bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses
Authors: Ma Bin , Gong Huimin , Xu Qianshuai , Gao Yuan , Guan Aohan , Wang Haoyu , Hua Kexin , Luo Rui , Jin Hui 
Published: January 2024

Abstract
Understanding phylogenetic relationships among species is essential for many biological studies, which call for an accurate phylogenetic tree to understand major evolutionary transitions. The phylogenetic analyses present a major challenge in estimation accuracy and computational efficiency, especially recently facing a wave of severe emerging infectious disease outbreaks. Here, we introduced a novel, efficient framework called Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) for new sample placement for viruses. In this study, a brand-new recoding method called Frequency Vector Recoding was implemented to approximate the phylogenetic distance, and the Phylogenetic Simulated Annealing Search algorithm was developed to match the recoded distance matrix with the phylogenetic tree. Meanwhile, the indel (insertion/deletion) was heuristically introduced to foreign sequence recognition for the first time. Here, we compared the Bd-RPC with the recent placement software (PAGAN2, EPA-ng, TreeBeST) and evaluated it in Alphacoronavirus, Alphaherpesvirinae, and Betacoronavirus by using Split and Robinson-Foulds distances. The comparisons showed that Bd-RPC maintained the highest precision with great efficiency, demonstrating good performance in new sample placement on all three virus genera. Finally, a user-friendly website (http://www.bd-rpc.xyz) is available for users to classify new samples instantly and facilitate exploration of the phylogenetic research in viruses, and the Bd-RPC is available on GitHub (http://github.com/Bin-Ma/bd-rpc).
Detection of Traumatic Ankle Arthrotomies: Computed Tomography Scan vs. Saline Load Test
Authors: Kallevang LT Jonathan K. , Berault LT Thomas J. , Olsen LCDR Aaron A. , Zuppke Julia N. , Clark LCDR James K. , Douglas CDR Thomas J. , Smith CDR Christopher S. 
Published: January 2024

OBJECTIVE:
Periarticular wounds present a common diagnostic dilemma for emergency providers and orthopedic surgeons, as traumatic arthrotomies (TA) often necessitate different management from superficial soft tissue wounds. Historically, TA have been diagnosed with the saline load test (SLT). Computed tomography (CT) scan has been studied as an alternative to SLT in diagnosing TA in several joints, but there is limited data specifically pertaining to the ankle. This study aimed to compare the ability of a CT scan to identify an ankle TA versus a traditional SLT. The hypothesis was there would be no significant difference between a CT scan and SLT in diagnosing ankle TA in a cadaveric model.

METHODS:
This cadaveric study utilized ten thawed fresh-frozen cadaveric ankles. A baseline CT scan was performed to ensure no intra-articular air existed before simulated TA. After the baseline CT, a 1 cm TA was created in the anterolateral arthroscopy portal site location. The ankles then underwent a post-arthrotomy CT scan to evaluate for the presence of intra-articular air. After the CT scan, a 30 mL SLT was performed using the anteromedial portal site location.

RESULTS:
Following arthrotomy, intra-articular air was visualized in seven of ten cadavers in the post-arthrotomy CT scan. All the ankles had fluid extravasation during the SLT with less than 10 mL of saline. The sensitivity of the SLT for TA was 100% versus 70% for the CT scan.

CONCLUSION:
The SLT was more sensitive in diagnosing 1 cm ankle TA than a CT scan in a cadaveric model.
Medicaid Expansion and Racial–Ethnic and Sex Disparities in Cardiovascular Diseases Over 6 Years: A Generalized Synthetic Control Approach
Authors: Nianogo Roch A. , Zhao Fan , Li Stephen , Nishi Akihiro , Basu Sanjay 
Published: January 2024

Background:
Studies have suggested Medicaid expansion enacted in 2014 has resulted in a reduction in overall cardiovascular disease (CVD) mortality in the United States. However, it is unknown whether Medicaid expansion has a similar effect across race–ethnicity and sex. We investigated the effect of Medicaid expansion on CVD mortality across race–ethnicity and sex.

Methods:
Data come from the behavioral risk factor surveillance system and the US Centers for Disease Control’s Wide-ranging Online Data for Epidemiologic Research, spanning the period 2000–2019. We used the generalized synthetic control method, a quasi-experimental approach, to estimate effects.

