bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of Kalman filter in the epidemiological model: a robust approach to predict COVID-19 outbreak in Bangladesh
Authors: Islam Md. Shariful , Hoque Md. Enamul , Amin Mohammad Ruhul 
Published: October 2020

AbstractAs one of the most densely populated countries in the world, Bangladesh have been trying to contain the impact of a pandemic like COVID-19 since March, 2020. Although government announced an array of restricted measures to slow down the diffusion in the beginning of the pandemic, the lockdown has been lifted gradually by reopening all the industries, markets and offices with a notable exception of educational institutes. As the physical geography of Bangladesh is highly variable across the largest delta, the population of different regions and their lifestyle also differ in the country. Thus, to get the real scenario of the current pandemic across Bangladesh, it is essential to analyze the transmission dynamics over the individual districts. In this article, we propose to integrate the Unscented Kalman Filter (UKF) with classic SIRD model to explain the epidemic evolution of individual districts in the country. We show that UKF-SIRD model results in a robust prediction of the transmission dynamics for 1-4 months. Then we apply the robust UKF-SIRD model over different regions in Bangladesh to estimates the course of the epidemic. Our analysis demonstrate that in addition to the densely populated areas, industrial areas and popular tourist spots are in the risk of higher COVID-19 transmission. In the light of these outcomes, we provide a set of suggestions to contain the pandemic in Bangladesh. All the data and relevant codebase is available athttps://mjonyh.github.io.HighlightsWe integrate the UKF with classic SIRD model for the better estimation of the COVID-19 diffusion of 64 districts in Bangladesh.Nationwide analysis show the strong correlation between population density and the number of COVID-19 positive cases in the country.Industrial zones and popular tourists spots are at greater risk of spreading the Coronavirus.With the better assessment of the COVID-19 cases dynamics, the Government will find effective policies to contain the current pandemic.
The timeout procedure in pediatric surgery - effective tool or lip service? A randomized prospective observational study
Authors: Muensterer Oliver J. , Kreutz Hendrik , Poplawski Alicia , Goedeke Jan 
Published: October 2020

ABSTRACTBackgroundFor over a decade, the preoperative timeout procedure has been implemented in most pediatric surgery units. In our hospital, a standardized team-timeout is performed before every operation. However, the impact of this intervention has not been systematically studied.PurposeThis study evaluates whether purposefully-introduced errors during the timeout routine are picked up by the operating team members.MethodsAfter ethics board approval and informed consent, deliberate errors were randomly and clandestinely introduced into the timeout routine for elective surgical procedures by a pediatric surgery attending. Errors were randomly selected among wrong name, site, side, allergy, intervention, birthdate, and gender items. The main outcome measure was how frequent an error was picked up by the team, and by whom.ResultsOver the course of 16 months, 1800 operations and timeouts were performed. Errors were randomly introduced in 120 cases (6.7%). Overall, 54% of the errors were picked up, the remainder went unnoticed. Errors were picked up most frequently by an anesthesiologists (64%), followed by nursing staff (28%), residents-in-training (6%) and medical students (1%).ConclusionsErrors in the timeout routine go unnoticed by the team in almost half of cases. Therefore, even if preoperative timeout routines are strictly implemented, mistakes may be overlooked. Hence, the timeout procedure in its current form appears unreliable. Future developments may be useful to improve the quality of the surgical timeout and should be studied in detail.
Systemic immune mediators predict therapeutic response and tumor-infiltrating lymphocyte intensity in triple-negative breast cancer
Authors: Lopes Ananda D. , Galdino Nayane A.L. , Figueiredo Amanda B. , Brianese Rafael C. , Morais Katia L.P. , De Brot Marina , A.B.T Cynthia , Osório  , Teixeira-Carvalho Andrea , Calsavara Vinicius F. , Evangelista Guilherme F.B. , Alves Natalia S. , Makdissi Fabiana B. , Sanches Solange M. , Cordeiro de Lima Vladmir C. , Carraro Dirce M. , Gollob Kenneth J. 
Published: October 2020

