bluuebunny/crossref_metadata_2025_split huggingface dataset:
SoxY
gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers
Authors: Sudo Marta , Osvatic Jay , Taylor John D. , Dufour Suzanne C. , Prathep Anchana , Wilkins Laetitia G. E. , Rattei Thomas , Yuen Benedict , Petersen Jillian M. 
Published: May 2024

ABSTRACT

Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of
soxY
in these genomes, with up to five distinct copies per genome. Symbionts harboring only the “canonical”
soxY
were typically ecological “specialists” that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent
soxY
genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the
soxY
gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.

IMPORTANCE
Sulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological “specialists,” and some are “generalists,” but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be “generalists,” revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.
Effectiveness of exercise-based sports injury prevention programmes in reducing injury rates in adolescents and their implementation in the community: a mixed-methods systematic review
Authors: Zhang Zhe Xin , Lai Joseph , Shen Liang , Krishna Lingaraj 
Published: May 2024

ObjectiveDespite evidence supporting the efficacy of sport injury prevention programmes (SIPPs) in adolescents, implementation of SIPPs in community settings is low. This review aims to synthesise and integrate evidence on the efficacy of exercise-based SIPPs in reducing injury rates in adolescents with implementation strategies for such programmes in the community.DesignA systematic review with meta-analysis, narrative synthesis and meta-aggregation was conducted, followed by a convergent segregated approach to integrate the findings. Sensitivity and subgroup analyses were conducted. Study appraisal was performed using Joanna Briggs Institute Critical Appraisal Checklists and Mixed Methods Appraisal Tool.Data sourcesLiterature search of nine databases was carried out to identify studies in English from January 2012 to December 2022.Eligibility criteriaIncluded were randomised controlled trials (RCTs), qualitative or mixed-methods studies. Population included adolescents (10–19 years). Interventions included SIPPs. Outcomes were injury rate and rate ratio (IRR). Phenomena of interest were facilitators and barriers to the implementation of SIPPs.Results23 studies were included for analysis. Meta-analysis for 16 RCTs showed a protective effect of SIPP (IRR 0.63, 95% CI 0.53 to 0.74, p<0.00001) in adolescents. Meta-aggregation of seven qualitative/mixed-method studies revealed four sets of synthesised findings that impact implementation namely players’ perceptions and beliefs, coaches as key facilitators, organisational support and characteristics of the SIPP.ConclusionImplementation of SIPPs provides a 37% risk reduction in adolescents but requires targeting key stakeholders through a top-down multifaceted approach for its efficacy to be translated. Future research should investigate the effectiveness of SIPPs and implementation strategies in adolescents in community settings.
Clinical perspectives on the frequency of hypoglycemia in treat-to-target randomized controlled trials comparing basal insulin analogs in type 2 diabetes: a narrative review
Authors: Rosenstock Julio , Bajaj Harpreet S , Lingvay Ildiko , Heller Simon R 
Published: May 2024

The objective of this review was to comprehensively present and summarize trends in reported rates of hypoglycemia with one or two times per day basal insulin analogs in individuals with type 2 diabetes to help address and contextualize the emerging theoretical concern of increased hypoglycemic risk with once-weekly basal insulins.Hypoglycemia data were extracted from treat-to-target randomized clinical trials conducted during 2000–2022. Published articles were identified on PubMed or within the US Food and Drug Administration submission documents. Overall, 57 articles were identified: 44 assessed hypoglycemic outcomes in participants receiving basal-only therapy (33 in insulin-naive participants; 11 in insulin-experienced participants), 4 in a mixed population (insulin-naive and insulin-experienced participants) and 9 in participants receiving basal-bolus therapy. For the analysis, emphasis was placed on level 2 (blood glucose <3.0 mmol/L (<54 mg/dL)) and level 3 (or severe) hypoglycemia.Overall, event rates for level 2 or level 3 hypoglycemia across most studies ranged from 0.06 to 7.10 events/person-year of exposure (PYE) for participants receiving a basal-only insulin regimen; the rate for basal-bolus regimens ranged from 2.4 to 13.6 events/PYE. Rates were generally lower with second-generation basal insulins (insulin degludec or insulin glargine U300) than with neutral protamine Hagedorn insulin or first-generation basal insulins (insulin detemir or insulin glargine U100). Subgroup categorization by sulfonylurea usage, end-of-treatment insulin dose or glycated hemoglobin reduction did not show consistent trends on overall hypoglycemia rates. Hypoglycemia rates reported so far for once-weekly basal insulins are consistent with or lower than those reported for daily-administered basal insulin analogs.
Predictors of mortality within 1 year after primary ovarian cancer surgery: a nationwide cohort study
Authors: Ørskov Mette , Iachina Maria , Guldberg Rikke , Mogensen Ole , Mertz Nørgård Bente 
Published: May 2024

