bluuebunny/crossref_metadata_2025_split huggingface dataset:
The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain
Authors: Weber Lisa Marie , Jia Yulin , Stielow Bastian , Gisselbrecht Stephen S , Cao Yinghua , Ren Yanpeng , Rohner Iris , King Jessica , Rothman Elisabeth , Fischer Sabrina , Simon Clara , Forné Ignasi , Nist Andrea , Stiewe Thorsten , Bulyk Martha L , Wang Zhanxin , Liefke Robert 
Published: December 2022

Abstract
The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.
Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding
Authors: Her Cheenou , Phan Tien M , Jovic Nina , Kapoor Utkarsh , Ackermann Bryce E , Rizuan Azamat , Kim Young C , Mittal Jeetain , Debelouchina Galia T 
Published: December 2022

Abstract
Heterochromatin protein 1α (HP1α) is a crucial element of chromatin organization. It has been proposed that HP1α functions through liquid-liquid phase separation (LLPS), which allows it to compact chromatin into transcriptionally repressed heterochromatin regions. In vitro, HP1α can undergo phase separation upon phosphorylation of its N-terminus extension (NTE) and/or through interactions with DNA and chromatin. Here, we combine computational and experimental approaches to elucidate the molecular interactions that drive these processes. In phosphorylation-driven LLPS, HP1α can exchange intradimer hinge-NTE interactions with interdimer contacts, which also leads to a structural change from a compacted to an extended HP1α dimer conformation. This process can be enhanced by the presence of positively charged HP1α peptide ligands and disrupted by the addition of negatively charged or neutral peptides. In DNA-driven LLPS, both positively and negatively charged peptide ligands can perturb phase separation. Our findings demonstrate the importance of electrostatic interactions in HP1α LLPS where binding partners can modulate the overall charge of the droplets and screen or enhance hinge region interactions through specific and non-specific effects. Our study illuminates the complex molecular framework that can fine-tune the properties of HP1α and that can contribute to heterochromatin regulation and function.
Sleep duration and cognitive function among older adults with chronic kidney disease: results from the National Health and Nutrition Examination Survey (2011–2014)
Authors: Warsame Fatima , Chu Nadia M , Hong Jingyao , Mathur Aarti , Crews Deidra C , Bayliss George , Segev Dorry L , McAdams-DeMarco Mara A 
Published: December 2022

ABSTRACTBackgroundShort and long sleep durations are associated with cognitive dysfunction. Given the increased prevalence of sleep abnormalities in the chronic kidney disease (CKD) population, we tested whether the association between sleep duration and cognitive function differed between older adults with and without CKD.MethodsThis was a study of 3215 older adults (age ≥60 years) enrolled in the National Health and Nutrition Examination Survey (2011–14) evaluating sleep duration, cognitive function (immediate recall, delayed recall, verbal fluency, executive function and processing speed and global cognition) and kidney function. We quantified the association between sleep duration and cognitive function using linear regression and tested whether the associations differed among those with CKD and without using a Wald test for interaction.ResultsAmong 3215 participants, 13.3% reported 2–5 hours of sleep/day, 75.2% reported 6–8 hours, and 11.5% reported ≥9 hours. Persons with CKD were more likely to sleep ≥9 hours [odds ratio 1.73 (95% confidence interval 1.22–2.46)]. Among participants with CKD, those with a sleep duration ≥9 hours demonstrated worse global cognitive function (P for interaction = .01), immediate recall (P for interaction = .01) and verbal fluency (P for interaction = .004) than those with a sleep duration of 6–8 h; no differences were observed for participants with CKD who slept 2–5 hours. Among participants without CKD, sleep was not associated with any measures of cognitive function.ConclusionsLonger sleep duration is associated with worse cognitive function only among persons with CKD, and global cognition, delayed recall and verbal fluency are particularly affected. Studies should identify interventions to improve sleep patterns and quality in this population.
Population-based prevalence and incidence estimates of mixed connective tissue disease from the Manhattan Lupus Surveillance Program
Authors: Hasan Ghadeer , Ferucci Elizabeth D , Buyon Jill P , Belmont H Michael , Salmon Jane E , Askanase Anca , Bathon Joan M , Geraldino-Pardilla Laura , Ali Yousaf , Ginzler Ellen M , Putterman Chaim , Gordon Caroline , Helmick Charles G , Parton Hilary , Izmirly Peter M 
Published: December 2022

Abstract

Objective
Epidemiological data for MCTD are limited. Leveraging data from the Manhattan Lupus Surveillance Program (MLSP), a racially/ethnically diverse population-based registry of cases with SLE and related diseases including MCTD, we provide estimates of the prevalence and incidence of MCTD.

