bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct-to-Consumer Chat-Based Remote Care Before and During the COVID-19 Outbreak
Authors: Zeltzer Dan , Vodonos Alina , Paz Edo , Malka Roy 
Published: July 2020

AbstractObjectiveTo compare the patient population, common complaints, and physician recommendations in direct-to-consumer chat-based consults, before and during the COVID-19 outbreak.Data sourcesData on patient characteristics, patient complaints, and physician recommendations from 36,864 chat-based telemedicine consults with physicians in an online-clinic by patients from across the United States between April 2019 and April 2020.Study DesignWe perform a retrospective analysis comparing patient characteristics, visit characteristics, and physician recommendation before and after the COVID-19 outbreak. We examine patient age and gender, visit time, patient chief complains, and physician medical recommendation (including prescription drugs, reassurance, and referrals).Principal FindingsBefore March 2020, most patients were female (75 percent) and 18–44 years old (89 percent). Common complaints such as abdominal pain, dysuria, or sore throat suggested minor acute conditions. Most cases (67 percent) were resolved remotely, mainly via prescriptions; a minority were referred. Since March 2020, the COVID-19 emergency has led to a sharp (fourfold) increase in case volume, including more males (from 25 to 29 percent), patients aged 45 and older (from 11 to 17 percent), and more cases involving mental health complaints and complaints related to COVID-19. Across all symptoms, significantly more cases (78 percent) have been resolved remotely.ConclusionsThe COVID-19 outbreak in the United States has been associated with a sharp increase in the use of chat-based telemedicine services, including by new patient demographics, an increase in both COVID-19 and mental health complains, and an increase in remote case resolutions.
COMPARATIVE SEROLOGIC PROFILES OF HEPATITIS B VIRUS (HBV) BETWEEN HIV/HBV CO-INFECTED AND HBV MONO-INFECTED PATIENTS IN ILE-IFE, NIGERIA
Authors: Osasona Oluwadamilola Gideon , Ariyo Olumuyiwa Elijah , Oguzie Judith , J.Olumade Testimony , George Uwem , Adewale-Fasoro Opeoluwa , Oguntoye Oluwatosin Oluwagbenga 
Published: July 2020

ABSTRACTIntroductionHepatitis B virus(HBV) infects about 2 billion people globally and accounts for mortality of about 800,000 from liver cirrhosis and hepatocellular carcinoma. Sub-Saharan Africa accounts for 70% of Human Immunodeficiency Virus (HIV) global burden. HIV/HBV co-infection results in early development of HBV complications, alterations of serological biomarkers of HBV.MethodsTwo hundred and fifty patients with HIV/AIDS were screened for HBV and 20 (8%) were identified. Same number of HBV mono-infected individuals were recruited into the study and subsequently, HBV serological profiles which includes HBsAg, HBsAb, HBeAg, HBeAb,HBcAbIgM and HBcAbIgG were assayed using HBV ELISA kits.ResultMean age of patients in the HBV/HIV cohort was 45.5 years while the HBV mono-infected infected cohort was 30.5 years. Majority of the HBV/HIV co-infected individuals were females (85%). Frequency of HBeAg among HIV/HBV co-infected cohort was 25% and 15% for HBV mono-infected, while the frequency of HBeAb was higher (60%) among cohort of HBV/HIV co-infected patients in comparison with the HBV mono-infected cohorts(50%). Two patients among the HIV/HBV co-infected cohort have the isolated anti-HBcAg serologic pattern.ConclusionThe study broadened the available evidence of comparative serologic profiles of Hepatitis B virus between cohorts of HBV/HIV co-infected individuals and HBV mono-infected patients in Nigeria.
Bioinformatic analysis of shared B and T cell epitopes amongst relevant coronaviruses to human health: Is there cross-protection?
Authors: Pacheco-Olvera Diana Laura , Remy-Hernández Stephanie Saint , Acevedo-Ochoa Ernesto , Arriaga-Pizano Lourdes , Cérbulo-Vázquez Arturo , Ferat-Osorio Eduardo , Rivera-Hernández Tania , López-Macías Constantino 
Published: July 2020

