bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast Targeted Metabolomics for Analyzing Metabolic Diversity of Bacterial Indole Derivatives in ME/CFS Gut Microbiome
Authors: Tian Huidi , Wang Lei , Aiken Elizabeth , Ortega Robert Jervine V. , Hardy Rachel , Placek Lindsey , Kozhaya Lina , Unutmaz Derya , Oh Julia , Yao Xudong 
Published: July 2024

ABSTRACTDisruptions in microbial metabolite interactions due to gut microbiome dysbiosis and metabolomic shifts may contribute to Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and other immune-related conditions. The aryl hydrocarbon receptor (AhR), activated upon binding various tryptophan metabolites, modulates host immune responses. This study investigates whether the metabolic diversity—the concentration distribution—of bacterial indole pathway metabolites can differentiate bacterial strains and classify ME/CFS samples. A fast targeted liquid chromatography-parallel reaction monitoring method at a rate of 4 minutes per sample was developed for large-scale analysis. This method revealed significant metabolic differences in indole derivatives amongB. uniformisstrains cultured from human isolates. Principal component analysis identified two major components (PC1, 68.9%; PC2, 18.7%), accounting for 87.6% of the variance and distinguishing two distinctB. uniformisclusters. The metabolic difference between clusters was particularly evident in the relative contributions of indole-3-acrylate and indole-3-aldehyde. We further measured concentration distributions of indole derivatives in ME/CFS by analyzing fecal samples from 10 patients and 10 healthy controls using the fast targeted metabolomics method. An AdaBoost-LOOCV model achieved moderate classification success with a mean LOOCV accuracy of 0.65 (Control: precision of 0.67, recall of 0.60, F1-score of 0.63; ME/CFS: precision of 0.64, recall of 0.7000, F1-score of 0.67). These results suggest that the metabolic diversity of indole derivatives from tryptophan degradation, facilitated by the fast targeted metabolomics and machine learning, is a potential biomarker for differentiating bacterial strains and classifying ME/CFS samples. Mass spectrometry datasets are accessible at the National Metabolomics Data Repository (ST002308, DOI: 10.21228/M8G13Q; ST003344, DOI: 10.21228/M8RJ9N; ST003346, DOI: 10.21228/M8RJ9N).
Templating of Monomeric Alpha-Synuclein Induces Inflammation and SNpc Dopamine Neuron Death in a Genetic Mouse Model of Synucleinopathy
Authors: Byrne Matthew D. , Petramfar Peyman , Smeyne Richard J 
Published: July 2024

AbstractWhile the etiology of most cases of Parkinson’s disease (PD) are idiopathic, it has been estimated that 5-10% of PD arise from known genetic mutations. The first mutations described that leads to the development of an autosomal dominant form of PD are in the SNCA gene that codes for the protein alpha-synuclein (α-syn). α-syn is an abundant presynaptic protein that is natively disordered and whose function is still unclear. In PD, α-syn misfolds into multimeric β-pleated sheets that aggregate in neurons (Lewy Bodies/neurites) and spread throughout the neuraxis in a pattern that aligns with disease progression. Here, using IHC, HPLC, and cytokine analysis, we examined the sequelae of intraparenchymal brain seeding of oligomeric pre-formed fibrils (PFFs) and monomeric α-syn in C57BL/6J (WT) and A53T SNCA mutant mice. We found that injection of PFFs, but not monomeric α-syn, into the striatum of C57BL/6J mice induced spread of aggregated α-syn, loss of SNpc DA neurons and increased neuroinflammation However, in A53T SNCA mice, we found that both PFFs and monomeric α-syn induced this pathology. This suggests that the conformation changes in α-syn seen in the A53T strain can recruit wild-type α-syn to a pathological misfolded conformation which may provide a mechanism for the induction of PD in humans with SNCA duplication/triplication.
The Unkempt RNA binding protein reveals a local translation program in centriole overduplication
Authors: Martinez Abraham , Stemm-Wolf Alexander J. , Sheridan Ryan M. , Taliaferro Matthew J. , Pearson Chad G. 
Published: July 2024

