bluuebunny/crossref_metadata_2025_split huggingface dataset:
Substance Use, Mental Health Problems, and Physical and Sexual Violence Additively Increase HIV Risk Between Male Sex Workers and Their Male Clients in Northeastern United States
Authors: Mimiaga Matthew J. , Hughto Jaclyn M. W. , Klasko-Foster Lynne , Jin Harry , Mayer Kenneth H. , Safren Steven A. , Biello Katie B. 
Published: November 2020

Background:
Male sex workers (MSW) are disproportionately affected by HIV/AIDS, with an estimated HIV prevalence in the United States of 19.3%. Existing research suggests that MSW are also at risk of adverse psychosocial problems. Cross-sectional studies of MSW have suggested that co-occurring epidemics or a “syndemic” of psychosocial problems may increase vulnerability to HIV acquisition/transmission by elevated sexual risk. To the best of our knowledge, there are no published studies examining this relationship longitudinally among MSW. This study examined how a syndemic of 6 psychosocial problems result in additive risk for condomless anal sex (CAS) with male clients among a multicity, longitudinal cohort of MSW.

Setting:
Community-based organization and health center in 2 Northeastern US cities.

Methods:
Between 2015 and 2017, 100 MSW from Boston, MA and Providence, RI completed behavioral/psychosocial surveys at baseline, 6 months, and 12months. Generalized estimating equation modeling was used to examine the prospective relationship of additive psychosocial problems and subsequent CAS with male clients, adjusting for age, site, race/ethnicity, MSW-type, and HIV serostatus.

Results:
Mean age = 34.7 (SD = 11.8); 62% racial/ethnic minority; and 20% HIV+. The prevalence of 6 psychosocial syndemic problems was substantial at baseline and remained high at each time point (all within the past 6 months): 74% problematic depressive symptoms, 27% polydrug use (3+ drugs, not including stimulants), 57% stimulant (methamphetamine/cocaine/crack) use, 44% hazardous drinking, 15% experienced client-specific physical/sexual violence, and 57% childhood sexual abuse. Looking at the number of psychosocial problems experienced, 7% had zero, 27% had 1, 24% had 2, 27% had 3, and 15% had 4 or more. We identified a statistically significant positive “dose-response” relationship between the number of psychosocial problems and CAS with male clients over time, with the greatest odds of engaging in CAS with a male client over follow-up among those with 4 or more psychosocial problems (adjusted odds ratio = 5.18, 95% CI: 1.61 to 16.62).

Conclusions:
Internet escorts and street-based MSW are likely to experience psychosocial problems and engaging in HIV sexual risk with male clients. The accumulation of psychosocial problems additively predicted CAS with male clients in a prospective cohort of MSW. The specification of psychosocial problems presents distinct treatment targets for HIV prevention among MSW in the United States.
Effect of Emotional Response on the Performance of a Simulated Laparoscopic Task
Authors: Yang Jin , Zheng Bin , Cai Xiujun , Wang Zhifei , Yu Hong , Cheng Yun , Yu Xiaojun 
Published: November 2020

Introduction
An emotional state impacts task performance and cognition. However, evidence of the effect of an induced emotional state on laparoscopic performance has not yet been documented. We investigated whether surgical residents in whom a positive emotion had been induced would produce a better laparoscopic task performance than residents in whom a negative emotional state had been induced.

Methods
This controlled laboratory study recruited a total of 53 junior surgical residents who were divided into 3 groups. Each group was required to watch 1 of 3 ten-minute videos designed to evoke a positive, neutral, or negative emotion before performing a laparoscopic cholecystectomy on a virtual simulation model. Task performances, as evaluated by a global assessment form and psychomotor metrics that included task time, errors, and path lengths, were compared between the 3 groups.

