bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stressful life events in electronic health records: a scoping review
Authors: Scherbakov Dmitry , Mollalo Abolfazl , Lenert Leslie 
Published: February 2024

AbstractObjectivesStressful life events, such as going through divorce, can have an important impact on human health. However, there are challenges in capturing these events in electronic health records (EHR). We conducted a scoping review aimed to answer 2 major questions: how stressful life events are documented in EHR and how they are utilized in research and clinical care.Materials and MethodsThree online databases (EBSCOhost platform, PubMed, and Scopus) were searched to identify papers that included information on stressful life events in EHR; paper titles and abstracts were reviewed for relevance by 2 independent reviewers.ResultsFive hundred fifty-seven unique papers were retrieved, and of these 70 were eligible for data extraction. Most articles (n = 36, 51.4%) were focused on the statistical association between one or several stressful life events and health outcomes, followed by clinical utility (n = 15, 21.4%), extraction of events from free-text notes (n = 12, 17.1%), discussing privacy and other issues of storing life events (n = 5, 7.1%), and new EHR features related to life events (n = 4, 5.7%). The most frequently mentioned stressful life events in the publications were child abuse/neglect, arrest/legal issues, and divorce/relationship breakup. Almost half of the papers (n = 7, 46.7%) that analyzed clinical utility of stressful events were focused on decision support systems for child abuse, while others (n = 7, 46.7%) were discussing interventions related to social determinants of health in general.Discussion and ConclusionsFew citations are available on the prevalence and use of stressful life events in EHR reflecting challenges in screening and storing of stressful life events.
“Disgust” and “Disgrace”: Cultural Evangelicals’ Reaction to Jimmy Carter’s Draft Evader Pardon and Early Memory of the Vietnam War in Texas
Authors: Nanninga David 
Published: February 2024

Abstract
This article examines the reactions of cultural evangelicals in Texas to Jimmy Carter’s pardon of Vietnam War draft evaders. This article seeks to answer two questions: Did cultural evangelicals agree or disagree with Carter’s pardon, and why? This article finds that the vast majority vehemently disagreed with the pardon for a variety of reasons, but one reason loomed above all: These cultural evangelicals thought that the pardon was profoundly disrespectful to veterans of the Vietnam War because, in their minds, it appeared to give draft evaders, whom many cultural evangelicals saw as cowards, moral approval from the White House. To make this argument, this article takes a microhistorical approach and focuses on the cities of Waco and Amarillo, Texas, and uses sources like letters to the editor of local newspapers, news articles, opinion editorials, and, most critically, constituent letters to US members of Congress. Ultimately, this article provides another lens for understanding Carter–evangelicals relations and demonstrates how the understanding of white evangelicalism put forth by Kristin Kobes Du Mez in Jesus and John Wayne: How White Evangelicals Corrupted a Faith and Fractured a Nation can be used in a political and religious microhistory.
Stress experienced by dental students performing clinical training in different dental disciplines: a cross-sectional study
Authors: Alamoush Rasha A , Al-sawaeir Sereen , Baker Dima Abu , Aljamani Sanaa A , Alomoush Salah A , AL-Omiri Mahmoud K 
Published: February 2024

Abstract
Objectives: To assess the stress level, the impact of stress factors, and discrepancies between fourth- and fifth-year undergraduate clinical students at the University of Jordan.
Methods: A cross-sectional study was conducted in the academic year 2022/2023. The study group included fourth- and fifth-year dental students at the University of Jordan (n = 382) who were asked to voluntarily fill in an online dental environment stress (DES) questionnaire. Analysis was conducted using Mann-Whitney U test, independent t-test, χ2 test, and Spearman ρ rank correlations. Statistical significance was inferred when P &lt; .05.
Results: Fourth-year students reported higher levels of nervousness before treating patients for the first time. Fifth-year students faced more difficulty, higher stress, and/or fear regarding the amount of assigned work, provided treatment, completed requirements, failing the course, time to finish assignments, patient comprehensive care, and financial expenses of the course. Comparison between groups revealed that the fifth-year students scored higher levels of stress on the total DES score and all partial DES scores. Furthermore, the total DES questionnaire scores were significantly correlated with grade point average (GPA) among the total study sample and the prosthodontics clinical course marks among the fourth-year students’ group.
Conclusions: The stress level among students in clinical courses was influenced by their academic performance, gender, year level, and the type and time needed for the provided treatment. Completing course requirements was among the most commonly faced stressors. Future research endeavors might be considered to study each clinical factor, its impact on students’ stress level, and how to manage and positively improve these factors.
Integration of pharmacodynamics and metabolomics to reveal rhubarb anthraquinone protection against nonalcoholic fatty liver disease rat model
Authors: Zhang Fang , Wu Rui , Liu Yanfang , Dai Shu , Gong Xiaohong , Li Yunxia 
Published: February 2024

