bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of naturally-acquired immunity using a self-matched negative control design
Authors: Northrup Graham R. , Qian Lei , Bruxvoort Katia , Marx Florian M. , Whittles Lilith K. , Lewnard Joseph A. 
Published: March 2020

ABSTRACTHost adaptive immune responses may protect against infection or disease when a pathogen is repeatedly encountered. The hazard ratio of infection or disease, given previous infection, is typically sought to estimate the strength of protective immunity. However, variation in individual exposure or susceptibility to infection may introduce frailty bias, whereby a tendency for infections to recur among individuals with greater risk confounds the causal association between previous infection and susceptibility. We introduce a self-matched “case-only” inference method to control for unmeasured individual heterogeneity, making use of negative-control endpoints not attributable to the pathogen of interest. To control for confounding, this method compares event times for endpoints due to the pathogen of interest and negative-control endpoints during counterfactual risk periods, defined according to individuals’ infection history. We derive a standard Mantel-Haenszel (matched) odds ratio conveying the effect of prior infection on time to recurrence. We compare performance of this approach to several proportional hazards modeling frameworks, and estimate statistical power of the proposed strategy under various conditions. In an example application, we use the proposed method to re-estimate naturally-acquired protection against rotavirus gastroenteritis using data from previously-published cohort studies. This self-matched negative-control design may present a flexible alternative to existing approaches for analyzing naturally-acquired immunity, as well as other exposures affecting the distribution of recurrent event times.
Electronic data capture for large scale typhoid surveillance, household contact tracing, and health utilisation survey: Strategic Typhoid Alliance across Africa and Asia
Authors: Thindwa Deus , Farooq Yama G , Shakya Mila , Saha Nirod , Tonks Susan , Anokwa Yaw , Gordon Melita A , Hartung Carl , Meiring James E , Pollard Andrew J , Heyderman Robert S 
Published: March 2020

AbstractBackgroundElectronic data capture systems (EDCs) have the potential to achieve efficiency and quality in collection of multisite data. We quantify volume, time, accuracy and costs of an EDC using large-scale census data from the STRATAA consortium, a comprehensive programme assessing population dynamics and epidemiology of typhoid fever in Malawi, Nepal and Bangladesh to inform vaccine and public health interventions.ResultsA census form was developed through a structured iterative process and implemented using Open Data Kit Collect running on Android-based tablets. Data were uploaded to Open Data Kit Aggregate, then auto-synced to MySQL-defined database nightly. Data were backed-up daily from 3 sites centrally, and auto-reported weekly. Pre-census materials’ costs were estimated. Demographics of 308,348 individuals from 80,851 households were recorded within average of 14.7 weeks range (13-16) using 65 fieldworkers. Overall, 21.7 errors (95% confidence interval: 21.4, 22.0) per 10,000 data points were found: 13.0 (95% confidence interval: 12.6, 13.5) and 24.5 (95% confidence interval: 24.1, 24.9) errors on numeric and text fields respectively. These values meet standard quality threshold of 50 errors per 10,000 data points. The EDC’s total variable cost was estimated at US$13,791.82 per site.ConclusionsIn conclusion, the EDC is robust, allowing for timely and high volume accurate data collection, and could be adopted in similar epidemiological settings.
Globus pallidus dynamics reveal covert strategies for behavioral inhibition
Authors: Gu Bon-Mi , Schmidt Robert , Berke Joshua D. 
Published: March 2020

AbstractFlexible behavior requires restraint or cancellation of actions that are no longer appropriate. This behavioral inhibition critically relies on frontal cortex - basal ganglia circuits. A central node within the basal ganglia, the globus pallidus pars externa (GPe), has been hypothesized to mediate “proactive” inhibition: being prepared to stop an action if needed. Here we investigate the population dynamics of rat GPe neurons during preparation-to-stop, stopping, and going. Rats could selectively engage proactive inhibition towards one specific action, as shown by slowed reaction times (RTs) for that action. While proactive inhibition was engaged, GPe population activity occupied state-space locations farther from the trajectory followed during normal movement initiation. Furthermore, the specific state-space location was predictive of distinct types of errors: failures to stop, failures to go, and incorrect choices. The slowed RTs on correct proactive trials reflected a starting bias towards the alternative action, which was overcome before making progress towards action initiation. Our results demonstrate that rats can exert cognitive control via strategic positioning of their GPe network state.
How to differentiate COVID-19 pneumonia from heart failure with computed tomography at initial medical contact during epidemic period
Authors: Zhu Zhaowei , Tang Jianjun , Chai Xiangping , Fang Zhenfei , Liu Qiming , Hu Xinqun , Xu Danyan , He Jia , Tang Liang , Tai Shi , Wu Yuzhi , Zhou Shenghua 
Published: March 2020

