bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of Factor H family proteins associates with meningococcal disease severity
Authors: van Beek Anna E. , Pouw Richard B. , Wright Victoria J. , Sallah Neneh , Inwald David , Hoggart Clive , Brouwer Mieke C. , Galassini Rachel , Thomas John , Calvo-Bado Leo , Fink Colin , Jongerius Ilse , Hibberd Martin , Wouters Diana , Levin Michael , Kuijpers Taco W. 
Published: February 2021

ABSTRACTNeisseria meningitidis, the causative agent of meningococcal disease (MD), evades complement-mediated clearance upon infection by ‘hijacking’ the human complement regulator factor H (FH). The FH protein family also comprises the homologous FH-related (FHR) proteins, hypothesized to act as antagonists of FH, and FHR-3 has recently been implicated to play a major role in MD susceptibility. Here, we show that, next to FH and FHR-3, the circulating levels of all FH family proteins are equally decreased during pediatric MD. We did not observe a specific consumption of FH or FHR-3 byN. meningitidisduring the first days of infection and the levels recovered over time. MD severity associated predominantly with a loss of FH. Strikingly, loss of FH and FHRs associated strongly with renal failure, suggesting insufficient protection of host tissue by the FH protein family. Retaining higher levels of FH family proteins may thus limit tissue injury during MD.
How effective was Newfoundland & Labrador’s travel ban to prevent the spread of COVID-19? An agent-based analysis
Authors: Aleman Dionne M. , Tham Benjamin Z. , Wagner Sean J. , Semelhago Justin , Mohammadi Asghar , Price Paul , Giffen Randy , Rahman Proton 
Published: February 2021

AbstractBackgroundTo prevent the spread of COVID-19 in Newfoundland & Labrador (NL), NL implemented a wide travel ban in May 2020. We estimate the effectiveness of this travel ban using a customized agent-based simulation (ABS).MethodsWe built an individual-level ABS to simulate the movements and behaviors of every member of the NL population, including arriving and departing travellers. The model considers individual properties (spatial location, age, comorbidities) and movements between environments, as well as age-based disease transmission with pre-symptomatic, symptomatic, and asymptomatic transmission rates. We examine low, medium, and high travel volume, traveller infection rates, and traveller quarantine compliance rates to determine the effect of travellers on COVID spread, and the ability of contact tracing to contain outbreaks.ResultsInfected travellers increased COVID cases by 2-52x (8-96x) times and peak hospitalizations by 2-49x (8-94x), with (without) contact tracing. Although contact tracing was highly effective at reducing spread, it was insufficient to stop outbreaks caused by travellers in even the best-case scenario, and the likelihood of exceeding contact tracing capacity was a concern in most scenarios. Quarantine compliance had only a small impact on COVID spread; travel volume and infection rate drove spread.InterpretationNL’s travel ban was likely a critically important intervention to prevent COVID spread. Even a small number of infected travellers can play a significant role in introducing new chains of transmission, resulting in exponential community spread and significant increases in hospitalizations, while outpacing contact tracing capabilities. With the presence of more transmissible variants, e.g., the UK variant, prevention of imported cases is even more critical.
A wind speed threshold for increased outdoor transmission of coronavirus: An ecological study
Authors: Clouston Sean A. P. , Morozova Olga , Meliker Jaymie R. 
Published: February 2021