Results
Video watching induced different emotions, as measured by a Visual Analog Scale on feelings. The task time was significantly shorter in the positive (13.7 ± 2.5 minutes) than in the neutrally (17.7 ± 3.9 minutes) and the negatively (18.5 ± 3.8 minutes) induced-emotion groups (P < 0.001).
Participants in the positive emotion group completed a laparoscopic cholecystectomy with a significantly lower error rate (2 vs. 4 vs. 7, P = 0.036) and shorter right-handed path length (1089.6 ± 250.6 cm vs. 1287.2 ± 355.5 cm vs. 1410.3 ± 304.1 cm, P = 0.010) than the participants in the neutral and negative emotion groups.

Conclusions
A positive emotion can enhance a simulated laparoscopic task performance as assessed by task time and path length. The results indicate that we might improve surgical task performance by adjusting the surgeon's emotional state. We plan a future study that will continue to investigate whether positive emotions can facilitate skill learning.
Psychometric Validation of Central Venous Catheter Insertion Mastery Learning Checklist Data and Decisions
Authors: McGaghie William C. , Adams William H. , Cohen Elaine R. , Wayne Diane B. , Barsuk Jeffrey H. 
Published: November 2020

Introduction
Resident physicians are expected to acquire competence at central venous catheter (CVC) insertion to a mastery standard. Valid competence decisions about resident physicians' CVC performance rely on reliable data and rigorous achievement standards. This study used data from 3 CVC simulation-based mastery learning studies involving internal medicine (IM) and emergency medicine (EM) residents to address 2 questions: What is the effectiveness of a CVC mastery learning education intervention? Are minimum passing standards (MPSs) set by faculty supported by item response theory (IRT) analyses?

Methods
Pretraining and posttraining skills checklist data were drawn from 3 simulation-based mastery learning research reports about CVC internal jugular (IJ) and subclavian (SC) insertion skill acquisition. Residents were required to meet or exceed a posttest skills MPS. Generalized linear mixed effect models compared checklist performance from pre to postintervention. Minimum passing standards were determined by Angoff and Hofstee standard setting methods. Item response theory models were used for cut-score evaluation.

Results
Internal medicine and EM residents improved significantly on every IJ and SC checklist item after mastery learning. Item response theory analyses support the IJ and SC MPSs.

Conclusions
Mastery learning is an effective education intervention to achieve clinical skill acquisition among IM and EM residents. Item response theory analyses reveal desirable measurement properties for the MPSs previously set by expert faculty panels. Item response theory analysis is useful for evaluating standards for mastery learning interventions. The CVC mastery learning curriculum, reliable outcome data, and high achievement standards together contribute to reaching valid decisions about the competence of resident physicians to perform the clinical procedure.
Rapid Cycle Deliberate Practice Simulation Curriculum Improves Pediatric Trauma Performance
Authors: Yan Diana Hou , Slidell Mark B. , McQueen Alisa 
Published: November 2020

Introduction
Simulation-based medical education allows learners to refine and maintain clinical skills especially for high-stake situations such as trauma resuscitation. Despite the primary and secondary survey being its foundation, literature shows poor adherence with overall rates as low as 13%. This study evaluates the impact of rapid cycle deliberate practice (RCDP) on primary and secondary survey skill retention. We hypothesized that RCDP-trained surgery residents will have real-world clinical improvement in their survey completion in pediatric trauma resuscitations.

Methods
We developed an RCDP trauma resuscitation curriculum. Videos of trauma resuscitations before and after curriculum implementation were scored by 2 blinded reviewers using a modified Pediatric Trauma Assessment Scoring Tool. Actual trauma care by residents who had received the curriculum (study group) was compared with care provided by residents who had not received the curriculum (precurriculum historical control group and a concurrent control group who provided care without receiving the curriculum).

Results
One hundred eighty-eight videos were scored with 98 in study group, 33 in concurrent control group, and 57 in historical control group. There was a significant improvement in primary survey performance between study group and historical control group (P < 0.001), but no difference between study group and concurrent control group. There was a significant improvement between study group and 2 control groups in secondary survey performance (both P < 0.001).

