bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mendelian randomization to evaluate the causal relationship between household income status and the risk of knee osteoarthritis
Authors: Weng Mingjie , Zhang Min 
Published: November 2023

Abstract

Objective
To explore the causal relationship between household income status and knee osteoarthritis (KOA) risk using a two-sample Mendelian randomization (MR) approach.
Methods
In order to assess the causal relationship between household income status and knee osteoarthritis (KOA), we utilized the Genome-wide association studies (GWAS) data. Our selection process involved identifying the single nucleotide polymorphisms (SNPs) as instrumental variables (IVs). Among these SNPs, we specifically chose the significant ones for the MR analysis. To determine the causal relationship, we employed three methods of MR analysis, namely inverse variance weighted (IVW), weighted median (WM), and MR-Egger regression. This analysis allowed us to calculate Odds Ratios (OR) for the relationship between household income status and KOA. Additionally, we also conducted heterogeneity and pleiotropy analyses to further validate the MR results.
Results
Higher household income tended to reduce the risk of knee osteoarthritis (OR: 0.71, 95% CI: 0.60 to 0.85, p < 0.001), while reverse MR studies showed no causal association between knee osteoarthritis and household income status. The intercept of MR-Egger regression was 0.014 (P = 0.1), indicating that the causal estimation results were unaffected by pleiotropy.
Conclusion
The findings showed that individuals with higher household incomes had a decreased risk of knee osteoarthritis.
The effect of online point of care ultrasound training coupled with 1:1 sessions on medical learner comfort level and intended use
Authors: Mikhail Pierre , Leung Deborah , Belanger Jacob , Hogenbirk John , Allen Lisa 
Published: November 2023

Abstract
Background
Point of Care Ultrasound (POCUS) is gaining popularity in the clinical setting as it provides important bedside clinical information in real-time. There are numerous barriers in POCUS training that impede access, training, and subsequent use. This study was developed to introduce and evaluate the use of a novel course, the Huntsville Integrated Simulation Program (HIP-Sim). The study objective was to investigate the feasibility and clinical relevance of the HIP-Sim program, to learn if completing modules coupled with select 1:1 sessions will improve confidence in ultrasound skills and potential incorporation of POCUS into practice.
Method
Participants included physicians, undergraduate and graduate medical learners in rural northern Ontario. Pre-and post-interventional responses were collected from participants. Data was assessed using descriptive analyses and Wilcoxon Signed Rank Tests. Laurentian University research ethics board, certificate number #2020-02-01.
Results
There were 40 unique respondents, twenty completing both the pre-and post-intervention surveys. Respondents reported a significant increase in comfort level for Abdomen FAST, IVC/ volume assessment, POCUS in general, and Basic Cardiac assessment, which increased by 1.13 points or more. Respondents strongly agreed that “the HIP-SIM course was an effective use of my time” (18/27 = 66.7%) or that “the training was appropriate to my learning needs” (20/27 = 74.1%). Almost 90% (24/27) would recommend the HIP SIM training program to others. Many respondents indicated that they would “recommend the HIP-Sim program to their colleagues and medical learners” and that it was “an excellent mix of self-directed learning and learning from the experts”.
Conclusion
The HIP-Sim program increased comfort in numerous POCUS scans. The hybrid format of electronic self-directed learning and in-person teaching was appreciated by physicians and medical learners alike. This study demonstrates preliminary evidence that HIP-Sim is a feasible and clinically relevant POCUS learning course.
The Hidden Oases: Unveiling Trophic Dynamics in Namib's Fog Plant Ecosystem
Authors: Gan Huei Ying , Hohberg Karin , Schneider Clément , Ebner Martin , Marais Eugene , Miranda Tatiana , Lehmitz Ricarda , Maggs-Kölling Gillian , Bocherens Hervé 
Published: November 2023

