bluuebunny/crossref_metadata_2025_split huggingface dataset:
The complete genome sequence of a
Paenibacillus tundrae
strain MLY93 isolated from spot disease-infected tobacco leaves in China
Authors: Lin Guan , Yang Xianhai , Xiang Dong , Yang Lei , Liu Yong , Zhang Huilin , Liu Shiwang 
Published: September 2024

ABSTRACT

This study presents the complete gene sequence of a
Paenibacillus tundrae
strain isolated from tobacco spot disease leaves in Xingyi, Guizhou Province, China. The genetic understanding of
P. tundrae
is advanced by this research.
Magmatic processes in the plumbing system of the Cenozoic ultrapotassic volcanic rocks in the southeastern Tibetan Plateau
Authors: Ma Rui , Bi Xian-Wu , Xu Lei-Luo , Yang Zong-Yong , Huang Ming-Liang , Liu Gong 
Published: September 2024

Abstract
Although great effort has been put into characterizing the sources of the Cenozoic ultrapotassic volcanic rocks in the southeastern Tibetan Plateau, insufficient attention has been paid to the magmatic processes in the magma plumbing systems of these rocks. We filled this gap by analyzing clinopyroxene (Cpx) phenocrysts of these rocks from the Wozhong area for major and trace elements and Sr isotopes. Based on textural and Mg# variations, Cpx phenocrysts were classified into five subtypes: type 1 has three zones (core, mantle, and rim) with decreasing Mg# outward (normal zoning); type 2 has two zones (core and rim) with normal zoning; type 3 has three zones with reverse zoning; type 4 has a homogeneous core and an oscillatory-zoned rim; and type 5 has fine oscillatory zoning. Estimated crystallization temperatures and pressures for the different types/zones are variable at grain scale, suggesting that the crystallization of a single crystal took place at various depths. The prevalence of oscillatory and reverse zoning, parallel trace-element patterns, and overlapping chemical-isotopic compositions of the Cpx phenocrysts with relatively high Mg# (87–93) indicate that magma recharge and mixing took place in the magma plumbing system. All of the Cpx data together show two different compositional evolution trends that are consistent with fractional crystallization and melt-mush reactions induced by magma recharge in the magmatic plumbing system. Trace elements and Sr isotopes of the most primitive Cpx (Mg# 87–93) support the interpretation that the parental magma for the Wozhong ultrapotassic volcanic rocks was originally derived from a metasomatized mantle source.
Dissolution of Ta–Nb and Nb Minerals in Granitoid Melts
Authors: Chevychelov V. Yu. , Viryus A. A. 
Published: September 2024

Abstract
The effective solubilities (maximum contents) of Ta and Nb in model felsic lithium-fluoride melts of variable alkalinity and alumina content were experimentally determined at the dissolution of Ta–Nb and Nb minerals: pyrochlore, microlite, ilmenorutile, and ferrotapiolite at T = 650–850°C and P = 100 and 400 MPa. The Ta and Nb partitioning in the mineral-melt systems was also studied. When pyrochlore is dissolved in granitoid melts at P = 100 MPa and T = 650–850°C, the highest effective solubilities of Nb (0.7–1.8 wt %) are obtained in alkaline melt, and they significantly decrease (to 0.03–0.5 wt %) in subaluminous and peraluminous melts. A temperature increase increases the solubility (content) of Nb in the melt. Similar dependences were obtained for Ta solubility by dissolving microlite. In peraluminous granitoid melt, microlite remains stable, while pyrochlore becomes unstable. A pressure decrease from 400 to 100 MPa in alkaline and subaluminous melts was found out to not significantly affect on the dissolution of microlite and pyrochlore, whereas Ta and Nb contents in the peraluminous melt noticeably decrease. The dependences of Nb solubility and its partitioning between granitoid melts and ilmenorutile on the alkalinity–alumina content of the melt are similar to those for the dissolution of columbite and tantalite. The dependences obtained by dissolving ferrotapiolite, pyrochlore, and microlite differ from them.
Associations of genetic variants for refractive error and axial length in adults with ocular endophenotypes in children: a cross-sectional and longitudinal study
Authors: Zaabaar Ebenezer , Shing Erica , Zhang Xiu Juan , Wang Yuyao , Kam Ka Wai , Zhang Yuzhou , Yip Wilson W. K. , Young Alvin L. , Tam Pancy O. S. , Tham Clement C. , Pang Chi Pui , Yam Jason C. , Chen Li Jia 
Published: September 2024

