bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Home Neighborhood Tree Canopy Coverage on Mental Health Outcomes: A Traumatic Brain Injury Model Systems Investigation
Authors: Juengst Shannon B. , Kumar Raj G. , Holland Alexandra , Cohen Achituv , Nelson Trisalyn A. , Corrigan John D. , Sander Angelle M. , Perrin Paul B. , Venkatesan Umesh M. , Rabinowitz Amanda , Driver Simon , Wilmoth Kristin , Tefertiller Candace 
Published: February 2025

Objective: Explore the relationship between tree canopy coverage (TCC) in one’s home neighborhood and mental health outcomes, and how these relationships differ by home neighborhood factors, among persons with traumatic brain injury (TBI) in the United States. Setting: Community. Participants: Enrolled in the TBI Model Systems National Database with completed follow-up interview after January 1, 2017. Design: Secondary analysis of cross-sectional data. Main Measures: Neighborhood (census tract) Percent TCC, depressive (Patient Health Questionnaire-9) and anxiety (General Anxiety Disorder-7) symptoms (scores ≥10 on each measure), personal/demographic (age, sex, education, homebound status), and neighborhood factors (type, socioeconomic disadvantage). Results: Separate negative binomial regression models were constructed for the 2 mental health outcomes (depression and anxiety symptoms). Covariates in final models were age, sex, neighborhood type, Functional Independence Measure (FIM) total (concurrent), driving status, homebound status, and neighborhood-level socioeconomic disadvantage. The interaction between Percent TCC and neighborhood type (but not homebound status) was significant for depression and anxiety symptoms. The nature of the significant interaction was such that, for both mental health outcomes, those living in rural neighborhoods with higher Percent TCC were more likely to have moderate to severe mental health symptoms. However, this effect was attenuated after adding neighborhood level socioeconomic disadvantage, suggesting that part of the effect may be due to socioeconomic characteristics of rural versus other neighborhoods. Conclusions: After adjusting for SDoH, the direct effect of TCC on mental health after TBI was small and opposite the direction hypothesized (higher TCC associated with poorer mental health), particularly for those living in rural neighborhoods potentially more likely to experience socioeconomic disadvantage. Our findings highlight the importance of evaluating interactions between different aspects of the social (eg, SDoH), natural (eg, greenspace), and built (eg, neighborhood type) environment to provide a comprehensive understanding of factors affecting health after TBI.
Update on diagnosis and management of radiation retinopathy
Authors: Lovett Eric A. , Fan Jason , Williams Basil K. , Di Nicola Maura 
Published: February 2025

Purpose of review
Radiation retinopathy is a vision-threatening complication of radiotherapy involving the eye or surrounding structures. This review aims to summarize recent advances in understanding the incidence, risk factors, pathophysiology, and utilization of new diagnostic imaging tools for radiation retinopathy. It will also focus on the current prophylaxis approaches to prevent or delay the development of radiation-related side effects and treatment strategies once radiation retinopathy occurs.

Recent findings
The incidence of radiation retinopathy is influenced by radiation dose, fractionation schedule, and patient-specific factors such as diabetes mellitus and hypertension. Advances in imaging techniques, including optical coherence tomography angiography (OCTA) and ultra-widefield fluorescein angiography (UWFA), have enhanced early detection by identifying subclinical retinal changes. Novel insights into pathophysiology suggest a role for endothelial damage, inflammation, and oxidative stress in disease progression. Prophylactic approaches, such as intravitreal antivascular endothelial growth factor (anti-VEGF) agents, have shown promise in reducing the onset of retinopathy in high-risk patients. Therapeutic options, including intravitreal anti-VEGF and corticosteroids, have demonstrated efficacy in managing macular edema and preserving vision. However, the outcomes remain variable, necessitating personalized treatment strategies. To address some of these unanswered questions, the Diabetic Retinopathy Clinical Research Network (DRCR) Protocol AL is currently enrolling patients and preparing to analyze the long-term effects of treating patients prophylactically with intravitreal faricimab or the 0.19 mg fluocinolone acetonide implant compared to observation, to identify which patients will benefit from which specific regimen, therefore moving towards a personalized approach for this condition as well.