Results:
Medicaid expansion was associated with −5.36 (mean difference [MD], 95% confidence interval [CI] = −22.63, 11.91) CVD deaths per 100,000 persons per year among Blacks; −4.28 (MD, 95% CI = −30.08, 21.52) among Hispanics; −3.18 (MD, 95% CI = −8.30, 1.94) among Whites; −5.96 (MD, 95% CI = −15.42, 3.50) among men; and −3.34 (MD, 95% CI = −8.05, 1.37) among women. The difference in mean difference (DMD) between the effect of Medicaid expansion in Blacks compared with Whites was −2.18; (DMD, 95% CI = −20.20, 15.83); between that in Hispanics compared with Whites: −1.10; (DMD, 95% CI = −27.40, 25.20) and between that in women compared with men: 2.62; (DMD, 95% CI = −7.95, 13.19).

Conclusions:
Medicaid expansion was associated with a reduction in CVD mortality overall and in White, Black, Hispanic, male, and female subpopulations. Also, our study did not find any difference or disparity in the effect of Medicaid on CVD across race–ethnicity and sex–gender subpopulations, likely owing to imprecise estimates.
Nephrologist follow-up care for the acute kidney injury-chronic kidney disease continuum and clinical outcomes: A systematic review and meta-analysis
Authors: Hsieh Chih-Chieh , Chen Sheng-Yin , Chen Jui-Yi , Pan Heng-Chih , Liao Hung-Wei , Wu Vin-Cent 
Published: January 2024

Background:
Acute kidney injury (AKI) to chronic kidney disease (CKD) continuum will increase patients’ risk of mortality and long-term dialysis. The aim of the present meta-analysis is to explore the effectiveness of nephrologist care and focus on the follow-up in patients with AKI.

Methods:
A systematic search of studies on nephrologist care for the AKI to CKD continuum has been conducted from PubMed and other different databases. Briefly, the primary outcome is the odds ratio of mortality as well as the secondary outcome is de novo renal replacement therapy.

Results:
This research includes one randomized controlled trial (RCT) and four cohort studies comprised of 15 541 participants in total. The quantitative analysis displays a lower mortality rate with nephrologist care versus non-nephrologist care in patients’ discharge after a hospitalization complicated by AKI (odds ratio: 0.768; 95% CI, 0.616-0.956). By means of Trial Sequential Analysis (TSA), we conclude that nephrologist care after an AKI episode declines 30% relative risks of all-cause mortality.

Conclusion:
Nephrologist care for AKI patients after a hospitalization significantly has reduced mortality compared to those followed up by non-nephrologists. There is a trend toward a potentially superior survival rate with nephrologist care has been going well in the recent years.
Characteristics of bone metabolism in the male patients with diabetic neuropathy
Authors: Huang Dong-Ni , Zeng Yue , Ding Hui-Ru , Zhang Zi-Kai , Wang Yu , Han Dong-Xu , Zhang Xiu-Zhen , Song Li-Ge 
Published: January 2024

Background:
This study aimed to evaluate the characteristics of bone metabolism and fracture risk in the type 2 diabetes mellitus (T2DM) patients with distal symmetric polyneuropathy (DSPN).

Methods:
A total of 198 T2DM individuals were recruited from January 2017 to December 2020. Patients with DSPN were evaluated by strict clinical and sensory thresholds. Biochemical parameters and bone mineral density (BMD) were measured. The BMD, bone turnover markers, and probability of fracture were compared between two groups, and the factors related to BMD and probability of hip fracture in 10 years were further explored.

Results:
Compared with type 2 diabetes mellitus without distal symmetric polyneuropathy (T2DN−) patients, type 2 diabetes mellitus with distal symmetric polyneuropathy (T2DN+) patients had lower level of cross-linked C-telopeptide (CTX) (0.32 ± 0.19 vs 0.38 ± 0.21 ng/mL, p = 0.038) and higher level of bone-specific alkaline phosphatase (BALP) (15.28 ± 5.56 vs 12.58 ± 4.41 μg/mL, p = 0.003). T2DN+ patients had higher BMD of lumbar L1-L4 (1.05 ± 0.19 vs 0.95 ± 0.37, p = 0.027) and higher probability of hip fracture (0.98 ± 0.88 vs 0.68 ± 0.63, p = 0.009) as compared to T2DN− individuals. Univariate correlation analysis showed that BALP level (coefficient (coef) = −0.054, p = 0.038), CTX level (coef = −2.28, p = 0.001), and hip fracture risk (coef = −1.02, p < 0.001) were negatively related to the BMD of L1-L4. As for the risk of hip fracture evaluated by WHO Fracture Risk Assessment Tool (FRAX), age (coef = 0.035, p < 0.001), use of insulin (coef = 0.31, p =0.015), and levels of BALP (coef = 0.031, p = 0.017) and CTX (coef = 0.7, p = 0.047) were positively related to the risk of hip fracture. Multivariate regression analysis showed that CTX level (coef = −1.41, p = 0.043) was still negatively related to BMD at the lumbar spine.

