bluuebunny/crossref_metadata_2025_split huggingface dataset:
Independent effects of the glucose-to-glycated hemoglobin ratio on mortality in critically ill patients with atrial fibrillation
Authors: Fu Yuqing , Wei Xing , Cong Xu  , Guifu Wu  
Published: July 2024

Abstract
Background
The glucose-to-glycated hemoglobin ratio (GAR) represents stress hyperglycemia, which has been closely associated with adverse outcomes in cardio-cerebrovascular diseases. No studies have examined the association between stress hyperglycemia and atrial fibrillation (AF) in critically ill patients. This study aims to explore the relationship between GAR and the prognosis of critically ill patients with AF.

Methods
A retrospective cohort of patients was selected from the Medical Information Mart for Intensive Care IV (MIMIC-IV) database. The GAR was calculated based on fasting blood glucose and glycated hemoglobin levels measured after admission. The primary outcome was the 30-day mortality rate, with secondary outcomes being the 90-day and 365-day mortality rates. The GAR was divided into tertiles, and Kaplan–Meier analysis was employed to compare differences in mortality rates between groups. The Cox proportional hazards model and restricted cubic splines (RCS) were utilized to evaluate the relationship between the GAR and mortality. Subsequently, a segmented regression model was constructed to analyze threshold effects in cases where nonlinear relationships were determined.

Results
In this cohort, the second tertile of the GAR exhibited lower mortality rates at 30 days (10.56% vs 6.33% vs 14.51%), 90 days (17.11% vs 10.09% vs 17.88%), and 365 days (25.30% vs 16.15% vs 22.72%). In the third tertile, the risk of mortality at 30 days increased by 165% (HR = 2.65, 95% CI 1.99–3.54, p < 0.001), at 90 days increased by 113% (HR = 2.13, 95% CI 1.68–2.70, p < 0.001), and at 365 days increased by 70% (HR = 1.70, 95% CI 1.68–2.70, p < 0.001). The association between the GAR and patient mortality demonstrated a “J-shaped” non-linear correlation. Once the GAR exceeded 15.915, each incremental unit increase in the ratio was associated with a 27.2% increase in the risk of 30-day mortality in critically ill atrial fibrillation patients (HR = 1.262, 95% CI 1.214–1.333, p < 0.001).

Conclusion
The GAR is associated with both short-term and long-term mortality in critically ill patients with AF in a J-shaped relationship. Both low and excessively high GAR values indicate poor prognosis.
Isolation of lytic bacteriophages and their relationships with the adherence genes of Staphylococcus saprophyticus
Authors: Rafiee Maryam , Tabarraei Alijan , yazdi Mahsa , Ghaemi Ezzat Allah 
Published: July 2024

AbstractObjectiveThis study aimed to introduce a lytic bacteriophage againstStaphylococcus saprophyticusfrom wastewater in Gorgan, northern Iran.ResultsThe vB_SsapS-46 phage was isolated from urban wastewater and formed round and clear plaques on bacterial culture. It was visualized by electron microscopy and had a large head (approximately 106 nm) and a long tail (approximately 150 nm), indicating that it belongs to the Siphoviridae family. The host range of vB_SsapS-46 was determined using a spot test on 35S. saprophyticusclinical isolates, and it was able to lyse 12 of the 35 clinical isolates (34%). Finally, the relationship between phage sensitivity and adherence genes was assessed, revealing no significant correlation between phage sensitivity and the frequency of adherence genes. The vB_SsapS-46 phage can be used alone or in a mixture in future studies to control urinary tract infections caused by this bacterium, especially in the elimination of drug-resistant pathogens.
The upregulation of POLR3G correlates with increased malignancy of bladder urothelium
Authors: Liu Xianhui , Zhu Lin , Li Diancheng , Chen Xiao 
Published: July 2024

