bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved resolution of microbial diversity in deep-sea surface sediments using PacBio long-read 16S rRNA gene sequencing
Authors: Gao Jie , Wang Ziming , Deng Wenjie , Sa Boxuan , Chen Xiaoxia , Cai Ruanhong , Yan Yi , Jiao Nianzhi , Leung Elaine Lai-Han , Liu Di , Yan Wei 
Published: November 2024

ABSTRACT

16S rRNA gene sequencing is the gold standard for identifying microbial diversity in environmental communities. The Illumina short-read platform is widely used in marine environment studies due to its cost-effectiveness and high accuracy, but its limited read length restricts taxonomic identification mainly to genus or family levels. Recently, the PacBio long-read sequencing platform was developed. This method has exceptional base-level resolution exceeding 99%, thereby effectively mitigating the challenges associated with high error rates commonly observed in long-read sequencing technologies. However, few studies have compared the PacBio long-read and Illumina short-read platforms in marine deep-sea sediments. Here, the PacBio long-read and Illumina short-read platforms were compared with samples collected from the deep-sea surface sediments from the cold seep in the Shenhu area of the South China Sea offshore Pearl River Estuary. Comparisons revealed a more comprehensive taxonomic identification, α-diversity, and β-diversity by PacBio long-reads. The PacBio long-read platform exhibited higher classified rates and classified taxonomy at all levels, particularly at the species level. The PacBio long-read platform was also more accurate at capturing fine spatial-scale variations in microbial communities in sediments. Our studies will facilitate the selection of 16S rRNA sequencing platforms for investigating fine spatial-scale patterns in microbial communities in deep-sea surface sediments and serve as a crucial methodological reference for future studies on microbial diversity.

IMPORTANCE
The PacBio long-read platform, with its exceptional base-level resolution exceeding 99%, has advanced our comprehension of deep-sea microbial diversity. By comparing microbial community analyses conducted using the Illumina short-read and PacBio long-read sequencing platforms, we have provided an enhanced understanding of fine spatial-scale patterns in microbial community diversity with depth across a deep-sea sediment core, as well as methodological insights that will be valuable for future research in this field.
Femoral diaphyseal reconstruction using free non-vascularised fibular graft in a paediatric case of postinfective gap non-union
Authors: Agrawal Alok Chandra , Singh Jagprit , Garg Ankit Kumar , chauhan Shivam 
Published: November 2024

Free non-vascularised fibular grafts are an autologous grafting option that requires a simple technique and minimal expertise to replicate. However, due to limited intrinsic biological activity, they are less preferred than their vascularised counterparts for reconstructing large bone defects. We present a case of a female child in her middle childhood with limb length discrepancy due to extensive femoral diaphyseal bone loss following successful treatment of chronic osteomyelitis of the femur. In this case, successful reconstruction of the femoral diaphysis was achieved using a free non-vascularised fibular graft, resulting in a good range of motion around the knee with no graft donor site morbidity at the latest follow-up.Therefore, we conclude that with adequate soft tissue coverage and vascularity for large bone defects, even a free, non-vascularised fibular graft can yield promising results with complete union and hypertrophy at the graft host junction.
Oculopharyngeal muscular dystrophy, myasthenia gravis, systemic lupus erythematosus: overlap and interactions
Authors: M Barbosa Joana , A Pereira Pedro 
Published: November 2024

Ptosis and proximal weakness may develop in multiple diseases including oculopharyngeal muscular dystrophy (OPMD) and myasthenia gravis (MG). These two entities can be challenging to differentiate since they may have important clinical and neurophysiological overlap. Systemic lupus erythematosus (SLE), a common autoimmune disease, has been described in association with MG.We present a woman in her 60s with fluctuating bilateral ptosis and proximal muscle weakness. Single fibre electromyography showed increased jitter. Her brother has genetically proven OPMD. The investigation revealed a positive genetic test for OPMD and positive antibodies for acetylcholine receptor. Additionally, she has SLE, treated with hydroxychloroquine for more than 30 years.This case highlights the importance of a thoughtful anamnesis with personal and familial history and raises awareness for the rare coexistence of three pathologies with some common clinical characteristics but different treatments and management.
Statins are rarely prescribed for incidentally discovered covert cerebrovascular disease: a retrospective cohort in a large electronic health record (EHR) identified using natural language processing
Authors: Leung Lester Y , Puttock Eric , Kallmes David F , Luetmer Patrick , Fu Sunyang , Zheng Chengyi X , Liu Hongfang , Chen Wansu , Kent David M 
Published: November 2024

