bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal dynamics of soil microbiome in response to dry–wet alternation along the Jinsha River Dry-hot Valley
Authors: Jiang Hao , Chen Xiaoqing , Li Yongping , Chen Jiangang , Wei Li , Zhang Yuanbin 
Published: November 2024

Abstract
Background
Soil microorganisms play a key role in nutrient cycling, carbon sequestration, and other important ecosystem processes, yet their response to seasonal dry–wet alternation remains poorly understood. Here, we collected 120 soil samples from dry-hot valleys (DHVs, ~ 1100 m a.s.l.), transition (~ 2000 m a.s.l.) and alpine zones (~ 3000 m a.s.l.) along the Jinsha River in southwest China during both wet and dry seasons. Our aims were to investigate the bacterial microbiome across these zones, with a specific focus on the difference between wet and dry seasons.

Results
Despite seasonal variations, bacterial communities in DHVs exhibit resilience, maintaining consistent community richness, diversity, and coverage. This suggests that the microbes inhabiting DHVs have evolved adaptive mechanisms to withstand the extreme dry and hot conditions. In addition, we observed season-specific microbial clades in all sampling areas, highlighting their resilience to environmental fluctuations. Notably, we found similarities in microbial clades between soils from DHVs and the transition zones, including the phyla Actinomycetota, Chloroflexota, and Pseudomonadota. The neutral community model respectively explained a substantial proportion of the community variation in DHVs (87.7%), transition (81.4%) and alpine zones (81%), indicating that those were predominantly driven by stochastic processes. Our results showed that migration rates were higher in the dry season than in the wet season in both DHVs and the alpine zones, suggesting fewer diffusion constraints. However, this trend was reversed in the transition zones.

Conclusions
Our findings contribute to a better understanding of how the soil microbiome responds to seasonal dry–wet alternation in the Jinsha River valley. These insights can be valuable for optimizing soil health and enhancing ecosystem resilience, particularly in dry-hot valleys, in the context of climate change.
Exploring the characteristics, methods and reporting of systematic reviews with meta-analyses of time-to-event outcomes: a meta-epidemiological study
Authors: Goldkuhle Marius , Hirsch Caroline , Iannizzi Claire , Zorger Ana-Mihaela , Bender Ralf , van Dalen Elvira C. , Hemkens Lars G. , Monsef Ina , Kreuzberger Nina , Skoetz Nicole 
Published: November 2024

Abstract
Background
Time-to-event analysis is associated with methodological complexities. Previous research identified flaws in the reporting of time-to-event analyses in randomized trial publications. These hardships impose challenges for meta-analyses of time-to-event outcomes based on aggregate data. We examined the characteristics, reporting and methods of systematic reviews including such analyses.

Methods
Through a systematic search (02/2017-08/2020), we identified 50 Cochrane Reviews with ≥ 1 meta-analysis based on the hazard ratio (HR) and a corresponding random sample (n = 50) from core clinical journals (Medline; 08/02/2021). Data was extracted in duplicate and included outcome definitions, general and time-to-event specific methods and handling of time-to-event relevant trial characteristics.

Results
The included reviews analyzed 217 time-to-event outcomes (Median: 2; IQR 1–2), most frequently overall survival (41%). Outcome definitions were provided for less than half of time-to-event outcomes (48%). Few reviews specified general methods, e.g., included analysis types (intention-to-treat, per protocol) (35%) and adjustment of effect estimates (12%). Sources that review authors used for retrieval of time-to-event summary data from publications varied substantially. Most frequently reported were direct inclusion of HRs (64%) and reference to established guidance without further specification (46%). Study characteristics important to time-to-event analysis, such as variable follow-up, informative censoring or proportional hazards, were rarely reported. If presented, complementary absolute effect estimates calculated based on the pooled HR were incorrectly calculated (14%) or correct but falsely labeled (11%) in several reviews.