AbstractExcess centrosomes cause defects in mitosis, cell-signaling, and cell migration, and therefore their assembly is tightly regulated. Plk4 controls centriole duplication at the heart of centrosome assembly, and elevation of Plk4 promotes centrosome amplification (CA), a founding event of tumorigenesis. Here, we investigate the transcriptional consequences of elevated Plk4 and find Unkempt, a gene encoding an RNA binding protein with roles in translational regulation, to be one of only two upregulated mRNAs. Unk protein localizes to centrosomes and Cep131-positive centriolar satellites and is required for Plk4-induced centriole overduplication in an RNA-binding dependent manner. Translation is enriched at centrosomes and centriolar satellites with Unk and Cep131 promoting this localized translation. A transient centrosomal downregulation of translation occurs early in Plk4-induced CA. CNOT9, an Unk interactor and component of the translational inhibitory CCR4-NOT complex, localizes to centrosomes at this time. In summary, centriolar satellites and Unk promote local translation as part of a translational program that ensures centriole duplication.
Effects of two different compounds on seizure suppression using the zebrafish PTZ-seizure model
Authors: Araujo Fernández Jhonathan Angel , de Moura Thatiane Cristina , Vila Sabela Fernández , Gaytán Juan Andrés Rubiolo , López-Díaz Iñaki , Learte-Aymamí Soraya , Vázquez M. Eugenio , Mayán Maria D. , Sánchez Laura , Maurer-Morelli Claudia Vianna 
Published: July 2024

AbstractEpilepsies are a common and severe neurological condition characterized by spontaneous and recurrent seizures. Although anti-seizure medications are effective for most patients, about 30% remain pharmacoresistant. Moreover, uncontrolled seizures are associated with risk factors and shortened life expectancy for individuals with refractory epilepsy. Preclinical studies are an essential step for drug discovery and the zebrafish (Danio rerio) has been successfully employed for this purpose. In this study, we applied the zebrafish PTZ-seizure model to investigate the effect of two compounds on seizure suppression, Tripeptide (p-BTX-I) and the Cx43 peptide CX2. Zebrafish larvae at 6 days post-fertilization (dpf) were exposed to both compounds, according to their group, 24h prior to PTZ-seizure induction. We quantified the compounds’ effect on seizure latency, number of seizures and transcript levels of genes related to inflammation, oxidative stress, and apoptosis (il1b, tnfa, cox1, cox2a, il6, casp3a, casp9, baxa, bcl2a, nox1, sod1andcat).Our results showed that CX2 at a concentration of 0.1 μM/mL yielded the best outcome for seizure suppression as it reduced the number of seizures and increased the seizure latency. Additionally, CX2 treatment before PTZ-induced seizures decreased the transcript ofil1b, il6, tnfaandcox1genes, all related to inflammation. A bio-distribution study showed that the CX2 reached the zebrafish brain at both times investigated, 1h and 6h. Similarly, the tripeptide exhibited anti-inflammatory and anti-apoptotic action, reducing mRNA expression of theil1bandcasp9genes. Our findings suggest that both Tripeptide and CX2 hold translational potential for seizure suppression.
Understanding the Pathogenicity of Parkin Catalytic Domain Mutants
Authors: Wagner Julian P. , Sauvé Véronique , Gehring Kalle 
Published: July 2024

