bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lymphocyte subset alterations with disease severity, imaging manifestation, and delayed hospitalization in COVID-19 patients
Authors: Wu Daxian , Wu Xiaoping , Huang Jiansheng , Rao Qunfang , Zhang Qi , Zhang Wenfeng 
Published: August 2020

ABSTRACTBackgroundCOVID-19 continuously threated public health heavily. Present study aimed to investigate the lymphocyte subset alterations with disease severity, imaging manifestation, and delayed hospitalization in COVID-19 patients.MethodsLymphocyte subsets was classified using flow cytometry with peripheral blood collected from 106 patients.ResultsMultivariate logistic regression showed that chest tightness, lymphocyte count, and γ-glutamyl transpeptidase were the independent predictors for severe COVID-19. The T cell, CD4+ T cell and B cell counts in severe patients were significantly lower than that in mild patients (p = 0.004, 0.003 and 0.046, respectively). Only the T cell count was gradually decreased with the increase of infiltrated quadrants of lesions in computed tomography (CT) (p = 0.043). The T cell, CD4+ T cell, and CD8+ T cell counts were gradually decreased with the increase of infiltrated area of the maximum lesion in CT (p = 0.002, 0.003, 0.028; respectively). The T cell count, as well as CD4+ T cell, CD8+ T cell, and NK cell counts were gradually decreased with the increased delayed hospitalization (p = 0.003, 0.002, 0.013, and 0.012; respectively). The proportion of T cell was gradually decreased but B cell was gradually increased with the increased delayed hospitalization (p = 0.031 and 0.003, respectively).ConclusionT cell and CD4+ T cell counts negatively correlated with disease severity, CT manifestation and delayed hospitalization. CD4+ T cell was mainstay of immunity response in COVID-19 patients.
Alcohol, calories and obesity: A rapid systematic review and meta-analysis of consumer knowledge, support and behavioural effects of energy labelling on alcoholic drinks
Authors: Robinson Eric , Humphreys Gabrielle , Jones Andrew 
Published: August 2020

AbstractMandatory energy (calorie) labelling of alcoholic drinks is a public health measure that could be used to address both alcohol consumption and obesity. We systematically reviewed studies examining consumer knowledge of the energy content of alcoholic drinks, public support for energy labelling and the effect of energy labelling of alcoholic drinks on consumption behaviour. Eighteen eligible studies (from 16 sources) were included. Among studies examining consumer knowledge of the energy content of alcoholic drinks (N=8) and support for energy labelling (N=9), there was moderate evidence that people tend to be unaware of the energy content of alcoholic drinks (pooled estimate: 74% [95% CIs 64-82%] of participants inaccurate estimating energy content) and support energy labelling (pooled estimate: 64% [95% CIs 53%-73% support policy]. Six studies examined the effect of energy labelling on consumer behaviour and findings were indicative of no likely effect of labelling. However, the majority of studies were of low methodological quality, used proxy outcome measures and none of the studies were conducted in real-world settings, resulting in a very low level of evidence. Further research is required to determine whether energy labelling of alcoholic drinks affects consumer behaviour and is likely to be an effective public health policy.
A comparison of Emergency Department presentations for Medically Unexplained Symptoms in Frequent Attenders during COVID-19
Authors: Daniels Natasha Faye , Ridwan Raiiq , Barnard Ed B G , Amanullah Talha Muneer , Hayhurst Catherine 
Published: August 2020

