bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are Video Recordings Reliable for Assessing Surgical Performance? A Prospective Reliability Study Using Generalizability Theory
Authors: Frithioff Andreas , Frendø Martin , Foghsgaard Søren , Sørensen Mads Sølvsten , Andersen Steven Arild Wuyts 
Published: October 2022

Introduction
Reliability is pivotal in surgical skills assessment. Video-based assessment can be used for objective assessment without physical presence of assessors. However, its reliability for surgical assessments remains largely unexplored. In this study, we evaluated the reliability of video-based versus physical assessments of novices' surgical performances on human cadavers and 3D-printed models—an emerging simulation modality.

Methods
Eighteen otorhinolaryngology residents performed 2 to 3 mastoidectomies on a 3D-printed model and 1 procedure on a human cadaver. Performances were rated by 3 experts evaluating the final surgical result using a well-known assessment tool. Performances were rated both hands-on/physically and by video recordings. Interrater reliability and intrarater reliability were explored using κ statistics and the optimal number of raters and performances required in either assessment modality was determined using generalizability theory.

Results
Interrater reliability was moderate with a mean κ score of 0.58 (range 0.53–0.62) for video-based assessment and 0.60 (range, 0.55–0.69) for physical assessment. Video-based and physical assessments were equally reliable (G coefficient 0.85 vs. 0.80 for 3D-printed models and 0.86 vs 0.87 for cadaver dissections). The interaction between rater and assessment modality contributed to 8.1% to 9.1% of the estimated variance. For the 3D-printed models, 2 raters evaluating 2 video-recorded performances or 3 raters physically assessing 2 performances yielded sufficient reliability for high-stakes assessment (G coefficient >0.8).

Conclusions
Video-based and physical assessments were equally reliable. Some raters were affected by changing from physical to video-based assessment; consequently, assessment should be either physical or video based, not a combination.
Older Women with lower lean mass values have hypermethylated sites in the PI3K-Akt pathway
Authors: Correia Igor Massari , da Silva Rodrigues Guilherme , Noronha Natália Yumi , de Almeida Mariana Luciano , da Silva Sobrinho Andressa Crystine , Nonino Carla Barbosa , Júnior Carlos Roberto Bueno 
Published: October 2022

ABSTRACTThe increase in lean mass is directly related to the loss of independence, muscle strength, and worse quality of life over the years. Studies in epigenetics can provide accurate answers about lean mass, demonstrating changes in DNA methylation patterns and possible changes in gene expression. The objective of this study was to verify whether there is a difference in the methylation profile among Brazilian women aged 50 to 70 years with greater or lesser lean mass. A cross-sectional study comprised 22 women aged 50 to 70 years, with 2 groups of 11 participants (Low Lean Mass and More Lean Mass). Lean mass was measured by dualenergy X-ray emission densitometry (DEXA). Blood DNA was collected for methylation assays using the Illumina 850k EPIC Infinium Methylation BeadChip, analyzing data from the Bioconductor chAMP data package medium in RStudio software. We obtained 1,913 differentially methylated (p ≤ 0.005 of delta β > 5% and delta β < −5 %) with a total of 979 genes with different methylation sites between groups (p ≤ 0.005; −5% > delta β > 5%). In addition, the pathway with the greatest power of significance was PI3K-Akt, presenting an FDR of 4.6 x 10-3. Thus, our results demonstrate a differentiation between specific sites of different genes, which have essential functions in body composition and energy metabolism, supporting future studies that aim to relate lean mass with epigenetics.
Natural Variation inBrachypodium distachyonResponses to Combined Abiotic Stresses
Authors: Ludwig Ella , Polydore Seth , Berry Jeffrey , Sumner Joshua , Ficor Tracy , Agnew Erica , Haines Kristina , Greenham Kathleen , Fahlgren Noah , Mockler Todd C. , Gehan Malia A. 
Published: October 2022