Conclusions
Our findings indicate that limitations in reporting of trial time-to-event analyses translate to the review level as well. Inconsistent reporting of meta-analyses of time-to-event outcomes necessitates additional reporting standards.
How power and knowledge hierarchies affect communication in intrapartum care: findings from public health facilities in two southern Indian districts
Authors: Rao Abha , Srinidhi V. , Karachiwala Baneen , Santosh Sanjana , Seshadri Shreelata Rao , Thomas Sophia , Chattopadhyay Sreeparna , Sreevathsa Anuradha , Sen Gita 
Published: November 2024

Abstract
Background
Effective communication is a key element of medical care; it can foster a warm interpersonal relationship, facilitate the exchange of information, and enable shared decision-making. In the context of obstetric care, it is associated with a range of positive clinical and social outcomes for mother and baby. Extant communication frameworks and respectful maternity care (RMC) guidelines emphasize the importance of effective communication during intrapartum care. Yet, studies conducted in Indian public health settings suggest that there are gaps in the implementation of RMC guidelines.

Methods
As part of a larger study on disrespect and abuse in Indian public hospitals, we studied the nature of communication in the intrapartum context and the extent to which it is respectful. The study is based on interviews with 29 providers across different levels of public health facilities. Interviews were translated, transcribed, and thematically coded. We examined codes related to communication to understand what kinds of communication occur during intrapartum care and the role played by knowledge and power hierarchies. We then considered their implications for RMC.

Results
We identified four types of communication that occurred in the context of intrapartum care: (a) compassionate, to comfort and support the laboring woman, (b) factual, to obtain or provide information or updates, (c) prescriptive, to obtain consent and cooperation from the woman and her family members, and (d) defensive, to protect against accusations of poor care. Knowledge and power hierarchies operated differently in each type of communication, with prescriptive and defensive communication more likely to be disrespectful than others.

Conclusions
Our findings suggest that successful implementation of RMC guidelines requires greater attention to knowledge and power hierarchies, and an understanding of the ways in which they operate in a clinical setting. Integrating this understanding into guidelines, medical education, training programmes, and interventions will facilitate effective and respectful communication during maternity care.
Associations between ethnicity and mental health problems among children and adolescents in the United Kingdom: A systematic review and narrative synthesis
Authors: Guan Shengjia , Coughlan Barry , Evans Kate , Duschinsky Robbie 
Published: November 2024

Abstract
Background
The associations between ethnicity and mental health problems (MHPs) among children and adolescents in the UK have been reported in recent years. However, this is the first review to compare and synthesise these associations and provides a deep understanding of child MHPs across ethnic groups in the UK.

Method
A comprehensive literature search across seven electronic databases and fifteen websites was conducted. The inclusion criteria focused on studies reporting quantitative associations between ethnicity and MHPs for children and adolescents aged 0–19 residing in the UK. Given the high heterogeneity of the studies, a narrative synthesis was adopted to analyse the associations.

Results
Twelve studies met the inclusion criteria, involving a total of 48,281 participants. The review reports no significant differences in the risk of experiencing general MHPs among children from Indian, Pakistani, Bangladeshi, and Black Caribbean groups compared to their White British counterparts. However, Black African children were less likely to develop general MHPs, while children in the Pakistani, Bangladeshi, and Black Caribbean groups showed a higher risk for internalising problems. Externalising and conduct problems were similarly likely among children from Pakistani and Bangladeshi backgrounds compared to White children, with Black Caribbean children showing a higher likelihood of these issues.

Conclusion
The findings suggest that most ethnic minority children and adolescents in the UK have comparable risks of MHPs to their White counterparts, although specific risks vary by ethnicity and MHP types. The results underscore the need for multifaceted analyses considering socioeconomic and cultural factors, beyond simple ethnic categorisations, to inform mental health services that effectively meet the diverse needs of the UK’s child population. This review calls for more detailed and uniform categorisation in future research to understand and address the mental health disparities across different ethnic groups.
Clinical and radiographic evaluation of non-surgical therapy with and without ozone gel application in controlled type 2 diabetic patients with periodontitis: a randomized controlled clinical trial
Authors: Barahim Abeer Abubaker , Shemais Nesma , Mousa Arwa , Darhous Mona 
Published: November 2024

Abstract
Background
The current study aimed to assess the clinical and radiographic outcomes of the effect of subgingival application of ozonated gel as an adjunct to scaling and root planing (SRP) in diabetic patients with stage III periodontitis.