AbstractWithin the last 30 years 3 coronaviruses, SARS-CoV, MERS-CoV and SARS-CoV-2, have evolved and adapted to cause disease and spread amongst the human population. From the three, SARS-CoV-2 has spread world-wide and to July 2020 it has been responsible for more than 11 million confirmed cases and over half a million deaths. In the absence of an effective treatment or vaccine, social distancing has been the most effective measure to control the pandemic. However it has become evident that as the virus spreads the only tool that will allow us to fully control it is an effective vaccine. There are currently more than 150 vaccine candidates in different stages of development using a variety of viral antigens, with the S protein being the most targeted antigen. Although some new experimental evidence suggests cross-reacting responses between coronaviruses are present in the population, it remains unknown whether potential shared antigens between different coronaviruses could provide cross-protection. Given that coronaviruses are emerging pathogens and continue to represent a threat to global health, the development of a SARS-Cov-2 vaccine that could provide ‘universal’ protection against other coronaviruses should be pushed forward. Here we present a thorough review of reported B and T cell epitopes shared between SARS-CoV-2 and other relevant coronaviruses, in addition we used web-based tools to predict novel B and T cell epitopes that have not been reported before. Analysis of experimental evidence that is constantly emerging complemented with the findings of this study allow us support the hypothesis that cross-reactive responses, particularly those coming from T cells, might play a key role in controlling infection by SARS-CoV-2. We hope that with the evidence presented in this manuscript we provide arguments to encourage the study of cross-reactive responses in order to elucidate their role in immunity to SARS-CoV-2. Finally we expect our findings will aid targeted analysis of antigen-specific immune responses and guide future vaccine design aiming to develop a cross reactive effective vaccine against respiratory diseases caused by coronaviruses.
Multi-sample Full-length Transcriptome Analysis of 22 Breast Cancer Clinical Specimens with Long-Read Sequencing
Authors: Namba Shinichi , Ueno Toshihide , Kojima Shinya , Tanaka Yosuke , Inoue Satoshi , Kishigami Fumishi , Maeda Noriko , Ogawa Tomoko , Hazama Shoichi , Shiraishi Yuichi , Mano Hiroyuki , Kawazu Masahito 
Published: July 2020

AbstractAlthough transcriptome alteration is considered as one of the essential drivers of carcinogenesis, conventional short-read RNAseq technology has limited researchers from directly exploring full-length transcripts, only focusing on individual splice sites. We developed a pipeline for Multi-Sample long-read Transcriptome Assembly, MuSTA, and showed through simulations that it enables construction of transcriptome from the transcripts expressed in target samples and more accurate evaluation of transcript usage. We applied it to 22 breast cancer clinical specimens to successfully acquire cohort-wide full-length transcriptome from long-read RNAseq data. By comparing isoform existence and expression between estrogen receptor positive and triple-negative subtypes, we obtained a comprehensive set of subtype-specific isoforms and differentially used isoforms which consisted of both known and unannotated isoforms. We have also found that exon-intron structure of fusion transcripts tends to depend on their genomic regions, and have found three-piece fusion transcripts that were transcribed from complex structural rearrangements. For example, a three-piece fusion transcript resulted in aberrant expression of an endogenous retroviral gene,ERVFRD-1, which is normally expressed exclusively in placenta and supposed to protect fetus from maternal rejection, and expression of which were increased in several TCGA samples withERVFRD-1fusions. Our analyses of real clinical specimens and simulated data provide direct evidence that full-length transcript sequencing in multiple samples can add to our understanding of cancer biology and genomics in general.
COVID-19 effective reproductive ratio determination: An application, and analysis of issues and influential factors
Authors: Baibás Luis Alfredo Bautista , Conesa Mario Gil , Caravaca Gil Rodríguez , Baibás Blanca Bautista 
Published: July 2020

