bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae)
Authors: Palacios Catalina , Wang Pengcheng , Wang Nan , Brown Megan A , Capatosto Lukas , Du Juan , Jiang Jiahu , Zhang Qingze , Dahal Nishma , Lamichhaney Sangeet 
Published: September 2023

Abstract
Species residing across elevational gradients display adaptations in response to environmental changes such as oxygen availability, ultraviolet radiation, and temperature. Here, we study genomic variation, gene expression, and long-term adaptation in Tibetan Partridge (Perdix hodgsoniae) populations residing across the elevational gradient of the Tibetan Plateau. We generated a high-quality draft genome and used it to carry out downstream population genomic and transcriptomic analysis. The P. hodgsoniae populations residing across various elevations were genetically distinct, and their phylogenetic clustering was consistent with their geographic distribution. We identified possible evidence of gene flow between populations residing in &lt;3,000 and &gt;4,200 m elevation that is consistent with known habitat expansion of high-altitude populations of P. hodgsoniae to a lower elevation. We identified a 60 kb haplotype encompassing the Estrogen Receptor 1 (ESR1) gene, showing strong genetic divergence between populations of P. hodgsoniae. We identified six single nucleotide polymorphisms within the ESR1 gene fixed for derived alleles in high-altitude populations that are strongly conserved across vertebrates. We also compared blood transcriptome profiles and identified differentially expressed genes (such as GAPDH, LDHA, and ALDOC) that correlated with differences in altitude among populations of P. hodgsoniae. These candidate genes from population genomics and transcriptomics analysis were enriched for neutrophil degranulation and glycolysis pathways, which are known to respond to hypoxia and hence may contribute to long-term adaptation to high altitudes in P. hodgsoniae. Our results highlight Tibetan Partridges as a useful model to study molecular mechanisms underlying long-term adaptation to high altitudes.
Diverse regulatory pathways modulate bet hedging of competence induction in epigenetically-differentiated phase variants ofStreptococcus pneumoniae
Authors: Kwun Min Jung , Ion Alexandru V , Oggioni Marco R , Bentley Stephen D , Croucher Nicholas J 
Published: September 2023

AbstractDespite enabling Streptococcus pneumoniae to acquire antibiotic resistance and evade vaccine-induced immunity, transformation occurs at variable rates across pneumococci. Phase variants of isolate RMV7, distinguished by altered methylation patterns driven by the translocating variable restriction-modification (tvr) locus, differed significantly in their transformation efficiencies and biofilm thicknesses. These differences were replicated when the corresponding tvr alleles were introduced into an RMV7 derivative lacking the locus. RNA-seq identified differential expression of the type 1 pilus, causing the variation in biofilm formation, and inhibition of competence induction in the less transformable variant, RMV7domi. This was partly attributable to RMV7domi’s lower expression of ManLMN, which promoted competence induction through importing N-acetylglucosamine. This effect was potentiated by analogues of some proteobacterial competence regulatory machinery. Additionally, one of RMV7domi’s phage-related chromosomal island was relatively active, which inhibited transformation by increasing expression of the stress response proteins ClpP and HrcA. However, HrcA increased competence induction in the other variant, with its effects depending on Ca2+ supplementation and heat shock. Hence the heterogeneity in transformation efficiency likely reflects the diverse signalling pathways by which it is affected. This regulatory complexity will modulate population-wide responses to synchronising quorum sensing signals to produce co-ordinated yet stochastic bet hedging behaviour.
The Perceived Usability of Virtual Visits Among Black Adults’ Receiving Oncology Care: A Qualitative Analysis
Authors: Tam Samantha , Neslund-Dudas Christine , Barrett Amy M , Barrow Lauren C J , Fridman Ilona , Kinlaw Alan C , Puviindran Praveen , Royce Trevor J , Smith Angela B , Stein Jacob N , Wood William A , Elston Lafata Jennifer 
Published: September 2023

Abstract

Background
With the COVID-19 pandemic came rapid uptake in virtual oncology care. During this, sociodemographic inequities in access to virtual visits (VVs) have become apparent. To better understand these issues, we conducted a qualitative study to describe the perceived usability and acceptability of VVs among Black adults diagnosed with cancer.