Methods
Twenty-four patients with type II diabetes mellitus (DM) were randomized into two groups, with 12 patients in each group. Group I served as the intervention group, receiving both SRP and ozone gel application (SRP + Ozone), while Group II served as the control group, undergoing SRP alone. Clinical attachment level was evaluated as primary outcome, with secondary outcomes including probing pocket depth, full mouth plaque score, full mouth bleeding score, dentinal hypersensitivity, radiographic linear defect depth, radiographic defect angle, and periodontal ligament widening space assessed at 3 and 6 months.

Results
The results revealed statistically significant intragroup differences between the two groups (p < 0.05). In contrast, intergroup differences revealed no statistically significant difference across the various time intervals (p > 0.05). The reduction in PD in the SRP + Ozone group at three months was statistically significant (p = 0.04). The SRP + Ozone group showed a significant radiographic improvement compared to the SRP group. The Visual Analogue Scale (VAS) also demonstrated statistically significant differences between the two groups. Glycated hemoglobin (HbA1c) significantly decreased after 6 months, with no significant signifcant differences between groups (p > 0.05).

Conclusions
Ozone gel is suggested to be a promising potential natural adjunctive therapy for diabetic patients to enhance periodontal health, with no reported adverse effects.

Trial registration
ID: NCT05538078, Date of Registration: 09/09/2022. (https://register.clinicaltrials.gov/prs/app/action/DownloadReceipt?uid=U0006D54&ts=3&sid=S000CGX4&cx=g1wreh).
The golden genome annotation of Ganoderma lingzhi reveals a more complex scenario of eukaryotic gene structure and transcription activity
Authors: Wang Lining , Shi Peiqi , Ping Zhaohua , Huang Qinghua , Jiang Liqun , Ma Nianfang , Wang Qingfu , Xu Jiang , Zou Yajie , Huang Zhihai 
Published: November 2024

Abstract
Background
It is generally accepted that nuclear genes in eukaryotes are located independently on chromosomes and expressed in a monocistronic manner. However, accumulating evidence suggests a more complex landscape of gene structure and transcription. Ganoderma lingzhi, a model medicinal fungus, currently lacks high-quality genome annotation, hindering genetic studies.

Results
Here, we reported a golden annotation of G. lingzhi, featuring 14,147 high-confidence genes derived from extensive manual corrections. Novel characteristics of gene structure and transcription were identified accordingly. Notably, non-canonical splicing sites accounted for 1.99% of the whole genome, with the predominant types being GC-AG (1.85%), GT-AC (0.05%), and GT-GG (0.04%). 1165 pairs of genes were found to have overlapped transcribed regions, and 92.19% of which showed opposite directions of gene transcription. A total of 5,412,158 genetic variations were identified among 13 G. lingzhi strains, and the manually corrected gene sets resulted in enhanced functional annotation of these variations. More than 60% of G. lingzhi genes were alternatively spliced. In addition, we found that two or more protein-coding genes (PCGs) can be transcribed into a single RNA molecule, referred to as polycistronic genes. In total, 1272 polycistronic genes associated with 2815 PCGs were identified.

Conclusions
The widespread presence of polycistronic genes in G. lingzhi strongly complements the theory that polycistron is also present in eukaryotic genomes. The extraordinary gene structure and transcriptional activity uncovered through this golden annotation provide implications for the study of genes, genomes, and related studies in G. lingzhi and other eukaryotes.
Development of a clinical metagenomics workflow for the diagnosis of wound infections
Authors: Halford Carl , Le Viet Thanh , Edge Katie , Russell Paul , Moore Nathan , Trim Fiona , Moragues-Solanas Lluis , Lukaszewski Roman , Weller Simon A. , Gilmour Matthew 
Published: November 2024

Abstract
Background
Wound infections are a common complication of injuries negatively impacting the patient’s recovery, causing tissue damage, delaying wound healing, and possibly leading to the spread of the infection beyond the wound site. The current gold-standard diagnostic methods based on microbiological testing are not optimal for use in austere medical treatment facilities due to the need for large equipment and the turnaround time. Clinical metagenomics (CMg) has the potential to provide an alternative to current diagnostic tests enabling rapid, untargeted identification of the causative pathogen and the provision of additional clinically relevant information using equipment with a reduced logistical and operative burden.