AbstractBackgroundTo examine whether outdoor transmission may contribute to the COVID-19 epidemic, we hypothesized that slower outdoor wind speed is associated with increased risk of transmission when individuals socialize outside.MethodsDaily COVID-19 incidence reported in Suffolk County, NY, between March 16th– December 31st, 2020, was the outcome. Average wind speed and maximal daily temperature were collated by the National Oceanic and Atmospheric Administration. Negative binomial regression was used to model incidence rates while adjusting for susceptible population size.ResultsCases were very high in the initial wave but diminished once lockdown procedures were enacted. Most days between May 1st, 2020, and October 24th, 2020, had temperatures 16-28°C and wind speed diminished slowly over the year and began to increase again in December 2020. Unadjusted and multivariable-adjusted analyses revealed that days with temperatures ranging between 16-28°C where wind speed was <8.85 kilometers per hour (KPH) had increased COVID-19 incidence (aIRR=1.45, 95% C.I.=[1.28-1.64], P<0.001) as compared to days with average wind speed ≥8.85 KPH.ConclusionThroughout the U.S. epidemic, the role of outdoor shared spaces such as parks and beaches has been a topic of considerable interest. This study suggests that outdoor transmission of COVID-19 may occur by noting that the risk of transmission of COVID-19 in the summer was higher on days with low wind speed. Outdoor use of increased physical distance between individuals, improved air circulation, and use of masks may be helpful in some outdoor environments where airflow is limited.
PesTrapp mobile app: A trap setting application for real-time entomological field and laboratory study
Authors: Ling Cheong Yoon , Rasli Rosilawati , Che Ibrahim Mohd Khairuddin , Farahininajua Fikri Siti Futri , Nazarudin Nur Ayuni , Hock Lim Kuang , Muhamed Khairul Asuad , Tajul Hassan Mohd Zahari , Yahya Umpong Mohd Izral , Taib Mohd Zainuldin , Ahmad Nazni Wasi , Lim Lee Han 
Published: February 2021

AbstractZoonotic diseases such as malaria, dengue, Zika and chikungunya remain endemic in many countries. Setting and deploying trap to capture the host/vector species are fundamental to understand their density and distribution. Human effort to manage the trap data accurately and timely is an exhaustive endeavour when the study area expands and study period prolongs. One stop mobile app to manage and monitor the process of animal trapping, from field to laboratory level is still scarce. We developed a new mobile app named “PesTrapp” especially for medical entomologists to acquire the vector density index based on the mobile updates of ovitraps and species information in field and laboratory. This study aimed to highlight the mobile app’s development and design, describe the user experience and evaluate the preliminary user assessment of the mobile app. The mobile app was developed using mobile framework and database. User evaluation of the mobile app was based on the adjusted Mobile App Rating Scale and Standardized User Experience Percentile Rank Questionnaire. The process flows of system design and detailed screen layouts were described. The user experiences of using the app in a project to study Aedes surveillance in six study sites in Selangor, Malaysia were described. The overall mean user evaluation score of the mobile app was 4.0 (SD=0.6), which showed its acceptability by the users. The PesTrapp, a one-stop solution, is anticipated to improve the entomological surveillance work processes. This new mobile app can contribute as a tool in the vector control countermeasure strategies.
The kinetic variations of anti-nucleocapsid antibody in SARS-CoV-2 infection
Authors: Kawada Shoji , Ogata Atsushi , Kato Yasuhiro , Okamoto Masashi , Yamaguchi Yuta , Morita Takayoshi , Kumanogoh Atsushi 
Published: February 2021

AbstractThe humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a pivotal role in controlling coronavirus disease 2019 (COVID-19) infections. However, little is known about the persistence of the antibody response.We evaluated that the kinetics of anti-nucleocapsid protein antibody of SARS-CoV2 infected healthcare workers in COVID-19 cluster occurred hospital. The long-term kinetics of anti-N antibody was classified high and keep pattern, high and decay pattern, and low and keep pattern. COVID-19 contact and symptomaticity was not related to kinetic patterns.The reason of kinetic difference was still unclear. However natural anti-SARS-CoV-2 antibody persistence was not uniform, suggesting inter-individual difference of SARS-CoV2 vaccine efficacy.
ADHD in adults with recurrent depression
Authors: Powell Victoria , Agha Sharifah Shameem , Jones Rhys Bevan , Eyre Olga , Thapar Anita , Rice Frances 
Published: February 2021

