bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and clinical course of 1000 patients with COVID-19 in New York: retrospective case series
Authors: Argenziano Michael G , Bruce Samuel L , Slater Cody L , Tiao Jonathan R , Baldwin Matthew R , Barr R Graham , Chang Bernard P , Chau Katherine H , Choi Justin J , Gavin Nicholas , Goyal Parag , Mills Angela M , Patel Ashmi A , Romney Marie-Laure S , Safford Monika M. , Schluger Neil W , Sengupta Soumitra , Sobieszczyk Magdalena E , Zucker Jason E , Asadourian Paul A , Bell Fletcher M , Boyd Rebekah , Cohen Matthew F , Colquhoun MacAlistair I , Colville Lucy A , de Jonge Joseph H , Dershowitz Lyle B , Dey Shirin A , Eiseman Katherine A , Girvin Zachary P , Goni Daniella T , Harb Amro A , Herzik Nicholas , Householder Sarah , Karaaslan Lara E , Lee Heather , Lieberman Evan , Ling Andrew , Lu Ree , Shou Arthur Y , Sisti Alexander C , Snow Zachary E , Sperring Colin P , Xiong Yuqing , Zhou Henry W , Natarajan Karthik , Hripcsak George , Chen Ruijun 
Published: April 2020

AbstractObjectiveTo characterize patients with coronavirus disease 2019 (COVID-19) in a large New York City (NYC) medical center and describe their clinical course across the emergency department (ED), inpatient wards, and intensive care units (ICUs).DesignRetrospective manual medical record review.SettingNewYork-Presbyterian/Columbia University Irving Medical Center (NYP/CUIMC), a quaternary care academic medical center in NYC.ParticipantsThe first 1000 consecutive patients with laboratory-confirmed COVID-19.MethodsWe identified the first 1000 consecutive patients with a positive RT-SARS-CoV-2 PCR test who first presented to the ED or were hospitalized at NYP/CUIMC between March 1 and April 5, 2020. Patient data was manually abstracted from the electronic medical record.Main outcome measuresWe describe patient characteristics including demographics, presenting symptoms, comorbidities on presentation, hospital course, time to intubation, complications, mortality, and disposition.ResultsAmong the first 1000 patients, 150 were ED patients, 614 were admitted without requiring ICU-level care, and 236 were admitted or transferred to the ICU. The most common presenting symptoms were cough (73.2%), fever (72.8%), and dyspnea (63.1%). Hospitalized patients, and ICU patients in particular, most commonly had baseline comorbidities including of hypertension, diabetes, and obesity. ICU patients were older, predominantly male (66.9%), and long lengths of stay (median 23 days; IQR 12 to 32 days); 78.0% developed AKI and 35.2% required dialysis. Notably, for patients who required mechanical ventilation, only 4.4% were first intubated more than 14 days after symptom onset. Time to intubation from symptom onset had a bimodal distribution, with modes at 3-4 and 9 days. As of April 30, 90 patients remained hospitalized and 211 had died in the hospital.ConclusionsHospitalized patients with COVID-19 illness at this medical center faced significant morbidity and mortality, with high rates of AKI, dialysis, and a bimodal distribution in time to intubation from symptom onset.
Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns
Authors: Wood Valerie , Carbon Seth , Harris Midori A. , Lock Antonia , Engel Stacia R. , Hill David P. , Van Auken Kimberly , Attrill Helen , Feuermann Marc , Gaudet Pascale , Lovering Ruth C. , Poux Sylvain , Rutherford Kim M. , Mungall Christopher J. 
Published: April 2020

AbstractBiological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally, and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes likely reflects errors in literature curation, ontology structure, or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g., amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 2.5 million automatically propagated annotations across all taxa.
Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection
Authors: Chen Qipian , He Ziwen , Feng Xiao , Yang Hao , Shi Suhua , Wu Chung-I 
Published: April 2020

