bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 serology at population scale: SARS-CoV-2-specific antibody responses in saliva
Authors: Randad Pranay R. , Pisanic Nora , Kruczynski Kate , Manabe Yukari C. , Thomas David , Pekosz Andrew , Klein Sabra L. , Betenbaugh Michael J. , Clarke William A. , Laeyendecker Oliver , Caturegli Patrizio P. , Larman H. Benjamin , Detrick Barbara , Fairley Jessica K. , Sherman Amy C. , Rouphael Nadine , Edupuganti Srilatha , Granger Douglas A. , Granger Steve W. , Collins Matthew , Heaney Christopher D. 
Published: May 2020

AbstractNon-invasive SARS-CoV-2 antibody testing is urgently needed to estimate the incidence and prevalence of SARS-CoV-2 infection at the general population level. Precise knowledge of population immunity could allow government bodies to make informed decisions about how and when to relax stay-at-home directives and to reopen the economy. We hypothesized that salivary antibodies to SARS-CoV-2 could serve as a non-invasive alternative to serological testing for widespread monitoring of SARS-CoV-2 infection throughout the population. We developed a multiplex SARS-CoV-2 antibody immunoassay based on Luminex technology and tested 167 saliva and 324 serum samples, including 134 and 118 negative saliva and serum samples, respectively, collected before the COVID-19 pandemic, and 33 saliva and 206 serum samples from participants with RT-PCR-confirmed SARS-CoV-2 infection. We evaluated the correlation of results obtained in saliva vs. serum and determined the sensitivity and specificity for each diagnostic media, stratified by antibody isotype, for detection of SARS-CoV-2 infection based on COVID-19 case designation for all specimens. Matched serum and saliva SARS-CoV-2 antigen-specific IgG responses were significantly correlated. Within the 10-plex SARS-CoV-2 panel, the salivary anti-nucleocapsid (N) protein IgG response resulted in the highest sensitivity for detecting prior SARS-CoV-2 infection (100% sensitivity at ≥10 days post-SARS-CoV-2 symptom onset). The salivary anti-receptor binding domain (RBD) IgG response resulted in 100% specificity. Among individuals with SARS-CoV-2 infection confirmed with RT-PCR, the temporal kinetics of IgG, IgA, and IgM in saliva were consistent with those observed in serum. SARS-CoV-2 appears to trigger a humoral immune response resulting in the almost simultaneous rise of IgG, IgM and IgA levels both in serum and in saliva, mirroring responses consistent with the stimulation of existing, cross-reactive B cells. SARS-CoV-2 antibody testing in saliva can play a critically important role in large-scale “sero”-surveillance to address key public health priorities and guide policy and decision-making for COVID-19.40-word summaryA multiplex immunoassay to detect SARS-CoV-2-specific antibodies in saliva performs with high diagnostic accuracy as early as ten days post-COVID-19 symptom onset. Highly sensitive and specific salivary COVID-19 antibody assays could advance broad immuno-surveillance goals in the USA and globally.
Utility of Pan-Family Assays for Rapid Viral Screening: Reducing Delays in Public Health Responses During Pandemics
Authors: Erlichster Michael , Chana Gursharan , Zantomio Daniela , Goudey Benjamin , Skafidas Efstratios 
Published: May 2020

