bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the Thematic Nature of Microaggression among Racial and Ethnic Minority Surgeons
Authors: Appah-Sampong Abena , Zakrison Tanya , Vela Monica , Saunders Milda , Zhang Lindsey , Dorsey Chelsea 
Published: July 2022

BACKGROUND:
It is well documented that surgeons who identify as racial and ethnic minorities experience discrimination while navigating the surgical environment. There is evidence to suggest that the most prevalent form of discrimination experienced is microaggressions. This study sought to identify common microaggressions experienced in the surgical workplace by racial and ethnic minority surgeons with the use of a validated scale.

METHODS:
A one-time, deidentified survey was administered to surgeons who identified as a racial and ethnic minority via email. The survey included demographic questions and a shortened version of the Racial Microaggressions Scale, a validated 32-item scale developed to measure microaggressions in everyday life. Subscale means were calculated and compared using sample t-tests along with an analysis of variance.

RESULTS:
A total of 185 surgeons completed the survey with 166 included in the final analysis (97 male-identifying, 67 female-identifying). Significantly different microaggression experiences between race and ethnicity were found on the environmental (p < 0.001), foreigner/not belonging (p ≤ 0.001), low achieving/undesirable (p < 0.001), criminality (p < 0.001), and invisibility (p < 0.001) subscales with higher scores denoting more frequent experiences. Black and African American surgeons scored higher than Asian and Asian American and Hispanic and Latino surgeons on the low achieving/undesirable subscale (1.7 vs 0.9 and 1.2, respectively) and the invisibility subscale (1.5 vs 0.8 and 0.8, respectively). In addition, Asian and Asian American and Hispanic and Latino surgeons scored significantly higher on the foreigner/not belonging subscale compared with Black and African American surgeons (1.6 and 1.6 vs 0.9, respectively).

CONCLUSIONS:
The current study suggests that surgeons who identified as a racial and ethnic minority experience microaggressions in various ways. Understanding the specific experience of racial and ethnic minority surgeons is important as the surgical workplace strives to create more inclusive environments by acknowledging the lived experience of its diverse workforce.
Upregulation of Activation Induced Cell Markers (AIM) among Severe COVID-19 patients in Bangladesh
Authors: Bhuiyan Taufiqur Rahman , Banna Hasan Al , Kaisar M Hasanul , Karmakar Polash Chandra , Hakim Al , Akter Afroza , Ahmed Tasnuva , Tauheed Imam , Islam Shaumik , Hasnat Mohammad Abul , Sumon Mostafa Aziz , Rashed Asif , Ghosh Shuvro , Clemens John D , Banu Sayera , Shirin Tahmina , Weiskopf Daniela , Sette Alessandro , Chowdhury Fahima , Qadri Firdausi 
Published: July 2022

ABSTRACTCOVID-19 caused by SARS-CoV-2 can develop the disease with different degree of clinical severity including fatality. In addition to antibody responses the antigen specific T cells may play a critical role in defining this protective immune response against this virus. As a part of a longitudinal cohort study in Bangladesh to investigate B and T cell specific immune responses, we sought to evaluate the activation induced cell marker (AIM) and the status of different immune cell subsets during infection. A total of 115 participants were analyzed in this study which included participants with asymptomatic, mild, moderate and severe clinical symptoms. In addition, healthy controls (19 in each group) were analysed. Specimens from participants collected during the pre-pandemic period were also analyzed (n=10). Follow-up visits were conducted on day 7, 14, and 28 for all the cases since the enrollment (day 1). In this study 10 participants among the moderate and severe cases expired during the course of follow up. We observed a decrease in mucosa associated invariant T (MAIT) cell frequency on the initial days (day 1 and day 7) in comparison to later days of the COVID-19 infection. However, natural killer (NK) cells were found to be elevated in symptomatic patients just after the onset of disease compared to both asymptomatic patients and healthy individuals. Moreover, we found AIM+ (both OX40+ CD137+ and OX40+ CD40L+) CD4+ T cells to show significant increase in moderate and severe COVID-19 patients in response to SARS-CoV-2 peptides (specially spike peptide) compared to prepandemic controls, who are unexposed to SARS-CoV-2. Notably, we did not observe any significant difference in the CD8+ AIM markers (CD137+ CD69+), which indicates the exhaustion of CD8+ T cells during COVID-19 infection. These findings suggest that the patients who recovered from moderate and severe COVID-19 were able to mount a strong CD4+ T cell response against shared viral determinants that ultimately induced the T cells to mount further immune responses to SARS-CoV-2.
Effect of Vitamin D3 supplementation vs. dietary-hygienic measures on SARS-COV-2 infection rates in hospital workers with 25-hydroxyvitamin D3 [25(OH)D3] levels ≥20 ng/mL
Authors: Romero-Ibarguengoitia Maria Elena , Gutiérrez-González Dalia , Cantú-López Carlos , Sanz-Sánchez Miguel Angel , González-Cantú Arnulfo 
Published: July 2022

