bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 – implementation of Swiss-wide diagnostic screening and whole genome sequencing
Authors: Cabecinhas Ana Rita Goncalves , Roloff Tim , Stange Madlen , Bertelli Claire , Huber Michael , Ramette Alban , Chen Chaoran , Nadeau Sarah , Gerth Yannick , Yerly Sabine , Opota Onya , Pillonel Trestan , Schuster Tobias , Metzger Cesar M.J.A. , Sieber Jonas , Bel Michael , Wohlwend Nadia , Baumann Christian , Koch Michel C. , Bittel Pascal , Leuzinger Karoline , Brunner Myrta , Suter-Riniker Franziska , Berlinger Livia , Søgaard Kirstine K. , Beckmann Christiane , Noppen Christoph , Redondo Maurice , Steffen Ingrid , Seth-Smith Helena M.B. , Mari Alfredo , Lienhard Reto , Risch Martin , Nolte Oliver , Eckerle Isabella , Lucchini Gladys Martinetti , Hodcroft Emma B. , Neher Richard A. , Stadler Tanja , Hirsch Hans H. , Leib Stephen L. , Risch Lorenz , Kaiser Laurent , Trkola Alexandra , Greub Gilbert , Egli Adrian 
Published: February 2021

AbstractThe rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations by the European Center for Disease Prevention and Control (ECDC) and World Health Organization (WHO) for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological definitions based on travel history and the S gene dropout in certain diagnostic systems. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 3492 VoCs have been identified since the detection of the first Swiss case in October 2020, with 1370 being B1.1.7, 61 B.1.351, and none P.1. The remaining 2061 cases of VoCs have been described without further lineage specification. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.
Learning Where to Look for COVID-19 Growth: Multivariate Analysis of COVID-19 Cases Over Time using Explainable Convolution-LSTM
Authors: Yudistira Novanto , Sumitro Sutiman Bambang , Nahas Alberth , Riama Nelly Florida 
Published: February 2021

AbstractDeterminant factors which contribute to the prediction should take into account multivariate analysis for capturing coarse-to-fine contextual information. From the preliminary descriptive analysis, it shows that environmental factor such as UV (ultraviolet) is one of the essential factors that should be considered to observe the COVID-19 epidemic drivers, During summer, UV can inactivate viruses that live in the air and on the surface of the objects especially at noon in tropical or subtropical countries. However, it may not be significant in closed spaces like workspace and areas with the intensive human-to-human transmission, especially in densely populated areas. Different COVID-19 pandemic growth patterns in northern subtropical, southern subtropical and tropical countries occur over time. Moreover, there are education, government, morphological, health, economic, and behavioral factors contributing to the growth of COVID-19. Multivariate analysis via visual attribution of explainable Convolution-LSTM is utilized to see high contributing factors responsible for the growth of daily COVID-19 cases. For future works, data to be analyzed should be more detailed in terms of the region and the period where the time-series sample is acquired. The explainable Convolution-LSTM code is available here:https://github.com/cbasemaster/time-series-attribution
AIBx, artificial intelligence model to risk stratify thyroid nodules
Authors: Thomas Johnson , Haertling Tracy 
Published: February 2021

AbstractBackgroundCurrent classification systems for thyroid nodules are very subjective. Artificial intelligence (AI) algorithms have been used to decrease subjectivity in medical image interpretation. 1 out of 2 women over the age of 50 may have a thyroid nodule and at present the only way to exclude malignancy is through invasive procedures. Hence, there exists a need for noninvasive objective classification of thyroid nodules. Some cancers have benign appearance on ultrasonogram. Hence, we decided to create an image similarity algorithm rather than image classification algorithm.MethodsUltrasound images of thyroid nodules from patients who underwent either biopsy or thyroid surgery from February of 2012 through February of 2017 in our institution were used to create AI models. Nodules were excluded if there was no definitive diagnosis of benignity or malignancy. 482 nodules met the inclusion criteria and all available images from these nodules were used to create the AI models. Later, these AI models were used to test 103 thyroid nodules which underwent biopsy or surgery from March of 2017 through July of 2018.ResultsNegative predictive value of the image similarity model was 93.2%. Sensitivity, specificity, positive predictive value and accuracy of the model was 87.8%, 78.5%, 65.9% and 81.5% respectively.ConclusionWhen compared to published results of ACR TIRADS and ATA classification system, our image similarity model had comparable negative predictive value with better sensitivity specificity and positive predictive value. By using image similarity AI models, we can eliminate subjectivity and decrease the number of unnecessary biopsies. Using image similarity AI model, we were able to create an explainable AI model which increases physician’s confidence in the predictions.
Risk-taking behavior and sustained attention after a night shift: an observational study in healthcare professionals
Authors: Bruno S. , Cruz-Sanabria F. , Bazzani A. , Frumento P. , Faraguna U. 
Published: February 2021