ABSTRACTOBJECTIVESTo compare chest CT findings in heart failure with those of Corona Virus Disease 2019 (COVID-19) pneumonia.BACKGROUNDDuring epidemic period, chest computed tomography (CT) has been highly recommended for screening patients with suspected COVID-19. However, the comparison of CT imaging between heart failure and COVID-19 pneumonia has not been fully elucidated.METHODSPatients with heart failure (n=12), COVID-19 pneumonia (n=12) and one patient with both diseases were retrospectively enrolled. Clinical information and imaging of chest CT were collected and analyzed.RESULTSThere was no difference of ground glass opacity (GGO), consolidation, crazy paving pattern, lobes affected and septal thickening between heart failure and COVID-19 pneumonia. However, less rounded morphology (8.3% vs. 67%, p=0.003), more peribronchovascular thickening (75% vs. 33%, p=0.041) and fissural thickening (33% vs. 0%, p=0.028), less peripheral distribution (33% vs. 92%, p=0.003) were found in heart failure group than that in COVID-19 group. Importantly, there were also more patients with upper pulmonary vein enlargement (75% vs. 8.3%, p=0.001), subpleural effusion and cardiac enlargement in heart failure group than that in COVID-19 group (50% vs. 0%, p=0.005, separately). Besides, more fibrous lesions were found in COVID-19 group although there was no statistical difference (25% vs. 0%, P=0.064)CONCLUSIONSAlthough there are some overlaps of CT imaging between heart failure and COVID-19, CT is still a useful tool in differentiating COVID-19 pneumonia.
The effectiveness of Ear Nose and Throat outreach programs for Aboriginal and Torres Strait Islander Australians: a systematic review
Authors: Gotis-Graham Anna , Macniven Rona , Kong Kelvin , Gwynne Kylie 
Published: March 2020

AbstractBackgroundAboriginal and Torres Strait Islander children experience a higher prevalence of ear, nose, and throat (ENT) diseases than non-Indigenous children. Many programs exist that aim to prevent and treat these diseases. Culturally appropriate and timely specialist outreach services may help improve access, service use, and outcomes but there has been a lack of rigorous evaluation of ENT outreach programs to date.ObjectiveTo examine the ability of ENT outreach programs to improve health outcomes among Aboriginal and Torres Strait Islander peopleMethodsWe performed a systematic literature search of nine databases (Medline, CINAHLS, PsychINFO, Embase, Cochrane, Scopus, Global health, Informit Rural health database and Indigenous collection) and grey literature sources for primary studies evaluating ENT outreach services for Aboriginal and Torres Strait Islander Australians. Two authors independently evaluated the eligible articles and extracted relevant information.ResultsOf the 506 studies identified, 15 were included in this review. These 15 studies evaluated eight different programs/activities. Studies were heterogeneous in design so a meta-analysis could not be conducted. Seven studies measured health-related outcomes in middle ear or hearing status; six reported overall positive changes one reported no clinically significant improvements. Five programs/activities and their corresponding studies involved Aboriginal and Torres Strait Islander people and organisations in delivery and evaluation, but involvement in program or study design was unclear.ConclusionWhile some studies demonstrated improved outcomes, the overall ability of ENT programs/activities to improve health outcomes for Aboriginal and Torres Strait Islander children is unclear. The impact of ENT outreach may be limited by a lack of evidence quality, a lack of coordination of services, and the provision of potentially unsustainable services. Improvements in the quality of evidence, service coordination and sustainability would likely improve health outcomes.Strengths and limitations of this studyStudies were identification based on a clearly defined and extensive search strategy based on a priori inclusion and exclusion criteriaStudy appraisal was performed using a relevant tool for mixed methods studiesThe involvement of Aboriginal and Torres Strait Islander people in all aspects of programs and their evaluation was examinedPROSPERO registration numberCRD42019134757
Optimal Random Avoidance Strategy in Prey-Predator Interactions
Authors: Abe Masato S. , Kasada Minoru 
Published: March 2020