AbstractTriple-negative breast cancer (TNBC) is an aggressive form of breast cancer defined by the lack of expression of estrogen receptor, progesterone receptors, and of the human epithelial growth factor receptor 2. Neoadjuvant chemotherapy has proven efficacy in the treatment of TNBC, and a pathological complete response (pCR) is predictive of improved long-term survival. The immune response exerts a vital role in response to neoadjuvant chemotherapy, as indicated by the relation between the percentage of stromal tumor-infiltrating lymphocytes (TILs) in pre-treated tumor tissue samples and the likelihood of achieving pCR. Despite this, the relationship between the systemic immune response and the tumor microenvironment is unclear. In this prospective study, we determined the systemic plasma immune profile of TNBC patients before treatment using a panel of 27 immune mediators and measured the percentage of TILs from the same patients. Patients who demonstrated pCR had significantly higher systemic immune mediators; GM-CSF, FGF-basic, VEGF, IL-2, and IL-5, than the non-responders. Moreover, responders displayed a strong positive correlation between the cytokines IFN-γ and IL-7 with the percentage of TILs, while non-responders had a negative or no correlation. Finally, systemic immune mediator levels before treatment predict pCR (AUC range 0.64 - 0.71), and the combination of immune mediators and TILs improved pCR prediction (AUC 0.71 - 0.82). In conclusion, increased systemic immune mediators reflect increased TILs percentage and act as potential predictive biomarkers of pCR for TNBC patients submitted to neoadjuvant chemotherapy.
A phenome-wide multi-directional Mendelian randomization analysis of atrial fibrillation
Authors: Wang Qin , Richardson Tom G , Sanderson Eleanor , Ala-Korpela Mika , Smith George Davey , Holmes Michael V 
Published: October 2020

AbstractBackgroundThe prevalence of atrial fibrillation (AF) is increasing with an aging worldwide population, yet a comprehensive understanding of its causes and consequences remains limited.ObjectivesTo assess the causes and consequences of AF via a multi-directional Mendelian randomization (MR) analysis scanning thousands of traits in a hypothesis-free approach.MethodsWe used publicly available GWAS data centralised and harmonised by the IEU open GWAS database. We assessed the potential causal role of 5048 exposures on risk of AF and the causal role of genetic liability to AF on 10,308 outcomes via two-sample MR analysis. Multivariable MR analysis was further conducted to explore the comparative role of identified risk factors.ResultsMR analysis suggested that 55 out of 5048 exposure traits, including four proteins, play a causal role in AF (P < 1e-5 allowing for multiple comparisons). Multivariable analysis suggested that higher body mass index, height, systolic blood pressure as well as genetic liability to coronary artery diseases independently cause AF. Three out of the four proteins (DUSP13, TNFSF12 and IL6R) had a drug prioritising score for atrial fibrillation of 0.26, 0.38 and 0.88, respectively (values closer to 1 indicating stronger evidence of the protein as a potential drug target). Genetic liability to AF was linked to a higher risk of cardioembolic ischemic stroke.ConclusionsBody mass index, height, systolic blood pressure and genetic liability to coronary artery diseases are independent causal risk factors for AF. Several proteins including DUSP13, IL-6R and TNFSF12 may represent therapeutic potential for preventing AF.
Individuals with recurrent low back pain exhibit further altered trunk control in remission than when in pain
Authors: Shih Hai-Jung Steffi , Van Dillen Linda , Kutch Jason , Kulig Kornelia 
Published: October 2020

