bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determinants of Persistent Post COVID-19 symptoms: Value of a Novel COVID-19 symptoms score
Authors: Galal Islam , Hussein Aliae AR Mohamed , Amin Mariam T , Saad Mahmoud M , Zayan Hossam Eldeen E , Abdelsayed Mustafa Z , Moustafa Mohamed M , Ezzat Abdel Rahman , Helmy Radwa ED , Abd- Elaal Howaida K , Massry Nasrallah A Al , Soliman Mohamed A. , Ismail Asmaa M , Kholief Karima MS , Fathy Enas , Hashem Maiada K 
Published: November 2020

AbstractBackgroundBeing a newly emerging disease little is known about its long-lasting post COVID-19 consequences. Aim of this work is to assess the frequency, patterns and determinants of persistent post COVID-19 symptoms and to evaluate the value of a proposed Novel COVID-19 symptoms score. Patients with confirmed COVID-19 in the registry were included in a cross sectional study. The patient demographics, comorbid disorders, the mean duration since the onset of the symptoms, history of hospital or ICU admittance, and treatment taken during acute state, as well as symptoms score before and after convalescence were recorded.ResultsThe most frequent constitutional and neurological symptoms were myalgia (60.0%), arthralgia (57.2%), restriction of daily activities (57.0%), sleeping troubles (50.9%), followed by anorexia (42.6%), chest pain (32.6%), gastritis (32.3%), cough (29.3%) and dyspnea (29.1%). The mean total score of acute stage symptoms was 31.0 ± 16.3 while post COVID 19 symptoms score was 13.1±12.6 (P<0.001). The main determinants of the persistent post COVID-19 symptoms were the need for oxygen therapy (P<0.001), pre-existing hypertension (P=0.039), chronic pulmonary disorders (P=0.012), and any chronic comorbidity (P=0.004). There was a correlation between the symptom score during the acute attack and post COVID-19 stage (P<0.001, r=0.67). The acute phase score had 83.5% sensitivity and 73.3% specificity for the cutoff point > 18 to predict occurrence of Post-COVID-19 symptoms.ConclusionsCOVID-19 can present with a diverse spectrum of long-term post COVID-19 symptoms. Increased acute phase symptom severity and COVID-19 symptom score > 18 together with the presence of any comorbid diseases increase the risk for persistent post COVID-19 manifestations and severity.
Inferring temporal organization of postembryonic development from high-content behavioral tracking
Authors: Faerberg Denis F. , Gurarie Victor , Ruvinsky Ilya 
Published: November 2020

AbstractUnderstanding temporal regulation of development remains an important challenge. Whereas average, species-typical timing of many developmental processes has been established, less is known about inter-individual variability and correlations in timing of specific events. We addressed these questions in the context of postembryonic development inCaenorhabditis elegans. Based on patterns of locomotor activity of freely moving animals, we inferred durations of four larval stages (L1-L4) in over 100 individuals. Analysis of these data supports several notable conclusions. Individuals have consistently faster or slower rates of development because durations of L1 through L3 stages are positively correlated. The last larval stage, the L4, is less variable than earlier stages and its duration is largely independent of the rate of early larval development, implying existence of two distinct larval epochs. We argue that characteristic patterns of variation and correlation arise because duration of each stage tends to scale relative to total developmental time. This scaling relationship suggests that each larval stage is not limited by an absolute duration, but is instead terminated when a subset of events that must occur prior to adulthood have been completed. The approach described here offers a scalable platform that will facilitate the study of temporal regulation of postembryonic development.
EARLY FLOWERING 3controls temperature responsiveness of the circadian clock
Authors: Zhu Zihao , Quint Marcel , Anwer Muhammad Usman 
Published: November 2020

