bluuebunny/crossref_metadata_2025_split huggingface dataset:
From Data to Insights: A Tool for Comprehensive Quantification of Continuous Glucose Monitoring (QoCGM)
Authors: Cichosz Simon Lebech , Hangaard Stine , Kronborg Thomas , Vestergaard Peter , Jensen Morten Hasselstrøm 
Published: January 2025

AbstractContinuous Glucose Monitoring (CGM) has become a important technology in the management and research of both type 1 and type 2 diabetes, providing real-time data on glucose fluctuations that were previously inaccessible with traditional monitoring methods. Numerous analytical tools, such as cgmquantify, iglu, GLU, rGV, and CGManalyzer, have been developed for platforms like R and Python to calculate standard metrics and extract insights from CGM data. However, these tools often fail to address the full spectrum of analytical requirements. Furthermore, there is a significant lack of updated, open-source tools tailored for MATLAB—a platform widely used by the research community. To address this gap, we introduce Quantification of Continuous Glucose Monitoring (QoCGM), a comprehensive, open-source analytical tool for CGM data specifically designed for MATLAB. A case study involving 324 individuals with insulin-treated type 2 diabetes mellitus (T2DM) demonstrates the utility of QoCGM, highlighting the distinct aspects of glucose dynamics captured by different CGM-derived metrics through an analysis of their coefficients of determination (R²).
Evaluation of Candidate “Kill or Cure” Strategies to Treat MFN2-related Lipodystrophy
Authors: Luijten Ineke , Weng Xiong , Kibildyte Ula , Buchan Jana , Onishi Ami , Mann Jake , McKay Eleanor , Savage David , Semple Robert K. 
Published: January 2025

AbstractThe R707W mutation in mitofusin 2, encoded by MFN2, causes a form of Multiple Symmetrical Lipomatosis (MFN2-MSL). This resembles sporadic, alcohol-associated MSL, combining loss of lower body adipose tissue with upper body adipose hyperplasia. Morbidity and sometimes mortality arise both from mechanical complications of head and neck adipose overgrowth, and metabolic complications. We reasoned that interventions that either mitigate the underlying cellular pathology, or that exacerbate it to induce selective death of hyperplastic adipose tissue may be beneficial. We thus assessed the effect of a metabolic or pharmacologic stressors or rapamycin inMfn2R707W/R707Wmice and or derived preadipocytes. 50mmol ethanol had little effect on WT orMfn2R707W/R707Wwhite preadipocytes, but increased mitochondrial content and blunted mitolysosome formation inMfn2R707W/R707Wbrown preadipocytes.Daily consumption of 20% EtOH increased brown adipose tissue mass in femaleMfn2R707W/R707Wmice, and serum lactate in males. 200nM rapamycin – a candidate treatment - increased size and mitolysosome content of WT andMfn2R707W/R707Wwhite and brown preadipocytes, but these effects were blunted inMfn2R707W/R707Wcells. In male but not femaleMfn2R707W/R707Wmice, rapamycin reduced or reversed weight gain, reduced brown adipose mass, and increased serum Fgf21. Finally, a panel of other metabolic and pharmacological mitochondrial stressors solicited no selective death or ISR inMfn2R707W/R707Wpreadipocytes. We conclude that ethanol mildly exacerbates MFN-MSL in mice, while rapamycin is tolerated. Lack of sensitisation to mitochondrial stressors implies that the MSL-inducing effect of MFN2 R707W may not be exerted through compromised oxidative phosphorylation.
Hepatic fructose metabolism is antagonized by growth hormone/insulin-like growth factor signaling via regulation of ketohexokinase expression
Authors: Elsaid Salaheldeen , Meesala Prathibha , Choi Youngshim , Yu Liqing , Xiao Yang , Lazar Mitchell A. , Perez-Matute Patrica , List Edward O. , Faccioli Lanuza AP , Sun Yiyue , Florentino Rodrigo M , Pichel Jose G. , Berryman Darlene E. , Mayer Dirk , Kopchick John J. , Tee Sui Seng 
Published: January 2025

