bluuebunny/crossref_metadata_2025_split huggingface dataset:
exploring the molecular mechanism of sepsis comprehensively based on multi-omics analysis
Authors: He Wenjing , Li Chunyan , Wei Zhen , Han Songji , Zhou Suansuan , Cheng Zhe , Ta Guang 
Published: October 2024

Abstract

Background: Sepsis remains a life-threatening disease with a high mortality rate that causes millions of deaths worldwide every year. However, the molecular mechanism remains incompletely unknown. Bioinformatics analysis has been widely used in microarray data to identify biomarkers of sepsis and perform subsequent analysis to identify potential therapeutic interventions.
Methods: The GSE175453, GSE185263 and GSE28750 datasets were obtained from Gene Expression Omnibus (GEO) database and eQTL data comes from the eQTLGen consortium database. Limma package and ClusterProfiler analysis were used to identify differentially expressed genes and explore the functional correlation of these genes. Functional analysis and immune infiltration analysis were used to investigate the biological characteristics and immune cell enrichment in sepsis patients. Then the correlation between pyroptosis-related genes and immune cells was analyzed and the diagnostic value of the selected genes was assessed using the receiver operating characteristic curve. Mendelian randomization (MR) analysis was first conducted to investigate the hub genes related to sepsis. Sensitivity analyses were applied to validate the reliability of MR results. Then artificial neural network models were constructed for diagnosis and immune cell infiltration analysis was performed to explore the potential molecular mechanisms. Cmap drug prediction was made to discover the therapeutic effect on sepsis.
Results: Our investigation revealed 204 differentially expressed genes (DEGs) in sepsis datasets including 124 up-regulated genes and 80 down-regulated genes. The MR analysis showed six hub genes (CA1, CD96, IL18R1, ORM1, S100P, SLC26A8) may be associated with a high or low risk of sepsis. Analyzes suggested that key genes are closely related to the level of immune cell infiltration and play an important role in the immune microenvironment. We constructed an artificial neural network model with high diagnostic and studied the specific signaling pathways enriched in 6 key genes performance. Furthermore, by transcriptional regulation analysis, corresponding transcription factors of key genes were displayed and Cmap drug prediction showed expression profiles perturbed by drugs such as Entecavir, Linsitinib, SDZ-205-557, and Triacsin C had a significant negative correlation with the disease which may have therapeutic effective.
Conclusion: Our investigation revealed six key genes related to sepsis, displayed the signaling pathways enriched in the key genes to explore the molecular mechanisms of sepsis, and offered potential therapeutic targets or biomarkers, shed light on the immune microenvironment by immune infiltration analysis, and proposed prospective alternative pathways for targeted therapeutic interventions by multi-omics analysis initially.
What works better with LSTM, decomposition or deseasonalisation for rainfall forecasting?
Authors: Lama Achal , Rakshit Debopam , Singh K N , Das Pankaj , Das Ritwika , Verma Satyam , Gurung Bishal 
Published: October 2024

Abstract

Forecasting rainfall is crucial for countries like India where farming is the livelihood for around half of the population and rainfall is their most important water source. The intensity of rainfall varies for different seasons and is not spread evenly across the country. Over the years, different researchers used various statistical models for rainfall forecasting. This article uses the monthly rainfall series for all India and five sub-divisions, namely Central North East, North East, North West, Peninsular and West Central for modeling and forecasting. It has been observed that, as a time series, these series follow nonlinearity and non-normality but are stationary. Again, all the series are seasonal. Decomposition or deseasonalised (DS) based hybrid models may be useful for this type of complex scenario. The variational mode decomposition (VMD) is applied to the both actual rainfall series and deseasonalised series (DS) and the Intrinsic Mode Functions (IMFs) are obtained. The Long Short-Term Memory (LSTM) model is fitted to these IMFs. LSTM is also applied to the deseasonalised series leading to DS-LSTM model. The traditional seasonal autoregressive integrated moving average (SARIMA) and LSTM model also fitted directly to the actual rainfall series. The DS- -LSTM hybrid model established its superiority in forecasting compared to the standalone SARIMA, LSTM, VMD-LSTM and DS-VMD-LSTM models based on Root Mean Squared Error (RMSE) and Mean Absolute Error (MAE) in the model testing set for all the series. Hence, establishing the importance of deseasonalisation of the series before applying appropriate model to it.
Filamentation activates bacterial NLR-like antiviral protein
Authors: Zheng Jianting , Wang Yiqun , Tian Yuqing , Yang Xu , Yu Feng 
Published: October 2024