IntroductionWhile incidentally discovered covert cerebrovascular diseases (id-CCD) are associated with future stroke, it is not known if patients with id-CCD are prescribed statins.MethodsPatients age ≥50 with id-CCD on neuroimaging from 2009 to 2019 with no prior ischaemic stroke, transient ischaemic attack or dementia were identified using natural language processing in a large real-world cohort. Robust Poisson multivariable regression was used to assess statin prescription among patients without prior statins.ResultsAmong 2 41 050 patients, 74 975 patients (31.1%; 4.7% with covert brain infarcts (CBI); 29.0% with white matter disease (WMD)) had id-CCD. 53.5% (95% CI 53.2 to 53.9%) were not on statins within 6 months prior to the scan. Of those, 12.0% (95% CI 11.7 to 12.3%) were prescribed statins in the next 6 months compared with 9.3% (95% CI 9.1 to 9.4%) in those without CCD, a 2.7% (95% CI 2.4 to 3.1%) absolute increase in statin prescription for those with id-CCD. In adjusted analyses, the presence of id-CCD was only associated with minor increases in statin prescription (CBI or WMD (risk ratio (RR) 1.09, 95% CI 1.05 to 1.13), CBI alone (RR 1.34, 95% CI 1.21 to 1.47), WMD alone (RR 1.05, 95% CI 1.01 to 1.09), and CBI and WMD (RR 1.23, 95% CI 1.12 to 1.35)).DiscussionIdentification of id-CCD is not associated with substantial changes in statin prescription in routine clinical practice.
Fertility-sparing surgery versus radical surgery for micropapillary serous borderline ovarian tumours: a systematic review protocol
Authors: Zhao Anqi , Wang Jingyi , Xu Jin , Dong Peng , Jiang Shan , Wang Shijun 
Published: November 2024

IntroductionMicropapillary serous borderline ovarian tumours (MP-SBOTs) are an aggressive subtype of serous borderline ovarian tumours (SBOTs). Surgery is the mainstay of treatment. Radical surgery (RS, including debulking) is an alternative. However, for patients who are of reproductive age, another treatment option is fertility-sparing surgery (FSS). Up to now, the best surgical approach for MP-SBOTs and whether different procedures will have an impact on postoperative recurrence are still up for debate. This protocol outlines a systematic review and meta-analysis to investigate whether FSS adversely affected outcomes compared with RS in patients with MP-SBOTs. Additionally, we will do a prognosis analysis of BOTs with no microcapillary pattern and MP-SOBTs, if possible.Methods and analysisThis protocol will consider non-randomised studies comparing outcomes in patients with MP-SBOTs treated with RS or FSS. The following databases will be searched: Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, MEDLINE, Embase Medline, PubMed, Web of Science, China Biological Medicine Database, China National Knowledge Infrastructure and Wan Fang database. We will try our best to search the grey literature to avoid missing crucial research. Data collection and extraction will be performed according to the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines. Risk of Bias in Non-randomised Studies of intervention will be used to assess non-randomized studies. We will assess the certainty of the evidence using the GRADEpro methodology and describe the degree of certainty of our results using suggested wording based on the GRADEpro assessment. We will conduct a meta-analysis and offer summary statistics for each result if there is enough data available. Instead, we will report the findings narratively where the data do not permit a statistical assessment.Ethics and disseminationEthics approval was not required for this study. Results will be published through a peer-reviewed publication and communicated at scientific events once complete.PROSPERO registration numberCRD42023439136.
Research and development investment of Chinese chemical pharmaceutical companies under the national pooled procurement: a retrospective panel data analysis, 2013–2022
Authors: Lei Qianrun , Wu Qiyou , Wang Zhitao , Sun Jing , Liu Yuanli 
Published: November 2024

