bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between glioblastoma location and O6-methylguanine-DNA methyltransferase promoter methylation percentage
Authors: Sansone Giulio , Lombardi Giuseppe , Maccari Marta , Gaiola Matteo , Pini Lorenzo , Cerretti Giulia , Guerriero Angela , Volpin Francesco , Denaro Luca , Corbetta Maurizio , Salvalaggio Alessandro 
Published: December 2024

Abstract
A large literature assessed the relationships between the O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status and glioblastoma location with inconsistent results. Studies assessing this association using the percentage of methylation are lacking. This cross-sectional study aimed at investigating relationships between glioblastoma topology and MGMT promoter methylation, both as categorical (presence/absence) and continuous (percentage) status. We included patients with diagnosis of isocitrate dehydrogenase wild-type glioblastoma [World Health Organization (WHO) 2021 classification], available pre-surgical MRI, known MGMT promoter methylation status. Quantitative methylation assessment was obtained through pyrosequencing. Several analyses were performed for categorical and continuous variables (χ2, t-tests, ANOVA and Pearson’s correlations), investigating relationships between MGMT methylation and glioblastoma location in cortex/white matter/deep grey matter nuclei, lobes, left/right hemispheres and functional grey and white matter network templates. Furthermore, we assessed at the voxel-wise level location differences between (i) methylated and unmethylated glioblastomas and (ii) highly and lowly methylated glioblastomas. Lastly, we investigated the linear relationship between glioblastoma-voxel location and the MGMT methylation percentage. Ninety-three patients were included (66 males; mean age: 62.3 ± 11.3 years), and 42 were MGMT methylated. The mean methylation level was 33.9 ± 18.3%. No differences in glioblastoma volume and location were found between MGMT-methylated and MGMT-unmethylated patients. No specific anatomical regions were associated with MGMT methylation at the voxel-wise level. MGMT methylation percentage positively correlated with cortical localization (R = 0.36, P = 0.021) and negatively with deep grey matter nuclei localization (R = −0.35, P = 0.025). To summarize, we investigated relationships between MGMT methylation status and glioblastoma location through multiple approaches, including voxel-wise analyses. In conclusion, MGMT promoter methylation percentage positively correlated with cortical glioblastoma location, while no specific anatomical regions were associated with MGMT methylation status.
Perspectives on Contraception, Pregnancy, and Reproductive Health Counseling from Young Women With Inflammatory Bowel Disease
Authors: Brenner Erica J , Grewe Mary E , Berenblum Tobi Catalina , Bryant Amy G , Dubinsky Marla C , Zhang Xian , Long Millie D , Kappelman Michael D , Buchbinder Mara 
Published: December 2024

Abstract

Background/Aims
Active inflammatory bowel disease (IBD) increases the risk of pregnancy complications and contraceptive side effects, and contraceptive use may impact the clinical course of IBD. Although young people are at elevated risk for unintended pregnancy, those with IBD receive minimal disease-specific contraceptive guidance. We characterized perspectives and preferences on contraception and reproductive health counseling from young cis-women with IBD.

Methods
We conducted 60-min semi-structured interviews with cis-women with IBD ages 18-30 (recruited nationwide and from North Carolina IBD clinics; February–June 2023). Interview guides included questions about reproductive health and preferences for receiving reproductive health information. Audio-recordings were professionally transcribed and coded using an inductive, thematic approach and Dedoose software.

Results
Participants included 30 cis-women with IBD (ages 18-30, 77% White, 7% Hispanic, and 55% Crohn’s disease). Some participants shared that IBD increased their menstrual symptom burden, prompting contraceptive use to control menses. Participants discussed the impact of IBD on their contraceptive decision-making, including concerns regarding blood clots. For a participant subset, IBD did not impact contraceptive decision-making. Participants discussed how IBD impacted their perspectives on childbearing, including concerns about IBD heritability, infertility, and peripartum IBD flares. Participants wanted their gastroenterology provider to proactively address reproductive health, provide appropriate resources, and coordinate care with reproductive health providers.