ObjectivesTo identify predictors of mortality within 1 year after primary surgery for ovarian cancer.DesignProspective nationwide cohort study from 1 January 2005 to 31 December 2012.SettingEvaluation of data from the Danish Gynaecology Cancer Database and the Danish Civil Registration System.Participants2654 women who underwent surgery due to a diagnosis of primary ovarian cancer.Outcome measuresOverall survival and predictors of mortality within 0–180 and 181–360 days after the primary surgery. Examined predictors were age, preoperative American Society of Anesthesiologists (ASA) score, body mass index (BMI), International Federation of Gynaecology and Obstetrics (FIGO) stage, residual tumour tissue after surgery, perioperative blood transfusion and calendar year of surgery.ResultsThe overall 1-year survival was 84%. Within 0–180 days after surgery, the 3 most important predictors of mortality from the multivariable model were residual tumour tissue >2 cm versus no residual tumour (HR=4.58 (95% CI 3.20 to 6.59)), residual tumour tissue ≤2 cm versus no residual tumour (HR=2.50 (95% CI 1.63 to 3.82)) and age >64 years versus age ≤64 years (HR=2.33 (95% CI 1.69 to 3.21)). Within 181–360 days after surgery, FIGO stages III–IV versus I–II (HR=2.81 (95% CI 1.75 to 4.50)), BMI<18.5 vs 18.5–25 kg/m2(HR=2.08 (95% CI 1.18 to 3.66)) and residual tumour tissue >2 cm versus no residual tumour (HR=1.84 (95% CI 1.25 to 2.70)) were the 3 most important predictors.ConclusionsThe most important predictors of mortality within 1 year after surgery were residual tumour tissue (0–180 days after surgery) and advanced FIGO stage (181–360 days after surgery). However, our results suggest that the surgeon should not just aim at radical surgery, but also pay special attention to comorbidity, nutritional state, age >64 years and the need for perioperative blood transfusion.
Facilitators and barriers to self-management in Iranian men with chronic obstructive pulmonary disease: a qualitative study
Authors: Rafii Forough , Alinejad-Naeini Mona , Soleymani Babadi Akbar , Shahriari Elahe , Heidari Beni Farshad 
Published: May 2024

IntroductionSelf-management, as the most common method of chronic obstructive pulmonary disease (COPD) management, is not an isolated behaviour, but a set of physical, social, cultural, psychological and existential factors affecting it.AimThis study aimed to explore the facilitators and barriers to self-management in men with COPD in the unique social, cultural, political and economic context of Iran.MethodsThis paper reports part of the findings of a qualitative grounded theory study aimed at exploring the process of self-management in Iranian men with COPD, which was conducted in Iran from January 2019 to July 2023. Participants included men with COPD, their family members and pulmonologists. The selection of participants in this research began with the purposeful sampling method. Data was collected using semistructured interviews. Data collection continued until the data saturation was achieved. A total of 15 interviews were conducted with nine patients, three family members of patients and three pulmonologists. The data was analysed using the constant comparative analysis method.ResultsThe findings of this study showed that knowledge, education, experience, family involvement and financial support are the factors that facilitate self-management. Factors related to deficits include lack of education, lack of treatment support, family cooperation deficit, financial problems, medication obtaining problems and factors related to disease impacts include specific nature of the disease, residual effect, comorbidity and factors related to negative patients characteristics include false beliefs, poor self-efficacy, feeling shame and non-adherence are barriers to self-management in men with COPD.ConclusionBased on results of this study, healthcare providers and health planners can strengthen the factors that facilitate self-management and weaken or remove the barriers to self-management, so that these patients use self-management strategies with maximum capacity to control the disease.
Examining the hospital costs of children born into relative deprivation in England
Authors: Dale Veronica , Gutacker Nils , Bradshaw Jonathan , Bloor Karen 
Published: May 2024

