bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bibliometric study of eDNA diatom for environmental change: An initial study for developing eDNA research in North Coast Area of Central Java
Authors: Falah M H A , Soeprobowati T R , Hadiyanto H , Rahim A , Faradisa N Z , Jasir M I 
Published: December 2024

Abstract
The land surface of Central Java’s coastal area can decrease due to rising sea levels and/or land subsidence caused by land conversion. Semarang, the capital city of Central Java, has experienced land subsidence of around 3.96 cm/year. Diatoms are unicellular organisms that can be used as bioindicators of environmental change because their cell walls are silica, protecting them against fossilization. Diatom studies in Indonesia are still limited to morphological and taxonomic studies, so identification methods using DNA still have the opportunity to be developed and applied. However, to start with eDNA diatom, it is necessary to analyze the literature from previous research. Bibliometric analysis is a technique for discovering scientific trends and organizing research. Based on bibliometric analysis, the papers used as sources are journals sourced from Scopus within the last five years (2018-2023). The VOSviewer 1.6.19 and RStudio Biblioshiny (Bibliometrix) v2023.03.1 were used to visualize the analyzed dataset retrieved from the Scopus database. Four hundred ninety-four articles were retrieved from the Scopus database and analyzed based on several parameters, such as title, author, keywords, and the author’s institution. eDNA diatom analysis has become quite an interesting trend because it is considered faster and more accurate. This paper will help authors and researchers in Indonesia develop research on eDNA diatom.
Rnalib: a Python library for custom transcriptomics analyses
Authors: Popitsch Niko , Ameres Stefan L 
Published: December 2024

Abstract

Motivation
The efficient and reproducible analysis of high-throughput sequencing datasets necessitates the development of methodical and robust computational pipelines that integrate established and bespoke bioinformatics analysis tools, often written in high-level programming languages such as Python. Despite the increasing availability of programming libraries for genomics, there is a noticeable lack of tools specifically focused on transcriptomics. Key tasks in this area include the association of gene features (e.g. transcript isoforms, introns or untranslated regions) with relevant subsections of (large) genomics datasets across diverse data formats, as well as efficient querying of these data based on genomic locations and annotation attributes.

Results
To address the needs of transcriptomics data analyses, we developed rnalib, a Python library designed for creating custom bioinformatics analysis methods. Built on existing Python libraries like pysam and pyBigWig, rnalib offers random access support, enabling efficient access to relevant subregions of large, genome-wide datasets. Rnalib extends the filtering and access capabilities of these libraries and includes additional checks to prevent common errors when integrating genomics datasets. The library is centred on an object-oriented Transcriptome class that provides methods for stepwise annotation of gene features with both, local and remote data sources. The rnalib Application Programming Interface cleanly separates immutable genomic locations from associated, mutable data, and offers a wide range of methods for iterating, querying, and exporting collated datasets. Rnalib establishes a fast, readable, reproducible, and robust framework for developing novel transcriptomics data analysis tools and methods.

Availability and implementation
Source code, documentation, and tutorials are available at https://github.com/popitsch/rnalib.
From bugs to brain: unravelling the GABA signalling networks in the brain-gut-microbiome axis
Authors: Belelli Delia , Lambert Jeremy J , Wan Murphy Lam Yim , Monteiro Ana Rita , Nutt David J , Swinny Jerome D 
Published: December 2024