AbstractEvidence for biological adaptation is often obtained by studying DNA sequence evolution. Since the analyses are affected by both positive and negative selection, studies usually assume constant negative selection in the time span of interest. For this reason, hundreds of studies that conclude adaptive evolution might have reported false signals caused by relaxed negative selection. We test this suspicion two ways. First, we analyze the fluctuation in population size, N, during evolution. For example, the evolutionary rate in the primate phylogeny could vary by as much as 2000 fold due to the variation in N alone. Second, we measure the variation in negative selection directly by analyzing the polymorphism data from four taxa (Drosophila, Arabidopsis, primates, and birds, with 64 species in total). The strength of negative selection, as measured by the ratio of nonsynonymous/synonymous polymorphisms, fluctuates strongly and at multiple time scales. The two approaches suggest that the variation in the strength of negative selection may be responsible for the bulk of the reported adaptive genome evolution in the last two decades. This study corroborates the recent report1on the inconsistent patterns of adaptive genome evolution. Finally, we discuss the path forward in detecting adaptive sequence evolution.
Iterative inhibition of commissural growth cone exploration, not post-crossing barrier, ensures forward midline navigation through SlitC-PlxnA1 signaling
Authors: Ducuing Hugo , Gardette Thibault , Pignata Aurora , Kindbeiter Karine , Bozon Muriel , Thoumine Olivier , Delloye-Bourgeois Céline , Tauszig-Delamasure Servane , Castellani Valérie 
Published: April 2020

SummarySensitization to Slits and Semaphorin (Sema)3B floor plate repellents after midline crossing is thought to be the mechanism expelling commissural axons contralaterally and preventing their back-turning. We studied the role of Slit-C terminal fragment sharing with Sema3B the Plexin (Plxn) A1 receptor, newly implicated in midline guidance. We generated a knock-in mouse strain baring PlxnA1Y1815F mutation altering SlitC but not Sema3B responses and observed recrossing phenotypes. Using fluorescent reporters, we found that Slits and Sema3B form clusters decorating an unexpectedly complex mesh of ramified FP glia basal processes spanning the entire navigation path. Time-lapse analyzes revealed that impaired SlitC sensitivity destabilized axon trajectories by inducing high levels of growth cone exploration from the floor plate entry, increasing risk of aberrant decisions. Thus, FP crossing is unlikely driven by post-crossing sensitization to SlitC. Rather, SlitC limits growth cone plasticity and exploration through reiterated contacts, continuously imposing a straight and forward-directed trajectory.
Half of the world’s tree biodiversity is unprotected and is increasingly threatened by human activities
Authors: Guo Wen-Yong , Serra-Diaz Josep M. , Schrodt Franziska , Eiserhardt Wolf L. , Maitner Brian S. , Merow Cory , Violle Cyrille , Anand Madhur , Belluau Michaël , Bruun Hans Henrik , Byun Chaeho , Catford Jane A. , Cerabolini Bruno E. L. , Chacón-Madrigal Eduardo , Ciccarelli Daniela , Cornelissen Johannes H. C. , Dang-Le Anh Tuan , de Frutos Angel , Dias Arildo S. , Giroldo Aelton B. , Guo Kun , Gutiérrez Alvaro G. , Hattingh Wesley , He Tianhua , Hietz Peter , Hough-Snee Nate , Jansen Steven , Kattge Jens , Klein Tamir , Komac Benjamin , Kraft Nathan , Kramer Koen , Lavorel Sandra , Lusk Christopher H. , Martin Adam R. , Mencuccini Maurizio , Michaletz Sean T. , Minden Vanessa , Mori Akira S. , Niinemets Ülo , Onoda Yusuke , Onstein Renske E. , Peñuelas Josep , Pillar Valério D. , Pisek Jan , Robroek Bjorn J.M. , Schamp Brandon , Slot Martjin , Sosinski Ênio , Soudzilovskaia Nadejda A. , Thiffault Nelson , van Bodegom Peter , van der Plas Fons , Wright Ian J. , Xu Wu-Bing , Zheng Jingming , Enquist Brian J. , Svenning Jens-Christian 
Published: April 2020