Abstract

Objectives
The objective of the present study was to investigate the effect of Rhubarb anthraquinone (RA) on a high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD) rat model, and explore potential biomarker and metabolic pathways by using the metabolomics method.

Materials and methods
We established HFD rats as the NAFLD model. Forty Sprague–Dawley rats were randomly divided into a control group, model group, RA low-dose group, RA medium-dose group, and RA high-dose group, and evaluated the protective effect of RA on NAFLD by detecting biochemical indicators of serum and pathological changes of liver tissue. Investigating potential biomarkers and metabolic pathways connected with RA’s protective effects against NAFLD by UHPLC–Q-TOF-MS untargeted metabolomics.

Results
The results showed that RA significantly reversed the increase of TG, TC, ALT, AST, and ALP (P &lt; .05), the decrease of HDL-C (P &lt; .05), and alleviated pathological conditions in NAFLD rats. Based on potential biomarker analysis, RA affected metabolic pathways such as fatty acids biosynthesis, bile acids biosynthesis, and pentose phosphate pathway, delaying the progression of NAFLD.

Conclusion
RA improved blood lipid levels, liver function, and pathological conditions of NAFLD rats. Meanwhile, affected the metabolic pathways and regulated the synthesis of fatty acids and bile acids in NAFLD rats.
‘Bit’ off more than he could chew: asymptomatic foreign body in the appendix
Authors: Waarala Zachary M S , Santucci Christopher , Sandberg Jay H 
Published: February 2024

Abstract
This report details the case of a 69-year-old male who had presented to the emergency department at the suggestion of his dentist after ingesting a diamond-tipped drill bit during a routine dental procedure. Through the use of radiograph, computed tomography, and colonoscopy, the drill bit was determined to be lodged in the distal vermiform appendix. Throughout his clinical course, the patient remained asymptomatic but was monitored closely for signs of complications of a retained foreign body in the appendix. Gastroenterology and general surgery were consulted on the case but ultimately non-surgical approaches prevailed and the drill bit passed in the stool. This patient’s case highlights the success of noninvasive measures for appendiceal foreign body removal.
Interacting galaxies in the IllustrisTNG simulations – VII: the connection between the most luminous active galactic nuclei and galaxy interactions
Authors: Byrne-Mamahit Shoshannah , Patton David R , Ellison Sara L , Bickley Robert , Ferreira Leonardo , Hani Maan , Quai Salvatore , Wilkinson Scott 
Published: February 2024

