bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Full Window Data Independent Acquisition Method for Deeper Top-down Proteomics
Authors: Sun Chen , Zhang Wenjing , Zhou Mowei , Myu Martin , Xu Wei 
Published: November 2024

AbstractTop-down proteomics (TDP) is emerging as a vital tool for the comprehensive characterization of proteoforms. However, as its core technology, top-down mass spectrometry (TDMS) still faces significant analytical challenges. While data-independent acquisition (DIA) has revolutionized bottom-up proteomics and metabolomics, they are rarely employed in TDP. The unique feature of protein ions in an electrospray mass spectrum, as well as the data complexity require the development of new DIA strategies. This study introduces a machine learning assisted Full Window DIA (FW-DIA) method that eliminates precursor ion isolation, making it compatible with a wide range of commercial mass spectrometers. Moreover, FW-DIA leverages all precursor protein ions to generate high-quality tandem mass spectra, enhancing signal intensities by ∼50-fold and protein sequence coverage by threefold in a modular protein analysis. The method was successfully applied to the analysis of a five-protein mixture under native conditions andEscherichia coliribosomal proteoform characterization.
Green synthesis, characterization, and potential antimicrobial studies of Ag-MgO nanocomposites mediated fromTalinum triangulareleaf extract
Authors: Gildas Fonye Nyuyfoni , Awawou Paboudam Gbambie , Leonard Kwati , Ndzeidze Gilbert Njowir , Meva Francois Eya’ane 
Published: November 2024

ABSTRACTIn this study, Ag-MgONCs (silver-magnesium oxide nanocomposites) were fabricated usingTalinum triangulareleaf extract as a renewable, mild reducing, and stabilizing agent. The synthesis process involved molecular interactions between pre-prepared AgNPs (silver nanoparticles) andin situ-prepared MgO. Confirmation of the nanocomposites came from micrographic images obtained through SEM-EDX analysis. Dynamic light scattering (DLS) revealed a characteristic nanocomposite size of 295 nm. The infrared spectrum (FTIR) proved interactions betweenT. triangulareand Ag. Additionally, X-ray patterns of AgNPs and Ag-MgONCs confirmed hexagonal and cubic crystalline states, respectively, with average particle sizes of 17 nm. Furthermore, anin vitroanalysis against five bacterial strains (Escherichia coli,Acinetobacter baumannii,Pseudomonas aeruginosa,Klebsiella pneumoniae, andProteus mirabilis) revealed pronounced activity of the nanocomposites, particularly againstProteus mirabilis, indicating bactericidal potential.
Systematics investigation of key drivers of lung adenocarcinoma: A focus on genes, pathways, and miRNAs
Authors: Navaei Maryam , Karami Fatemeh , Jahanimoghadam Aria , Zareei Sara , Khorsand Babak 
Published: November 2024

AbstractIntroductionLung cancer remain a leading cause of cancer-related death, largely due to its asymptomatic progression in early stages and the development of drug resistance. Non-small cell lung cancer (NSCLC) accounts for 80% of all lung cancer cases, with lung adenocarcinoma (LUAD) being the most prevalent subtype. Despite advancements in treatment, the 5-year survival rate for LUAD remains low. Therefore, exploring gene networks may reveal novel therapeutic targets and pave the way for improvedMethodA comprehensive literature review was conducted across various databases containing multi- level genomic information. From this, a robust list of LUAD-related genes was curated. These genes were used to construct a weighted network based on KEGG pathway similarity. The network was subjected to clustering, hub gene detection, and gene ontology analysis. In parallel, a protein-protein interaction (PPI) network was constructed around these genes, which was further enriched with miRNA data to develop a gene-miRNA regulatory network.ResultsFollowing our analysis, 48 genes were identified as crucial to LUAD. Many of these genes, along with their corresponding miRNAs, were found to be either upregulated or downregulated in LUAD tissues. The hub genes and miRNAs identified are believed to play key roles in the initiation and progression of LUAD. Our network analysis highlighted PIK3CA, BRAF, EGFR, ERBB2, FGFR3, MTOR, and TP53, along with KRAS, MET, and FGFR2, as potential biomarkers. Additionally, miR-17-5p and miR-27a-3p, which are notably implicated in LUAD, emerged as novel biomarker candidates.ConclusionIn conclusion, we employed a combination of bioinformatics techniques and database mining to derive a refined list of genes and miRNAs with high potential for further research in LUAD. We also identified core pathways that play a critical role in LUAD pathogenesis, providing a foundation for future studies aimed at developing more targeted therapeutic approaches.
Dynamic changes in methadone distribution for opioid use disorder treatment from 2019 to 2023
Authors: Golden Amelia G , Piper Brian J 
Published: November 2024