AbstractAn essential indicator of COVID-19 transmission is the effective reproduction number (Rt), the number of cases which an infected individual is expected to infect at a particular point in time; curves of the evolution of Rt over time (transmission curves) reflect the impact of preventive measures and whether an epidemic is controlled. We have created a Shiny/R web application (https://alfredob.shinyapps.io/estRO/) with user-selectable features: open data sources with daily COVID-19 incidences from all countries and many regions, customizable preprocessing options (smoothing, proportional increment, backwards distribution of negative corrections, etc), different MonteCarlo-Markov-Chain estimates of the generation time or serial interval distributions and state-of-the-art Rt estimation frameworks (EpiEstim, R0). We have analyzed the impact of these factors in the obtained transmission curves. We also have obtained curves at the national and sub-national level and analyzed the impact of epidemic control strategies, superspreading events, socioeconomic factors and outbreaks.We conclude that country wealth and, to a lesser extent, mitigation strategies, were associated with poorer epidemic control. Dataset quality was an important factor, and sometimes dictated the necessity of time series smoothing. We couldn’t find conclusive evidence regarding the impact of alleged superspreading events. In the reopening phase, outbreaks had an impact on transmission curves. This application could be used interactively as a tool both to obtain transmission estimates and to perform interactive sensitivity analysis.
Risk factors mediating the effect of body-mass index and waist-to-hip ratio on cardiovascular outcomes: Mendelian randomization analysis
Authors: Gill Dipender , Zuber Verena , Dawson Jesse , Pearson-Stuttard Jonathan , Carter Alice R. , Sanderson Eleanor , Karhunen Ville , Levin Michael G. , Wootton Robyn E. ,   VA Million Veteran Program, Klarin Derek , Tsao Philip S. , Tsilidis Konstantinos K. , Damrauer Scott M. , Burgess Stephen , Elliott Paul 
Published: July 2020

AbstractBackgroundHigher body-mass index (BMI) and waist-to-hip ratio (WHR) increase the risk of cardiovascular disease, but the extent to which this is mediated by blood pressure, diabetes, lipid traits and smoking is not fully understood.MethodsUsing consortia and UK Biobank genetic association summary data from 140,595 to 898,130 participants predominantly of European ancestry, MR mediation analysis was performed to investigate the degree to which genetically predicted systolic blood pressure (SBP), diabetes, lipid traits and smoking mediated an effect of genetically predicted BMI and WHR on risk of coronary artery disease (CAD), peripheral artery disease (PAD) and stroke.ResultsThe 49% (95% confidence interval [CI] 39%-60%) increased risk of CAD conferred per 1-standard deviation increase in genetically predicted BMI attenuated to 34% (95% CI 24%-45%) after adjusting for genetically predicted SBP, to 27% (95% CI 17%-37%) after adjusting for genetically predicted diabetes, to 47% (95% CI 36%-59%) after adjusting for genetically predicted lipids, and to 46% (95% CI 34%-58%) after adjusting for genetically predicted smoking. Adjusting for all the mediators together, the increased risk attenuated to 14% (95% CI 4%-26%). A similar pattern of attenuation was observed when considering genetically predicted WHR as the exposure, and PAD or stroke as the outcomes.ConclusionsMeasures to reduce obesity will lower risk of cardiovascular disease primarily by impacting on downstream metabolic risk factors, particularly diabetes and hypertension. Reduction of obesity prevalence alongside control and management of its mediators is likely to be most effective for minimizing the burden of obesity.
Cultural adaptation and content validity of a Chinese translation of the “Person-Centered Primary Care Measure”: findings from cognitive debriefing
Authors: Tse Tsui Yee Emily , Lam Lo Kuen Cindy , Wong King Ho Carlos , Yee Chin Weng , Etz Rebecca S. , Zyzanski Stephen J. , Stange Kurt C. 
Published: July 2020