Summary
Radiation retinopathy remains a significant challenge in ophthalmology. Early recognition through advanced imaging and tailored interventions, including prophylaxis and treatment, are crucial for optimizing visual outcomes. Further research into underlying mechanisms and novel therapies is essential to reduce the burden of this condition and improve patient quality of life.
Association Between Sociodemographic Risk Factors and No-Show Propensity in a Glaucoma Population Before and During Covid-19 Pandemic
Authors: Kamdar Amey , Yohannes Gelila B. , Swaminathan Swarup S. 
Published: February 2025

Précis:
Greater social vulnerability, younger age, non-white race, Hispanic ethnicity, non-English speaking, Medicaid insurance, and milder glaucoma were associated with higher no-show propensity, which worsened during the Covid-19 pandemic among those subjects who were older and more socially vulnerable.

Purpose:
To identify sociodemographic risk factors for higher likelihood to no-show among glaucoma subjects before and during the Covid-19 pandemic using the no-show propensity factor (NSPF), a novel attendance metric, which improves upon no-show percentages by adjusting for number of visits.

Methods:
We analyzed de-identified demographic, visit attendance, and social risk factor data (social vulnerability index (SVI) and area deprivation index (ADI) scores) of de-identified glaucoma subjects from the Bascom Palmer Glaucoma Repository, computed NSPF, and categorized scores as low, intermediate, or high by the 75th and 90th percentiles for the pre-pandemic and pandemic periods. We identified predictors of NSPF scores using univariable, multivariable, and logistic regression analyses.

Results:
Of 15,342 subjects, 11,474, 2,238, and 1,630 subjects had low, intermediate, and high NSPF scores respectively with no-show rates of 9.5%, 39.2%, and 57.8% respectively. Age (β=−0.039 per decade, P<0.001), Black race (β=0.152, P<0.001), Hispanic ethnicity (β=0.115, P<0.001), Medicaid (β=0.073, P<0.001), Spanish primary language (β=0.076, P<0.001), SVI scores (β=0.047 per 25% increase, P<0.001), ADI ranking (β=0.057 for highest quartile, P<0.001), and baseline moderate (β=−0.046, P<0.001) or severe (β=−0.077, P<0.001) glaucomatous disease were significant predictors of NSPF. Older age (odds ratio (OR) 1.15 per decade, P<0.001), higher overall SVI (OR 1.09 per 25% increase, P<0.001), Medicare/Tricare insurance (OR 1.13, P=0.044), and non-English/Spanish primary language (OR 1.43, P=0.020) were associated with worsening NSPF during the pandemic.

Conclusion:
Younger age, non-white race, Hispanic ethnicity, non-English primary language, Medicaid, milder glaucoma, and residence in vulnerable areas are risk factors for greater propensity to no-show.
Exploring the mechanism of SLXG for treating nonalcoholic fatty liver disease based on network pharmacology and molecular docking
Authors: Wang Yang , Wang Jiaxing , Chen Zitong , Liu Bin , Wang Wujie , Li Yuliang 
Published: February 2025

Background:
The Shugan Lidan Decoction and Chaihu Shugan formula are traditional Chinese medicine formulas for treating liver diseases, with a history of over a 1000 years. By comprehensively improving 2 traditional Chinese medicinal formulas, Shugan Lidan Xiaoshi Granules (SLXG) has been developed for the treatment of nonalcoholic fatty liver disease (NAFLD) and other liver-related metabolic diseases.

Methods:
First, the effective active ingredients and targets of SLXG were determined using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database. The treatment targets for NAFLD were identified using the GeneCards, OMIM, and CTD databases, and the intersection of the decoction and disease targets was obtained. The intersection targets were then subjected to protein–protein interaction network analysis, Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, and gene ontology enrichment analysis. KEGG enrichment analysis revealed enrichment of the NAFLD pathway. Molecular docking was performed to validate the binding between the crucial targets enriched in this pathway and the corresponding active ingredients in SLXG.