ABSTRACTStudy ObjectivesNight work plays an irreplaceable role in healthcare systems. However, sleep loss due to night shifts can negatively affect healthcare workers’ cognition. Identifying individual variables predicting night shift tolerance may help to mitigate the negative consequences of sleep loss on workers’ and patients’ safety. This study aims to explore, in a healthcare workers’ sample, which variables predict the possible impairment in sustained attention and increase in risk-taking behavior after a night shift.Methods22 healthcare workers (avg. age 39.4 ± 11.5 y, 63% females) participated in the experiment. Participants wore a wrist actigraph during a night shift and the preceding 6 days. At the beginning (t0) and at the end (t1) of the night shift, they underwent an assessment of sustained attention (Psychomotor Vigilance Task, PVT) and risk-taking behavior (Balloon Analogue Risk Task, BART). Questionnaires on risk propensity (Domain-Specific Risk Taking, DOSPERT) and on demographics were also administered. Linear regression models were estimated to disentangle the effect of age, risk propensity and actigraphically-defined sleep metrics on cognitive variables.ResultsWake after sleep onset (WASO) significantly predicted t1-t0 PVT metric “major lapses” (β=-0.11, p=0.0007) while age and DOSPERT significantly predicted t1-t0 BART score (β=-0.26, p=0.023 and β=-0.097, p=0.043, respectively).ConclusionsSleep parameters predict the impairment in sustained attention, while the combination of age and risk propensity predicts an increase in risk-taking behavior. The implementation of measures to prevent cognitive decline during night shifts should be designed according to the type of tasks workers must accomplish.
RCGAToolbox: A real-coded genetic algorithm software for parameter estimation of kinetic models
Authors: Maeda Kazuhiro , Boogerd Fred C. , Kurata Hiroyuki 
Published: February 2021

AbstractSummaryKinetic modeling is essential in understanding the dynamic behavior of biochemical networks, such as metabolic and signal transduction pathways. However, parameter estimation remains a major bottleneck in the development of kinetic models. We present RCGAToolbox, software for real-coded genetic algorithms (RCGAs), which accelerates the parameter estimation of kinetic models. RCGAToolbox provides two RCGAs: the unimodal normal distribution crossover with minimal generation gap (UNDX/MGG) and real-coded ensemble crossover star with just generation gap (REXstar/JGG), using the stochastic ranking method. The RCGAToolbox also provides user-friendly graphical user interfaces.Availability and implementationRCGAToolbox is available fromhttps://github.com/kmaeda16/RCGAToolboxunder GNU GPLv3, with application examples. The user guide is provided in the Supplementary Material. RCGAToolbox runs on MATLAB in Windows, Linux, and macOS.Contactkmaeda@bio.kyutech.ac.jpSupplementary informationSupplementary Material is available atBioinformaticsonline.
A hands-on tutorial on network and topological neuroscience
Authors: Centeno Eduarda Gervini Zampieri , Moreni Giulia , Vriend Chris , Douw Linda , Santos Fernando Antônio Nóbrega 
Published: February 2021