Conclusions
Young cis-women with IBD may have IBD-specific concerns about contraceptives, pregnancy, and menstrual symptoms and desire better IBD-related reproductive health counseling. Inflammatory bowel disease providers can improve reproductive health counseling by proactively addressing IBD-specific reproductive health questions, providing reproductive health resources, and coordinating care.
Success rate and factors affecting stability of infrazygomatic miniscrew implants: a systematic review and meta-analysis
Authors: Katyal Sakshi , Bhatia Navleen Kaur , Sardana Rinkle , Singh Surjit , Chugh Ankita , Shamim Muhammad Aaqib , Anil Abhishek , Negi Anurag , Chugh Vinay Kumar 
Published: December 2024

Abstract

Background
The infrazygomatic miniscrew implants (IZC-MSI) serve as innovative temporary anchorage devices placed parallel to the roots of molars in the infrazygomatic crest region, leveraging their extra-radicular location to support the en masse distalization and intrusion of the maxillary dentition. The efficacy and stability of these screws are crucial for their application in contemporary orthodontic practices.

Objectives
This systematic review aimed to estimate the success rate and factors affecting the stability of IZC-MSI.

Search methods
An electronic search was conducted on 7 February 2024 across the following databases: PubMed, Scopus, EMBASE, and Cochrane databases without any restriction on language and time of publication.

Selection criteria
The review included clinical trials (both randomized and non-randomized) and retrospective cohort studies that utilized infrazygomatic miniscrew anchorage for orthodontic tooth movement in human participants.

Data collection and analysis
The proportion of success rate was calculated and factors affecting stability (patient and implant-related factors) such as age, sex, implant position, and loading characteristics were subjected to subgroup analysis and meta-regression. The quality assessment of studies was done using the Cochrane risk-of-bias tools for randomized (RoB 2.0) and non-randomized trials (ROBINS-I).

Results
Fourteen studies (n = 1683 IZC-MSI) were included in the meta-analysis revealing a 92% success rate of IZC-MSI (C.I. 87%–95%; prediction interval: 66%–99%; I2 = 80%). Studies with sample size &gt; 100 presented a 94% success rate (C.I. 91%–96%; I2 = 63%) and moderate heterogeneity. Meta-regression analysis revealed no significant relation between age and success rate. Significant heterogeneity was observed in the subgroup analysis of host-, implant- and other related risk factors affecting stability and limited correlation was found. The risk-of-bias assessment revealed high risk in five, moderate in five, and low in four studies.

Conclusions
IZC-MSI have shown a good success rate for their clinical application. Although some factors appear to influence IZC-MSI stability, the majority of them necessitate additional investigation due to the low quality of evidence. Furthermore, high-quality studies are needed to confirm the results of this meta-analysis and address other important factors such as operator’s experience, insertion torque, and sinus penetration that could not be analysed due to limited data.

Registration
CRD42024469048.
Co-regulation of cooperative and private traits by PsdR in Pseudomonas aeruginosa
Authors: Qiu Huifang , Dandekar Ajai A , Dai Weijun 
Published: December 2024

Abstract
Social interactions profoundly shape the dynamics and functionality of microbial populations. However, mechanisms governing the regulation of cooperative or individual traits have remained elusive. Here, we investigated the regulatory mechanisms of social behaviors by characterizing the fitness of transcriptional regulator PsdR mutants in cooperating Pseudomonas aeruginosa populations. In a canonical model described previously, PsdR was shown to solely have a nonsocial role in adaptation of these populations by controlling the intracellular uptake and processing of dipeptides. In addition to these known private traits, we found that PsdR mutants also enhanced cooperation by increasing the production of quorum sensing (QS)-regulated public goods. Although private dipeptide utilization promotes individual absolute fitness, it only partially accounts for the growth advantage of PsdR mutants. The absence of the QS master regulator LasR delayed the appearance of PsdR variants in an evolution experiment. We also demonstrated that the growth fitness of PsdR mutants is determined by a combination of the QS-mediated cooperative trait and the dipeptide metabolism-related private trait. This dual trait is co-regulated by PsdR, leading to the rapid spread of PsdR variants throughout the population. In conclusion, we identified a new social model of co-regulating cooperative and private traits in PsdR variants, uncovering the social and nonsocial roles of this transcriptional regulator in cooperating bacterial populations. Our findings advance the fundamental understanding of bacterial social interactions and provide insights into population evolution, pathogen infection control and synthetic biotechnology.
Effects of a Physical Activity Intervention on Perceived Stress, Fatigue, and Depressive Symptoms in Older Adults: A Secondary Analysis of the LIFE Study
Authors: Smail Emily J , Kaufmann Christopher N , King Abby C , Espeland Mark A , Anton Stephen , Manini Todd M 
Published: December 2024