Methods
Adults who self-identified as Black and had a diagnosis of prostate, multiple myeloma, or head and neck cancer were recruited from 2 academic medical centers, and their community affiliates to participate in a semi-structured interview, regardless of prior VV experience. A patient and family advisory board was formed to inform all components of the study. Interviews were conducted between September 2, 2021 and February 23, 2022. Transcripts were organized topically, and themes and subthemes were determined through iterative and interpretive immersion/crystallization cycles.

Results
Of the 49 adults interviewed, 29 (59%) had participated in at least one VV. Three overarching themes were derived: (1) VVs felt comfortable and convenient in the right contexts; (2) the technology required for VVs with video presented new challenges, which were often resolved by an audio-only telephone call; and (3) participants reported preferring in-person visits, citing concerns regarding gaps in nonverbal communication, trusting providers, and distractions during VV.

Conclusion
While VVs were reported to be acceptable in specific circumstances, Black adults reported preferring in-person care, in part due to a perceived lack of interpersonal connectedness. Nonetheless, retaining reimbursement for audio-only options for VVs is essential to ensure equitable access for those with less technology savvy and/or limited device/internet capabilities.
The landscape of innate and adaptive immune cell subsets in patients with adult-onset Still’s disease
Authors: Chi Huihui , Hong Xinyue , Dai Ningqi , Chen Longfang , Zhang Hao , Liu Honglei , Cheng Xiaobing , Ye Junna , Shi Hui , Hu Qiongyi , Meng Jianfen , Zhou Zhuochao , Jia Jinchao , Liu Tingting , Wang Fan , Wang Mengyan , Ma Yuning , Chen Xia , You Yijun , Zhu Dehao , Tang Zihan , Yang Chengde , Teng Jialin , Su Yutong , Sun Yue 
Published: September 2023

Abstract

Objective
Adult-onset Still’s disease (AOSD) is a systemic autoinflammatory disorder. The understanding of the changes in adaptive immune cells and the crosstalk between innate and adaptive immune systems in AOSD is limited. This study aimed to examine the peripheral immune cell composition and inflammatory protein levels in AOSD patients.

Methods
Twenty-nine active AOSD patients were enrolled. Flow cytometry was used to analyse the cell populations in peripheral blood. Antibody chips were utilized to detect the protein expression profile in serum.

Results
In active AOSD patients, there was an increase in the percentage of classical and non-classical monocytes among peripheral blood mononuclear cells. The proportion of natural killer (NK) cells decreased, with an increase in CD56dim NK1 cells and a decrease in CD56bright NK2 cells compared with healthy controls (HCs). The percentage of naïve central memory T cells was decreased, while the percentage of effector and effector memory T cells was increased among adaptive lymphocytes. The proportion of naïve B and memory B cells was decreased, while plasma cells were increased in AOSD patients, indicating activation of the adaptive immune system. Additionally, the serum levels of 40 proteins were elevated in AOSD patients, primarily involved in cytokine–cytokine receptor interaction, inflammatory response and regulation of mitogen-activated protein kinase cascade.

Conclusion
Our findings showed the activation of the innate and adaptive immune system in AOSD. The protein–protein interaction analysis suggested potential communication between innate and adaptive cell subsets. These findings provide new insights into the pathogenesis of the disease and the development of targeted therapies.
Efficacy and safety of anti-interleukin-1 treatment in familial Mediterranean fever patients: a systematic review and meta-analysis
Authors: Kilic Berkay , Guler Yelin , Azman Feyza N , Bostanci Ece , Ugurlu Serdal 
Published: September 2023

Abstract

Objectives
FMF is the most common hereditary monogenic fever syndrome marked by recurrent attacks of fever and polyserositis. Colchicine is the current recommended first-line treatment for FMF. However, a small portion of FMF patients are unresponsive or intolerant to colchicine. Anti-IL-1 agents are alternative treatment options for colchicine-resistant or -intolerant FMF patients. This systematic review and meta-analysis aimed to provide qualitative and quantitative evidence for the efficacy and safety of anti-IL-1 agents in adult and paediatric FMF patients.