Abstract

Bacterial antiviral STANDs (Avs) are evolutionarily related to the nucleotide-binding leucine-rich repeat containing receptors (NLRs) widely distributed in immune systems across animals and plants. EfAvs5, an Avs type 5 protein from Escherichia fergusonii, contains an N-terminal SIR2 effector domain, a nucleotide-binding oligomerization domain (NOD) and a C-terminal sensor domain, conferring protection against diverse phage invasions. Despite the established roles of SIR2 and STAND in prokaryotic and eukaryotic immunity, the mechanism underlying their collaboration remains unclear. Here we present cryo-EM structures of EfAvs5 filaments, elucidating the mechanisms of dimerization, filamentation, filament clustering, ATP binding and NAD+ hydrolysis, all of which are crucial for anti-phage defense. The SIR2 domains and NODs engage in the intra- and inter-dimer interaction to form an individual filament, while the outward C-terminal domains contribute to bundle formation. Filamentation potentially stabilizes the dimeric SIR2 configuration, thereby activating the NADase activity of EfAvs5. EfAvs5 is deficient in the ATPase activity, but elevated ATP concentrations can impede its NADase activity. Together, we uncover the filament assembly of Avs5 as a unique mechanism to switch enzyme activities and perform anti-phage defenses, emphasizing the conserved role of filamentation in immune signaling across diverse life forms.
Morphological Characteristics of Microenvironment in the Human Thymus During Fetal Development
Authors: Maletin Nemanja , Denda Nikola , Borocki Stefan , Golušin Zoran , Rašković Aleksandar , Fejsa Aleksandra Levakov , Amidžić Jelena 
Published: October 2024

Abstract

Background
The thymus is a key organ for the development of T cells. T cell precursors first migrate from the bone marrow to the thymus. During maturation, these precursors require interactions with various types of cells that form the thymic microenvironment, such as epithelial, mesenchymal, and other immune cells not belonging to the T lineage. The aim of this study was to examine the changes in the number and diameter of Hassall's corpuscles, as well as the density and distribution of epithelial cells (p63+) and macrophages (CD68+).
Methods
Twenty-five fetal thymus samples were examined, divided into five groups according to gestational age. The samples were processed using standard histological methods and immunohistochemical staining.
Results
The study showed that the number and diameter of Hassall's corpuscles gradually increased during fetal development, with a significant increase from the 14th to the 38th gestational week. The average diameter of Hassall's corpuscles was largest in the age group of 34–38 weeks. The density of p63 + epithelial cells decreased in correlation with gestational age, while the density of CD68 + macrophages significantly increased, particularly in the thymic medulla, towards the end of the fetal period.
Conclusions
An increase in the number and size of Hassall's corpuscles during fetal development was recorded, while the density of epithelial cells decreased and the density of macrophages increased.
Different environmental contexts, different responses: Evaluating the drivers of red fox occupancy patterns in Portugal
Authors: Quezado Luisa , Ferreira Eduardo , Barroqueiro Carlos , Linck Paloma , Ares-Pereira Guilherme , Pinto Nuno , Rossa Mariana , Teixeira Daniela , Carvalho João , Negrões Nuno , Torres Rita T. , Rosalino Luís Miguel 
Published: October 2024