AbstractAlthough trees are key to ecosystem functioning, many forests and tree species across the globe face strong threats. Preserving areas of high biodiversity is a core priority for conservation; however, different dimensions of biodiversity and varied conservation targets make it difficult to respond effectively to this challenge. Here, we (i) identify priority areas for global tree conservation using comprehensive coverage of tree diversity based on taxonomy, phylogeny, and functional traits; and (ii) compare these findings to existing protected areas and global biodiversity conservation frameworks. We find thatca. 51% of the top-priority areas for tree biodiversity are located in current protected areas. The remaining half top-priority areas are subject to moderate to high human pressures, indicating conservation actions are needed to mitigate these human impacts. Our findings emphasize the effectiveness of using tree conservation priority areas for future global conservation planning.
Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design
Authors: Inoue Keiichi , Karasuyama Masayuki , Nakamura Ryoko , Konno Masae , Yamada Daichi , Mannen Kentaro , Nagata Takashi , Inatsu Yu , Yura Kei , Béjà Oded , Kandori Hideki , Takeuchi Ichiro 
Published: April 2020

AbstractMicrobial rhodopsins are photoreceptive membrane proteins utilized as molecular tools in optogenetics. In this paper, a machine learning (ML)-based model was constructed to approximate the relationship between amino acid sequences and absorption wavelengths using ~800 rhodopsins with known absorption wavelengths. This ML-based model was specifically designed for screening rhodopsins that are red-shifted from representative rhodopsins in the same subfamily. Among 5,558 candidate rhodopsins suggested by a protein BLAST search of several protein databases, 40 were selected by the ML-based model. The wavelengths of these 40 selected candidates were experimentally investigated, and 32 (80%) showed red-shift gains. In addition, four showed red-shift gains > 20 nm, and two were found to have desirable ion-transporting properties, indicating that they were potentially useful in optogenetics. These findings suggest that an ML-based model can reduce the cost for exploring new functional proteins.
Parallel factor analysis enables quantification and identification of highly-convolved data independent-acquired protein spectra
Authors: Buric Filip , Zrimec Jan , Zelezniak Aleksej 
Published: April 2020

AbstractHigh-throughput data-independent acquisition (DIA) is the method of choice for quantitative proteomics, combining the best practices of targeted and shotgun proteomics approaches. The resultant DIA spectra are, however, highly convolved and with no direct precursor-fragment correspondence, complicating the analysis of biological samples. Here we present PARADIAS (PARAllel factor analysis of Data Independent Acquired Spectra), a GPU-powered unsupervised multiway factor analysis framework that deconvolves multispectral scans to individual analyte spectra, chromatographic profiles, and sample abundances, using the PARAFAC tensor decomposition method based on variation of informative spectral features. The deconvolved spectra can be annotated with traditional database search engines or used as a high-quality input forde novosequencing methods. We demonstrate that spectral libraries generated with PARADIAS substantially reduce the false discovery rate underlying the validation of spectral quantification. PARADIAS covers up to 33 times more total ion current than library-based approaches, which typically use less than 5 % of total recorded ions, thus allowing the quantification and identification of signals from unexplored DIA spectra.
Analysis of continuous neuronal activity evoked by natural speech with computational corpus linguistics methods
Authors: Schilling Achim , Tomasello Rosario , Henningsen-Schomers Malte R. , Zankl Alexandra , Surendra Kishore , Haller Martin , Karl Valerie , Uhrig Peter , Maier Andreas , Krauss Patrick 
Published: April 2020

AbstractIn the field of neurobiology of language, neuroimaging studies are generally based on stimulation paradigms consisting of at least two different conditions. Designing those paradigms can be very time-consuming and this traditional approach is necessarily data-limited. In contrast, in computational linguistics analyses are often based on large text corpora, which allow a vast variety of hypotheses to be tested by repeatedly re-evaluating the data set. Furthermore, text corpora also allow exploratory data analysis in order to generate new hypotheses. By drawing on the advantages of both fields, neuroimaging and corpus linguistics, we here present a unified approach combining continuous natural speech and MEG to generate a corpus of speech-evoked neuronal activity.
The early development and physiology ofXenopus laevistadpole lateral line system
Authors: Saccomanno Valentina , Love Heather , Sylvester Amy , Li Wen-Chang 
Published: April 2020

