bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surveillance by age-class and prefecture for emerging infectious febrile diseases with respiratory symptoms, including COVID-19
Authors: Ueno Tomoaki , Kurita Junko , Sugawara Tamie , Sugishita Yoshiyuki , Ohkusa Yasushi , Kawanohara Hirokazu , Kamei Miwako 
Published: April 2020

AbstractObjectThe COVID-19 outbreak emerged in late 2019 in China, expanding rapidly thereafter. Even in Japan, epidemiological linkage of transmission was probably lost already by February 18, 2020. From that time, it has been necessary to detect clusters using syndromic surveillance.MethodWe identified common symptoms of COVID-19 as fever and respiratory symptoms. Therefore, we constructed a model to predict the number of patients with antipyretic analgesics (AP) and multi-ingredient cold medications (MIC) controlling well-known pediatric infectious diseases including influenza or RS virus infection. To do so, we used the National Official Sentinel Surveillance for Infectious Diseases (NOSSID), even though NOSSID data are weekly data with 10 day delays, on average. The probability of a cluster with unknown febrile disease with respiratory symptoms is a product of the probabilities of aberrations in AP and MIC, which is defined as one minus the probability of the number of patients prescribed a certain type of drug in PS compared to the number predicted using a model. This analysis was conducted prospectively in 2020 using data from October 1, 2010 through 2019 by prefecture and by age-class.ResultsThe probability of unknown febrile disease with respiratory symptom cluster was estimated as less than 60% in 2020.DiscussionThe most severe limitation of the present study is that the proposed model cannot be validated. A large outbreak of an unknown febrile disease with respiratory symptoms must be experienced, at which time, practitioners will have to “wing it”. We expect that no actual cluster of unknown febrile disease with respiratory symptoms will occur, but if it should occur, we hope to detect it.
Rapid prototyping and clinical testing of a reusable face shield for health care workers responding to the COVID-19 pandemic
Authors: Mostaghimi Arash , Antonini M.-J. , Plana Deborah , Anderson Philip D. , Beller Brandon , Boyer Edward W. , Fannin Amber , Freake Jacob , Oakley Richard , Sinha Michael S. , Smith Leanne , Van Christopher , Yang Helen , Sorger Peter K. , LeBoeuf Nicole R. , Yu Sherry H. 
Published: April 2020

AbstractDue to supply chain disruption, the COVID-19 pandemic has caused severe shortages in personal protective equipment (PPE) for health care professionals. Local fabrication based on 3D printing is one way to address this challenge, particularly in the case of simple products such as protective face shields. As a consequence, many public domain designs for face shields have become available. No clear path exists, however, for introducing a locally fabricated and unapproved product into a clinical setting. In a US health care setting, face shields are regulated by the Food and Drug Administration (FDA); similar policies exist in other countries. We describe a research protocol under which rapid iteration on an existing design, coupled with clinical feedback and real-world testing in an emergency department, allowed a face shield to be implemented by the members of the incident command team at a major academic medical center. We describe our design and testing process and provide an overview of regulatory considerations associated with fabrication and testing of face shields and related products. All designs, materials used, testing protocols, and survey results are reported in full to facilitate the execution of similar face shield efforts in other clinical settings. Our work serves as a case study for development of a robust local response to pandemics and other health care emergencies, with implications for healthcare professionals, hospital administrators, regulatory agencies and concerned citizens.
Pregnancy outcomes, Newborn complications and Maternal-Fetal Transmission of SARS-CoV-2 in women with COVID-19: A systematic review of 441 cases
Authors: Gajbhiye Rahul K , Modi Deepak N , Mahale Smita D 
Published: April 2020