Methods
MEDLINE, EMBASE, CENTRAL and Web of Science were screened from inception to May 2023. We included adult and paediatric FMF patients who received continuous treatment with at least one of the anti-IL-1 drugs: anakinra, canakinumab and rilonacept. The primary efficacy outcome was the proportion of patients who achieved complete remission of attacks and the primary safety outcome was the proportion of patients who experienced at least one adverse event during treatment. A random-effects meta-analysis was performed for the quantitative synthesis.

Results
Fourty-four reports consisting of 1399 FMF patients were included. Sixty percent (95% CI 49%, 72%) of the adult patients and 81% (95% CI 72%, 89%) of the paediatric patients achieved complete remission. Anti-IL-1 agents significantly decreased levels of inflammatory markers. At least one adverse event was observed in 25% (95% CI 13%, 37%) of the adult patients and 12% (95% CI 3%, 21%) of the paediatric patients.

Conclusion
Anti-IL-1 agents were effective and demonstrated a low adverse event profile in paediatric and adult FMF patients.
Prevalence of Hyperacusis Diagnosis in Veterans Who Use VA Healthcare
Authors: Theodoroff Sarah M. , Reavis Kelly M. , Norrholm Seth D. 
Published: September 2023

Objectives:
The primary objective was to estimate the prevalence of hyperacusis diagnosis in treatment-seeking Veterans, paying attention to when it is diagnosed in conjuncture with common comorbid conditions.

Design:
This retrospective observational study used Veteran electronic health records from January 2015 to July 2021. Hyperacusis and comorbid conditions were identified using International Classification of Disease diagnostic codes.

Results:
The prevalence of hyperacusis diagnosis was 0.06%. Veterans diagnosed with tinnitus, posttraumatic stress disorder, headache, or traumatic brain injury were between two and seven times more likely to have an International Classification of Disease code for hyperacusis.

Conclusions:
The estimated prevalence of hyperacusis diagnosis using electronic health records is grossly below what is reported in the literature. This is likely due to lack of standardized methods to diagnosis hyperacusis and when present with comorbid conditions, uncertainty when it should be coded as a secondary diagnosis. Future clinical and research efforts prioritizing hyperacusis are desperately needed.
Long-Term Evaluation of Ulnar Nerve Function in Patients with Distal Humerus Fractures Treated with Open Reduction and Internal Fixation: A Nerve Conduction Study
Authors: Bayram Serkan , Gökçeoğlu Yaşar Samet , Kendirci Alper Şükrü , Şahin Koray , Şentürk Fatih , Baslo Mehmet Barış , Erşen Ali 
Published: September 2023

Abstract

Objectives:
To investigate the long-term evaluation with electromyography of ulnar nerve function in patients with distal humerus fractures (DHFs) treated with open reduction and internal fixation.

Design:
Retrospective cohort study.

Setting:
Level 1 trauma center.

Patients:
Fifty-two patients (20 men and 32 women) with DHFs.

Interventions:
All patients underwent open reduction and internal fixation between 2002 and 2017 with a minimum five years’ follow-up.

Main outcome measurements:
The nerve conduction test was done for evaluation ulnar nerve function. Secondary outcomes were modified McGowan grading system for symptoms of ulnar neuropathy.

Results:
The mean follow-up time was 112.7 ± 39 months after surgery. 28.8% (15) of the patients scored in Grade I, 30 (57.6%) in Grade II, and 7 (13.6%) in Grade III on the affected side according to McGowan grading scale. According to EMG results, 40.1% (21/52) of patients had abnormal results. There was significant difference between fracture and unaffected side regarding ulnar nerve motor wrist CMAP amplitude, motor below elbow CMAP amplitude, above elbow CMAP amplitude, above elbow MNCV, and sensory wrist amplitude. Ulnar nerve motor wrist-ADM latency (p = 0.01; r = 0.446) and ulnar nerve sensory conduction velocity (p < 0.001, r = −0.504) were significant correlation with McGowan grading scale.

Conclusion:
There were significant difference ulnar nerve motor amplitude and sensory wrist amplitude between fracture and unaffected side. A mean decrease in sensory amplitude of fracture elbow was found 25% compared to the unaffected side in our result.