Abstract

The Namib Desert is a hyperarid coastal desert where fog is a major moisture source. We hypothesized that the fog-harvesting grass Stipagrostis sabulicola establishes an important ecological niche in the extreme Namib Sand Sea ecosystem, referred to as "Fog-Plant-Oases (FPO)". Using a combination of extraction methods, we collected and described the above- and belowground FPO invertebrate communities and inferred their trophic feedings based on stable carbon and nitrogen isotope values. Our findings revealed a complex trophic structure and a unique food web, all of which revolve around a single fog plant as the primary producer. We demonstrated that S. sabulicola serves as the primary energy source for the aboveground food web, encompassing a diverse range of trophic levels. Nevertheless, the distinctive stable isotope values of bacterial- and fungal-feeding nematodes indicated the separation of the aboveground niche, which is primarily sustained by S. sabulicola, from the belowground niche, where wind-blown sediments serve as the main energy source. These findings further accentuate the role of S. sabulicola not only as a primary producer but also as a source of moisture and habitat provider for belowground invertebrates.
Huei Ying Gan, Karin Hohberg, and Clément Schneider contributed equally to this work.
Antibacterial activity of Streptomyces sp. strain NELs-60 against Methicillin-resistant Staphylococcus aureus
Authors: Rajaofera Mamy Jayne Nelly , Wang Yanshuang , Chen Chuizhe , Li Xuemiao , Kang Xun , Zhang Nan , Kuang Dai , Xia Qianfeng 
Published: November 2023

Abstract
Streptomyces sp. strain NELs-60 isolated from the coastal city Dongfang in Hainan province of China was investigated for its antibacterial potential. The isolate showed strong activity against Methicillin-resistant Staphylococcus aureus ATCC 43300. Using the Plackett Burman design, the culture condition was optimized to achieve the maximum production. Five variables and 12 run experiment were adopted, and the result evinced pH, inoculum time, and agitation speed highly influenced bioactive compound production. Solvent extraction method was applied for taking out of bioactive metabolites from the strain and highest activity was obtained from ethyl acetate. The active metabolites had obvious inhibitory effect, with MIC and MBC of 125 µg/mL and 500 µg/mL, respectively. Based on GC–MS, the active metabolites of NELs-60 were preliminarily analyzed. Different compounds were detected, suggesting their contribution towards the anti-MRSA activities. Ethyl acetate extract was found fully stable and showed decreases in biofilm formation, lower virulence and less toxicity when comparing on non-treated ones. The results of this study indicate the potential of NELs-60 as a promising source of anti-MRSA and antibiofilm compounds and warrants further study.
AAC: An anomaly aware time series compression algorithm towards green computing
Authors: Meng Jingwen , Liu Liang , Liu Yulei , Wang Ning 
Published: November 2023

Abstract
The storage of time series big data in Internet of Things (IoT) requires a lot of environmentally unfriendly servers that generate a large amount of energy consumption. Reducing the number of storage servers with efficient time series compression techniques is one of the available solutions to decrease energy consumption to realize green computing. Therefore, in this paper, we propose an Anomaly Aware Compression algorithm (AAC) aiming to achieve green storage by obtaining higher compression ratios. Anomalies appear frequently in time series data in scenarios such as IoT, but no compression algorithm has been designed for them. AAC realizes better compression results by dividing and compressing abnormal and normal data separately. For the two types of data, we present Window Delta encoding and Dispersion Tolerant encoding to efficiently compress them. Our experimental results demonstrate that the approach achieves about 5% - 120% improvement in compression ratio compared to the state of art.
A Study on the Association Between Vaginal Microecology Imbalances During Pregnancy and the Risk of Spontaneous Preterm Birth: A Prospective Cohort Study
Authors: Ren Siling , Liu Liping , Xiao Xuejuan , He Tingde , Guo Quanyi , Ling Ting , Li Tingting , Jiang Lingling 
Published: November 2023

Abstract

Background
Spontaneous preterm birth remains a paramount challenge in obstetrics with potential adverse implications for maternal and neonatal health. The vaginal microecology during pregnancy plays a pivotal role in orchestrating normal parturition, and its dysbiosis is associated with an escalated risk of Spontaneous preterm birth.
Methods
A prospective study encompassing 79 pregnant women was conducted to elucidate the nexus between gestational vaginal microecology imbalances and the susceptibility to preterm birth. Based on pregnancy outcomes, participants were stratified into preterm and term groups. At the 24th gestational week and close to parturition, vaginal secretions from the pregnant women were both qualitatively and semi-quantitatively assessed in accordance with the clinical consensus on vaginal microbiota evaluation.
Results
Significant disparities were discerned between the preterm and term cohorts, notably regarding the lactobacillus proportion and the Nugent score and Aerobic Vaginitis score. By the 24th gestational week, the preterm group exhibited a pronounced decrement in lactobacillus proportion coupled with elevated Nugent score and Aerobic Vaginitis score. Despite interventions at the 24th gestational week for those with detrimental vaginal environments, which significantly improved Nugent score and Aerobic Vaginitis score by term, the lactobacillus proportion did not show corresponding recovery.
Conclusions
The study underscores a tangible association between diminished lactobacillus proportion, heightened Nugent score, and Aerobic Vaginitis score at 24 weeks of gestation, and an augmented Spontaneous preterm birth risk. These metrics offer pivotal insights for clinical practice concerning preterm birth susceptibility and emphasize the importance of preserving a healthy vaginal microbiota milieu.
A complete mass spectrometry-based immunopeptidomics pipeline for neoantigen identification and validation
Authors: Li Ming , Tran Ngoc Hieu , Peng Chao , Lei Qingyang , Xin Lei , Lang Jingxiang , Zhang Qing , Li Wenting , Qiao Rui , Qin Haiming , Bu Dongbo , Zhang Haicang , Yu Chungong , Liu Xiaolong , Shan Baozhen , Wu Ping , Miao Haofei , Zhang Yi 
Published: November 2023

