bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variant graph craft (VGC): a comprehensive tool for analyzing genetic variation and identifying disease-causing variants
Authors: Li Jennifer , Yang Andy , Carneiro Benedito A. , Gamsiz Uzun Ece D. , Massingham Lauren , Uzun Alper 
Published: September 2024

Abstract
Background
The variant call format (VCF) file is a structured and comprehensive text file crucial for researchers and clinicians in interpreting and understanding genomic variation data. It contains essential information about variant positions in the genome, along with alleles, genotype calls, and quality scores. Analyzing and visualizing these files, however, poses significant challenges due to the need for diverse resources and robust features for in-depth exploration.

Results
To address these challenges, we introduce variant graph craft (VGC), a VCF file visualization and analysis tool. VGC offers a wide range of features for exploring genetic variations, including extraction of variant data, intuitive visualization, and graphical representation of samples with genotype information. VGC is designed primarily for the analysis of patient cohorts, but it can also be adapted for use with individual probands or families. It integrates seamlessly with external resources, providing insights into gene function and variant frequencies in sample data. VGC includes gene function and pathway information from Molecular Signatures Database (MSigDB) for GO terms, KEGG, Biocarta, Pathway Interaction Database, and Reactome. Additionally, it dynamically links to gnomAD for variant information and incorporates ClinVar data for pathogenic variant information. VGC supports the Human Genome Assembly Hg37 and Hg38, ensuring compatibility with a wide range of data sets, and accommodates various approaches to exploring genetic variation data. It can be tailored to specific user needs with optional phenotype input data.

Conclusions
In summary, VGC provides a comprehensive set of features tailored to researchers working with genomic variation data. Its intuitive interface, rapid filtering capabilities, and the flexibility to perform queries using custom groups make it an effective tool in identifying variants potentially associated with diseases. VGC operates locally, ensuring data security and privacy by eliminating the need for cloud-based VCF uploads, making it a secure and user-friendly tool. It is freely available at https://github.com/alperuzun/VGC.
Aerosolization ocular surface microorganisms accumulation effect during non-contact tonometer measurements
Authors: Shen Xinyi , Xu Yi , Ye Yuee , Huai Shuo , Wu Peiyu , Huang Jinzhi , Zhou Weihe , Li Chunchun , Chen Yanyan 
Published: September 2024

Abstract
Purpose
This study aimed to verify that aerosolization ocular surface microorganisms (AOSMs) accumulated during non-contact tonometry (NCT) measurements.

Methods
A total of 508 participants (740 eyes) were enrolled in the study. In Experiment 1, before NCT was performed on each eye, the air was disinfected, and environment air control samples were collected via Air ideal® 3P (Bio Merieux). During NCT measurements, microbial aerosol samples were collected once from each eye. In Experiment 2, we collected initial blank control samples and then repeated Experiment 1. Finally, in Experiment 3, after the background microbial aerosol investigation, we cumulatively sampled AOSMs from each 10 participants then culture once, without any interventions to interrupt the accumulation. The collected samples were incubated and identified using matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF-MS).

Results
Pathogenic Aerococcus viridans and other microorganisms from human eyes can spread and accumulate in the air during NCT measurements. The species and quantity of AOSMs produced by NCT measurements can demonstrate an accumulation effect.

Conclusion
AOSMs generated during NCT measurements are highly likely to spread and accumulate in the air, thereby may increase the risk of exposure to and transmission of bio-aerosols.
Newman’s theory of health as expanding consciousness: an evolutionary concept analysis
Authors: Li Hongman , Xiong Ying , Ye Zengjie 
Published: September 2024

Abstract
Background
The health as expanding consciousness (HEC) theory posits that health and disease are interconnected components of a comprehensive process aimed at expanding consciousness.

Aim
The objective of this study is to introduce the concept, research status and applications of HEC and offer a comprehensive understanding of its various key components.

Data sources
Databases including EMBASE, PubMed, ScienceDirect, ProQuest, Wiley, Web of Science, Sinomed, China National Knowledge Infrastructure, Wanfang, and CQVIP, covering the period from 1986 to 2023.

Method
Employing Rodgers’ evolutionary concept analysis approach, this study included and analysed 70 studies.