Conclusion:
This study indicates that T2DM patients with DSPN have special bone metabolism represented by higher BALP level and lower CTX level which may increase BMD at the lumbar spine.
Reliability of a Musculoskeletal Imaging Competency Examination for Physical Therapists
Authors: Burley Troy , Cahanin Richard L. , Brody Lori T. , Boissonnault William G. , Ross Michael D. 
Published: January 2024

Introduction.
The Burley Readiness Examination (BRE) for Musculoskeletal (MSK) Imaging Competency assesses physical therapists' baseline MSK imaging competency. Establishing its reliability is essential to its value in determining MSK imaging competency. The purpose of this study was to test the reliability of the BRE for MSK Imaging Competency among physical therapists (PTs) with varying levels of training and education.

Review of Literature.
Previous literature supports PTs' utility concerning diagnostic imaging; however, no studies directly measure their competency. With PTs expanding their practice scope and professional PT education programs, increasing their MSK imaging instruction, assessing competency becomes strategic in determining the future of MSK education and training.

Subjects.
One hundred twenty-three United States licensed PTs completed the BRE.

Methods.
Physical therapists completed the BRE through an online survey platform. Point biserial correlation (rpb) was calculated for each examination question. Final analyses were based on 140 examination questions. Examination scores were compared using independent sample t-test and one-way analysis of variance. Chi-square tests and odds ratios (ORs) assessed the relationship of a passing examination score (≥75%) and the type of training. Reliability of the BRE was assessed using Cronbach's alpha (α).

Results.
Mean overall examination score was 75.89 ± 8.56%. Seventy PTs (56.9%) obtained a passing score. Physical therapists with additional MSK imaging training, board certification, and residency or fellowship training scored significantly higher (P < .001) compared with those with only entry-level PT program education. Physical therapists with additional MSK imaging training scored significantly higher (x̄ = 81.07% ± 8.93%) and were almost 5 times (OR = 4.74, 95% CI [1.95–11.50]) as likely to achieve a passing score than those without. The BRE demonstrated strong internal consistency (Cronbach's α = 0.874).

Discussion and Conclusions.
The BRE was reliable, consistently identifying higher examination scores among those with increased MSK imaging training. Training in MSK imaging influenced competency more than other factors. The BRE may be of analytical value to PT professional and postprofessional programs.
A Rare Presentation of Pica Disorder in Soap Ingestion Variant
Authors: Sousa Rui , Cunha Francisco , Abreu Joana , Cunha Nuno 
Published: January 2024

Abstract
Pica indicates the persistent ingestion of inedible substances over a period of at least 1 month, being discordant to the individual's cognitive development level and not directly attributable to cultural or social normative practices. The literature suggests that the prevalence of pica varies significantly according to the social and clinical context. It can co-occur with psychiatric disorders, with its etiology being poorly understood and most likely multifactorial. In this article, we report the case of a patient in her 50s with a clinical setting compatible with soap ingestion variant of pica disorder. In addition to the variety of ingested substances, pica can be associated with heterogeneous behavior, mainly of the obsessive-compulsive spectrum. Despite recent research, this condition is still a target of much speculation. This is a very rare and challenging presentation of a soap ingestion variant of pica with very few similar cases described to date.
Correlates of Menarcheal Age in a Psychiatric Sample of Adolescents
Authors: Stumper Allison , Thomas Sarah A. , Zaidi Zaharah A. , Fydenkevez Megan A. , Maron Micaela , Wolff Jennifer C. , Peters Jessica R. 
Published: January 2024

