bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP
Authors: Li Rongyuan , Wu Jingli , Li Gaoshi , Liu Jiafei , Xuan Junbo , Zhu Qi 
Published: November 2023

Abstract
Background
Although gene expression data play significant roles in biological and medical studies, their applications are hampered due to the difficulty and high expenses of gathering them through biological experiments. It is an urgent problem to generate high quality gene expression data with computational methods. WGAN-GP, a generative adversarial network-based method, has been successfully applied in augmenting gene expression data. However, mode collapse or over-fitting may take place for small training samples due to just one discriminator is adopted in the method.

Results
In this study, an improved data augmentation approach MDWGAN-GP, a generative adversarial network model with multiple discriminators, is proposed. In addition, a novel method is devised for enriching training samples based on linear graph convolutional network. Extensive experiments were implemented on real biological data.

Conclusions
The experimental results have demonstrated that compared with other state-of-the-art methods, the MDWGAN-GP method can produce higher quality generated gene expression data in most cases.
DG-Affinity: predicting antigen–antibody affinity with language models from sequences
Authors: Yuan Ye , Chen Qushuo , Mao Jun , Li Guipeng , Pan Xiaoyong 
Published: November 2023

Abstract
Background
Antibody-mediated immune responses play a crucial role in the immune defense of human body. The evolution of bioengineering has led the progress of antibody-derived drugs, showing promising efficacy in cancer and autoimmune disease therapy. A critical step of this development process is obtaining the affinity between antibodies and their binding antigens.

Results
In this study, we introduce a novel sequence-based antigen–antibody affinity prediction method, named DG-Affinity. DG-Affinity uses deep neural networks to efficiently and accurately predict the affinity between antibodies and antigens from sequences, without the need for structural information. The sequences of both the antigen and the antibody are first transformed into embedding vectors by two pre-trained language models, then these embeddings are concatenated into an ConvNeXt framework with a regression task. The results demonstrate the superiority of DG-Affinity over the existing structure-based prediction methods and the sequence-based tools, achieving a Pearson’s correlation of over 0.65 on an independent test dataset.

Conclusions
Compared to the baseline methods, DG-Affinity achieves the best performance and can advance the development of antibody design. It is freely available as an easy-to-use web server at https://www.digitalgeneai.tech/solution/affinity.
Delving into the lifestyle of Sundarban Wetland resident, biofilm producing, halotolerant Salinicoccus roseus: a comparative genomics-based intervention
Authors: Dutta Bhramar , Halder Urmi , Chitikineni Annapurna , Varshney Rajeev K. , Bandopadhyay Rajib 
Published: November 2023

Abstract
Background
Microbial community played an essential role in ecosystem processes, be it mangrove wetland or other intertidal ecologies. Several enzymatic activities like hydrolases are effective ecological indicators of soil microbial function. So far, little is known on halophilic bacterial contribution and function on a genomic viewpoint of Indian Sundarban Wetland. Considering the above mentioned issues, the aims of this study was to understand the life style, metabolic functionalities and genomic features of the isolated bacterium, Salinicoccus roseus strain RF1H. A comparative genome-based study of S. roseus has not been reported yet. Henceforth, we have considered the inclusion of the intra-species genome comparison of S. roseus to gain insight into the high degree of variation in the genome of strain RF1H among others.

Results
Salinicoccus roseus strain RF1H is a pink-red pigmented, Gram-positive and non-motile cocci. The bacterium exhibited high salt tolerance (up to 15% NaCl), antibiotic resistance, biofilm formation and secretion of extracellular hydrolytic enzymes. The circular genome was approximately 2.62978 Mb in size, encoding 574 predicted genes with GC content 49.5%. Presence of genomic elements (prophages, transposable elements, CRISPR-Cas system) represented bacterial virulence and multidrug-resistance. Furthermore, genes associated with salt tolerance, temperature adaptation and DNA repair system were distributed in 17 genomic islands. Genes related to hydrocarbon degradation manifested metabolic capability of the bacterium for potential biotechnological applications. A comparative pangenome analysis revealed two-component response regulator, modified C4-dicarboxylate transport system and osmotic stress regulated ATP-binding proteins. Presence of genes encoding arginine decarboxylase (ADC) enzyme being involved in biofilm formation was reported from the genome. In silico study revealed the protein is thermostable and made up with ~ 415 amino acids, and hydrophilic in nature. Three motifs appeared to be evolutionary conserved in all Salinicoccus sequences.