Results
The characteristics of HEC comprise aspects such as movement, time, space, energy, rhythm, and paradigm of health. The antecedents of HEC encompass disease, chaos, binding, centring, and choice point. Consequences associated with HEC include self-transcendence, unbinding, decentring, expanded consciousness, real freedom, pattern recognition, absolute consciousness, and death.

Conclusion
This study has identified substitute terms, related concepts, attributes, antecedents, consequences, and empirical references associated with HEC. The findings provide valuable information applicable across various domains of nursing, encompassing practice, education, research, and management.
Integrative microbiome and metabolome profiles reveal the impacts of periodontitis via oral-gut axis in first-trimester pregnant women
Authors: Cheng Tianfan , Wen Ping , Yu Rong , Zhang Feng , Li Huijun , Xu Xiaoyi , Zhao Dan , Liu Fang , Su Weilan , Zheng Zheng , Yang Hong , Yao Jilong , Jin Lijian 
Published: September 2024

Abstract
Background
Periodontitis results from host-microbe dysbiosis and the resultant dysregulated immunoinflammatory response. Importantly, it closely links to numerous systemic comorbidities, and perplexingly contributes to adverse pregnancy outcomes (APOs). Currently, there are limited studies on the distal consequences of periodontitis via oral-gut axis in pregnant women. This study investigated the integrative microbiome-metabolome profiles through multi-omics approaches in first-trimester pregnant women and explored the translational potentials.

Methods
We collected samples of subgingival plaques, saliva, sera and stool from 54 Chinese pregnant women at the first trimester, including 31 maternal periodontitis (Perio) subjects and 23 Non-Perio controls. By integrating 16S rRNA sequencing, untargeted metabolomics and clinical traits, we explored the oral-gut microbial and metabolic connection resulting from periodontitis among early pregnant women.

Results
We demonstrated a novel bacterial distinguisher Coprococcus from feces of periodontitis subjects in association with subgingival periodontopathogens, being different from other fecal genera in Lachnospiraceae family. The ratio of fecal Coprococcus to Lachnoclostridium could discriminate between Perio and Non-Perio groups as the ratio of subgingival Porphyromonas to Rothia did. Furthermore, there were differentially abundant fecal metabolic features pivotally enriched in periodontitis subjects like L-urobilin and kynurenic acid. We revealed a periodontitis-oriented integrative network cluster, which was centered with fecal Coprococcus and L-urobilin as well as serum triglyceride.

Conclusions
The current findings about the notable influence of periodontitis on fecal microbiota and metabolites in first-trimester pregnant women via oral-gut axis signify the importance and translational implications of preconceptional oral/periodontal healthcare for enhancing maternal wellbeing.
Sensory dysfunction in SMA type 2 and 3 - adaptive mechanism or concomitant target of damage?
Authors: Koszewicz Magdalena , Ubysz Jakub , Dziadkowiak Edyta , Wieczorek Malgorzata , Budrewicz Slawomir 
Published: September 2024

Abstract
Background
The motor neuron survival protein performs numerous cellular functions; hence, spinal muscular atrophy (SMA) is considered to be a multi-organ disease with possible sensory system damage. The controversy surrounding the presence of sensory disturbances, prompted us to conduct standard electrophysiological studies and assess the sensory thresholds for different modalities in adults with SMA types 2 and 3. The study group consisted of 44 adult SMA patients (types 2 and 3). All patients underwent neurological examination using the Hammersmith Functional Motor Scale – Expanded (HFMSE). Standard sensory electrophysiological studies in the ulnar nerve and the estimation of vibratory, temperature, and warm- and cold-induced pain thresholds with temperature dispersion assessment were performed using quantitative sensory testing (QST).

Results
The most repeatable result was the high amplitude of the sensory nerve action potentials (SNAP) in SMA patients compared to controls. This was higher in type 2 patients compared to type 3a and 3b patients and patients with low HFSME scores. Patients with SMA, especially type 3b presented a longer sensory latency and slower conduction velocity than did controls. Cold pain threshold was higher and warm dispersion larger in SMA. The vibratory limit was higher in patients with high HFSME scores.

