bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mothers’ Parenting in an Era ofProactive Policing
Authors: Turney Kristin 
Published: July 2021

AbstractA family systems perspective suggests the repercussions of adolescent police contact likely extend beyond the adolescent to proliferate to the broader family unit, but little research investigates these relationships. I used data from the Fragile Families and Child Wellbeing Study, a longitudinal survey of children who became adolescents during an era of proactive policing, to examine the relationship between adolescent police contact and four aspects of family life: mothers’ parenting stress, mothers’ monitoring, mothers’ discipline, and the mother-adolescent relationship. Adolescent police contact, especially invasive police contact, is associated with increased parenting stress, increased discipline, and decreased engagement, net of adolescent and family characteristics that increase the risk of police contact. There is also evidence that suggests adolescent police contact is more consequential for family life when mothers themselves had experienced recent police contact. These findings suggest the repercussions of police contact extend beyond the individual and proliferate to restructure family relationships.
How trees thrive in a dry climate: diurnal and seasonal hydrology and water relations in a riparian cottonwood grove
Authors: Phelan Colleen A , Pearce David W , Franks Carmen G , Zimmerman Oscar , Tyree Melvin T , Rood Stewart B 
Published: July 2021

Abstract
In semi-arid ecoregions, trees are restricted to river valley floodplains where river water supplements the limited precipitation. To characterize the associated diurnal and seasonal dynamics in hydrology and water relations, we studied narrowleaf cottonwoods (Populus angustifolia) along a prairie river in Canada. From June through August, the shallow soil moisture was depleted but moisture remained higher above the alluvial groundwater table, which dropped to 2.3 m along with river recession. Throughout the summer, with the daily rise in temperature and insolation, foliar stomatal conductance (gs) and transpiration (E) increased to midday and then fell, thus maintaining the midday leaf water potential (Ψmd) above ~−1.7 MPa. This Ψmd approximated the water potential associated with 12% loss of xylem conductivity due to cavitation for branches (P12); the Ψmd and P12 varied independently across eight trees, providing differences in relative hydraulic risk. Sap flux density (Fd) was measured with thermal dissipation probes, and revealed diurnal patterns similar to foliar E. In contrast to our expectation, the daily Fd maxima were consistent through the summer despite the seasonal recession in water supply. Canopy conductances (GS), derived from Fd, sapwood area and canopy area, declined with vapor pressure deficit (D) and fell slightly in late summer along with stomatal sensitivity, which reflects the magnitude of decrease in GS with increasing D. For spatial up-scaling, satellite-derived near-infrared reflectance of vegetation revealed the woodland phenology, with leaf expansion from May through June and gradual decline in photosynthetic productivity through the summer. Thus, the phreatophytic cottonwoods: (i) sustained substantial water use and productivity through the warm and dry summer, by (ii) accessing shallow soil moisture and then deeper alluvial groundwater, and (iii) providing diurnal stomatal regulation, to (iv) avoid xylem cavitation and (v) maintain fairly constant hydraulic conductance.
Discovering Monogenic Patients with a Confirmed Molecular Diagnosis in Millions of Clinical Notes with MonoMiner
Authors: Wu David Wei , Bernstein Jonathan A. , Bejerano Gill 
Published: July 2021