AbstractBackgroundDepression is highly heterogeneous in its clinical presentation. Those with attention deficit/hyperactivity disorder (ADHD) may be at risk of a more chronic and impairing depression compared to those with depression alone according to studies of young people. However, no studies to date have examined ADHD in recurrently depressed adults in mid-life.AimsTo investigate ADHD in women in mid-life with a history of recurrent depression.MethodIn a sample of women in mid-life (n=148) taken from a UK based prospective cohort of adults with a history of recurrent depression, we investigated the prevalence of ADHD and the association of ADHD with clinical features of depression.Results12.8% of the recurrently depressed women had elevated ADHD symptoms and 3.4% met DSM-5 diagnostic criteria for ADHD. None of the women reported having a diagnosis of ADHD from a medical professional. ADHD was associated with earlier age of depression onset, higher depression associated impairment, a greater recurrence of depressive episodes and increased persistence of subthreshold depression symptoms over the study period, higher levels of irritability and increased risk of self-harm or suicide attempt. ADHD symptoms were associated with increased risk of hospitalisation and receiving non-first line antidepressant medication.ConclusionsHigher ADHD symptoms appear to index a worse clinical presentation for depression. Findings suggest that in women with early onset, impairing and recurrent depression, the possibility of underlying ADHD masked by depression needs to be considered.
The antibody response to SARS-CoV-2 infection persists over at least 8 months in symptomatic patients
Authors: Levi Riccardo , Ubaldi Leonardo , Pozzi Chiara , Angelotti Giovanni , Sandri Maria Teresa , Azzolini Elena , Salvatici Michela , Savevski Victor , Mantovani Alberto , Rescigno Maria 
Published: February 2021

AbstractThe factors involved in the persistence of antibodies to SARS-CoV-2 are unknown. We evaluated the antibody response to SARS-CoV-2 in personnel from 10 healthcare facilities and its association with individuals’ characteristics and COVID-19 symptoms in an observational study. We enrolled 4735 subjects (corresponding to 80% of all personnel) for three time points over a period of 8-10 months. For each participant, we determined the rate of antibody increase or decrease over time in relation to 93 features analyzed in univariate and multivariate analyses through a machine learning approach. In individuals positive for IgG (≥ 12 AU/mL) at the beginning of the study, we found an increase [p= 0.0002] in antibody response in symptomatic subjects, particularly with anosmia/dysgeusia (OR 2.75, 95% CI 1.753 – 4.301), in a multivariate logistic regression analysis. This may be linked to the lingering of SARS-CoV-2 in the olfactory bulb.
Disparities After Discharge: The Association of Limited English Proficiency and Post-Discharge Patient Reported Issues
Authors: Malevanchik Lev , Wheeler Margaret , Gagliardi Kristin , Karliner Leah , Shah Sachin J. 
Published: February 2021

AbstractBackgroundPatients with limited English proficiency (LEP) experience worse outcomes following hospital discharge. Care transition programs are common, yet little is known about the disparities in quality (process and outcome measures) experienced by patients with LEP.MethodsWe conducted a retrospective cohort study to determine the association of LEP and care transition quality at an urban, US academic hospital. We examined all adults discharge home from the hospital from May 2018 through April 2019. All patients received a multilingual, automated telephone call three days after discharge to assess and address patient-reported issues. We determined care transition quality using process measures (reach rate, time to resolve reported issue) and outcome measures (discharge instructions questions, difficulty obtaining prescriptions, medication concerns, follow up care questions, new or worsening symptoms, any other clinical issues). All results were adjusted for measured confounders; we used predicted probabilities and average marginal effect (AME) to describe associations.Results13,860 patients were included in the study; 11% had LEP. The program reached most patients regardless of LEP status but was less likely to reach patients with LEP (AME 3.3%; 95% CI, 1.4% to 5.1%). After adjustment, patients with LEP reported high rates of all measured patient-reported outcomes: discharge instruction (AME 4.8%; 95% CI, 2.7% to 6.9%), obtaining prescriptions (AME 2.9%; 95% CI, 0.6% to 5.1%), medications concerns (AME 2.3%; 95% CI, 0.0% to 4.6%), follow up questions (AME 2.8%; 95% CI, 0.3% to 5.3%), new or worsening symptoms (AME 3.2%; 95% CI, 0.7% to 5.8%), and any other clinical issues (AME 3.6%; 95% CI, 1.1% to 6.1%). When issues were identified, the association between LEP and time to resolution of an issue was statistically, but not clinically, significant.Conclusion and RelevanceAmong patients with LEP, substantial disparities exist in patient-reported post-discharge outcome measures indicating a need for better discharge processes that focus on quality and health equity. Following discharge, relatively minor disparities were observed in the processes of a care transitions program that supports non-English languages.
Predicted distribution of a rare and understudied forest carnivore: Humboldt martens (Martes caurina humboldtensis)
Authors: Moriarty Katie , Thompson Joel , Delheimer Matthew , Barry Brent , Linnell Mark , Levi Taal , Hamm Keith , Early Desiree , Gamblin Holly , Gunther Micaela Szykman , Ellison Jordan , Prevéy Janet S. , Hartman Jennifer , Davis Ray 
Published: February 2021