Conclusion
The first report of whole genome analysis of Salinicoccus roseus strain RF1H provided information of metabolic functionalities, biofilm formation, resistance mechanism and adaptation strategies to thrive in climate-change induced vulnerable spot like Sundarban. Comparative genome analysis highlighted the unique genome content that contributed the strain’s adaptability. The biomolecules produced during metabolism are important sources of compounds with potential beneficial applications in pharmaceuticals.
Association between intraoperative mean arterial pressure variability and postoperative delirium after hip fracture surgery: a retrospective cohort study
Authors: Zhang Chuangxin , Song Yuxiang , Wu Xiaodong , Miao Ran , Lou Jingsheng , Ma Yulong , Li Mengmeng , Mi Weidong , Cao Jiangbei 
Published: November 2023

Abstract
Background
Postoperative delirium (POD) is a common complication in elderly patients after hip fracture surgery. Our study was to investigate whether intraoperative mean arterial pressure variability (MAPV) was associated with POD in elderly patients after hip fracture surgery.

Methods
In this retrospective cohort study, patients aged 65 years and older undergoing hip fracture surgery were included. The correlation between MAPV and POD was investigated using univariate and multivariate logistic regression. Covariate-related confounding effects were eliminated with propensity score matching (PSM) analysis. Then, a subgroup analysis was conducted to further examine the associations between MAPV and POD.

Results
Nine hundred sixty-three patients with a median age of 80 years (IQR: 73–84) were enrolled. POD occurred in 115/963 (11.9%) patients within 7 days after surgery. According to multivariate regression analysis, MAPV > 2.17 was associated with an increased risk of POD (OR: 2.379, 95% CI: 1.496–3.771, P < 0.001). All covariates between the two groups were well balanced after PSM adjustment. A significant correlation between MAPV and POD was found in the PSM analysis (OR: 2.851, 95% CI: 1.710–4.746, P < 0.001).

Conclusions
An increased intraoperative MAPV may be a predictor for POD.
Staff’s insights into fall prevention solutions in long-term care facilities: a cross-sectional study
Authors: Albasha Neah , Curtin Catriona , McCullagh Ruth , Cornally Nicola , Timmons Suzanne 
Published: November 2023

Abstract
Background
Falls are one of the most common and serious health issues in long-term care facilities (LTCFs), impacting not just residents, but staff and the healthcare system. This study aimed to explore LTCF staff’s current practices around falls prevention, and their suggested solutions for better falls prevention.

Methods
In the southwest of Ireland, a descriptive cross-sectional study was conducted in 13 LTCF sites, across a range of provider types and facility sizes. A survey, measuring staff knowledge, skills and attitudes, was distributed in physical and online formats. Staff suggestions for prioritising fall and fall-related injury prevention activities, and current staff practices regarding fall incidents were also sought. Content analysis was used to analyse responses, mapping categories and subcategories to the refined theoretical domains framework (TDF) and to an existing fall prevention guideline.

Results
There were 155 respondents (15% response rate), from staff of the LTCFs. Environmental reviews and modifications (aligned to the TDF environmental context and resource domain) were the most common suggestions for preventing both falls and fall-related injuries. Other common suggestions for preventing falls were staff education, monitoring of residents, and using alarm/calling systems, while few staff members, across all roles, reported assessing residents, exercises, reviewing medications, and vitamin D supplements. For preventing fall-related injuries, suggestions included protective equipment, hip protectors and alarm/calling systems. Staff used a standardised approach when responding to a fall incident, with intensive and holistic post-fall control measures. HCAs focussed on transferring residents safely, while nurses of all grades focused more on post-fall assessment. Respondents believed that staff education, communication, increasing staffing levels and enhancing specialist care could support their practice.