AbstractBackgroundMovement alterations due to low back pain (LBP) could lead to long-term adverse consequences if they do not resolve after symptom subsides. This study aims to determine if altered trunk control associated with recurrent low back pain persists beyond symptom duration.MethodsTwenty young adults with recurrent low back pain were tested once during an LBP episode and once in symptom remission, and twenty matched back-healthy participants served as controls. Participants walked on a treadmill with five prescribed step widths. Motion capture and surface electromyography were used to record frontal plane trunk kinematics and muscle activation. Thorax-pelvis coordination was calculated using vector coding technique, and bilateral longissimus activation and co-activation were analyzed.FindingsYoung adults with recurrent LBP exhibited a “looser” trunk control strategy in the frontal plane during gait that was persistent regardless of pain status across multiple step widths compared to back-healthy controls. This was demonstrated by a greater pelvis-only, less thorax-only coordination pattern, and decreased bilateral longissimus co-activation in individuals with recurrent LBP than controls. The looser trunk control strategy was further amplified when individuals with recurrent LBP were in symptom remission and exhibited greater trunk excursion and reduced in-phase coordination.InterpretationThe amplification of aberrant movement during symptom remission may suggest that movement patterns or anatomical factors existing prior to the tested painful episode underlie the altered trunk control in individuals with recurrent LBP. The symptom remission period of recurrent LBP patients may be a critical window into clinical evaluation and treatment.
A Comparative Analysis of System Features Used in the TREC-COVID Information Retrieval Challenge
Authors: Chen Jimmy , Hersh William R. 
Published: October 2020

AbstractThe COVID-19 pandemic has resulted in a rapidly growing quantity of scientific publications from journal articles, preprints, and other sources. The TREC-COVID Challenge was created to evaluate information retrieval methods and systems for this quickly expanding corpus. Based on the COVID-19 Open Research Dataset (CORD-19), several dozen research teams participated in over 5 rounds of the TREC-COVID Challenge. While previous work has compared IR techniques used on other test collections, there are no studies that have analyzed the methods used by participants in the TREC-COVID Challenge. We manually reviewed team run reports from Rounds 2 and 5, extracted features from the documented methodologies, and used a univariate and multivariate regression-based analysis to identify features associated with higher retrieval performance. We observed that fine-tuning datasets with relevance judgments, MS-MARCO, and CORD-19 document vectors was associated with improved performance in Round 2 but not in Round 5. Though the relatively decreased heterogeneity of runs in Round 5 may explain the lack of significance in that round, fine-tuning has been found to improve search performance in previous challenge evaluations by improving a system’s ability to map relevant queries and phrases to documents. Furthermore, term expansion was associated with improvement in system performance, and the use of the narrative field in the TREC-COVID topics was associated with decreased system performance in both rounds. These findings emphasize the need for clear queries in search. While our study has some limitations in its generalizability and scope of techniques analyzed, we identified some IR techniques that may be useful in building search systems for COVID-19 using the TREC-COVID test collections.
Informal coercion during childbirth: risk factors and prevalence estimates from a nationwide survey among women in Switzerland
Authors: Oelhafen Stephan , Trachsel Manuel , Monteverde Settimio , Raio Luigi , Müller Eva Cignacco 
Published: October 2020

AbstractBackgroundIn many countries, the increase in facility births is accompanied by a high rate of obstetric interventions. Lower birthrates or elevated risk factors such as women’s higher age at childbirth and thus a higher need for control and security cannot entirely explain this rise in obstetric interventions. Another potential factor is that women feel coerced to agree to interventions; however, the prevalence of coercive interventions is unknown.MethodsIn a nationwide cross-sectional online survey, we assessed mothers’ satisfaction with childbirth and the prevalence of informal coercion during childbirth and of women at risk for postpartum depression. We used multivariable logistic regression to estimate the risk associated with multiple individual and contextual factors. Women at least 18 years old who gave birth in Switzerland within the previous 12 months were recruited online via Facebook ads or offline via various channels.ResultsA total of 6’054 women completed the questionnaire (drop-out rate 16.2%). An estimated 26.7% experience some form of informal coercion during childbirth. Having a cesarean section or instrumental vaginal birth was associated with an increased risk to experience informal coercion (all risk ratios > 1.5). The risk was also increased for women with a migrant background, women living in more urban regions and women with a risk pregnancy. Also, women to whom having a self-determined vaginal birth is important reported on informal coercion more often. Being at risk for postpartum depression was mostly associated with having an emergency cesarean section, having been transferred to hospital and the experience of informal coercion. Also, women with a migrant background seem to be at a higher risk to develop postpartum depression or having other mental health issues. Finally, women who had a non-instrumental vaginal birth reported higher satisfaction with childbirth experience and women who experienced informal coercion reported lower satisfaction.ConclusionsOne in four women experience informal coercion during childbirth, and this experience is associated with being at risk for postpartum depression and lower satisfaction with childbirth. Health care professionals should make every effort to prevent informal coercion and ensure sensitive aftercare for all new mothers in order to prevent traumatic effects.
Genome-wide analysis of blood lipid metabolites in over 5,000 South Asians reveals biological insights at cardiometabolic disease loci
Authors: Harshfield Eric L. , Fauman Eric B. , Stacey David , Paul Dirk S. , Ziemek Daniel , Ong Rachel M. Y. , Danesh John , Butterworth Adam S. , Rasheed Asif , Sattar Taniya , Zameer-ul-Asar  , Saleem Imran , Hina Zoubia , Ishtiaq Unzila , Qamar Nadeem , Mallick Nadeem Hayat , Yaqub Zia , Saghir Tahir , Hasan Rizvi Syed Nadeem , Memon Anis , Ishaq Mohammad , Rasheed Syed Zahed , Memon Fazal-ur-Rehman , Jalal Anjum , Abbas Shahid , Frossard Philippe , Saleheen Danish , Wood Angela M. , Griffin Julian L. , Koulman Albert 
Published: October 2020

