bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative multi-center study on the clinical and imaging features of confirmed and unconfirmed patients with COVID-19
Authors: Miao Congliang , Zhuang Jinqiang , Jin Mengdi , Xiong Huanwen , Huang Peng , Zhao Qi , Miao Li , Du Jiang , Yang Xinying , Huang Peijie , Hong Jiang 
Published: March 2020

AbstractBackgroundPrevious studies had described the differences in clinical characteristics between ICU and non-ICU patients. However, seldom study focused on confirmed and unconfirmed groups. Our aim was to compare clinical and imaging characteristics of COVID-19 patients outside Hubei province between confirmed and unconfirmed group.MethodsWe retrospectively enrolled 163 consecutive adult patients with suspected COVID-19 from three tertiary hospitals in two provinces outside Hubei province from January 12, 2020 to February 13, 2020 and the differences in epidemiological, clinical, laboratory and imaging characteristics between the two groups were compared.ResultsThis study enrolled 163 patients with 62 confirmed cases and 101 unconfirmed cases. Most confirmed patients were clustered (31, 50.0%) and with definite epidemiological exposure. Symptoms of COVID-19 were nonspecific, largely fever and dry cough. Laboratory findings in confirmed group were characterized by normal or reduced white blood cell count, reduced the absolute value of lymphocytes, and elevated levels of C-reactive protein (CRP) and accelerated Erythrocyte sedimentation rate (ESR). The typical chest CT imaging features of patients with confirmed COVID-19 were peripherally distributed multifocal GGO with predominance in the lower lung lobe. Compared with unconfirmed patients, confirmed patients had significantly higher proportion of dry cough, leucopenia, lymphopenia and accelerated ESR (P<0.05); but not with alanine aminotransferase, aspartate aminotransferase, D-dimer, lactic dehydrogenase, and myoglobin (P>0.05). Proportion of peripheral, bilateral or lower lung distribution and multi-lobe involvement, GGO, crazy-paving pattern, air bronchogram and pleural thickening in the confirmed group were also higher (P<0.05).ConclusionsSymptoms of COVID-19 were nonspecific. Leukopenia, lymphopenia and ESR, as well as chest CT could be used as a clue for clinical diagnosis of COVID-19.
Analysis of psychological state and clinical psychological intervention model of patients with COVID-19
Authors: Yang Lu , Wu Danjuan , Hou Yanbin , Wang Xunqiang , Dai Ni , Wang Guanjun , Yang Qing , Zhao Wenhui , Lou Zhongze , Ji Yunxin , Ruan Liemin 
Published: March 2020

AbstractBackgroundPatients with the 2019 coronavirus disease (COVID-19) have different degrees of psychological pain, such as anxiety and depression, which may related to their prognosis. Psychological intervention can be conducted in different ways to improve psychological pain and improve the treatment effect.ObjectiveThe present study aimed to investigate and analyze the psychological status of patients with COVID-19 during the course of illness, and to evaluate the effect and influencing factors of psychological crisis intervention, so as to explore the effective mode of clinical psychological intervention in acute patients under isolation environment.MethodsA total of 143 persons participated in the study, including 26 patients diagnosed with COVID-19 in the isolation ward (COVID-19 group), 87 patients with general pneumonia in the observation ward (General Pneumonia group) and 30 healthy volunteers (Normal group). All the patients in the ward received comprehensive psychological intervention, including telephone psychological counseling (active and passive), self-adjustment of written materials and one-to-one psychological crisis intervention. Hamilton depression scale (HAMD) and Hamilton anxiety scale (HAMA) were used to evaluate the mental health status of all patients on the day of admission and 1 week after treatment.ResultsThe scores of HAMA and HAMD of all patients (including isolation ward and observation ward) were significantly higher than the healthy volunteers at the time of admission. The total score of HAMA and HAMD in CVOID-19 group were both higher than that General Pneumonia group. After 1 week’s hospitalization with comprehensive psychological intervention, the scores of HAMA and HAMD in CVOID-19 group were significantly decreased.ConclusionPatients those who diagnosed with COVID-19 in the isolation ward and/or general pneumonia in observation ward have different degrees of anxiety, depression and sleep problems. While receiving antiviral treatment, patients also need psychological intervention. Comprehensive psychological intervention model has been proved to be effective.
Using early data to estimate the actual infection fatality ratio from COVID-19 in France
Authors: Roques Lionel , Klein Etienne , Papaïx Julien , Sar Antoine , Soubeyrand Samuel 
Published: March 2020