AimsTo investigate the associations of genetic variants previously linked to axial length (AL) and spherical equivalent refraction (SE) in adults with refractive error and related endophenotypes in children, at baseline and 3-year follow-up.Methods15 candidate single-nucleotide polymorphisms (SNPs), selected from previous Genome-Wide Association Studies and meta-analyses, were genotyped in 2819 Chinese children, who had undergone baseline and 3-year follow-up cycloplegic refraction, ocular biometry and ocular health examinations. Linear regression analyses were conducted to assess the associations of the SNPs with baseline measurements and longitudinal changes in SE, spherical power (SPH), AL, corneal radius of curvature (CR) and AL/CR ratio.ResultsSNPsZMAT4rs7829127,ZMAT4rs16890057,TOXrs7837791,GRIA4rs11601239 andRDH5rs3138142 were associated with SE (β=0.233, p=4.21×10−4; β=0.221, p=7.87×10−4; β=0.106, p=0.0076; β=0.084, p=0.041; β=0.14, p=0.013, respectively) and SPH (β=0.24, p=2.3×10−4; β=0.232, p=3.8×10−4; β=0.088, p=0.025; β=0.086, p=0.034; β=0.14, p=0.012, respectively). Among them,ZMAT4rs7829127 and rs16890057, were also associated with AL (β=−0.128, p=5.6×10−4; β=−0.128, p=5.21×10−4) and AL/CR ratio (β=−0.014, p=0.0028; β=−0.014, p=0.0034), whereasTOXrs7837791 was associated with AL (β=−0.062, p=0.0058) andGRIA411 601 239 with AL/CR ratio (β=−0.0058, p=0.049). Additionally,CD55rs1652333 andRDH5rs3138142 were associated with 3-year longitudinal changes in AL (β=0.062, p=0.018; β=−0.079, p=0.029) and CR (β=0.014, p=0.027; β=−0.018, p=0.035).ConclusionAmong SNPs previously associated with AL and SE in adults, variants inZMAT4,TOXandGRIA4were associated with AL, SE, SPH, and/or AL/CR ratio, while variants inRDH5andCD55showed associations with AL and CR changes in children.
Arthroscopic partial meniscectomy versus exercise therapy for degenerative meniscal tears: 10-year follow-up of the OMEX randomised controlled trial
Authors: Berg Bjørnar , Roos Ewa M , Englund Martin , Kise Nina Jullum , Engebretsen Lars , Eftang Cathrine Nørstad , Risberg May Arna 
Published: September 2024

ObjectiveTo evaluate radiographic knee osteoarthritis (OA) progression, development of knee OA, patient-reported outcomes and knee muscle strength at 10-year follow-up after arthroscopic partial meniscectomy (APM) or exercise therapy for degenerative meniscal tears.MethodsRandomised controlled trial including 140 participants, with a degenerative meniscal tear and no or minimal radiographic OA changes. Participants were randomised to either APM or 12 weeks of exercise therapy (1:1 ratio). The primary outcome was knee OA progression assessed by the Osteoarthritis Research Society International (OARSI) atlas sum score (sum of medial and lateral compartment joint space narrowing and osteophyte score). Secondary outcomes included incidence of radiographic and symptomatic knee OA, patient-reported pain and knee function and isokinetic knee muscle strength.ResultsThe adjusted mean difference in change in the OARSI sum score was 0.39 (95% CI −0.19 to 0.97), with more progression in the APM group. The incidence of radiographic knee OA was 23% in the APM group and 20% in the exercise group (adjusted risk difference 3% (95% CI −13% to 19%)). No clinically relevant differences were found in patient-reported outcomes or isokinetic knee muscle strength.ConclusionNo differences in radiographic knee OA progression and comparable rates of knee OA development were observed 10 years following APM and exercise therapy for degenerative meniscal tears. Both treatments were associated with improved patient-reported pain and knee function.Trial registration numberNCT01002794.
Impact of the degree of synergy between patient and nurse perceptions on the clinical outcome of pressure injury prevention: a mixed-methods systematic review protocol
Authors: Trozic Irhad , Fischer Lisa , Deckert Stefanie , Gmeinwieser Kerstin 
Published: September 2024