SummaryBackgroundThe SARS-CoV-2 pandemic has highlighted deficiencies in the testing capacity of many developed countries during the early stages of emerging pandemics. Here we describe the potential for pan-family viral assays to improve early accessibility of large-scale nucleic acid testing.MethodsCoronaviruses and SARS-CoV-2 were used as a case-study for investigating the utility of pan-family viral assays during the early stages of a novel pandemic. Specificity of a pan-coronavirus (Pan-CoV) assay for viral detection was assessed using the frequency of common human coronavirus (HCoV) species in key populations. A reported Pan-CoV assay was assessed to determine sensitivity to SARS-CoV-2 and 59 other coronavirus species. The resilience of the primer target regions of this assay to mutation was assessed in 8893 high quality SARS-CoV-2 genomes to predict ongoing utility during pandemic progression.FindingsDue to infection with common HCoV species, a Pan-CoV assay would return a false positive for as few as 1% of asymptomatic adults, but up to 30% of immunocompromised patients displaying symptoms of respiratory disease. Two of the four reported pan-coronavirus assays would have identified SARS-CoV-2 and we demonstrate that with small adjustments to the primers, these assays can accommodate novel variation observed in animal coronaviruses. The assay target region of one well established Pan-CoV assay is highly resistant to mutation compared to regions targeted by other widely applied SARS-CoV-2 RT-PCR assays.InterpretationPan-family assays have the potential to greatly assist management of emerging public health emergencies through prioritization of high-resolution testing or isolation measures, despite limitations in test specificity due to cross-reactivity with common pathogens. Targeting highly conserved genomic regions make pan-family assays robust and resilient to mutation of a given virus. This approach may be applicable to other viral families and has utility as part of a strategic stockpile of tests maintained to better contain spread of novel diseases prior to the widespread availability of specific assays.
Cytoplasmic pool of spliceosome protein SNRNP70 regulates the axonal transcriptome and development of motor connectivity
Authors: Nikolaou Nikolas , Gordon Patricia M. , Hamid Fursham , Taylor Richard , Makeyev Eugene V. , Houart Corinne 
Published: May 2020

SUMMARYRegulation of pre-mRNA splicing and polyadenylation plays a profound role in neurons by diversifying the proteome and modulating gene expression during development and in response to physiological cues. Although most pre-mRNA processing reactions are thought to occur in the nucleus, numerous splicing regulators are also found in neurites. Here, we show that U1-70K/SNRNP70, a major spliceosomal component, localizes in RNA-associated granules in axons. We identify the cytoplasmic pool of SNRNP70 as an important local regulator of motor axonal growth, nerve-dependent acetylcholine receptor (AChR) clustering and neuromuscular synaptogenesis. This cytoplasmic pool has a protective role for a limited number of axonal transcripts preventing them from degradation. Moreover, non-nuclear SNRNP70 is able to locally regulates splice variants of transcripts such asagrin, thereby locally controlling formation of synapses. Our results point to an unexpected, yet essential, function of local SNRNP70 in axonal development and indicate a role of splicing factors in local RNA metabolism during establishment and maintenance of neuronal connectivity.
The persistence of NontypeableHaemophilus influenzaefuels airway inflammation
Authors: Saliu Fabio , Rizzo Giulia , Bragonzi Alessandra , Cariani Lisa , Cirillo Daniela M. , Colombo Carla , Daccò Valeria , Girelli Daniela , Rizzetto Sara , Sipione Barbara , Cigana Cristina , Lorè Nicola I. 
Published: May 2020

•AbstractNontypeableHaemophilus influenzae(NTHi) is commonly isolated from airway of cystic fibrosis (CF) patients. However, to what extent NTHi persistence contributes to the lung inflammatory burden during CF chronic airway disease is controversial. Here, we aimed at determining the pathological role of NTHi persistence in a cohort of CF patients and in a newly generated mouse model of NTHi persistence.In our study cohort, we found that CF patients chronically colonized by NTHi had significantly higher levels of IL-8 and CXCL1 than those who were not colonized. To better define the impact of NTHi persistence in fuelling inflammatory response, we developed a new mouse model using both laboratory and CF clinical strains. NTHi persistence was associated with chronic inflammation of the lung, characterized by recruitment of neutrophils and cytokine release (KC, G-CFS, IL-6 and IL-17A) at 2 and 14 days postinfection. An increased burden of T cell mediated response (CD4+and γδ cells) and higher levels of matrix metalloproteinase 9, known to be associated with tissue remodelling, were observed at 14 days post-infection. Of note we found that both CD4+IL-17+cells and levels of IL-17 cytokine were enriched in mice at advanced stage of NTHi chronic infection. Moreover, by immunohistochemistry we found CD3+, B220+and CXCL-13+cells localized in bronchus-associated lymphoid tissue-like structures at day 14.Our results demonstrate that NTHi persistence exerts a pro-inflammatory activity in the human and murine lung, and could therefore contribute to the exaggerated burden of lung inflammation in CF patients.
Structural Insights on Fusion Mechanisms of Extracellular Vesicles with Model Plasma Membrane
Authors: Perissinotto Fabio , Rondelli Valeria , Senigagliesi Beatrice , Brocca Paola , Almásy László , Bottyan Laszlo , Merkel Dániel Géza , Amenitsch Heinz , Sartori Barbara , Pachler Karin , Mayr Magdalena , Gimona Mario , Rohde Eva , Casalis Loredana , Parisse Pietro 
Published: May 2020