AbstractThe number of screening tests carried out in France and the methodology used to target the patients tested do not allow for a direct computation of the actual number of cases and the infection fatality ratio (IFR). The main objective of this work is to estimate the actual number of people infected with COVID-19 and to deduce the IFR during the observation window in France. We develop a ‘mechanistic-statistical’ approach coupling a SIR epidemiological model describing the unobserved epidemiological dynamics, a probabilistic model describing the data acquisition process and a statistical inference method. The actual number of infected cases in France is probably higher than the observations: we find here a factor ×8 (95%-CI: 5–12) which leads to an IFR in France of 0.5% (95%-CI: 0.3 – 0.8) based on hospital death counting data. Adjusting for the number of deaths in nursing homes, we obtain an IFR of 0.8% (95%-CI: 0.45 – 1.25). This IFR is consistent with previous findings in China (0.66%) and in the UK (0.9%) and lower than the value previously computed on the Diamond Princess cruise ship data (1.3%).
Social distancing strategies for curbing the COVID-19 epidemic
Authors: Kissler Stephen , Tedijanto Christine , Lipsitch Marc , Grad Yonatan H. 
Published: March 2020

AbstractThe SARS-CoV-2 pandemic is straining healthcare resources worldwide, prompting social distancing measures to reduce transmission intensity. The amount of social distancing needed to curb the SARS-CoV-2 epidemic in the context of seasonally varying transmission remains unclear. Using a mathematical model, we assessed that one-time interventions will be insufficient to maintain COVID-19 prevalence within the critical care capacity of the United States. Seasonal variation in transmission will facilitate epidemic control during the summer months but could lead to an intense resurgence in the autumn. Intermittent distancing measures can maintain control of the epidemic, but without other interventions, these measures may be necessary into 2022. Increasing critical care capacity could reduce the duration of the SARS-CoV-2 epidemic while ensuring that critically ill patients receive appropriate care.SummaryOne-time distancing results in a fall COVID-19 peak. Intermittent efforts require greater hospital capacity and surveillance.
Nuclear envelope-vacuole contacts mitigate nuclear pore complex assembly stress
Authors: Lord Christopher L. , Wente Susan R. 
Published: March 2020

AbstractThe intricacy of nuclear pore complex (NPC) biogenesis imposes risks of failure that can cause defects in nuclear transport and nuclear envelope morphology, however, cellular mechanisms utilized to alleviate NPC assembly stress are not well-defined. In the budding yeastSaccharomyces cerevisiae, we demonstrate thatNVJ1- andMDM1-enriched nuclear envelope (NE)-vacuole contacts increase when NPC assembly is compromised in severalnupmutants, includingnup116ΔGLFGcells. These interorganelle nucleus-vacuole junctions (NVJs) cooperate with lipid droplets to maintain viability and enhance NPC formation in assembly mutants. Additionally, NVJs function withATG1to promote vacuole-dependent remodeling innup116ΔGLFGcells, which also correlates with proper NPC formation. Importantly, NVJs significantly improve the physiology of NPC assembly mutants, despite having only negligible effects when NPC biogenesis is unperturbed. Collectively, these results define how NE-vacuole interorganelle contacts coordinate responses to mitigate deleterious cellular effects caused by disrupted NPC assembly.SummaryHow cells respond to deleterious effects imposed by disrupted nuclear pore complex (NPC) assembly are not well-defined. The authors demonstrate nuclear envelope-vacuole interactions expand in response to perturbed NPC assembly to promote viability, nuclear envelope remodeling, and proper NPC biogenesis.
Mass spectrometric characterisation of the circulating peptidome following oral glucose ingestion in control and gastrectomised patients
Authors: Kay Richard G. , Foreman Rachel E. , Roberts Geoff P. , Hardwick Richard , Reimann Frank , Gribble Fiona M. 
Published: March 2020