AbstractBladder cancer remains a significant health challenge due to its high recurrence and progression rates. This study aims to evaluate the role of POLR3G in the development and progression of bladder cancer and the potential of POLR3G to serve as a novel therapeutic target. We constructed a bladder cancer model in Wistar rats by administering N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN), which successfully induced a transition from normal mucosa to hyperplasia and ultimately to urothelial carcinoma. We observed a progressive upregulation of POLR3G expression during the bladder cancer development and progression. To investigate the functional role of POLR3G, we performed functional experiments in bladder cancer cell lines. The results demonstrated that knocking down POLR3G significantly inhibited cell proliferation, migration, and invasion. We further conducted RNA sequencing on POLR3G-knockdown bladder cancer cells, and Metascape was employed to perform the functional enrichment analysis of the differentially expressed genes (DEGs). Enrichment analysis revealed the enrichment of DEGs in the RNA polymerase and apoptotic cleavage of cellular proteins pathways, as well as their involvement in the Wnt and MAPK signaling pathways. The downregulation of Wnt pathway-related proteins such as Wnt5a/b, DVL2, LRP-6, and phosphorylated LRP-6 upon POLR3G knockdown was further confirmed by Western blotting, indicating that POLR3G might influence bladder cancer behavior through the Wnt signaling pathway. Our findings suggest that POLR3G plays a crucial role in bladder cancer progression and could serve as a potential therapeutic target. Future studies should focus on the detailed mechanisms by which POLR3G regulates these signaling pathways and its potential as a biomarker for early detection and prognosis of bladder cancer.
MIDASim: a fast and simple simulator for realistic microbiome data
Authors: He Mengyu , Zhao Ni , Satten Glen A. 
Published: July 2024

Abstract
Background
Advances in sequencing technology has led to the discovery of associations between the human microbiota and many diseases, conditions, and traits. With the increasing availability of microbiome data, many statistical methods have been developed for studying these associations. The growing number of newly developed methods highlights the need for simple, rapid, and reliable methods to simulate realistic microbiome data, which is essential for validating and evaluating the performance of these methods. However, generating realistic microbiome data is challenging due to the complex nature of microbiome data, which feature correlation between taxa, sparsity, overdispersion, and compositionality. Current methods for simulating microbiome data are deficient in their ability to capture these important features of microbiome data, or can require exorbitant computational time.

Methods
We develop MIDASim (MIcrobiome DAta Simulator), a fast and simple approach for simulating realistic microbiome data that reproduces the distributional and correlation structure of a template microbiome dataset. MIDASim is a two-step approach. The first step generates correlated binary indicators that represent the presence-absence status of all taxa, and the second step generates relative abundances and counts for the taxa that are considered to be present in step 1, utilizing a Gaussian copula to account for the taxon-taxon correlations. In the second step, MIDASim can operate in both a nonparametric and parametric mode. In the nonparametric mode, the Gaussian copula uses the empirical distribution of relative abundances for the marginal distributions. In the parametric mode, a generalized gamma distribution is used in place of the empirical distribution.

Results
We demonstrate improved performance of MIDASim relative to other existing methods using gut and vaginal data. MIDASim showed superior performance by PERMANOVA and in terms of alpha diversity and beta dispersion in either parametric or nonparametric mode. We also show how MIDASim in parametric mode can be used to assess the performance of methods for finding differentially abundant taxa in a compositional model.

Conclusions
MIDASim is easy to implement, flexible and suitable for most microbiome data simulation situations. MIDASim has three major advantages. First, MIDASim performs better in reproducing the distributional features of real data compared to other methods, at both the presence-absence level and the relative-abundance level. MIDASim-simulated data are more similar to the template data than competing methods, as quantified using a variety of measures. Second, MIDASim makes few distributional assumptions for the relative abundances, and thus can easily accommodate complex distributional features in real data. Third, MIDASim is computationally efficient and can be used to simulate large microbiome datasets.
Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China
Authors: Liang Jie-Liang , Feng Shi-wei , Jia Pu , Lu Jing-li , Yi Xinzhu , Gao Shao-ming , Wu Zhuo-hui , Liao Bin , Shu Wen-sheng , Li Jin-tian 
Published: July 2024

Abstract
Background
Soil giant viruses are increasingly believed to have profound effects on ecological functioning by infecting diverse eukaryotes. However, their biogeography and ecology remain poorly understood.