ABSTRACTObjectiveThe aim of this systematic review was to examine the maternal and fetal outcomes in pregnant women with COVID-19 and also assess the incidence of maternal-fetal transmission of SARS CO-V-2 infection.Data sourcesWe searched PUMBED. Medline, Embase, MedRxiv and bioRxiv databases upto 3rdMay 2020 utilizing combinations of word variants for “coronavirus” or “COVID-19” or “severe acute respiratory syndrome” or “SARS-COV-2” and “pregnancy”. We also included data from preprint articles.Study eligibility criteriaOriginal case reports and case series on pregnant women with diagnosis of SARS-CoV-2 infection.Study appraisal and synthesis methodsWe included 50 studies reporting the information on 441 pregnant women and 391 neonates. The primary outcome measures were maternal health characteristics and adverse pregnancy outcomes, neonatal outcomes and SARS-CoV-2 infection in neonates was extracted. Treatments given to pregnant women with COVID-19 were also recorded.ResultsOut of 441 women affected by COVID-19 in pregnancy, 387 women have delivered. There are nine maternal deaths reported. In pregnant women with COVID-19, the most common symptoms were fever (56%), cough (43%), myalgia (19%), dyspnea (18%) and diarrhea (6%). Pneumonia was diagnosed by CT scan imaging in 96 % of COVID-19 pregnant women. Pregnancy complications included delivery by cesarean section (80%), preterm labor (26%), fetal distress (8%) and premature rupture of membranes (9%). Six still births (2%) are reported. The most common co-morbidities associated with pregnant women with COVID-19 were hypertensive disorders (10%), diabetes (9%), placental disorders (2%), co-infections (3%), scarred uterus (3%) and hypothyroidism (3%). Amongst the neonates of COVID-19 mothers, preterm birth (25%), respiratory distress syndrome (8%), pneumonia (8%) were reported. There were four neonatal deaths reported. Vertical transmission rate of SARS-CoV-2 is estimated to be 8%.ConclusionIn pregnant women with COVID-19, hypertensive disorders and diabetes are common comorbidities and there is a risk of preterm delivery and maternal death. Amongst the neonates born to mothers with COVID-19, respiratory distress syndrome and pneumonia are common occurrence. There are reports of still births and neonatal deaths. There is an evidence of vertical transmission of SARS-CoV-2 infection in women with COVID-19.
Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL proteasein vitro
Authors: Su Haixia , Yao Sheng , Zhao Wenfeng , Li Minjun , Liu Jia , Shang WeiJuan , Xie Hang , Ke Changqiang , Gao Meina , Yu Kunqian , Liu Hong , Shen Jingshan , Tang Wei , Zhang Leike , Zuo Jianping , Jiang Hualiang , Bai Fang , Wu Yan , Ye Yang , Xu Yechun 
Published: April 2020

AbstractHuman infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause coronavirus disease 19 (COVID-19) and there is currently no cure. The 3C-like protease (3CLpro), a highly conserved protease indispensable for replication of coronaviruses, is a promising target for development of broad-spectrum antiviral drugs. To advance the speed of drug discovery and development, we investigated the inhibition of SARS-CoV-2 3CLpro by natural products derived from Chinese traditional medicines. Baicalin and baicalein were identified as the first non-covalent, non-peptidomimetic inhibitors of SARS-CoV-2 3CLpro and exhibited potent antiviral activities in a cell-based system. Remarkably, the binding mode of baicalein with SARS-CoV-2 3CLpro determined by X-ray protein crystallography is distinctly different from those of known inhibitors. Baicalein is perfectly ensconced in the core of the substrate-binding pocket by interacting with two catalytic residues, the crucial S1/S2 subsites and the oxyanion loop, acting as a “shield” in front of the catalytic dyad to prevent the peptide substrate approaching the active site. The simple chemical structure, unique mode of action, and potent antiviral activitiesin vitro, coupled with the favorable safety data from clinical trials, emphasize that baicalein provides a great opportunity for the development of critically needed anti-coronaviral drugs.
Mechanics Of Flight Feathers: Effects Of Captivity?
Authors: Portugal Steven J. , Nudds Robert L. , Green Jonathan A. , Alexander R. McNeil , Butler Patrick J. , Ker Robert F. 
Published: April 2020

ABSTRACTFeathers act as aerodynamic cantilevers, and to withstand the prolonged cyclical loading that occurs during flight, feathers must be stiff, lightweight and strong. We experimentally tested the differences in feather structure, primarily stiffness and size, between (a) wild and captive Barnacle GeeseBranta leucopsis,and (b) primary feathers dropped during the annual flight feather moult, and those feathers freshly regrown during the moult process. We found that, despite having undergone a 5,000km round-trip migration, flight feathers dropped during moult in the wild geese were stiffer than those measured in the captive geese, both for those dropped during moult and those re-grown. We propose that this may be related to diet or stress in the captive geese.
Identifying flow modules in ecological networks using Infomap
Authors: Farage Carmel , Edler Daniel , Eklöf Anna , Rosvall Martin , Pilosof Shai 
Published: April 2020

AbstractAnalysing how species interact in modules is a fundamental problem in network ecology. Theory shows that a modular network structure can reveal underlying dynamic ecological and evolutionary processes, influence dynamics that operate on the network and affect the stability of the ecological system.Although many ecological networks describe flows, such as biomass flows in food webs or disease trans-mission, most modularity analyses have ignored network flows, which can hinder our understanding of the interplay between structure and dynamics.Here we present Infomap, an established method based on network flows to the field of ecological networks. Infomap is a flexible tool that can identify modules in virtually any type of ecological network and is particularly useful for directed, weighted and multilayer networks. We illustrate how Infomap works on all these network types. We also provide a fully documented repository with additional ecological examples. Finally, to help researchers analyse their networks with Infomap, we introduce the open source R package infomapecology.Analysing flow-based modularity is useful across ecology and transcends to other biological and non-biological disciplines. A dynamic approach for detecting modular structure has strong potential to provide new insights into the organisation of ecological networks.
Triplet-based similarity score for fully multi-labeled trees with poly-occurring labels
Authors: Ciccolella Simone , Bernardini Giulia , Denti Luca , Bonizzoni Paola , Previtali Marco , Della Vedova Gianluca 
Published: April 2020