Abstract

Identifying the drivers and ecological mechanisms that shape species occupancy patterns at large scales is decisive in understanding how species respond to environmental changes. In this study, we compiled camera trapping data from different scientific projects and monitoring programs to conduct the first assessment of the relevant ecological drivers of red fox (Vulpes vulpes) occupancy patterns at the national level in Portugal. Here, using single-species/single-season occupancy models, we target two regions with different environmental contexts - north and south of River Tagus. Our results show that the red fox occupancy drivers change depending on the environmental context. In the northern region (more mountainous and densely forested), occupancy patterns were mostly shaped by direct human-associated disturbance, positively associated with dogs’ relative abundance index. On the other hand, in the southern region (plain areas dominated by agroforestry systems), the variation in red fox occupancy patterns was best explained by the habitat characteristics, with foxes showing a higher probability of occupying areas with greater habitat diversity. Considering these results, we conclude that the red fox’s generalist character is highlighted by its capacity to adopt two different occupancy strategies depending on the environmental context: the use of more humanized areas, along with free-ranging dogs, in the Northern region, and the use of areas with more diversified resources in the Southern region. Therefore, our study reinforces the red fox's highly adaptive character, adding crucial information to tailor red fox management and conservation actions to the different regional environmental contexts of Portugal.
Efficacy and Safety of Eight-Week Therapy with Ashwagandha Root Extract in Improvement of Sexual Health in Healthy Men: Findings of a Prospective, Randomized, Double-Blind, Placebo-Controlled Study
Authors: Mutha Amit Shrenikraj , Mutha Sonali Amit , Tejuja Anupama Hem , Beldar Amit Shashikant , Mulay Alok Mahendra , langade Deepak 
Published: October 2024

Abstract

Ashwagandha, a traditional Indian Ayurvedic remedy, an adaptogen, may improve sexual dysfunction in men and women. This 8-week prospective, double-blind, randomized, placebo-controlled study evaluated the efficacy and safety of Ashwagandha Root Extract (ARE) on improving sexual health in healthy adult men based on Satisfying Sexual Events (SSEs), the Sexual Desire Inventory (SDI-2), the International Index of Erectile Function (IIEF) score, semen parameters and the Quality Of Life (QOL) using the SF-12 tool. A total of 100 healthy men aged 30 to 50 years were randomly assigned to receive ARE 300 mg twice daily (n=50), or identical placebo (n=50) in a 1:1 ratio for 8 weeks. Study assessments were done at baseline, week 2, week 4, and week 8. Three participants from ARE and four participants from the placebo group were excluded due to follow-up loss. The efficacy analyses were done on Per-Protocol (PP) dataset of 93, whereas safety analyses were done on all 100 participants. Significant improvements were observed with ARE for semen volume (p=0.005), sperm number (p=0.006), sperm concentration (p=0.007), and sperm morphology (p=0.007). The improvement in scores was better with ARE for SDI-2 (p<0.05), orgasm and sexual desire domains of IIEF (p<0.05), and SF-12 (p<0.0001). No adverse events were reported in the study.
Exploring the Causal Role of Gut Microbiota and Inflammatory Proteins in Neuromyelitis Optica Spectrum Disorder: a Mendelian randomization study with mediation analysis
Authors: Yin Ziqian , Qiu Youjia , Yang Yayi , Wang Menghan , Yue Sijia , Song Bingyi , Chen Zhouqing , Wu Jiang , Wang Zhong 
Published: October 2024

Abstract

Background: Observational studies have highlighted a strong association between gut microbiota (GM) and the onset of neuromyelitis optica spectrum disorder (NMOSD), however, the causality remains unclear.
Method: A Mendelian randomization (MR) study was conducted to determine the causal effect of GM on NMOSD and to explore the role of inflammatory proteins as mediators. Genetic data from GWAS were analyzed using the Inverse Variance Weighted (IVW) method, alongside weighted median andMR-Egger methods. Sensitivity analyses, including MR-Egger intercept, leave-one-out, Cochrane’s Q-test, and MR-PRESSO, were performed to validate the MR estimations. Two-sample MR and reverse MR were utilized to assess causality and potential reverse causation.
Result: The MR analysis revealed nine significant causal links between GM and NMOSD. Four inflammatory proteins were also found to have positive causal associations with NMOSD. Sensitivity analyses confirmed these findings. However, mediated MR analysis did not find evidence supporting inflammatory proteins as mediators in the GM-NMOSD pathway.
Conclusion: The study presents evidence for a causal relationship between GM, inflammatory proteins, and NMOSD. Notably, inflammatory proteins do not mediate the pathway from GM to NMOSD, contributing to a deeper understanding of the interplay between GM and NMOSD.
The Influence of Social Determinants and 5Cs of Positive Youth Development on the Mental Health of Chilean Adolescents
Authors: Marín-Gutiérrez Mauricio , Caqueo-Urízar Alejandra 
Published: October 2024

