous regions to varying degrees of resolution. K-core performs a hierarchical decomposition which partitions the graph into shells containing nodes having degree at least K, called K-shells, yieldingO(V + E) complexity compared to exact betweenness centrality complexity ofO(V E) found in prior related approaches. We show through rigorous validation on simulated, synthetic, and real metagenomic datasets that KOMB accurately recovers and profiles repetitive and homologous genomic regions across organisms in the sample. KOMB can also identify functionally-rich regions in Human Microbiome Project (HMP) datasets, and can be used to analyze longitudinal data and identify pivotal taxa in fecal microbiota transplantation (FMT) samples. In summary, KOMB represents a novel approach to microbiome characterization that can efficiently identify sequences of interest in metagenomes.
Extracting the Dynamics of Behavior in Decision-Making Experiments
Authors: Roy Nicholas A. , Bak Ji Hyun ,   The International Brain Laboratory, Akrami Athena , Brody Carlos D. , Pillow Jonathan W. 
Published: May 2020

AbstractUnderstanding how animals update their decision-making behavior over time is an important problem in neuroscience. Decision-making strategies evolve over the course of learning, and continue to vary even in well-trained animals. However, the standard suite of behavioral analysis tools is ill-equipped to capture the dynamics of these strategies. Here, we present a flexible method for characterizing time-varying behavior during decision-making experiments. We show that it successfully captures trial-to-trial changes in an animal’s sensitivity to not only task-relevant stimuli, but also task-irrelevant covariates such as choice, reward, and stimulus history. We use this method to derive insights from training data collected in mice, rats, and human subjects performing auditory discrimination and visual detection tasks. With this approach, we uncover the detailed evolution of an animal’s strategy during learning, including adaptation to time-varying task statistics, suppression of sub-optimal strategies, and shared behavioral dynamics between subjects within an experimental population.
The dorsal and ventral default mode networks are dissociably modulated by the valence and vividness of imagined events
Authors: Lee Sangil , Parthasarathi Trishala , Kable Joseph W. 
Published: May 2020

AbstractRecent work has shown that the brain’s default mode network (DMN) is active when people imagine the future. Here we test whether future imagination can be decomposed into two dissociable psychological processes linked to different subcomponents of the DMN. While measuring brain activity with fMRI as subjects imagine future events, we manipulate the vividness of these events to modulate the demands for scene construction, and we manipulate the valence of these events to modulate the demands for evaluation. We found that one subcomponent of the DMN, the ventral DMN or medial temporal lobe subsystem, responds to the vividness but not the valence of imagined events. In contrast, another subcomponent, the dorsal or core DMN, responds to the valence but not the vividness of imagined events. This separate modifiability of different subcomponents of the DMN by vividness and valence provides strong evidence for a neurocognitive dissociation between (1) the construction of novel, imagined scenes from individual components from memory and (2) the evaluation of these constructed events as desirable or undesirable.Significance StatementPrevious work has suggested that imagination may depend on separate neural networks involved in the construction and evaluation of imagined future events. This study provides strong neural evidence for this dissociation by demonstrating that two components of the brain’s default mode network (DMN) uniquely and specifically respond to different aspects of imagination. The vividness of imagined events modulates the ventral DMN, but not the dorsal DMN, while the valence of imagined events modulates the dorsal DMN, but not the ventral DMN. This supports the dissociable engagement of these sub-networks in constructing and evaluating imagined future events.
Machine learning analysis of the bleomycin-mouse model reveals the compartmental and temporal inflammatory pulmonary fingerprint
Authors: Bordag Natalie , Biasin Valentina , Schnoegl Diana , Valzano Francesco , Jandl Katharina , Nagy Bence M. , Sharma Neha , Wygrecka Malgorzata , Kwapiszewska Grazyna , Marsh Leigh M. 
Published: May 2020