ABSTRACT
We investigate the connection between the most luminous active galactic nuclei (AGN), galaxy pairs, and post-mergers in the IllustrisTNG simulation. We select galaxy pairs and post-mergers with a mass ratio between 1:10 &lt; μ &lt; 1:1 and a redshift between 0 &lt; z &lt; 1. We compare the incidence of luminous AGN in pairs with matched non-pair controls, finding that AGN with luminosity Lbol &gt; 1044 erg s−1 occur in ∼26 per cent of paired galaxies with a companion within 20 kpc, compared with ∼14 per cent in controls (a fractional excess of ∼2). The enhancement of AGN in galaxy pairs is luminosity dependent, with the highest excess (a factor of ∼6 ± 2 at the closest separations) for AGN with Lbol &gt; 1045 erg s−1. Additionally, pairs exhibit a modest yet statistically significant excess of luminous AGN up to ∼150 kpc in separation. For pairs which merge between 0 &lt; z &lt; 1, AGN fractions are elevated between 1.5 Gyr before and after coalescence, with the highest excess closest to coalescence. Our results indicate that pre-coalescence interactions drive excesses of luminous AGN, but that luminous AGN in galaxy pairs are not ubiquitous. Finally, we investigate what fraction of AGN can be associated with an interaction (either having a companion within 100 kpc or a merger within the last 500 Myr). For AGN with Lbol &gt; 1045 erg s−1, ∼55 per cent are interacting, compared with a 30 per cent interaction fraction in AGN with 1044 &lt; Lbol &lt; 1044.5 erg s−1. Our results support a picture in which interactions play a dominant role in (but are not the sole cause of) triggering the most luminous AGN.
Time resolved spectroscopy of a GRS 1915 + 105 flare during its unusual low state using AstroSat
Authors: Boked Sajad , Maqbool Bari , V Jithesh , Misra Ranjeev , Bhat Naseer I , Bhulla Yashpal 
Published: February 2024

ABSTRACT
Since its discovery in 1992, GRS 1915 + 105 has been among the brightest sources in the X-ray sky. However, in early 2018, it dimmed significantly and has stayed in this faint state ever since. We report on AstroSat and NuSTAR observation of GRS 1915 + 105 in its unusual low/hard state during 2019 May. We performed time-resolved spectroscopy of the X-ray flares observed in this state and found that the spectra can be fitted well using highly ionized absorption models. We further show that the spectra can also be fitted using a highly relativistic reflection dominated model, where for the lamp post geometry, the X-ray emitting source is always very close to the central black hole. For both interpretations, the flare can be attributed to a change in the intrinsic flux, rather than dramatic variation in the absorption or geometry. These reflection dominated spectra are very similar to the reflection dominated spectra reported for active galactic nuclei in their low flux states.
Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression
Authors: Nagy Gergely , Bojcsuk Dóra , Tzerpos Petros , Cseh Tímea , Nagy László 
Published: February 2024

Abstract
Mammalian promoters consist of multifarious elements, which make them unique and support the selection of the proper transcript variants required under diverse conditions in distinct cell types. However, their direct DNA-transcription factor (TF) interactions are mostly unidentified. Murine bone marrow-derived macrophages (BMDMs) are a widely used model for studying gene expression regulation. Thus, this model serves as a rich source of various next-generation sequencing data sets, including a large number of TF cistromes. By processing and integrating the available cistromic, epigenomic and transcriptomic data from BMDMs, we characterized the macrophage-specific direct DNA-TF interactions, with a particular emphasis on those specific for promoters. Whilst active promoters are enriched for certain types of typically methylatable elements, more than half of them contain non-methylatable and prototypically promoter-distal elements. In addition, circa 14% of promoters—including that of Csf1r—are composed exclusively of ‘distal’ elements that provide cell type-specific gene regulation by specialized TFs. Similar to CG-rich promoters, these also contain methylatable CG sites that are demethylated in a significant portion and show high polymerase activity. We conclude that this unusual class of promoters regulates cell type-specific gene expression in macrophages, and such a mechanism might exist in other cell types too.
RNAvigate: efficient exploration of RNA chemical probing datasets
Authors: Irving Patrick S , Weeks Kevin M 
Published: February 2024

Abstract
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA, including local nucleotide flexibility, RNA secondary structure, protein and ligand binding, through-space interaction networks, and multistate structural ensembles. Deep understanding of RNA structure–function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multilayered relationships. Current platforms lack the broad accessibility, flexibility and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library that automatically parses 21 standard file formats (primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures) and outputs 18 plot types. RNAvigate enables efficient exploration of nuanced relationships between multiple layers of RNA structure information and across multiple experimental conditions. Compatibility with Jupyter notebooks enables nonburdensome, reproducible, transparent and organized sharing of multistep analyses and data visualization strategies. RNAvigate simplifies and accelerates discovery and characterization of RNA-centric functions in biology.
A Seminested PCR Method for the Diagnosis of Invasive Fungal Infections in Combat Injured
Authors: Ellis Graham C , Shaikh Faraz , Carson M Leigh , Sercy Erica , Stewart Laveta , Andrews Jared M , Campbell Wesley R , Mende Katrin , Yabes Joseph M , Tribble David R , Bialek Ralf , Wickes Brian L , Ganesan Anuradha 
Published: February 2024