Abstract

This study analyzes the influence of social determinants (SD) and positive youth development (PYD) on the mental health (MH) of Chilean adolescents. A nonexperimental, cross-sectional, correlational-explanatory design was adopted to analyze data from 612 adolescents (43.46% males and 56.54% females) aged between 11 and 19 years (M = 14.92, SD = 1.50). The SD evaluated included parental educational level, family affluence, gender, migratory status, and ethnicity. PYD was assessed via the 5Cs model (Competence, Confidence, Connection, Character, and Caring). MH was conceptualized through the dual-factor model, which encompasses positive mental health (PMH) and negative mental health (NMH). The analyses included confirmatory factor analysis to assess the measurement models and structural equation modeling to examine the direct and indirect effects of the hypothesized relationships. The findings indicate that family affluence and gender are the factors most consistently associated with the dimensions of PYD and MH. Confidence and connection positively influence MH, improving PMH and reducing NMH, and mediate the relationship between SD and MH. The importance of considering the socioeconomic context and individual capabilities in mental health promotion strategies is highlighted, proposing an integral approach that addresses both the positive and negative aspects of adolescent well-being.
RETRACTED: Ecofriendly Synthesis of BiVO4 Nanoparticles from Ipomoea Campanulata Leaf Extracts: Advances in Photocatalysis and Electrochemical Sensing
Authors: C Sunil Kumar K , V Lakshmi Rnaganatha , L Soundarya T , S Chandra , G Nagaraju , C Mallikarjunaswamy 
Published: October 2024

Abstract

The authors have requested that this preprint be removed from Research Square.
Is there any light at the end of the tunnel? Validation of the Perceived Hope Scale in Arabic-speaking adults living in Gaza in the midst of war, destruction and death
Authors: Fekih-Romdhane Feten , Jebreen Kamel , Swaitti Tasnim , Jebreen Mohammed , Radwan Eqbal , Kammoun-Rebai Wafa , Samra Mahmoud A. Abu , Hallit Souheil 
Published: October 2024

Abstract

Background: Despite its obvious relevance for clinical practice and research, it is surprising that yet no hope measure is available for use among Arabic-speaking populations, especially those most vulnerable who have been going through major humanitarian crises. This paper proposed to provide novel insights into psychometric information on hope scales, by examining, for the first time, the psychometric properties of an Arabic translation of the Perceived Hope Scale (PHS) in Palestinians living in Gaza who have endured several months of suffering since the war began in October 2023.
Method: This study had a cross-sectional design and applied a quantitative research approach. It was carried-out over a month period (September 2024) using an anonymous self-report questionnaire that was shared through social networks and the snowball sampling technique. A total of 534 Arabic-speaking Palestinian adults aged over 18 years and currently living in Gaza took part in the study.
Results: The factorial structure of the Arabic PHS was explored using Confirmatory Factor Analyses, and showed that the fit indexes of the one-factor solution reached the standard of good model fit. Furthermore, our results suggest that the Arabic PHS possesses excellent internal consistency reliability, with a Cronbach’s alpha value of .90 for the total score. Invariance was established in our sample at the metric and scalar levels in terms of sex groups. PHS scores significantly and positively correlated with religiosity, resilience and post-traumatic growth. In addition, and as expected, PHS inversely correlated with anxiety and depression.
Conclusion: Overall, our results add to the measurement assessment of the PHS, lending further support to its value as a sound measure to assess perceived hope in a new context and cultural background of Muslim, Arabic-speaking adults and fragile survivors of several decades of war that dramatically escalated over the past months.
The Hidden Carbon Debt: Rethinking Electric Vehicles in India’s Coal-Powered Future
Authors: Kavya Amaya , Yadav Seema 
Published: October 2024