SummaryPredictable changes in light and temperature during a diurnal cycle are major entrainment cues that enable the circadian clock to generate internal biological rhythms that are synchronized with the external environment. With the average global temperature predicted to keep increasing, the intricate light-temperature coordination that is necessary for clock functionality is expected to be seriously affected. Hence, understanding how temperature signals are perceived by the circadian clock has become an important issue, especially in light of climate change scenarios. InArabidopsis, the clock componentEARLY FLOWERING 3(ELF3) not only serves as an essential lightZeitnehmer, but also functions as a thermosensor participating in thermomorphogenesis. However, the role ofELF3in temperature entrainment of the circadian clock is not fully understood. Here, we report thatELF3is essential for delivering temperature input to the clock. We demonstrate that in the absence ofELF3, the oscillator was unable to properly respond to temperature changes, resulting in an impaired gating of thermoresponses. Consequently, clock-controlled physiological processes such as rhythmic growth and cotyledon movement were disturbed. Together, our results reveal thatELF3is an essentialZeitnehmerfor temperature sensing of the oscillator, and thereby for coordinating the rhythmic control of thermoresponsive physiological outputs.
Bedshift: perturbation of genomic interval sets
Authors: Gu Aaron , Cho Hyun Jae , Sheffield Nathan C. 
Published: November 2020

Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. Many tools have been developed to analyze region sets, including computing similarity metrics to compare them. However, there is no way to objectively evaluate the effectiveness of region set similarity metrics. In this paper we presentBedshift, a command-line tool and Python API to generate new BED files by making random perturbations to an original BED file. Perturbed files have known similarity to the original file and are therefore useful to benchmark similarity metrics. To demonstrate, we used Bedshift to create an evaluation dataset of hundreds of perturbed files generated by shifting, adding, and dropping regions from a reference BED file. Then, we compared four similarity metrics: Jaccard score, coverage score, Euclidean distance, and cosine similarity. Our results highlight differences in behavior among these metrics, such as that Jaccard score is most sensitive to added or dropped regions, while coverage score is most sensitive to shifted regions. Together, we show that Bedshift is a useful tool for creating randomized region sets for a variety of uses.AvailabilityBSD2-licensed source code and documentation can be found athttps://bedshift.databio.org.
Repression precedes the stepwise evolution of a highly specific gene expression pattern
Authors: Pu Jian , Wang Zinan , Cong Haosu , Chin Jacqueline S.R. , Justen Jessa , Yew Joanne Y. , Chung Henry 
Published: November 2020

AbstractWell-controlled gene expression is critical for the proper development and function of many traits. Highly-specific temporal and spatial expression patterns are often due to the overlapping activities of activator and repressor sequences that formcis-regulatory elements called enhancers. While many studies have shown that evolutionary changes in enhancers can result in novel traits, few studies illuminate how enhancers originate, how activator and repressor sequences interact during enhancer evolution, and the order in which they evolve. Here, we traced the evolutionary origin of a recently evolved enhancer that drives the expression of the fatty acyl-CoA elongase,bond, specifically in the semicircular wall epithelium (swe) of theDrosophilamale ejaculatory bulb (EB). We show that this enhancer consists of two activator regions that drivebondexpression in the entire EB and a repressor region that restricts expression specifically to the EB swe. Interestingly, the repressor region preceded the evolution of the two activator regions. The evolution of the first activator region, consisting of two putativeAbdominal-Bsites, did not drive expression in the EB due to the action of the repressor region. Expression ofbondin the EB swe requires the evolution of the second activator region, which does not drive expression on its own, but synergizes with the first activator region and the repressor region to produce a highly-specific spatial expression pattern. Our results show that the origin and evolution of a novel enhancer require multiple steps and the evolution of repressor sequences can precede the evolution of activator sequences.
Dynamic Domain Specificity In Human Ventral Temporal Cortex
Authors: Bankson Brett B. , Boring Matthew J. , Richardson R. Mark , Ghuman Avniel Singh 
Published: November 2020