AbstractIt has recently been reported that individual animals, ranging from insects to birds and mammals, exhibit a special class of random walks, known as Lévy walks, which can lead to higher search efficiency than normal random walks. However, the role of randomness or unpredictability in animal movements is not very well understood. In the present study, we used a theoretical framework to explore the advantage of Lévy walks in terms of avoidance behaviour in prey-predator interactions and analysed the conditions for maximising the prey’s survival rate. We showed that there is a trade-off relationship between the predictability of the prey’s movement and the length of time of exposure to predation risk, suggesting that it is difficult for prey to decrease both parameters in order to survive. Then, we demonstrated that the optimal degree of randomness in avoidance behaviour could change depending on the predator’s ability. In particular, Lévy walks resulted in higher survival rates than normal random walks and straight movements when the physical ability of the predators was high. This indicates that the advantage of Lévy walks may also be present in random avoidance behaviour and provides new insights into why Lévy walks can evolve in terms of randomness.
Inferring Multiple Metagenomic Association Networks based on Variation of Environmental Factors
Authors: Yang Yuqing , Wang Xin , Xie Kaikun , Zhu Congmin , Chen Ning , Chen Ting 
Published: March 2020

AbstractIdentifying significant biological relationships or patterns is central to many metagenomic studies. Methods that estimate association networks have been proposed for this purpose, but they assume that associations are static, neglecting the fact that relationships in a microbial ecosystem may vary with changes in environmental factors, which can result in inaccurate estimations. We propose a computational model, k-Lognormal-Dirichlet-Multinomial model (kLDM), which estimates multiple association networks that correspond to specific environmental conditions according to values of environmental factors (EFs), and simultaneously infers microbe-microbe and environmental factor-microbe associations for each network. We showed the effectiveness of kLDM on synthetic data, a colorectal cancer dataset, as well as the TARA Oceans and American Gut project datasets. The results showed that the widely used Spearman’s rank correlation coefficient (SCC) performed much worse than other methods, indicating the importance of separating samples by environmental conditions. We compared cancer fecal samples with cancer-free samples, and our estimation showed fewer associations among microbes but stronger associations between specific bacteria such as five colorectal cancer (CRC)-associated OTUs, indicating gut microbe translocation in cancer patients. Some environmental-factor-dependent associations were found within marine eukaryotic community, and gut microbial heterogeneity of irritable bowel disease (IBD) patients was detected. Results demonstrated that kLDM could successfully unravel the underlying biological associations. In summary, our study presents a computational framework that can elucidate the complex associations within microbial ecosystems. The kLDM program, R, and python scripts, together with all experimental datasets are all accessible at Github (https://github.com/tinglab/kLDM.git).
A dataset of speed-resolved blood perfusion and oxygen saturation in human skin response to thermal stimulation
Authors: Jia Shuyong , Song Xiaojing , Zhang Weibo , Wang Guangjun 
Published: March 2020

AbstractThe functional status of vessels can be determined by assessing blood perfusion. By integrating diffuse reflectance spectroscopy (DRS) and laser Doppler Flowmetry (LDF), the speed-resolved blood perfusion and blood oxygen saturation can be measured simultaneously by Enhanced Perfusion and Oxygen Saturation (EPOS). The dataset presented in this descriptor contains EPOS data recorded from a forearm point exposed to different levels of thermal stimulation, the classical LDF at control points, the R-R time series and data regarding characteristics of subjects. All data were recorded from 60 recruited healthy subjects. Half of the subjects received different levels of thermal stimulation, and half of them were blank controls. We believe that this dataset will lead to the development of local blood perfusion methods that can be used to index vessel function assessments. This publicly available dataset will be beneficial to the microcirculation evaluation.
Learning from local to global - an efficient distributed algorithm for modeling time-to-event data
Authors: Duan Rui , Luo Chongliang , Schuemie Martijn J. , Tong Jiayi , Liang Jason C. , Chang Howard H. , Boland Mary Regina , Bian Jiang , Xu Hua , Holmes John H. , Forrest Christopher B. , Morton Sally C. , Berlin Jesse A. , Moore Jason H. , Mahoney Kevin B. , Chen Yong 
Published: March 2020