Results
In this study, we analyzed 333 soil metagenomes from 5 habitat types (farmland, forest, grassland, Gobi desert, and mine wasteland) across China and identified 533 distinct giant virus phylotypes affiliated with nine families, thereby greatly expanding the diversity of soil giant viruses. Among the nine families, Pithoviridae were the most diverse. The majority of phylotypes exhibited a heterogeneous distribution among habitat types, with a remarkably high proportion of unique phylotypes in mine wasteland. The abundances of phylotypes were negatively correlated with their environmental ranges. A total of 76 phylotypes recovered in this study were detectable in a published global topsoil metagenome dataset. Among climatic, geographical, edaphic, and biotic characteristics, soil eukaryotes were identified as the most important driver of beta-diversity of giant viral communities across habitat types. Moreover, co-occurrence network analysis revealed some pairings between giant viral phylotypes and eukaryotes (protozoa, fungi, and algae). Analysis of 44 medium- to high-quality giant virus genomes recovered from our metagenomes uncovered not only their highly shared functions but also their novel auxiliary metabolic genes related to carbon, sulfur, and phosphorus cycling.

Conclusions
These findings extend our knowledge of diversity, habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses.
Wisdom affinity in the general population
Authors: Muschalla Beate 
Published: July 2024

Abstract
Background
Wisdom is an important coping resource for difficult and ambiguous life situations. Wisdom trainings have been developed in clinical and non-clinical settings. What has been missing so far are representative data on wisdom affinity from the general population. These are important regarding needs assessments and identification of risk groups with low wisdom affinity and potential problems in coping with difficult and ambiguous life situations.

Method
The study examined a population-representative sample of 2509 persons. Socio-demographic data, presence of chronic and mental illnesses was assessed, and wisdom attitudes by the 12-WD Wisdom Scale. The surveys were carried out by means of interviews and self-report questionnaires at the respondents’ homes, done by an experienced social research company (USUMA GmbH).

Results
Only 6% of the whole sample appeared to be highly wisdom-affirmative (12-WD mean score 10 on scale 0–10), whereas 4% may appear low wisdom-affirm, due to very low agreement (12 WD mean score 0–4). Most of the moderately wisdom-affirm people had a religious denomination (70.9%), whereas only 57–59% of the high or low wisdom-affirm persons reported religious affiliations. Low wisdom-affirm were most often chronically ill (25%), with mental or physical illness in similar frequency, and had significantly more unemployment times than persons with higher wisdom scores. Wisdom affinity was independent from age, gender and age, household situation, and higher school education.

Conclusion
It must be assumed that people with socio-medical risk factors also have impairments in their wisdom-related problem-solving strategies, and that these can be of interest for transdiagnostic wisdom trainings in prevention or rehabilitation, which has shown positive effects.
Study on train safety control of high-speed railway bridge under the action of near-fault earthquake
Authors: Lei Hujun , Feng Hancong , Liu Wei 
Published: July 2024

AbstractIn order to study the effect of the velocity pulse on the dynamic response of the train-bridge system of the high-speed railway simple supported beam bridge, the velocity pulse is simulated by the trigonometric function method and superimposed with the far-field earthquake without pulse to synthesize the pulse with different pulse types, pulse periods and pulse peaks. A 10$$\times$$
×
32m typical high-speed railway simple supported beam bridge is considered an case illustrating study. Then, the dynamic response of train-track-bridge coupling system is calculated by train-track-bridge seismic analysis software TTBSAS. Afterwards, the influence of pulse near-field earthquakes parameters and vertical components on dynamic response of train-bridge system and the safety of the train on the bridge are discussed in detail.The new derailment evaluation index is adopted to evaluate driving safety under earthquakes. The train safety control of simply supported beam bridge under the action of near-field earthquake is studied. The results show that the impact of pulse ground motion on the dynamic response of the train-track-bridge coupling system is significantly higher than that of no-pulse ground motion, especially the impact on the bridge and rail subsystem is more significant than that of train subsystem. Under the excitation of ground motion intensity of 0.05g$$\sim$$
∼
0.15g, the safe speed threshold of pulse near-field ground motion is smaller than that of far-field ground motion. When the ground motion intensity is 0.20g$$\sim$$
∼
0.30g, the safe speed threshold of pulse near-field ground motion and far field ground motion is 200km/h. So, the pulse near-field earthquake poses a greater threat to the safety of the train on the bridge than the far-field earthquake. Therefore, the influence of pulse near-field earthquakes should be considered in the seismic design. The research results of this paper can provide theoretitcal support for the design of a high-speed railway bridge in the near-field area.
Natural Language Processing Algorithm to Extract Multiple Myeloma Stage From Oncology Notes in the Veterans Affairs Healthcare System
Authors: Goryachev Sergey D. , Yildirim Cenk , DuMontier Clark , La Jennifer , Dharne Mayuri , Gaziano J. Michael , Brophy Mary T. , Munshi Nikhil C. , Driver Jane A. , Do Nhan V. , Fillmore Nathanael R. 
Published: July 2024