AbstractMeal ingestion triggers secretion of a variety of gut and endocrine peptides, several of which are routinely measured in research studies by commercial immunoassays. We developed an LC-MS/MS based assay for parallel monitoring of multiple peptides in small volumes of human plasma, providing the benefit of analysing exact peptide sequences rather than immuno-reactivity, and potential advantages of cost and sample volumes for measuring multiple peptide hormones. The method involves acetonitrile precipitation of larger proteins, followed by solid phase extraction and nano-LC-MS/MS using an untargeted approach on an orbitrap mass spectrometer. Analysis of plasma from control subjects and patients who have undergone gastrectomy with Roux-en-Y reconstruction, revealed elevated levels of a number of peptides following glucose ingestion. These included GLP-1(7-36), GLP-1(9-36), glicentin, oxyntomodulin, GIP(1-42), GIP(3-42), PYY(1-36), PYY(3-36), neurotensin, insulin and C-peptide, as well as motilin, which decreased following glucose ingestion. Results showed good correlation with those peptides measured previously by immunoassay in the same samples. The gastrectomy group had higher, but non-glucose-dependent, circulating levels of peptides from PIGR and DMBT1.Overall, the method is fast, generic, reproducible and inexpensive, and requires only small plasma samples, making it potentially adaptable for multiplexed measurement of a variety of peptides.
A transient decrease in mitochondrial activity is required to establish the ganglion cell fate in retina adapted for high acuity vision
Authors: Brodier Laurent , Rodrigues Tania , Matter-Sadzinski Lidia , Matter Jean-Marc 
Published: March 2020

SUMMARYAlthough the plan of the retina is well conserved in vertebrates, there are considerable variations in cell type diversity and number, as well as in the organization and properties of the tissue. The high ratios of retinal ganglion cells (RGCs) to cones in primate fovea and bird retinas favor neural circuits essential for high visual acuity and color vision. The role that cell metabolism could play in cell fate decision during embryonic development of the nervous system is still largely unknown. Here, we describe how subtle changes of mitochondrial activity along the pathway converting uncommitted progenitors into newborn RGCs increase the recruitment of RGC-fated progenitors. ATOH7, a proneural protein dedicated to the production of RGCs in vertebrates, activates transcription of the Hes5.3 gene in pre-committed progenitors. The HES5.3 protein, in turn, regulates a transient decrease in mitochondrial activity via the retinoic acid signaling pathway few hours before cell commitment. This metabolic shift lengthens the progression of the ultimate cell cycle and is a necessary step for upregulating Atoh7 and promoting RGC differentiation.GRAPHICAL ABSTRACT
A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development
Authors: Betting Valerie , Joosten Joep , Halbach Rebecca , Thaler Melissa , Miesen Pascal , Van Rij Ronald P. 
Published: March 2020

ABSTRACTPIWI-interacting (pi)RNAs are small silencing RNAs that are crucial for the defense against transposable elements in germline tissues of animals. In Aedes aegypti mosquitoes, the piRNA pathway also contributes to gene regulation in somatic tissues, illustrating additional roles for piRNAs and PIWI proteins besides transposon repression. Here, we identify a highly abundant endogenous piRNA (propiR1) that associates with both Piwi4 and Piwi5. PropiR1-mediated target silencing requires base pairing in the seed region with supplemental base pairing at the piRNA 3’ end. Yet, propiR1 represses a limited set of targets, among which the lncRNA AAEL027353 (lnc027353). Slicing of lnc027353 initiates production of responder and trailer piRNAs from the cleavage fragment. Expression of propiR1 commences early during embryonic development and mediates degradation of maternally provided lnc027353. Both propiR1 and its lncRNA target are conserved in the closely related Aedes albopictus mosquito, underscoring the importance of this regulatory network for mosquito development.
trans-homolog interaction regulates the sex-biased expression of an X-linked gene
Authors: Galouzis Charalampos Chrysovalantis , Prud’homme Benjamin 
Published: March 2020