AbstractXenopus laevishas a lateral line mechanosensory system throughout its full life cycle. Previous studies of the tadpole lateral line system revealed that it may play a role in escape behaviour. In this study, we used DASPEI staining to reveal the location of tadpole lateral line neuromasts. Destroying these neuromasts with neomycin resulted in loss of escape responses in tadpoles. We then studied the physiology of anterior lateral line in immobilised tadpoles. Activating the neuromasts behind one eye could evoke asymmetrical motor nerve discharges when the tadpole was resting, suggestive of turning/escape, followed by fictive swimming. When the tadpole was already producing fictive swimming however, anterior lateral line activation reliably led to the termination of swimming. The anterior lateral line had spontaneous afferent discharges at rest, and when activated showed typical adaptation. There were also efferent activities during tadpole swimming, the activity of which was loosely in phase with ipsilateral motor nerve discharges, implying modulation by the motor circuit from the same side. Calcium imaging experiments located sensory interneurons in the primary anterior lateral line nucleus in the hindbrain. Future studies are needed to reveal how sensory information is processed by the central circuit to determine tadpole motor behaviour.Summary statementActivating tadpole anterior lateral line evokes escape responses followed by swimming and halts ongoing swimming. The afferent and efferent activities and sensory interneuron locations in the hindbrain are reported.
Intrinsic/extrinsic duality of large-scale neural functional integration in the human brain
Authors: Sjøgård Martin , Bourguignon Mathieu , Costers Lars , Dumitrescu Alexandru , Coolen Tim , Roshchupkina Liliia , Destoky Florian , Bertels Julie , Niesen Maxime , Ghinst Marc Vander , van Schependom Jeroen , Nagels Guy , Urbain Charline , Peigneux Philippe , Goldman Serge , Woolrich Mark W. , De Tiège Xavier , Wens Vincent 
Published: April 2020

AbstractHuman brain activity is not merely responsive to environmental context but includes intrinsic dynamics, as suggested by the discovery of functionally meaningful neural networks at rest, i.e., even without explicit engagement of the corresponding function. Yet, the neurophysiological coupling mechanisms distinguishing intrinsic (i.e., task-invariant) from extrinsic (i.e., task-dependent) brain networks remain indeterminate. Here, we investigated functional brain integration using magnetoencephalography throughout rest and various tasks recruiting different functional systems and modulating perceptual/cognitive loads. We demonstrated that two distinct modes of neural communication continually operate in parallel: extrinsic coupling supported by phase synchronization and intrinsic integration encoded in amplitude correlation. Intrinsic integration also contributes to phase synchronization, especially over short (second-long) timescales, through modulatory effects of amplitude correlation. Our study establishes the foundations of a novel conceptual framework for human brain function that fundamentally relies on electrophysiological features of functional integration. This framework blurs the boundary between resting-state and task-related neuroimaging.
Defining Epidermal Stem Cell Fate Infidelity and Immunogenicity in Hidradenitis Suppurativa at the Single-Cell Resolution
Authors: Marohn Meaghan , Lin Meng-ju , Yu Wei-wen , Mendoza Ciara Mae , Remark Juliana , Khodadadi-Jamayran Alireza , Chiu Ernest S. , Lu Catherine Pei-ju 
Published: April 2020

AbstractHidradenitis suppurativa (HS) is a severe chronic inflammatory skin disease affecting human apocrine sweat gland-bearing skin regions. One unique feature of HS is the development of keratinized sinus tracts that grow extensively deep in the dermis and are highly immunogenic. Here, we demonstrated that the stem cell fate infidelity exists in the HS sinus tracts, which exhibit features of both surface epidermis and appendages. Using single cell transcriptome analyses, we finely dissected different compartments of the HS epithelium and identified their respective changes in cytokine expression during disease progression and the critical interactions with the immune cells. Together, our work provides advanced understanding of the pathological epidermal remodeling and important implications for HS therapeutics.
White matter microstructure across the adult lifespan: A mixed longitudinal and cross-sectional study using advanced diffusion models and brain-age prediction
Authors: Beck Dani , de Lange Ann-Marie , Maximov Ivan I. , Richard Geneviève , Andreassen Ole A. , Nordvik Jan E. , Westlye Lars T. 
Published: April 2020