AbstractExtracellular vesicles (EVs) represent a potent intercellular communication system. Within a lipid bilayer such small vesicles transport biomolecules between cells and throughout the body, strongly influencing the fate of recipient cells. Due to their specific biological functions they have been proposed as biomarkers for various diseases and as optimal candidates for therapeutic applications. Despite of their extreme biological relevance, the small size (30 to a few hundred nanometers in diameter) of EVs still poses a great challenge for their isolation, quantification and biophysical/biochemical characterization, therefore the complex network of EVs and cells as well as their interaction remains to be further revealed. Here we propose a multiscale platform based on Atomic Force Microscopy, Small Angle X-ray Scattering, Small Angle Neutron Scattering and Neutron Reflectometry to reveal structure-function correlations of purified EVs through the analysis of their interaction with model membrane systems, in form of both supported lipid bilayers and suspended unilamellar vesicles of variably complex composition. The analysis reveals a strong interaction of EVs with the model membranes and preferentially with liquid ordered raft-like lipid domains, and opens the way to understand uptake mechanisms in different vesicle to cell membrane relative compositions.
Population structure-guided profiling of antibiotic resistance patterns in clinicalListeria monocytogenesisolates from Germany identifiespbpB3alleles associated with low levels of cephalosporin resistance
Authors: Fischer Martin A. , Wamp Sabrina , Fruth Angelika , Allerberger Franz , Flieger Antje , Halbedel Sven 
Published: May 2020

AbstractCase numbers of listeriosis have been increasing in Germany and the European Union during the last decade. In addition reports on the occurrence of antibiotic resistance inListeria monocytogenesin clinical and environmental isolates are accumulating. The susceptibility towards 14 antibiotics was tested in a selection of clinicalL. monocytogenesisolates to get a more precise picture of the development and manifestation of antibiotic resistance in theL. monocytogenespopulation. Based on the population structure determined by core genome multi locus sequence typing (cgMLST) 544 out of 1,220 sequenced strains collected in Germany between 2009 and 2019 were selected to cover the phylogenetic diversity observed in the clinicalL. monocytogenespopulation. All isolates tested were susceptible towards ampicillin, penicillin and co-trimoxazole - the most relevant antibiotics in the treatment of listeriosis. Resistance to daptomycin and ciprofloxacin was observed in 493 (91%) and in 71 (13%) of 544 isolates, respectively. While all tested strains showed resistance towards ceftriaxone, the minimal inhibitory concentrations (MIC) observed varied widely between 4 mg/L up to >128 mg/L. An allelic variation of the penicillin binding protein genepbpB3could be identified as the cause of this difference in ceftriaxone resistance levels. This study is the first population structure-guided analysis of antimicrobial resistance in recent clinical isolates and confirms the importance of penicillin binding protein B3 (PBP B3) for the high level of intrinsic cephalosporin resistance ofL. monocytogeneson a population-wide scale.
COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM
Authors: Lemoine Frédéric , Blassel Luc , Voznica Jakub , Gascuel Olivier 
Published: May 2020

AbstractMotivationThe first cases of the COVID-19 pandemic emerged in December 2019. Until the end of February 2020, the number of available genomes was below 1,000, and their multiple alignment was easily achieved using standard approaches. Subsequently, the availability of genomes has grown dramatically. Moreover, some genomes are of low quality with sequencing/assembly errors, making accurate re-alignment of all genomes nearly impossible on a daily basis. A more efficient, yet accurate approach was clearly required to pursue all subsequent bioinformatics analyses of this crucial data.ResultshCoV-19 genomes are highly conserved, with very few indels and no recombination. This makes the profile HMM approach particularly well suited to align new genomes, add them to an existing alignment and filter problematic ones. Using a core of ∼2,500 high quality genomes, we estimated a profile using HMMER, and implemented this profile in COVID-Align, a user-friendly interface to be used online or as standalone via Docker. The alignment of 1,000 genomes requires less than 20mn on our cluster. Moreover, COVID-Align provides summary statistics, which can be used to determine the sequencing quality and evolutionary novelty of input genomes (e.g. number of new mutations and indels).Availabilityhttps://covalign.pasteur.cloud,hub.docker.com/r/evolbioinfo/covid-alignContactsolivier.gascuel@pasteur.fr,frederic.lemoine@pasteur.frSupplementary informationSupplementary information is available atBioinformaticsonline.
High-Efficiency Electroporation of Chytrid Fungi
Authors: Swafford Andrew J.M. , Hussey Shane P. , Fritz-Laylin Lillian K. 
Published: May 2020