AbstractBackgroundOpioid-related overdoses are a major concern in the United States (US) stemming from the high rates of Opioid Use Disorder (OUD). The rates of US overdoses continue to exceed one-hundred thousand per year. Methadone, a medication used as a treatment for OUD, is effective in reducing cravings and withdrawal symptoms which improves the quality of life for OUD. This study analyzed the distribution of methadone to Opioid Treatment Programs (OTP) across the US including the District of Columbia and Puerto Rico.MethodsThe weight of methadone (in grams) was gathered from the Drug Enforcement Administration’s Automated Reports and Consolidated Ordering System (ARCOS) database and population data from the US Census Bureau. The number of OTPs per state from the ARCOS Database was obtained. GraphPad Prism Version10.2.3 was used to make figures and perform data analysis. A paired t-test compared distribution in 2019 to 2023. Datawrapper was used to create heat maps.ResultsAnalyzing the population-adjusted percent change by state from 2019 to 2023 showed 32 states had a positive percent change (61.5%), 19 states had a negative one (36.5%), and one state had no change (1.9%). The percent change between 2019 and 2023 (+6.2%) was statistically significant (p=0.047). When looking at the number of OTPs (population-adjusted), there was a twenty-fold state-level difference in 2023.DiscussionAlthough there was a modest increase overall, there were pronounced state-level differences in methadone distribution across the nation. An emphasis on establishing policies to make a positive change widespread over the nation is crucial. New policies are urgently needed to increase the availability of OUD treatments more widely by initiating more OTPs and a more treatment retention focused program to reverse the escalation in overdose deaths.
Effects of Joint Mobilization on Pain, Range of Motion, and Function in Patients with Knee Osteoarthritis: A Systematic Review and Meta-analysis of Randomized Controlled Trials
Authors: Chen Xiaotin , Yu Debiao , Lin Yaoyu , Chen Peng , Shao Bin , Wu Fuchun 
Published: November 2024

AbstractsBackgroundKnee osteoarthritis (KOA) is a common degenerative joint disease that severely affects patients’ quality of life. Joint-mobilization technique reportedly improves joint pain, limited mobility, and dysfunction significantly. This meta-analysis aimed to systematically assess the clinical efficacy of joint-mobilization technique treatment on the level of knee pain, function, and mobility in patients with KOA. We also aimed to provide evidence-based medical data for the clinical management of KOA.MethodsWe searched four English databases (PubMed, Web of Science, Embase, and Cochrane) and three Chinese databases (China Biomedical Literature Database, CNKI, VIP, and Wanfang). The search date was from the date of inception to February 1, 2024 for each database. Randomized controlled trials investigating the efficacy of joint release in KOA were identified. Meta-analysis was performed using RevMan 5.4 and Stata 17.0.ResultsA total of 8 studies involving 432 patients with KOA were included. Our meta-analysis showed that compared with the control group, the experimental group showed a significant improvement in knee pain level (SMD=-1.69, 95% CI [-1.74, -0.82] Z=3.96 P<0.0001), WOMAC scale (SMD=-0.74 95% CI [-1.39, -0.10] Z= 2.25 P=0.02) were significantly improved. However, they were not superior to controls in knee flexion (SMD=2.3 95% CI [0.98, 3.62] Z=3.41 P=0.00006) and extension mobility (SMD=1.79, 95% CI [1.38, 2.20], Z=8.54,P<0.00001).ConclusionJoint-mobilization technique has some advantages in improving the degree of knee pain and dysfunction in patients with KOA, but it is not better than the control group in improving knee mobility. This study provides theoretical support for the promotion of joint-mobilization technique in KOA treatment.
The loss of both pUL16 and pUL21 in HSV-1 infected cells abolishes cytoplasmic envelopment
Authors: Roddy Kellen , Grzesik Peter , Smith Barbara , Ko Nathan , Vashee Sanjay , Desai Prashant J. 
Published: November 2024