AbstractOverconsumption of added sugars such as fructose has been associated with a remarkable decline in metabolic health. Fructose is primarily metabolized by the small intestines and the liver, via phosphorylation mediated by ketohexokinase (KHK). KHK activity is traditionally viewed as lacking negative feedback mechanisms, such as those present to limit glucose metabolism, leading to excessive fat accumulation characteristic of metabolic dysfunction-associated liver disease (MASLD). In this study, we observe KHK downregulation in hepatocytes of diet-induced and genetic models of MASLD. Reduced KHK coincides with decreased flux of fructose-derived carbons into glycolytic and amino acid metabolic pathways, suggesting the presence of mechanisms that limit KHK-mediated fructolysis in the liver. We subsequently focused on the growth hormone (GH)/insulin-like growth factor (IGF) signaling pathway as a potential mechanism antagonizing KHK expression. In transgenic mice with enhanced GH signaling, KHK levels are reduced, whereas reduced GH activity leads to increased KHK expression. Additionally, administration of GH and IGF-1 in liver cell cultures induces time-dependent degradation of KHK, facilitated by direct interactions between KHK and the IGF-1 receptor (IGF-1R). Single-nuclei RNA sequencing revealed elevated IGF-1R expression in hepatocytes from diet-induced MASLD mice, supported by human MASLD patient samples, which also show reduced KHK expression. Taken together, these findings describe a novel pathway by which GH/IGF-1 signaling regulates KHK, offering new insights into how the liver adapts to metabolic stress to limit fructose-driven liver dysfunction.
G-Quadruplex-Protein Interactome at Human Gene Promoters
Authors: Duan Rui-fang , Zheng Jin-ping , Hao Yu-hua , Tan Zheng 
Published: January 2025

AbstractDNA-protein interactions at gene promoters play a critical role in gene expression. The promoters of human cells are highly enriched in guanine-rich sequences, which can form four-stranded G-quadruplex (G4) structures. G4s are emerging as a distinct class of structure-based regulatory elements in gene regulation, and their interaction with proteins is essential for the role G4s play. Currently, our understanding of G4-protein interaction is mainly on a case-by-case basis, without systematic information. In this work, we examined the spatial occupancy of 1,183 human DNA-binding proteins, including transcription factors, histones and their modifying enzymes, around the consensus G4-forming region, G4(+), using data from the ENCODE project. We found that the G4(+), its immediate proximal side, and its distal side serve as three primary protein binding sites. Nearly all proteins are either enriched or depleted at these sites, likely due to competition, or in a spatiotemporal transition between the sites, resulting in different degrees of variation or persistence within or across cell/tissue types. Notably, histones were excluded from the proximal side of G4(+), and their binding to G4(+) was turned on and off by acetylation and methylation, respectively. Furthermore, the distal side is preferentially enriched for H3K23me2 and H3K4me2. Our experiments also revealed corresponding patterns of G4-protein interaction. Taken together, our results suggest a general role for G4s in dynamically defining and coordinating chromatin architecture and DNA-protein interactions at gene promoters for transcriptional regulation, a task that is unlikely to be accomplished by sequence-based DNA recognition.Abstract FigureGraphical abstract:A protein can be either enriched or suppressed at G-quadruplexes (G4s), at the proximal side of G4s, or enriched at the distal side of G4s in a 2 kb neighborhood. Regulatory roles of proteins may result from spatial transitions between the different binding regions.
A tool to dissect heterotypic determinants of homotypic protein phase behavior
Authors: Kimbrough Hannah , Jensen Jacob , Weber Caleb , Miller Tayla , Maddera Lucinda E. , Babu Vignesh , Redwine William B. , Halfmann Randal 
Published: January 2025