AbstractObjectivesTo develop an equivalent Chinese translation of the Person-Centered Primary Care Measure (PCPCM) and to establish its cultural adaptability and content validity through cognitive debriefing.DesignThe original English PCPCM was first translated into Chinese by double forward-translation by professional translators. The reconciliated Chinese version was then doubly back-translated into English by two other professional translators blinded to the forward-translation. Upon affirmation on its linguistic equivalence with the developers of the original English PCPCM, the reconciliated Chinese PCPCM was sent for cognitive debriefing with twenty Chinese-speaking primary care subjects by a trained interviewer using structured probing questions to collect their opinions on the clarity, comprehensibility and relevance of each item and response option in the Measure.SettingSubjects were invited from a primary care clinic in Hong Kong to undergo the cognitive debriefing interviews. The interviews were divided into four groups chronologically to allow revision of the items to be made in between.ParticipantsTen males of age ranged from twenty-eight to sixty-eight and ten females of age ranged from thirty-seven to seventy completed the cognitive interviews. They were all Cantonese-speaking Chinese recruited by convenience sampling. Subjects with cognitive impairment, could not read Chinese, too old or too sick to complete the interviews were excluded from the study.ResultsAn average of 3.3 minutes (range 3 to 4 minutes) was required for the subjects to self-complete the Measure. All items were generally perceived to be easily understood and relevant. Modifications were made to items with the content validity index on clarity or understanding <0.8 in each round of the interviews or if a majority of the subjects suggested rewording. Revisions were made to two items in the Chinese PCPCM throughout the whole cognitive debriefing process before the final version was confirmed. The average content validity index (CVI) on clarity of the Chinese PCPCM items ranged from 0.75 to 1. The average CVI on understanding ranged from 0.7 to 1. The average CVI on relevance ranged from 0.55 to 1.ConclusionsThe content validity of the PCPCM was good enough to allow further testing of its psychometric properties in a larger population.Key PointsQuestionIs our Chinese translation of The Person-Centered Primary Care Measure (PCPCM) a culturally adaptable and valid measure?FindingOur Chinese version of the PCPCM was confirmed to be culturally adaptable. It showed high content validity indices regarding its clarity, understanding and relevance through cognitive debriefing.MeaningThis Chinese version of the PCPCM is ready for further testing of its psychometric properties in a larger population.
Patient acceptability of ctDNA testing in endometrial cancer follow-up
Authors: Relton A , Collins A , Guttery DS , Gorsia D , McDermott HJ , Moss EL 
Published: July 2020

ABSTRACTObjectiveCirculating tumour DNA (ctDNA) is emerging as a potential option to detect disease recurrence in many cancer types however, ensuring patient acceptability of changing clinical practice and the introduction of new technology is paramount. This study aimed to explore women’s opinions on the acceptability of ctDNA to monitor for endometrial cancer (EC) recurrence.MethodsWomen enrolled on a non-intervention cohort study determining the ability of ctDNA to detect recurrent endometrial cancer were invited to participate in a semi-structured interview. Data was analysed using Template Analysis.ResultsEighteen women were interviewed. Participants represented a mix of cases, including early stage high-risk EC, metastatic disease at diagnosis and EC recurrence, to ensure a wide range of participant experiences were captured. A ctDNA blood test was viewed by participants as more physically and psychologically acceptable than clinical examination to monitor for EC recurrence. In particular, participants expressed overwhelming preference for a blood test rather than pelvic examination. Although participants acknowledged that an abnormal ctDNA result could cause anxiety, they expressed a preference to be informed of their results, even if a recurrence was too small to detect radiologically. Explanations for these opinions were a desire for certainty whether their cancer would recur or not, and knowledge would help them be more aware of symptoms that should be reported to their clinician.ConclusionsctDNA monitoring to identify EC recurrence appears to be acceptable to patients, and for many, may be preferable to clinical examination.
Possible fates of the dispersion of SARS-COV-2 in the Mexican context
Authors: Santamaría-Holek I. , Castaño V. 
Published: July 2020

AbstractThe determination of the adequate time for house confinement and when social distancing restrictions should end are now two of the main challenges that any country has to face in an effective battle against. The possibility of a new outbreak of the pandemic and how to avoid it is, nowadays, one of the primary objectives of epidemiological research. In this work, we go deep in this subject by presenting an innovative compartmental model, that explicitly introduces the number of active cases, and employing it as a conceptual tool to explore the possible fates of the dispersion of SARS-COV-2 in the Mexican context. We incorporated the impact of starting, inattention, and end of restrictive social policies on the time evolution of the pandemics via time-in-run corrections to the infection rates. The magnitude and impact on the epidemic due to post-social restrictive policies are also studied. The scenarios generated by the model can help authorities to determine an adequate time and population load that may be allowed to reassume normal activities.
Estimate of airborne transmission of SARS-CoV-2 using real time tracking of health care workers
Authors: Hota Bala , Stein Brian , Lin Michael , Tomich Alex , Segreti John , Weinstein Robert A. 
Published: July 2020