AbstractPurposeCohort building is a powerful foundation for improving clinical care, performing research, clinical trial recruitment, and many other applications. We set out to build a cohort of all patients with monogenic conditions who have received a definitive causal gene diagnosis in a 3 million patient hospital system.MethodsWe define a subset of half (4,461) of OMIM curated diseases for which at least one monogenic causal gene is definitively known. We then introduce MonoMiner, a natural language processing framework to identify molecularly confirmed monogenic patients from free-text clinical notes.ResultsWe show that ICD-10-CM codes cover only a fraction of known monogenic diseases, and even where available, code-based patient retrieval offers 0.12 precision. Searching by causal gene symbol offers great recall but an even worse 0.09 precision. MonoMiner achieves 7-9 times higher precision (0.82), with 0.88 precision on disease diagnosis alone, tagging 4,259 patients with 560 monogenic diseases and 534 causal genes, at 0.48 recall.ConclusionMonoMiner enables the discovery of a large, high-precision cohort of monogenic disease patients with an established molecular diagnosis, empowering numerous downstream uses. Because it relies only on clinical notes, MonoMiner is highly portable, and its approach is adaptable to other domains and languages.
Sustaining effective COVID-19 control in Malaysia through large-scale vaccination
Authors: Jayasundara Pavithra , Peariasamy Kalaiarasu M. , Law Kian Boon , Abd Rahim Ku Nurhasni Ku , Lee Sit Wai , Ghazali Izzuna Mudla M. , Abayawardana Milinda , Le Linh-Vi , K.S.Khalaf Rukun , Razali Karina , Le Xuan , Chong Zhuo Lin , McBryde Emma S , Meehan Michael T , Caldwell Jamie M. , Ragonnet Romain , Trauer James M 
Published: July 2021

AbstractIntroductionAs of 3rdJune 2021, Malaysia is experiencing a resurgence of COVID-19 cases. In response, the federal government has implemented various non-pharmaceutical interventions (NPIs) under a series of Movement Control Orders and, more recently, a vaccination campaign to regain epidemic control. In this study, we assessed the potential for the vaccination campaign to control the epidemic in Malaysia and four high-burden regions of interest, under various public health response scenarios.MethodsA modified susceptible-exposed-infectious-recovered compartmental model was developed that included two sequential incubation and infectious periods, with stratification by clinical state. The model was further stratified by age and incorporated population mobility to capture NPIs and micro-distancing (behaviour changes not captured through population mobility). Emerging variants of concern (VoC) were included as an additional strain competing with the existing wild-type strain. Several scenarios that included different vaccination strategies (i.e. vaccines that reduce disease severity and/or prevent infection, vaccination coverage) and mobility restrictions were implemented.ResultsThe national model and the regional models all fit well to notification data but underestimated ICU occupancy and deaths in recent weeks, which may be attributable to increased severity of VoC or saturation of case detection. However, the true case detection proportion showed wide credible intervals, highlighting incomplete understanding of the true epidemic size. The scenario projections suggested that under current vaccination rates complete relaxation of all NPIs would trigger a major epidemic. The results emphasise the importance of micro-distancing, maintaining mobility restrictions during vaccination roll-out and accelerating the pace of vaccination for future control. Malaysia is particularly susceptible to a major COVID-19 resurgence resulting from its limited population immunity due to the country’s historical success in maintaining control throughout much of 2020.
Associations between cardiovascular risk factors, stroke severity, and post-stroke cognition: a moderated mediation analysis
Authors: Hua Jianian , Zhou Yixiu , Chen Licong , Diao Shanshan , Fang Qi 
Published: July 2021