Abstract
Convergent data, across species, paint a compelling picture of the critical role of the gut and its resident microbiota in several brain functions and disorders. The chemicals mediating communication along these sophisticated highways of the brain-gut-microbiome (BGM) axis include both microbiota metabolites and classical neurotransmitters. Amongst the latter, GABA is fundamental to brain function where it mediates the majority of neuronal inhibition. Until recently, GABA’s role and specific molecular targets in the periphery within the BGM axis had received limited attention. Yet, GABA is produced by neuronal and non-neuronal elements of the BGM, and recently GABA-modulating bacteria have been identified as key players in GABAergic gut systems, indicating that GABA-mediated signalling is likely to transcend not only physiological boundaries, but also species.
We review available evidence with a view to better understand how GABA facilitates integration of molecularly and functionally disparate systems to bring about overall homeostasis, and how GABA perturbations within the BGM axis can give rise to multi-system medical disorders, thereby magnifying the disease burden and the challenges for patient care.
Analysis of transcriptomic databases revealed significant overlaps between GABAAR subunits expressed in the human brain and gut. However, in the gut, there are notable expression profiles for a select number of subunits that have received limited attention to date but could be functionally relevant for BGM axis homeostasis.
GABAergic signalling, via different receptor subtypes, directly regulates BGM homeostasis by modulating the excitability of neurons within brain centres responsible for gastrointestinal (GI) function, in a sex-dependent manner, potentially revealing mechanisms underlying the greater prevalence of GI disturbances in females. Apart from such top-down regulation of the BGM axis, a diverse group of cell types, including enteric neurons, glia, enteroendocrine cells, immune cells and bacteria - integrate peripheral GABA signals to influence brain functions and potentially contribute to brain disorders.
We propose several priorities for this field, including the exploitation of available technologies to functionally dissect components of these GABA pathways within the BGM, with a GI and brain-behaviour-disease focus. Furthermore, in silico ligand-receptor docking analyses, using relevant bacterial metabolomic datasets, coupled with advances in knowledge of GABAAR 3D structures, could uncover new ligands with novel therapeutic potential. Finally, targeted design of dietary interventions is imperative to advance their therapeutic potential to support GABA homeostasis across the BGM axis.
Fast and interpretable mortality risk scores for critical care patients
Authors: Zhu Chloe Qinyu , Tian Muhang , Semenova Lesia , Liu Jiachang , Xu Jack , Scarpa Joseph , Rudin Cynthia 
Published: December 2024

Abstract

Objective
Prediction of mortality in intensive care unit (ICU) patients typically relies on black box models (that are unacceptable for use in hospitals) or hand-tuned interpretable models (that might lead to the loss in performance). We aim to bridge the gap between these 2 categories by building on modern interpretable machine learning (ML) techniques to design interpretable mortality risk scores that are as accurate as black boxes.

Material and Methods
We developed a new algorithm, GroupFasterRisk, which has several important benefits: it uses both hard and soft direct sparsity regularization, it incorporates group sparsity to allow more cohesive models, it allows for monotonicity constraint to include domain knowledge, and it produces many equally good models, which allows domain experts to choose among them. For evaluation, we leveraged the largest existing public ICU monitoring datasets (MIMIC III and eICU).

Results
Models produced by GroupFasterRisk outperformed OASIS and SAPS II scores and performed similarly to APACHE IV/IVa while using at most a third of the parameters. For patients with sepsis/septicemia, acute myocardial infarction, heart failure, and acute kidney failure, GroupFasterRisk models outperformed OASIS and SOFA. Finally, different mortality prediction ML approaches performed better based on variables selected by GroupFasterRisk as compared to OASIS variables.

Discussion
Group Faster Risk’s models performed better than risk scores currently used in hospitals, and on par with black box ML models, while being orders of magnitude sparser. Because GroupFasterRisk produces a variety of risk scores, it allows design flexibility—the key enabler of practical model creation.

Conclusion
Group Faster Risk is a fast, accessible, and flexible procedure that allows learning a diverse set of sparse risk scores for mortality prediction.
Association of smartphone overuse and neck pain: a systematic review and meta-analysis
Authors: Chen Yan-Jyun , Hu Ching-Yuan , Wu Wen-Tien , Lee Ru-Ping , Peng Cheng-Huan , Yao Ting-Kuo , Chang Chia-Ming , Chen Hao-Wen , Yeh Kuang-Ting 
Published: December 2024

Abstract

Background
Smartphone overuse is associated with both psychological and physical health problems, including depression and musculoskeletal disorders. However, the association between smartphone overuse and neck pain remains unclear. We performed a meta-analysis to examine the relation between smartphone overuse and neck pain, and to identify high-risk usage patterns.

Methods
PubMed, Embase, and Cochrane CENTRAL databases were searched for relevant studies published up to 16 August 2023, using keywords including “smartphone” and “neck pain”. Prospective, retrospective, and case-controlled studies assessing the correlation between smartphone overuse and neck pain were eligible. The Newcastle-Ottawa Scale was used to assess the quality of the included studies. Meta-regression and sensitivity analysis using the leave-one-out approach were performed to test the robustness of the results (PROSPERO registration number: CRD42024599227).

