bluuebunny/crossref_metadata_2025_split huggingface dataset:
Navigating The complexity of churg-strauss syndrome presenting as acute abdomen: A comprehensive review and case report
Authors: Boda Subbarayudu , Badipatla Venkata Narayana , Divya Erramelli Nag , Dutta Palak , Ganduboina Rohit 
Published: February 2024

Introduction and importance:
Churg-Strauss syndrome (CSS) is a rare multisystemic condition characterized by asthma, blood and tissue eosinophilia, and vasculitis. The purpose of this work is to present a detailed overview of CSS, focusing on its epidemiology, clinical symptoms, histological criteria, gastrointestinal involvement, and therapy.

Case presentation:
We report a case of a 40-year-old woman with CSS who had peripheral eosinophilia, small vessel vasculitis, and bronchial asthma. Diagnosed with symmetric polyarthritis six months ago, experienced abdominal pain, vomiting, and loose feces. Diagnostic tests revealed CSS with systemic involvement. In addition, we undertake a literature analysis to emphasize essential elements of CSS, such as its rarity and the difficulties in diagnosing and managing it.

Clinical discussion:
CSS can cause gastrointestinal symptoms including stomach pain, diarrhea, mucosal ulcers, rectal bleeding, and bowel perforations. Corticosteroids and immunosuppressives are routinely used in treatment, with caution due to the risks of long-term steroid use. The goal of treatment should be to induce remission while minimizing side effects.

Conclusion:
CSS is a rare condition, with an annual incidence of 2.4 per million and a prevalence of 1.3 per 100,000. The illness typically presents with necrotizing vasculitis, extravascular granulomas, and eosinophilic tissue infiltration. CSS is a complex and rare condition that requires high clinical suspicion, especially when patients present with gastrointestinal symptoms in addition to asthma and eosinophilia. This case study adds to our understanding of CSS and emphasizes the significance of a holistic strategy for its management.
Examining the Perspectives of Nurse Managers on Missed Nursing Care in Surgical Units
Authors: Kohanová Dominika , Kirwan Marcia , Bartoníčková Daniela , Gurková Elena , Žiaková Katarína 
Published: February 2024

OBJECTIVE
To examine nurse managers' perspectives on missed nursing care (MNC) on surgical units.

BACKGROUND
The phenomenon of MNC is an important concern for nurse researchers. However, the reality of how it is experienced by clinical nurse managers is largely unexplored. Understanding nurse managers' experiences with MNC could help develop useful approaches to reducing levels of MNC.

METHODS
A descriptive qualitative study was conducted between December and June 2020, using face-to-face semistructured interviews with 10 nurse managers.

RESULTS
Five themes were identified: 1) awareness of MNC; 2) rationale for MNC; 3) consequences of MNC; 4) questions of reporting; and 5) management of MNC.

CONCLUSIONS
Nurse managers must use their positions and leadership skills to expect appropriate staffing approaches and material resources for surgical units, effective process for newly hired nurses, and the establishment of a reporting system for MNC to reduce the phenomenon in practice.
Prevalence of Urogenital Mycoplasma genitalium Infection at 2 US Army Medical Facilities
Authors: Romo Matthew L. , Moreland Sarah C. , Yates Adam M. , Crowell Trevor A. , Sevilla Maureen , MacArthur John L. , Faestel Paul , Kunz Anjali , Ake Julie A. , Calvano Tatjana , Colby Donn J. 
Published: February 2024

Background
Sexually transmitted infections (STIs) have a high incidence in the US Armed Forces and can adversely impact service members' ability to perform their duties. Better knowledge of Mycoplasma genitalium (MG) epidemiology in the military is needed to understand the potential impact of this emerging pathogen on force readiness.

Methods
We conducted cross-sectional analyses of data from US Army service members and other Military Health System beneficiaries participating in a trial of an STI/HIV behavioral intervention at Fort Liberty, NC, and Joint Base Lewis-McChord, WA. At enrollment, participants completed questionnaires and provided biological specimens for nucleic acid amplification testing for MG, Chlamydia trachomatis (CT), and Neisseria gonorrhoeae (NG). We used principal component analysis and robust Poisson regression to examine associations between participant characteristics and prevalent urogenital MG.