Conclusions
The RCDP curriculum led to significant improvement in surgical residents' trauma survey performance and had clinical impact on actual patients, which is rare in pediatric trauma simulation literature.
A comparison of treatment regimens for autoimmune hemolytic anemia: A network meta-analysis protocol
Authors: Deng Jiawen 
Published: November 2020

ABSTRACTAutoimmune hemolytic anemia (AIHA) is a rare blood disorder that result in the hemolysis of red blood cells (RBCs) due to the presence of autoantibodies in the serum. There are a variety of treatment regimens available for AIHA, including glucocorticoids, monoclonal antibody rituximab and splenectomy. We propose a network meta-analysis that investigates whether the use of different regimens can decrease adverse events, increase remission rate and improve lab results, including hemoglobin, RBC, reticulocyte counts, hematocrit and total bilirubin.
Response to neoadjuvant chemoradiotherapy in rectal cancer is associated with RAS/AKT pathway dysregulation and high tumour mutational burden
Authors: Stockton Joanne D , Tee Louise , Whalley Celina , James Jonathan , Dilworth Mark , Wheat Rachel , Nieto Thomas , Geh Ian , Beggs Andrew D 
Published: November 2020

ABSTRACTPurposePathological complete response (pathCR) in rectal cancer, seen in examination of the pathological specimen post-surgery is the phenomenon whereby a tumour completely regresses under treatment with chemoradiotherapy. This is beneficial as up to 75% of patients do not experience regrowth of the primary tumour, allowing organ preservation and is poorly understood. We aimed to characterise the processes involved in pathCR.Materials & MethodsTwo groups of patients were identified with either complete response (pathCR group) or no response (poor response group) and biopsy and/or resection specimen blocks were retrieved. These underwent high read depth amplicon sequencing, exome sequencing, methylation arrays and immunohistochemistry for DNA repair pathway proteins. Sequencing data underwent analysis and the two cohorts were compared.ResultsSeven patients who underwent pathological complete response and twenty four who underwent poor response (to act as opposite “extreme phenotypes”) underwent molecular characterisation. Patients in the complete response group had significantly higher tumour mutational burden, neoantigen load and enrichments for mutations in the PI3K/AKT/mTOR signalling pathway as well as significantly lower numbers of structural variants. There were no differences in copy number variants or tumour heterogeneity. Methylation analysis demonstrated enrichment for changes in the PI3K/AKT/mTOR signalling pathway.ConclusionsThe phenomenon of pathCR in rectal cancer appears to be related to immunovisibility caused by a high tumour mutational burden phenotype. Resistance mechanisms seem to involve the PI3K/AKT/mTOR signalling pathway and tumour heterogeneity does not seem to play a role in resistance.
Estimating the risk on outbreak spreading of 2019-nCoV in China using transportation data
Authors: Yuan Hsiang-Yu , Hossain M. Pear , Tsegaye Mesfin , Zhu Xiaolin , Jia Pengfei , Junus Alvin , Wen Tzai-Hung , Pfeiffer Dirk 
Published: November 2020

AbstractA novel corona virus (2019-nCoV) was identified in Wuhan, China and has been causing an unprecedented outbreak in China. The spread of this novel virus can eventually become an international emergency. During the early outbreak phase in Wuhan, one of the most important public health tasks is to prevent the spread of the virus to other cities. Therefore, full-scale border control measures to prevent the spread of virus have been discussed in many nearby countries. At the same time, lockdown in Wuhan cityu (border control from leaving out) has been imposed. The challenge is that many people have traveled from Wuhan to other cities before the border control. Thus, it is difficult to forecast the number of imported cases at different cities and estimate their risk on outbreak emergence.Here, we have developed a mathematical framework incorporating city-to-city connections to calculate the number of imported cases of the novel virus from an outbreak source, and the cumulative number of secondary cases generated by the imported cases. We used this number to estimate the arrival time of outbreak emergence using air travel frequency data from Wuhan to other cities, collected from the International Air Transport Association database. In addition, a meta-population compartmental model was built based on a classical SIR approach to simulate outbreaks at different cities.We consider the scenarios under three basic reproductive number (R0) settings using the best knowledge of the current findings, from high (2.92), mild (1.68), to a much lower numbers (1.4). The mean arrival time of outbreak spreading has been determined. Under the high R0, the critical time is 17.9 days after December 31, 2019 for outbreak spreading. Under the low R0, the critical time is between day 26.2 to day 35 after December 31, 2019. To make an extra 30 days gain, under the low R0 (1.4), the control measures have to reduce 87% of the connections between the source and target cities. Under the higher R0 (2.92), the effect on reducing the chance of outbreak emergence is generally low until the border control measure was enhanced to reduce more than 95% of the connections.
Transfer learning applied to the forecast of mosquito-borne diseases
Authors: Coelho Flávio Codeço , de Holanda Nicolaus Linneu , Coimbra Beatriz 
Published: November 2020