Abstract
Here we proposed DeepImmu, a complete pipeline for neoantigen identification and validation that was based solely on mass spectrometry (MS) immunopeptidomics. In particular, a new enrichment kit was developed for HLA peptide purification from a small amount of biopsied tissue as low as 18mg. To identify candidate neoantigens from such a small amount of sample, we built DeepNovo Peptidome, a highly sensitive de novo sequencing-based workflow for HLA peptide identification. Furthermore, we developed DeepSelf, a personalized model for immunogenicity prediction based on the central tolerance of T cells, which could be used to prioritize candidate neoantigens from de novo HLA peptides for in vitro validation. Finally, we presented a new MS-based immunopeptidomics study of native tumor tissues from five patients with cervical cancer. We applied DeepImmu pipeline to identify and prioritize candidate neoantigens from low amounts of tumor tissues, and then performed in vitro validation of autologous neoantigen-specific T cell responses to confirm our results. Our MS-based de novo sequencing approach provides an unbiased solution for neoantigen discovery, because it does not depend on prior knowledge of protein databases, RNA sequencing data, or the source of neoantigens. By reducing the amount of sample to biopsy size, our DeepImmu pipeline can be easily performed in routine clinical applications.
Biogenic synthesis of selenium nanoparticles by moderate halophilic bacteria and evaluation of its anti-bacterial and anti-biofilm activity
Authors: Selvaraj Bharathi , A Kishore Kumar , S Kumaran , G Suresh 
Published: November 2023

Abstract
In the present investigation, the selenium nanoparticles (SeNPs) were biosynthesized from moderate halophilic bacteria (that can grow optimally at 3–15% NaCl) isolated from Pichavaram mangrove sediments. The bacterial strain S8 was found to be efficient for SeNPs synthesis and hence identified by 16s r RNA sequencing as Shewanella sp. In UV- spectral analysis the SeNPs displayed peak at 320 nm due to surface plasmon resonance (SPR). The cell free extract of Shewanella sp. and SeNPs clearly indicate that the various functional groups in the cell free extract were mainly involved in synthesis and stabilisation of SeNPs. The SeNPs had a spherical form and a 20 nm size, according to the FESEM analysis. The EDX show the distinctive peaks of selenium at 1.37, 11.22.12.49 Kev. In agar well diffusion method the SeNPs shows inhibitory activity against all the test pathogens with the highest activity was noted against P. aeruginosa with zone of inhibition of 23 ± 0.5mm. In the micro broth dilution method, lowest minimal inhibitory concentration (MIC) value was recorded against P. aeruginosa with 8µg/200µl and minimal bactericidal concentration (MBC) of 16 µg/100µl. SeNPs at concentrations of more than 50 µg/ml were found to inhibit P. aeruginosa biofilm by 85% in the anti-biofilm study.
Integrated transcriptomic and metabolomic analyses reveals anthocyanin biosynthesis in leaf coloration of quinoa (Chenopodium quinoa Willd.)
Authors: Zhang Min , Wang Hongxia , Yang Xinlei , Wang Mei , Wang Junling , Li Yueyou , Lu Chuan , Sun Xinbo , Liu Xiaoqing , Lv Wei , Mu Guojun 
Published: November 2023