SummaryThe bleomycin mouse-model is the extensively used model to study pulmonary fibrosis, however, the inflammatory cell kinetics and their compartmentalisation is still incompletely understood. Here we assembled historical flow cytometry data, totalling 303 samples and 16 inflammatory-cell populations, and applied advanced data modelling and machine learning methods to conclusively detail these kinetics.Three days post-bleomycin, the inflammatory profile was typified by acute innate inflammation, pronounced neutrophilia, especially of SiglecF+neutrophils, and alveolar macrophage loss. Between 14 and 21 days, rapid-responders were increasingly replaced by T and B cells, and monocyte-derived alveolar macrophages. Multi-colour imaging revealed the spatial-temporal cell distribution and the close association of T cells with deposited collagen.Unbiased immunophenotyping and data modelling exposed the dynamic shifts in immune-cell composition over the course of bleomycin-triggered lung injury. These results and workflow provides a reference point for future investigations, and can easily be applied in the analysis of other datasets.
High burden ofMycoplasma genitaliumand other reproductive tract infections among pregnant women in Papua New Guinea
Authors: Scoullar Michelle J. L. , Boeuf Philippe , Peach Elizabeth , Fidelis Ruth , Tokmun Kerryanne , Melepia Pele , Elijah Arthur , Bradshaw Catriona S. , Fehler Glenda , Siba Peter M. , Erskine Simon , Mokany Elisa , Kennedy Elissa , Umbers Alexandra J. , Luchters Stanley , Robinson Leanne J. , Wong Nicholas C. , Vallely Andrew , Badman Steven G. , Vallely Lisa M. ,   HMHB Study Team, Fowkes Freya J. I. , Morgan Christopher , Pomat William , Crabb Brendan S. , Beeson James G. 
Published: May 2020

ABSTRACTThere is a pressing need for detailed knowledge of the range of pathogens, extent of co-infection and clinical impact of reproductive tract infections (RTIs) among pregnant women. Here, we report on RTIs (Mycoplasma genitalium, Chlamydia trachomatis,Neisseria gonorrhoeae,Trichomonas vaginalis,Treponema pallidum subspecies pallidum,bacterial vaginosis and vulvovaginal candidiasis) and other sexual and reproductive health indicators among 699 pregnant women in Papua New Guinea (PNG). We found widespreadM. genitaliuminfection (12.5% of women), the first time this pathogen has been reported in PNG, with no evidence of macrolide resistance. Most pregnant women (76.2%) had at least one RTI, most of which are treatable. Excluding syphilis, sexually-transmitted infections were detected in 37.8% women. Syndromic management of infections is greatly inadequate and there was remarkably little use of contraception; 98.4% report never having used barrier contraception. This work has implications for improving maternal and child health in PNG.ARTICLE SUMMARY LINEThis first report ofMycoplasma genitaliumin Papua New Guinea finds a high burden (12.5%) among 699 pregnant women. Additionally, more than one in two women were positive for a treatable reproductive tract infection associated with poor health outcomes.
Supramodal executive control of attention: evidence from unimodal and crossmodal dual conflict effects
Authors: Spagna Alfredo , Wu Tingting , Kim Kevin , Fan Jin 
Published: May 2020

AbstractAlthough we have demonstrated that the executive control of attention acts supramodally as shown by significant correlation between conflict effects measures in visual and auditory tasks, no direct evidence of the equivalence in the computational mechanisms governing the allocation of executive control resources within and across modalities has been found. Here, in two independent groups of 40 participants, we examined the interaction effects of conflict processing in both unimodal (visual) and crossmodal (visual and auditory) dual-conflict paradigms (flanker conflict processing in Task 1 and then in the following Task 2) with a manipulation of the stimulus onset asynchrony (SOA). In both the unimodal and the crossmodal dual-conflict paradigms, the conflict processing of Task 1 interfered with the conflict processing of Task 2 when the SOA was short, reflecting an additive interference effect of Task 1 on Task 2 under the time constraints. These results suggest that there is a unified entity that oversees conflict processing acting supramodally by implementing comparable mechanisms in unimodal and crossmodal scenarios.
Severe murine schistosomiasis results from disruption of the modulation of anti-egg CD4 T cell response by immunodominance of a single egg epitope
Authors: Finger Eduardo , Coimbra Thaissa Melo Galante , Finardi de Souza Alessandra 
Published: May 2020