AbstractHere we apply the concept of transfer learning to time series forecasting models for mosquito-borne diseases. Transfer learning, in this application, allows us to use knowledge obtained from modeling one disease to predict an emerging one for which extensive data is still not available. Here we discuss the performances of two families of models for predicting Chikungunya and Zika using models trained with dengue time series, in two Brazilian cities: Rio de Janeiro and Fortaleza.
IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs
Authors: Yu Fengchao , Haynes Sarah E. , Nesvizhskii Alexey I. 
Published: November 2020

AbstractMissing values weaken the power of label-free quantitative proteomic experiments to uncover true quantitative differences between biological samples or experimental conditions. Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem mass spectra in one run are transferred to another by inference based on m/z, charge state, retention time, and ion mobility when applicable. Though tolerances are used to ensure such transferred identifications are reasonably located and meet certain quality thresholds, little work has been done to evaluate the statistical confidence of MBR. Here, we present a mixture model-based approach to estimate the false discovery rate (FDR) of peptide and protein identification transfer, which we implement in the label-free quantification tool IonQuant. Using several benchmarking datasets generated on both Orbitrap and timsTOF mass spectrometers, we demonstrate superior performance of IonQuant with FDR-controlled MBR compared to MaxQuant (19-38 times faster; 6-18% more proteins quantified and with comparable or better accuracy). We further illustrate the performance of IonQuant, and highlight the need for FDR-controlled MBR, in two single-cell proteomics experiments, including one acquired with the help of high-field asymmetric ion mobility spectrometry (FAIMS) separation. Fully integrated in FragPipe computational environment, IonQuant with FDR-controlled MBR enables fast and accurate peptide and protein quantification in label-free proteomics experiments.
Strengthening the BioCompute Standard by Crowdsourcing on PrecisionFDA
Authors: Stephens Sarah H , King Charles Hadley , Watford Sean , Patel Janisha , Dean Dennis A. , Koc Soner , Xiao Nan , Donaldson Eric F. , Thompson Elaine E. , Purkayastha Anjan , Mazumder Raja , Johanson Elaine , Keeney Jonathon 
Published: November 2020