AbstractThe latest advances in cancer sequencing, and the availability of a wide range of methods to infer the evolutionary history of tumors, have made it important to evaluate, reconcile and cluster different tumor phylogenies.Recently, several notions of distance or similarities have been proposed in the literature, but none of them has emerged as the golden standard. Moreover, none of the known similarity measures is able to manage mutations occurring multiple times in the tree, a circumstance often occurring in real cases.To overcome these limitations, in this paper we propose MP3, the first similarity measure for tumor phylogenies able to effectively manage cases where multiple mutations can occur at the same time and mutations can occur multiple times. Moreover, a comparison of MP3 with other measures shows that it is able to classify correctly similar and dissimilar trees, both on simulated and on real data.
Schistosoma mansonieggs modulate the timing of granuloma formation to promote transmission
Authors: Takaki Kevin K. , Rinaldi Gabriel , Berriman Matthew , Pagán Antonio J. , Ramakrishnan Lalita 
Published: April 2020

SUMMARYSchistosome eggs provoke the formation of granulomas, organized immune aggregates, around them. For the host, the granulomatous response can be both protective and pathological. Granulomas are also postulated to facilitate egg extrusion through the gut lumen, a necessary step for parasite transmission. We used zebrafish larvae to visualize the granulomatous response toSchistosoma mansonieggs and inert egg-sized beads. Mature eggs rapidly recruit macrophages, which form granulomas within days. Egg-sized inert beads also induce granulomas rapidly, through a foreign body response. Strikingly, immature eggs evade macrophage recruitment altogether, revealing that the eggshell is immunological inert. These findings suggest that the parasite modulates the timing of granuloma formation to its advantage, inhibiting foreign body granuloma formation until it reaches the optimal maturation and location for extrusion. At this point, the parasite secretes specific antigens through the eggshell to trigger granulomas that might facilitate egg extrusion.
Structural insights into the mechanism of rhodopsin phosphodiesterase
Authors: Ikuta Tatsuya , Shihoya Wataru , Sugiura Masahiro , Yoshida Kazuho , Watari Masahito , Tokano Takaya , Yamashita Keitaro , Katayama Kota , Tsunoda Satoshi P. , Uchihashi Takayuki , Kandori Hideki , Nureki Osamu 
Published: April 2020

AbstractRhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase (Rh-GC) and photosensitive adenylyl cyclase (PAC). Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The 2.6 Å resolution crystal structure of the transmembrane domain revealed a new topology of rhodopsin, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the transmembrane and PDE domain (2.1 Å) with their connecting linkers. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins.
A faster implementation of association mapping from k-mers
Authors: Mehrab Zakaria , Mobin Jaiaid , Tahmid Ibrahim Asadullah , Rahman Atif 
Published: April 2020

AbstractGenome wide association studies (GWAS) attempt to map genotypes to phenotypes in organisms. This is typically performed by genotyping individuals using microarray or by aligning whole genome sequencing reads to a reference genome. Both approaches require knowledge of a reference genome which limits their application to organisms with no or incomplete reference genomes. This caveat can be removed using alignment-free association mapping methods based on k-mers from sequencing reads. Here we present an implementation of an alignment free association mapping method [1] to improve its execution time and flexibility. We have tested our implementation on anE. Coliampicillin resistance dataset and observe improvement in performance over the original implementation while maintaining accuracy in results. Finally, we demonstrate that the method can be applied to find sex specific sequences.
The prevalence and genomic context of Shiga toxin 2a genes inE. colifound in cattle
Authors: Jinnerot Tomas , Tomaselli Angeles Tatiana Ponton , Johannessen Gro S , Söderlund Robert , Urdahl Anne Margrete , Aspán Anna , Sekse Camilla 
Published: April 2020