AbstractMutations in the E3 ubiquitin ligase parkin cause a familial form of Parkinson’s disease (PD). Parkin and the mitochondrial kinase PINK1 assure quality control of mitochondria through selective autophagy of mitochondria (mitophagy). Whereas numerous parkin mutations have been functionally characterized and their structural basis revealed, several pathogenic PD mutations found in the catalytic RING2 domain remain poorly understood. Here, we characterize two pathogenic RING2 mutants, T415N and P437L and shed light on the underlying structural causes. For this purpose, we use biochemicalin vitroassays in combination with AlphaFold modeling. We demonstrate that both mutants exhibit impaired activity using autoubiquitination and ubiquitin vinyl sulfone assays. After determining the parkin minimal ubiquitin binding region, we show that both mutants display impaired binding to the ubiquitin molecule charged onto the E2 enzyme. Finally, we employ the most recent version of AlphaFold 3 to generate a structural model of the phospho-parkin/phospho-ubiquitin/ubiquitin-charged E2 complex. This model consolidates our findings and provides a structural understanding for the pathogenicity of these two parkin variants. A better understanding of the different PD mutations at the molecular level can pave the way for personalized treatments and the design of small molecule therapeutics for the treatment of PD.
Exploring potential targets for quercetin treatment of colorectal cancer through network pharmacology and molecular docking technology
Authors: Qian Yuanyuan , Wang Zhaojunli , Ji Jiancheng , Fu Wenlong 
Published: July 2024

AbstractObjectiveTo explore the potential targets of quercetin in the treatment of colorectal cancer through network pharmacology and molecular docking technology.MethodDownload the 3D structure of quercetin from Pubchem database, use PharmaMapper database for reverse docking, and screen protein targets based on zscore; GEO database screening for colorectal cancer datasets and screening for differentially expressed genes; Screening common genes for protein targets and differentially expressed genes using Wayne diagrams; Use DAVID database for GO and KEGG analysis. Use ChemDraw, 20.0 AutoDock, and Pymol for molecular docking.ResultThe results showed that 24 common genes and 13 signaling pathways were identified from the reverse docking data of quercetin and the GSE33113 gene chip data of colorectal cancer; Molecular docking results showed that quercetin showed good binding energy with 1ykc, 1k3y, 1kbq, 2bkz, 1xo2, 1og5, 2bsm.ConclusionQuercetin may exert its therapeutic effect on colorectal cancer through a multi target and multi channel mechanism.
A new tuna specimen (GenusAuxis) from the Duho Formation (Miocene) of South Korea
Authors: Suh Dayun , Kim Su-Hwan , Nam Gi-Soo 
Published: July 2024

AbstractA partially preserved caudal vertebrae imprint of a tuna was discovered from the Duho Formation (Miocene) of South Korea. This specimen was assigned to the genusAuxisand represents the second record of fossilAuxisfound in South Korea and in the world. We compared the vertebral morphology of the studied specimen to that of currently known species ofAuxis, including extinct taxa. However, the specimen could not be assigned to any extant or new species ofAuxisdue to anatomical differences and a lack of comparability. The discovery of a new specimen ofAuxisaligns with theories of high marine biodiversity in the East Sea (Sea of Japan) and its opening in the Early to Middle Miocene. A widely opened East Sea and upwelling activities might have increased the abundance and diversity of large oceanic fishes such as tunas during the deposition of the Duho Formation. The specimen supports paleoenvironmental interpretations of the Duho Formation as pelagic and subtropical. A taphonomic scenario of the specimen was inferred based on the lack of anal pterygiophores and the leaf imprint on the matrix. The specimen would have been exposed for at least a month in a low-energy sedimentary environment at the deep-sea bottom and would have undergone disintegration before being buried.
Exploring optimization strategies for support vector machine-based half-cell potential prediction
Authors: Pandey Shikha , Murthy Yogesh Iyer , Gandhi Sumit 
Published: July 2024

Purpose
This study aims to assess support vector machine (SVM) models' predictive ability to estimate half-cell potential (HCP) values from input parameters by using Bayesian optimization, grid search and random search.

Design/methodology/approach
A data set with 1,134 rows and 6 columns is used for principal component analysis (PCA) to minimize dimensionality and preserve 95% of explained variance. HCP is output from temperature, age, relative humidity, X and Y lengths. Root mean square error (RMSE), R-squared, mean squared error (MSE), mean absolute error, prediction speed and training time are used to measure model effectiveness. SHAPLEY analysis is also executed.

Findings
The study reveals variations in predictive performance across different optimization methods, with RMSE values ranging from 18.365 to 30.205 and R-squared values spanning from 0.88 to 0.96. Additionally, differences in training times, prediction speeds and model complexities are observed, highlighting the trade-offs between model accuracy and computational efficiency.