AbstractThe brain is an extraordinarily complex system that facilitates the efficient integration of information from different regions to execute its functions. With the recent advances in technology, researchers can now collect enormous amounts of data from the brain using neuroimaging at different scales and from numerous modalities. With that comes the need for sophisticated tools for analysis. The field of network neuroscience has been trying to tackle these challenges, and graph theory has been one of its essential branches through the investigation of brain networks. Recently, topological data analysis has gained more attention as an alternative framework by providing a set of metrics that go beyond pair-wise connections and offer improved robustness against noise. In this hands-on tutorial, our goal is to provide the computational tools to explore neuroimaging data using these frameworks and to facilitate their accessibility, data visualisation, and comprehension for newcomers to the field. We will start by giving a concise (and by no means complete) overview of the field to introduce the two frameworks, and then explain how to compute both well-established and newer metrics on resting-state functional magnetic resonance imaging. We use an open-source language (Python) and provide an accompanying publicly available Jupyter Notebook that uses data from the 1000 Functional Connectomes Project. Moreover, we would like to highlight one part of our notebook that is solely dedicated to realistic visualisation of high order interactions in brain networks. This pipeline provides three-dimensional (3-D) plots of pair-wise and higher-order interactions projected in a brain atlas, a new feature tailor-made for network neuroscience.
OBSTRUCTIVE APNEAS IN A MOUSE MODEL OF CONGENITAL CENTRAL HYPOVENTILATION SYNDROME
Authors: Madani Amélia , Pitollat Gabriel , Sizun Eléonore , Cardoit Laura , Ringot Maud , Bourgeois Thomas , Ramanantsoa Nelina , Delclaux Christophe , Dauger Stéphane , d’Ortho Marie-Pia , Thoby-Brisson Muriel , Gallego Jorge , Matrot Boris 
Published: February 2021

AbstractRationaleCongenital Central Hypoventilation Syndrome (CCHS) is characterized by life-threatening sleep hypoventilation, and is caused byPHOX2Bgene mutations, most frequently thePHOX2B27Ala/+mutation, with patients requiring lifelong ventilatory support. It is unclear whether obstructive apneas are part of the syndrome.ObjectivesTo determine whetherPhox2b27Ala/+mice, which present the main symptoms of CCHS and die within hours after birth, also express obstructive apneas, and to investigate potential underlying mechanisms.MethodsApneas were classified as central, obstructive or mixed by using a novel system combining pneumotachography and laser detection of abdominal movement immediately after birth. Several respiratory nuclei involved in airway patency were examined by immunohistochemistry and electrophysiology in brainstem-spinal cord preparation.Measurements and Main ResultsThe median (interquartile range) of obstructive apnea frequency was 2.3/min (1.5-3.3) inPhox2b27Ala/+pups versus 0.6/min (0.4-1.0) in wildtypes (P< 0.0001). Obstructive apnea duration was 2.7s (2.3-3.9) inPhox2b27Ala/+pups versus 1.7s (1.1-1.9) in wildtypes (P< 0.0001). Central and mixed apneas presented similar, significant differences. InPhox2b27Ala/+preparations, the hypoglossal nucleus had fewer (P< 0.05) and smaller (P< 0.01) neurons, compared to wildtypes. Importantly, coordination of phrenic and hypoglossal motor activities was disrupted, as evidenced by the longer and variable delay of hypoglossal with respect to phrenic activity onset (P< 0.001).ConclusionsThePhox2b27Ala/+mutation predisposed pups not only to hypoventilation and central apneas, but also to obstructive and mixed apneas, likely due to hypoglossal dysgenesis. These results thus demand attention towards obstructive events in infants with CCHS.
Gender and geographical disparity in editorial boards of journals in psychology and neuroscience
Authors: Palser Eleanor R. , Lazerwitz Maia , Fotopoulou Aikaterini 
Published: February 2021