ObjectiveTo examine the association between being born into relative deprivation and hospital costs during childhood.DesignRetrospective cohort study.MethodsWe created a birth cohort using Hospital Episode Statistics for children born in NHS hospitals in 2003/2004. The Index of Multiple Deprivation (IMD) rank at birth was missing from 75% of the baby records, so we linked mother and baby records to obtain the IMD decile from the mother’s record. We aggregated and costed each child’s hospital inpatient admissions, and outpatient and emergency department (ED) attendances up to 15 years of age. We used 2019/2020 NHS tariffs to assign costs. We constructed an additional cohort, all children born in 2013/2014, to explore any changes over time, comparing the utilisation and costs up to 5 years of age.ResultsOur main cohort comprised 567 347 babies born in 2003/2004, of which we could include 91%. Up to the age of 15 years, children born into the most deprived areas used more hospital services than those born in the least deprived, reflected in higher costs of inpatient, outpatient and ED care. The highest costs and greatest differences are in the year following birth. Comparing this with the later cohort (up to age 5 years), the average cost per child increased across all deprivation deciles, but differences between the most and least deprived deciles appeared to narrow slightly.ConclusionsHealthcare utilisation and costs are consistently higher for children who are born into the most deprived areas compared with the least.
Association of postabsorptive glucose and acetate metabolism with feed intake, growth, and efficiency in finishing beef heifers
Authors: Foote Andrew P. , Rathert-Williams Abigail R. , Salisbury Carlee M. , McConnell Hunter , Lalman David 
Published: May 2024

The objective of this experiment was to determine whether acetate and glucose metabolism and insulin response to glucose are associated with the growth, feed intake, and feed efficiency of finishing heifers. Charolais heifers ( n = 18; initial body weight = 415.7 ± 45.17 kg) were acclimated to restraint with a halter and fed a finishing diet ad libitum using an Insentec feeding system. Following a 12 h fast, a jugular catheter was inserted, and an acetate clearance test was performed followed by a glucose clearance test. Four days after the metabolic tests, heifers began an 84-day DMI and ADG test period. Heifers gained 1.69 ± 0.03 kg/day and consumed 10.4 ± 0.19 kg/day. Acetate and glucose clearance rates were not associated with any production trait ( P ≥ 0.40). Insulin time to peak concentration after the glucose challenge was associated ( r = 0.69; P = 0.003) with G:F, but not peak concentration ( P = 0.45). The increased time to insulin peak could indicate that efficient heifers have pancreatic β-cell dysfunction, which is a contributor to insulin resistance. These data indicate that insulin resistance early in the finishing period could be related to improved feed efficiency in finishing heifers.
Integrability of Dirac equations in static spherical space-times
Authors: Cianci Roberto , Vignolo Stefano , Fabbri Luca 
Published: May 2024

AbstractWe consider the Dirac equations in static spherically-symmetric space-times, and we present a type of spinor field whose structure allows the separation of elevation angle and radial coordinate in very general situations. We demonstrate that after such a separation of variables the Dirac equations reduce to two equations that can always be integrated, at least in principle. To prove that ours is a fully-working method, we find an explicit exact solution in the special case of the de Sitter universe.
Investigation of structural, dielectric and optical properties of the (Bi0.5La0.5Fe)0.5(Bi0.5Na0.5Ti)0.5O3perovskite for some electronic devices
Authors: Bhuyan R. K. , Parida S. K. 
Published: May 2024