Methods
MLSP cases were identified from rheumatologists, hospitals and population databases using a variety of International Classification of Diseases, Ninth Revision codes. MCTD was defined as one of the following: fulfilment of our modified Alarcon-Segovia and Kahn criteria, which required a positive RNP antibody and the presence of synovitis, myositis and RP; a diagnosis of MCTD and no other diagnosis of another CTD; and a diagnosis of MCTD regardless of another CTD diagnosis.

Results
Overall, 258 (7.7%) cases met a definition of MCTD. Using our modified Alarcon-Segovia and Kahn criteria for MCTD, the age-adjusted prevalence was 1.28 (95% CI 0.72, 2.09) per 100 000. Using our definition of a diagnosis of MCTD and no other diagnosis of another CTD yielded an age-adjusted prevalence and incidence of MCTD of 2.98 (95% CI 2.10, 4.11) per 100 000 and 0.39 (95% CI 0.22, 0.64) per 100 000, respectively. The age-adjusted prevalence and incidence were highest using a diagnosis of MCTD regardless of other CTD diagnoses and were 16.22 (95% CI 14.00, 18.43) per 100 000 and 1.90 (95% CI 1.49, 2.39) per 100 000, respectively.

Conclusions
The MLSP provided estimates for the prevalence and incidence of MCTD in a diverse population. The variation in estimates using different case definitions is reflective of the challenge of defining MCTD in epidemiologic studies.
Phylogenomics of the Ancient and Species-Depauperate Gars Tracks 150 Million Years of Continental Fragmentation in the Northern Hemisphere
Authors: Doran Brownstein Chase , Yang Liandong , Friedman Matt , Near Thomas J 
Published: December 2022

AbstractReconstructing deep-time biogeographic histories is limited by the comparatively recent diversification of most extant lineages. Ray-finned fishes, which include nearly half of all living vertebrates, are no exception. Although most lineages of ray-finned fishes radiated around the Cretaceous-Paleogene boundary, a handful of ancient, species-poor clades still persist. These lineages can illuminate very old biogeographic trends, but their low species richness can also limit the reconstruction of these patterns. The seven extant species of gars distributed in freshwater habitats in North America and Cuba are an old clade with a fossil record spanning over 150 million years of Earth history. Using a genomic data set of DNA sequences of 1105 exons for the seven living species and an updated morphological matrix of all extant and extinct taxa, we infer the phylogenetic relationships of gars and test how divergence times and biogeographic reconstructions are influenced by sequential and joint estimation and the effect on these inferences when using different taxon sets based on fossil completeness. Our analyses consistently show that the two extant gar genera Atractosteus and Lepisosteus diverged approximately 105 million years ago and many of the inferred divergences in the gar time-calibrated phylogeny closely track major Mesozoic tectonic events, including the separation of the Americas, the expansion of the early Atlantic, and the Cretaceous reorganization of North American river systems. The crown clades Atractosteus and Lepisosteus originated in the Cenozoic of eastern North America, implying that this region has served as both the origin of extant gar diversity and the refugium of this iconic ancient lineage. These results exemplify how combining phylogenomics with the fossil record provides congruence around the evolutionary history of ancient clades like gars and can reveal long-lost biogeographic patterns. [Lepisosteidae; fossilized birth death; biogeography; phylogenomics; paleontology.]
The Complete Genome Resource of Xanthomonas oryzae pv. oryzae CIX2779 Includes the First Sequence of a Plasmid for an African Representative of This Rice Pathogen
Authors: Sciallano Coline , Auguy Florence , Boulard Gabriel , Szurek Boris , Cunnac Sébastien 
Published: December 2022

The bacterial plant pathogen Xanthomonas oryzae pv. oryzae is responsible for the foliar rice bacterial blight disease. Genetically contrasted, continent-specific, sublineages of this species can cause important damages to rice production both in Asia and Africa. We report on the genome of the CIX2779 strain of this pathogen, previously named NAI1 and originating from Niger. Oxford Nanopore long reads assembly and Illumina short reads polishing produced a genome sequence composed of a 4,725,792-bp circular chromosome and a 39,798-bp-long circular plasmid designated pCIX2779_1. The chromosome structure and base-level sequence are highly related to reference strains of African X. oryzae pv. oryzae and encode identical transcription activator-like effectors for virulence. Importantly, our in silico analysis strongly indicates that pCIX2779_1 is a genuine conjugative plasmid, the first indigenous one sequenced from an African strain of the X. oryzae species. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Trauma-Informed Care Curricula for the Health Professions: A Scoping Review of Best Practices for Design, Implementation, and Evaluation
Authors: Burns Courtney Julia , Borah Luca , Terrell Stephanie M. , James LaTeesa N. , Erkkinen Elizabeth , Owens Lauren 
Published: December 2022

Purpose
Trauma-exposed persons often experience difficulties accessing medical care, remaining engaged in treatment plans, and feeling psychologically safe when receiving care. Trauma-informed care (TIC) is an established framework for health care professionals, but best practices for TIC education remain unclear. To remedy this, the authors conducted a multidisciplinary scoping literature review to discern best practices for the design, implementation, and evaluation of TIC curricula for health care professionals.