AbstractBackgroundMedically Unexplained Symptoms (MUS) refer to symptoms with no identified organic aetiology, and are amongst the most challenging for patients and Emergency Department (ED) staff. Providers working in our ED perceived an increase in severity and frequency of these types of presentations during the COVID-19 pandemic.MethodsA retrospective list of frequent attenders (FA) presenting five or more times to the ED between two 122-day periods were examined: 01 Mar to 30 Jun 2019 (Control) and 2020 (COVID-19). The FA group were then examined to identify patients presenting with MUS (FA-MUS). Data were analysed in Prism; presented as n(%), % (95% confidence interval (95%CI) – Wilson/Brown method). Proportions were compared with a two-tailed Fisher’s exact test. A Baptista-Pike odds ratio was used to estimate magnitude and precision.ResultsThe total number of ED attendances during the control period was n=42,785 which reduced to n=28,806 in the COVID-19 period, a decrease of 32.7%. The control FA cohort had n=44 FA-MUS patients with 149 ED visits. This increased to n=65 FA-MUS patients with 267 visits during COVID-19, p=0.44. There was a significant increase in the proportion of all ED visits that were FA-MUS: 0.3% (control) compared to 0.9% (COVID-19); OR 2.7, p<0.001. There was a significant increase in shortness of breath amongst MUS during the COVID-19 pandemic relative to the control period (p<0.01), with no significant difference in any other MUS category.ConclusionWhilst the total number of ED attendances reduced by almost one third during COVID-19, the actual number of all visits by frequent attenders with MUS increased and the proportion of attendances by these tripled during the same period. This presents an increasing challenge to ED clinicians who may feel underprepared to manage these patients effectively.What is already knownMedically Unexplained Symptoms (MUS) are those that have no identified organic aetiology - they are amongst the most challenging presentations for patients and Emergency Department (ED) staff.During times of stress and uncertainty, frequent attenders (FA) appear to be disproportionately affected by MUS. However, there are few data examining the impact of COVID-19 on the FA population.What this paper addsThere was a significant increase in the proportion of all ED visits by FAs during the first four months of the COVID-19 pandemic.There was a significant increase in the proportion of all ED visits by FAs with MUS during the first four months of the COVID-19 pandemic.The proportion of MUS presentations that were ‘shortness of breath’ was significantly higher in the COVID-19 period compared to the control period. There were no other proportional differences observed in MUS categories.
Effectiveness of Localized Lockdowns in the COVID-19 Pandemic
Authors: Li Yige , Undurraga Eduardo A. , Zubizarreta José R. 
Published: August 2020

ABSTRACTNon-pharmaceutical interventions, such as social distancing and lockdowns, have been essential to control the COVID-19 pandemic. In particular, localized lockdowns in small geographic areas have become an important policy intervention to prevent viral spread in cases of resurgence. These localized lockdowns can result in lower social and economic costs compared to larger-scale suppression strategies. Using an integrated dataset from Chile (March 3 through June 15, 2020) and a novel synthetic control approach, in this paper we estimate the effect of localized lockdowns, disentangling its direct and indirect causal effects on SARS-CoV-2 transmission. Our results show that the effects of localized lockdowns are strongly modulated by their duration and are influenced by indirect effects from neighboring geographic areas. Our estimates suggest that extending localized lockdowns can slow down the pandemic; however, localized lockdowns on their own are insufficient to control pandemic growth in the presence of indirect effects from contiguous neighboring areas that do not have lockdowns. These results provide critical empirical evidence about the effectiveness of localized lockdowns in interconnected geographic areas.
WITHDRAWN: Rad5 and Rad51 act at telomeres through two partially distinct pathways
Authors: Henninger Erin E. , Jolivet Pascale , Berardi Prisca , Fallet Emilie , Benmounah Mohcen , Zeinoun Bechara , Charvin Gilles , Xu Zhou , Mattarocci Stefano , Teixeira Maria Teresa 
Published: August 2020

Withdrawal StatementThe authors have withdrawn their manuscript because, upon reanalyzing the primary data it appears that the methods used by one of the authors, S.M., might have compromised the reliability of the data presented in Figure 1. We sincerely apologize for any harm or confusion this may cause to BioRxiv and its users.
Natural enemies have inconsistent impacts on the coexistence of competing species
Authors: Terry J. Christopher D. , Chen J. , Lewis O. T. 
Published: August 2020