ABSTRACTObjectivesWe developed and evaluated a privacy-preservingOne-shotDistributedAlgorithm to fit a multi-centerCox proportional hazard model (ODAC) without sharing patient-level information across sites.MethodsUsing patient-level data from a single site combined with only aggregated information from other sites, we constructed a surrogate likelihood function, approximating the Cox partial likelihood function obtained using patient-level data from all sites. By maximizing the surrogate likelihood function, each site obtained a local estimate of the model parameter, and the ODAC estimator was constructed as a weighted average of all the local estimates. We evaluated the performance of ODAC with (1) a simulation study, and (2) a real-world use case study using four datasets from the Observational Health Data Sciences and Informatics (OHDSI) network.ResultsOur simulation study showed that ODAC provided estimates nearly the same as the estimator obtained by analyzing, in a single dataset, the combined patient-level data from all sites (i.e., the pooled estimator). The relative bias was less than 0.1% across all scenarios. The accuracy of ODAC remained high across different sample sizes and event rates. On the other hand, the metaanalysis estimator, which was obtained by the inverse variance weighted average of the sitespecific estimates, had substantial bias when the event rate is less than 5%, with the relative bias reaching 20% when the event rate is 1%. In the OHDSI network application, the ODAC estimates have a relative bias less than 5% for 15 out of 16 log hazard ratios; while the meta-analysis estimates had substantially higher bias than ODAC.ConclusionsODAC is a privacy-preserving and non-iterative method for implementing time-to-event analyses across multiple sites. It provides estimates on par with the pooled estimator and substantially outperforms the meta-analysis estimator when the event is uncommon, making it extremely suitable for studying rare events and diseases in a distributed manner.
Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasets
Authors: Feuerborn Tatiana R. , Palkopoulou Elle , van der Valk Tom , von Seth Johanna , Munters Arielle R. , Pečnerová Patrícia , Dehasque Marianne , Ureña Irene , Ersmark Erik , Lagerholm Vendela Kempe , Krzewinska Maja , Rodríguez-Varela Ricardo , Götherström Anders , Dalén Love , Díez-del-Molino David 
Published: March 2020

AbstractBackgroundAfter over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.ResultsHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.ConclusionsWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
CDR3 and V- genes show distinct reconstitution patterns in T-cell repertoire post allogeneic bone marrow transplantation
Authors: Tickotsky-Moskovitz N , Dvorkin S , Rotkopf A , Kuperman A.A. , Efroni Sol , Louzoun Y 
Published: March 2020

AbstractBackgroundRestoration of T-cell repertoire diversity after allogeneic bone marrow transplantation (allo-BMT) is crucial for immune recovery. T-cell diversity is produced by rearrangements of germline gene segments (V (D) and J) of the T-cell receptor (TCR) α and β chains, and selection induced by binding of TCRs to MHC-peptide complexes. This diversity can be measured by many measures. We here focus on the V gene usage and the CDR3 sequences of the beta chain. We compared multiple T-cell repertoires to follow T cell repertoire changes post allo-BMT in HLA-matched related donor and recipient pairs.ResultsOur analyses of the differences between donor and recipient complementarity determining region 3 (CDR3) beta composition and V-gene profile show that the CDR sequence composition does not change during restoration, implying its dependence on the HLA typing. In contrast, V gene usage followed a time-dependent pattern, got following the donor profile post transplant and then shifting back to the recipients’ profile. The final long-term repertoire was more similar to that of the recipient’s original one than the donor’s.; some recipients converged within months while others took multiple years.ConclusionBased on the results of our analyses, we propose that donor-recipient V-gene distribution differences may serve as clinical biomarkers for monitoring immune recovery.
m6A RNA methylation regulates promoter proximal pausing of RNA Polymerase II
Authors: Akhtar Junaid , Renaud Yoan , Albrecht Steffen , Ghavi-Helm Yad , Roignant Jean-Yves , Silies Marion , Junion Guillaume 
Published: March 2020