Method
The research team searched Ovid MEDLINE, Cochrane Library, Elsevier’s Scopus, Elsevier’s Embase, Web of Science, and the PTSDpubs database from the database inception date until May 14, 2021. Worldwide English language studies on previously implemented TIC curricula for trainees or professionals in health care were included in this review.

Results
Fifty-five studies met the inclusion criteria, with medicine being the most common discipline represented. The most prevalent learning objectives were cultivating skills in screening for trauma and responding to subsequent disclosures (41 studies [74.5%]), defining trauma (34 studies [61.8%]), and understanding trauma’s impact on health (33 studies [60.0%]). Fifty-one of the studies included curricular evaluations, with the most common survey items being confidence in TIC skills (38 studies [74.5%]), training content knowledge assessment (25 studies [49.0%]), participant demographic characteristics (21 studies [41.2%]), and attitudes regarding the importance of TIC (19 studies [37.3%]).

Conclusions
Future curricula should be rooted in cultural humility and an understanding of the impacts of marginalization and oppression on individual and collective experiences of trauma. Moreover, curricula are needed for clinicians in more diverse specialties and across different cadres of care teams. Additional considerations include mandated reporting, medical record documentation, and vicarious trauma experienced by health care professionals.
Drama Training as a Tool to Teach Medical Trainees Communication Skills: A Scoping Review
Authors: Landry-Wegener Bernard A. , Kaniecki Timothy , Gips Julia , Lebo Rachael , Levine Rachel B. 
Published: December 2022

Purpose
Recognizing the similarities between the skills an actor needs and those required of a physician in clinical communication, medical educators have begun to create drama-based interventions to teach communication skills. The purpose of this scoping review was to summarize existing educational interventions that use drama training to teach medical trainees communication skills.

Method
The authors searched PubMed, CINAHL Plus, Embase, ERIC, and Web of Science Core Collection multiple times beginning in March 2020 through March 2022. Articles were included if they (1) described components of an educational intervention, (2) used an active intervention based on drama training, (3) stated a curricular goal of improving learners’ communication skills, and (4) included medical trainee learners. Data extracted included the details of the targeted learners and educational interventions, assessment tools, and outcomes. The quality of each study was assessed.

Results
Thirty articles met the inclusion criteria. Twenty-five (83%) articles included acting and improvisation exercises, 9 (30%) used some or all of the conventions of forum theater, and 3 (10%) used dramatic performance. The interventions included undergraduate, graduate, and continuing medical education learners. Most were elective and involved a member of the theatrical community. Although low overall study quality (average MERSQI score was 8.5) limited the strength of the evidence, of the 8 articles that evaluated learners’ knowledge, skills, and/or behaviors, the majority showed an initial improvement in communication skills post-intervention.

Conclusions
This review is the first, to the authors’ knowledge, to focus on the curricular goal of improving communication skills and to include a broader scope (beyond medical improv) of drama trainings. While the included articles represent a diverse group of interventions, generally they reported an outcome of improved communication skills in their learners. More high-quality studies are needed to determine best practices and the generalizability of drama-based initiatives.
Predicting Intensive Care Delirium with Machine Learning: Model Development and External Validation
Authors: Gong Kirby D. , Lu Ryan , Bergamaschi Teya S. , Sanyal Akaash , Guo Joanna , Kim Han B. , Nguyen Hieu T. , Greenstein Joseph L. , Winslow Raimond L. , Stevens Robert D. 
Published: December 2022

Background
Delirium poses significant risks to patients, but countermeasures can be taken to mitigate negative outcomes. Accurately forecasting delirium in intensive care unit (ICU) patients could guide proactive intervention. Our primary objective was to predict ICU delirium by applying machine learning to clinical and physiologic data routinely collected in electronic health records.

Methods
Two prediction models were trained and tested using a multicenter database (years of data collection 2014 to 2015), and externally validated on two single-center databases (2001 to 2012 and 2008 to 2019). The primary outcome variable was delirium defined as a positive Confusion Assessment Method for the ICU screen, or an Intensive Care Delirium Screening Checklist of 4 or greater. The first model, named “24-hour model,” used data from the 24 h after ICU admission to predict delirium any time afterward. The second model designated “dynamic model,” predicted the onset of delirium up to 12 h in advance. Model performance was compared with a widely cited reference model.