Abstract

Background
Among combat injured, invasive fungal infections (IFIs) result in significant morbidity. Cultures and histopathology are the primary diagnostic methods for IFIs, but they have limitations. We previously evaluated a panfungal polymerase chain reaction assay, which was 83% sensitive and 99% specific for angioinvasive IFIs. Here, we evaluated 3 less resource-intensive seminested assays targeting clinically relevant fungi in the order Mucorales and genera Aspergillus and Fusarium.

Methods
Formalin-fixed paraffin-embedded tissue specimens from a multicenter trauma IFI cohort (2009-2014) were used. Cases were US military personnel injured in Afghanistan with histopathologic IFI evidence. Controls were patients with similar injury patterns and no laboratory IFI evidence (negative culture and histopathology). Seminested assays specific to Mucorales (V4/V5 regions of 18S rDNA), Aspergillus (mitochondrial tRNA), and Fusarium (internal transcribed spacer [ITS]/28A regions of DNA) were compared with a panfungal assay amplifying the internal transcribed spacer 2 region of rDNA and to histopathology.

Results
Specimens from 92 injury sites (62 subjects) were compared with control specimens from 117 injuries (101 subjects). We observed substantial agreement between the seminested and panfungal assays overall, especially for the order Mucorales. Moderate agreement was observed at the genus level for Aspergillus and Fusarium. When compared with histopathology, sensitivity and specificity of seminested assays were 67.4% and 96.6%, respectively (sensitivity increased to 91.7% when restricted to sites with angioinvasion).

Conclusions
Prior studies of seminested molecular diagnostics have focused on culture-negative samples from immunocompromised patients. Our findings underscore the utility of the seminested approach in diagnosing soft-tissue IFIs using formalin-fixed paraffin-embedded tissue samples, especially with angioinvasion.
Irrigation strengthens climate resilience: Long-term evidence from Mali using satellites and surveys
Authors: BenYishay Ariel , Sayers Rachel , Singh Kunwar , Goodman Seth , Walker Madeleine , Traore Souleymane , Rauschenbach Mascha , Noltze Martin 
Published: February 2024

Abstract
Agriculture in the Sahel and much of sub-Saharan Africa remains to a large extent rainfed. At the same time, climate change is already causing less predictable rainfall patterns in the region, even as rising temperatures increase the amount of water needed for agricultural production. We assess to what extent irrigation can strengthen the climate resilience of farming communities. Our study sample consists of nearly 1,000 distinct locations in Mali in which small-scale, river-based irrigation was introduced over the past two decades, as weather conditions worsened and political upheaval erupted. Using the staggered roll-out of the irrigation and repeated observations over 20 years allows us to compare the pre- and postirrigation outcomes of locations while adjusting for confounding factors. We geospatially link data on irrigation interventions with agricultural conditions measured using satellite imagery and surveys, as well as child nutrition and health outcomes and conflict event data. Using a two-way fixed effects model to quasi-experimentally estimate counterfactual outcomes, we find that the introduction of irrigation led to substantial increases in agricultural production on supported fields, with these gains persisting even a decade later. Children in nearby communities are less likely to be stunted or wasted due to the irrigation, and conflict risks decrease in the closest communities. Some of these gains are offset by worsening conditions farther away from the newly installed irrigation. These findings suggest that, even with political conflicts in semi-arid areas already increasing, sustainable irrigation may offer a valuable tool to improve communities' long-term well-being and social cohesion.
Disease activity–guided dose optimization including discontinuation of TNF inhibitors in rheumatoid arthritis is effective for up to 10 years: an observational follow-up of the DRESS study
Authors: van der Togt Céleste J T , den Broeder Nathan , Boonstra Marleen S , van der Maas Aatke , den Broeder Alfons A , van Herwaarden Noortje 
Published: February 2024

Abstract

Objective
The objective of this study was to investigate the safety and effectiveness of disease activity–guided dose optimization of TNF inhibitors in RA over 10 years.