AbstractPreviously, we had developed synthetic genomics methods to assemble an infectious clone of herpes simplex virus type-1 (HSV-1). To do this, the genome was assembled from 11 separate cloned fragments in yeast using transformation associated recombination. The eleven fragments or “parts” spanned the 152 kb genome and recombination was achieved because of the overlapping homologous sequences between each fragment. To demonstrate the robustness of this genome assembly method for reverse genetics, we engineered different mutations that were located in distant loci on the genome and built a collection of HSV-1 genomes that contained single and different combination of mutations in 5 conserved HSV-1 genes. The five genes: UL7, UL11, UL16, UL21 and UL51 encode virion structural proteins and have varied functions in the infected cell. Each is dispensable for virus replication in cell culture, however, combinatorial analysis of deletions in the five genes revealed “synthetic-lethality” of some of the genetic mutations. Thus, it was discovered that any virus that carried a UL21 mutation in addition to the other gene was unable to replicate in Vero cells. Replication was restored in a complementing cell line that provided pUL21 in trans. One particular combination (UL16-UL21) was of interest because the proteins encoded by these genes are known to physically interact and are constituents of the tegument structure. Furthermore, their roles in HSV-1 infected cells are unclear. Both are dispensable for HSV-1 replication, however, in HSV-2 their mutation results in nuclear retention of assembled capsids. We thus characterized these viruses that carry the single and double mutant. What we discovered is that in cells where both pUL16 and pUL21 are absent, cytoplasmic capsids were evident but did not mature into enveloped particles. The capsid particles isolated from these cells showed significantly lower levels of incorporation of both VP16 and pUL37 when compared to the wild-type capsids. These data now show that of the tegument proteins, like the essential pUL36, pUL37 and VP16; the complex of pUL16 and pUL21 should be considered as important mediators of cytoplasmic maturation of the particle.
The Microbial Ecology of Serpentinites
Authors: Colman Daniel R. , Templeton Alexis S. , Spear John R. , Boyd Eric S. 
Published: November 2024

ABSTRACTSerpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that are challenging for life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, serpentinite-hosted biospheres offer insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the ability of serpentinites to support abundant microbial communities was only recognized ∼20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of marine and continental serpentinite-hosted biospheres in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo ofin situevolution, and the extent to which modern serpentinites serve as analogs for those on early Earth. These topics are explored herein from a microbial perspective to outline key knowledge-gaps that should be a focus of future research.
Rare and novelRELAvariants are common in systemic autoimmunity
Authors: Downes Morgan B. , Nambadan Sonia B. , Chow Joanne , Davies Ainsley , Hart Gemma , Andrews Thomas D. , Lehmann Nicole , Bales Isabella , Vengatasalam Alamelu , Kitching Arthur Richard , Walters Giles , Athanasopoulos Vicki , Jiang Simon 
Published: November 2024