AbstractSex-biased gene expression patterns in animals are generally controlled by the somatic sex-determination hierarchies. How the different tiers of these hierarchies act on sexually dimorphic gene regulation is still poorly understood. In the developingDrosophila biarmipeswing, the X-linked geneyellowis expressed in males in a specific distal spot pattern that prefigures a corresponding adult pigmentation pattern. Thisyellowexpression pattern is controlled by thespotenhancer, but the origin ofyellowsexually dimorphic expression is unknown. Here we find that the functional interaction between homologousyellowalleles silences specifically thespotenhancer, which is therefore active in males (XY) but not in females (XX). We show that insertingyellowat homologous positions on autosomes recapitulates, in either sex, the homologous-dependent silencing of thespotenhancer. We further find that this silencing requires theyellowintron as well as the architectural protein Mod(mdg4). Finally, we show that Mod(mdg4) is also necessary for the sex-biased expression of some X-linked genes in the brain. Our results demonstrate that regulatory interactions between X-linked homologous alleles promote their sex-biased expression, independently of the canonical sex-determination hierarchy. More generally, they illustrate the biological significance of homologous chromosome pairing andtrans-homolog interactions for the sexually dimorphic regulation of X-linked genes.
Mitotic spindle assembly is controlled by the APC/C localized at the centrosome
Authors: Tischer Thomas , Yang Jing , Barford David 
Published: March 2020

AbstractThe control of protein abundance is a fundamental regulatory mechanism during mitosis. The anaphase promoting complex/cyclosome (APC/C) is the main protein ubiquitin ligase responsible for the temporal regulation of mitotic progression. It has long been speculated that the APC/C might fulfil other functions including assembly of the mitotic spindle. Here, we show that the APC/C localizes to centrosomes, the organizers of the eukaryotic microtubule cytoskeleton, specifically during mitosis. The APC/C is recruited to spindle poles by the centrosomal protein Cep152, and we identified Cep152 as both a novel APC/C interaction partner, and as an APC/C substrate. Importantly, this revealed a mitotic function of Cep152 that is reciprocally regulated by the APC/C. A destruction-defective mutant of Cep152 showed that the timely regulation of Cep152 levels at the centrosome controls spindle assembly and chromosome segregation. The APC/C-mediated degradation of Cep152 at the centrosome releases Cep57 from an inhibitory complex to enable its interaction with pericentrin, a critical step in promoting microtubule nucleation. Thus, our study extends the function of the APC/C from being a regulator of mitosis to also acting as a positive governor of spindle assembly. The APC/C thereby integrates control of these two important processes in a temporal manner.
Cortico-motor control dynamics orchestrates visual sampling
Authors: Tomassini Alice , Maris Eric , Hilt Pauline , Fadiga Luciano , D’Ausilio Alessandro 
Published: March 2020

AbstractMovements overtly sample sensory information, making sensory analysis an active-sensing process. In this study, we show that visual information sampling is not just locked to the (overt) movement dynamics, but it is structured by the internal (covert) dynamics of cortico-motor control. We asked human participants to perform an isometric motor task – based on proprioceptive feedback – while detecting unrelated near-threshold visual stimuli. The motor output (Force) shows zero-lag coherence with brain activity (recorded via electroencephalography) in the beta-band, as previously reported. In contrast, cortical rhythms in the alpha-band systematically forerun the motor output by 200ms. Importantly, visual detection is facilitated when cortico-motor alpha (not beta) synchronization is enhanced immediately before stimulus onset, namely at the optimal phase relationship for sensorimotor communication. These findings demonstrate an automatic gating of visual inputs by the ongoing motor control processes, providing evidence of an internal and alpha-cycling visuomotor loop.
Whole Genome Sequencing ofPlasmodium vivaxIsolates Reveals Frequent Sequence and Structural Polymorphisms in Erythrocyte Binding Genes
Authors: Ford Anthony , Kepple Daniel , Abagero Beka Raya , Connors Jordan , Pearson Richard , Auburn Sarah , Getachew Sisay , Ford Colby , Gunalan Karthigayan , Miller Louis H. , Janies Daniel A. , Rayner Julian C. , Yan Guiyun , Yewhalaw Delenasaw , Lo Eugenia 
Published: March 2020