Methods
The study involved an observational long-term extension of a randomized study of participants who completed the 3-year extension of the DRESS-study. After the randomized phase (months 0–18), disease activity–guided dose optimization was allowed for all. The main outcomes were mean time-weighted DAS28-CRP; biologic and targeted synthetic DMARD (b/tsDMARD) use per year, as proportion of daily defined dose; proportion of patients reaching discontinuation; durability and effectiveness of subsequent dose reduction attempts; and radiographic progression between years 3 and 10 using the Sharp–van der Heijde score.

Results
A total of 170 patients were included, of whom 127 completed the 10-year follow-up. The mean disease activity remained low (DAS28-CRP 2.13, 95% CI 2.10–2.16), while the b/tsDMARD dose reduced from 97% at baseline (95% CI 96–99%, n = 170) to 56% at year 10 (95% CI 49–63%, n = 127). Of 161 participants with an optimization attempt, 119 (74%) reached discontinuation with a median duration of 7 months (interquartile range 3–33 months), and 25 participants never had to restart their b/tsDMARD (21%, 95% CI 14–29%). The mean dose reduction after dose optimization was 48% (n = 159) for the first optimization attempt, and 33% for a subsequent attempt (n = 86). Of the 86 participants, 41 (48%) had radiographic progression exceeding the smallest detectable change (5.7 units), and progression was associated with disease activity, not b/tsDMARD use.

Conclusion
Long-term disease activity–guided dose optimization of TNF inhibitors in RA, including discontinuation and multiple tapering attempts, remains safe and effective.
Correlation between surgical booking by a PA and surgical procedure performed
Authors: Gandhi Deep A. , Colón-Sanchez Kaity , Ellsworth Pamela 
Published: February 2024

ABSTRACT

Objective:
This study evaluated the concordance between clinical evaluation and diagnosis by a physician associate/assistant (PA) and the preoperative and intraoperative evaluations by a pediatric urologic surgeon.

Methods:
A retrospective chart review was performed for patients independently evaluated and scheduled for surgery by a single PA between 2017 and 2020. Concordance was measured by comparing the PA's office note with the surgeon's preoperative note and operative report.

Results:
Of the 242 patients scheduled for surgery, 11 underwent an operative report procedure change and 11 others underwent a preoperative note procedure change. Concordance increased from 89.09% in 2017 to 92.31% in 2020; this was not statistically significant (P = .230). Urologic conditions evaluated demonstrated an increase in the variety and complexity of conditions.

Conclusions:
A supervisory/collaborative model involving a well-trained PA yields excellent outcomes in terms of concordance with surgical scheduling and procedure performed.
Managing heartburn and reflux in primary care
Authors: Provenza Delaney , Gillette Christopher , Peacock Brian , Rejeski Jared 
Published: February 2024

ABSTRACT
This article describes an algorithmic approach to caring for patients presenting with heartburn and reflux, including empiric treatment with acid-suppression therapy and a data-driven approach to diagnostic testing. This article also reviews the efficacy and safety profile of the widely available and commonly used proton pump inhibitors. Refining our approach to diagnostic testing can reduce time to diagnosis, better control patients' symptoms, and limit complications of longstanding disease.
Peer feedback
Authors: Gallant Alexandra , Erdman Laura , McBeth Lauren , Ngov Li-Kheng , Misky Gregory 
Published: February 2024

ABSTRACT
The increasing use of physician associates/assistants (PAs) and NPs on clinical teams creates an opportunity for colleagues to provide feedback that can drive growth and improvement in PA and NP clinical skills. Through a needs assessment, month-long pilot, and buy-in from our academic hospital medicine group, we initiated a peer feedback platform that sought to highlight individual faculty strengths, facilitate thoughtful and constructive feedback, and create effective collaboration among colleagues. Three months after implementation, results indicated that the platform provided important information on clinical skills and identified areas for growth and opportunities for additional training. Peer feedback can also improve working relationships among PAs, NPs, and physicians by highlighting the clinical skill sets and value of all team members.