AbstractRNA Polymerase II (RNAP II) pausing is essential to precisely control gene expression and is critical for development of metazoans. Here, we show that the m6A RNA modification regulates promoter-proximal RNAP II pausing. The m6A methyltransferase complex (MTC), with the nuclear reader Ythdc1, are recruited to gene promoters. Depleting the m6A MTC leads to a decrease in RNAP II pause release and in Ser2P occupancy on the gene body, and affects nascent RNA transcription. Tethering Mettl3 to a heterologous gene promoter is sufficient to increase RNAP II pause release, an effect that relies on its m6A catalytic domain. Collectively, our data reveal an important link between RNAP II pausing and the m6A RNA modification, thus adding another layer to m6A-mediated gene regulation.
Molecular characterization of clonal human renal forming cells
Authors: Osnat Cohen-Zontag , Rotem Gershon , Orit Harari-Steinberg , Itamar Kanter , Dorit Omer , Oren Pleniceanu , Gal Tam , Sarit Oriel , Herzl Ben-Hur , Guy Katz , Dotan Zohar , Tomer Kalisky , Benjamin Dekel , Naomi Pode-Shakked 
Published: March 2020

AbstractThe adult kidney replaces its parenchymain vivoin steady state and during regeneration by segment-specific clonal cell proliferation.To understand human adult kidney clonal cell growth, we derived tissue from human nephrectomies and performed limiting dilution to establish genuine clonal cultures from one single cell.Clonal efficiency of the human kidney was x%. Remarkably, a single renal cell could give rise to up to 3.3*10(6) cells. Phenotypically, two types of clonal cultures were apparent; a stably proliferating cuboidal epithelial-like appearing (EL) and a rapidly proliferating fibroblast-like appearing (FL). RNA sequencing of all clonal cultures separated FL from EL cultures according to proximal-distal/collecting renal epithelial tubular identity, respectively. Moreover, distinct molecular features in respect to cell-cycle, epithelial-mesenchymal transition, oxidative phosphorylation, BMP signaling pathway and cell surface markers were observed for each clone type. Surprisingly, clonal expansion (>3 months) was sustained in EL clones harboring markers of mature kidney epithelia (high CD24, CDH1, EpCAM, EMA) in contrast to de-differentiated FL clones (high NCAM1, serpine1), which showed fast lineage amplification and exhausted in a few weeks.Thus, the human adult kidney harbors progenitor cell function in which segment identity and the level of epithelial differentiation dictate clonal characteristics.
7,000 years of turnover: historical contingency and human niche construction shape the Caribbean’s Anthropocene biota
Authors: Kemp Melissa E. , Mychajliw Alexis M. , Wadman Jenna , Goldberg Amy 
Published: March 2020

AbstractThe human-mediated movement of species across biogeographic boundaries—whether intentional or accidental—is dramatically reshaping the modern world. Yet, humans have been reshaping ecosystems and translocating species for millennia, and acknowledging the deeper roots of these phenomena is important for contextualizing present-day biodiversity loss, ecosystem functioning, and management needs. Here, we present the first database of terrestrial vertebrate species introductions spanning the entire anthropogenic history of a system: the Caribbean. We employ this ~7,000 year dataset to assess the roles of historical contingency and priority effects in shaping present-day community structure and conservation outcomes, finding that serial human colonization events contributed to habitat modifications and species extinctions that shaped the trajectories of subsequent species introductions by other human groups. We contextualized spatial and temporal patterns of species introductions within cultural practices and population histories of Indigenous, colonial, and modern human societies, and show that the taxonomic and biogeographic diversity of introduced species reflects diversifying reasons for species introductions through time. Recognition of the complex social and economic structures across the 7,000-year human history of the Caribbean provides the necessary context for interpreting the formation of an Anthropocene biota.