Results
Seven retrospective studies including 10 715 participants were included in the systematic review and meta-analysis. The mean age of the participants ranged from 19.9 to 42.9 years. The meta-analysis revealed that compared to participants without smartphone overuse, those who overused a smartphone had a significantly higher risk of neck pain (pooled adjusted odds ratio = 2.34, 95% confidence interval: 1.44–3.82).

Conclusions
These results indicate a significant association between smartphone overuse and increased risk of neck pain. Our findings underscore the necessity of addressing smartphone overuse as a health concern, especially considering its growing prevalence in modern society.
Returning to Work is Associated with Higher Quality of Life: A LIMB-Q Analysis in Patients with Limb-Threatening Injuries
Authors: Wang Sabrina M. , McKibben Natasha , Azad Chao Long , Njoroge Moreen W. , Kraenzlin Franca , O’Hara Nathan N. , De Jong Tim , Hollenbeck Scott T. , Gage Mark J. , Mundy Lily R. 
Published: December 2024

OBJECTIVES:
To identify clinical, demographic, and patient-reported outcomes (PROs) associated with return to work after lower extremity traumatic injury requiring amputation or limb salvage.

METHODS:
Design: Cross-sectional study.

Setting:
Multi-center across 25 countries.

Patient Selection Criteria:
Working patients who sustained lower extremity trauma requiring soft-tissue reconstruction or amputation.

Outcome Measures and Comparisons:
The main outcome measurements were LIMB-Q scores. Regression analyses were performed to evaluate associations between functional and quality of life outcomes by return to work status.

RESULTS:
Responses were received from 258 participants with 66% males (n=173) and a mean age of 40 years old (IQR: 19-78) . Of respondents that worked prior to injury, 67% (n=173) returned to work after a mean 16 months (SD 39). Divorced or widowed status [p=0.006; OR 0.107 (95% CI 0.022-0.531)], bilateral injuries [p=0.004; OR 0.093 (95% CI 0.019-0.471)], and having a manual labor job [p=0.002; OR 0.191 (95% CI 0.027-0.395)] were negatively associated with return to work. Increased time since injury [p=0.036, OR 1.08 (95% 1.02, 1.16)] and higher educational status [p=0.024; OR 5.12 (95% CI 1.24, 21.0)] were positively associated with return to work status. Reconstruction or amputation was not associated with return to work [p=0.087, OR (95% CI 0.190-1.11)]. LIMB-Q Function (p=0.033; 95% CI [-11.3, -0.49]), and LIMB-Q Life Impact (p=0.008; 95% CI [-13.5, -2.01]) scores were significantly increased in patients that returned to work after injury.

CONCLUSIONS:
Patients who returned to work after lower extremity injury reported higher levels of function and overall return to normalcy in their lives. Returning to work may improve quality of life in patients following lower extremity trauma.

LEVEL OF EVIDENCE:
Prognostic Level III
Associations of gestation length and offspring birthweight for gestational age with menopausal symptoms and age of natural menopause at midlife among women enrolled in a prebirth longitudinal cohort
Authors: Cohen Nathan J. , Rifas-Shiman Sheryl L. , Soria-Contreras Diana C. , Perng Wei , Hivert Marie-France , Oken Emily , Chavarro Jorge E. , Minguez-Alarcon Lidia 
Published: December 2024

Abstract

Objective
Reproductive history may help identify women at higher risk for experiencing menopausal symptoms. We hypothesized that gestation length and offspring birthweight for gestational age z-scores would be associated with menopausal symptoms and age at natural menopause in midlife among women in a longitudinal prebirth cohort.

Methods
Among 691 women enrolled in pregnancy and followed to midlife, we examined associations of gestation length and offspring birthweight for gestational age z-score at the index pregnancy with total menopausal symptoms assessed with the 11-item Menopause Rating Scale (MRS) using linear regression models, with individual menopausal symptoms using binomial regression models with a log link function, and with age at natural menopause using Cox proportional hazards models. We adjusted all models for age at enrollment, education, parity, annual household income, and prepregnancy body mass index.

Results
Mean (SD) MRS total score was 7.9 (5.8) points at age 52.1 (3.8) years, and mean (SD) age at natural menopause was 50.8 (3.7) years. We observed null associations of gestation length (β = −0.07 points per week, 95% confidence interval [CI] = −0.32 to 0.18) and birthweight for gestational age z-score (β = 0.16 points per z-score, 95% CI = −0.31 to 0.63) with the MRS total score in adjusted models. We also observed null associations of gestation length (adjusted hazards ratio = 0.99 per week, 95% CI = 0.94-1.06) and birthweight for gestational age z-score (adjusted hazards ratio = 1.06 per z-score, 95% CI = 0.94-1.19) with age of onset of natural menopause.