AbstractThis study exploits the consistent correlation between immunodominance of the major egg antigen Sm-p40234-246, a robust Th1/Th17 anti-egg CD4 response and severe liver immunopathology in experimental murine schistosomiasis as an experimental platform to analyze how different degrees of immunodominance affect CD4 modulation and disease outcome. The results show that strong immunodominance of a restricted egg epitope repertoire skews CD4 modulation towards a pathogenic Th1/Th17 pro-inflammatory response and that neutralizing this immunodominance generates an opposite and restorative effect. These results identify immunodominance as an important pathogenic component that influences CD4 modulation in experimental murine schistosomiasis and can be manipulated to treat this and maybe other CD4 mediated diseases.SummaryAntigen informed CD4 modulation determines how efficiently the immune system neutralizes a threat; however, this process and its components are not fully comprehended. This study analyzes immunodominance as one component able to disrupt CD4 modulation and turn pathogenic an otherwise healthy immune response.
The frequency-dependent effect of electrical fields on the mobility of intracellular vesicles in astrocytes
Authors: Wang Yihua , Burghardt Thomas P. , Worrell Gregory A. , Wang Hai-Long 
Published: May 2020

AbstractSlow-wave sleep, defined by low frequency (<4 Hz) electrical brain activity, is a basic brain function affecting metabolite clearance and memory consolidation. Although the origin of low-frequency activity is related to cortical up and down states, the underlying cellular mechanism of how low-frequency activity becomes effective has remained elusive. We applied electrical stimulation to cultured glial astrocytes while monitored the trafficking of GFP-tagged intracellular vesicles using TIRFM. We found a frequency-dependent effect of electrical stimulation that electrical stimulation in low frequency elevates the mobility of astrocytic intracellular vesicles. We suggest a novel mechanism of brain modulation that electrical signals in the lower range frequencies embedded in brainwaves modulate the functionality of astrocytes for brain homeostasis and memory consolidation. This finding suggests a physiological mechanism whereby endogenous low-frequency brain oscillations enhance astrocytic function that may underlie some of the benefits of slow-wave sleep and highlights possible medical device approach for treating neurological diseases.
A Modular Microarray Imaging System for Highly Specific COVID-19 Antibody Testing
Authors: Hedde Per Niklas , Abram Timothy J. , Jain Aarti , Nakajima Rie , de Assis Rafael Ramiro , Pearce Trevor , Jasinskas Algis , Toosky Melody N. , Khan Saahir , Felgner Philip L. , Gratton Enrico , Zhao Weian 
Published: May 2020

AbstractTo detect the presence of antibodies in blood against SARS-CoV-2 in a highly sensitive and specific manner, here we describe a robust, inexpensive ($200), 3D-printable portable imaging platform (TinyArray imager) that can be deployed immediately in areas with minimal infrastructure to read coronavirus antigen microarrays (CoVAMs) that contain a panel of antigens from SARS-CoV-2, SARS-1, MERS, and other respiratory viruses. Application includes basic laboratories and makeshift field clinics where a few drops of blood from a finger prick could be rapidly tested in parallel for the presence of antibodies to SARS-CoV-2 with a test turnaround time of only 2-4 h. To evaluate our imaging device, we probed and imaged coronavirus microarrays with COVID-19-positive and negative sera and achieved a performance on par with a commercial microarray reader 100x more expensive than our imaging device. This work will enable large scale serosurveillance, which can play an important role in the months and years to come to implement efficient containment and mitigation measures, as well as help develop therapeutics and vaccines to treat and prevent the spread of COVID-19.
Dementias Platform UK Clinical Studies and Great Minds register: Protocol of a targeted brain health studies re-contact database
Authors: Koychev Ivan , Young Simon , Holve Heather , Yehuda Michael Ben , Gallacher John 
Published: May 2020