AbstractWhile certain metrics of diversity have seen great improvement in recent years in academic psychology and neuroscience, unequal representation remains for many positions of power. Here, we reviewed publicly available information in order to infer the proportion of editors by gender and their country of affiliation in the top 50 journals worldwide in each of the two fields. The sample included a total of 2,864 editors for psychology journals and 3,093 editors for neuroscience journals. There was a statistically significant difference in the proportion of male and female editors in both fields, both across editorial roles, and within various role categories, including editor-in-chief and their deputies at neuroscience journals, associate and section editors in both fields, and editorial and advisory board members in both fields. The only category in which there was not a significant imbalance of male and female scholars was the editors-in-chief of psychology journals and their deputies. Geographically, USA-based academics significantly outnumbered those from other countries as editors in both psychology and neuroscience. Results also indicated that over three quarters of psychology journals (76%) were comprised of more than 50% male editors, while only 20% had a similar proportion of female editors. In neuroscience, 88% of journals were comprised of more than 50% male editors, while only 10% of journals included a similar, proportional majority of female editors. Findings suggest that editorial positions in academic journals, possibly one of the most powerful decision-making roles in academic psychology and neuroscience, are not balanced in gender or geographical representation.
The Relationship between Birth Timing, Circuit Wiring, and Physiological Response Properties of Cerebellar Granule Cells
Authors: Shuster S. Andrew , Wagner Mark J. , Pan-Doh Nathan , Ren Jing , Grutzner Sophie M. , Beier Kevin T. , Kim Tony Hyun , Schnitzer Mark J. , Luo Liqun 
Published: February 2021

AbstractCerebellar granule cells (GrCs) are usually regarded as a uniform cell type that collectively expands the coding space of the cerebellum by integrating diverse combinations of mossy fiber inputs. Accordingly, stable molecularly or physiologically defined GrC subtypes within a single cerebellar region have not been reported. The only known cellular properties that distinguishes otherwise homogeneous GrCs is the correspondence between GrC birthtime and the depth of the molecular layer to which their axons (parallel fibers) project. To determine the role birth timing plays in GrC wiring and function, we developed genetic strategies to access early- and late-born GrCs. We initiated retrograde monosynaptic rabies virus tracing from control, early-born, and late-born GrCs, revealing the different patterns of mossy fiber input to GrCs in vermis lobule 6 and simplex, as well as to early- and late-born GrCs of vermis lobule 6: sensory and motor nuclei provide more input to early-born GrCs, while basal pontine and cerebellar nuclei provide more input to late-born GrCs.In vivomulti-depth 2-photon Ca2+imaging of parallel fibers of early- and late-born GrCs revealed representations of diverse task variables and stimuli by both populations, with differences in the proportions of parallel fibers encoding movement, reward anticipation, and reward consumption. Our results suggest neither organized parallel processing nor completely random organization of mossy fiber→GrC circuitry, but instead a moderate influence of birth timing on GrC wiring and encoding. Our imaging data also suggest that GrCs can represent general aversiveness, in addition to recently described reward representations.Significance StatementCerebellar granule cells (GrCs) comprise the majority of all neurons in the mammalian brain and are usually regarded as a uniform cell type. However, the birth timing of an individual GrC dictates where its axon projects. Using viral-genetic techniques, we find that early- and late-born GrCs receive different proportions of inputs from the same set of input regions. Usingin vivomulti-depth 2-photon Ca2+imaging of axons of early- and late-born GrCs, we found that both populations represent diverse task variables and stimuli, with differences in the proportions of axons in encoding of a subset of movement and reward parameters. These results indicate that birth timing contributes to the input selection and physiological response properties of GrCs.
Protocol for Safe, Affordable, and Reproducible Isolation and Quantitation of SARS-CoV-2 RNA from Wastewater
Authors: Trujillo Monica , Cheung Kristen , Gao Anna , Hoxie Irene , Kannoly Sherin , Kubota Nanami , San Kaung Myat , Smyth Davida S. , Dennehy John J. 
Published: February 2021

ABSTRACTThe following protocol describes our workflow for processing wastewater with the goal of detecting the genetic signal of SARS-CoV-2. The steps include pasteurization, virus concentration, RNA extraction, and quantification by RT-qPCR. We include auxiliary steps that provide new users with tools and strategies that will help troubleshoot key steps in the process. This protocol is one of the safest, cheapest, and most reproducible approaches for the detection of SARS-CoV-2 RNA in wastewater. Furthermore, the RNA obtained using this protocol, minus the pasteurization step, can be sequenced both using a targeted approach sequencing specific regions or the whole genome. The protocol was adopted by the New York City Department of Environmental Protection in August 2020 to support their efforts in monitoring SARS-CoV-2 prevalence in wastewater in all five boroughs of the city. Owing to a pasteurization step, it is safe for use in a BSL1+ facility. This step also increases the genetic signal of the virus while making the protocol safe for the personnel involved. This protocol could be used to isolate a variety of other clinically relevant viruses from wastewater and serve as a foundation of a wastewater surveillance strategy for monitoring community spread of known and emerging viral pathogens.
Bacteria elicit a phage tolerance response subsequent to infection of their neighbors
Authors: Tzipilevich Elhanan , Pollak-Fiyaksel Osher , Ben-Yehuda Sigal 
Published: February 2021