AbstractShiga toxin-producingEscherichia coli(STEC) that cause severe disease predominantly carry the toxin gene variantstx2a. However, the role of Shiga toxin in the ruminant reservoirs of this zoonotic pathogen is poorly understood and strains that cause severe disease in humans (HUSEC) likely constitute a small and atypical subset of the overall STEC flora. The aim of this study was to investigate the presence ofstx2ain samples from cattle and to isolate and characterizestx2a-positiveE. coli. In nationwide surveys in Sweden and Norway samples were collected from individual cattle or from cattle herds, respectively. Samples were tested for Shiga toxin genes by real-time PCR and amplicon sequencing andstx2a-positive isolates were whole genome sequenced. Among faecal samples from Sweden,stx1was detected in 37%,stx2in 53% andstx2ain 5% and in skin samples in 64%, 79% and 2% respectively. In Norway, 79% of the herds were positive forstx1, 93% forstx2and 17% forstx2a. Based on amplicon sequencing the most commonstx2types in samples from Swedish cattle werestx2aandstx2d. Multilocus sequence typing (MLST) of 39stx2a-positive isolates collected from both countries revealed substantial diversity with 19 different sequence types. Only a few classical LEE-positive HUSEC were found among thestx2a-positive isolates, notably a single O121:H19 and an O26:H11. Known LEE-negative HUSEC lineages were also recovered including O113:H21 (ST-223), O130:H11 (ST-297), and O101:H33 (ST-330). We conclude thatE. coliencodingstx2ain cattle are ranging from well-known HUSEC to unknown STEC variants. Comparison of isolates from human HUS cases to related STEC from the ruminant reservoirs can help identify combinations of virulence attributes necessary to cause HUS, as well as provide a better understanding of the routes of infection for rare and emerging pathogenic STEC.
One is not enough: on the effects of reference genome for the mapping and subsequent analyses of short-reads
Authors: Valiente-Mullor Carlos , Beamud Beatriz , Ansari Iván , Francés-Cuesta Carlos , García-González Neris , Mejía Lorena , Ruiz-Hueso Paula , González-Candelas Fernando 
Published: April 2020

AbstractMapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species were selected as reference sequences, and read alignment statistics, SNP calling, recombination rates, dN/dS ratios, and phylogenetic trees were evaluated depending on the mapping reference. The choice of different reference genomes proved to have an impact on almost all the parameters considered in the five species. In addition, these biases had potential epidemiological implications such as including/excluding isolates of particular clades and the estimation of genetic distances. These findings suggest that the single reference approach might introduce systematic errors during mapping that affect subsequent analyses, particularly for data sets with isolates from genetically diverse backgrounds. In any case, exploring the effects of different references on the final conclusions is highly recommended.Author summaryMapping consists in the alignment of reads (i.e., DNA fragments) obtained through high-throughput genome sequencing to a previously assembled reference sequence. It is a common practice in genomic studies to use a single reference for mapping, usually the ‘reference genome’ of a species —a high-quality assembly. However, the selection of an optimal reference is hindered by intrinsic intra-species genetic variability, particularly in bacteria. Biases/errors due to reference choice for mapping in bacteria have been identified. These are mainly originated in alignment errors due to genetic differences between the reference genome and the read sequences. Eventually, they could lead to misidentification of variants and biased reconstruction of phylogenetic trees (which reflect ancestry between different bacterial lineages). However, a systematic work on the effects of reference choice in different bacterial species is still missing, particularly regarding its impact on phylogenies. This work intended to fill that gap. The impact of reference choice has proved to be pervasive in the five bacterial species that we have studied and, in some cases, alterations in phylogenetic trees could lead to incorrect epidemiological inferences. Hence, the use of different reference genomes may be prescriptive to assess the potential biases of mapping.
Characterizing the portability of RecT-mediated oligonucleotide recombination
Authors: Filsinger Gabriel T. , Wannier Timothy M. , Pedersen Felix B. , Lutz Isaac D. , Zhang Julie , Stork Devon A. , Debnath Anik , Gozzi Kevin , Kuchwara Helene , Volf Verena , Wang Stan , Rios Xavier , Gregg Christopher J. , Lajoie Marc J. , Shipman Seth L. , Aach John , Laub Michael T. , Church George M. 
Published: April 2020

AbstractBacterial genome editing methods are used to engineer strains for biotechnology and fundamental research. Homologous recombination (HR) is the most versatile method of genome editing, but traditional techniques using endogenous RecA-mediated pathways are inefficient and laborious. Phage encoded RecT proteins can improve HR over 1000-fold, but these proteins have limited portability between species. UsingEscherichia coli,Lactococcus lactis, Mycobacterium smegmatis, Lactobacillus rhamnosus, andCaulobacter crescentuswe investigated the hostlimited functionality of RecTs. We find that these proteins specifically recognize the 7 C-terminal amino acids of the bacterial single-stranded DNA-binding protein (SSB), and are portable between species only if compatibility with this host domain is maintained. Furthermore, in some species, we find that co-expressing otherwise incompatible RecTs with a paired bacterial SSB is sufficient to establish functionality. Finally, we demonstrate that high-efficiency HR surpasses the mutational capacity of more widely used error-prone methods for genome diversification, and can be used to identify exceptional phenotypes inaccessible through sequential nucleotide conversions.