Results
Among 432 participants enrolled between November 2020 and February 2023, 43 had MG (prevalence, 10.0%), of whom 13 had coinfection with another bacterial STI (all 13 were positive for CT, with 1 also positive for NG). The prevalence of MG was significantly higher among female (13.5%) versus male (7.6%; P = 0.048) participants and non-Hispanic Black (14.9%) versus non-Hispanic White participants (6.6%; P = 0.045). Single relationship status and increased number of recent sexual partners were correlated, and their component was associated with higher MG prevalence (adjusted prevalence ratio, 2.11; 95% confidence interval, 1.29–3.48).

Conclusions
The high prevalence of urogenital MG among Military Health System beneficiaries highlights the importance of understanding the potential clinical sequelae of MG and conducting additional epidemiologic research in military settings.
Clinical Diagnosis Is Highly Predictive of Laboratory-Confirmed Mpox in a Sexual Health Clinic
Authors: Cannon Chase A. , Karmarkar Ellora N. , Ramchandani Meena S. , Dombrowski Julia C. , Golden Matthew R. 
Published: February 2024

Background
Promptly recognizing mpox can facilitate earlier diagnosis and appropriate treatment. How accurately clinicians can diagnose mpox based on clinical data and before receiving molecular test results is not known.

Methods
Leveraging public health and clinical data collected in Seattle–King County's Sexual Health Clinic (SHC) from July 29, 2022, to September 30, 2022, we analyzed the proportion of patients who received presumptive versus results-based tecovirimat when clinicians had a high, intermediate, or low suspicion for mpox after clinical evaluation. We calculated the sensitivity, specificity, and positive (PPV) and negative predictive value (NPV) of this approach against criterion standard mpox polymerase chain reaction (PCR) results.

Results
Of 321 patients evaluated for mpox in the SHC, median age was 34.5 years and 88% were cisgender men. Overall, 121 of 319 (38%) tested positive by mpox PCR. Clinicians had high suspicion for mpox in 122 patients and offered empiric tecovirimat to 92 (88%), of whom 85 (92%) tested PCR positive. Of 13 intermediate suspicion patients offered presumptive therapy, all accepted but none tested positive by PCR. The sensitivity, specificity, PPV, and NPV of high/intermediate clinical suspicion for mpox were 99%, 90%, 86%, and 99%, respectively. A higher proportion of people with HIV were diagnosed with mpox (57% vs. 36%, P = 0.01, χ
2 test), and sensitivity and PPV of high/intermediate clinical suspicion in this subgroup were 100% and 86%, respectively.

Conclusions
Clinical providers working in a high-volume, public SHC were able to both accurately identify and rule out mpox based on clinical examination before receiving PCR test results.
Comparison of Ultrasound Guided Saline Enema and X-ray-Guided Air Enema in the Treatment of Intussusception Reduction in Children
Authors: Lian Dan-Dan , Sun Chen 
Published: February 2024

Abstract
To compare the effect of ultrasound guided saline enema (USGSE) and x-ray fluoroscopic air enema in the reduction of intussusception in children, 80 children with intussusception were randomly divided into ultrasonic-guided saline enema reduction in 40 cases (USGSE group) and x-ray air enema reduction in 40 cases (air enema group). The enema pressure, success rate, average time, and cost of the 2 methods were compared. The average operation time of the USGSE group was lower than that of the air group ([5.35 ± 1.79] min vs [6.03 ± 2.41] min, P = 0.159), the average pressure of the air group was higher than that of the air group ([10.95 ± 1.54] kPa vs [9.6 ± 1.26] kPa; P < 0.001), the success rate of resetting was higher than that of the air group (87.5% vs 85.0%; P = 0.745), and the cost of USGSE was lower than that of the air group ([339.23 ± 10.73] yuan vs [378.23 ± 18.20] yuan, P < 0.001). Subgroup analysis showed that the success rate of enema treatment in children with onset time <48 hours was significantly higher than that in children with onset time ≥48 hours (98.30% vs 54.50%, continuous correction χ2 = 22.16; P < 0.001). The success rate and operation time of USGSE in pediatric intussusception reduction are similar to that of air enema, and the advantages of low cost and no radiation are worthy of popularization. For children with onset time ≥48 hours, enema reduction is safe and effective, but the conversion rate to open is high. It is necessary to carefully identify the symptoms of intestinal perforation and necrosis on the basis of strictly following the indications to avoid delayed treatment.
Belonging in Surgery
Authors: Acker Rachael C. , Sharpe James , Shea Judy A. , Ginzberg Sara P. , Bakillah Emna , Rosen Claire B. , Finn Caitlin B. , Roberts Sanford E. , Ajmera Sonia , Kelz Rachel R. 
Published: February 2024

Objective:
The aim of this study was to develop and validate an instrument to measure Belonging in Surgery among surgical residents.