Conclusion
Noting the low response rate, the results suggest an awareness gap regarding some evidence-based, resident-focussed falls prevention solutions, such as pro-active fall-risk assessment, exercise, medication review, and Vitamin D supplements. These aspects should be included in future fall prevention education programmes in LTCFs.
Erythroderma combined with deeper dermal dermatophytosis due to Trichophyton rubrum in a patient with myasthenia gravis: first case report and literature review
Authors: Si Henan , Li Yang , Huang Zhiyang , Cui Yan , Li Shanshan 
Published: November 2023

Abstract
Background
Dermatophytes are the most common causative pathogens of mycoses worldwide and usually cause superficial infections. However, they can enter deep into the dermis lead to invasive dermatophytosis such as deeper dermal dermatophytosis on rare occasions. Erythroderma is a severe dermatological manifestation of various diseases resulting in generalized skin redness, but erythroderma due to fungi infections is barely reported. In this article, we reported the first case of erythroderma combined with deeper dermal dermatophytosis due to Trichophyton rubrum (T. rubrum) in a patient with myasthenia gravis.

Case presentation
A 48-year-old man was hospitalized because of erythema with scaling and nodules covering his body for a month. The patient had a history of myasthenia gravis controlled by regularly taking prednisolone for > 10 years and accompanied by onychomycosis and tinea pedis lasting > 8 years. Based on histopathological examinations, fungal cultures, and DNA sequencing results, the patient was finally diagnosed with dermatophyte-induced erythroderma combined with deeper dermal dermatophytosis caused by T. rubrum. After 2 weeks of antifungal treatment, the patient had recovered well.

Conclusions
This case report shows that immunosuppressed patients with long histories of superficial mycoses tend to have a higher risk of developing invasive dermatophytic infections or disseminated fungal infections. Dermatologists should be alert to this condition and promptly treat the superficial dermatophytosis.
Characterization of Salmonella enterica serovar Isangi from South Africa, 2020–2021
Authors: Myataza Asive , Thomas Juno , Smith Anthony M. 
Published: November 2023

Abstract
Background
We describe the genotypic characteristics and antimicrobial resistance (AMR) determinants of Salmonella enterica serovar Isangi (Salmonella Isangi) clinical isolates in South Africa from 2020 through 2021.

Methods
During the years 2020 to 2021, the Centre for Enteric Diseases of the National Institute for Communicable Diseases, a national reference centre in South Africa for human infections resulting from enteric bacterial pathogens, investigated a total of 3549 clinical isolates of Salmonella species. Whole genome sequencing (WGS) was performed using Illumina NextSeq Technology. WGS data was analyzed using Centre for Genomic Epidemiology-based tools and EnteroBase web-based platform. Genotypic relatedness and cluster analysis was investigated based on core-genome multilocus sequence typing.

Results
Forty-nine isolates were confirmed to be Salmonella Isangi, with most submitted from Gauteng Province (24/49, 49%). The most prevalent sequence type was ST335 (48/49, 98%), and the remaining 1 isolate was ST216. All ST335 isolates were genotypically multidrug-resistant (MDR), with resistance to fluoroquinolones, chloramphenicol, trimethoprim-sulfamethoxazole and tetracycline; the ST216 isolate was resistant only to aminoglycosides. All ST335 isolates carried ESBL genes, the most common being blaCTX-M-15. Five clusters (consisting of isolates related within five allele differences) were detected, all being ST335.

Conclusions
Most Salmonella Isangi isolates in South Africa are MDR and ESBL-positive. Ongoing monitoring of the epidemiology and AMR profile of this serovar is important for public health and treatment guidelines.
High throughput method for detecting murine brain atrophy using a clinical 3T MRI
Authors: Linzey Michael , DiSano Krista , Welsh Nora , Ford James C. , Gilli Francesca , Wishart Heather , Pachner Andrew 
Published: November 2023

Abstract
Background
There is a lack of understanding of the mechanisms by which the CNS is injured in multiple sclerosis (MS). Since Theiler’s murine encephalomyelitis virus (TMEV) infection in SJL/J mice is an established model of progressive disability in MS, and CNS atrophy correlates with progressive disability in MS, we used in vivo MRI to quantify total ventricular volume in TMEV infection. We then sought to identify immunological and virological biomarkers that correlated with increased ventricular size.