ABSTRACTBackgroundGenetic, lifestyle, and environmental factors can lead to perturbations in circulating lipid levels and increase risk of cardiovascular and metabolic diseases. However, how changes in individual lipid species contribute to disease risk is often unclear. Moreover, little is known about the role of lipids on cardiovascular disease in Pakistan, a population historically underrepresented in cardiovascular studies.MethodsWe characterised the genetic architecture of the human blood lipidome in 5,662 hospital controls from the Pakistan Risk of Myocardial Infarction Study (PROMIS) and 13,814 healthy British blood donors from the INTERVAL study. We applied a candidate causal gene prioritisation tool to link the genetic variants associated with each lipid to the most likely causal genes, and Gaussian Graphical Modelling network analysis to identify and illustrate relationships between lipids and genetic loci.ResultsWe identified 359 genetic associations with 255 lipids measured using direct infusion high-resolution mass spectrometry in PROMIS, and 616 genetic associations with 326 lipids in INTERVAL. Our analyses revealed new biological insights at genetic loci associated with cardiometabolic diseases, including novel lipid associations at the LPL, MBOAT7, LIPC, APOE-C1-C2-C4, SGPP1, and SPTLC3 loci.ConclusionsOur findings, generated using a distinctive lipidomics platform in an understudied South Asian population, strengthen and expand the knowledge base of the genetic determinants of lipids and their association with cardiometabolic disease-related loci.
Vascular Risk Factor Prevalence and Trends in Native Americans With Ischemic Stroke - A National Inpatient Sample Analysis
Authors: Jillella Dinesh V. , Crawford Sara , Lopez Rocio , Zafar Atif , Tang Anne S. , Uchino Ken 
Published: October 2020