Conclusions
A high SNAP amplitude suggests sensory fibre hyperactivity, which may be based on overactivation of metabolic pathways as an adaptive mechanism in response to SMN protein deficiency with additionally coexisting small C- and A-delta fibre damage. SMA patients seem to have a concomitant, mild demyelinating process present at the early SMA stage.
Identification of treatment elements for adolescents with callous unemotional traits: a systematic narrative review
Authors: Waaler Pamela M. , Bergseth Josefine , Vaskinn Linda , Espenes Kristin , Holtan Thale , Kjøbli John , Bjørnebekk Gunnar 
Published: September 2024

AbstractAdolescents with callous unemotional (CU) traits are at risk for poor quality-of-life outcomes such as incarceration, suicide, and psychopathy. It is currently unknown which treatments are implemented with CU adolescents specifically and which elements make up these interventions. A narrative systematic review was used to identify the treatments and common elements used with CU adolescents (12–18 years). Eligible studies were randomized controlled trials and quasi-experimental studies evaluating psychosocial interventions, delivered within a clinical context, and directed towards the adolescent or their family. Eight studies with 1291 participants were included. Significant decreases in CU traits were demonstrated only in a minority of studies. The most utilized practice elements were set goals for treatment, practice interpersonal/communication skills, prepare for termination, and teach parents skills and strategies; the most utilized process elements were formal therapy, practice exercises, important others, and flexible/adaptive. A majority of the studies did not report an implementation element. While theoretical frameworks for CU children are employed with CU adolescents, there is still uncertainty regarding their suitability for this age group. Given the limited empirical evidence, there is a critical need for further exploration.
Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR
Authors: Flynn Sean M. , Dhir Somdutta , Herka Krzysztof , Doyle Colm , Melidis Larry , Simeone Angela , Hui Winnie W. I. , Araujo Tavares Rafael de Cesaris , Schoenfelder Stefan , Tannahill David , Balasubramanian Shankar 
Published: September 2024

AbstractMethods to measure chromatin contacts at genomic regions bound by histone modifications or proteins are important tools to investigate chromatin organization. However, such methods do not capture the possible involvement of other epigenomic features such as G-quadruplex DNA secondary structures (G4s). To bridge this gap, we introduce ViCAR (viewpoint HiCAR), for the direct antibody-based capture of chromatin interactions at folded G4s. Through ViCAR, we showcase the first G4-3D interaction landscape. Using histone marks, we also demonstrate how ViCAR improves on earlier approaches yielding increased signal-to-noise. ViCAR is a practical and powerful tool to explore epigenetic marks and 3D genome interactomes.
Laser enhanced photothermal effect of silver nanoparticles synthesized by chemical and green method on Gram-positive and Gram-negative bacteria
Authors: Mostafa Elham M. , Badr Y. , Ramadan Marwa A. , Hashem Mohamed M. M. , Abo-El-Sooud Khaled , Deif Heba N. , Faid Amna H. 
Published: September 2024

Abstract
Purpose
The antibacterial properties of silver nanoparticles (AgNPs) are extensively identified. In large quantities, they might be harmful. So many fields of nanotechnology have shown a great deal of interest in the development of an environmentally friendly, efficient method for synthesizing metal nanoparticles. Because of its antibacterial and antifungal properties toward a wide range of microbes, chitosan silver nanoparticles (AgNPs@Cs) constitute a newly developing class of bio-nanostructured hybrid materials. Furthermore, the use of photothermal therapy (PTT) has been suggested as a means of elimination of germs. These light-stimulated treatments are minimally invasive and have a few side effects. In the present work, the antibacterial effect of AgNPs at low concentrations; prepared by chemical and green methods as antimicrobial and photothermal agents in photothermal therapy; with laser irradiation were explored as combined treatment against MRSA, Pseudomonas aeruginosa, and Klebsiella pneumoniae.

Methods
Silver nanoparticles were produced in two ways. First, by sodium borohydrides, second, by chitosan (as a natural eco-friendly reducing, and capping agent). The nanostructure of AgNPs and AgNPs@Cs was confirmed by UV–visible spectrometer, transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIRs), and direct light scattering (DLS). The antibacterial activity of the prepared nanoparticles and the laser irradiation was tested against three bacterial species of zoonotic importance; MRSA, Pseudomonas aeruginosa, and Klebsiella pneumoniae; and was evaluated by measuring their minimum inhibitory concentrations (MIC).