ABSTRACTAn enduring neuroscientific debate concerns the extent to which neural representation is restricted to neural populations specialized for particular domains of perceptual input, or distributed outside of highly selective populations as well. A critical level for this debate is the neural representation of the identity of individual images, such as individual-level face or written word recognition. Here, intracranial recordings throughout ventral temporal cortex across 17 human subjects were used to assess the spatiotemporal dynamics of individual word and face processing within and outside regions strongly selective for these categories of visual information. Individual faces and words were first discriminable primarily only in strongly selective areas, beginning at about 150 milliseconds after word or face onset, and then discriminable both within and outside strongly selective areas approximately 170 milliseconds later. Regions of ventral temporal cortex that were and were not strongly selective both contributed non-redundant information to the discrimination of individual images. These results can reconcile previous results endorsing disparate poles of the domain specificity debate by highlighting the temporally segregated contributions of different functionally defined cortical areas to individual level representations. This work supports a dynamic model of neural representation characterized by successive domain-specific and distributed processing stages.
Glia actively sculpt sensory neurons by controlled phagocytosis to tune animal behavior
Authors: Raiders Stephan , Black Erik Calvin , Bae Andrea , MacFarlane Stephen , Shaham Shai , Singhvi Aakanksha 
Published: November 2020

ABSTRACTGlia in the central nervous system engulf neuron fragments during synapse remodeling and recycling of photoreceptor outer-segments. Whether glia passively clear shed neuronal debris, or actively remove neuron fragments is unknown. How pruning of single-neuron endings impacts animal behavior is also unclear. Here we report that adultC. elegansAMsh glia engulf sensory endings of the AFD thermosensory neuron. Engulfment is regulated by temperature, AFD’s sensory input, and tracks AFD activity. Phosphatidylserine (PS) flippase TAT-1/ATP8A, functions with glial PS-receptor PSR-1/PSR and PAT-2/α-integrin to initiate engulfment. Glial CED-10/Rac1 GTPase, acting through a conserved GEF complex, executes phagocytosis using the actin-remodeler WSP-1/nWASp and the membrane-sealing factor EFF-1 fusogen. CED-10 levels determine engulfment rates, and engulfment-defective mutants exhibit altered AFD-ending shape and thermosensory behavior. Our findings reveal a molecular pathway underpinning glia-dependent phagocytosis in a peripheral sense-organ, and demonstrate that glia actively engulf neuron-fragments, with profound consequences on neuron shape and animal behavior.
Neural support for contributions of utility and narrative processing of evidence in juror decision making
Authors: Castrellon Jaime J. , Hakimi Shabnam , Parelman Jacob M. , Yin Lun , Law Jonathan R. , Skene Jesse A.G. , Ball David A. , Malekpour Artemis , Beskind Donald H. , Vidmar Neil , Pearson John M. , Carter R. McKell , Pate Skene J. H. 
Published: November 2020

AbstractEfforts to explain complex human decisions have focused on competing theories emphasizing utility and narrative mechanisms. These are difficult to distinguish using behavior alone. Both narrative and utility theories have been proposed to explain juror decisions, which are among the most consequential complex decisions made in a modern society. Here, we asked jury-eligible male and female subjects to rate the strength of a series of criminal cases while recording the resulting patterns of brain activation. We compared patterns of brain activation associated with evidence accumulation to patterns of brain activation derived from a large neuroimaging database to look for signatures of the cognitive processes associated with different models of juror decision making. Evidence accumulation correlated with multiple narrative processes, including reading and recall. Of the cognitive processes traditionally viewed as components of utility, activation patterns associated with uncertainty, but not value, were more active with stronger evidence. Independent of utility and narrative, activations linked to reasoning and relational logic also correlated with increasing evidence. Hierarchical modeling of cognitive processes associated with evidence accumulation supported a more prominent role for narrative in weighing evidence in complex decisions. However, utility processes were also associated with evidence accumulation. These complementary findings support an emerging view that integrates utility and narrative processes in complex decisions.Significance StatementThe last decade has seen a sharply increased interest in narrative as a central cognitive process in human decision making and as an important factor in the evolution of human societies. However, the roles of narrative versus utility models of decision making remain hotly debated. While available models frequently produce similar behavioral predictions, they rely on different cognitive processes and so their roles can be separated using the right neural tests. Here, we use brain imaging during mock juror decisions to show that cognitive processes associated with narrative, and to a lesser extent utility, were engaged while subjects evaluated evidence. These results are consistent with interactions between narrative and utility processes during complex decision making.
A Markov Random Field Model for Network-based Differential Expression Analysis of Single-cell RNA-seq Data
Authors: Li Hongyu , Zhu Biqing , Xu Zhichao , Adams Taylor , Kaminski Naftali , Zhao Hongyu 
Published: November 2020