Methods
Mice, both infected and control, were followed for 6 months. Cerebral ventricular volumes were determined by MRI, and disability was assessed by Rotarod. A range of immunological and virological measures was obtained using standard techniques.

Results
Disability was present in infected mice with enlarged ventricles, while infected mice without enlarged ventricles had Rotarod performance similar to sham mice. Ventricular enlargement was detected as soon as 1 month after infection. None of the immunological and virological measures correlated with the development of ventricular enlargement.

Conclusions
These results support TMEV infection with brain MRI monitoring as a useful model for exploring the biology of disability progression in MS, but they did not identify an immunological or virological correlate with ventricular enlargement.
Association between physical activity and health literacy in patients with Parkinson’s disease: an online web survey
Authors: Nagaki Koichi , Mishima Takayasu , Ohura Tomoko , Kurihara Kanako , Fujioka Shinsuke , Tsuboi Yoshio 
Published: November 2023

Abstract
Background
For patients with Parkinson's disease (PwPD), promotion of habitual physical activity (PA) assists in the prevention of disease progression. Patients' health literacy (HL) is integral for meeting PA standards and turning it into a habit. This study evaluated the association between PA level and each HL domain in PwPD.

Methods
Online web-based assessment instruments and self-administered questionnaires, including the PA Questionnaire (IPAQ) Short Form and the Functional, Communicative, and Critical Health Literacy (FCCHL) scale, were used to assess PA levels and health literacy domains of PwPD.

Results
The mean age of PwPD (n = 114) was 65.9 (SD = 11.6) years; 59.6% female, and the mean duration of disease was 6.4 (SD = 5.1) years. Of participants, 47.4% met the recommended criteria for PA. When comparing each HL domain by PA level, participants with lower PA had significantly lower critical HL (p = 0.03). Logistic regression analysis revealed that PA level correlated with critical HL (OR = 2.46; 95% CI = 1.16–5.19; p = 0.02).

Conclusions
Adherence to recommended PA standards was associated with critical HL, but not other HL domains. Proactive attitudes to critically evaluate and utilize as well as understand health information may positively influence the promotion of PA.
Maternal multimorbidity - experiences of women seeking asylum during pregnancy and after childbirth: a qualitative study
Authors: Rowe Anna , Bhardwaj Minakshi , McCauley Mary 
Published: November 2023

Abstract
Background
Many women seeking asylum during pregnancy and after childbirth have ill-health but detection and assessment of all physical, psychological, and social health needs (maternal multimorbidity) are often difficult as part of routine maternity care. Healthcare providers are key for the early identification and management of vulnerable pregnant women who have additional physical, psychological, and social health needs. We sought to explore the impact of the asylum-seeking process, understanding of wellbeing, expressed health needs (in terms of maternal multimorbidity), and the experiences of maternity care of women seeking asylum during pregnancy and after childbirth in Liverpool, United Kingdom. Enabling factors and barriers to access woman-centred care were also explored.

Methods
Key informant interviews (n = 10) and one focus group discussion (n = 4) were conducted with women attending a non-profit charitable pregnancy support group. Transcribed interviews were coded by topic and then grouped into categories. Thematic framework analysis was undertaken to identify emerging themes.

Results
The asylum-seeking process negatively impacted women making them feel anxious and depressed with little control or choice over their future. Women reported feeling stressed regarding poor standard of accommodation, low income, dispersal and the uncertainty of their asylum application outcome. Wellbeing during pregnancy and after childbirth was understood to be multifactorial and women understood that their physical health needs were interlinked and negatively impacted by complex psychological and social factors. Women reported that their expectations of maternity services were often exceeded, but information giving, and the use of language interpreters needed to be improved. Women expressed the need for more psychological and social support throughout pregnancy and after childbirth.