Results:
A total of 219 disease intersection genes related to NAFLD were identified from the GeneCards, OMIM, and CTD databases, and 239 non-duplicated drug targets were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database. A total of 24 intersection target genes were obtained from both drug- and disease-related databases, with 6 genes enriched in the KEGG NAFLD pathway. Molecular docking results showed that the 13 gene–active ingredient bindings had a binding energy of less than −6.5.

Conclusion:
The use of network pharmacology and molecular docking technology has revealed the mechanism of action of SLXG in NAFLD treatment, thus laying a theoretical foundation for the clinical application of SLXG in NAFLD therapy.
A comparison of the efficacy and safety of Chinese patent medicine combined with Western medicine for Helicobacter pylori-related gastric ulcer: A systematic review and network meta-analysis
Authors: Zhong Meiqi , Sun Qifang , Ren Baoping , Yu Chang , Zhou Shunhua , Gao Qing , Wang Xiaojuan , Yuan Chengzhi , Lu Jing , Peng Qinghua , Zeng Meiyan , Song Houpan 
Published: February 2025

Background:
The aim of this network meta-analysis (NMA) was to compare the effectiveness and safety of different Chinese patent medicines (CPMs) combined with Western medicines (WMs) regimen versus WMs alone in the treatment of Helicobacter pylori-related gastric ulcer (GU).

Methods:
A comprehensive search was conducted on databases from their inception to May 31, 2023, to identify all randomized controlled trials (RCTs) that investigated the efficacy of CPMs in combination with conventional WMs in the treatment of patients with H pylori-related GU. Using Cochrane risk of bias assessment tool, we evaluated the methodological quality of RCTs. R version 4.2.3 and Stata version 15.1 software were cross-merged to conduct pairwise NMA.

Results:
A total of 35 studies involving 4667 patients and 11 CPMs were identified. Eleven CPMs were analyzed, including Pingwei Capsule (PWC), Kangfuxin Solution (KFXS), Shugan Jieyu Capsule (SGJYC), Weisu Granule (WSG), Qiwei Weitong Capsule (QWWTC), Beiling Weitong Granule (BLWTG), Anweiyang Capsule (AWYC), Jinghua Weikang Capsule (JHWKC), Weifuchun Tablet (WFCT), Wenweishu Capsule (WWSC), and Weidean Capsule (WDAC). Results showed that the combination of CPM and WM was more effective relative to the WM regimen alone. NMA revealed that WWSC combined with the WM yielded superior results in enhancing clinical outcomes and mitigating GU recurrence rates. PWC combined with the WM showed the best performance in improving the H pylori eradication rate. WFCT combined with the WM had the most optimal performance in controlling gastrin (GAS) and motilin (MTL) levels. KFXS combined with the WM showed the best results in terms of reducing the incidence of adverse events.

Conclusion:
Our NMA findings indicate that the combination of WWSC, PWC, WFCT, and KFXS with WM may be more effective and advantageous outcomes compared to other CPMs. Due to the limitations of this study, future research should employ larger sample sizes and multicenter RCTs to conduct real-world clinical studies.
Primary cutaneous Mycobacteria avium complex infection in a systemic lupus erythematosus patient: A case report and review
Authors: Yao Qi-Hao , Xia Xiu-Jiao , Xu Jun-Zhu , Shen Hong , Yang Yang , Liu Ze-Hu 
Published: February 2025

Rationale:
Nontuberculous mycobacteria infection is becoming more and more common in clinical practice, while skin and soft tissue infection is an important part. The evaluation of the immune status of patients has certain reference value for diagnosis and treatment.

Patient concerns:
A 48-year-old woman developed an erythematosus nodule with purulent discharge on the right hip for 4 months. She had a history of systemic lupus erythematosus for more than 20 years, in stable control with prednisone 10 mg/d, azathioprine 50 mg/12 h, and hydroxychloroquine 200 mg/12 h. There was no trauma prior to the lesion.

Diagnoses:
After excluding other sites involved, the patient was diagnosed as Mycobacterium avium primary cutaneous infection based on laboratory culture, biopsy, and sequencing techniques.

Interventions:
After surgical resection, a combination of oral azithromycin, rifampicin, and ethambutol hydrochloride was given.