AbstractBackgroundRecent development of single cell sequencing technologies has made it possible to identify genes with different expression (DE) levels at the cell type level between different groups of samples. In this article, we propose to borrow information through known biological networks to increase statistical power to identify differentially expressed genes (DEGs).ResultsWe develop MRFscRNAseq, which is based on a Markov Random Field (MRF) model to appropriately accommodate gene network information as well as dependencies among cell types to identify cell-type specific DEGs. We implement an Expectation-Maximization (EM) algorithm with mean field-like approximation to estimate model parameters and a Gibbs sampler to infer DE status. Simulation study shows that our method has better power to detect cell-type specific DEGs than conventional methods while appropriately controlling type I error rate. The usefulness of our method is demonstrated through its application to study the pathogenesis and biological processes of idiopathic pulmonary fibrosis (IPF) using a single-cell RNA-sequencing (scRNA-seq) data set, which contains 18,150 protein-coding genes across 38 cell types on lung tissues from 32 IPF patients and 28 normal controls.ConclusionsThe proposed MRF model is implemented in the R package MRFscRNAseq available on GitHub. By utilizing gene-gene and cell-cell networks, our method increases statistical power to detect differentially expressed genes from scRNA-seq data.
The effect of soil potassium and carbohydrates on xylem conductivity and embolism in an evergreen angiosperm tree and a gymnosperm tree before and after drought
Authors: Wagner Yael , Brumfeld Vlad , Grünzweig José M. , Klein Tamir 
Published: November 2020

AbstractXylem embolism is a major threat to tree function and survival under drought, in natural and agricultural settings alike, with its impact increasing in light of global climate change. Conversely, potassium (K+) has been shown to increase xylem conductivity (Ks) in trees, and carbohydrates were reported to impact leaf gas exchange.In this study we examined the effects of K+and carbohydrates on Ksin two divergent evergreen tree species that are regularly exposed to drought: pine (Pinus brutia) and lemon (Citrus × limon). Five-year-old trees were pretreated with zero, moderate, and high K+, and with ambient or elevated CO2, to experimentally increase their xylem K+or carbohydrates levels, respectively. Trees were then monitored for Ksand embolism (using a microCT), along with leaf gas exchange and water potential, before and after a 1.5-2.5 month drought period.Potassium fertigation had a positive effect on Ks, in both species when irrigated, which was eliminated following drought. Drought decreased Ksabout 10-fold in lemon, with little effect in pine. CO2-treated trees had the same Ksas control trees before and after drought.Our results indicate a positive effect of K+on tree hydraulics, which was more pronounced in lemon than in pine, supporting the hypothesis of interaction with the angiosperm pit membrane, and not with the gymnosperm bordered pit. Yet, the elimination of this benefit following drought, and the lack of benefit from elevated carbohydrates following a short-term CO2treatment, question the relevance of these components to tree drought resistance mechanisms.Key massagePotassium fertigation increases hydraulic conductivity and reduces xylem embolism in the gymnosperm pine, and more so in the angiosperm lemon tree, benefits which were eliminated following drought.
Critical care workers have lower seroprevalence of SARS-CoV-2 IgG compared with non-patient facing staff in first wave of COVID19
Authors: Baxendale H.E. , Wells D. , Gronlund J. , Nadesalingam A. , Paloniemi M. , Carnell G. , Tonks P. , Ceron-Gutierrez L. , Ebrahimi S. , Sayer A. , Briggs J.A.G. , Xiong X. , Nathan J.A. , Grice G.L. , James L.C. , Luptak J. , Pai S. , Heeney J.L. , Doffinger R. 
Published: November 2020