Background:
Belonging is the essential human need to maintain meaningful relationships and connections to one’s community. Increased belongingness is associated with better well-being, job performance, and motivation to learn. However, no tools exist to measure belonging among surgical trainees.

Methods:
A panel of experts adapted a belonging instrument for use among United States surgery residents. After administration of the 28-item instrument to residents at a single institution, a Cronbach alpha was calculated to measure internal consistency, and exploratory principal component analyses were performed. Multiple iterations of analyses with successively smaller item samples suggested the instrument could be shortened. The expert panel was reconvened to shorten the instrument. Descriptive statistics measured demographic factors associated with Belonging in Surgery.

Results:
The overall response rate was 52% (114 responses). The Cronbach alpha among the 28 items was 0.94 (95% CI: 0.93−0.96). The exploratory principal component analyses and subsequent Promax rotation yielded 1 dominant component with an eigenvalue of 12.84 (70% of the variance). The expert panel narrowed the final instrument to 11 items with an overall Cronbach alpha of 0.90 (95% CI: 0.86, 0.92). Belonging in Surgery was significantly associated with race (Black and Asian residents scoring lower than White residents), graduating with one’s original intern cohort (residents who graduated with their original class scoring higher than those that did not), and inversely correlated with resident stress level.

Conclusions:
An instrument to measure Belonging in Surgery was validated among surgical residents. With this instrument, Belonging in Surgery becomes a construct that may be used to investigate surgeon performance and well-being.
SHIP-1 differentially regulates IgE-induced IL-10 and antiviral responses in human monocytes
Authors: Solleti Siva Kumar , Matthews Bailey E. , Rowe Regina K. 
Published: February 2024

AbstractIgE-mediated stimulation of monocytes regulates multiple cellular functions including cellular maturation, cytokine release, antiviral responses, and T cell priming and differentiation. The high affinity IgE receptor, FcεRI, is closely linked to serum IgE levels and atopic disease. The signaling molecules which regulate effector functions of this receptor have been well studied in mast cells and basophils, however, less is known about the signaling components, regulatory molecules, and mechanisms downstream of receptor activation in monocytes. This study sought to identify regulators of IgE-mediated cytokine release in human monocytes. SHIP-1 was identified as a negative regulator of IgE-induced IL-10 production. It was also determined that IgE-mediated stimulation and SHIP-1 inhibition decreased antiviral IP-10 production after liposomal poly(I:C) stimulation, indicating differential regulation by SHIP-1 in IgE-driven and antiviral response pathways. Both SHIP-1 and NF-κB were activated following IgE-mediated stimulation of primary monocytes, and NF-κB activation was related to both SHIP-1 and FcεRIα expression levels in monocytes. To our knowledge this is the first study to identify a role for SHIP-1 in regulating IgE-driven responses and antiviral responses in human monocytes. Given the importance of monocytes in inflammation and immune responses, a better understanding of the signaling and regulatory mechanisms downstream of FcεRI receptor could lead to new therapeutic targets in allergic disease.
CoCoPyE: feature engineering for learning and prediction of genome quality indices
Authors: Birth Niklas , Leppich Nicolina , Schirmacher Julia , Andreae Nina , Steinkamp Rasmus , Blanke Matthias , Meinicke Peter 
Published: February 2024

AbstractThe exploration of the microbial world has been greatly advanced by the reconstruction of genomes from metagenomic sequence data. However, the rapidly increasing number of metagenome-assembled genomes has also resulted in a wide variation in data quality. It is therefore essential to quantify the achieved completeness and possible contamination of a reconstructed genome before it is used in subsequent analyses. The classical approach for the estimation of quality indices solely relies on a relatively small number of universal single copy genes. Recent tools try to extend the genomic coverage of estimates for an increased accuracy. CoCoPyE is a fast tool based on a novel two-stage feature extraction and transformation scheme. First it identifies genomic markers and then refines the marker-based estimates with a machine learning approach. In our simulation studies, CoCoPyE showed a more accurate prediction of quality indices than the existing tools.
scGrapHiC : Deep learning-based graph deconvolution for Hi-C using single cell gene expression
Authors: Murtaza Ghulam , Butaney Byron , Wagner Justin , Singh Ritambhara 
Published: February 2024