Abstract
Quinoa leaves demonstrate a diverse array of colors, offering a potential enhancement to landscape aesthetics and the development of leisure-oriented sightseeing agriculture in semi-arid regions. This study utilized combined transcriptomic and metabolomic analyses to investigate the mechanisms underlying anthocyanin synthesis in both emerald green and pink quinoa leaves. Differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were analyzed between two different germplasms at different periods. Several key genes, including 4CL, C3'H, HCT, CHS, CHI, ANR, CYP75B1, UGT79B1, FG3, FG2, CYP73A, MYC2, bHLH14, HY5, and TGA, were identified in anthocyanin biosynthesis using DEG analysis. GO enrichment analysis revealed seven closely related GO Terms. KEGG enrichment analysis identified six metabolic pathways that were significantly associated with anthocyanin biosynthesis, with flavonoid biosynthesis (ko00941) emerging as the most pivotal. Metabolomic analysis confirmed cyanidin 3-O-(3'',6''-O-dimalonyl glucoside) and naringenin as key DAMs in pink leaves. Combined transcriptomic and metabolomic analyses indicated that both the flavonoid biosynthesis pathway (ko00941) and anthocyanin biosynthesis pathway (ko00942) were involved in the anthocyanin biosynthesis pathway. Ten DEGs, including PAL, CHI, CYP75B1, F3H, FG3, CYP73A, HCT, C3'H, 4CL, and CHS, were verified through qRT-PCR, with the results across the nine comparison groups consistent with that from transcriptomic sequencing. These findings provide a foundation for elucidating the molecular regulatory mechanisms governing flavonoid synthesis in quinoa leaves.
Rapid evaluation of the implementation of a disinfectant spray in hospital during the COVID-19 pandemic: a mixed-methods qualitative study.
Authors: Saman Razan , Pini Simon , Higham Ruchi , Helliwell Jack , Jayne David , Kowal Mikolaj , Lewthwaite Penny , Moriarty Catherine , Stocken Deborah , Young Nicola , Rousseau Nikki , Quyn Aaron 
Published: November 2023

Abstract
Background
A spray-based disinfectant (VIRUSENDTM) was developed in collaboration with the British Army to provide protection for its service-people from COVID-19. The Critical evaluation of the implementation of VIRUSENDTM in clinical settings (CLEAN) study sought to assess the potential utility of the spray-based disinfectant to enhance infection prevention and control (IPC) in hospital settings during the COVID-19 pandemic. It is a study of the rapid evaluation of a novel product in a high-pressure environment.
Methods
We conducted a single centre, prospective, rapid mixed-methods, implementation study. Participants were recruited to use the spray as part of their routine IPC practice and data collection followed. Initial observations and pre-implementation survey informed the framework for the post-implementation survey and interviews. Rapid qualitative analysis methodology was used.
The study was conducted at a major tertiary referral teaching hospital in the United Kingdom. One hundred and eighty-two staff participants were recruited from ten different clinical environments, selected to represent a diverse level of COVID-19 infection risk.
Results
One hundred and two participants completed the first survey, 66 completed the second survey and 23 participated in interviews. The interviews with staff regarding their views and experiences of the spray-based disinfectant illuminated the survey responses. Five themes were identified: Is there a need for a spray-based disinfectant? integration of the spray into IPC processes; issues of cleaning vs disinfection; design and functionality; negative consequences of spray use.
Conclusions
Most people liked using VIRUSENDTM and said that they would continue to use it at work if it was available to them. A key barrier was that VIRUSENDTM whilst being a multi-organism disinfectant, was marketed specifically at COVID-19. In hospitals cleaning and disinfection needs to address a range of infectious organisms. Furthermore, economic evaluation will be required prior to any wider uptake. A rapid evaluation approach identified key issues related to feasibility and acceptability of a novel product in a high-pressure environment. This approach could be usefully applied to the assessment of other potential healthcare interventions where timely information is needed.
Comprehensive Computational Analysis of Differentially Expressed miRNAs and Their Target Genes in Breast Cancer: Implications for Diagnostic and Prognostic Insights
Authors: Phoebe Grace Lydia , Christy.H Jemmy 
Published: November 2023