AbstractIntroductionNative Americans have a higher incidence and prevalence of stroke and the highest stroke-related mortality among race-ethnic groups in the United States. We aimed to analyze trends in the prevalence of vascular risk factors among Native Americans with ischemic stroke over the last two decades along with a comparison to the other race-ethnic groups.MethodsNational/Nationwide Inpatient Sample (NIS) database was used to explore the prevalence of risk factors among hospitalized ischemic stroke patients during 2000 - 2016. Ischemic stroke and risk factors of interest were identified using validated ICD-9/10 codes. The race-ethnic groups of interest were Native American, White, Black, Hispanic, Asian/Pacific Islanders, and others. Crude and age-and sex-standardized prevalence estimates were calculated for each risk factor within each race-ethnic group in 6 time periods: 2000-02, 2003-05, 2006-08, 2009-11, 2012-14, and 2015-16. We explored linear trends over the defined time periods using linear regression models, with differences in trends between the Native American group and each of the other race-ethnic groups assessed using interaction terms. The analysis accounted for the complex sampling design, including hospital clusters, NIS stratum, and trend weights for analyzing multiple years of NIS data.ResultsOf the 1,278,784 ischemic stroke patients that were included in the analysis, Native Americans constituted 5472. The age-and-sex-standardized prevalence of hypertension (trend slope = 2.24, p < 0.001), hyperlipidemia (trend slope = 6.29, p < 0.001), diabetes (trend slope = 2.04, p = 0.005), atrial fibrillation/flutter (trend slope = 0.80, p = 0.011), heart failure (trend slope = 0.73, p = 0.036) smoking (trend slope = 3.65, p < 0.001), and alcohol (slope = 0.60, p = 0.019) increased during these time periods among Native Americans, while coronary artery disease prevalence remained unchanged. Similar upward trends of several risk factors were noted across other race-ethnic groups with Native Americans showing larger increases in hypertension prevalence compared to Blacks, Hispanics, and Asian/Pacific Islanders and in smoking prevalence compared to Hispanics and Asian/Pacific Islanders. By the year 2015-2016, Native Americans had the highest overall prevalence of diabetes, coronary artery disease, smoking, and alcohol among all the race-ethnic groups.ConclusionThe prevalence of most vascular risk factors among ischemic stroke patients has increased in Native Americans and other race-ethnic groups over the last two decades. Significantly larger increases in the prevalence of hypertension and smoking were seen in Native Americans compared to other groups along with them having the highest prevalence in multiple risk factors in recent years.
The implications of religious event and holidays on the transmission of SARS-CoV2 : the impact of behavioral changes on transmission
Authors: Abdulrahman Abdulkarim , AlMajthoob Muath , AlAwadhi Abdulla I , AlQahtani Manaf M 
Published: October 2020

AbstractIntroductionThe risk factors for transmission of SARS-CoV2 have been widely studied and it was evident that a population’s behavior has a direct effect on the risk of transmission. Public health measures and regulation are largely kept to control and direct these behaviors. In this study, we describe the change in transmission in SARS-CoV2 in relation to demographics before and after two major religious events: “Eid Alfitr” and “Ashura”MethodsThis is a national observational study conducted in Bahrain in September 2020 to compare the number and demographics of all newly diagnosed cases before and after Eid Alfitr (religious holiday) and Ashura religious event. A 10 day period before the event was compared to a 10 day period after the event by ten days. Data on the number of tests, number of new cases, their demographics (age, gender, nationality) and presence of symptoms were collected and analyzed.ResultsThere was significant increase in the number of COVID-19 cases after both Eid Alfitr (1997 more cases, with a 67% increase) and Ashura (4232 more cases with 2.19 times more cases). The majority of new cases after the religious events were found in local Bahrainis, from 472 cases to 2169 cases after Eid, and from 2201 to 6639 cases after Ashura. The rise was most notable in females (increased by 4.89 times after Eid and by 2.69 times after Ashura), children (increased by 4.69 times after Eid and by 5 times after Ashura) and elderly above the age of 60 years (increased by 5.7 times after Eid and by 3.23 times after Ashura).ConclusionIt is evident that religious events and holidays have important implications on the transmission of SARS-CoV2. This increased in transmission is related mainly to the behavior of the population in those days. Children, female, and elderly were the most affected categories due to these events. A thorough public health plan to limit the spread of the infection at these events should be planned and implemented ahead of time.
Real-time tracking and prediction of COVID-19 infection using digital proxies of population mobility and mixing
Authors: Leung Kathy , Wu Joseph T , Leung Gabriel M 
Published: October 2020

AbstractDigital proxies of human mobility and physical mixing have been used to monitor viral transmissibility and effectiveness of social distancing interventions in the ongoing COVID-19 pandemic. We developed a new framework that parameterizes disease transmission models with age-specific digital mobility data. By fitting the model to case data in Hong Kong, we were able to accurately track the local effective reproduction number of COVID-19 in near real time (i.e. no longer constrained by the delay of around 9 days between infection and reporting of cases) which is essential for quick assessment of the effectiveness of interventions on reducing transmissibility. Our findings showed that accurate nowcast and forecast of COVID-19 epidemics can be obtained by integrating valid digital proxies of physical mixing into conventional epidemic models.