IntroductionPressure injuries are a common and significant concern in clinical practice, often serving as a vital quality indicator. While (clinical) practice guidelines have been established to offer recommendations for mitigating hospital-acquired pressure injuries, adherence among stakeholders remains inconsistent. The subjective perceptions of stakeholders, such as patients and nurses, may impede adherence to pressure ulcer prevention guidelines, potentially reducing the effectiveness of these interventions. However, there is currently insufficient evidence to comprehensively understand this influence. Therefore, this review aims to offer a broader understanding of how the perspectives of patients and nurses engaged in pressure injury prevention affect the effectiveness of specific interventions for pressure ulcer management.Methods and analysisWe will conduct a convergent, segregated mixed-methods systematic review and perform a narrative synthesis with a focus on evidence of the effectiveness of pressure injury prevention strategies and patient and nurse perceptions. Our search will encompass several databases, including the 'Centre for Reviews and Dissemination' (CRD) Database, Medline (via Ovid), CINAHL (via Ebsco) and Scopus (via Elsevier). Additionally, we will cross-check reference lists from all included systematic reviews. Two independent reviewers will screen titles, abstracts, and full texts and extract data from the included studies. The quality of methodology of systematic reviews will be assessed using 'A Measurement Tool to Assess Systematic Reviews-2' (AMSTAR 2) and the risk of bias using 'Risk of Bias in Systematic Reviews' (ROBIS). Qualitative studies will undergo critical appraisal using appropriate Joanna Briggs checklists. If it is feasible to pool data from included studies, we will synthesise them accordingly, using meta-analysis for quantitative reviews and meta-aggregation for qualitative studies. The results from both qualitative and quantitative analyses will be compared with derive new recommendations for healthcare practice aimed at enhancing the quality of care.Ethics and disseminationEthical approval is not required due to the nature of this intended review. The results of this review will be disseminated through publications, reports and conference presentations.PROSPERO registration numberCRD42023438792
Determinants of physical activity commitment in adolescents and young adults with cancer: sociological protocol for a hospital-based mixed methods study (ETAPE-AJA)
Authors: Bruneau Charlotte , Perrin Claire , Bertrand Amandine , Mongondry Rodolf , Marec-Berard Perrine , Fervers Béatrice , Pérol Olivia 
Published: September 2024

IntroductionAdolescents and young adults (AYA) with cancer undergo physical transformations due to disease and treatments occurring alongside puberty and adolescence. Although physical activity is recommended for its benefits, its practice among AYA with cancer remains insufficient. The aim of the Éducation Thérapeutique et Activité Physique: Engagement des Adolescents et Jeunes Adultes atteints de cancer study is to identify the evolution of AYA with cancer medical knowledge and powers (power to act, to express oneself) over life and cancer care, and their role in commitment in adapted physical activity (APA) and therapeutic patient education during and after oncological treatments.Methods and analysisThis prospective mixed methods monocentre study will be conducted in a French comprehensive cancer centre. Observations will be conducted two times a week during medical consultations, APA interventions and therapeutic education sessions for AYA with cancer. Semidirective interviews will involve 70 participants, including AYA with cancer aged 15–25, health professionals, APA teachers and parents. Quantitative data will be collected on AYA’s social characteristics and participation in physical activity intervention and therapeutic education sessions. A correspondence factor analysis will supplement inductive analysis of ethnographic qualitative data, involving patient coresearchers. The results will help to improve the understanding of AYAs’ medical knowledge and powers, their commitment in physical activity and to develop strategies to increase their participation.Ethics and disseminationThis study complies with reference methodology MR004 of the French National Data Protection Authority and was registered by the Data Protection Officer of the Leon Berard Cancer Center on the activity registry of the institution (Ref. N°R201-004-259; 5 July 2022). Ethics approval has been obtained from the Centre Léon Bérard ethics board (Ref. N°2022–006; 20 July 2022). Oral informed consent will be obtained from all participants before data collection. The results of this study will be published in peer-reviewed scientific journals, national and international conferences.
Efficacy and safety of esketamine hydrochloride adjunct to sufentanil in non-surgical patients under mechanical ventilation in the ICU (SENSATION trial): protocol for a multicentre, single-blind, randomised controlled trial
Authors: Long Yi , Hong Donghuang , Ni Haibin , Zhou Dandan , Zhou Tingfa , Liu Songwu , Luo Xiang , Liu Qian , Li Rui , Jiang Zhengying , Ke Lu 
Published: September 2024