ObjectiveTo generate evidence about changes in the research and development (R&D) investment of Chinese chemical pharmaceutical companies before and after the implementation of the national pooled procurement, to respond to the concerns that significant price reductions might negatively affect R&D investment, and to facilitate the evidence-based decision-making for improvement of the national pooled procurement.MethodsThis retrospective study employed the fixed-effects models with robust SEs to analyse the changes in R&D investment intensities of 76 A-share listed Chinese chemical pharmaceutical companies before and after the procurement implementation in 2019. The analyses were based on a panel data set between 2013 and 2022. Subgroup analyses were conducted to account for the heterogeneity of the target companies. The bootstrap hypothesis test method was employed to assess potential variations across the different subgroups.ResultsFollowing the procurement implementation, the R&D investment intensity (RDI) of the target companies increased by 1.9% (p<0.05) compared with the RDI before the procurement implementation. Successful bidders exhibited a higher RDI of 2.2% (p<0.01) compared with that of the other suppliers. The RDI of companies engaged in traditional Chinese medicine (TCM) production was found to be 2.4% lower (p<0.01) than that of companies not involved in TCM production. Similarly, the companies engaged in the production of active pharmaceutical ingredients (APIs) had a 1.6% lower (p<0.01) RDI than those not involved in API production.ConclusionsThis study found that the enthusiasm of Chinese chemical medicines companies towards investing in R&D following the medicines regulatory reforms was not suppressed when the pilot pooled procurement was expanded and continued. The overall level of RDI following the pilot was higher than that before the pilot during the entire observation period. The enhanced investment in R&D has been a distinctive feature of Chinese chemical pharmaceutical companies that position themselves with more substantial market competitiveness.
Methodological standards in the design and reporting of pilot and feasibility studies in emergency medicine literature: a systematic review
Authors: Ruangsomboon Onlak , Lima João Pedro , Eltorki Mohamed , Worster Andrew 
Published: November 2024

ObjectivePilot and feasibility studies are intended to ensure that subsequent randomised controlled trials (RCTs) are feasible, economical and rigorous, especially in a challenging research environment such as emergency medicine (EM). We aimed to evaluate the methodological quality in conducting and reporting randomised pilot and feasibility studies in the EM literature and propose recommendations to improve their quality.DesignMethodological systematic review.Data sources and eligibilityWe searched MEDLINE and Embase (2018–29 September 2023) for pilot or feasibility RCTs published as full texts in the five top-ranked and other first-quartile EM journals according to Scimago.Data extraction and analysisWe assessed their methodological features and reporting quality primarily based on the Consolidated Standards of Reporting Trials (CONSORT) extension.ResultsA total of 24 randomised trials identified as pilot (n=13), feasibility (n=3) or both (n=8) were included. At least one feasibility outcome was assessed in 9 trials (feasibility trials), while 15 others only focused on treatment efficacy (efficacy trials). Only three (12.5%) studies progressed to the main trials. Among 12 feasibility trials, 55.6% reported their outcomes with uncertainty estimates, and 33.3% had clear progression criteria. Efficacy trials tended to draw clinical implications on their results. Studies from the five top-ranked journals had better methodological and reporting quality than those from other first-quartile journals.ConclusionMain methodological concerns for pilot and feasibility studies in first-quartile EM literature include misconceptions, misuses and suboptimal design and reporting quality. These issues were more prominent in lower-ranked first-quartile journals. Our findings highlight the need for resources and training for researchers, journal editors and peer reviewers on the value, objectives and appropriate conduct of pilot and feasibility studies. The conceptual framework and standardised methodological components should be emphasised. EM journals should reinforce the reporting standards and support their publication. These actions can lead to more methodologically rigorous pilot and feasibility studies in EM.PROSPERO registration numberCRD42023468437.
Different interventions to prevent preterm birth in pregnant women with cervical shortening during pregnancy: a protocol for a network meta-analysis
Authors: Luo JieFeng , Liu Dan , Liu Jiyong 
Published: November 2024