Abstract

Background
Engaging in physical activity is critical for maintaining well-being in older adults, particularly those at heightened risk for mobility disability. We assessed the effects of a physical activity (PA) intervention on perceived stress, fatigue, and depressive symptoms compared to a health education (HE) program in older adults with mobility challenges and evaluated differential effects of the interventions among those with the poorest self-rated mental health at baseline.

Methods
Secondary data analysis of the Lifestyle Interventions and Independence for Elders (LIFE) Study, a single-blinded, parallel randomized controlled trial conducted between February 2010 and December 2013. The PA intervention included walking, strength exercises, balance training, and flexibility activities. The HE intervention consisted of workshops on health topics for older adults. The main outcomes for our analysis included standardized scales with participants self-reporting their stress, fatigue, and depressive symptoms at baseline, 12 months, and 24 months postrandomization.

Results
Results from the 1 495 participants (Mage = 78 years; 66% female in both groups) showed no significant between-group differences in perceived stress, fatigue, or depressive symptom scores over time. However, in both intervention groups, participants with worse baseline scores showed a steady improvement in symptom scores over time compared to the remaining participants, who showed some decline (p value for interaction &lt; .05).

Conclusions
Among mobility-impaired individuals, a long-duration, group-based PA intervention had no more impact on stress, fatigue, or depressive symptoms compared to a group-based HE intervention. However, participants with higher symptoms at baseline showed improvement over time in both intervention groups.
The Fifth Annual Symposium of the Midwest Aging Consortium
Authors: Reader Brenda F , Rosas Lorena , Knopf Bailey Anna , Liu Yang , Alzate-Correa Diego , Bhat Ajay , Carey Anna , Cuervo Ana Maria , Dayal Sanjana , Demarco Rafael S , Elliehausen Christian J , Englund Davis A , Hamilton Haylee L , Johnston Matthew , Kang Ping , Konopka Adam R , Lepola Noah , Presley Carolyn J , Schafer Marissa J , Serrano Joan , Singer Benjamin D , Song Min-Ae , Stanford Kristin I , Taylor Jackson , Wei Wei , Yeh Chung-Yang , Zhang Lei , Zhang Lei , Anderson Rozalyn M , Bai Hua , Robbins Paul D , Lamming Dudley W , Mihaylova Maria M , Rojas Mauricio , Mora Ana L 
Published: December 2024

Abstract
As the healthcare burden caused by an increasingly aging population rapidly rises, a pressing need exists for innovative geroscience research that can elucidate aging mechanisms and precipitate the development of therapeutic interventions to support healthy aging. The Fifth Annual Midwest Aging Consortium Aging Research symposium, held from April 28 to 30, 2024, was hosted by The Ohio State University in Columbus, Ohio, and featured presentations from investigators across the Midwestern United States. This report summarizes the research presented at the symposium, whose topics included cellular senescence and the aging brain, metabolism and metabolic interventions, nutrition, redox mechanisms and biomarkers, and stress mechanisms. Abstract presentations and short talks highlighted early-stage and young investigators, whereas 2 keynote presentations anchored the symposium. Overall, this symposium showed the robustness of aging research in the Midwest and underscored the advantages of a collaborative approach to geroscience research.
scGraph2Vec: a deep generative model for gene embedding augmented by graph neural network and single-cell omics data
Authors: Lin Shiqi , Jia Peilin 
Published: December 2024

Abstract

Background
Exploring the cellular processes of genes from the aspects of biological networks is of great interest to understanding the properties of complex diseases and biological systems. Biological networks, such as protein–protein interaction networks and gene regulatory networks, provide insights into the molecular basis of cellular processes and often form functional clusters in different tissue and disease contexts.