AbstractProteins commonly self-assemble to create liquid or solid condensates with diverse biological activities. The mechanisms of assembly are determined by each protein’s sequence and cellular context. We previously developed distributed amphifluoric FRET (DAmFRET) to analyze sequence determinants of self-assembly in cells. Here, we extend DAmFRET by creating a nanobody (mEosNb) against the fluorescent protein mEos3 to physically tether and thereby recruit candidate modifier proteins to mEos3-fused query proteins. This accessorization allows us to rapidly screen for effects on the phase behavior of query proteins by modulating the expression level and valency of mEosNb-fused modifiers. We show that our system recapitulates known effects of multivalency on liquid-liquid phase separation and can discriminate between nucleation mechanisms of amyloid and amyloid-like assemblies. Our approach adds a new experimental dimension for interrogating the mechanisms of intracellular phase transitions.Lay summaryProtein self-assemblies are essential for cellular function, but can also contribute to disease. We develop a new tool to study how their formation is influenced by other cellular factors. This tool allows us to control the location and number of interactions between a protein of interest and other proteins that may influence it. Our results provide new insight into mechanisms of self-assembly and will aid research toward treating diseases associated with aberrant assembly.
Discrimination betweenMycobacterium tuberculosisandMycobacterium bovisusing Fourier Transform Infrared Spectroscopy
Authors: Guterres Kevim B. , Silva-Pereira Taiana Tainá , Oliveira Rodrigo , Moonen Carolyn G.J. , Heinemann Marcos Bryan , Araújo Flábio , Palaci Moisés , de Souza Gisele Oliveira , Guimarães Nathália Silveira , Guimarães Ana Marcia Sá 
Published: January 2025

ABSTRACTZoonotic tuberculosis (TB) caused byMycobacterium bovis(Mb) is a neglected disease that hinders efforts to eradicate human tuberculosis. Developing a rapid, high-throughput diagnostic test to distinguish Mb fromMycobacterium tuberculosis(Mtb) isolates could enhance global zoonotic TB diagnostics and surveillance. This study aimed to evaluate the ability of Fourier Transform Infrared Spectroscopy (FT-IRS), using the IR Biotyper® system, to differentiate clinical isolates of Mb and Mtb. Two bacterial inactivation protocols— paraformaldehyde and boiling—were tested using Mtb and BCG strains grown in liquid culture. While both methods allowed FT-IRS analysis, boiling was preferred due to its ease of use and efficiency in biomass recovery. Subsequently, Mtb and Mb isolates were analyzed using FT-IRS, and the resulting spectra were used to construct a sample classifier employing machine learning algorithms. Linear Discriminant Analysis (LDA) and a UPGMA dendrogram demonstrated clear separations between Mtb and Mb ecotypes. Additionally, a classifier built and internally validated using artificial neural networks achieved 99% accuracy in distinguishing Mb and Mtb. Further FT-IRS analysis of few availableMycobacterium africanum(Maf) strains demonstrated its capacity to differentiate Maf from Mtb and Mb, expanding its utility in regions where Maf is endemic. This is the first study to apply FT-IRS to distinguish tuberculous mycobacteria. FT-IRS proved to be a highly effective, rapid, and accurate diagnostic tool for differentiating Mb and Mtb strains, with promising applications for other tuberculous mycobacteria such as Maf.IMPORTANCEZoonotic tuberculosis (TB) caused byMycobacterium bovis(Mb) remains a major threat due to its clinical similarity to human TB, higher rates of extrapulmonary cases, and resistance to pyrazinamide, complicating treatment. Current diagnostic methods used to differentiateM. tuberculosis(Mtb) from Mb and are limited by costs, resource needs, and technical complexity. We developed a method based on Fourier Transform Infrared Spectroscopy (FT-IRS) to differentiate Mb and Mtb clinical isolates with high accuracy. This diagnostic assay offers advantages over traditional molecular techniques by eliminating the need for DNA extraction, requiring less technical expertise, and providing fast, accurate differentiation of Mtb and Mb strains. This innovative approach can improve global diagnostics and surveillance of zoonotic TB.
Surveying the Literature on Implementation Determinants and Strategies for HIV Structural Interventions: A Systematic Review Protocol
Authors: zamantakis alithia , Chandra Shruti , Donoso Valeria A. , Paton R. Mariajose , Powers Alec , Mustanski Brian , Benbow Nanette 
Published: January 2025