AbstractIntroductionCognitive impairment may affect one third of the stroke survivors. Cardiovascular risk factors have been described to be risk factors for lower cognition after stroke. However, most previous studies only used multivariate regression models to learn the association. The aim of our study was to investigate whether the effect of cardiovascular risk factors on cognition after stroke was mediated by stroke severity, the estimated effect of direct and indirect pathways, and the moderated association.MethodIn this incident cross-sectional study, 300 stroke patients received cognitive test within seven days after stroke. Cognitive tested was performed by the Chinese version of Mini-Mental State Examination (MMSE). A second stage dual moderated mediation model was used the select moderation variables. Finally, we constructed a structural equation model to test the indirect effects of cardiovascular and demographic factors on cognition stroke severity, the direct effects of predictors on cognition, and the moderated effects of hypertension.ResultsAge (estimate, -0.114; 95% bias-corrected CI, -0.205, -0.032; P<0.001), female (estimate, -2.196; 95% bias-corrected CI, -4.359, -0.204; P=0.009), lower education (estimate, -0.893; 95% bias-corrected CI, -1.662, --0.160; P<0.001), stroke severity (estimate, -1.531; 95% bias-corrected CI, -3.015, -0.095), hypertension (estimate, -2.242; 95% bias-corrected CI, -4.436, -0.242; P=0.003) and atrial fibrillation (estimate, -4.930; 95% bias-corrected CI, -12.864, -0.126; P=0.048) were directly associated with lower cognitive function after stroke. We found no evidence that cardiovascular risk factors indirectly correlated cognitive function through stroke severity. The combination of hypertension could alleviate the negative effect of atrial fibrillation on cognition (estimate, -3.928; 95% bias-corrected CI, -7.954, 0.029; P=0.009).ConclusionsWe explored the complex relationship between cardiovascular risk factors, stroke severity, and cognitive function after stroke. Using our method, researchers using other dataset could repeat the analysis and achieve a better understanding of the relationship. Future researchers are needed to find whether the moderated associations were casual or modifiable.
Epidemic preparedness -Leishmania tarentolaeas an easy-to-handle tool to produce antigens for viral diagnosis: application to COVID-19
Authors: Varotto-Boccazzi Ilaria , Manenti Alessandro , Dapporto Francesca , Gourlay Louise J. , Bisaglia Beatrice , Gabrieli Paolo , Forneris Federico , Faravelli Silvia , Bollati Valentina , Zuccotti Gian Vincenzo , Montomoli Emanuele , Epis Sara , Bandi Claudio 
Published: July 2021

AbstractTo control future epidemics, discovery platforms are urgently needed, for the rapid development of diagnostic assays. Molecular diagnostic tests for COVID-19 emerged shortly after the isolation of SARS-CoV-2, however, serological tests based on antiviral antibody detection, revealing previous exposure to the virus, required longer developmental phases, due to the need for correctly folded and glycosylated antigens. The delay between the identification of a new virus and the development of reliable serodiagnostic tools limits our readiness for the control of a future epidemic. In this context, we propose the protozoanLeishmania tarentolaeas an easy-to-handle micro-factory for the rapid production of viral antigens, to be used at the forefront of emerging epidemics. As a study model, we engineeredL. tarentolaeto express the SARS-CoV-2 Receptor Binding Domain (RBD) and report the ability of the purified RBD antigen to detect SARS-CoV-2 infection, with a sensitivity and reproducibility comparable to that of a reference antigen produced in human cells. This is the first application of an antigen produced inL. tarentolaefor the serodiagnosis of a Coronaviridae infection. Based on our results, we proposeL. tarentolaeas an effective system for viral antigen production, even in countries that lack high-tech cell factories.
Better Antimicrobial Resistance Data Analysis & Reporting in Less Time
Authors: Luz Christian F. , Berends Matthijs S. , Zhou Xuewei , Lokate Mariëtte , Friedrich Alex W. , Sinha Bhanu , Glasner Corinna 
Published: July 2021

AbstractIntroductionThe global challenge of antimicrobial resistances (AMR) requires the rational and responsible use of antimicrobials. Insights and knowledge about the local AMR levels and epidemiology are essential to guide optimal decision-making processes in antimicrobial use. However, dedicated tools for reliable and reproducible AMR data analysis and reporting are often lacking. Previously, we have developed a novel approach to AMR data analysis and reporting using open-source software tools. In this study, we aimed at comparing the effectiveness and efficiency of traditional analysis and reporting versus this new approach for reliable and reproducible AMR data analysis in a clinical setting.MethodsTen professionals in the field of AMR that routinely work with AMR data were recruited to participate and provided with one year’s blood culture test results from a tertiary care hospital results including antimicrobial susceptibility test results. Participants were asked to perform a detailed AMR data analysis in a two-step process: first (round 1) using their analysis software of choice and next (round 2) using the previously developed open-source software tools. Accuracy of the results and time spent were compared between the two rounds. Paired student’s t-tests were used to test for statistical significance. Finally, participants rated the usability of the tools using the systems usability scale.ResultsThe mean time spent on creating a comprehensive AMR report reduced from 93.7 (SD ±21.6) minutes to 22.4 (SD ±13.7) minutes (p < 0.001). Average task completion per round changed from 56% (SD: ±23%) to 96% (SD: ±5.5%) (p<0.05). The proportion of correct answers in the available results increased from 37.9% in the first round to 97.9% in the second round (p < 0.001). The usability of the new AMR reporting tool was rated with a median of 83.8 (out of 100) on the system usability scale.ConclusionThis study demonstrated the significant improvement in efficiency and accuracy in standard AMR data analysis and reporting workflows through the use of open-source software tools in a clinical setting. Integrating these tools in clinical settings can democratise the access to fast and reliable insights about local microbial epidemiology and associated AMR levels. Thereby, our approach can support evidence-based decision-making processes in the use of antimicrobials.
Socio-economic Transition in an Indian Rural Setting and Its Impact on Health: Pune Maternal Nutrition Study
Authors: Shukla S R. , Kumaran K , Radkar A , Bhalerao A J. , Solat V A. , Chougule S D. , Deokar T M. , Yajnik P C. , Fall C HD. , Yajnik C S. 
Published: July 2021