This paper outlines the investigation of structural, dielectric, complex impedance and optical properties of lanthanum-modified (Bi[Formula: see text]La[Formula: see text]Fe)[Formula: see text](Bi[Formula: see text]Na[Formula: see text]Ti)[Formula: see text]O3(BLF–BNT) single perovskite oxide synthesized by conventional solid-state reaction method. From Rietveld refinement, the crystal structure of the BLF–BNT ceramic has confirmed a tetragonal and the estimated average crystallite size is found to be 43.6[Formula: see text]nm. The dielectric properties of the La-doped BLF–BNT ceramic reveal the presence of Maxwell–Wagner-type dielectric dispersion. This suggests the occurrence of charge accumulation at grain boundaries and interfaces within the material. The complex impedance and complex electric modulus studies were employed to gain insight into the microscopic dielectric relaxations and conduction processes of the material. The electric modulus spectroscopy reveals the existence of nonDebye-type relaxation processes, including localized and long-range relaxation processes. The Nyquist and Cole–Cole plots show the semiconducting nature of the BLF–BNT ceramic. With the help of the Arrhenius method based on the imaginary portion of the electrical impedance and modulus, activation energies and relaxation times have been estimated. These parameters contribute to a deeper understanding of the electrical properties and conduction mechanisms within the material. Further, Raman spectroscopy, a nondestructive chemical analysis technique, was conducted to confirm the composition and structural integrity of the proposed system through its atomic vibrations. Also, the bandgap energy of the material has been estimated using Tauc’s relation and is found to be 1.69[Formula: see text]eV.This signifies that the BLF–BNT ceramic possesses a suitable bandgap for certain device applications, making it a promising candidate in various technological fields. Moreover, the overall comprehensive study of the proposed ceramic provides valuable insight and opens new possibilities for its potential applications in various electronic devices.
Overcoming Nutrient Stress: Integrin αvβ3-Driven Metabolic Adaptation Supports Tumor Initiation
Authors: Rainero Elena 
Published: May 2024

AbstractNutrient stress accompanies several stages of tumor progression, including metastasis formation. Metabolic reprogramming is a hallmark of cancer, and it has been associated with stress tolerance and anchorage-independent cell survival. Adaptive responses are required to support cancer cell survival under these conditions. In this issue of Cancer Research, Nam and colleagues showed that the extracellular matrix (ECM) receptor integrin β3 was upregulated in lung cancer cells in response to nutrient starvation, resulting in increased cell survival that was independent from ECM binding. Delving into the molecular mechanisms responsible for this, the authors found that integrin β3 promoted glutamine metabolism and oxidative phosphorylation (OXPHOS) by activating a Src/AMPK/PGC1α signaling pathway. Importantly, in vivo experiments confirmed that OXPHOS inhibition suppressed tumor initiation in an orthotopic model of lung cancer, while β3 knockout completely abrogated tumor initiation. These observations indicate that targeting signaling pathways downstream of αvβ3 could represent a promising therapeutic avenue to prevent lung cancer progression and metastasis.See related article by Nam et al., p. 1630
Role of Gut Microbiome in Neoadjuvant Chemotherapy Response in Urothelial Carcinoma: A Multi-institutional Prospective Cohort Evaluation
Authors: Bukavina Laura , Ginwala Rashida , Eltoukhi Mohamed , Sindhani Mohit , Prunty Megan , Geynisman Daniel M. , Ghatalia Pooja , Valentine Henkel , Calaway Adam , Correa Andres F. , Brown Jason R. , Mishra Kirtishri , Plimack Elizabeth R. , Kutikov Alexander , Ghannoum Mahmoud , Elshaer Mohammed , Retuerto Mauricio , Ponsky Lee , Uzzo Robert G. , Abbosh Philip H. 
Published: May 2024