Results
Silver nanoparticles produced by the two methods had spherical shapes with nearly the same particle size. The analysis of DLS showed that AgNPs were very stable with zeta potential − 28.8 mv, and 47.7 mv by chemical and chitosan synthesis, respectively. Furthermore, AgNPs@Cs showed higher antibacterial activity toward the tested bacterial species than AgNPs by chemical method. Additionally, the bacterial viability using photothermal laser therapy was reduced compared to laser and AgNPs alone. The bactericidal activities were higher when laser diode was coupled with AgNPs@Cs than by chemical reduction.

Conclusion
The laser combined treatment had a higher antimicrobial effect than AgNPs alone or laser irradiation alone.
Variation in the prion protein gene (PRNP) open reading frame sequence in French cervids
Authors: Laubier Johann , Van De Wiele Anne , Barboiron Aurélie , Laloë Denis , Saint-Andrieux Christine , Castille Johan , Meloni Emma , Ernst Sonja , Pellerin Maryline , Floriot Sandrine , Daniel-Carlier Nathalie , Passet Bruno , Merlet Joël , Verheyden Hélène , Béringue Vincent , Andréoletti Olivier , Houston Fiona , Vilotte Jean-Luc , Bourret Vincent , Moazami-Goudarzi Katayoun 
Published: September 2024

AbstractThe recent emergence of chronic wasting disease (CWD) in Europe has become a new public health risk for monitoring of wild and farmed cervids. This disease, due to prions, has proliferated in North America in a contagious manner. In several mammalian species, polymorphisms in the prion protein gene (PRNP) play a crucial role in the susceptibility to prions and their spread. To obtain a reliable picture of the distribution of PRNP polymorphisms in the two most common cervid species in France, we sequenced the open reading frame (ORF) of this gene in 2114 animals, 1116 roe deer (Capreolus capreolus) and 998 red deer (Cervus elaphus). Selection criteria such as historical origin, spatial distribution and sex ratio have been integrated to establish this sample collection. Except for one heterozygous animal with a non-synonymous mutation at codon 37 (G37A), all the 1116 French roe deer were monomorphic. Red deer showed greater variation with two non-synonymous substitutions (T98A; Q226E), three synonymous substitutions (codons 21, 78 and 136) and a new 24pb deletion (Δ69-77). We found significant regional variations between French regions in the frequency of the identified substitutions. After cloning of the PRNP ORF from animals presenting multiple non-synonymous polymorphisms, we identified six haplotypes and obtained a total of twelve genotypes. As in other European countries, we highlighted the apparent homogeneity of PRNP in the French roe deer and the existence of a greater diversity in the red deer. These results were in line with European phylogeographic studies on these two species.
Effectiveness of lifestyle interventions for glycaemic control among adults with type 2 diabetes in West Africa: a systematic review and meta-analysis protocol
Authors: Peprah Ellen Barnie , Jahan Yasmin , Danso-Appiah Anthony , Abdul-Samed Abdul-Basit , Mirzoev Tolib , Antwi Edward , Balabanova Dina , Agyepong Irene 
Published: September 2024

Abstract
Background
Lifestyle interventions are key to the control of diabetes and the prevention of complications, especially when used with pharmacological interventions. This protocol aims to review the effectiveness of lifestyle interventions in relation to nutrition and physical activity within the West African region. This systematic review and meta-analysis seeks to understand which interventions for lifestyle modification are implemented for the control of diabetes in West Africa at the individual and community level, what evidence is available on their effectiveness in improving glycaemic control and why these interventions were effective.

Methods
We will review randomised control trials and quasi-experimental designs on interventions relating to physical activity and nutrition in West Africa. Language will be restricted to English and French as these are the most widely spoken languages in the region. No other filters will be applied. Searching will involve four electronic databases — PubMed, Scopus, Africa Journals Online and Cairn.info using natural-language phrases plus reference/citation checking.
Two reviewers will independently screen results according to titles and abstracts against the inclusion and exclusion criteria to identify eligible studies. Upon full-text review, all selected studies will be assessed using Cochrane’s Collaboration tool for assessing the risk of bias of a study and the ROBINS-I tool before data extraction. Evidence will be synthesised narratively and statistically where appropriate. We will conduct a meta-analysis when the interventions and contexts are similar enough for pooling and compare the treatment effects of the interventions in rural to urban settings and short term to long term wherever possible.