AbstractBackgroundThe field of bioinformatics has grown at such a rapid pace that a gap in standardization exists when reporting an analysis. In response, the BioCompute project was created to standardize the type and method of information communicated when describing a bioinformatic analysis. Once the project became established, its goals shifted to broadening awareness and usage of BioCompute, and soliciting feedback from a larger audience. To address these goals, the BioCompute project collaborated with precisionFDA on a crowdsourced challenge that ran from May 2019 to October 2019. This challenge had a beginner track where participants submitted BCOs based on a pipeline of their choosing, and an advanced track where participants submitted applications supporting the creation of a BCO and verification of BCO conformance to specifications.ResultsIn total, there were 28 submissions to the beginner track (including submissions from a bioinformatics master’s class at George Washington University) and three submissions to the advanced track. Three top performers were selected from the beginner track, while a single top performer was selected for the advanced track. In the beginner track, top performers differentiated themselves by submitting BCOs that included more than the minimally compliant content. Advanced track submissions were very impressive. They included a complete web application, a command line tool that produced a static result, and a dockerized container that automatically created the BCO as the tool was run. The ability to harmonize the correct function, a simple user experience, and the aesthetics of the tool interface differentiated the tools.ConclusionsDespite being new to the concept, most beginner track scores were high, indicating that most users understood the fundamental concepts of the BCO specification. Novice bioinformatics students were an ideal cohort for this Challenge because of their lack of familiarity with BioCompute, broad diversity of research interests, and motivation to submit high-quality work. This challenge was successful in introducing the BCO to a wider audience, obtaining feedback from that audience, and resulting in a tool novices may use for BCO creation and conformance. In addition, the BCO specification itself was improved based on feedback illustrating the utility of a “wisdom of the crowd” approach to standards development.
Synergistic Coding of Carbon Dioxide and a Human Sweat Odorant in the Mosquito Brain
Authors: Shankar Shruti , Tauxe Genevieve M. , Spikol Emma D. , Li Ming , Akbari Omar S. , Giraldo Diego , McMeniman Conor J. 
Published: November 2020

AbstractThe yellow fever mosquitoAedes aegyptiemploys olfaction to locate humans. We applied neural activity mapping to define the molecular and cellular logic of how the mosquito brain is wired to detect two human odorants that are attractive when blended together. We determined that the human breath volatile carbon dioxide (CO2) is detected by the largest unit of olfactory coding in the antennal lobe of the mosquito brain. Synergistically, CO2detection gates pre-synaptic calcium signaling in olfactory sensory neuron axon terminals that innervate unique antennal lobe regions tuned to the human sweat odorant L-(+)-lactic acid. We propose that simultaneous detection of the signature human volatiles CO2and L-(+)-lactic acid disinhibits a multimodal olfactory network for hunting humans in the mosquito brain.
Influence of nutritional status on eating habits and food choice determinants among Brazilian women during the COVID-19 pandemic
Authors: Mazzolani Bruna Caruso , Smaira Fabiana Infante , Esteves Gabriel Perri , Santo André Heloísa C. , Amarante Milla Cordeiro , Castanho Daniela , Campos Karen , Benatti Fabiana Braga , Jéssica Pinto Ana , Roschel Hamilton , Gualano Bruno , Ferreira Carolina Nicolleti 
Published: November 2020

ABSTRACTWe aimed to evaluate the influence of nutritional status on eating habits and food choice determinants among Brazilian women during the COVID-19 outbreak. This cross-sectional survey was conducted between June and September, 2020, period in which social distancing measures were in place. Participants (n=1,183) were classified as normal weight (60.4%), overweight (26.2%) and obese (13.4%). Eating habits changed during quarantine irrespective of nutritional status. The number of women participating in grocery shopping was reduced by 34% during quarantine (p<0.001, OR=0.55, 0.79), whereas participation in cooking and ordering delivery service increased by 28% (p=0.004, OR=1.08, 1.51) and 146% (p<0.001, OR=2.06, 2.95), respectively. The number of participants reporting the habit of snacking (p=0.005, OR=1.07, 1.43) and eating at the table increased by 24% and 40% (p<0.001, OR=1.20, 1.64). Interestingly, the number of participants reporting the habit of dieting decreased by 41% (p<0.001, OR=0.59 [0.50, 0.70]). During the quarantine, “liking”, “need and hunger”, and “habits” were the most commonly reported determinants of food choice overall. “Health”, “natural concerns” and “need and hunger” were less important determinants for participants with overweight/obesity compared to those with normal weight. Regression models showed that(i)“health”, “natural concerns” and “affect regulation”;(ii)“health”, “pleasure”, “convenience”, and “natural concerns”; and(iii)“visual appeal” and “pleasure” were the food choice determinants more associated with eating habits among women with normal weight, overweight and obesity, respectively. In conclusion, eating habits were influenced during the pandemic despite nutritional status, whereas food choice determinants differed between overweight/obesity and normal weight women.