AbstractWith the first 2020 surge of the COVID-19 pandemic, many health care workers (HCW) were re-deployed to critical care environments to support intensive care teams to look after high numbers of patients with severe COVID-19. There was considerable anxiety of increased risk of COVID19 for staff working in these environments.Using a multiplex platform to assess serum IgG responses to SARS-CoV-2 N, S and RBD proteins, and detailed symptom reporting, we screened over 500 HCW (25% of the total workforce) in a quaternary level hospital to explore the relationship between workplace and evidence of exposure to SARS-CoV-2.Whilst 45% of the cohort reported symptoms that they consider may have represented COVID-19, overall seroprevalence was 14% with anosmia and fever being the most discriminating symptoms for seropositive status. There was a significant difference in seropositive status between staff working in clinical and non-clinical roles (9% patient facing critical care, 15% patient facing non-critical care, 22% nonpatient facing). In the seropositive cohort, symptom severity increased with age for men and not for women. In contrast, there was no relationship between symptom severity and age or sex in the seronegative cohort reporting possible COVID-19 symptoms. Of the 12 staff screened PCR positive (10 symptomatic), 3 showed no evidence of seroconversion in convalescence.ConclusionThe current approach to Personal Protective Equipment (PPE) appears highly effective in protecting staff from patient acquired infection in the critical care environment including protecting staff managing interhospital transfers of COVID-19 patients. The relationship between seroconversion and disease severity in different demographics warrants further investigation. Longitudinally paired virological and serological surveillance, with symptom reporting are urgently required to better understand the role of antibody in the outcome of HCW exposure during subsequent waves of COVID-19 in health care environments.
Upper Limb Motor Improvement after TBI: Systematic Review of Interventions
Authors: Subramanian Sandeep K. , Fountain Melinda A. , Hood Ashley F. , Verduzco-Gutierrez Monica 
Published: November 2020

AbstractBackgroundTraumatic Brain Injury (TBI) is a leading cause of adult morbidity and mortality. Individuals with TBI have impairments in both cognitive and motor domains. Motor improvements post-TBI are attributable to adaptive neuroplasticity and motor learning. Majority of the studies focus on remediation of balance and mobility issues. There is limited understanding on the use of interventions for upper limb (UL) motor improvements in this population.ObjectiveWe examined the evidence regarding the effectiveness of different interventions to augment UL motor improvement after a TBI.MethodsWe systematically examined the evidence published in English from 1990-2020. The modified Downs and Black checklist helped assess study quality (total score:28). Studies were classified as excellent:24-28, good:19-23, fair:14-18 and poor:≤13 in quality. Effect sizes helped quantify intervention effectiveness.ResultsTwenty-three studies were retrieved. Study quality was excellent(n=1), good(n=5) or fair(n=17). Interventions used included strategies to decrease muscle tone (n=6), constraint induced movement therapy (n=4), virtual reality gaming (n=5), noninvasive stimulation (n=3), arm motor ability training (n=1), stem-cell transplant (n=1); task-oriented training (n=2) and feedback provision (n=1). Motor impairment outcomes included Fugl-Meyer Assessment, Modified Ashworth Scale, and kinematic outcomes (error and movement straightness). Activity limitation outcomes included Wolf Motor Function Test and Motor Activity Log. Effect sizes for majority of the interventions ranged from medium(0.5-0.79) to large(≥0.8). Only ten studies included retention testing.ConclusionThere is preliminary evidence that using some interventions may enhance UL motor improvement after a TBI. Answers to emergent questions can help select the most appropriate interventions in this population.