AbstractPlasmodium vivaxmalaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. Recently, there has been a dramatic increase in the reporting ofP. vivaxcases in Africa, with a high number of them being in Duffy negative individuals, potentially indicatingP. vivaxhas evolved an alternative invasion mechanism that can overcome Duffy negativity. Here, we analyzed single nucleotide polymorphism (SNP) and copy number variation (CNV) in Whole Genome Sequence (WGS) data from 44P. vivaxsamples isolated from symptomatic malaria patients in southwestern Ethiopia, where both Duffy positive and Duffy negative individuals are found. A total of 236,351 SNPs were detected, of which 21.9% was nonsynonymous and 78.1% was synonymous mutations. The largest number of SNPs were detected on chromosomes 9 (33,478 SNPs; 14% of total) and 10 (28,133 SNPs; 11.9%). There were particularly high levels of polymorphism in erythrocyte binding gene candidates including reticulocyte binding protein 2c (RBP2c), merozoite surface protein 1 (MSP1), and merozoite surface protein 3 (MSP3.5,MSP3.85 andMSP3.9). Thirteen genes related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. Variation in gene copy number was also concentrated in genes involved in host-parasite interactions, including the expansion of the Duffy binding protein gene (PvDBP) on chromosome 6 and severalPIRgenes. Based on the phylogeny constructed from the whole genome sequences, the expansion of these genes was an independent process among theP. vivaxlineages in Ethiopia. We further inferred transmission patterns ofP. vivaxinfections among study sites and showed various levels of gene flow at a small geographical scale. The genomic features ofP. vivaxprovided baseline data for future comparison with those in Duffy-negative individuals, and allowed us to develop a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale.
Eigenvector alignment: assessing functional network changes in amnestic mild cognitive impairment and Alzheimer’s disease
Authors: Clark Ruaridh , Nikolova Niia , McGeown William J. , Macdonald Malcolm 
Published: March 2020

AbstractEigenvector alignment, introduced herein to investigate human brain functional networks, is adapted from methods developed to detect influential nodes and communities in networked systems. It is used to identify differences in the brain networks of subjects with Alzheimer’s disease (AD), amnestic Mild Cognitive Impairment (aMCI) and healthy controls (HC). Well-established methods exist for analysing connectivity networks composed of brain regions, including the widespread use of centrality metrics such as eigenvector centrality. However, these metrics provide only limited information on the relationship between regions, with this understanding often sought by comparing the strength of pairwise functional connectivity. Our holistic approach, eigenvector alignment, considers the impact of all functional connectivity changes before assessing the strength of the functional relationship, i.e. alignment, between any two regions. This is achieved by comparing the placement of regions in a Euclidean space defined by the network’s dominant eigenvectors. Eigenvector alignment recognises the strength of bilateral connectivity in cortical areas of healthy control subjects, but also reveals degradation of this commissural system in those with AD. Surprisingly little structural change is detected for key regions in the Default Mode Network, despite significant declines in the functional connectivity of these regions. In contrast, regions in the auditory cortex display significant alignment changes that begin in aMCI and are the most prominent structural changes for those with AD. Alignment differences between aMCI and AD subjects are detected, including notable changes to the hippocampal regions. These findings suggest eigenvector alignment can play a complementary role, alongside established network analytic approaches, to capture how the brain’s functional networks develop and adapt when challenged by disease processes such as AD.
Shifts in evolutionary balance of microbial phenotypes under environmental changes
Authors: Kleshnina M. , McKerral J. C. , González-Tokman C. , Filar J. A. , Mitchell J.G. 
Published: March 2020

AbstractEnvironmental conditions shape entire communities by driving microbial interactions. These interactions then find their reflection in the evolutionary outcome of microbial competition. In static, homogeneous environments a robust, or evolutionary stable, outcome in microbial communities is reachable, if it exists. However, introducing heterogeneity and time-dependence in microbial ecology leads to stochastic evolutionary outcomes determined by specific environmental changes. We utilise evolutionary game theory to provide insight into phenotypic competition in dynamic environments. We capture these effects in a perturbed evolutionary game describing microbial interactions at a phenotypic level. We show that under regular periodic environmental fluctuations a stable state that preserves dominant phenotypes is reached. However, rapid environmental shifts, especially in a cyclic interactions, can lead to critical shifts in the evolutionary balance among phenotypes. Our analysis suggests that an understanding of the robustness of the systems current state is necessary to understand when system will shift to the new equilibrium. This can be done by understanding the systems overall margin of safety, that is, what level of perturbations it can take before its equilibrium changes. In particular, the extent to which an environmental shift affects the system’s behaviour.