Abstract
Early pubertal timing is associated with more adverse childhood experiences (ACEs) and increased risk for psychopathology during adolescence. However, most work to date has used community or epidemiological samples, and it remains unclear whether these associations persist in acute clinical samples. The present study examined associations between age at menarche and ACEs, psychiatric symptoms, and emotion regulation difficulties in a sample of N = 140 adolescents on a psychiatric inpatient unit. Youth with early menarche reported higher levels of depressive symptoms, more severe suicidal ideation, and greater difficulty with emotion regulation than youth with normative age at menarche. There was a marginal effect of youth with early menarche reporting more ACEs and more anxiety symptoms. These results suggest menarcheal age, and ACEs may be useful risk factors to assess in inpatient settings to predict risk for more severe outcomes, and future research on pubertal timing in high acuity settings is warranted.
Differences in STI/HIV Burden and Sexual Health Care–Seeking Behavior Among First- and Second-Generation Migrant and Western-Born Male Sex Workers Who Have Sex With Men in the Netherlands: A Retrospective Cohort Study
Authors: Peters Charlotte M.M. , Evers Ymke J. , Kampman Carolina J.G. , Theunissen-Lamers Marie-José , Van Den Elshout Mark A.M. , Dukers-Muijrers Nicole H.T.M. , Hoebe Christian J.P.A. 
Published: January 2024

Background
Globally, migrant sex workers have a higher burden of sexually transmitted infections (STI)/human immunodeficiency virus (HIV). This large study aimed to assess demographics, STI/HIV burden, and sexual health care–seeking behavior of first-generation migrant and second-generation migrant male sex workers who have sex with men (MSW-MSM) versus Western-born MSW-MSM.

Methods
Coded STI clinic consultations (n = 6970) from 3116 individual MSW-MSM attending any Dutch STI clinic between 2016 and 2021 were included. First-generation migrant: born outside of northern/central/southern/western Europe/North America/Oceania. Second-generation migrant: ≥1parent born outside of northern/central/southern/western Europe/North America/Oceania. Multivariable logistic regression analysis assessed associations between MSW-MSM groups and STI in first consultation in the data. A Cox proportional hazard regression compared the incidence of a first repeat consultation between migration groups, stratified by STI in first consultation. All analyses were adjusted for age and urbanity of STI clinic region.

Results
First-generation migrant MSW-MSM (n = 1085) were mostly born in Latin America (50%), whereas second-generation migrant MSW-MSM (n = 368) mostly originated from North Africa (30.4%). The proportion of STI diagnoses differed (33.2%, 29.3%, 23.3%; P < 0.001) between the first-generation migrant, second-generation migrant, and Western-born MSW-MSM. First-generation migrant MSW-MSM versus Western-born had an adjusted odds ratio of 1.6 (95% confidence interval, 1.3–1.9) of STI diagnosis in the first consultation. First-generation migrant MSW-MSM versus Western-born had an adjusted hazard ratio of 1.5 (95% confidence interval, 1.3–1.8) of having a first repeat consultation at any time, when stratified for no STI in the first consultation.

Conclusions
The STI/HIV burden is high among all 3 MSW-MSM groups. First-generation migrants have higher odds of STI, but retention in care seems similar. Results highlight the importance of low-threshold STI testing and care for (migrant) MSW-MSM.
Possible Role of Netrin-1/Deleted in Colorectal Cancer/Vascular Endothelial Growth Factor Signaling Pathway in the Pathogenesis of Placenta Accreta Spectrum: A Case-control Study
Authors: Badary Dalia M. , Elsaied Huda , Abdel-Fadeil Mahmoud R. , Ali Mohammed K. , Abou-Taleb Hisham , Iraqy Heba M. 
Published: January 2024

Summary
Netrin-1, an epithelial-secreted protein, plays a key role in placental formation through the promotion of cytotrophoblast proliferation and placental vascular development. These effects are mediated through several receptors, including the deleted in colorectal cancer (DCC) receptor. Placenta accreta spectrum (PAS) is an exaggerated trophoblastic invasion into the uterine myometrium. The exact etiology is unknown, but it is believed that increased trophoblastic invasion, defect decidualization, and/or abnormal angiogenesis might play a role. Our study aimed to investigate the suggested role of macrophage-induced netrin-1/DCC/vascular endothelial growth factor (VEGF) signaling in PAS pathogenesis. A total of 29 women with PAS (as cases) and 29 women with normal pregnancies (as controls) were enrolled in the study. At delivery, placental tissues of both groups were collected and processed for the evaluation of placental netrin-1 level by enzyme-linked immunoassay technique and immunohistochemical analysis of tissue DCC receptor. Placental tissue netrin-1 level of PAS cases showed a statistically significantly higher value than those in the normal group. Significant overexpression of DCC receptors, VEGF, and enhanced macrophage recruitment was noted in PAS cases in comparison to the normal placenta. Macrophage-induced netrin-1/DCC/VEGF signaling might be involved in PAS pathogenesis through the enhancement of trophoblastic angiogenesis.
Subjective Long-Term Outcomes After Vaginal Native Tissue Hysteropexy: Cohort Study
Authors: Lange Sören , Carlin Greta , Zängle Roxana , Heinzl Florian , Umek Wolfgang , Bodner-Adler Barbara 
Published: January 2024

Importance
There are still doubts about long-term satisfaction rates of native tissue uterine preserving surgical techniques for pelvic organ prolapse.