Abstract

Electric vehicles (EVs) are often positioned as a cornerstone of sustainable mobility, promising to combat climate change by reducing emissions from transportation. However, in nations like India, where coal powers over 70% of the electricity grid, the actual environmental impact of EVs remains underexplored. This paper presents a comprehensive lifecycle assessment (LCA) of EVs in India, examining their carbon footprint from the manufacturing of lithium-ion batteries to the operation and disposal phases. The findings challenge the perception that EVs are inherently eco-friendly, revealing that their lifecycle emissions are significantly impacted by the carbon intensity of India’s coal-dependent energy infrastructure. Battery production alone contributes to a substantial share of an EV’s emissions, and with India’s limited battery recycling infrastructure, the end-of-life phase adds further environmental strain. When factoring in these realities, EVs in India may deliver only marginal greenhouse gas (GHG) reductions compared to internal combustion engine vehicles (ICEVs)—and in some cases, their emissions may even be higher. To unlock the true potential of EVs, this study emphasizes the urgent need for India to decarbonize its energy grid and implement robust battery recycling policies. By unveiling the hidden carbon costs of EVs in coal-powered regions, this paper calls for a more balanced, data-driven approach to sustainable transportation.
Technology and Continuous Glucose Monitoring Access, Literacy, and Use Among Patients at the Diabetes Center of an Inner-City Safety-Net Hospital: Mixed Methods Study
Authors: Sabben Gaëlle , Telfort Courtney , Morales Marissa , Zhang Wenjia Stella , Espinoza Juan C , Pasquel Francisco J , Winskell Kate 
Published: October 2024

Background
Despite the existence of an increasing array of digital technologies and tools for diabetes management, there are disparities in access to and uptake and use of continuous glucose monitoring (CGM) devices, particularly for those most at risk of poor diabetes outcomes.

Objective
This study aims to assess communication technology and CGM access, literacy, and use among patients receiving treatment for diabetes at an inner-city safety-net hospital.

Methods
A survey on digital technology ownership and use was self-administered by 75 adults with type 1 and type 2 diabetes at the diabetes clinic of Grady Memorial Hospital in Atlanta, Georgia. In-depth interviews were conducted with 16% (12/75) of these patient participants and 6 health care providers (HCPs) to obtain additional insights into the use of communication technology and CGM to support diabetes self-management.

Results
Most participants were African American (66/75, 88%), over half (39/75, 52%) were unemployed or working part time, and 29% (22/75) had no health insurance coverage, while 61% (46/75) had federal coverage. Smartphone ownership and use were near universal; texting and email use were common (63/75, 84% in both cases). Ownership and use of tablets and computers and use and daily use of various forms of media were more prevalent among younger participants and those with type 1 diabetes, who also rated them as easier to use. Technology use specifically for diabetes and health management was low. Participants were supportive of a potential smartphone app for diabetes management, with a high interest in such an app helping them track blood sugar levels and communicate with their care teams. Younger participants showed higher levels of interest, perceived value, and self-efficacy for using an app with these capabilities. History of CGM use was reported by 56% (42/75) of the participants, although half (20/42, 48%) had discontinued use, above all due to the cost of the device and issues with its adhesive. Nonuse was primarily due to not being offered CGM by their HCP. Reasons given for continued use included convenience, improved blood glucose control, and better tracking of blood glucose. The in-depth interviews (n=18) revealed high levels of satisfaction with CGM by users and supported the survey findings regarding reasons for continued use. They also highlighted the value of CGM data to enhance communication between patients and HCPs.

Conclusions
Smartphone ownership was near universal among patients receiving care at an inner-city hospital. Alongside the need to address barriers to CGM access and continued use, there is an opportunity to leverage increased access to communication technology in combination with CGM to improve diabetes outcomes among underresourced populations.