AbstractSingle-cell Hi-C (scHi-C) protocol helps identify cell-type-specific chromatin interactions and sheds light on cell differentiation and disease progression. Despite providing crucial insights, scHi-C data is often underutilized due the high cost and the complexity of the experimental protocol. We present a deep learning framework, scGrapHiC, that predicts pseudo-bulk scHi-C contact maps using pseudo-bulk scRNA-seq data. Specifically, scGrapHiC performs graph deconvolution to extract genome-wide single-cell interactions from a bulk Hi-C contact map using scRNA-seq as a guiding signal. Our evaluations show that scGrapHiC, trained on 7 cell-type co-assay datasets, outperforms typical sequence encoder approaches. For example, scGrapHiC achieves a substantial improvement of 23.2% in recovering cell-type-specific Topologically Associating Domains over the baselines. It also generalizes to unseen embryo and brain tissue samples. scGrapHiC is a novel method to generate cell-type-specific scHi-C contact maps using widely available genomic signals that enables the study of cell-type-specific chromatin interactions.Availabilityhttps://github.com/rsinghlab/scGrapHiCContactritambhara@brown.edu
A common set of structurally distinct endogenous retroviruses predict survival in multiple human tumor types
Authors: Massa Alexandra L. , Chintalapudi Himanshu , Coppenbarger Evelyn C. , Peterson Jake M. , Moss Walter N. , Frost H. Robert , Leach Steven D. 
Published: February 2024

AbstractAccumulating evidence suggests that viral mimicry induction in cancer cells through the expression of human endogenous retroviral elements (ERVs) enhances tumor immunogenicity and improves response to immunotherapy. However, the characterization of ERV expression across multiple tumor types, their clinical relevance, and their role in tumor immunity remain limited. Here, we assessed the prognostic and immune-related consequences of ERV expression across 8 different tumor types from The Cancer Genome Atlas (TCGA). We applied a recently developed tool, Telescope, to quantify the expression of 14,968 ERVs in bulk tumor RNA-sequencing data. Approximately 15-22% of Telescope’s ERVs (navg= 2,736) were expressed in each tumor cohort. We identified both tissue-specific and commonly expressed ERVs across cohorts. Over 50% of tissue-specific ERVs were ubiquitously expressed (n = 1,709) across all 8 tumor types. Using patient clinical data, we identified a subset of 94 ERVs whose expression levels were significantly associated with overall survival, of which 42 were favorably prognostic. Prognostic ERVs displayed unique structural characteristics, including more frequent inverted repeats and more stable secondary structures. Patients were classified based on ERV expression, allowing identification of patient cohorts with greater than 6-fold differences in overall survival. We also found that expression of positively prognostic ERVs was associated with enrichment for selected anti-tumor immune response gene expression signatures. This analysis extends previous results identifying patterns of ERV expression in bulk tumor RNA-seq datasets, providing further insight into the role of ERVs in tumor clinicopathology and immunogenicity.
Marine phytoplankton and heterotrophic bacteria rapidly adapt to future pCO2conditions in experimental co-cultures
Authors: Lu Zhiying , Entwistle Elizabeth , Kuhl Matthew D. , Durrant Alexander R. , Filho Marcelo Malisano Barreto , Goswami Anuradha , Morris J. Jeffrey 
Published: February 2024

ABSTRACTThe CO2content of Earth’s atmosphere is rapidly increasing due to human consumption of fossil fuels. Models based on short-term culture experiments predict that major changes will occur in marine phytoplankton communities in the future ocean, but these models rarely consider how the evolutionary potential of phytoplankton or interactions within marine microbial communities may influence these changes. Here we experimentally evolved representatives of four phytoplankton functional types (silicifiers, calcifiers, coastal cyanobacteria, and oligotrophic cyanobacteria) in co-culture with a heterotrophic bacterium,Alteromonas, under either present-day or predicted future pCO2conditions. Growth rates of cyanobacteria generally increased under both conditions, and the growth defects observed in ancestralProchlorococcuscultures at elevated pCO2and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except forProchlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but mostAlteromonaslineages showed evidence of directional selection, especially when co-cultured with eukaryotic phytoplankton, where evolution appeared to favor a broad metabolic switch from growth on small organic acids to catabolism of more complex carbon substrates. EvolvedAlteromonaswere also poorer “helpers” forProchlorococcus, supporting the assertion that the interaction betweenProchlorococcusand heterotrophic bacteria is not a true mutualism but rather a competitive interaction stabilized by Black Queen processes. This work provides new insights on how phytoplankton will respond to anthropogenic change and on the evolutionary mechanisms governing the structure and function of marine microbial communities.
Global genomic epidemiology ofblaGES-5carbapenemase-associated integrons
Authors: Matlock William , Shaw Liam P. , Stoesser Nicole 
Published: February 2024