PURPOSE Stage in multiple myeloma (MM) is an essential measure of disease risk, but its measurement in large databases is often lacking. We aimed to develop and validate a natural language processing (NLP) algorithm to extract oncologists' documentation of stage in the national Veterans Affairs (VA) Healthcare System. METHODS Using nationwide electronic health record (EHR) and cancer registry data from the VA Corporate Data Warehouse, we developed and validated a rule-based NLP algorithm to extract oncologist-determined MM stage. To that end, a clinician annotated MM stage within over 5,000 short snippets of clinical notes, and annotated MM stage at MM treatment initiation for 200 patients. These were allocated into snippet- and patient-level development and validation sets. We developed MM stage extraction and roll-up algorithms within the development sets. After the algorithms were finalized, we validated them using standard measures in held-out validation sets. RESULTS We developed algorithms for three different MM staging systems that have been in widespread use (Revised International Staging System [R-ISS], International Staging System [ISS], and Durie-Salmon [DS]) and for stage reported without a clearly defined system. Precision and recall were uniformly high for MM stage at the snippet level, ranging from 0.92 to 0.99 for the different MM staging systems. Performance in identifying for MM stage at treatment initiation at the patient level was also excellent, with precision of 0.92, 0.96, 0.90, and 0.86 and recall of 0.99, 0.98, 0.94, and 0.92 for R-ISS, ISS, DS, and unclear stage, respectively. CONCLUSION Our MM stage extraction algorithm uses rule-based NLP and data aggregation to accurately measure MM stage documented in oncology notes and pathology reports in VA's national EHR system. It may be adapted to other systems where MM stage is recorded in clinical notes.
Stockholm3 in a Multiethnic Cohort for Prostate Cancer Detection (SEPTA): A Prospective Multicentered Trial
Authors: Vigneswaran Hari T. , Eklund Martin , Discacciati Andrea , Nordström Tobias , Hubbard Rebecca A. , Perlis Nathan , Abern Michael R. , Moreira Daniel M. , Eggener Scott , Yonover Paul , Chow Alexander K. , Watts Kara , Liss Michael A. , Thoreson Gregory R. , Abreu Andre L. , Sonn Geoffrey A. , Palsdottir Thorgerdur , Plym Anna , Wiklund Fredrik , Grönberg Henrik , Murphy Adam B. ,   on behalf of the SEPTA STHLM3 Study Group
Published: July 2024

PURPOSE
Asian, Black, and Hispanic men are underrepresented in prostate cancer (PCa) clinical trials. Few novel prostate cancer biomarkers have been validated in diverse cohorts. We aimed to determine if Stockholm3 can improve prostate cancer detection in a diverse cohort.