AbstractBackgroundA suite of mammalian species have experienced range contractions following European settlement and post-settlement development of the North American continent. For example, while North American martens (American marten,Martes americana; Pacific marten,M. caurina) generally have a broad range across northern latitudes, local populations have experienced substantial reductions in distribution and some extant populations are small and geographically isolated. The Humboldt marten (M. c. humboldtensis), a subspecies of Pacific marten that occurs in coastal Oregon and northern California, was recently designated as federally threatened in part due to its reduced distribution. To inform strategic conservation actions, we assessed Humboldt marten occurrence by compiling all known records from their range.MethodsWe compiled Humboldt marten locations since their rediscover to present (1,692 marten locations, 1996-2020). We spatially-thinned locations to 500-m to assess correlations with variables across contemporary Humboldt marten distribution (n=384). Using maximum entropy modeling (Maxent), we created distribution models with variables optimized for spatial scale; pre-selected scales were associated with marten ecology (50 to 1170 m radius). Marten locations were most correlated with abiotic factors (e.g., precipitation), which are unalterable and therefore uninformative within the context of restoration or management actions. Thus, we created variables to focus on hypothesized marten habitat relationships, including understory conditions such as predicted suitability of shrub species.ResultsHumboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon), mast producing trees), increased pine (Pinus sp) overstory cover and precipitation at home-range spatial scales, areas with low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature on the species, we found little evidence that Humboldt marten locations were associated with old growth structural indices, perhaps because of a potential mismatch in the association between this index and shrub cover. As with any species distribution model, there were gaps in predicted distribution where Humboldt martens have been located during more recent surveys, for instance the southeastern portion of Oregon’s coast range. Conservation efforts and our assessment of potential risks to Humboldt marten populations would benefit from additional information on range extent, population sizes, and fine-scale habitat use. Like many rare and lesser-known species, this case study provides an example of how limited information can provide differing interpretations, emphasizing the need for study-level replication in ecology.
Intraspecific trait changes have large impacts on community functional composition but do not affect ecosystem function
Authors: Pichon Noémie A. , Cappelli Seraina L. , Allan Eric 
Published: February 2021

AbstractPlant functional traits can provide a more mechanistic understanding of community responses to global change and effects on ecosystem functions. In particular, nitrogen enrichment shifts trait composition by promoting dominance of fast growing, acquisitive plants (with high specific leaf area [SLA] and low leaf dry matter content [LDMC]), and such fast species have higher aboveground biomass production. Changes in mean trait values can be due to a shift in species identity, a shift in species relative abundance and/or a shift in intraspecific trait values. However, we do not know the relative importance of these three shifts in determining responses to global change and effects on function.We quantified the relative importance of composition, abundance and intraspecific shifts in driving variation in SLA and LDMC. We collected leaf samples in a large grassland experiment, which factorially manipulates functional composition (slow vs. fast species), plant species richness, nitrogen enrichment and foliar fungal pathogen removal. We fitted structural equation models to test the relative importance of abundance shifts, intraspecific shifts and sown trait composition in contributing to overall variation in community weighted mean traits and aboveground and belowground biomass production.We found that intraspecific shifts were as important as abundance shifts in determining community weighted mean traits, and even had large effects relative to a wide initial gradient in trait composition. Intraspecific trait shifts resulted in convergence towards intermediate SLA, in diverse communities, although convergence was reduced by nitrogen addition and enhanced by pathogen removal. In contrast, large intraspecific shifts in LDMC were not influenced by the treatments. Belowground biomass was reduced by SLA and increased by LDMC, while aboveground biomass increased in communities dominated by high SLA species. However, despite large intraspecific trait shifts, intraspecific variation in these traits had no effect on above or belowground biomass production.Our results add to a growing body of literature showing large intraspecific trait variation and emphasise the importance of using field sampled data to determine community composition. However, they also show that intraspecific variation does not affect ecosystem functioning and therefore trait response-effect relationships may differ between vs. within species.
An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees
Authors: Almodaresi Fatemeh , Khan Jamshed , Madaminov Sergey , Pandey Prashant , Ferdman Michael , Johnson Rob , Patro Rob 
Published: February 2021