AbstractBackgroundThere is scant information on the effect of supplementation with vitamin D3 in SARS-COV-2 infection cases when patient 25-hydroxyvitamin D3 [25(OH)D3] levels are between 20-100ng/mL. Our aim was to evaluate the effect of supplementation with vitamin D3 vs. dietary-hygienic measures on the SARS-COV-2 infection rate in participants with serum 25(OH)D3 levels ≥20ng/mL.MethodsWe invited hospital workers with 25(OH)D3 levels between 20-100 ng/mL and no previous SARS-COV-2 infection; they were randomized as follows: treatment options were a) vitamin D3 supplementation (52,000 IU monthly, G1) or b) dietary-hygienic measures (G2). We conducted a 3- to 6-month follow-up of SARS-COV-2 infections. Participants with 25(OH)D3 levels <20 ng/mL were also analyzed. We divided these latter participants depending on whether they were supplemented (G3) or not (G4).ResultsWe analyzed 198 participants, with an average age of 44.4 (SD 9) years, and 130 (65.7%) were women. G1 had less cases of SARS-COV-2 infection than G2 after a follow-up of 3- to 6-months (p<0.05). There were no differences between G3 and G4 at the 3- and 6-month follow-up cutoff points (p>0.05). Using mixed effect Cox regression analysis in 164 participants that completed six months of follow-up, vitamin D3 supplementation appeared to act as a protective factor against SARS-COV-2 infection (HR 0.21, p=0.008) in G1 and G2. None of the participants treated with the supplementation doses had serum 25(OH)D3 levels > 100ng/mL.ConclusionVitamin D3 supplementation in participants with 25(OH)D3 levels between 20-100 ng/mL have a lower rate of SARS-COV-2 infection in comparison with the use of dietary-hygienic measures at six months follow-up.
Health care utilization of fine-scale identity by descent clusters in a Los Angeles biobank
Authors: Caggiano Christa , Boudaie Arya , Shemirani Ruhollah , Petter Ella , Chiu Alec , Johnson Ruth , Ercelen Defne , Pasaniuc Bogdan , Kenny Eimear , Shortt Jonathan , Gignoux Chris , Balliu Brunilda , Arboleda Valerie , Belbin Gillian , Zaitlen Noah 
Published: July 2022

1AbstractAn individual’s disease risk is affected by the populations that they belong to, due to shared genetics and shared environment. The study of fine-scale populations in clinical care will be important for reducing health disparities and for developing personalized treatments. In this work, we developed a novel health monitoring system, which leverages biobank data and electronic medical records from over 40,000 UCLA patients. Using identity by descent (IBD), we analyzed one type of fine-scale population, an IBD cluster. In total, we identified 376 IBD clusters, including clusters characterized by the presence of many significantly understudied communities, such as Lebanese Christians, Iranian Jews, Armenians, and Gujaratis. Our analyses identified thousands of novel associations between IBD clusters and clinical diagnoses, physician offices, utilization of specific medical specialties, pathogenic allele frequencies, and changes in diagnosis frequency over time. To enhance the impact of the research and engage the broader community, we provide a web portal to query our results:www.ibd.la
Platinum vs non-platinum chemotherapy for platinum-resistant ovarian cancer: a systematic review and meta-analysis
Authors: Rumyantsev Alexey , Tyulyandina Alexandra , Fedyanin Mikhail , Pokataev Ilya , Glazkova Elena , Tjulandin Sergey 
Published: July 2022