AbstractThe macro- and microstructural architecture of human brain white matter undergoes substantial alterations throughout development and ageing. Most of our understanding of the spatial and temporal characteristics of these lifespan adaptations come from magnetic resonance imaging (MRI), including diffusion MRI (dMRI), which enables visualisation and quantification of brain white matter with unprecedented sensitivity and detail. However, with some notable exceptions, previous studies have relied on cross-sectional designs, limited age ranges, and diffusion tensor imaging (DTI) based on conventional single-shell dMRI. In this mixed cross-sectional and longitudinal study (mean interval: 15.2 months) including 702 multi-shell dMRI datasets, we combined complementary dMRI models to investigate age trajectories in healthy individuals aged 18 to 94 years (57.12% women). Using linear mixed effect models and machine learning based brain age prediction, we assessed the age-dependence of diffusion metrics, and compared the age prediction accuracy of six different diffusion models, including diffusion tensor (DTI) and kurtosis imaging (DKI), neurite orientation dispersion and density imaging (NODDI), restriction spectrum imaging (RSI), spherical mean technique multi-compartment (SMT-mc), and white matter tract integrity (WMTI). The results showed that the age slopes for conventional DTI metrics (fractional anisotropy [FA], mean diffusivity [MD], axial diffusivity [AD], radial diffusivity [RD]) were largely consistent with previous research, and that the highest performing advanced dMRI models showed comparable age prediction accuracy to conventional DTI. Linear mixed effects models and Wilk’s theorem analysis showed that the ‘FA fine’ metric of the RSI model and ‘orientation dispersion’ (OD) metric of the NODDI model showed the highest sensitivity to age. The results indicate that advanced diffusion models (DKI, NODDI, RSI, SMT mc, WMTI) provide sensitive measures of age-related microstructural changes of white matter in the brain that complement and extend the contribution of conventional DTI.
An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins
Authors: Koda Shin-ichi , Saito Shinji 
Published: April 2020

ABSTRACTThe biological clock of cyanobacteria is composed of three proteins, KaiA, KaiB, and KaiC. The KaiB-KaiC binding brings the slowness into the system, which is essential for the long period of the circadian rhythm. However, there is no consensus as to the origin of the slowness due to the pre-binding conformational transition of either KaiB or KaiC. In this study, we propose a simple KaiB-KaiC binding scheme in a hexameric form with an attractive interaction between adjacent bound KaiB monomers, which is independent of KaiB’s conformational change. We then show that the present scheme can explain several important experimental results on the binding, including that used as evidence for the slow conformational transition of KaiB. The present result thus indicates that the slowness arises from KaiC rather than KaiB.
Endoplasmic Reticulum Associated Degradation (ERAD) Deficiency Promotes Mitochondrial Dysfunction and Transcriptional Rewiring in Human Hepatic Cells
Authors: Yang Xiaoqing , Liu Qingqing , Long Guangyu , Hu Yabin , Gu Zhenglong , Boisclair Yves R. , Long Qiaoming 
Published: April 2020

AbstractMitochondrial dysfunction has been associated with a variety of human diseases including neurodegeneration, diabetes, non-alcohol fatty liver disease (NAFLD) and cancer, but its underlying causes are incompletely understood. Endoplasmic reticular associated degradation (ERAD) is a protein quality control process essential for maintaining ER homeostasis. Using the human hepatic cell line HepG2 as a model, we show here that ERAD is critically required for mitochondrial function in mammalian cells. Pharmacological inhibition or genetic ablation of ERAD increases cell death under both basal conditions and in response to proinflammatory cytokines. Decreased viability of ERAD-deficient HepG2 cells was traced to impaired mitochondrial functions including reduced ATP production, enhanced reactive oxygen species (ROS) accumulation and increased mitochondrial outer membrane permeability (MOMP). Transcriptome profiling reveals widespread down-regulation in the expression of genes underpinning mitochondrial functions, and up-regulation in the genes with association to tumor growth and aggression. These results highlight a critical role for ERAD in maintaining mitochondrial functional and structural integrity and raise the possibility to improve cellular and organismal mitochondrial function via enhancing cellular ERAD capacity.