AbstractMotivationIn the past few years, researchers have proposed numerous indexing schemes for searching large databases of raw sequencing experiments. Most of these proposed indexes are approximate (i.e. with one-sided errors) in order to save space. Recently, researchers have published exact indexes—Mantis, VariMerge, and Bifrost—that can serve as colored de Bruijn graph representations in addition to serving ask-mer indexes. This new type of index is promising because it has the potential to support more complex analyses than simple searches. However, in order to be useful as indexes for large and growing repositories of raw sequencing data, they must scale to thousands of experiments and support efficient insertion of new data.ResultsIn this paper, we show how to build a scalable and updatable exact sequence-search index. Specifically, we extend Mantis using the Bentley-Saxe transformation to support efficient updates. We demonstrate Mantis’s scalability by constructing an index of≈40K samples from SRA by adding samples one at a time to an initial index of 10K samples.Compared to VariMerge and Bifrost, Mantis is more efficient in terms of index-construction time and memory, query time and memory, and index size. In our benchmarks, VariMerge and Bifrost scaled to only 5K and 80 samples, respectively, while Mantis scaled to more than 39K samples. Queries were over 24×faster in Mantis than in Bifrost (VariMerge does not immediately support general search queries we require). Mantis indexes were about 2.5×smaller than Bifrost’s indexes and about half as big as VariMerge’s indexes.AvailabilityThe updatable Mantis implementation is available athttps://github.com/splatlab/mantis/tree/mergeMSTs.Contactrob@cs.umd.eduSupplementary informationSupplementary data are available online.
Recombinant chimpanzee adenovirus AdC7 expressing dimeric tandem-repeat RBD of SARS-CoV-2 spike protein protects mice against COVID-19
Authors: Xu Kun , An Yaling , Li Qunlong , Huang Weijin , Han Yuxuan , Zheng Tianyi , Fang Fang , Liu Hui , Liu Chuanyu , Gao Ping , Xu Senyu , Liu William J. , Bi Yuhai , Wang Youchun , Zhou Dongming , Wang Qinghan , Hou Wenli , Xia Qianfeng , Gao George F. , Dai Lianpan 
Published: February 2021

AbstractA safe and effective vaccine is urgently needed to control the unprecedented COVID-19 pandemic. Four adenovirus vectored vaccines expressing spike (S) protein have advanced into phase 3 trials, with three approved for use. Here, we generated several recombinant chimpanzee adenovirus (AdC7) vaccines expressing S, receptor-binding domain (RBD) or dimeric tandem-repeat RBD (RBD-tr2). We found vaccination via either intramuscular or intranasal route was highly immunogenic in mice to elicit both humoral and cellular (Th1-based) immune responses. AdC7-RBD-tr2 showed higher antibody responses compared with both AdC7-S and AdC7-RBD. Intranasal administration of AdC7-RBD-tr2 additionally induced mucosal immunity with neutralizing activity in bronchoalveolar lavage fluid. Either single-dose or two-dose mucosal administration of AdC7-RBD-tr2 protected mice against SARS-CoV-2 challenge, with undetectable subgenomic RNA in lung and relieved lung injury. These results support AdC7-RBD-tr2 as a promising COVID-19 vaccine candidate.