AbstractBackgroundrecurrent ovarian cancer (OC) patients with platinum-free interval (PFI) <6 mo. are usually considered platinum-resistant and treated with non-platinum based chemotherapy. However, this was never confirmed in proper-conducted randomized trials.Methodswe queried the PubMed database for all full-text articles and abstracts on the treatment of patients with platinum-resistant ovarian cancer (PROC) in 01/01/2000-01/06/2019 timeframe. The PRISMA tool was used to ensure transparent reporting of the results. Inclusion criteria were: 1) morphologically confirmed epithelial ovarian cancer; 2) recurrent disease within 6 months after completion of platinum-based chemotherapy; 3) treatment with platinum- or non-platinum chemotherapy with agents that are routinely used for OC; 4) no concomitant therapy with targeted or investigational agents or non-platinum doublets; 5) defined response rate (RR) and assessment criteria. Proportion meta-analysis (random-effect model) and beta-regression were conducted to assess the impact of platinum agents on response rate as well as significance of other variables. In the beta-regression model response rate was a dependent variable, while platinum agents (yes or no), used non-platinum drugs and method of response assessment were independent variables. Statistical analysis was dose with meta, metafor and betareg packages of R software.Resultswe identified 7156 articles and screened them for title and abstract, 157 studies for further analysis. Overall, 6327 patients were included in the analysis, efficacy of non-platinum- and platinum-based therapy was assessed in 113 (n = 5272) and 44 (n = 1055) trials respectively. In meta-proportion random-effect model RR among patients treated with platinum-based and non-platinum chemotherapy RR was 36% (95% CI 30-41; I2 = 62%) and 16% (95% CI 14-19; I2=70%) respectively. For sensitivity analysis various regression models were made with different subsets of the trials and additional variables (including year of the trial, percentage of serous subtype of OC and median of prior therapy lines). Platinum was the strongest predictor of response in every developed model.Conclusionthis meta-analysis shows that patients with ‘platinum-resistant’ ovarian carcinoma may derive significant benefit from reintroduction of platinum agents. These results support recent ESMO-ESGO consensus on treatment of recurrent ovarian cancer.
Evolutionary innovation through transcription factor promiscuity in microbes is constrained by pre-existing gene regulatory network architecture
Authors: Shepherd Matthew J. , Pierce Aidan P. , Taylor Tiffany B. 
Published: July 2022

AbstractThe survival of a population during environmental shifts depends on whether the rate of phenotypic adaptation keeps up with the rate of changing conditions. A common way to achieve this is via change to gene regulatory network (GRN) connections – known as rewiring – that facilitate novel interactions and innovation of transcription factors. To understand the success of rapidly adapting organisms, we therefore need to determine the rules that create and constrain opportunities for GRN rewiring.Here, using an experimental microbial model system we reveal a hierarchy among transcription factors that are rewired to rescue lost function, with alternative rewiring pathways only unmasked after the preferred pathway is eliminated. We identify three key properties - high activation, high expression, and pre-existing low-level affinity for novel target genes – that facilitate transcription factor innovation via gain of functional promiscuity. Ease of acquiring these properties is constrained by pre- existing GRN architecture, which was overcome in our experimental system by both targeted and global network alterations. This work reveals the key properties that determine transcription factor evolvability, and as such, the evolution of GRNs.
Microstructural and crystallographic evolution of palaeognath (Aves) eggshells
Authors: Choi Seung , Hauber Mark E , Legendre Lucas J , Kim Noe-Heon , Lee Yuong-Nam , Varricchio David J 
Published: July 2022