Methods
This study presents the development and demonstration of a CMg workflow for wound swab samples. This workflow was applied to samples prospectively collected from patients with a suspected wound infection and the results were compared to routine microbiology and real-time quantitative polymerase chain reaction (qPCR).

Results
Wound swab samples were prepared for nanopore-based DNA sequencing in approximately 4 h and achieved sensitivity and specificity values of 83.82% and 66.64% respectively, when compared to routine microbiology testing and species-specific qPCR. CMg also enabled the provision of additional information including the identification of fungal species, anaerobic bacteria, antimicrobial resistance (AMR) genes and microbial species diversity.

Conclusions
This study demonstrates that CMg has the potential to provide an alternative diagnostic method for wound infections suitable for use in austere medical treatment facilities. Future optimisation should focus on increased method automation and an improved understanding of the interpretation of CMg outputs, including robust reporting thresholds to confirm the presence of pathogen species and AMR gene identifications.
Co-occurring mutations identify prognostic subgroups of microsatellite stable colorectal cancer
Authors: Nunes Luís , Stenersen Jakob Mørkved , Kryeziu Kushtrim , Sjöblom Tobias , Glimelius Bengt , Lothe Ragnhild A. , Sveen Anita 
Published: November 2024

Abstract
Background
Co-occurring mutations in pairs of genes can pinpoint clinically relevant subgroups of cancer. Most colorectal cancers (CRCs) are microsatellite stable (MSS) and have few frequent mutations. Large patient cohorts and broad genomic coverage are needed for comprehensive co-mutation profiling.

Methods
Co-mutations were identified in a population-based Swedish cohort analyzed by whole-genome sequencing (n=819 stage I-IV MSS CRCs). Prognostic value was further evaluated in a publicly available dataset of clinically sequenced metastatic CRCs (MSK-IMPACT; n=934 MSS). Multivariable Cox proportional hazards analyses with clinicopathological parameters were performed for locoregional (stage I-III) and metastatic (stage IV and recurrent) cancers separately.

Results
Prevalent co-mutations were detected in 23 unique gene pairs, 20 of which included APC, TP53, KRAS and/or PIK3CA. Several co-mutations involving APC were associated with good overall survival in locoregional CRC, including APC-TCF7L2 (multivariable HR: 0.49, 95% CI 0.27-0.89). This co-mutation was prognostic also in metastatic cancers (multivariable HR: 0.49 and 0.37, 95% CI: 0.24-0.98 and 0.17-0.82 in the Swedish and MSK cohorts, respectively). APC-SOX9 co-mutations were mutually exclusive with APC-TCF7L2, and the co-mutations combined had stronger prognostic associations than APC alone in both metastatic cohorts. BRAF p.V600E-RNF43 co-mutations were associated with poor overall and recurrence-free survival in locoregional CRC (multivariable HR: 4.13 and 3.2, 95% CI: 1.78-9.54 and 1.53-8.04, respectively).

Conclusions
We report a genome-wide evaluation of co-occurring mutations in MSS CRCs, and suggest that co-mutations can improve the prognostic stratification compared to single mutations alone.
Two-year scale-up dissemination study of a multi-strategic community-wide intervention promoting physical activity: a single-arm pre-post hybrid effectiveness-implementation trial
Authors: Tsuzuki Aoi , Kamada Masamitsu , Amagasa Shiho , Kitayuguchi Jun , Miyashita Takuma , Abe Takafumi , Gomi Tatsunosuke , Okuyama Kenta , Taguri Masataka , Inoue Shigeru 
Published: November 2024

Abstract
Background
Intervention trials that have demonstrated significant effects may not always replicate those effects when scaled up. This study aimed to test whether scaling-up a successful cluster randomized trial (the COMMUNICATE study, 9 intervention communities), which promoted population-level physical activity (PA), could promote PA in a broader citywide setting (29 communities) after two years, as a mid-term evaluation of the six-year scaled-up trial.

Methods
This is a single-arm, pre-post comparison of a multi-strategic community-wide intervention covering the entire Unnan City, Japan. The intervention for middle-aged and older people consisted of three components: information delivery, education, and support delivery. The intervention method followed the COMMUNICATE study but adapted and introduced new initiatives tailored to local resources. A baseline survey (n = 3,718) among randomly selected residents aged 40–79 years in 2016 and a follow-up survey with the same respondents two years later were conducted. The primary outcome was the change in the percentage of people who practiced the recommended levels of PA, analyzed with a generalized linear mixed model to account for clusters at individual and community levels. Additionally, we examined the dose–response relation of the effect based on the intervention doses in each community. The RE-AIM framework assessed intervention dissemination and implementation.