AbstractObjectivePhenotypic diversity of autoimmune diseases presents an ongoing diagnostic and drug development challenge for clinicians and scientists. Recent discovery of mutations inRELA(encoding RELA) in patients with different diagnoses has highlighted that different pathogenic molecular mechanisms are at play and may explain the observed phenotypic diversity. We identified seven novel/rareRELAvariants in patients with autoimmune diseases and examine the functional consequences on immune signalling.MethodsWild type and mutant RELA proteins were ectopically expressed in HEK293 cells. Western blot and NF-κB/IFNβ luciferase reporter assays were used to determine RELA expression and transcriptional activity, respectively. In patients (n=3), B and T cell populations were examined via flow cytometry and NF-κB and interferon stimulated genes in PBMCs were assessed via qPCR following toll-like receptor activation.ResultsRELAI250V, RELAR295Hand RELAE3*displayed a loss in NF-κB transcriptional activity. Comparative to RELAWT, RELAI250Vprotein expression was reduced. Two variants,RELAI250VandRELAR295H, induced hyperactivation of theIFNβpromoter. An elevated IFN gene signature was not detected in patient PBMCs following toll-like receptor activation, however the patient heterozygous for I250V had elevatedIFNβtranscripts at baseline and after TLR7/8 activation. A reduction in transitional, unswitched memory and memory B cell and cTfh (CCR6-CXCR3-) T cell subsets was shared by the patient group.ConclusionWe expand upon the clinical syndromes linked to RELA dysfunction and uncover rare and novel variants that have distinct functional effects on gene transcription downstream ofNF-κBandIFNβpromoter elements. These findings reinforce an important role for RELA in a range of autoimmune and autoinflammatory diseases.
Oscillatory coupling between thalamus, cerebellum and motor cortex in essential tremor
Authors: Steina Alexandra , Sure Sarah , Butz Markus , Vesper Jan , Schnitzler Alfons , Hirschmann Jan 
Published: November 2024

AbstractBackgroundEssential tremor is hypothesized to emerge from synchronized oscillatory activity within the cerebello-thalamo-cortical circuit. However, this hypothesis has not yet been tested using local field potentials directly recorded from the thalamus alongside signals from both the cortex and cerebellum, leaving a gap in the understanding of essential tremor.ObjectivesTo clarify the importance of cerebello-thalamo-cortical oscillatory coupling for essential tremor.MethodsWe investigated oscillatory coupling between thalamic local field potentials and simultaneously recorded magnetoencephalography in 19 essential tremor patients with externalized deep brain stimulation electrodes. Brain activity was measured while patients repeatedly adopted a tremor-provoking posture and while pouring rice from one cup to another. In a whole-brain analysis of coherence between the ventral intermediate nucleus of the thalamus and cortex, we contrasted epochs containing tremor and epochs lacking tremor.ResultsBoth postural and kinetic tremor were associated with an increase of thalamic power and thalamo-cortex coherence at individual tremor frequency in the bilateral cerebellum and primary sensorimotor cortex contralateral to tremor. These areas also exhibited an increase in corticomuscular coherence in the presence of tremor. The coupling of motor cortex to both thalamus and muscle correlated with tremor amplitude during postural tremor.ConclusionsThese results demonstrate that essential tremor is indeed associated with increased oscillatory coupling at tremor frequency within a cerebello-thalamo-cortical network, with coupling strength directly reflecting tremor severity.
Do the technological anxiety, privacy and physical risks matter in retail customers'‏ ‏adoption of AR‏ ‏apps? An extended UTAUT2 approach
Authors: Elsotouhy Mohamed M. , Khashan Mohamed A. , Thabet Mumen Z. , Galal Hany M. , Ghonim Mohamed A. 
Published: November 2024