Results
We present scGraph2Vec, a deep learning framework for generating informative gene embeddings. scGraph2Vec extends the variational graph autoencoder framework and integrates single-cell datasets and gene–gene interaction networks. We demonstrate that the gene embeddings are biologically interpretable and enable the identification of gene clusters representing functional or tissue-specific cellular processes. By comparing similar tools, we showed that scGraph2Vec clearly distinguished different gene clusters and aggregated more biologically functional genes. scGraph2Vec can be widely applied in diverse biological contexts. We illustrated that the embeddings generated by scGraph2Vec can infer disease-associated genes from genome-wide association study data (e.g., COVID-19 and Alzheimer's disease), identify additional driver genes in lung adenocarcinoma, and reveal regulatory genes responsible for maintaining or transitioning melanoma cell states.

Conclusions
scGraph2Vec not only reconstructs tissue-specific gene networks but also obtains a latent representation of genes implying their biological functions.
Soil pH modulates the activity of low-affinity methane oxidation in soils from the Amazon region
Authors: Fonseca de Souza Leandro , Nakamura Fernanda Mancini , Kroeger Marie , Obregon Dasiel , de Moraes Moacir Tuzzin , Vicente Mariana Gomes , Moreira Marcelo Zacharias , Pellizari Vivian Helena , Tsai Siu Mui , Nüsslein Klaus 
Published: December 2024

Abstract

Aims
In the Amazon region, pastures are the main land use subsequent to deforestation and this change can result in soil acidification and degradation. Liming is a management practice to increase soil pH, important to recover degraded lands and increase soil fertility, but its impacts on soil methane cycling in tropical soils are unknown. Here we investigate the role of soil pH on methane uptake under high concentrations of the gas, manipulating pasture and forest soils pH by liming and evaluating the active methane cycling microbial community.

Methods and Results
Top layer of forest and pasture soils were subjected to liming treatment and incubated with ∼10 000 ppm of 13CH4. Soil DNA was evaluated with Stable Isotopic Probing (SIP-DNA), methanotrophic abundance was quantified (pmoA gene), and high throughput sequencing of 16S rRNA was performed. Liming increased the methane uptake in both forest (∼10%) and pasture (∼25%) soils. Methanotrophs Methylocaldum spp. (type I) and potential methanotrophs in Beijerinckiaceae (type II) were identified to actively incorporate carbon from methane in limed pasture soils. In limed forest soils, Nitrososphaeraceae were identified as 13C-enriched taxa, indicating that ammonia oxidizers can oxidize methane in these soils.

Conclusions
Liming Amazonian pasture soils not only contributes to the fertility and recovery of degraded areas but also has the potential to improve the oxidation of methane at high concentrations of this gas.
Effects of antioxidants on in vitro growth of Thecaphora frezzii
Authors: Figueroa Ana Cristina , Díaz María Soledad , Turco Mauricio , Fernández Trotta Andrea , Marino Bibiana , Soria Néstor Walter , Beltramo Dante Miguel , Alasino Roxana Valeria 
Published: December 2024

Abstracts

Aims
Thecaphora frezzii, the causal agent of peanut smut, causes significant grain losses in Argentina. Current control strategies are insufficient to manage this pathogen. We investigate the effect of antioxidants on the in vitro development of T. frezzii hyphae, to identify compounds with antifungal activity, also evaluate protein and lipid profiles as potential targets for these compounds.

Methods and results
The antifungal activity was evaluated in both, solid and liquid media, and minimum inhibitory concentration and minimum fungicidal concentration were calculated. The protein profile was assessed using sodium dodecyl sulfate polyacrylamide gel electrophoresis, while lipids were analyzed by thin-layer chromatography (TLC) and gas chromatography with flame ionization detection, both before and after hyphal treatment. Lipase activity was analyzed using agar Tween 20 and TLC, while lipid peroxidation was evaluated by the thiobarbituric acid-reactive substance (TBARS)assay. Microscopy was used to observe morphological and metabolic changes. Butylated hydroxyanisole, methylparaben, and lipoic acid showed inhibitory effects on T. frezzii. Lipoic acid was chosen for further study due to its lack of environmental toxicity. Lipoic acid induced the loss of cytosolic proteins, hydrolysis of triglycerides, and increased levels of free fatty acids, monoacylglycerols, and diacylglycerols. It also caused a decrease in ergosterol levels and alterations in the fungal cell wall and membrane, ultimately leading to cell death.