Level of Evidence:
Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Golgi Protein 73 Promotes LPS-Induced Cardiac Dysfunction via Mediating Myocardial Apoptosis and Autophagy
Authors: Xing Yaqi , Gao Zhenqiang , Bai Yunfei , Wang Wen , Chen Chen , Zheng Yuanyuan , Meng Yan 
Published: September 2023

Abstract:
Sepsis-induced cardiac dysfunction represents a major cause of high mortality in intensive care units with limited therapeutic options. Golgi protein 73 (GP73) has been implicated in various diseases. However, the role of GP73 in lipopolysaccharide (LPS)-induced cardiac dysfunction is unclear. In this study, we established a sepsis-induced cardiac dysfunction model by LPS administration in wild-type and GP73 knockout (GP73

−/−
) mice. We found that GP73 was increased in LPS-treated mouse hearts and LPS-cultured neonatal rat cardiomyocytes (NRCMs). Knockout of GP73 alleviated myocardial injury and improved cardiac dysfunction. Moreover, depletion of GP73 in NRCMs relieved LPS-induced cardiomyocyte apoptosis and activated myocardial autophagy. Therefore, GP73 is a negative regulator in LPS-induced cardiac dysfunction by promoting cardiomyocyte apoptosis and inhibiting cardiomyocyte autophagy.
Association of serum thyroid hormone and coronary artery calcification in patients who underwent invasive coronary angiography: an observational study
Authors: Shen Xueqian , Jian Wen , Shi Yuchen , Liu Jinghua 
Published: September 2023

Background
Thyroid hormones (TH) are known to have a range of effects on the cardiovascular system. However, there is still controversy regarding the relationship between thyroid function and coronary artery calcification (CAC). The purpose of this paper is to investigate the relationship between TH and CAC, especially severe CAC, in patients who underwent invasive coronary angiography (ICA). This may provide further insights into the potential role of TH in the development and progression of cardiovascular disease.

Method
This observational study included 4221 patients who underwent ICA after completing CTA in a single center. We collected demographic, clinical, and laboratory data from electronic medical records and measured CAC scores via non-contrast cardiac CT.

Result
The study found that there is a negative correlation between the CAC score and FT3 level, even after adjusting for potential confounding factors, but there was no correlation between the CAC score and FT4 or TSH. When categorized into quartiles, the highest quartile of FT3 was associated with a decrease (β = −104.37, 95%CI: −172.54, −36.21) in calcification score compared to the lowest quartile. This correlation was more significant in the subgroup of individuals with diabetes or hypertension.

Conclusion
The study found a negative correlation between FT3 and CAC in patients who underwent ICA. The correlation was consistent with other studies and may suggest that low levels of FT3 are associated with severe CAC. The study may provide new evidence for future research on CAC and potential therapeutic approaches.
Effect of repeated, on-field sprints on kinematic variables in wheelchair rugby players
Authors: Bakatchina Sadate , Brassart Florian , Dosseh Kossivi , Weissland Thierry , Pradon Didier , Faupin Arnaud 
Published: September 2023

Abstract

Objective
To evaluate the influence of repeated sprints on kinematic performance and propulsion variables during the acceleration and constant peak velocity phases in wheelchair rugby players classified as defensive (LP-D) or offensive players (HP-O).

Design
22 players (13 LP-D and 9 HP-O) performed 6 × 20 m repeated sprint field tests. We calculated peak wheelchair velocities, propulsion phase times, deceleration phase times, cycle times, and left-right velocity asymmetry of the best and last sprints during the acceleration and constant peak velocity phases; the rate of decline in performance variables between the best and the last sprint and a fatigue index.

Results
Peak velocities during the acceleration and constant peak velocity phases and mean velocity over the whole sprint were significantly higher during the best than last sprint. Peak velocities were higher during the acceleration and constant peak velocity phases for the best and last sprint for HP-O. The rate of decline in peak velocity during the constant peak velocity phase was higher for LP-D. Fatigue index and rate of decline in velocities and sprint time were higher for LP-D.

Conclusions
Performance variables and the rate of decline in performance variables depended on functional capacity and wheelchair type.
Successful Multidrug-Resistant Tuberculosis Treatment Without HIV Viral Suppression: A Missed Opportunity
Authors: Geiger Keri , Patil Amita , Budhathoki Chakra , Dooley Kelly E. , Lowensen Kelly , Ndjeka Norbert , Ngozo Jacqueline , Farley Jason E. 
Published: September 2023

Background:
Coinfection with multidrug-resistant tuberculosis (MDR-TB) and HIV is common, but few published studies examine how undergoing MDR-TB treatment affects HIV disease indicators.