AbstractIntroductionEfforts to de-risk neurodegenerative research have been hampered by the expense and time required to gather the rich longitudinal data needed for stratified experimental study recruitment. Dementias Platform UK (DPUK) is a public-private partnership that brings together data from over 40 cohorts in a standardised framework, which represents an until now unavailable opportunity to create such a resource through a streamlined brain health re-contact platform based on existing cohorts, as well as prospectively collected data.Methods and analysisThe DPUK re-contact platform consists of an opt-in (Great Minds, GM) and an opt-out component (Clinical Studies register, CSR). GM requires invited DPUK cohort participants to consent to targeted re-contact at the GM website. Participants complete prospective browser- and smartphone-based cognitive tests and are given the option for remote genetic and actigraphy testing. The GM data is linked to the retrospective DPUK cohort dataset, including genotypic and longitudinal phenotypic data. The CSR is a solution for cohorts explicitly allowing targeted re-contact. Approved studies provide pre-screening criteria on the basis of the CSR/GM dataset, and individuals meeting these criteria are offered participation directly (GM) or through the parent DPUK cohort (CSR).Ethics and disseminationThe database was approved by the South Central - Oxford C Research Ethics Committee, reference 18/SC/0268 on the 27th of June 2018 and amended on the 1st of November 2019. The availability of the Register to researchers will be disseminated through DPUK’s official communication channels as well as national and international scientific meetings.Article SummaryStrengths and limitations of this study-Solution for stratified recruitment into brain health studies on the basis of genetics and cross-cohort retrospective phenotypic data-Prospective standardised data collection: medical history, cognition, actigraphy-Explicit consent for re-contact on the basis of perceived dementia risk-Recruitment on the basis of retrospective data limited by data variance between cohorts-Limited scope for recruitment of symptomatic individuals due to need to register interest for research and respond to study offers through digital technology
Brain-behaviour relationships in the perceptual decision-making process through cognitive processing stages
Authors: Imani Elaheh , Harati Ahad , Pourreza Hamidreza , Moazami Goudarzi Morteza 
Published: May 2020

AbstractPerceptual decision making, as a process of detecting and categorizing information, has been studied extensively over the last two decades. In this study, we investigated the neural characterization of the whole decision-making process by discovering the information processing stages. Such that, the timing and the neural signature of the processing stages were identified for individual trials. The association of stages duration with the stimulus coherency and spatial prioritization factors also revealed the importance of the evidence accumulation process on the speed of the whole decision-making process. We reported that the impact of the stimulus coherency and spatial prioritization on the neural representation of the decision-making process was consistent with the behavioral characterization as well. This study demonstrated that uncovering the cognitive processing stages provided more insights into the decision-making process.
Neuroepithelial progenitors generate and propagate non-neuronal action potentials across the spinal cord
Authors: Arulkandarajah Kalaimakan Hervé , Osterstock Guillaume , Lafont Agathe , Le Corronc Hervé , Escalas Nathalie , Corsini Silvia , Le Bras Barbara , Boeri Juliette , Czarnecki Antonny , Mouffle Christine , Bullier Erika , Hong Elim , Soula Cathy , Legendre Pascal , Mangin Jean-Marie 
Published: May 2020

SUMMARYIn the developing central nervous system, electrical signaling is thought to rely exclusively on differentiating neurons as they acquire the ability to generate action potentials. Accordingly, the neuroepithelial progenitors (NEPs) giving rise to all neurons and glial cells during development have been reported to remain electrically passive. Here, we investigated the physiological properties of NEPs in the mouse spinal cord at the onset of spontaneous neural activity (SNA) initiating motor behavior in embryos. Using patch-clamp recordings, we discovered that spinal NEPs exhibit spontaneous membrane depolarizations during episodes of SNA. These recurrent depolarizations exhibited a ventral-to-dorsal gradient with the highest amplitude located in the floor-plate – the ventral-most part of the neuroepithelium. Paired-recordings revealed that NEPs are extensively coupled via gap-junctions and form a single electrical syncytium. Although other NEPs were electrically passive, we discovered that floor-plate NEPs have the unique ability to generate large Na+/Ca++action potentials. Unlike neurons, floor-plate action potentials relied primarily on the activation of voltage-gated T-type calcium channels (TTCCs).In situhybridization showed that all 3 known subtypes of TTCCs are highly and predominantly expressed in the floor-plate. During SNA, we found that acetylcholine released by motoneurons recurrently trigger floor-plate action potentials by acting through nicotinic acetylcholine receptors. Finally, by expressing the genetically encoded calcium indicator GCaMP6f in the floor plate, we demonstrated that neuroepithelial action potentials are associated with calcium waves and propagate along the entire length of the spinal cord. By unraveling a novel physiological mechanism generating electrical signals which can propagate independently from neurons across a neural structure, our work significantly changes our understanding of the development, origin and extent of electrical signaling in the central nervous system.HIGHLIGHTSSpinal neuroepithelial progenitors (NEP) are depolarized during spontaneous neural activityNEPs form a single electrical syncytium connected by gap junctionsFloor-plate NEPs generate large Na+/Ca++action potentials in response to acetylcholineNeuroepithelial action potentials propagate across the entire spinal cord