Outcomes:
The lesion healed after 4 months with no relapse.

Lessons:
Primary cutaneous nontuberculous mycobacteria infection should raise more attention in immunocompromised and even immunocompetent populations.
Afipia dichlorophenoxyacetatis sp. nov., isolated from field soil in Japan, degrades 2,4-dichlorophenoxyacetic acid
Authors: Sawada Hiroyuki , Sakai Yoriko , Takashima Yusuke , Naito Ken , Horita Mitsuo , Satou Mamoru 
Published: February 2025

Bacterial strains, designated DD3T and DDX28, were isolated from field soil in Japan. The strains had the ability to use 2,4-dichlorophenoxyacetic acid as the sole carbon source. They were Gram-reaction-negative, oxidase-positive, weakly catalase-positive, aerobic and non-spore-forming. Their cells were rod-shaped and often lacked flagella, but some exhibited motility due to the presence of one or two polar flagella. The genomic DNA G+C content was 58.8 mol%, and the major cellular fatty acids (>10% of the total fatty acids) were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), C18 : 0 and C17 : 0 cyclo. Phylogenetic analyses based on gyrB gene sequences and phylogenomic analysis using whole-genome sequences confirmed that the strains belong to the genus Afipia; however, their phylogenetic position did not match that of any known species of this genus. Comparative studies of the average nucleotide identity and digital DNA–DNA hybridization with closely related species revealed values lower than the thresholds used for prokaryotic species delineation (95–96 and 70%, respectively), with the highest values observed for Afipia broomeae ATCC 49717T (79.92 and 21.5%, respectively). Phenotypic characteristics, cellular fatty acid composition and specific metabolic processes and biosynthetic gene clusters could differentiate the strains from their closest relatives. Our phenotypic, chemotaxonomic and genotypic data indicate that DD3T/DDX28 constitute a novel Afipia species, for which we propose the name Afipia dichlorophenoxyacetatis sp. nov., with DD3T (MAFF 311804T=ICMP 25015T) as the type strain.
Evaluation of reproductive profiles, epigenetic aging, and mortality in post-menopausal women
Authors: Ye Qiaofeng , Ahamed Aaliya , Shalev Idan , Etzel Laura 
Published: February 2025

AbstractEvolutionary theories of aging indicate trade-offs between reproduction and longevity. Epigenetic clocks, such as PhenoAge, GrimAge, and DunedinPoAm, were designed to reflect biological age and be used as surrogates for mortality and healthspan. The current study investigated the connection between reproductive profiles, epigenetic aging and mortality among post-menopausal women (50-85 years) with data from the National Health and Nutrition Examination Survey across the United States (N=770). Using latent profile analysis, we identified four distinct reproductive profiles: high gravidity but average parity (Class 1); high gravidity and parity (Class 2); early menopause (Class 3); an average profile (Class 4). Women of Class 3 had an accelerated pace of aging as indicated by DunedinPoAm, but not an older epigenetic age as measured by PhenoAge or GrimAge. The association was significant among women who had ever used female hormones (β=0.521; 95%CI 0.014-1.027). Women of Class 1 or 2 did not exhibit accelerated epigenetic aging. Women of Class 3 had higher mortality (HR=1.40, 95%CI 1.08-1.81), and 36.3% of the effect was mediated through accelerated DunedinPoAm. Findings suggest that women with reproductive profiles characterized by early menopause may have altered epigenetic aging trajectories. Pace of aging may be more sensitive to the impact of reproductive profile variations than the status of biological age as indicated by PhenoAge or GrimAge. Clinically monitoring the pace of biological aging among women with early menopause and an appropriate application of hormone replacement therapy may minimize the negative consequence of accelerated biological aging and reduce premature mortality.
Decoding yeast transcriptional regulation via a data-and mechanism-driven distributed large-scale network model
Authors: Fan Xingcun , Xiang Guangming , Liao Wenbin , Xiao Luchi , He Siwei , Lu Hongzhong , Yan Xuefeng 
Published: February 2025