AbstractThe avian palaeognath phylogeny has been recently revised significantly due to the advancement of genome-wide comparative analyses and provides the opportunity to trace the evolution of the microstructure and crystallography of modern dinosaur eggshells. Here, eggshells of all major clades of Palaeognathae (including extinct taxa) and selected eggshells of Neognathae and non-avian dinosaurs are analysed with electron backscatter diffraction. Our results show the detailed microstructures and crystallographies of (previously) loosely categorized ostrich-, rhea-, and tinamou-style morphotypes of palaeognath eggshells. All rhea-style eggshell appears homologous, while respective ostrich-style and tinamou-style morphotypes are best interpreted as homoplastic morphologies (independently acquired). Ancestral state reconstruction and parsimony analysis additionally show that rhea-style eggshell represents the ancestral state of palaeognath eggshells both in microstructure and crystallography. The ornithological and palaeontological implications of the current study are not only helpful for the understanding of evolution of modern and extinct dinosaur eggshells, but also aid other disciplines where palaeognath eggshells provide useful archive for comparative contrasts (e.g. palaeoenvironmental reconstructions, geochronology, and zooarchaeology).
Improved detection of genetic effects on promoter usage with augmented transcript annotations
Authors: Vija Andreas , Alasoo Kaur 
Published: July 2022

AbstractDisease-associated non-coding variants can modulate their target genes by disrupting multiple mechanisms, including regulating total gene expression level, splicing, alternative polyadenylation or promoter usage. Quantifying promoter usage from standard RNA sequencing data is challenging due to incomplete reference transcriptome annotations and low read coverage observed at the ends of transcripts. We previously developed the txrevise tool (https://github.com/kauralasoo/txrevise) to quantify promoter usage events from RNA-seq data using reference transcriptome annotations. Here, we augment the txrevise promoter event annotations with experimentally identified Cap Analysis of Gene Expression (CAGE) promoters from the FANTOM5 project. Applying the new annotations to RNA-seq data from 358 individuals, we found that augmented promoter event annotations increased the power to detect promoter usage quantitative trait loci (puQTLs) by ~30%. However, concordance between puQTLs inferred from RNA-seq data and those directly measured using CAGE remained low, suggesting that additional experimental and computational improvements are needed to capture the full range of regulatory effects of non-coding variants.
Neonatal hyperoxia induces sex-dependent pulmonary cellular and transcriptomic changes in an experimental mouse model of bronchopulmonary dysplasia
Authors: Xia Sheng , Vila Ellis Lisandra , Winkley Konner , Menden Heather , Mabry Sherry M. , Louiselle Daniel , Gibson Margaret , Grundberg Elin , Chen Jichao , Sampath Venkatesh 
Published: July 2022

ABSTRACTHyperoxia (HOX) disrupts lung development in mice and causes bronchopulmonary dysplasia (BPD) in neonates. To investigate sex-dependent molecular and cellular programming involved in HOX, we surveyed the mouse lung using single cell RNA sequencing (scRNA-seq), and validated our findings in human neonatal lung cells in vitro. HOX-induced inflammation in alveolar type (AT) 2 cells gave rise to damage associated transient progenitors (DATP). It also induced a new subpopulation of AT1 cells with reduced expression of growth factors normally secreted by AT1 cells, but increased mitochondrial gene expression. Female alveolar epithelial cells had less EMT and pulmonary fibrosis signaling in HOX. In the endothelium, expansion of Car4+ EC (Cap2) was seen in HOX along with an emergent subpopulation of Cap2 with repressed VEGF signaling. This regenerative response was increased in females exposed to HOX. Mesenchymal cells had inflammatory signatures in HOX, with a new distal interstitial fibroblast subcluster characterized by repressed lipid biosynthesis and a transcriptomic signature resembling myofibroblasts. HOX-induced gene expression signatures in human neonatal fibroblasts and alveolar epithelial cells in vitro resembled mouse scRNA-seq data. These findings suggest that neonatal exposure to HOX programs distinct sex-specific stem cell progenitor and cellular reparative responses that underpin lung remodeling in BPD.
Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean
Authors: Bandillo Nonoy B. , Jarquin Diego , Posadas Luis G. , Lorenz Aaron J. , Graef George L. 
Published: July 2022