AbstractBackgroundThere is scant scientific information on socioeconomic transition and its effects on health parameters in India. The prospective data collection in the Pune Maternal Nutrition Study (PMNS) birth cohort provided an opportunity to examine the changes in socio-economic status (SES) and 1) its comparison against state and district indicators, 2) association with body size and cardio-metabolic risk factors.MethodWe followed up ∼700 families for biomedical information in the PMNS. SES data was collected in the index pregnancy (1993-96) and serially every six years (∼2001, ∼2007, ∼2013). Comparisons with rural Maharashtra and Pune were made using data from the National Family Health Survey 1999 and 2006 (NFHS II and III).ResultsThere was an increase in the proportion of those in the high Standard of Living Index (SLI, NFHS) from 64% to 90% between 2001 and 2013. The increase in SES in our study area was faster and greater compared to the state and district. Higher SLI was associated with higher weight, height, body fat percent and total cholesterol concentrations at each followup. However, there were no associations between transition and health parameters.ConclusionOur data suggest a rapid socio-economic transition in the study area which is faster than the state and district.
Modeling of leptospirosis outbreaks in relation to hydroclimatic variables in the northeast of Argentina
Authors: Gómez Andrea A. , López María Soledad , Müller Gabriela V. , López Leonardo , Sione Walter , Giovanini Leonardo 
Published: July 2021

AbstractThe transmission of leptospirosis is conditioned by climatic variables. In northeastern Argentina leptospirosis outbreaks occur mainly in coincidence with periods of abundant precipitation and high hydrometric level. A Susceptible-Infectious-Recovered Epidemiological Model (SIR) is proposed, which incorporates hydroclimatic variables for the three most populated cities in the area (Santa Fe, Paraná and Rosario), during the 2009 – 2018 period. Results obtained by solving the proposed SIR model for the 2010 outbreaks are in good agreement with the actual data, capturing the dynamics of the leptospirosis outbreak wave. However, the model does not perform very well when isolated cases appear outside the outbreak periods, probably due to non-climatic factors not explicitly considered in the present version of the model. Nevertheless, the dynamic modeling of infectious diseases considering hydroclimatic variables constitutes a climatic service for the public health system, not yet available in Argentina.
Wireless endovascular nerve stimulation with a millimeter-sized magnetoelectric implant
Authors: Chen Joshua C. , Kan Peter , Yu Zhanghao , Alrashdan Fatima , Garcia Roberto , Singer Amanda , Lai C.S. Edwin , Avants Ben , Crosby Scott , Felicella Michelle M. , Robledo Ariadna , Hartgerink Jeffrey D. , Sheth Sunil A. , Yang Kaiyuan , Robinson Jacob T. 
Published: July 2021