AbstractBackgroundDespite improvements in HIV prevention, treatment, and surveillance, vast disparities remain in access, uptake, and adherence of evidence-based interventions. These disparities are most pronounced among racially, sexually, and gender minoritized populations, as well as among those living in poverty and/or who use injectable drugs. Structural interventions, or interventions that target social and structural determinants of health like housing, transportation, or income, are needed to increase access to, use of, and adherence to HIV EBIs to advance the aims of the national Ending the HIV Epidemic initiative. However, it is unclear to what extent barriers and facilitators of structural interventions have been identified in the U.S. and what implementation strategies and adjunctive interventions have been developed to enhance their delivery.MethodsTo identify what implementation determinants, implementation strategies, and adjunctive interventions have been identified for HIV structural interventions, we carried out a broad database search between May and July 2024, identifying a total of 8,098 articles. We will use a multi-step process to identify articles to include in the systematic review. We will use natural language processing to identify articles for exclusion, followed by manual text review and extraction using COVIDENCE software. Literature on determinants will be coded according to the Consolidated Framework for Implementation Research. Implementation strategies and adjunctive interventions will be coded according to the Expert Recommendations for Implementing Change, the Theoretical Domains Framework, and COM-B. We will descriptively analyze determinants, implementation strategies, and adjunctive interventions, use natural language processing for thematic analysis of determinants, implementation strategies, and adjunctive interventions, and provide narrative description of implementation strategies and adjunctive interventions.DiscussionThis systematic review will identify key barriers and facilitators for HIV structural intervention implementation strategies, including multi-level approaches to address disparities among marginalized populations. Findings will provide insights for advancing equitable, scalable interventions to support the goals of the Ending the HIV Epidemic initiative.Systematic review registrationCRD42024554315
Novel Endogenous Retrovirus in the Slow Loris
Authors: Michie Charles , Free Hayley Beth , Nijman Vincent , Kanda Ravinder 
Published: January 2025

AbstractEndogenous retroviruses (ERVs) are the result of an exogenous infectious retrovirus becoming integrated within the host genome through infection of germline cells. The majority of ERV research has been conducted on humans and other great apes and research of them within other primates can provide unique insights. Screening the genome of two endangered slow lorisesNycticebus bengalensisandN. coucangwith a previously identified LTR, a novel ERV was identified within their genomes with varying levels of completeness and numerous solo LTRs. Phylogenetic analysis of the genes of this ERV indicates that it is a betaretrovirus most closely related to HERV-K. Despite being closely related to HERV-K, the ERV does not appear to be within humans and is only found in Asian lorises and absent in all other primates. Due to the staggering similarity of viral insertions of this ERV between the two species of slow lorises, indicates that the currentN. coucanggenome may actually be a hybrid of the two species or aN. bengalensisfrom a different population as the reference genome. This study highlights that studying ERVs in more distant primates provides information about the genomes and evolution of these species as well as viral evolution.
Kif11-haploinsufficient oocytes reveal spatially differential requirements for chromosome biorientation in the spindle
Authors: Mishina Tappei , Courtois Aurélien , Kiyonari Hiroshi , Kitajima Tomoya S. 
Published: January 2025

SummaryBipolar spindle assembly and chromosome biorientation are prerequisites for chromosome segregation during cell division. The kinesin motor KIF11 drives spindle bipolarization by sliding antiparallel microtubules bidirectionally, elongating a spherical spindle into a bipolar-shaped structure in oocytes. This process stretches chromosomes, establishing chromosome biorientation at the spindle equator. The quantitative requirement for KIF11 in spindle bipolarization and chromosome biorientation remains unclear. Here, using a genetic strategy to modulate KIF11 expression levels, we show thatKif11haploinsufficiency impairs spindle elongation, leading to the formation of a partially bipolarized spindle during meiosis I in mouse oocytes. While the partially bipolarized spindle allows chromosome stretching in the inner region of its equator, it fails to do so in the outer region. These findings demonstrate the necessity of biallelic functionalKif11for bipolar spindle assembly in oocytes and reveal a spatially differential requirement for chromosome biorientation within the spindle.
TheUstilago maydistranscription factor Nit2 regulates nitrate utilization during biotrophy and influences organic nitrogen metabolism in infected maize leaves under nitrogen limitation
Authors: Lopinski Philipp L. , Schulz Christin , Fischer Alicia , Reichl Nadine , Engelsdorf Timo , Braun Nadja , Voll Lars M. 
Published: January 2025