IntroductionPremature birth is the leading cause of neonatal mortality. Cervical length shortening during pregnancy serves as the gold standard for predicting preterm birth. Although several interventions have been applied to reduce the incidence of preterm birth in short cervix pregnant women, the optimal intervention in clinical practice remains controversial. The aim of this study is to conduct a network meta-analysis to explore the optimal intervention for preventing preterm birth among pregnant women with a short cervix.Methods and analysisWe will search electronic information databases including PubMed, Embase Ovid, Cochrane Library Ovid, Wanfang Data, China Science and Technology Journal Database(VIP) and clinical trial registry websites (US Clinical Trials Registry and China Clinical Trials Registry) until 1 January 2024. Randomised controlled trials (RCTs) comparing two or more interventions to prevent preterm birth in short cervix pregnant women will be included. The primary outcomes are preterm birth rate at <37 weeks and the composite neonatal adverse outcome, secondary outcomes include spontaneous preterm birth rate at <37 weeks, preterm birth rate at <34 weeks, spontaneous preterm birth rate at <34 weeks, week of gestation, birth weight of the newborn, perinatal mortality and neonatal admission rate. Risk of bias 2.0 (ROB 2.0） will be used to assess the risk of bias in the RCT, and the Confidence in Network Meta-Analysis software will be used to assess the certainty of the generated evidence. The network meta-analysis will be conducted using the gemtc package in R 4.2.2. Two investigators independently performed article screening, data extraction and quality assessment. In addition, subgroup analyses and sensitivity analyses will be used to assess the robustness of the findings.Ethics and disseminationEthical considerations will not be required. Results will be published in a peer-review journal.PROSPERO registration numberCRD42022315200.
Exploratory analysis of factors influencing hospital preferences among the Lebanese population: a cross-sectional study
Authors: El Zouki Christian-Joseph , Chahine Abdallah , Ghadban Elie , Harb Frederic , El-Eid Jamale , El Khoury Diala 
Published: November 2024

ObjectivesThe primary aim of this research is to uncover the underlying factors that shape hospital selection criteria among individuals in Lebanon.DesignCross-sectional study.SettingA survey was circulated across social media platforms and messaging applications in Lebanon from February to May 2023. This questionnaire aimed to gauge participants’ opinions on the importance of various factors in their hospital selection process.ParticipantsA total of 746 participants filled out the survey. We targeted Lebanese adults who were not hospitalised at the time of survey submission.Main outcome measuresWe performed an exploratory factor analysis to examine the underlying structure of our 70-question survey. Reliability analysis was conducted using Cronbach’s alpha and McDonald’s omega. Factor scores were derived by aggregating raw scores and computing the mean.ResultsThe survey results identified eight key factors that accounted for 58.02% of the total variance, with excellent sampling adequacy (Kaiser-Meyer-Olkin=0.921, Bartlett’s p<0.001). These factors exhibited good internal consistency, as indicated by Cronbach’s alpha values for each factor. Ranked by importance for hospital selection, the factors are: staff qualities (α=0.773), administrative services (α=0.801), reputation (α=0.773), ease of access (α=0.704), room attributes (α=0.796), architectural and physical surroundings (α=0.828), luxury amenities (α=0.849) and affiliation and ownership (α=0.661).ConclusionThis paper highlights the hospital characteristics that people may value before selecting a hospital. This insight provides an opportunity for hospital managers to refine their services, ensuring better resonance with people’s anticipations. Beyond this, it sheds light on areas where hospitals could strategically invest to elevate their competitive edge in the healthcare market.
Assessing if motives-based vignettes influence plans for drinking and alcohol cues: protocol for a randomised controlled trial
Authors: Crawford Joel , Collier Elizabeth , Cooke Richard , Ulfsdotter Gunnarsson Katarina , Shorter Gillian , Bendtsen Marcus 
Published: November 2024