IntroductionPain is common in patients receiving mechanical ventilation in the intensive care unit (ICU). Intravenous opioids are recommended as first-line therapy for pain management; however, opioids have adverse side effects. Based on low-quality evidence, low-dose ketamine is therefore recommended as an opioid adjunct to reduce opioid consumption. Esketamine is an alternative to ketamine with greater efficacy and fewer side effects. However, evidence on the use of esketamine in patients receiving mechanical ventilation is lacking. This study investigates the efficacy and safety of esketamine as an adjunct to sufentanil for analgesic therapy in non-surgical ICU patients under mechanical ventilation.Methods and analysisThis ongoing multicentre, single-blind, randomised controlled trial is being conducted at six ICUs in China. 132 non-surgical patients under mechanical ventilation will be randomly assigned to the standard care and S-ketamine groups at a 1:1 ratio. Patients in the standard care group received a minimal dose of sufentanil as the sole analgesic agent. Patients in the S-ketamine group received a minimal dose of sufentanil in addition to an esketamine infusion at a fixed rate of 0.2 mg/kg/hour for analgesia. The primary outcome is mean hourly sufentanil consumption during the treatment period.Ethics and disseminationThis study was approved by the Ethics Committee of Chongqing University Cancer Hospital (CZLS2022067-A). Participants are required to provide informed consent. The results of this trial will be reported in peer-reviewed journals and presented at conferences.Trial registration numberChiCTR2200058933.
Combining electronic health records data from a clinical research network with registry data to examine long-term outcomes of interventions and devices: an observational cohort study
Authors: Mao Jialin , Matheny Michael , Smolderen Kim G , Mena-Hurtado Carlos , Sedrakyan Art , Goodney Philip 
Published: September 2024

ObjectivesTo assess the feasibility of assessing long-term outcomes of peripheral vascular intervention (PVI) by linking data from a clinical registry to electronic health records (EHR) data from a clinical research network.DesignObservational cohort study.SettingVascular Quality Initiative registry linked to INSIGHT Clinical Research Network, which aggregated EHR data from multiple institutions in New York City.ParticipantsPatients receiving PVI during 1 January 2013–30 November 2021 in four centres in New York City.Primary and secondary outcome measuresWe examined the proportion of registry patients retained in EHR over time and predictors of EHR retention after year 1. We evaluated the implications of EHR attrition by examining amputation-free survival (AFS) in the observed data and predicted data when patients discontinued in the EHR were hypothesised to have increased risks of events than the observed average.ResultsWe included 1405 patients receiving PVI (age=70.8±11.2 years, 51.3% male). Among eligible patients, 75.2% were retained in EHR through year 3. Patients who aged 75 years or above (vs <65: OR 0.34, 95% CI 0.18 to 0.62), had Medicaid (vs Medicare: OR 0.41, 95% CI 0.22 to 0.79), congestive heart failure (OR 0.54, 95% CI 0.32 to 0.90), dialysis (OR 0.47, 95% CI 0.24 to 0.91) and reduced ambulation (OR 0.34, 95% CI 0.15 to 0.75) were less likely to be retained in EHR. When discontinued patients were hypothesised to have increased risks of death or amputation than observed, AFS estimates diverged from the observed data around 6–12 months.ConclusionsStudies using registry-EHR data may benefit from the timeliness of the data but may be most appropriate to focus on short-term to intermediate-term outcomes of interventions and devices. Future research is needed to investigate the value of registry-EHR linkage in facilitating short-term to intermediate-term outcome assessment following vascular interventions and advanced statistical approaches to account for non-random missing long-term data.
Maryland opioid overdose deaths from 2018 to 2022: occupational patterns and their sociodemographic variations
Authors: Amin-Esmaeili Masoumeh , Susukida Ryoko , Byregowda Himani , Zhou Zhiqing E , Mitchell Clifford S , Johnson Renee M 
Published: September 2024