Abstract

Neoadjuvant chemotherapy (NAC) is linked with clinical advantages in urothelial carcinoma for patients with muscle-invasive bladder cancer (MIBC). Despite comprehensive research into the influence of tumor mutation expression profiles and clinicopathologic factors on chemotherapy response, the role of the gut microbiome (GM) in bladder cancer chemotherapy response remains poorly understood. This study examines the variance in the GM of patients with bladder cancer compared with healthy adults, and investigates GM compositional differences between patients who respond to chemotherapy versus those who exhibit residual disease.
Our study reveals distinct clustering, effectively separating the bladder cancer and healthy cohorts. However, no significant differences were observed between chemotherapy responders and nonresponders within community subgroups. Machine learning models based on responder status outperformed clinical variables in predicting complete response (AUC 0.88 vs. AUC 0.50), although no single microbial species emerged as a fully reliable biomarker.
The evaluation of short chain fatty acid (SCFA) concentration in blood and stool revealed no correlation with responder status. Still, SCFA analysis showed a higher abundance of Akkermansia (rs = 0.51, P = 0.017) and Clostridia (rs = 0.52, P = 0.018), which correlated with increased levels of detectable fecal isobutyric acid. Higher levels of fecal Lactobacillus (rs = 0.49, P = 0.02) and Enterobacteriaceae (rs = 0.52, P &lt; 0.03) correlated with increased fecal propionic acid.
In conclusion, our study constitutes the first large-scale, multicenter assessment of GM composition, suggesting the potential for a complex microbial signature to predict patients more likely to respond to NAC based on multiple taxa.

Significance:
Our study highlights results that link the composition of the GM to the efficacy of NAC in MIBC. We discovered that patients with higher levels of Bacteroides experienced a worse response to NAC. This microbial signature shows promise as a superior predictor of treatment response over traditional clinical variables. Although preliminary, our findings advocate for larger, more detailed studies to validate these associations.
Identification of the Molecular Components of Enhancer-Mediated Gene Expression Variation in Multiple Tissues Regulating Blood Pressure
Authors: Yaacov Or , Mathiyalagan Prabhu , Berk-Rauch Hanna E. , Ganesh Santhi K. , Zhu Luke , Hoffmann Thomas J. , Iribarren Carlos , Risch Neil , Lee Dongwon , Chakravarti Aravinda 
Published: May 2024

BACKGROUND:
Inter-individual variation in blood pressure (BP) arises in part from sequence variants within enhancers modulating the expression of causal genes. We propose that these genes, active in tissues relevant to BP physiology, can be identified from tissue-level epigenomic data and genotypes of BP-phenotyped individuals.

METHODS:
We used chromatin accessibility data from the heart, adrenal, kidney, and artery to identify cis-regulatory elements (CREs) in these tissues and estimate the impact of common human single-nucleotide variants within these CREs on gene expression, using machine learning methods. To identify causal genes, we performed a gene-wise association test. We conducted analyses in 2 separate large-scale cohorts: 77 822 individuals from the Genetic Epidemiology Research on Adult Health and Aging and 315 270 individuals from the UK Biobank.

RESULTS:

We identified 309, 259, 331, and 367 genes (false discovery rate <0.05) for diastolic BP and 191, 184, 204, and 204 genes for systolic BP in the artery, kidney, heart, and adrenal, respectively, in Genetic Epidemiology Research on Adult Health and Aging; 50% to 70% of these genes were replicated in the UK Biobank, significantly higher than the 12% to 15% expected by chance (
P
<0.0001). These results enabled tissue expression prediction of these 988 to 2875 putative BP genes in individuals of both cohorts to construct an expression polygenic score. This score explained ≈27% of the reported single-nucleotide variant heritability, substantially higher than expected from prior studies.

CONCLUSIONS:
Our work demonstrates the power of tissue-restricted comprehensive CRE analysis, followed by CRE-based expression prediction, for understanding BP regulation in relevant tissues and provides dual-modality supporting evidence, CRE and expression, for the causality genes.