Originality/value
This study contributes to the understanding of SVM model efficacy in HCP prediction, emphasizing the importance of optimization techniques, model complexity and dimensionality reduction methods such as PCA.
Physically consistent temperature fields for geophysical inversion based on the parametrized location of an isotherm
Authors: Fernandez Mariano Tomás , Zlotnik Sergio , Diez Pedro 
Published: July 2024

Purpose
This paper aims to provide a method for obtaining physically sound temperature fields to be used in geophysical inversions in the presence of immersed essential conditions.

Design/methodology/approach
The method produces a thermal field in agreement with a given location of the interface between the Lithosphere and Asthenosphere. It leverages the known location of the interface to enforce the location of a given isotherm while relaxing other constraints known with less precision. The method splits the domain: in the Lithosphere the solution is immediately obtained by standard procedures, while in the Asthenosphere a minimization problem is solved to fulfill continuity of temperatures (strongly imposed) and fluxes at the interface (weakly imposed).

Findings
The numerical methodology, based on the relaxation of the bottom fluxes, correctly recovers the thermal field in the complete domain. To obtain bottom fluxes following geophysical expected values, a constrained minimization strategy is required. The sensitivity of the method could be improved by relaxing other quantities such as lateral fluxes or mantle velocities.

Originality/value
A statement of the energy balance problem in terms of a known immersed condition is presented. A novel numerical procedure based on a domain-splitting strategy allows the solution of the problem. The procedure is tailored to be used within geophysical inversions and provides physically sound solutions.
How to successfully adapt distribution strategy in exporting? The moderating effects of commitment and responsiveness
Authors: Sousa Carlos M.P. , Ruzo-Sanmartín Emilio , Varela-Neira Concepción , Tan Qun 
Published: July 2024

PurposeDrawing on the resource-based view, this study examines the effect of distribution adaptation on export performance. The study also examines the moderating role of responsiveness and commitment. Two distinct factors for commitment (i.e. managerial export commitment and financial export commitment) and two distinct factors for responsiveness (i.e. export customer responsiveness and export competitor responsiveness) are considered as moderators in the relationship between distribution adaptation and export performance.Design/methodology/approachUsing a Spanish governmental database of exporting firms, this study collected data from 208 firms to run the analysis.FindingsThe results indicate that distribution adaptation has a positive impact on export performance. Findings also support the moderating roles of the two types of commitment and the two types of responsiveness. Managerial export commitment positively moderates the relationship, whereas financial export commitment plays a negative moderating role. Both export customer responsiveness and export competitor responsiveness have a positive moderating impact.Originality/valueTo consider distribution adaptation as a distinct variable rather than mixing it with other elements of the marketing mix. This distinction facilitates a clearer comprehension of its unique contribution to export performance. Two distinct factors for commitment and two distinct factors for responsiveness are considered. This approach offers a more detailed analysis of how the different aspects of commitment and responsiveness moderate this relationship.
Digital shadows: analyzing factors influencing sentencing in child sexual abuse material (CSAM) cases
Authors: Choi Kyung-Shick , Chawki Mohamed , Basu Subhajit 
Published: July 2024

Purpose
Exhibiting an unprecedented rate of advancement, technology’s progression over the past two decades has regrettably led to a disturbing increase in the distribution of child sexual abuse materials (CSAM) online. Compounded by the emergence of an underground cryptocurrency market, which serves as a primary distribution channel for these materials, the investigation and sanctioning of CSAM present a complex and unique set of challenges. The purpose of this study is to accurately diagnose the CSAM sentencing landscape and build a more comprehensive, evidence-based legal framework in penology.

Design/methodology/approach
The study collected and analyzed case details regarding CSAM sanctions in a database sourced from the US Department of Justice for 2020. Various factors were analyzed such as the victim’s age, offender typology and previous conviction, accompanied by an analysis of how these factors affect the sentence length.