AbstractTwo species of parasitic fungi from the phylum Chytridiomycota (chytrids) are annihilating global amphibian populations. These chytrid species—Batrachochytrium dendrobatidisandB. salamandrivorans—have high rates of mortality and transmission. Upon establishing infection in amphibians, chytrids rapidly multiply within the skin and disrupt their hosts’ vital homeostasis mechanisms. Current disease models suggest that chytrid fungi locate and infect their hosts during a motile, unicellular ‘zoospore’ life stage. Moreover, other chytrid species parasitize organisms from across the tree of life, making future epidemics in new hosts a likely possibility. Efforts to mitigate the damage and spread of chytrid disease have been stymied by the lack of knowledge about basic chytrid biology and tools with which to test molecular hypotheses about disease mechanisms. To overcome this bottleneck, we have developed high-efficiency delivery of molecular payloads into chytrid zoospores using electroporation. Our electroporation protocols result in payload delivery to between 75-97% of living cells of three species:B. dendrobatidis, B. salamandrivorans,and a non-pathogenic relative,S. punctatus. This method lays the foundation for molecular genetic tools needed to establish ecological mitigation strategies and answer broader questions in evolutionary and cell biology.
Single-cell growth inference ofCorynebacterium glutamicumreveals asymptotically linear growth
Authors: Messelink Joris , Meyer Fabian , Bramkamp Marc , Broedersz Chase P. 
Published: May 2020

AbstractRegulation of growth and cell size is crucial for the optimization of bacterial cellular function. So far, single bacterial cells have been found to grow exponentially, which implies the need for tight regulation to maintain cell size homeostasis. Here, we characterize the growth behavior of the apically growing bacteriumCorynebacterium glutamicumusing a novel broadly applicable inference method for single-cell growth dynamics. Using this approach, we find thatC. glutamicumexhibits asymptotically linear single-cell growth. To explain this growth mode, we model elongation as being rate-limited by the apical growth mechanism. Our model accurately reproduces the inferred cell growth dynamics and is validated with elongation measurements on a transglycosylase deficientΔrodAmutant. Finally, with simulations we show that the distribution of cell lengths is narrower for linear than exponential growth, suggesting that this asymptotically linear growth mode can act as a substitute for tight division length and division symmetry regulation.
A network linking scene perception and spatial memory systems in posterior cerebral cortex
Authors: Steel Adam , Billings Madeleine M. , Silson Edward H. , Robertson Caroline E. 
Published: May 2020

AbstractHere, we report a network of brain areas bridging the spatial-memory and scene-perception systems of the human brain. Using fine-grained individual-subject fMRI, we reveal three cortical areas of the human brain, each lying immediately anterior to a region of the scene perception network in posterior cerebral cortex, that selectively activate when recalling familiar real-world locations. Despite their close proximity to the scene-perception areas, network analyses show that these regions constitute a distinct functional network that interfaces with memory systems during naturalistic scene understanding. These “place-memory areas” offer a new framework for understanding how the brain implements memory-guided visual behaviors, including navigation.
Preliminary analysis of scRNA sequencing of children’s lung tissues excludes the expression of SARS-CoV-2 entry related genes as the key reason for the milder syndromes of COVID-19 in children
Authors: Tao Yue , Yang Ruwen , Wen Chen , Fan Jue , Ma Jing , He Qiao , Zhao Zhiguang , Song Xinyu , Chen Hao , Shi Guocheng , Yin Minzhi , Fang Nan , Zhang Hao , Chen Huiwen , Mo Xi 
Published: May 2020