AbstractIncreasing the rate of genetic gain for seed yield remains the primary breeding objective in both public and private soybean breeding programs. Genomic selection (GS) has the potential to accelerate the rate of genetic gain for soybean seed yield. To date, limited studies have empirically validated accuracy of GS and compared to phenotypic selection (PS), and none has been done for soybean breeding. This study conducted the first empirical validation of GS for increasing seed yield using over 1,500 lines and over 7 years (2010-2016) of replicated experiments in the University of Nebraska soybean breeding program. The study was designed to capture the varying genetic relatedness of the training population to three validation sets: two large bi-parental populations (TBP-1 and TBP-2), and a large validation set comprised of 457 pre-selected advanced lines derived from 45 bi-parental populations in the variety development program (TMP). We found that prediction accuracy (0.54) from our validation experiments was competitive with what we obtained from a series of cross-validation experiments (0.64). Both GS and PS were more effective for increasing population mean performance with similar realized gain but significantly greater than random selection (RS). We found a selection advantage of GS over PS where higher genetic gain and identification of top-performing lines was maximized at higher selection stringency from 10 to 20% selected proportion. GS led to at least 2% increase in the mean genetic similarity vs. PS and RS, potentially causing a minimal loss of genetic diversity. We showed that loss of genetic variance in the GS set was presumably due to a significant shift on allelic frequencies towards the extremes. Across all loci, an average increase of 0.04 in allelic frequency in the GS set was observed after selection, which is about 5% higher than the base population when no selection was made. Overall, we demonstrate that GS performed as effectively as PS, and the implementation of GS in a public soybean breeding program should be warranted mainly for reducing breeding cycle time and lowering cost per unit gain.
Comparison of Very Short Answer Questions and Multiple Choice Questions in Medical Students: Reliability, Discrimination, Acceptability and Effect on Knowledge Retention
Authors: Janse Roemer J. , van Wijk Elise V. , Ruijter Bastian N. , Rohling Jos H.T. , van der Kraan Jolein , Crobach Stijn , de Jonge Mario , de Beaufort Arnout Jan , Dekker Friedo W. , Langers Alexandra M.J. 
Published: July 2022

AbstractIntroductionMultiple choice questions (MCQs) offer high reliability and easy machine-marking, but allow for cueing and stimulate recognition-based learning. Very short answer questions (VSAQs) may circumvent these limitations. We investigated VSAQ reliability, discriminative capability, acceptability, and knowledge retention compared to MCQs.MethodsDutch undergraduate medical students (n=375) were randomised to a formative exam with VSAQs first and MCQs second or vice versa in two courses, to determine reliability and discrimination. Next, acceptability (i.e., VSAQ review time) was determined in the summative exam. Knowledge retention at 2 and 5 months was determined by comparing score increase on the three-monthly progress test (PT) between students tested with VSAQs and students from previous years tested without VSAQs.ResultsReliability (Cronbach’s α) was 0.74 for VSAQs and 0.57 for MCQs in one course. In the other course, Cronbach’s α was 0.87 for VSAQs and 0.83 for MCQs. Discrimination (Rir) was 0.27 vs. 0.17 and 0.43 vs. 0.39 for VSAQs vs. MCQs, respectively. Reviewing time of one VSAQ for the entire student cohort was ±2 minutes on average. No clear effect on knowledge retention after 2 and 5 months was observed.DiscussionWe found increased reliability and discrimination of VSAQs compared to MCQs. Reviewing time of VSAQs was acceptable. The association with knowledge retention was unclear in our study. This study supports and extends positive results of previous studies on VSAQs regarding reliability, discriminative capability, and acceptability in Dutch undergraduate medical students.
RAFTS: A graphical tool to guide Flux Simulator transcriptome simulation for method development in de novo transcriptome assembly from short reads
Authors: Doering Matthew , Stout Jake M. 
Published: July 2022

AbstractDue to complexity of RNA transcripts expressed in any given cell or tissue, the assembly of de novo transcriptomes still represents a computational challenge when compared to genome assemblies. A number of modern transcriptome assembly algorithms have been developed to meet this challenge, and each of them have their own strengths and weaknesses dependent on the transcript abundance and complexity of the biological sample that is sequenced. As such, we are seeking to develop a transcriptome assembly pipeline in which multiple transcriptomes are generated, merged, and then redundancies are filtered out to produce a final transcriptome that should contain full length sequences of all transcripts. However, it is almost impossible to evaluate the efficacies of such novel assembly pipelines using short read sequencing data derived from biological samples due to not knowing a priori the transcript abundance and complexity. Thus, to test our pipelines we developed RAFTS. This tool is used to generate simulated short read sequencing datasets using annotated genomic data from model species.