Findings
The study found that the hierarchical agency-level interactions give insight into resource allocation prioritization, as well as confirming a close relationship between prior conviction history and sentence length, with the victim’s age inversely related to sentence length. Leveraging data-driven insights, the study paves the way for more targeted and effective sanctions, ultimately contributing to the broader goal of safeguarding children from online sexual exploitation.

Originality/value
The paper provides a critical analysis of the complex landscape surrounding CSAM distribution and judicial sentencing. By examining case details and leveraging data-driven insights, it offers valuable contributions to understanding the interplay between various factors such as victim age, offender typology and prior convictions on sentencing outcomes. This comprehensive approach not only sheds light on the dynamics of CSAM sanctions but also lays the groundwork for evidence-based legal frameworks in penology. Its originality lies in its nuanced examination of hierarchical agency interactions and its potential to inform more targeted interventions for safeguarding children from online exploitation.
Examining the ability of big data analytics to investigate financial reporting quality: a comprehensive bibliometric analysis
Authors: Aboelfotoh Ahmed , Zamel Ahmed Mohamed , Abu-Musa Ahmad A. , Frendy  , Sabry Sara H. , Moubarak Hosam 
Published: July 2024

PurposeThis study aims to examine the ability of big data analytics (BDA) to investigate financial reporting quality (FRQ), identify the knowledge base and conceptual structure of this research field and explore BDA techniques used over time.Design/methodology/approachThis study uses a comprehensive bibliometric analysis approach (performance analysis and science mapping) using software packages, including Biblioshiny and VOSviewer. Multiple analyses are conducted, including authors, sources, keywords, co-citations, thematic evolution and trend topic analysis.FindingsThis study reveals that the intellectual structure of using BDA in investigating FRQ encompasses three clusters. These clusters include applying data mining to detect financial reporting fraud (FRF), using machine learning (ML) to examine FRQ and detecting earnings management as a measure of FRQ. Additionally, the results demonstrate that ML and DM algorithms are the most effective techniques for investigating FRQ by providing various prediction and detection models of FRF and EM. Moreover, BDA offers text mining techniques to detect managerial fraud in narrative reports. The findings indicate that artificial intelligence, deep learning and ML are currently trending methods and are expected to continue in the coming years.Originality/valueTo the best of the authors’ knowledge, this study is the first to provide a comprehensive analysis of the current state of the use of BDA in investigating FRQ.
Well! Fun forms and friendship uplift frontline employees' positive affect for workplace well-being in the hospitality industry
Authors: Suneera K.K. , Mavoothu D. , Sajid Muhammed 
Published: July 2024

PurposeThis study aims to reveal the positive effects of workplace fun forms on employee positive affect state and workplace well-being. This study also aims to examine workplace friendship opportunity and workplace friendship prevalence in the context of fun events and workplace well-being.Design/methodology/approachThe research model developed and tested with responses from 1,000 thousand Indian frontline employees of five-star hotels who have worked in the hospitality industry for at least two years and who have been exposed to fun committees at their workplace.FindingsThis study revealed that workplace fun forms are the main causes of employee positive affective reactions, and they have positive effects on frontline employees' positive affect. The study also found that fun activities, customer interaction with fun and manager support for fun as workplace events are strong proximal causes for forming positive affect when they have workplace friendship opportunity. Coworker socialization can induce employee positive affect in the workplace, even without the moderating effect of workplace friendship opportunity. Additionally, the positive effect of positive affect was found to be significant on workplace well-being.Practical implicationsHospitality management is required to foster fun culture with fun activities, coworker socialization, manager support for fun and customer interaction with fun that enhance employee affective reactions to uplift employee positive affect state. This study also presents more interesting practical implications for practitioners and managers.Originality/valueThis study empirically tested deferential workplace fun forms on positive affect, and study provides novel insights into positive affect and workplace well-being. Four mediation mechanisms examined on fun forms and workplace well-being. Four moderating roles of workplace friendship opportunity tested on positive affect and fun events. Workplace friendship prevalence moderation on positive affect and workplace well-being helped to understand employee cognitive mechanism.