SummaryLittle is known on how filamentous phytopathogens adapt to nitrogen limitation in the host plant. In previous work, we have shown that the transcription factor Nit2 plays a major role for the utilization of non-favored nitrogen sources like nitrate, minor amino acids or nucleobases in saprotrophic sporidia of the basidiomycete corn smut fungusUstilago maydis.Here, we employedΔnit2mutants in the natural FB1 x FB2 background to identify Nit2 regulated genes during biotrophy and investigated the impact of Nit2 on the physiology of leaf galls in nitrogen replete versus nitrogen limited host plants. RNA-Seq analysis of galls caused by theU. maydis Δnit2mutant and by theU. maydiswild type, revealed that about one third of the genes affected by Nit2 deletion during fungal biotrophy are involved in nitrogen metabolism and transport. Induction of the nitrate assimilation cluster was completely dependent on Nit2 and under nitrogen limitation,Δnit2leaf galls accumulated nitrate and showed reduced accumulation of the nitrogen-rich phloem transport amino acids asparagine and glutamine compared to wild type galls. In nitrogen replete conditions, only asparagine content was reduced inΔnit2leaf galls compared to wild type galls. Since total protein content in galls and pathogenicity were comparable between fungal genotypes in both nitrogen regimes, our findings demonstrate that nitrate utilization is dispensable forUstilago maydisduring biotrophy and can likely be compensated by increased utilization of abundant organic nitrogen sources, like asparagine, GABA and glutamine, which occurs in a partially Nit2-dependent fashion.
Structure of high-performance work system and new product entry strategy: configuration based on manufacturing enterprises in China
Authors: Cheng Dejun , Huang Jie , Wang Xiaoyu , Zhao Shuming 
Published: January 2025

Purpose
There is a clear correspondence between different types of high performance work systems (HPWS), economic rents and market entry strategies. This correspondence is manifested through the strategic vertical fit and internal synergetic horizontal fit within HPWS, leading to a “core-periphery” structure in human resource management practice configurations. This study aims to depict the “core-periphery” structure within specific HPWSs by identifying human resource (HR) practice configurations and by analyzing the matching mechanisms and structural characteristics among different HR practices based on the interaction between vertical and horizontal fits.

Design/methodology/approach
This study uses a sample of 277 enterprises in East China and employs the ability-motivation-opportunity (AMO) framework and fuzzy-set qualitative comparative analysis (fsQCA) to identify and depict the “core-periphery” structure within HPWS. By integrating fsQCA with t-test, the study explores the interaction between vertical and horizontal fits within HPWS based on economic rent formation mechanisms.

Findings
Seven specific HR practice configurations, shown to effectively enhance organizational performance, have been identified and systematically classified into three typologies of HPWS, based on their distinct underlying mechanisms of horizontal and vertical fit.

Research limitations/implications
The data used in this study were sourced from manufacturing enterprises. Future research can enhance generalizability by expanding the dataset and examining whether efficient HPWS exist across different industries.

Practical implications
The findings of this study emphasize the crucial roles of interaction and complementarity among HR practices within HPWS. By extracting and synthesizing HR practice configurations from empirical data, this study provides practical insights for constructing effective HPWS in real-world settings.

Originality/value
First, this study incorporates both vertical and horizontal fits of HPWS into a unified analytical framework, emphasizing their interactive mechanisms and providing a more nuanced understanding of how these fits operate together. This contributes to the existing literature by validating and expanding the understanding of how specific HR practice configurations align with corporate strategies. Second, by adopting a configurational perspective, this study is able to conduct an in-depth exploration of the “core-periphery” structure within HPWS, thereby challenging the widely held assumption within the AMO framework that all HR practices carry equal significance within a specific HPWS. Third, the empirical analyses identify three specific types of HPWS that can be applicable to different new product strategies from a dynamic perspective, providing practical references for companies to select appropriate HPWS types based on their characteristics.