AbstractPlaque occurrence on a bacterial lawn manifests successive rounds of bacteriophage infection. Yet, mechanisms evolved by bacteria to limit plaque spread have been hardly explored. Here we investigated the dynamics of plaque development by lytic phages infecting the bacteriumBacillus subtilis. We report that plaque expansion is followed by a constriction phase owing to bacterial growth into the plaque zone. This phenomenon is caused by an adaptive process, herein termed “phage tolerance response”, elicited by non-infected bacteria located at the plaque rim upon sensing infection of their neighbors. The temporary phage-tolerance is executed by the stress response RNA polymerase sigma factor σX, primarily through activation of thedltoperon, encoding enzymes that catalyze D-alanylation of cell wall teichoic acid polymers, the major attachment sites for phages infecting Gram-positive bacteria. D-alanylation impedes phage binding and hence infection, thus enabling the uninfected bacteria to form a protective shield opposing plaque spread.
Dynamics ofhunchbacktranslation in real time and at single mRNA resolution in theDrosophilaembryo
Authors: Vinter Daisy J. , Hoppe Caroline , Minchington Thomas G. , Sutcliffe Catherine , Ashe Hilary L. 
Published: February 2021

AbstractThe Hunchback (Hb) transcription factor is critical for anterior-posterior patterning of theDrosophilaembryo. Despite the maternalhbmRNA acting as a paradigm for translational regulation, due to its repression in the posterior of the embryo, little is known about the translatability of zygotically transcribedhbmRNAs. Here we adapt the SunTag system, developed for imaging translation at single mRNA resolution in tissue culture cells, to theDrosophilaembryo to study the translation dynamics of zygotichbmRNAs. Using singlemolecule imaging in fixed and live embryos, we provide evidence for translational repression of zygoticSunTag-hbmRNAs. While the proportion ofSunTag-hbmRNAs translated is initially uniform, translation declines from the anterior over time until it becomes restricted to a posterior band in the expression domain. We discuss how regulatedhbmRNA translation may help establish the sharp Hb expression boundary, which is a model for precision and noise during developmental patterning. Overall, our data show how use of the SunTag method on fixed and live embryos is a powerful combination for elucidating spatiotemporal regulation of mRNA translation inDrosophila.
Delta C2 Domain β1-2 loop contributes to robust Notch signalling
Authors: Martins Torcato , Meng Yao , Korona Boguslawa , Suckling Richard , Johnson Steven , Handford Penny , Lea Susan M. , Bray Sarah 
Published: February 2021

SummaryAccurate Notch signalling is critical for organism development and homeostasis. Fine-tuning of Notch-ligand interactions have substantial impact on signalling-outputs. Recent structural studies identified a conserved N-terminal C2 domain in human Notch ligands which conferred phospholipid binding in vitro. Here we show that Drosophila ligands adopt the same C2 domain structure with analogous variations in the loop regions, including the so-called β1-2 loop that has been associated with phospholipid binding. Mutations in the β 1-2 loop of Delta C2 domain retain Notch binding but have impaired ability to interact with phospholipids in vitro. To investigate its role in vivo we deleted five residues within the β 1-2 loop of endogenous Delta by CRISPR/Cas9 gene editing. Strikingly, this change compromised ligand function. The modified Delta enhanced phenotypes produced by Delta loss of function alleles and suppressed that of Notch alleles. As the modified protein was present on the cell surface in normal amounts, these results argue that C2 domain phospholipid-binding is necessary for robust signalling in vivo where the balance of cis and trans ligand-receptor interactions is finely tuned.