AbstractBACKGROUNDWhether and to what degree SARS-CoV-2 is spread via the airborne route is unknown. Using data collected from health care worker interactions with hospitalized patients with COVID-19 illness, we calculated the transmissibility of SARS-CoV-2 via the airborne route.OBJECTIVES/METHODSHealthcare worker interaction with SARS-CoV-2 infected patients were tracked using a real time location system between March 18 and March 31. A value for q, the transmissibility expressed as quanta per hour, was estimated using a well-established model for airborne transmission.RESULTSSARS-CoV-2 infection prevalence among tracked HCWs was 2.21% (0.07-4.35). Transmissibility was estimated to be 0.225 quanta per hour, well below other well-characterized airborne pathogens. Simulations demonstrated that risk of infection is substantially reduced with increased ventilation of rooms.CONCLUSIONSOverall, our findings suggest that SARS-CoV-2 is not well transmitted via the airborne route in controlled conditions. We speculate that SARS-CoV-2 may be only opportunistically airborne, with most transmission occurring via droplet methods.One Sentence SummaryWe calculated the airborne transmissibility (q) of SARS-CoV-2 and the impact of masks and ventilation in a hospital setting.
Local Gazetteers Reveal Contrasting Patterns of Historical Distribution Changes between Apex Predators and Mesopredators in Eastern China
Authors: Hu Kaijin 
Published: July 2020

AbstractBackgroundHumans have been causing the sixth wave of mass extinction of biodiversity. The situation of predators, especially of carnivores, is a key indicator of biodiversity, and the mesopredator release is a typical phenomenon in ecosystem recess. Local gazetteers are a rich resource for historical biodiversity research. However there are obvious biases in previous studies focusing only on presence records and neglecting the absence records. I recollected and analyzed the records by fixed methods to research historical biodiversity change.MethodsInnovatively, this research used both presence and absence records from local gazetteers to reconstruct the distribution of 8 kinds of mammalian predators (i.e. large carnivores: tigers, leopards, and bears; medium-sized carnivores: wolves, foxes, civets, dholes, and mustelids) in eastern China from 1573C.E.(Common Era) to 1949C.E. (sorted into 4 periods). Then by utilizing statistics methods, e.g. Partial Least Squares Structural Equation Modeling(PLS-SEM), I analyzed the distribution changes(overall and sorted into 5 altitude groups), and the relation between carnivores and the influence from humans.Results & ConclusionsI reconstructed the specific distribution changes of the carnivores and found the changes match the mesopredator release phenomenon. Furthermore, I found the specific relation(e.g. trade-off effect) between carnivores and the influence of humans. Besides, I found that bears and civets may be potential members of the “Tigers - Leopards - Dholes” predator guild.ProspectsI have also collected records for other wild animals from local gazetteers in China. Based on this collection, I have built the Database of Wild Mammal Records in Chinese Local Gazetteers and am building the Database of Wild Bird Records in Chinese Local Gazetteers. I aim to continue relevant studies using these databases in the future.
GPR183 regulates interferons and bacterial growth duringMycobacterium tuberculosisinfection: interaction with type 2 diabetes and TB disease severity
Authors: Bartlett Stacey , Gemiarto Adrian Tandhyka , Dao Ngo Minh , Sajiir Haressh , Hailu Semira , Sinha Roma , Foo Cheng Xiang , Kleynhans Léanie , Tshivhula Happy , Webber Tariq , Bielefeldt-Ohmann Helle , West Nicholas P. , Hiemstra Andriette M. , MacDonald Candice E. , von Voss Christensen Liv , Schlesinger Larry S. , Walzl Gerhard , Rosenkilde Mette Marie , Mandrup-Poulsen Thomas , Ronacher Katharina 
Published: July 2020

AbstractOxidized cholesterols have emerged as important signaling molecules of immune function, but little is known about the role of these oxysterols during mycobacterial infections. We found that expression of the oxysterol-receptor GPR183 was reduced in blood from patients with tuberculosis (TB) and type 2 diabetes (T2D) compared to TB patients without T2D and was associated with TB disease severity on chest x-ray. GPR183 activation by 7α,25-hydroxycholesterol (7α,25-OHC) reduced growth ofMycobacterium tuberculosis(Mtb) andMycobacterium bovisBCG in primary human monocytes, an effect abrogated by the GPR183 antagonist GSK682753. Growth inhibition was associated with reduced IFN-β and IL-10 expression and enhanced autophagy. Mice lacking GPR183 had significantly increased lung Mtb burden and dysregulated IFNs during early infection. Together, our data demonstrate that GPR183 is an important regulator of intracellular mycobacterial growth and interferons during mycobacterial infection.Graphical Abstract