AbstractThe growing world population increases demand for agricultural production, which is more challenging as climate change increases global temperature and causes more extreme weather events. High-throughput phenotyping tools can be used to measure plant responses to the environment to identify genomic regions associated with response to stress. This study examines the phenotypic variation of 149 accessions ofBrachypodium distachyonunder drought, heat, and the combination of both stresses. Heat alone causes the largest amounts of tissue damage and the combination of heat and drought causes the largest decrease in plant biomass compared to other treatments. Notably, Bd21-0, the reference line forB. distachyon, was identified as not having very robust growth under stress conditions, especially in the heat-drought combined treatment. Climate data from the collection locations of these accessions (climate of origin) was used to assess whether climate of origin was correlated with responses to stresses and it was found to be significantly associated with height and percent of plant tissue damage. Additionally, genome wide association mapping found a number of genetic loci associated with changes in plant height, biomass, and the amount of damaged tissue under stress. Some SNPs found to be significantly associated with a response to heat or drought are also significantly associated in the combination of stresses, while others are not, and some significantly associated SNPs were only identified in the combined stress treatment. This, combined with the phenotypic data, indicates that the effects of these abiotic stresses are not simply additive, and the responses ofB. distachyonto the combined stresses differ from drought and heat alone. Significant SNPs were closely located to genes known to be involved in plant responses to abiotic stresses.
Targeting the BAG-1 family of co-chaperones in lethal prostate cancer
Authors: Neeb Antje , Figueiredo Ines , Bogdan Denisa , Cato Laura , Stober Jutta , Jimenez-Vacas Juan M. , Gourain Victor , Lee Irene I. , Seeger Rebecca , Muhle-Goll Claudia , Gurel Bora , Welti Jonathan , Rodrigues Daniel Nava , Rekowski Jan , Qiu Xintao , Jiang Yija , Di Micco Patrizio , Mateos Borja , Bielskutė Stasė , Riisnaes Ruth , Ferreira Ana , Miranda Susana , Crespo Mateus , Buroni Lorenzo , Ning Jian , Bräse Stefan , Jung Nicole , Gräßle Simone , Metzger Daniel , Swain Amanda , Salvatella Xavier , Plymate Stephen R. , Al-Lazikani Bissan , Long Henry , Yuan Wei , Brown Myles , Cato Andrew C. B. , de Bono Johann S. , Sharp Adam 
Published: October 2022

AbstractTherapies that abrogate persistent androgen receptor (AR) signaling in castration resistant prostate cancer (CRPC) remain an unmet clinical need. The N-terminal domain (NTD) of the AR drives transcriptional activity in CRPC but is intrinsically disordered and remains a challenging therapeutic target. Therefore, inhibiting critical co-chaperones, such as BAG-1L, is an attractive alternative strategy. We performed druggability analyses demonstrating the BAG domain to be a challenging drug target. Thio-2, a tool compound, has been reported to bind the BAG domain of BAG-1L and inhibit BAG-1L-mediated AR transactivation. However, despite these data, the mechanism of action of Thio-2 is poorly understood and the BAG domain which is present in all BAG-1 isoforms has not been validated as a therapeutic target. Herein, we demonstrate growth inhibiting activity of Thio-2 in CRPC cell lines and patient derived models with decreased AR genomic binding and AR signaling independent of BAG-1 isoform function. Furthermore, genomic abrogation of BAG-1 isoforms did not recapitulate the described Thio-2 phenotype, and NMR studies suggest that Thio-2 may bind the AR NTD, uncovering a potential alternative mechanism of action, although in the context of low compound solubility. Furthermore, BAG-1 isoform knockout mice are viable and fertile, in contrast to previous studies, and when crossed with prostate cancer mouse models, BAG-1 deletion does not significantly impact prostate cancer development and growth. Overall, these data demonstrate that Thio-2 inhibits AR signaling and growth in CRPC independent of BAG-1 isoforms, and unlike previous studies of the activated AR, therapeutic targeting of the BAG domain requires further validation before being considered a therapeutic strategy for the treatment of CRPC.
PSC niche develops into immune-responsive blood cells capable of transdifferentiating into lamellocytes inDrosophila
Authors: Hirschhäuser Alexander , Molitor Darius , Salinas Gabriela , Großhans Jörg , Rust Katja , Bogdan Sven 
Published: October 2022