Conclusions
A multidisciplinary team, with links and effective referral pathways to maternal mental health and social services, are necessary for women seeking asylum, to ensure a more integrated, comprehensive assessment of maternal multimorbidity and to provide maternity care in a way that meets all health needs.
Exploring the association between circRNA expression and pediatric obesity based on a case–control study and related bioinformatics analysis
Authors: Li Guobo , Xu Xingyan , Yang Le , Cai Yingying , Sun Yi , Guo Jianhui , Lin Yawen , Hu Yuduan , Chen Mingjun , Li Huangyuan , Wu Siying 
Published: November 2023

Abstract
Objective
Our present study utilized case–control research to explore the relationship between specific circRNAs and pediatric obesity through a literature review and bioinformatics and to predict their possible biological functions, providing ideas for epigenetic mechanism studies of pediatric obesity.

Methods
CircRNAs related to pediatric obesity were preliminarily screened by a literature review and qRT–PCR. CircRNA expression in children with obesity (n = 75) and control individuals (n = 75) was confirmed with qRT–PCR in a case–control study. This was followed by bioinformatics analyses, such as GO analysis, KEGG pathway analysis, and ceRNA network construction. Multivariate logistic regression was utilized to analyze the effects of circRNAs on obesity. A receiver operating characteristic (ROC) curve was also drawn to explore the clinical application value of circRNAs in pediatric obesity.

Results
Has_circ_0046367 and hsa_circ_0000284 were separately validated to be statistically downregulated and upregulated, respectively, in the peripheral blood mononuclear cells of children with obesity and revealed as independent indicators of increased CHD risk [hsa_circ_0046367 (OR = 0.681, 95% CI: 0.480 ~ 0.967) and hsa_circ_0000284 (OR = 1.218, 95% CI: 1.041 ~ 1.424)]. The area under the ROC curve in the combined analysis of hsa_circ_0046367 and hsa_circ_0000284 was 0.706 (95% CI: 0.623 ~ 0.789). Enrichment analyses revealed that these circRNAs were actively involved in neural plasticity mechanisms, cell secretion and signal regulation.

Conclusion
The present research revealed that low expression of hsa_circ_0046367 and high expression of hsa_circ_0000284 are risk factors for pediatric obesity and that neural plasticity mechanisms are closely related to obesity.
The latent profile analysis of Chinese adolescents’ gaming disorder: examination and validation
Authors: Zhang Lina , Liu Mengqi , Yuan Ming , Hou Mutian , Yang Cheng , Wang Yingying , Hao Wei , Liao Yanhui 
Published: November 2023

Abstract
Background
Gaming disorder is a new disease, which is included in the disease unit of disorder caused by addiction in the 11th revision of the International Classification of Diseases. This study examined the symptom characteristics of gaming disorders in Chinese adolescents using the latent profile analysis.

Methods
Totally, 5988 students (including 3285 boys and 2703 girls; aged 12–18 years) from junior high schools and senior high schools were enrolled. The Gaming Disorder Symptom Questionnaire-21 (GDSQ-21) was used to screen gaming disorder. A latent profile analysis was used for classifying the subgroups based on the extent of gaming usage. The relationship between adolescent gamers and demographic variables was analyzed by logistic regression.

Results
The results of latent profile analysis supported the models of four latent profiles, which were defined as healthy gamers (Profile 1, 56.83%), impaired control gamers (Profile 2, 26.09%), impaired control-game priority gamers (Profile 3, 9.72%) and gamers with disorder (Profile 4, 7.36%), respectively. Logistic regression analysis found that, compared with girls, boys were more likely to be classified into the group dominated by the impaired gamers, the impaired control-game priority gamers, and the gamers with disorder.

Conclusions
This study highlighted that the latent profile analysis identified four different groups of adolescent gamers, showing a clearer conceptualization of heterogeneous gamers. Gender and average weekly gaming time can predict the latent profile of adolescents. Our findings may facilitate the design of individualized assessment and early intervention programs for adolescent gamer users based on different gaming usage symptoms.