PurposeDue to augmented reality (AR) technology improvements, the retail industry has embraced smart retailing as its primary business model. Therefore, organizations must comprehend the intricacies of AR adoption to persuade clients to adopt this revolutionary technology effectively. Thus, the current study proposes and evaluates a comprehensive model that includes unified theory of acceptance and use of technology (UTAUT2), privacy concerns, physical risks and technological anxiety to predict customers’ intention to use AR apps in the retail industry in the Egyptian context.Design/methodology/approachThe current study examines 398 responses from Egyptian shoppers using partial least squares structural equation modeling (PLS-SEM). Snowball sampling was employed in the existing study. The participants were selected using a “self-selection” strategy, which is an excellent method for research investigations in which the participants freely participate.FindingsConsumers’ intentions to use AR apps in retail settings are positively impacted by task-technology fit, performance expectation, effort expectancy, social influence, facilitating conditions and hedonic motivation. Conversely, privacy and physical risks negatively affect customers’ intention to use AR apps in retail. Furthermore, technological anxiety serves as a moderator factor in these connections.Originality/valueTo the best of our knowledge, the current study is considered the first to test the role of UTAUT2, privacy and physical risks on users' behavioral intentions toward adopting AR apps in retail. It also examines technological anxiety as a moderator in the retail setting.
Self-rating scale in self-directed learning in workplace context: a case study of Thai operational employees in the petrochemical plant industry
Authors: Onsawarng Thitiporn , Wongdee Prapassorn , Pinit Pichet 
Published: November 2024

PurposeThis study addresses the need for a validated tool to assess self-directed learning (SDL) behaviors among Thai operational employees in the petrochemical industry. Understanding SDL capabilities is essential for effective human resource development, given the complexity of plant operations and the need for continuous skill enhancement.Design/methodology/approachThis research adapts the self-rating scale of self-directed learning (SRSSDL) to the Thai workplace context. The SRSSDL was translated into Thai and adapted for the workplace. Five experts validated the content, and validity and reliability testing was conducted with 50 operational employees from Thai petrochemical plants. Confirmatory factor analysis (CFA) and Cronbach’s alpha were used to assess the instrument’s reliability and validity.FindingsContent validation confirmed that all SRSSDL items had an item-objective congruence (IOC) score above 0.5. CFA results showed a good model fit (comparative fit index [CFI] = 0.99, Tucker–Lewis index [TLI] = 0.98, root mean square error of approximation [RMSEA] = 0.02 and standardized root mean square residual [SRMR] = 0.02). Reliability analysis showed Cronbach’s alpha values from 0.91 to 0.96, indicating excellent internal consistency.Originality/valueThis research is the first study to assess and prove the content validity, construct validity and reliability of the SRSSDL in the context of Thai workplaces, particularly in the petrochemical industry. The SRSSDL is a reliable and valid tool for assessing SDL behaviors among Thai operational employees. It enhances human resource development by identifying SDL capabilities and fostering continuous improvement and SDL.
How do socioeconomic indicators and fiscal decentralization affect stunting? Evidence from Indonesia
Authors: Hamzah Muhammad Zilal , Sofilda Eleonora , Kusairi Suhal 
Published: November 2024

Purpose
Stunting has emerged as a prominent concern on a global scale. Over the past seven years, the average prevalence has consistently exceeded the World Health Organization standards. This study aims to investigate the roots and model of stunting.

Design/methodology/approach
The samples were collected from 406 regencies (counties) and municipalities across 34 provinces in Indonesia from 2017 to 2022 and used the dynamic panel data analysis.

Findings
The findings showed that the food security index, poverty line, women’s years of schooling, the specific allocation of funds and hopeful family program negatively influenced stunting. Otherwise, village funds and fiscal decentralisation positively affect stunting. The results also confirmed that stunting had a dynamic impact. In addition, the effect of income per capita, the poverty severity index and government funds for education and health on stunting rates were inconclusive.

Practical implications
The policy implication of the study suggests that the government must consider the budgetary concerns of each region and focus on the regions that exhibit different needs.

Originality/value
This paper will contribute to the literature about the modelling of determinants of Stunting in Indonesia.