Conclusions
This study demonstrates the efficacy of lipoic acid in inhibiting the in vitro development of T. frezzii.
Etomoxir suppresses the expression of PPARγ2 and inhibits the thermogenic gene induction of brown adipocytes through pathways other than β-oxidation inhibition
Authors: Shimura Hiroki , Yamamoto Sota , Shiiba Isshin , Oikawa Mami , Uchinomiya Shohei , Ojida Akio , Yanagi Shigeru , Kadowaki Hisae , Nishitoh Hideki , Fukuda Toshifumi , Nagashima Shun , Yamaguchi Tomoyuki 
Published: December 2024

Abstract
Brown adipocytes are characterized by a high abundance of mitochondria, allowing them to consume fatty acids for heat production. Increasing the number of brown adipocytes is considered a promising strategy for combating obesity. However, the molecular mechanisms underlying their differentiation remain poorly understood. In this study, we demonstrate that etomoxir, an inhibitor of Carnitine Palmitoyltransferase 1 (CPT1), inhibits their differentiation through mechanisms independent of β-oxidation inhibition. In the presence of etomoxir during brown adipocyte differentiation, reduced expression of the thermogenic gene UCP1 and decreased lipid droplets formation were observed. Furthermore, a transient reduction in the expression of PPARγ2, a critical factor in adipocyte differentiation, was also observed in the presence of etomoxir. These findings suggest the presence of a regulatory mechanism that specifically enhances PPARγ2 expression during brown adipocyte differentiation, thereby modulating thermogenic gene expression.
Restoring the Regulated: The EU’s Nature Restoration Law
Authors: Lees Emma , Pedersen Ole W 
Published: December 2024

Abstract
To halt the decline of the natural environment, attention is increasingly directed towards nature restoration. A recent example of this is the EU’s Nature Restoration Law (NRL). This article presents an assessment of the NRL, arguing that the NRL is ambitious but that this ambition comes with a risk of it becoming a performative body of law. To test the NRL’s application in Member States, this article identifies four key ‘interpretive puzzles’: the relative priorities between the different obligations in the NRL; the correct approach to timescales and the concept of natural range; the ‘climate change causation defence’ and the interaction between the definition of restoration measures and pre-emptive measures. The article then articulates the central theme in relation to these four puzzles—the tension in the relationship between the mandated ‘plan-led’ approach, and a potential lack of Member State discretion in the contents of that plan.
Real-world treatment patterns and survival in extensive stage small-cell lung cancer in Japan
Authors: Horinouchi Hidehito , Chang Chia-Hsien Suzu , Shaw Jaime , Archangelidi Olga , Balasubramanian Akhila , Pundole Xerxes 
Published: December 2024

Abstract

Objective
To describe standard of care and inform the evolving unmet need among extensive stage small-cell lung cancer (ES-SCLC) patients in Japan since approval of first-line anti-PD-L1 therapies, we describe treatment patterns and overall survival by line of therapy.

Methods
We conducted a descriptive analysis of adult ES-SCLC patients in Japan using de-identified patient data within the MDV database (hospital-based claims) to describe treatment patterns and DeSC database (payer-based claims linked to mortality of municipality records) to describe both treatment patterns and real-world overall survival (rwOS).

Results
The study population of MDV and DeSC cohorts included 6302 and 903 patients, respectively. First-line anti-PD-L1 therapy-based regimens grew since their approval in 2019 and were used in ~35% and ~59% of patients in 2022, in the MDV and DeSC cohorts, respectively. Amrubicin monotherapy was the most common second-line (2 L) regimen before and after 1 L anti-PD-L1 approvals. No clear standard of care was identified in third-line (3 L) and fourth-line (4 L). Median rwOS following 1 L therapy was 10.6 months (95% CI: 9.0, 11.8) and 9.3 months (95% CI: 8.3, 10.3) in patients who did and did not receive anti-PD-L1 therapy, respectively. Following 2 L, 3 L, and 4 L therapy, median rwOS was 6.7 months (95% CI: 5.9, 7.4), 5.5 months (95% CI: 4.4, 6.4), and 4.7 months (95% CI: 3.4, 6.9), respectively.

Conclusions
Anti-PD-L1 therapies have become part of first-line standard of care but survival in treated Japanese ES-SCLC patients remains poor, highlighting the unmet medical need in the post anti-PD-L1 era.