AbstractDrosophilablood cells called hemocytes form an efficient barrier against infections and tissue damage. During metamorphosis, hemocytes undergo tremendous changes in their shape and behavior preparing them for tissue clearance. Yet, the diversity and functional plasticity of pupal blood cells have not been explored. Here, we combine single-cell transcriptomics and high-resolution microscopy to dissect the heterogeneity and plasticity of pupal hemocytes. We identified precursor and effector hemocytes with distinct molecular signatures and cellular functions clearly distinct from other stages of hematopoiesis. Strikingly, we identified that PSC cells, which function as lymph gland niche, are highly migratory and immune responsive cells in the pupa. PSC cells can transdifferentiate to lamellocytes triggered by wasp infection. Altogether, our data highlight a remarkable cell heterogeneity, and identifies a cell population that acts not only as a stem cell niche in larval hematopoiesis, but functions as cell reservoir to pupal and adult blood cells.
AVaccinia-based system for directed evolution of GPCRs in mammalian cells
Authors: Klenk Christoph , Scrivens Maria , Niederer Anina , Shi Shuying , Mueller Loretta , Gersz Elaine , Zauderer Maurice , Smith Ernest , Strohner Ralf , Plückthun Andreas 
Published: October 2022

AbstractLow stability and poor expression levels are inherent in many G protein-coupled receptors, hindering structural and biophysical analyses. Directed evolution in bacterial or yeast display systems has been successfully used to overcome both limitations in some cases. Yet, some receptors cannot be tackled in microbial systems, due to their complex molecular composition or due to unfavorable ligand properties. Here, we report an approach to evolve G protein-coupled receptors in mammalian cells. To achieve clonality of individual mutants, and a rather uniform gene copy number, both prerequisites for strict genotype-phenotype linkage in mammalian cells, we developed a highly efficient viral transduction system based onVacciniavirus. Using rational design of synthetic DNA libraries, we first evolved neurotensin receptor 1 for high stability and expression, reaching levels similar or higher to what has been achieved in bacterial systems. Second, using parathyroid hormone 1 receptor we demonstrate that also receptors with complex molecular architectures and large ligands can be readily evolved in mammalian cells. Furthermore, in our system, the physiological signaling environment in mammalian cells can be employed to evolve functional receptor properties. We obtained fully functional receptor variants exhibiting increased allosteric coupling between the ligand binding site and the G protein interface, resulting in higher signaling efficacy. Thus, our approach provides new means to readily improve the biophysical properties of receptors in a mammalian cellular environment. Moreover, it opens the possibility to modulate receptor signaling and to gain further insights into the intricate molecular interplay required for GPCR activation.
Borrelia burgdorferiDnaA and the nucleoid-associated protein EbfC coordinate expression of thednaX-ebfCoperon
Authors: Krusenstjerna Andrew C. , Arnold William K. , Saylor Timothy C. , Tucker Jamila S. , Stevenson Brian 
Published: October 2022

ABSTRACTBorrelia burgdorferi, the spirochete agent of Lyme disease, has evolved within a consistent infectious cycle between tick and vertebrate hosts. The transmission of the pathogen from tick to vertebrate is characterized by rapid replication and a change in the outer surface protein profile. EbfC, a highly conserved nucleoid-associated protein, binds throughout the borrelial genome affecting expression of many genes, including the Erp outer surface proteins. InB. burgdorferi, like many other bacterial species,ebfCis co-transcribed withdnaX, an essential component of the DNA polymerase III holoenzyme, which facilitates chromosomal replication. The expression of thednaX-ebfCoperon is tied to the spirochete’s replication rate, but the underlying mechanism for this connection was unknown. In this work, we provide evidence that the expression ofdnaX-ebfCis controlled by direct interactions of DnaA, the chromosomal replication initiator, and EbfC at the unusually longdnaX-ebfC5’ UTR region. Both proteins bind to the 5’ UTR DNA, with EbfC also binding to the RNA. The DNA binding of DnaA to this region was similarly impacted by ATP/ADP.In vitrostudies characterized DnaA as an activator ofdnaX-ebfCand EbfC as an anti-activator. We further found evidence that DnaA may regulate other genes essential for replication.IMPORTANCEThe dual-life cycle ofBorrelia burgdorferi, the causative agent of Lyme disease, is characterized by periods of rapid and slowed replication. The expression patterns of many of the spirochete’s virulence factors are impacted by these changes in replication rates. The connection between replication and virulence can be understood at thednaX-ebfCoperon. DnaX is a component of the DNA polymerase III holoenzyme that facilitates replication. EbfC is a nucleoid-associated protein that regulates the infection-associated outer surface Erp proteins, as well as other transcripts. The expression ofdnaX-ebfCis tied to replication rate, which we demonstrate is mediated by DnaA, the master chromosomal initiator protein and transcription factor, and EbfC.
Genomic characterization and molecular evolution of human Monkeypox viruses
Authors: Gröhs Ferrareze Patrícia Aline , Alves Pereira e Costa Rute , Thompson Claudia Elizabeth 
Published: October 2022