AbstractThe role of natural enemies in promoting coexistence of competing species has generated substantial debate. Modern coexistence theory provides a detailed framework to investigate this topic, but there have been remarkably few empirical applications to the impact of natural enemies.We tested experimentally the capacity for a generalist enemy to promote coexistence of competing insect species, and the extent to which any impact can be predicted by trade-offs between reproductive rate and susceptibility to natural enemies.We used experimental mesocosms to conduct a fully-factorial pairwise competition experiment for six rainforestDrosophilaspecies, with and without a generalist pupal parasitoid. We then parameterised models of competition and examined the coexistence of each pair ofDrosophilaspecies within the framework of modern coexistence theory.We found idiosyncratic impacts of parasitism on pairwise coexistence, mediated through changes in fitness differences, not niche differences. There was no evidence of an overall reproductive rate – susceptibility trade-off. Pairwise reproductive rate – susceptibility relationships were not useful shortcuts for predicting the impact of parasitism on coexistence.Our results exemplify the value of modern coexistence theory in multi-trophic contexts and the importance of contextualising the impact of natural enemies. In the set of species investigated, competition was affected by the higher trophic level, but the overall impact on coexistence cannot be easily predicted just from knowledge of relative susceptibility. Methodologically, our Bayesian approach highlights issues with the separability of model parameters within modern coexistence theory and shows how using the full posterior parameter distribution improves inferences. This method should be widely applicable for understanding species coexistence in a range of systems.
Coordinated interactions between endothelial cells and macrophages in the islet microenvironment promote β cell regeneration
Authors: Saunders Diane C. , Aamodt Kristie I. , Richardson Tiffany M. , Hopkirk Alec , Aramandla Radhika , Poffenberger Greg , Jenkins Regina , Flaherty David K. , Prasad Nripesh , Levy Sean E. , Powers Alvin C. , Brissova Marcela 
Published: August 2020

ABSTRACTEndogenous β cell regeneration could alleviate diabetes, but proliferative stimuli within the islet microenvironment are incompletely understood. We previously found that β cell recovery following hypervascularization-induced β cell loss involves interactions with endothelial cells (ECs) and macrophages (MΦs). Here we show that proliferative ECs modulate MΦ infiltration and phenotype during β cell loss, and recruited MΦs are essential for β cell recovery. Furthermore, VEGFR2 inactivation in quiescent ECs accelerates islet vascular regression during β cell recovery and leads to increased β cell proliferation without changes in MΦ phenotype or number. Transcriptome analysis of β cells, ECs, and MΦs reveals that β cell proliferation coincides with elevated expression of extracellular matrix remodeling molecules and growth factors likely driving activation of proliferative signaling pathways in β cells. Collectively, these findings suggest a new β cell regeneration paradigm whereby coordinated interactions between intra-islet MΦs, ECs, and extracellular matrix mediate β cell self-renewal.
Using Neutralization Landscapes to enumerate Antibody Behavior and Decompose Antibody Mixtures
Authors: Einav Tal , Creanga Adrian , Andrews Sarah F. , McDermott Adrian B. , Kanekiyo Masaru 
Published: August 2020

AbstractAntibodies constitute a key line of defense against the diverse pathogens we encounter in our lives. While the interactions between a single antibody and a single virus are routinely characterized in exquisite detail, the inherent tradeoffs between attributes such as potency and breadth remain unclear. In addition, there is a wide gap between the discrete interactions of single antibodies and how antibody mixtures collectively repel multiple viruses. Here, we develop a new form of antigenic cartography called a Neutralization Landscape that enumerates the full space of antibody-virus interactions for antibodies targeting the influenza hemagglutinin stem. This reference set of antibody behaviors transforms the potency-breadth tradeoff into a readily solvable geometry problem. Using the Neutralization Landscape, we decompose the collective neutralization from multiple antibodies to characterize the composition and functional properties of the stem antibodies within. Looking forward, this framework can leverage the serological assays routinely performed for influenza surveillance to analyze how an individual’s antibody repertoire evolves over time in response to vaccination or infection.One-Sentence SummaryWe describe the full range of behaviors for antibodies targeting the stem of influenza hemagglutinin, enabling us to decompose the collective behavior of antibody mixtures and characterize the individual antibodies within.
metabaR : an R package for the evaluation and improvement of DNA metabarcoding data quality
Authors: Zinger Lucie , Lionnet Clément , Benoiston Anne-Sophie , Donald Julian , Mercier Céline , Boyer Frédéric 
Published: August 2020