METHODS
An observational prospective multicentered (17 sites) clinical trial (2019-2023), supplemented by prospectively recruited participants (2008-2020) in a urology clinic setting included men with suspicion of PCa and underwent prostate biopsy. Before biopsy, sample was collected for measurement of the Stockholm3 risk score. Parameters include prostate-specific antigen (PSA), free PSA, KLK2, GDF15, PSP94, germline risk (single-nucleotide polymorphisms), age, family history, and previous negative biopsy. The primary endpoint was detection of International Society of Urological Pathology (ISUP) Grade ≥2 cancer (clinically significant PCa, csPC). The two primary aims were to (1) demonstrate noninferior sensitivity (0.8 lower bound 95% CI noninferiority margin) in detecting csPC using Stockholm3 compared with PSA (relative sensitivity) and (2) demonstrate superior specificity by reducing biopsies with benign results or low-grade cancers (relative specificity).

RESULTS
A total of 2,129 biopsied participants were included: Asian (16%, 350), Black or African American (Black; 24%, 505), Hispanic or Latino and White (Hispanic; 14%, 305), and non-Hispanic or non-Latino and White (White; 46%, 969). Overall, Stockholm3 showed noninferior sensitivity compared with PSA ≥4 ng/mL (relative sensitivity: 0.95 [95% CI, 0.92 to 0.99]) and nearly three times higher specificity (relative specificity: 2.91 [95% CI, 2.63 to 3.22]). Results were consistent across racial and ethnic subgroups: noninferior sensitivity (0.91-0.98) and superior specificity (2.51-4.70). Compared with PSA, Stockholm3 could reduce benign and ISUP 1 biopsies by 45% overall and between 42% and 52% across racial and ethnic subgroups.

CONCLUSION
In a substantially diverse population, Stockholm3 significantly reduces unnecessary prostate biopsies while maintaining a similar sensitivity to PSA in detecting csPC.
Exploring host–pathogen interactions in the Dictyostelium discoideum–Mycobacterium marinum infection model of tuberculosis
Authors: Guallar-Garrido Sandra , Soldati Thierry 
Published: July 2024

ABSTRACT
Mycobacterium tuberculosis is a pathogenic mycobacterium that causes tuberculosis. Tuberculosis is a significant global health concern that poses numerous clinical challenges, particularly in terms of finding effective treatments for patients. Throughout evolution, host immune cells have developed cell-autonomous defence strategies to restrain and eliminate mycobacteria. Concurrently, mycobacteria have evolved an array of virulence factors to counteract these host defences, resulting in a dynamic interaction between host and pathogen. Here, we review recent findings, including those arising from the use of the amoeba Dictyostelium discoideum as a model to investigate key mycobacterial infection pathways. D. discoideum serves as a scalable and genetically tractable model for human phagocytes, providing valuable insights into the intricate mechanisms of host–pathogen interactions. We also highlight certain similarities between M. tuberculosis and Mycobacterium marinum, and the use of M. marinum to more safely investigate mycobacteria in D. discoideum.
Cardiovascular physiology of decapod crustaceans: from scientific inquiry to practical applications
Authors: McGaw Iain J. , Ebrahim Rahana A. 
Published: July 2024

ABSTRACT
Until recently, the decapod crustacean heart was regarded as a simple, single ventricle, contraction of which forces haemolymph out into seven arteries. Differential tissue perfusion is achieved by contraction and relaxation of valves at the base of each artery. In this Review, we discuss recent work that has shown that the heart is bifurcated by muscular sheets that may effectively divide the single ventricle into ‘chambers’. Preliminary research shows that these chambers may contract differentially; whether this enables selective tissue perfusion remains to be seen. Crustaceans are unusual in that they can stop their heart for extended periods. These periods of cardiac arrest can become remarkably rhythmic, accounting for a significant portion of the cardiac repertoire. As we discuss in this Review, in crustaceans, changes in heart rate have been used extensively as a measurement of stress and metabolism. We suggest that the periods of cardiac pausing should also be quantified in this context. In the past three decades, an exponential increase in crustacean aquaculture has occurred and heart rate (and changes thereof) is being used to understand the stress responses of farmed crustaceans, as well as providing an indicator of disease progression. Furthermore, as summarized in this Review, heart rate is now being used as an effective indicator of humane methods to anaesthetize, stun or euthanize crustaceans destined for the table or for use in scientific research. We believe that incorporation of new biomedical technology and new animal welfare policies will guide future research directions in this field.