Methods:
Using data from a nested, retrospective cohort of people with HIV (PWH) and successful MDR-TB treatment outcomes, we built multivariable regression models to explore correlates of HIV viral suppression at MDR-TB treatment completion.

Results:
Among 531 PWH successfully treated for MDR-TB, mean age was 37.4 years (SD 10.2, interquartile range 30–43), 270 (50.8%) were male, 395 (74.4%) were virally suppressed at MDR-TB outcome, and 259 (48.8%) took bedaquiline. Older age (adjusted odds ratio [aOR] 1.04, 95% confidence interval [CI]: 1.01 to 1.06) increased odds of viral suppression, while having a prior TB episode (aOR 0.45, 95% CI: 0.31 to 0.64), having a detectable viral load at MDR-TB treatment initiation (aOR 0.17, 95% CI: 0.09 to 0.30), living in a township (aOR 0.49, 95% CI: 0.28 to 0.87), and being changed from efavirenz-based antiretroviral therapy (ART) to a protease inhibitor due to bedaquiline usage (aOR 0.19, 95% CI: 0.04 to 0.82) or not having an ART change while on bedaquiline (aOR 0.29, 95% CI: 0.11 to 0.75) lowered odds of viral suppression. Changing from efavirenz to nevirapine due to bedaquiline usage did not significantly affect odds of viral suppression (aOR 0.41, 95% CI: 0.16 to 1.04).

Conclusions:
Increased pill burden and adverse treatment effects did not significantly affect HIV viral suppression while switching ART to a protease inhibitor to accommodate bedaquiline or not changing ART while taking bedaquiline did, suggesting that PWH and MDR-TB may benefit from additional support if they must switch ART.
A Patient-Centered, Combination Intervention to Support Adherence to HIV Pre-exposure Prophylaxis During Pregnancy and Breastfeeding: A Randomized Pilot Study in Malawi
Authors: Chi Benjamin H. , Saidi Friday , Graybill Lauren A. , Phanga Twambilile , Mollan Katie R. , Amico K. Rivet , Freeborn Kellie , Rosenberg Nora E. , Hill Lauren M. , Hamoonga Twaambo , Richardson Brian , Kalua Thokozani , Phiri Sam , Mutale Wilbroad 
Published: September 2023

Background:
Daily oral pre-exposure prophylaxis (PrEP) can reduce HIV incidence in pregnant and breastfeeding women, but adherence is essential.

Methods:
We conducted a pilot randomized trial to evaluate an intervention package to enhance antenatal and postnatal PrEP use in Lilongwe, Malawi. The intervention was based on patient-centered counseling adapted from previous PrEP studies, with the option of a participant-selected adherence supporter. Participants were locally eligible for PrEP and randomized 1:1 to intervention or standard counseling (ie, control) and followed for 6 months. Participants received the intervention package or standard counseling at enrollment, 1, 3, and 6 months. Adherence was measured through plasma and intracellular tenofovir concentrations and scored using a published algorithm. Our primary outcome was retention in care with concentrations consistent with 4–7 doses/week.

Results:
From June to November 2020, we enrolled 200 pregnant women with the median gestational age of 26 (interquartile range: 19–33) weeks. Study retention was high at 3 months (89.5%) and 6 months (85.5%). By contrast, across the 2 time points, 32.8% of participants retained in the study had adherence scores consistent with 2–5 doses/week while 10.3% had scores consistent with daily dosing. For the composite primary end point, no substantial differences were observed between the intervention and control groups at 3 months (28.3% vs. 29.0%, probability difference: −0.7%, 95% confidence interval: −13.3%, 11.8%) or at 6 months (22.0% vs. 26.3%, probability difference: −4.3%, 95% confidence interval: −16.1%, 7.6%).

Conclusions:
In this randomized trial of PrEP adherence support, retention was high, but less than one-third of participants had pharmacologically confirmed adherence of ≥4 doses/week. Future research should focus on antenatal and postnatal HIV prevention needs and their alignment across the PrEP continuum, including uptake, persistence, and adherence.