IntroductionIn Sweden and the UK, there is a high prevalence of risky drinking, a pattern of drinking associated with adverse consequences. Drinking motives are a proximal predictor of risky drinking and subsequent consequences, suggesting it may be an apt intervention target. Currently, there is a lack of evidence regarding the applicability of motives for intervention efforts. The current study aims to test if motives-based materials are effective in impacting plans for future drinking and reactivity to alcohol-related cues. A secondary aim is to assess individuals’ perceptions of risky drinking as outlined by health authorities. The results of the study will inform the design of a motives-based digital alcohol intervention.Methods and analysisThe study is a three-arm, parallel group, randomised controlled trial. Vignettes will be used to present health information, framed in terms of gains from limiting drinking and losses from excess drinking. Control vignettes will present general health information framed in terms of gains or losses. Proxies for behaviour (intentions and self-efficacy) will be assessed with questionnaire items. A Stroop task will be used to assess reactivity to alcohol cues, and an open-ended item will be used to record perceptions of risky drinking. Outcomes will be contrasted with regression models and estimated using Bayesian inference, while qualitative data will be analysed using thematic analysis within a framework analysis.Ethics and disseminationEthical approval for the study was waived by the Swedish Ethical Review Authority on 16 December 2023 based on participants being anonymous (Dnr. 2023-06474-01). The results of the study will be disseminated in an academic journal and research conferences while also informing the design of a national digital alcohol intervention.Trial registration numberISRCTN12456514.
Maintenance immunosuppressive therapy in liver transplantation: results from CESIT study, an Italian retrospective cohort study
Authors: Bellini Arianna , Finocchietti Marco , Rosa Alessandro Cesare , Masiero Lucia , Trapani Silvia , Cardillo Massimo , Massari Marco , Spila Alegiani Stefania , Pierobon Silvia , Ferroni Eliana , Zanforlini Martina , Leoni Olivia , Ledda Stefano , Garau Donatella , Davoli Marina , Addis Antonio , Belleudi Valeria 
Published: November 2024

ObjectivesTo investigate the use of maintenance immunosuppressive treatments following liver transplantation and to compare their risk–benefit profiles in clinical practice.DesignRetrospective multicentrer cohort study.SettingFour Italian regions (Lombardy, Veneto, Lazio, Sardinia).MethodsData were integrated from the national transplant information system and administrative claims data from four Italian regions. All adults who underwent incident liver transplantation between 2009 and 2019 were identified and categorised into two groups: cirrhosis or hepatocellular carcinoma (HCC). The trend of immunosuppressive treatment over years was analysed, and their effectiveness/safety profiles were compared using multivariate Cox models (HR; 95% CI).Main outcome measuresMortality, transplant reject/graft failure, incidence of severe infections, cancer, diabetes, major adverse cardiovascular events and lipid-modifying agents use.ResultsThe study comprised 750 subjects in the cirrhosis cohort and 1159 in the HCC cohort. Over the study years, there was a decline in the use of cyclosporine-CsA, while combination therapy involving tacrolimus with other drugs increased compared with monotherapy. Overall, tacrolimus monotherapy use was slightly over 40% in both groups, followed by tacrolimus+mycophenolate (39.5%-cirrhosis; 30.6%-HCC) and tacrolimus+molecular target of rapamycin inhibitors (mTORi) (8.5%-cirrhosis; 13.3%-HCC). No significant differences emerged in risk–benefit profile of different tacrolimus-based therapies, except for a higher risk of mortality in cirrhosis subjects under tacrolimus monotherapy compared with tacrolimus+mycophenolate (HR: 2.07; 1.17 to 3.65).ConclusionsThe study highlights a shift over time in postliver transplant therapeutic patterns, favouring the use of tacrolimus in combination with mycophenolate or mTORi, rather than monotherapy. Moreover, a potential association between tacrolimus monotherapy and increased mortality in the cirrhosis cohort was identified. Further research is warranted to investigate these findings more deeply and to optimise treatment strategies for liver transplant recipients.