Conclusions
Birth outcomes were not associated with total menopause symptom scores or age at natural menopause.
Chinese guidelines for the diagnosis and treatment of human immunodeficiency virus infection/acquired immunodeficiency syndrome (2024 edition)
Authors:   Acquired Immunodeficiency Syndrome Professional Group, Society of Infectious Diseases, Chinese Medical Association; Chinese Center for Disease Control and Prevention
Published: December 2024

Abstract
The Acquired Immunodeficiency Syndrome Professional Group of the Society of Infectious Diseases of the Chinese Medical Association formulated the first edition of the Chinese Guidelines for the Diagnosis and Treatment of human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS) (referred to as the Guidelines) in 2005. The 2024 edition of the Guidelines has been compiled by updating the 2021 fifth edition, incorporating the latest research advancements in antiviral therapy, comprehensive management, opportunistic infections, concurrent tumors, and the prevention and intervention of HIV infection. The new edition also introduces a new section on “Incomplete immune reconstitution”, proposes the concept of “HIV vulnerable populations” for the first time with recommendations for their diagnosis and treatment. This edition of the Guidelines covers 14 sections: epidemiology, pathogenic characteristics, laboratory tests, pathogenesis, clinical presentation and staging, diagnostic criteria, common opportunistic infections, antiretroviral therapy, immune reconstitution inflammatory syndrome, incomplete immune reconstitution, AIDS-related neoplasms, prevention of mother-to-child transmission and conception in serodiscordant couples, pre- and post-exposure prophylaxis, and whole-course management of HIV infection. This edition of the Guidelines aims to assist clinical physicians in making informed decisions in the diagnosis, treatment, and management of HIV/AIDS and will be periodically revised and updated based on domestic and international research progress.
Periorbital Microcystic Adnexal Carcinoma With Distant Metastases
Authors: Mah Leonard J. , Sandler Gideon , Ngo, Quan , Estall, Vanessa , Vargas, Ana Cristina , Tumuluri, Krishna 
Published: December 2024

Purpose:
Microcystic adnexal carcinoma (MAC) is a locally aggressive adnexal carcinoma of the head and neck, which has a high tendency for recurrence. MAC rarely has distant metastasis, with only one previously reported case originating from the periorbital region. We present a patient with periorbital MAC with distant metastasis and a review of all reported patients with metastatic disease.

Method:
We present a patient with the youngest reported periorbital MAC with metastases along with a major review of metastatic MAC using PubMed/MEDLINE databases. Case reports or case series that described a case of MAC with metastases were included.

Results:
A 37-year-old man with left periorbital MAC had local resection and subsequent exenteration for orbital recurrence. Distal metastases were noted between 8 and 13 years postexenteration in the left parotid gland, left sartorius muscle, and right brachialis and trapezius muscles. There are 7 patients, including our patient, with distant metastasis in MAC, of which 2 were of periorbital origin. The median age was 62 with a male predominance (n = 5/7). Our patient is the youngest reported patient with metastatic MAC. The median time to metastasis was 8 years. Strategies to control disease included radiotherapy (n = 4/7) and chemotherapy (n = 4/7). Six of 7 cases passed away with disease or have ongoing disease.

Conclusion:
Periorbital MAC is a locally aggressive disease with potential for metastatic spread and all patients need long-term surveillance for local recurrence and distant metastases.
Corneal endothelial cell loss with different techniques of nucleus delivery in Manual Small Incision Cataract Surgery- Randomized Controlled Trial
Authors: Mol Fincy , Nagarajan Swathi , AR Rajalakshmi , Govindasamy Ezhumalai 
Published: December 2024

Purpose:
To compare corneal endothelial loss in manual small incision cataract surgery (MSICS) following three different techniques of nucleus delivery (Viscoexpression, Irrigating Vectis, Phacosandwich).