Discussion
We anticipate finding a number of studies missed by previous reviews and providing evidence of the effectiveness of different nutrition and physical activity interventions within the context of West Africa. This knowledge will support practitioners and policymakers in the design of interventions that are fit for context and purpose within the West African region.

Systematic review registration
This systematic review has been registered in the International Prospective Register for Systematic Reviews — PROSPERO, with registration number CRD42023435116. All amendments to this protocol during the process of the review will be explained accordingly.
Dietary recommendations for people with diabetes in special situations: a position statement report by Arabic Association for the Study of Diabetes and metabolism (AASD)
Authors: Soliman Amin Roshdy , Hegazy Mona , Ahmed Rabab Mahmoud , Abdelghaffar Shereen , Gomaa Mohammed , Alwakil Sahar , Soliman Dina , Sedky Lobna , Shaltout Inass 
Published: September 2024

Abstract
Background
Diabetes is a significant global health concern. Regional factors play a crucial role in determining the appropriate diet for patients.

Main body
The Arabic Association for the Study of Diabetes and Metabolism has developed a position statement that addresses the dietary needs of patients in the context of low income and cultural dietary habits. This statement aims to explore the most suitable diet for Middle East and North Africa (MENA) region and provide guidance for physicians to overcome barriers in optimal care. While most dietary guidelines focus on uncomplicated diabetes, it’s essential to recognize that diabetes often coexists with other common diseases in our region.

Conclusion
International guidelines cannot be directly applied to the Egypt and Arab countries due to cultural and dietary differences. Our position statement shares valuable insights into managing diabetes in special situations and diverse clinical settings within this region. These recommendations are flexible, considering personal, cultural, and traditional differences.
Bladder-Preserving Trimodality Treatment for High-Grade T1 Bladder Cancer: Results From Phase II Protocol NRG Oncology/RTOG 0926
Authors: Dahl Douglas M. , Rodgers Joseph P. , Shipley William U. , Michaelson M. Dror , Wu Chin-Lee , Parker William , Jani Ashesh B. , Cury Fabio L. , Hudes Richard S. , Michalski Jeff M. , Hartford Alan C. , Song Daniel , Citrin Deborah E. , Karrison Theodore G. , Sandler Howard M. , Feng Felix Y. , Efstathiou Jason A. 
Published: September 2024

PURPOSE
To investigate the use of radiation with radiosensitizing chemotherapy following repeated transurethral resection (trimodality therapy) as an alternative to radical cystectomy in T1 bladder cancer which has failed Bacillus Calmette-Guerin (BCG).

PATIENTS AND METHODS
Patients with recurrent T1 bladders who had failed BCG and were recommended to undergo cystectomy were treated with trimodality therapy. The primary end point was 3-year freedom from cystectomy. Secondary end points were distant metastasis at 3 and 5 years, local recurrence, disease-specific and overall survival (OS), and safety.

RESULTS
This single-arm phase II study enrolled 37 patients. Efficacy and safety were evaluated in 34 patients after three exclusions. The median follow-up was 5.1 years. The 3-year freedom from cystectomy rate was 88% (lower one-sided 97.5% confidence limit [CI], 72%), meeting the primary study goal. OS at 3 and 5 years was 69% (95% CI, 54 to 85) and 56% (95% CI, 39 to 74), respectively. The distant metastasis rates at 3 and 5 years were 12% (95% CI, 4 to 26) and 19% (95% CI, 7 to 34), respectively. Eight patients died due to urothelial cancer, 12 exhibited local recurrence at 3 years (cumulative incidence: 32%; 95% CI, 17 to 48), 18 experienced grade 3 adverse events, mostly hematological, and one developed grade 4 neutropenia.

CONCLUSION
Trimodality therapy is an effective potential alternative to radical cystectomy for recurrent high-grade T1 urothelial cancer of the bladder. At 3 years, 88% of the patients remained free of cystectomy.