AbstractDNA metabarcoding is becoming the tool of choice for biodiversity studies across taxa and large-scale environmental gradients. Yet, the artefacts present in metabarcoding datasets often preclude a proper interpretation of ecological patterns. Bioinformatic pipelines removing experimental noise have been designed to address this issue. However, these often only partially target produced artefacts, or are marker specific. In addition, assessments of data curation quality and the appropriateness of filtering thresholds are seldom available in existing pipelines, partly due to the lack of appropriate visualisation tools.Here, we presentmetabaR, an R package that provides a comprehensive suite of tools to effectively curate DNA metabarcoding data after basic bioinformatic analyses. In particular,metabaRuses experimental negative or positive controls to identify different types of artefactual sequences, i.e. reagent contaminants and tag-jumps. It also flags potentially dysfunctional PCRs based on PCR replicate similarities when those are available. Finally,metabaRprovides tools to visualise DNA metabarcoding data characteristics in their experimental context as well as their distribution, and facilitate assessment of the appropriateness of data curation filtering thresholds.metabaRis applicable to any DNA metabarcoding experimental design but is most powerful when the design includes experimental controls and replicates. More generally, the simplicity and flexibility of the package makes it applicable any DNA marker, and data generated with any sequencing platform, and pre-analysed with any bioinformatic pipeline. Its outputs are easily usable for downstream analyses with any ecological R package.metabaRcomplements existing bioinformatics pipelines by providing scientists with a variety of functions with customisable methods that will allow the user to effectively clean DNA metabarcoding data and avoid serious misinterpretations. It thus offers a promising platform for automatised data quality assessments of DNA metabarcoding data for environmental research and biomonitoring.
Aberrant RNA methylation triggers recruitment of an alkylation repair complex
Authors: Brickner Joshua R. , Tsao Ning , Rodell Rebecca , Oyeniran Clement , Lukinović Valentina , Bacolla Albino , Zhang Lisheng , Soll Jennifer M. , Casanova Alexandre G. , Ganguly Adit , He Chuan , Tainer John A. , Reynoird Nicolas , Mosammaparast Nima 
Published: August 2020

SummaryA critical question in genome stability is the nature of the chemical damage responsible for repair activation. We previously reported a novel pathway specifically activated during alkylation damage in human cells, where the E3 ubiquitin ligase RNF113A mediates the recruitment of the ASCC repair complex. Yet the mechanistic basis for the alkylation damage selectivity of this pathway remains unclear. Here, we demonstrate that RNA but not DNA alkylation is the initiating signal for this process. Aberrantly methylated RNA is sufficient to recruit ASCC, while an RNA dealkylase suppresses ASCC recruitment during chemical alkylation. This aberrant RNA methylation causes transcriptional repression in a manner dependent on the ASCC complex. We show that an alkylated pre-mRNA, or an RNA containing a single damaged base, is sufficient to activate RNF113A E3 activity in a phosphorylation-dependent manner. Together, our work identifies an unexpected role for RNA damage in eliciting a DNA repair response, and suggests that RNA may serve as the “canary in the coal mine” for sensing alkylation damage.
Organisation of afferents along the anterior-posterior and medial-lateral axes of the rat orbitofrontal cortex
Authors: Barreiros Ines V. , Panayi Marios C. , Walton Mark E. 
Published: August 2020

AbstractThe orbitofrontal cortex (OFC) has been anatomically divided into a number of subregions along its medial-lateral axis, which behavioural research suggests have distinct functions. Recently, evidence has emerged suggesting functional diversity is also present along the anterior-posterior axis of the rodent OFC. However, the patterns of anatomical connections that underlie these differences have not been well characterised. Here, we use the retrograde tracer cholera toxin subunit B to simultaneously label the projections into the anterior lateral (ALO), posterior lateral (PLO), and posterior ventral (PVO) portions of the rat OFC. Our methodological approach allowed us to simultaneously compare the density and input patterns into these OFC subdivisions. We observed distinct and topographically organised projection patterns into ALO, PLO, and PVO from the mediodorsal and the submedius nuclei of the thalamus. We also observed different levels of connectivity strength into these OFC subdivisions from the amygdala, motor cortex, sensory cortices and medial prefrontal cortical structures, including medial OFC, infralimbic and prelimbic cortices. Interestingly, while labelling in some of these input regions revealed only a gradient in connectivity strength, other regions seem to project almost exclusively to specific OFC subdivisions. Moreover, differences in input patterns between ALO and PLO were as pronounced as those between PLO and PVO. Together, our results support the existence of distinct anatomical circuits within lateral OFC along its anterior-posterior axis.
Color morphs of the coral,Acropora tenuis, show different responses to environmental stress and different expression profiles of fluorescent-protein genes
Authors: Satoh Noriyuki , Kinjo Koji , Shintaku Kohei , Kezuka Daisuke , Ishimori Hiroo , Yokokura Atsushi , Hagiwara Kazutaka , Hisata Kanako , Kawamitsu Mayumi , Koizumi Koji , Shinzato Chuya , Zayasu Yuna 
Published: August 2020