Objective
The objective of this study was to compare long-term subjective success rates and satisfaction rates between vaginal sacrospinous hysteropexy (SSHP) and vaginal hysterectomy with uterosacral ligament suspension (VH-USLS).

Study Design
This was a retrospective single-center, observational matched cohort study in women receiving either SSHP or VH-USLS between 2004 and 2021. Primary outcome was overall subjective success (combined outcome of absence of bulge nor retreatment, and satisfaction with operation) at least 12 months after surgery. Satisfaction with the operation was defined as a combined Patient Global Impression of Improvement rating ≤ 2 and a patient satisfaction score ≥7.

Results
Of 583 patients, 192 patients could be matched (SSHP, 96; VH-USLS, 96), with 55% (SSHP, 60; VH-USLS, 45) participating at the telephone interview. Mean follow-up time was 77 months for VH-USLS, and 36 months for SSHP, respectively. No difference in overall subjective success rates was found between the groups (45% VH-USLS and 51% SSHP; P = 0.54). Overall satisfaction was similar between both groups (70% vs 71%, P = 0.90). Logistic regression found no influence of duration of follow-up and the overall subjective success rate. Both procedures would be recommended to a relative or friend by a large majority of patients (88% vs 85%, P = 0.761). Operative time and hospitalization time were significantly shorter in the SSHP group. No serious complications were reported.

Conclusions
Overall success rates did not differ between both procedures after at least 1 year of follow-up with relatively high satisfaction rates. Sacrospinous hysteropexy had shorter operative time and shorter duration of hospitalization.
<xhtml:span xmlns:xhtml="http://www.w3.org/1999/xhtml" xml:lang="en">Comparative analysis of virulence gene profiles of&#160;<em>Escherichia coli</em>&#160;from clinical and non-clinical sources&#160;in Rivers State, Nigeria
</xhtml:span>
Authors: Abeni Barira Azeez , Frank-Peterside Nnenna , Otokunefor Kome 
Published: January 2024

Traditionally, the presence of virulence features have been thought to be a key factor in differentiating pathogenic from commensal strains. An understanding of virulence potential of Escherichia coli isolates from various sources is essential to help shed light on potential contamination/transmission rates between the various sources. This study was therefore aimed at exploring the occurrence of specific virulence genes and gene profiles associated with Escherichia coli from clinical and non-clinical sources in Rivers State, Nigeria.
Two hundred samples from clinical (urine and feces) and non-clinical (soil and poultry droppings) sources (50 each) were analyzed using standard microbiological procedures. DNA was extracted from isolates presumptively identified as Escherichia coli using PrestoTM Mini gDNA Bacteria-Kit Quick protocol following the manufacturer’s instructions. Isolate identities were confirmed using E. coli specific 16S rRNA primers and confirmed isolates screened for the presence of six virulence genes (Afimbriae binding adhesin (afa), type 1 fimbriae (fimH), P-fimbrial Usher Protein (papC)), iron acquisition systems: aerobactin (aer), Cytotoxic necrotizing factor I (cnf1) and alpha hemolysin (hly).
Results showed that all isolates haboured at least one of the tested virulence genes, with fimH (97%) as the most prevalent virulence gene and papC the least commonly occurring (35%). A higher occurrence of virulence genes was noted in non-clinical isolates though Hly and cnf were not detected at all in any of the isolates studied (0%). Ten different profiles were observed with the afaCc-aer-fimH profile the most commonly occurring virulence gene profile in general (33.3%). For non-clinical isolates however, the aer-afaCc-fimH-papC was the most commonly occurring profile (42.9%).
This study shows that the test clinical and non-clinical Escherichia coli do not carry distinct virulence gene profiles. Hence the virulence genes tested for in this study cannot be used to tell whether an isolate is of a clinical source or not.