AbstractAntimicrobial resistance (AMR) gene cassettes comprise an AMR gene flanked by short recombination sites (attI×attCorattC×attC). Integrons are genetic elements able to capture, excise, and shuffle these cassettes, providing ‘adaptation on demand’, and can be found on both chromosomes and plasmids. Understanding the patterns of integron diversity may help to understand the epidemiology of AMR genes. As a case study, we examined the clinical resistance geneblaGES-5, an integron-associated class A carbapenemase first reported in Greece in 2004 and since observed worldwide, which to our knowledge has not been the subject of a previous global analysis. Using a dataset comprising all NCBI contigs containingblaGES-5(n= 431), we developed a pangenome graph-based workflow to characterise and cluster the diversity ofblaGES-5-associated integrons. We demonstrate thatblaGES-5-associated integrons on plasmids are different to those on chromosomes. Chromosomal integrons were almost all identified inP. aeruginosaST235, with a consistent gene cassette content and order. We observed instances where insertion sequence IS110disruptedattCsites, which might immobilise the gene cassettes and explain the conserved integron structure despite the presence ofintI1integrase promoters, which would typically facilitate capture or excision and rearrangement. The plasmid-associated integrons were more diverse in their gene cassette content and order, which could be an indication of greater integrase activity and ‘shuffling’ of integrons on plasmids.
Parvalbumin Interneuron Impairment Leads to Synaptic Transmission Deficits and Seizures inSCN8AEpileptic Encephalopathy
Authors: Miralles Raquel M. , Boscia Alexis R. , Kittur Shrinidhi , Vundela Shreya R. , Wengert Eric R. , Patel Manoj K. 
Published: February 2024

AbstractSCN8Aepileptic encephalopathy (EE) is a severe epilepsy syndrome resulting fromde novomutations in the voltage-gated sodium channel Nav1.6, encoded by the geneSCN8A. Nav1.6 is expressed in both excitatory and inhibitory neurons, yet previous studies have primarily focused on the impactSCN8Amutations have on excitatory neuron function, with limited studies on the importance of inhibitory interneurons to seizure onset and progression. Inhibitory interneurons are critical in balancing network excitability and are known to contribute to the pathophysiology of other epilepsies. Parvalbumin (PV) interneurons are the most prominent inhibitory neuron subtype in the brain, making up about 40% of inhibitory interneurons. Notably, PV interneurons express high levels of Nav1.6. To assess the role of PV interneurons withinSCN8AEE, we used two mouse models harboring patient-derivedSCN8Again-of-function mutations,Scn8aD/+, where theSCN8Amutation N1768D is expressed globally, andScn8aW/+-PV, where theSCN8Amutation R1872W is selectively expressed in PV interneurons. Expression of the R1872WSCN8Amutation selectively in PV interneurons led to the development of spontaneous seizures inScn8aW/+-PV mice and seizure-induced death, decreasing survival compared to wild-type. Electrophysiology studies showed that PV interneurons inScn8aD/+andScn8aW/+-PV mice were susceptible to depolarization block, a state of action potential failure.Scn8aD/+andScn8aW/+-PV interneurons also exhibited increased persistent sodium current, a hallmark ofSCN8Again-of-function mutations that contributes to depolarization block. Evaluation of synaptic connections between PV interneurons and pyramidal cells showed an increase in synaptic transmission failure at high frequencies (80-120Hz) as well as an increase in synaptic latency inScn8aD/+andScn8aW/+-PV interneurons. These data indicate a distinct impairment of synaptic transmission inSCN8AEE, potentially decreasing overall cortical network inhibition. Together, our novel findings indicate that failure of PV interneuron spiking via depolarization block along with frequency-dependent inhibitory synaptic impairment likely elicits an overall reduction in the inhibitory drive inSCN8AEE, leading to unchecked excitation and ultimately resulting in seizures and seizure-induced death.