Results
For the 24-h model, delirium was identified in 2,536 of 18,305 (13.9%), 768 of 5,299 (14.5%), and 5,955 of 36,194 (11.9%) of patient stays, respectively, in the development sample and two validation samples. For the 12-h lead time dynamic model, delirium was identified in 3,791 of 22,234 (17.0%), 994 of 6,166 (16.1%), and 5,955 of 28,440 (20.9%) patient stays, respectively. Mean area under the receiver operating characteristics curve (AUC) (95% CI) for the first 24-h model was 0.785 (0.769 to 0.801), significantly higher than the modified reference model with AUC of 0.730 (0.704 to 0.757). The dynamic model had a mean AUC of 0.845 (0.831 to 0.859) when predicting delirium 12 h in advance. Calibration was similar in both models (mean Brier Score [95% CI] 0.102 [0.097 to 0.108] and 0.111 [0.106 to 0.116]). Model discrimination and calibration were maintained when tested on the validation datasets.

Conclusions
Machine learning models trained with routinely collected electronic health record data accurately predict ICU delirium, supporting dynamic time-sensitive forecasting.

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Improved Prediction of Surgical Site Infection after Colorectal Surgery Using Machine Learning
Authors: Chen Kevin A. , Joisa Chinmaya U. , Stem Jonathan , Guillem Jose G. , Gomez Shawn M. , Kapadia Muneera R. 
Published: December 2022

BACKGROUND:
Surgical site infection is a source of significant morbidity after colorectal surgery. Previous efforts to develop models that predict surgical site infection have had limited accuracy. Machine learning has shown promise in predicting post-operative outcomes by identifying non-linear patterns within large datasets.

OBJECTIVE:
We sought to use machine learning to develop a more accurate predictive model for colorectal surgical site infections.

DESIGN:
Patients who underwent colorectal surgery were identified in the American College of Surgeons National Quality Improvement Program database from years 2012-2019 and were split into training, validation, and test sets. Machine learning techniques included random forest, gradient boosting, and artificial neural network. A logistic regression model was also created. Model performance was assessed using area under the receiver operating characteristic curve.

SETTINGS:
A national, multicenter dataset.

PATIENTS:
Patients who underwent colorectal surgery.

MAIN OUTCOME MEASURES:
The primary outcome (surgical site infection) included patients who experienced superficial, deep, or organ-space surgical site infections.

RESULTS:
The dataset included 275,152 patients after application of exclusion criteria. 10.7% of patients experienced a surgical site infection. Artificial neural network showed the best performance with area under the receiver operating characteristic curve of 0.769 (95% CI 0.762 - 0.777), compared with 0.766 (95% CI 0.759 - 0.774) for gradient boosting, 0.764 (95% CI 0.756 - 0.772) for random forest, and 0.677 (95% CI 0.669 - 0.685) for logistic regression. For the artificial neural network model, the strongest predictors of surgical site infection were organ-space surgical site infection present at time of surgery, operative time, oral antibiotic bowel prep, and surgical approach.

LIMITATIONS:
Local institutional validation was not performed.

CONCLUSIONS:
Machine learning techniques predict colorectal surgical site infections with higher accuracy than logistic regression. These techniques may be used to identify patients at increased risk and to target preventative interventions for surgical site infection. See Video Abstract at http://links.lww.com/DCR/C88.
Single Port Endorobotic Rectal Mucosa Harvest For Urethral Reconstruction
Authors: Ozgur Ilker , Justiniano Carla F. , Wood Hadley M. , Gorgun Emre 
Published: December 2022

BACKGROUND:
Colorectal mucosal grafts for substitution urethroplasty are alternatives for patients when buccal mucosa is not adequate for long urethral strictures.

IMPACT OF INNOVATION:
To presents the first cases of single port endorobotic rectal mucosa harvesting for urethral reconstruction.

TECHNOLOGY MATERIALS AND METHODS:
The patients are 43- and 57-year-old males with medical histories of lichen sclerosis. The urethrograms demonstrated panurethral strictures requiring long mucosal grafts. The single-port robot was docked under general anesthesia in modified lithotomy position. The procedure began with submucosal injection of lifting agent. After achieving an adequate lift of the mucosa, the dissection was started 2 cm proximal to the sphincter complex with a hook and continued cephalad. The semi-flexible robotic platform eased and facilitated the dissection providing the required traction and counter-traction. The injecting needle and aspiration device were directed with the help of a silk knot at the tip of the tools to create a handle for robot arms. The procedure was continued with a spatula tip thinner than the hook, which delivers less energy to the dissection field and creates a precise cut. The harvested graft was provided to the urology team after pinning it for measurement. The urologists prepared and completed the reconstruction of the urethra with the autograft.

PRELIMINARY RESULTS:
The patient had no complications related to his rectal mucosa harvest.

CONCLUSIONS:
We report the first two cases of single port robotic rectal mucosal harvesting for long panurethral strictures with single port endorobotic submucosal dissection technique.

FUTURE DIRECTIONS:
The technique seems promising to facilitate the precise submucosal dissection with meticulous control of traction and delivered energy.