AbstractThe complex transcriptional regulatory relationships among genes influence gene expression levels and play crucial roles in determining cellular phenotypes. Here, we present a novel distributed large-scale transcriptional regulatory neural network model (DLTRNM) by integrating prior knowledge into the reconstruction of pre-trained machine learning models followed with fine-tuning. TakenS. cerevisiaeas the example, the transcriptional regulatory relationships, carefully compiled and documented, are utilized to define interactions between TFs and their TGs within DLTRNM. Subsequently, DLTRNM is pre-trained on pan-transcriptomic data and fine-tuned with time-series data, enabling it to accurately predict dynamic regulatory correlations between TFs and TGs, such as simulating TG responses by tuning the expression of TFs. In addition, DLTRNM can assist in identifying potential key TFs for a subset of genes, thus simplifying the complex and interrelated transcriptional regulatory networks (TRN). Based on the key TFs, it can also refine previously reported transcriptional regulatory subnetworks and highlight the core regulatory networks. DLTRNM offers a powerful tool for studying transcriptional regulation with reduced computational demands and enhanced interpretability. Thus, this study represents a significant step forward in systems biology for understanding the complicated transcriptional regulation within cells.
Molecular bases for the loss of type VI secretion system activity during enteroaggregativeE. coliexperimental evolution
Authors: Taillefer Boris , Desjardins Jonas B. , Cascales Eric 
Published: February 2025

ABSTRACTThe type VI secretion system (T6SS) is a nanoweapon deployed by Gram-negative to inject effectors into target cells and hence involved in pathogenesis and bacterial competition. While T6SS gene clusters are found in all recently isolated commensals or pathogenicEscherichia colistrains, they are absent from classical laboratory strains. TheseE. colistrains, which have been used since decades for bacterial genetics, were usually grown in pure cultures, suggesting that T6SS might have been lost during evolution in absence of competitors. Here, we conducted a 640-generation experimental evolution by passaging the enteroaggregativeE. coli(EAEC) 17-2 strain under controlled competition conditions against susceptible or immune recipient cells. EAEC T6SS activity was almost abolished when grown in the presence of immune recipients, while no difference with the ancestral strain was observed for EAEC grown in the presence of susceptible cells. Whole genome sequencing of 18 clones identified adaptative mutations responsible for the loss of T6SS activity, including mutations of the T6SS promoter and within genes encoding T6SS subunits, and revealed a novel regulatory mechanism involving RfaH-dependent antitermination. We further found that the RfaH binding siteopselement is present in T6SS gene clusters of several species, suggesting a conserved RfaH-dependent regulation of T6SSs across enterobacteria. This work exemplifies the power of experimental evolution to understand T6SS genetic adaptation and to unravel new players for its function.
The use of management information in process innovation: effects of knowledge conversion by socialization
Authors: Beuren Ilse Maria , Meurer Silvana Mannes , Ferraz Pazetto Celliane 
Published: February 2025

PurposeThe article analyzes the effects of using management information and knowledge conversion by socialization in process innovation.Design/methodology/approachA survey was conducted with 133 managers of Brazilian firms that received tax subsidies to develop technological innovation. For data analysis, structural equation modeling was used.FindingsResults show that the use of management information to score keeping and focusing organizational attention triggered higher levels of process innovation. In contrast, improving understanding and improving organizational learning did not show statistical significance, suggesting that these do not have the potential to influence directly process innovation. It was also found that managers’ skill to convert knowledge by socialization precedes process innovation. Furthermore, mediating effect of knowledge conversion by socialization between the use of management information and process innovation was statistically significant only in improving organizational learning.Practical implicationsThe finding that the use of management information for score keeping, focusing organizational attention directly and improving organizational learning indirectly reflects in higher levels of innovation can be used as part of the strategy and support organization’s management in process innovation. Furthermore, the organization can emphasize on knowledge conversion by socialization, both explicit and tacit knowledge, to leverage process innovation.Originality/valueThe study addresses recent calls to understand the potential of managers’ skills to convert knowledge through socialization. Evidence shows that, by socializing knowledge, managers expand and disseminate the organization’s tacit knowledge, which can stimulate process innovation. It also adds to the debate about which uses of information managers should emphasize to promote process innovation.