AbstractImplanted bioelectronic devices have the potential to treat disorders that are resistant to traditional pharmacological therapies; however, reaching many therapeutic nerve targets requires invasive surgeries and implantation of centimeter-sized devices. Here we show that it is possible to stimulate peripheral nerves from within blood vessels using a millimeter-sized wireless implant. By directing the stimulating leads through the blood vessels we can target specific nerves that are difficult to reach with traditional surgeries. Furthermore, we demonstrate this endovascular nerve stimulation (EVNS) with a millimeter sized wireless stimulator that can be delivered minimally invasively through a percutaneous catheter which would significantly lower the barrier to entry for neuromodulatory treatment approaches because of the reduced risk. This miniaturization is achieved by using magnetoelectric materials to efficiently deliver data and power through tissue to a digitally-programmable 0.8 mm2 CMOS system-on-a-chip. As a proof-of-principle we show wireless stimulation of peripheral nerve targets both directly and from within the blood vessels in rodent and porcine models. The wireless EVNS concept described here provides a path toward minimally invasive bioelectronics where mm-sized implants combined with endovascular stimulation enable access to a number of nerve targets without open surgery or implantation of battery-powered pulse generators.
Efficient gradient boosting for prognostic biomarker discovery
Authors: Li Kaiqiao , Yao Sijie , Zhang Zhenyu , Cao Biwei , Wilson Christopher M. , Kuan Pei Fen , Zhu Ruoqing , Wang Xuefeng 
Published: July 2021

AbstractMotivationGradient boosting decision tree (GBDT) is a powerful ensemble machine learning method that has the potential to accelerate biomarker discovery from high-dimensional molecular data. Recent algorithmic advances, such as Extreme Gradient Boosting (XGB) and Light Gradient Boosting (LGB), have rendered the GBDT training more efficient, scalable and accurate. These modern techniques, however, have not yet been widely adopted in biomarkers discovery based on patient survival data, which are key clinical outcomes or endpoints in cancer studies.ResultsIn this paper, we present a new R packageXsurvas an integrated solution which applies two modern GBDT training framework namely, XGB and LGB, for the modeling of censored survival outcomes. Based on a comprehensive set of simulations, we benchmark the new approaches against traditional methods including the stepwise Cox regression model and the original gradient boosting function implemented in the packagegbm. We also demonstrate the application ofXsurvin analyzing a melanoma methylation dataset. Together, these results suggest thatXsurvis a useful and computationally viable tool for screening a large number of prognostic candidate biomarkers, which may facilitate cancer translational and clinical research.AvailabilityXsurvis freely available as an R package at:https://github.com/topycyao/XsurvContactxuefeng.wang@moffitt.orgSupplementary informationSupplementary data are available atBioinformaticsonline.
SAFA facilitates chromatin opening of immune genes through interacting with nascent antiviral RNAs
Authors: Cao Lili , Li Yunfei , Luo Yujie , Guo Xuefei , Liu Shengde , Li Siji , Li Junhong , Zhang Zeming , Zhao Yingchi , Zhang Qiao , Gao Feng , Ji Xiong , Wang Yiguang , Gao Xiang , You Fuping 
Published: July 2021

SummaryRegulation of chromatin accessibility determines the transcription activities of genes, which endow the host with function-specific gene expression patterns. It remains unclear how chromatin accessibility is specifically directed, particularly, during host defense against viral infection. We previously reported that the nuclear matrix protein SAFA surveils viral RNA and regulates antiviral immune genes expression. However, how SAFA regulates the expression and what determines the specificity of antiviral immune genes remains unknown. Here, we identified that the depletion of SAFA specifically decreased the chromatin accessibility, activation and expression of virus induced genes in a genome-wide scale after VSV infection. SAFA exclusively bound with antiviral related RNAs, which mediated the specific opening of the according chromatin and robust transcription of these genes. Knockdown of these associated RNAs dampened the accessibility of corresponding genes in an extranuclear signaling pathway dependent manner. Moreover, VSV infection cleaved SAFA protein at the C-terminus which deprived its RNA binding ability for immune evasion. Thus, our results demonstrated that SAFA and the interacting RNA products during viral infection collaborate and remodel chromatin accessibility to facilitate antiviral innate immune response.