Abstract
Breast cancer, known for its complex and multifaceted nature, presents formidable challenges in both diagnosis and treatment. MicroRNAs (miRNAs) have emerged as promising biomarkers due to their distinctive expression patterns in tumor tissues and their stability in various biological fluids. This stability makes them valuable for early detection and precise prognostication. In this research endeavor, we conducted an exhaustive analysis to pinpoint differentially expressed miRNAs (DE-miRNAs) in breast tumor samples compared to their normal counterparts. To achieve this, we meticulously examined four microarray datasets (GSE45666, GSE2665, GSE44124, and GSE59247) acquired from the Gene Expression Omnibus (GEO) repository. Our analytical approach consistently unveiled eight DE-miRNAs (miR-21, miR-99a, miR-100, miR-125b, miR-130b, miR-195, miR-451, and miR-497) across all datasets. Subsequently, we delved into the interactions between these DE-miRNAs and identified a network of 387 target genes. This comprehensive network offers a visual representation of the intricate miRNA-target interactions. Furthermore, we embarked on a functional enrichment analysis rooted in gene ontology terms. This analysis illuminated several pivotal biological processes, including epithelial to mesenchymal transition, positive regulation of nuclear-transcribed mRNA poly(A) tail shortening, protein K27-linked deubiquitination, peptidyl-threonine phosphorylation, regulation of transcription by RNA polymerase, gene silencing by RNA, phosphorylation, negative regulation of nitrogen compound metabolic processes, and the cellular response to transforming growth factor beta. These processes are characterized by their diverse roles in cancer biology, influencing gene expression, protein activity, cellular signaling, and metabolic pathways. Dysregulation of these processes can indeed lead to uncontrolled cell growth, invasive behavior, and metastasis, all of which are hallmarks of cancer development and progression. In conclusion, our extensive computational analysis provides valuable insights into the potential use of miRNAs as markers for early breast cancer diagnosis and ongoing monitoring. By identifying DE-miRNAs and unraveling their interactions and associated biological processes, this study enhances our comprehension of the molecular intricacies of breast cancer and the potential for improved diagnostic and prognostic approaches.
Insilico screening to identify MAO-B inhibitor as Anti Alzheimer potential from natural compounds using ZINC database.
Authors: Chaudhari Somdatta Y. , Anawade Geeta , Borude Snehal Tukaram , Gaikwad Nikita , Bedse Anjali Prashant , Dhage Azad N. , Uttekar Pravin S. , Nemade Lalita S. , Banu S. Shakila , Sharma Prince 
Published: November 2023

Abstract

Alzheimer’s disease (AD) is a neuron degenerative disorder. The MAO enzymes are potential therapeutic targets for the treatment of neurological illnesses because of their crucial role in the breakdown of neurotransmitters that results in the formation of some hazardous compounds. Because MAO inhibition reduces the oxidative stress brought on the MAO enzymes, it has a significant anti-Alzheimer impact. Consequently, the purpose of this investigation was to find out potent natural compounds that could be used as a medication to treat AD without causing any side effects. In the study of MAO-B action on Alzheimer’s disease a database of the natural compounds of ZINC15 was used for virtually screened using computational methods. In computation methods we screened ZINC15 database. This database contained lakh of molecules which were screened using different parameters such as BBB (Blood brain Barrier), Log B, Toxicity and some more. After this we were left with 4210 compounds on which using Binding energy and MPO score we selected top 5 compounds, then Molecular Dynamics simulations of the top five compounds were performed using the software. Through Molecular dynamics study we found the RMSD, RMSF, Hydrogen bonding, Hydrophobic Interaction and other parameters, this were studied. According to overall studied we found one of the top 5 compound showed best activity and can be proceed for further studies for Alzheimer’s disease and can lead for a better treatment for Alzheimer’s disease.
Fabrication of SnO2/TiO2 composite by a chemical co-precipitation method for efficient electrocatalytic oxidation of methylene blue
Authors: Zhang Jie , Zhang Man , Wang Hui , XU Jiasheng 
Published: November 2023

Abstract
In the present research, the Tin dioxide/Titanium dioxide (SnO2/TiO2) composite has been successfully fabricated by a chemical co-precipitation method. SnO2/TiO2 composite precursors were calcined at different temperatures (400 °C, 500 °C 600 °C, 700 °C). The as-prepared composite has been characterized by XRD, XPS, SEM, EDX, TEM, FTIR, and EIS. The SnO2/TiO2 composite, polyvinylidene fluoride (PVDF) and acetylene black were fully ground (8:1:1), which were covered on the foam nickel, and then vacuum dried to form the work electrode. The degradation experiment of methylene blue dye using SnO2/TiO2 composite material was conducted to analyze the electrocatalytic performance. The degradation efficiency of the composite material can reach 96.6% (calcination at 500 °C). The process of electrocatalytic degradation of methylene blue follows a quasi-first order reaction kinetics. The composite material electrode calcinated at 500 °C has the fastest electrocatalytic decolorization reaction rate and the highest catalytic capacity, which is consistent with the results of degradation efficiency.