ABSTRACTMonkeypox virus is a member of the Poxviridae family, as variola and vaccinia viruses, presenting a linear double-strand DNA genome approximately ≈197 kb long, which encodes ≈190 non overlapping ORFs. Genomic comparison of Central and West African clades shows the presence of unique genes that promote different disease presentations according to the strain. Since the last smallpox vaccination efforts ended in the mid-1980s, nowadays, there is concern about the recent spread of human monkeypox disease around the world. Currently, almost 70,000 human monkeypox cases are diagnosed in the world, of which more than 7,800 are from Brazil. This study aims to evaluate genomic epidemiology and molecular evolution of hMpxV genomes. Using computational biology to analyze 604 hMpxV genomes from 1960 up to 2022, it was possible to observe synteny breaks and gene conservation between Central and West clade genomes, with the presence of strains associated with the 2022 outbreak assigned to West African clade. Evidence of diversifying selective pressure on specific sites from protein coding sequences acting on immunomodulatory processes was identified. The existence of different sites under diversifying - and purifying - selection in paralog genes denotes adaptation mechanisms underlying the host-pathogen interaction of Monkeypox virus in human species.HIGHLIGHTSSynteny breaks were identified among West and Central African genomes with sequence identity of 96.5%Positive selection evidence was found on sites from genes of immunomodulatory functionsDifferent sites under diversifying and purifying selection were observed in paralog genesGenomes from the 2022 outbreak are phylogenetically assigned to the West African clade
The faculty-to-faculty mentorship experience: a survey on challenges and recommendations for improvements
Authors: Sarabipour Sarvenaz , Niemi Natalie M , Burgess Steven J , Smith Christopher T , Bisson Filho Alexandre W , Ibrahim Ahmed , Clark Kelly 
Published: October 2022

AbstractFaculty at research institutions play a central role in advancing knowledge and careers, as well as promoting the well-being of students and colleagues in research environments. Faculty members must balance a host of activities - such as performing research, teaching, sourcing funds, administrative and service duties - with their roles as educators and mentors. Mentorship from experienced peers has been touted as critical for enabling these myriad roles to allow faculty development, career progression, and satisfaction. However, there is little information available on who supports faculty and best ways to structure a faculty mentorship program for early- and mid-career academics. Furthermore, the extent to which mentorship and mentoring programs have been offered to faculty members has not been widely characterized. It is also unclear what challenges faculty receiving mentorship may face and which aspects could be further improved. In the interest of advocating for increased and enhanced faculty mentoring and mentoring programs, we surveyed faculty (i.e., group leaders) around the world to gather data on whether and how they receive mentoring from peers, senior researchers, informal mentoring programs, or formal mentoring programs at their institutions. We received responses from 457 early- and mid-career faculty and found that a substantial portion of respondents either reported having no mentor or a lack of a formal mentoring scheme. Qualitative responses on the quality of mentorship revealed that the most common complaints regarding mentorship included lack of mentor availability, unsatisfactory commitment to mentorship, and non-specific or non-actionable advice. Our findings further identified key mentorship elements desired by faculty mentees. Based on these suggestions, we identify a need for training for faculty mentors as well as strategies for individual mentors, departments, and institutions for funding and design of more intentional and supportive mentorship programs for early- and mid-career faculty.
Transcriptional control ofhgcABby an ArsR-like regulator inPseudodesulfovibrio mercuriiND132
Authors: Gionfriddo Caitlin M. , Soren Ally Bullock , Wymore Ann , Hartnett D. Sean , Podar Mircea , Parks Jerry M. , Elias Dwayne A. , Gilmour Cynthia C. 
Published: October 2022