ABSTRACTCorals of the family Acroporidae are key structural components of reefs that support the most diverse marine ecosystems. Due to increasing anthropogenic stresses, coral reefs are in decline. Along the coast of Okinawa, Japan, three different color morphs ofAcropora tenuishave been recognized for decades. These include brown (N morph), yellow-green (G) and purple (P) forms. The tips of axial coral polyps exhibit specific fluorescence spectra. This attribute is inherited asexually, and color morphs do not change seasonally. In Okinawa Prefecture, during the summer of 2017, the N and P morphs experienced bleaching, in which some N morphs died while P morphs recovered. In contrast, G morphs successfully withstood the stress. Symbiotic dinoflagellates are essential symbiotic partners of scleractinian corals. Photosynthetic activity of symbionts was reduced in July in N and P morphs; however, the three color-morphs host similar sets of Clade-C zoothanthellae, suggesting that beaching of N and P morphs cannot be attributed to differences in symbiont clades. The decodedAcropora tenuisgenome includes five genes for green fluorescent proteins (GFP), two for cyan fluorescent proteins (CFP), three for red fluorescent proteins (RFP), and seven genes for chromoprotein (ChrP). A summer survey of gene expression profiles demonstrated that (a) expression of CFP and REP was quite low in all three morphs, (b) P morphs expressed higher levels of ChrP, (c) both N and G morphs expressed GFP highly, and (d) GFP expression was reduced in N morphs, compared to G morphs, which maintained higher levels of GFP expression throughout the summer. Although further studies are required to understand the biological significance of these color morphs ofAcropora tenuis, our results suggest that thermal stress resistance is modified by genetic mechanisms that coincidentally lead to diversification of color morphs.
Nuclear stiffness decreases with disruption of the extracellular matrix in living tissues
Authors: McCreery Kaitlin P. , Xu Xin , Scott Adrienne K. , Fajrial Apresio K. , Calve Sarah , Ding Xiaoyun , Neu Corey P. 
Published: August 2020

ABSTRACTReciprocal interactions between the cell nucleus and the extracellular matrix lead to macroscale tissue phenotype changes. The extracellular environment is physically linked to the nuclear envelope and provides cues to maintain nuclear structure and cellular homeostasis regulated in part by mechanotransduction mechanisms. However, little is known about how structure and properties of the extracellular matrix in living tissues impacts nuclear mechanics, and current experimental challenges limit the ability to detect and directly measure nuclear mechanics while cells are within the native tissue environment. Here, we hypothesized that enzymatic disruption of the tissue matrix results in a softer tissue, affecting the stiffness of embedded cell and nuclear structures. We aimed to directly measure nuclear mechanics without perturbing the native tissue structure to better understand nuclear interplay with the cell and tissue microenvironments. To accomplish this, we expanded an atomic force microscopy needle-tip probe technique that probes nuclear stiffness in cultured cells to measure the nuclear envelope and cell membrane stiffness within native tissue. We validated this technique by imaging needle penetration and subsequent repair of the plasma and nuclear membranes of HeLa cells stably expressing the membrane repair protein CHMP4B-GFP. In the native tissue environmentex vivo, we found that while enzymatic degradation of viable cartilage tissues with collagenase 3 (MMP-13) and aggrecanase-1 (ADAMTS-4) decreased tissue matrix stiffness, cell and nuclear membrane stiffness is also decreased. Finally, we demonstrated the capability for cell and nucleus elastography using the AFM needle-tip technique. These results demonstrate disruption of the native tissue environment that propagates to the plasma membrane and interior nuclear envelope structures of viable cells.