Setting:
Mahatma Gandhi Medical College and Research Institute, Puducherry, India

Design:
Prospective, single blinded, randomized controlled trial

Methods:
Willing patients > 40years of age with immature cataract and posted for MSICS were recruited for the study. Those with systemic or ocular comorbidities which may influence corneal endothelium, dilated pupil size of <5mm, intraoperative complications and postoperative corneal haze were excluded. They were randomly divided to one of the three groups (Group 1- Viscoexpression, Group 2- Irrigating Vectis, Group 3- Phacosandwich) for nucleus delivery. Visual acuity and corneal endothelial parameters were recorded preoperatively and postoperatively at 6-8weeks.

Results:
A total of 90 patients with mean age of 59.13 ± 9.42 years (range 40-82years) were studied with 30 patients in each group. Following MSICS there was a 12.12% (p=0.001) endothelial cell loss. It was 10.81% in viscoexpression group, 11.3% in irrigating vectis group and 14.28% in phacosandwich group. Post hoc analysis with Dunn Bon ferroni test showed endothelial cell loss following viscoexpression and irrigating vectis methods of nucleus delivery were comparable (p=0.096) and significantly lesser (p<0.001) than in Phacosandwich group.

Conclusion:
There was significant endothelial cell loss following MSICS. Nucleus delivery by viscoexpression and irrigating vectis had similar endothelial cell loss while it was greater with phacosandwich technique.
Factors Associated With Self-management in Adults With Type 1 or Type 2 Diabetes
Authors: Heo Seongkum , Barbé Tammy , Kim JinShil 
Published: December 2024

Background
Poor self-management in adults with type 1 diabetes (T1DM) or type 2 diabetes (T2DM) leads to increased diabetes complications. Factors associated with self-management in T1DM and T2DM may differ due to the different methods for controlling blood glucose.

Purpose
The aim of this study was to examine the associations of modifiable physical, cognitive, and psychosocial factors and the nonmodifiable factor of age with overall self-management, diet, exercise, blood glucose testing (BGT), foot care, and smoking in adults with T1DM or T2DM.

Methods
In this cross-sectional, correlational study, data were collected from adults with T1DM (n = 64; mean age, 51.2 years) or T2DM (n = 84; mean age, 62.5 years) using REDCap in 2023 and were analyzed using multiple regression analyses.

Results
Older age, lower body mass index, and stronger knowledge in T1DM (F
10,53 = 2.290, P = .026, R
2 = 0.302), and lower body mass index and higher levels of self-efficacy in T2DM were associated with better overall self-management (F
10,73 = 3.219, P = .002, R
2 = 0.306). Different combinations of age, body mass index, knowledge, resilience, and self-esteem were associated with different components of self-management, including diet, BGT, and foot care, in T1DM, whereas different combinations of body mass index, knowledge, self-efficacy, and depressive symptoms were associated with different components of self-management, including diet, exercise, and BGT, in T2DM.

Conclusions
Factors associated with self-management differed based on types of diabetes and components of self-management. Clinicians need to consider the 2 types of diabetes and distinct factors associated with each component of self-management to improve it.
The Leaky Preexposure Prophylaxis Cascade: Barriers and Facilitators to Preexposure Prophylaxis Uptake and Adherence Among Youth Experiencing Homelessness in the US South, a Mixed Methods Study
Authors: Santa Maria Diane , Paul Mary , Lightfoot Marguerita , Nyamathi Adeline , Quadri Yasmeen , Padhye Nikhil , Ocampo Eduardo , Babayev Roman , Ramos Melanie Watt , Malone-Thomas Sheryl L. , White Margaret , Carrillo Alejandro , Jones Jennifer Torres 
Published: December 2024

Abstract
Adherence to preexposure prophylaxis (PrEP) is lower among high-risk populations, including youth experiencing homelessness (YEH). This study determined the feasibility of urine PrEP adherence biomarker testing and examined the barriers and facilitators to PrEP uptake and adherence among YEH. YEH were recruited from a randomized control trial conducted in a large urban setting in southern United States. Interviews (N = 40) were conducted to identify barriers and facilitators to PrEP uptake and adherence. PrEP urine-based adherence testing feasibility was conducted among those who started on PrEP. Twenty-two participants obtained a prescription and 15 youth completed at least one adherence test. Facilitators and barriers were categorized as individual, interpersonal and community, and structural among PrEP starters and nonstarters. PrEP uptake and adherence were low for eligible YEH. Enriching the understanding of the challenges and facilitators experienced with accessing PrEP for YEH can improve engagement in HIV prevention among YEH.