ABSTRACTThehgcABgene pair encodes mercury (Hg) methylation capability in a diverse group of microorganisms, but its evolution and transcriptional regulation remain unknown. Working from the possibility that the evolutionary function of HgcAB may not be Hg methylation, we test a possible link to arsenic resistance. Using model Hg-methylatorPseudodesulfovibrio mercuriiND132, we specifically evaluated transcriptional control ofhgcABby a putative ArsR encoded upstream and co-transcribed withhgcAB. This regulator shares homology with ArsR repressors of arsenic resistance and S-adenosyl-homocysteine (SAH) responsive regulators of methionine biosynthesis but is distinct from other ArsR/SahR inPseudodesulfovibrio mercuriiND132. Using qPCR and RNA-seq analyses we confirmed this ArsR regulateshgcABtranscription, and is responsive to arsenic and SAH. Additionally, RNA-seq indicated a possible link betweenhgcABactivity and arsenic transformations byPseudodesulfovibrio mercuriiND132, with significant up-regulation of other ArsR-regulated arsenic resistance operons alongsidehgcAB. Interestingly, wild-type ND132 was less sensitive to AsV (but not AsIII) than anhgcABknockout strain, supporting the idea thathgcABmay be linked to arsenic resistance. Arsenic significantly impacted Hg-methylation rates by ND132, however, responses varied with culture conditions. Differences in growth and overall metabolic activity did not account for arsenic impacts on methylation. One goal of this research is to better predict MeHg production in nature. However, we found thathgcABgene and transcript abundance was not a good predictor of Hg-methylation rates. Our finding thathgcABactivity is linked to arsenic may hold clues to the possible environmental drivers of horizontal transfer ofhgcAB.IMPORTANCEThis work reveals a link between microbial mercury methylation and arsenic resistance and may hold clues to the evolution of mercury methylation genes (hgcAB). Microbes withhgcABproduce methylmercury, a strong neurotoxin that readily accumulates in the food web. This study addresses a critical gap in our understanding about the environmental factors that controlhgcABexpression. We show thathgcABexpression is controlled by an ArsR-like regulator responsive to both arsenic and S-adenosyl-homocysteine in our model organism,Pseudodesulfovibrio mercuriiND132. Exposure to arsenic also significantly impactedPseudodesulfovibrio mercuriiND132 mercury methylation rates. However, expression ofhgcABwas not always a good predictor of Hg methylation rates, highlighting the roles of Hg bioavailability and other biochemical mechanisms in methylmercury production. This study improves our understanding of the controls onhgcABexpression which is needed to better predict environmental methylmercury production.
CD8+ tissue-resident memory T cells triggered the erosion of oral lichen planus by the cytokine network
Authors: Qing Maofeng , Shang Qianhui , Yang Dan , Peng Jiakuan , Deng Jiaxin , Jiang Lu , Li Jing , Zhou Yu , Xu Hao , Chen Qianming 
Published: October 2022

ABSTRACTCD8+tissue-resident memory T (CD8+Trm) cells play key roles in many immune-inflammation-related diseases. However, their characteristics in the pathological process of oral lichen planus (OLP) are unclear. Therefore, we investigated the function of CD8+Trm cells in the process of OLP. Single-cell RNA sequencing profiling and spatial transcriptomics revealed that compared with non-erosive OLP, CD8+Trm cells, which were mainly distributed in the lamina propria close to the basement membrane, were increased and functionally more active by secreting multiple cytokines in patients with erosive oral lichen planus (EOLP), including IFN-γ, TNF-α, and IL17. And our clinical cohort of 1-year follow-up was also supported the above results in RNA level and protein level. In summary, this study provided a novel molecular mechanism for triggering OLP erosion by CD8+Trm cells to secrete multiple cytokines, and new insight into the pathological development of OLP.
Prioritizing Annotated miRNAs: Only a Small Percentage are Candidates for Biological Regulation
Authors: Johnson Krystal C. , Johnson Samantha T. , Liu Jing , Chu Yongjun , Corey David R. 
Published: October 2022

AbstractThe potential for miRNAs to regulate gene expression remains controversial. DROSHA initiates the biogenesis of miRNAs while Argonaute (AGO) and TNRC6 proteins form complexes with miRNAs that recognize RNA. Here we investigate the fate of miRNAs in the absence of critical RNAi protein factors. Knockout ofDROSHAexpression reduced levels of some miRNAs, but not others. Knocking out AGO proteins, which directly contact the mature miRNA, decreased expression of miRNAs. Quantitative analysis indicates compensation to maintain the overall pool of AGO after knockout of AGO variants. Evaluation of miRNA binding to AGO proteins revealed that association between AGO and miRNAs was similar for AGO1 - 4. Contrary to the assumptions underlying many peer-reviewed reports, not all annotated miRNAs have equal potential as biological regulators. Cellular abundance, DROSHA dependence, and physical association with AGO must be considered when forming hypotheses related to their function. Our data prioritize sixty miRNAs – under two percent of the overall annotated miRNA repertoire – as being most likely to function as robust gene regulators. Our approach will facilitate identifying biologically active miRNAs.