IntroductionWe aimed to describe the occupational pattern of opioid overdose deaths in Maryland between 2018 and 2022 and determine the occupations at higher risk of opioid overdose death.MethodsThe sample included undetermined or unintentional opioid overdose deaths among those aged 16 years or older in Maryland, drawn from the State Unintentional Drug Overdose Reporting System. We calculated population-based incidence overdose rates by occupation, stratified by sex and race. We further calculated the incidence rate ratios (IRRs) comparing each occupation with all other groups combined and estimated the IRRs among males versus females and non-Hispanic whites versus other racial/ethnic groups.ResultsThe pooled sample included 11 455 opioid overdose decedents (72% male and 55% non-Hispanic whites) of whom 80% were employed. The three occupation groups with the highest incidence rates were ‘construction and extraction’, ‘transportation and material moving’ and ‘installation/maintenance and repair’ with 291, 137 and 133 deaths per 100 000 workers in these respective occupational groups. Incidence rates were significantly higher in males than females in all categories except those ‘Not in Labour Force’ (IRR=0.51, p<0.001). Non-Hispanic whites relative to other racial/ethnic groups had a lower incidence of opioid overdose death in ‘Military-Specific’ occupations (IRR=0.53, p=0.031).ConclusionOpioid overdose deaths vary by type of occupation and certain occupations are at higher risk of overdose death. The findings highlight the need for priority setting in the implementation and expansion of existing strategies to target the workers most impacted by opioid overdose.
Military and occupational exposures among Veterans in the Million Veteran Program by survey self-report: a descriptive study
Authors: Sordillo Joanne E , Dey Andrew , Ho Yuk-Lam , Kosik Nicole , Harrington Kelly , Costa Lauren , Muralidhar Sumitra , Hauser Elizabeth , Gaziano John Michael , Cho Kelly , Whitbourne Stacey 
Published: September 2024

ObjectiveWe aimed to characterise self-reported military and occupational exposures including Agent Orange, chemical/biological warfare agents, solvents, fuels, pesticides, metals and burn pits among Veterans in the Department of Veterans Affairs Million Veteran Program (MVP).MethodsMVP is an ongoing longitudinal cohort and mega-biobank of over one million US Veterans. Over 500 000 MVP participants reported military exposures on the baseline survey, and over 300 000 reported occupational exposures on the lifestyle survey. We determined frequencies of selected self-reported occupational exposures by service era, specific deployment operation (1990–1991 Gulf War, Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF)), service in a combat zone and occupational categories. We also explored differences in self-reported exposures by sex and race.ResultsAgent Orange exposure was mainly reported by Vietnam-era Veterans. Gulf War and OEF/OIF Veterans deployed to a combat zone were more likely to report exposures to burn pits, chemical/biological weapons, anthrax vaccination and pyridostigmine bromide pill intake as compared with non-combat deployers and those not deployed. Occupational categories related to combat (infantry, combat engineer and helicopter pilot) often had the highest percentages of self-reported exposures, whereas those in healthcare-related occupations (dentists, physicians and occupational therapists) tended to report exposures much less often. Self-reported exposures also varied by race and sex.ConclusionsOur results demonstrate that the distribution of self-reported exposures varied by service era, demographics, deployment, combat experience and military occupation in MVP. Overall, the pattern of findings was consistent with previous population-based studies of US military Veterans.
Hybrid Algorithm Selection and Hyperparameter Tuning on Distribute Machine Learning Resources: Hierarchical Agent-based Approach
Authors: Esmaeili Ahmad , Rayz Julia , Matson Eric 
Published: September 2024

Algorithm selection and hyperparameter tuning are critical steps in both academic and applied machine learning (ML). These steps are becoming increasingly delicate due to the extensive rise in the number, diversity, and distributed nature of ML resources. Multi-agent systems, when applied to the design of ML platforms, bring about several distinctive characteristics, such as scalability, flexibility, and robustness, just to name a few. This article proposes a fully automatic and collaborative agent-based mechanism for selecting distributed ML algorithms and simultaneously tuning their hyperparameters. Our method builds upon an existing agent-based hierarchical ML platform and augments its query structure to support the aforementioned functionalities without being limited to specific learning, selection, and tuning mechanisms. We have conducted theoretical assessments, formal verification, and analytical study to demonstrate the correctness, resource utilization, and computational efficiency of our technique. According to the results, our solution is algorithmically correct and exhibits linear time and space complexity in relation to the size of available resources. To further verify its correctness and demonstrate its effectiveness and flexibility across a range of algorithmic options and datasets, the article also presents a series of empirical results on a system composed of 24 algorithms and 9 datasets. The findings not only highlight the efficiency and scalability of the proposed approach, but also show its flexibility and openness to responding to the dynamic and distributed ML ecosystem.