SUMMARYTo explore whether the expression levels of viral-entry associated genes might contribute to the milder symptoms in children, we analyzed the expression of these genes in both children and adults’ lung tissues by single cell RNA sequencing (scRNA-seq) and immunohistochemistry (IHC). Both scRNA-seq and IHC analyses showed comparable levels of the key genes for SARS-CoV-2 entry in children and adults, includingACE2, TMPRSS2andFURIN, suggesting that instead of lower virus intrusion rate, other factors are more likely to be the key reasons for the milder symptoms of SARS-CoV-2 infected children.
Periodontal therapy on disease activity of Rheumatoid Arthritis. Systematic review and meta-analysis
Authors: Novillo Francisco , Lai Shuheng , Cárdenas Geovanna , Verdugo Francisca , Rada Gabriel 
Published: May 2020

AbstractObjectiveThe objective of this systematic review is to assess the impact of periodontal therapy on disease activity of patients with Rheumatoid ArthritisData SourcesWe will conduct a comprehensive search in PubMed/Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Lilacs, the International Clinical Trials Registry Platform (ICTRP), ClinicalTrials.gov, US National Institutes of Health (NIH) and grey literature, to identify all relevant randomized controlled trials regardless of language or publication status (published, unpublished, in press and in progress).Elegibility Criteria for Selecting Studies and MethodsWe will include randomised trials evaluating the effect of periodontal therapy on disease activity of rheumatoid arthritis. Two reviewers will independently screen each study for eligibility, data extraction, and assess the risk of bias. We will pool the results using meta-analysis and will apply the GRADE system to assess the certainty of the evidence for each outcome.Ethics and DisseminationNo ethics approval is considered necessary. The results of this review will be disseminated via peer-reviewed publications, social networks and traditional media.PROSPERO Registration IDCRD42020150286.
What Can We Learn from the Time Evolution of COVID-19 Epidemic in Slovenia?
Authors: Bâldea Ioan 
Published: May 2020

AbstractA recent work (DOI 10.1101/2020.05.06.20093310) indicated that temporarily splitting larger populations into smaller groups can efficiently mitigate the spread of SARS-CoV-2 virus. The fact that, soon afterwards, on May 15, 2020, the two million people Slovenia was the first European country proclaiming the end of COVID-19 epidemic within national borders may be relevant from this perspective. Motivated by this evolution, in this paper we investigate the time dynamics of coronavirus cases in Slovenia with emphasis on how efficient various containment measures act to diminish the number of COVID-19 infections. Noteworthily, the present analysis does not rely on any speculative theoretical assumption; it is solely based on raw epidemiological data. Out of the results presented here, the most important one is perhaps the finding that, while imposing drastic curfews and travel restrictions reduce the infection rate k by a factor of four with respect to the unrestricted state, they only improve the κ-value by ~ 15% as compared to the much bearable state of social and economical life wherein (justifiable) wearing face masks and social distancing rules are enforced/followed. Significantly for behavioral and social science, our analysis of the time dependence κ = κ(t) may reveal an interesting self-protection instinct of the population, which became manifest even before the official lockdown enforcement.
Do investors’ reactions to CSR-related news communication differ by shareholder? An empirical analysis from Japan
Authors: Murashima Miho 
Published: May 2020

Purpose
This paper aims to examine the differences in investors’ reactions toward firms’ corporate social responsibility (CSR)-related news announcements between individuals and institutions.

Design/methodology/approach
Analyzed by the short-term event study and ordinary least squares (OLS) methods using a unique CSR data set collected from newspapers in Japan from 2001 to 2016.

Findings
The study finds, first, the different reactions toward CSR-related news announcements among shareholders. Second, the findings indicate that individual investors are more sensitive to CSR-related positive news, whereas institutional investors are more concerned about the negative news, providing one of the reasons for mixed results in the studies on the CSR and financial performance linkage. Those findings indicate that CSR-related news affects investors’ behaviors differently based on their purpose, ability and accessible information.

Practical implications
This study deepens the understanding of the different investing behaviors toward CSR-related announcements by shareholder type. Second, different attitudes among investors require different investor relations (IR) approaches depending on the type. It also provides valuable implications not only for Japanese business managers or policymakers but also for those from countries with a similar stage of market maturity in the CSR context.

Originality/value
This paper is original in two ways. First, to the best of the author’s knowledge, this is the first paper to deepen the understanding of investors’ reactions toward CSR-related events through analysis by the main shareholder, which provides some insights into mixed results in the previous studies. Second, the original CSR data set collected from newspapers by the author allows the analysis to use a larger data set than other research, resulting in more robust conclusions.