Results
The two-year intervention was implemented in all communities, reaching and involving various groups. The rate of people engaged in PA significantly increased in two years (adjusted change: + 8.0 percentage points [95% confidence interval: 6.1, 10.0]). Based on the type of PA, only muscle-strengthening activity showed a significant increase (+ 11.5% points [9.6, 13.5]), whereas walking (-1.8% points [-3.6, 0.1]) and flexibility activities (+ 0.3% points [-1.5, 2.0]) did not. The increase in PA in higher-dose areas was not significantly different but slightly larger than that in lower-dose areas (+ 8.4% points vs. + 7.6% points, adjusted difference in change: 0.8% points [-3.8, 5.5]).

Conclusion
The scaled-up citywide intervention promoted PA, especially muscle-strengthening activity. Collaboration with diverse organizations in different settings is crucial for multi-faceted interventions and requires balancing uncertainty in its implementation quality and quantity owing to collaborative decision-making.

Trial registration
UMIN-CTR, UMIN000024682. Registered 02 November 2016, https://center6.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000028377
Cost-effectiveness of high flow nasal cannula therapy versus continuous positive airway pressure for non-invasive respiratory support in paediatric critical care
Authors: Sadique Zia , Zapata Silvia Moler , Grieve Richard , Richards-Belle Alvin , Lawson Izabella , Darnell Robert , Lester Julie , Morris Kevin P. , Tume Lyvonne N. , Davis Peter J. , Peters Mark J. , Feltbower Richard G. , Mouncey Paul R. , Harrison David A. , Rowan Kathryn M. , Ramnarayan Padmanabhan ,   the FIRST-ABC RCT Investigators,   the Paediatric Critical Care Society Study Group
Published: November 2024

Abstract
Background
High flow nasal cannula therapy (HFNC) and continuous positive airway pressure (CPAP) are two widely used modes of non-invasive respiratory support in paediatric critical care units. The FIRST-ABC randomised controlled trials (RCTs) evaluated the clinical and cost-effectiveness of HFNC compared with CPAP in two distinct critical care populations: acutely ill children (‘step-up’ RCT) and extubated children (‘step-down’ RCT). Clinical effectiveness findings (time to liberation from all forms of respiratory support) showed that HFNC was non-inferior to CPAP in the step-up RCT, but failed to meet non-inferiority criteria in the step-down RCT. This study evaluates the cost-effectiveness of HFNC versus CPAP.

Methods
All-cause mortality, health-related Quality of Life (HrQoL), and costs up to six months were reported using FIRST-ABC RCTs data. HrQoL was measured with the age-appropriate Paediatric Quality of Life Generic Core Scales questionnaire and mapped onto the Child Health Utility 9D index score at six months. Quality-Adjusted Life Years (QALYs) were estimated by combining HrQoL with mortality. Costs at six months were calculated by measuring and valuing healthcare resources used in paediatric critical care units, general medical wards and wider health service. The cost-effectiveness analysis used regression methods to report the cost-effectiveness of HFNC versus CPAP at six months and summarised the uncertainties around the incremental cost-effectiveness results.

Results
In both RCTs, the incremental QALYs at six months were similar between the randomised groups. The estimated incremental cost at six months was − £4565 (95% CI − £11,499 to £2368) and − £5702 (95% CI − £11,328 to − £75) for step-down and step-up RCT, respectively. The incremental net benefits of HFNC versus CPAP in step-down RCT and step-up RCT were £4388 (95% CI − £2551 to £11,327) and £5628 (95% CI − £8 to £11,264) respectively. The cost-effectiveness results were surrounded by considerable uncertainties. The results were similar across most pre-specified subgroups, and the base case results were robust to alternative assumptions.

Conclusions
HFNC compared to CPAP as non-invasive respiratory support for critically-ill children in paediatric critical care units reduces mean costs and is relatively cost-effective overall and for key subgroups, although there is considerable statistical uncertainty surrounding this result.