bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroRNA signature predicts post-operative atrial fibrillation after coronary artery bypass grafting
Authors: Yerukala Sathipati Srinivasulu , Carter Tonia , Soodi Deepa , Somto Nwaedozie , Shukla Sanjay K , Petronovich John , Ingrid Glurich , Braxton John , Sharma Param 
Published: June 2024

AbstractBackgroundEarly detection of atrial fibrillation (AFib) is crucial for altering its natural progression and complication profile. Traditional demographic and lifestyle factors often fail as predictors of AFib, particularly in studies with small samples. This study investigated pre-operative, circulating microRNAs (miRNAs) as potential biomarkers for post-operative AFib (POAF) in patients undergoing coronary artery bypass grafting (CABG).MethodsWe used an array polymerase chain reaction method to detect pre-operative, circulating miRNAs in seven patients who subsequently developed POAF after CABG (cases) and eight patients who did not develop POAF after CABG (controls). The top 10 miRNAs from 84 candidates were selected and assessed for their performance in predicting POAF using machine learning models, including Random Forest, K-Nearest Neighbors (KNN), XGBoost, and Support Vector Machine (SVM).ResultsThe Random Forest and XGBoost models showed superior predictive performance, with test sensitivities of 0.76 and 0.83, respectively. Differential expression analysis revealed four upregulated miRNAs—hsa-miR-96-5p, hsa-miR-184, hsa-miR-17-3p, and hsa-miR-200-3p—that overlapped with the AFib-miRNA signature. The AFib-miRNA signature was significantly associated with various cardiovascular diseases, including acute myocardial infarction, hypertrophic cardiomyopathy, and heart failure. Biological pathway analysis indicated these miRNAs target key signaling pathways involved in cardiovascular pathology, such as the MAPK, PI3K-Akt, and TGF-beta signaling pathways.ConclusionThe identified miRNAs demonstrate significant potential as predictive biomarkers for AFib post-CABG, implicating critical cardiovascular pathways and highlighting their role in AFib development and progression. These findings suggest that miRNA signatures could enhance predictive accuracy for AFib, offering a novel, noninvasive approach to early detection and personalized management of this condition.
Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons
Authors: Vaysset Hugo , Meers Chance , Cury Jean , Bernheim Aude , Sternberg Samuel H. 
Published: June 2024

ABSTRACTTransposase genes are ubiquitous in all domains of life and provide a rich reservoir for the evolution of novel protein functions. Here we report deep evolutionary links between bacterial IS110 transposases, which catalyze RNA-guided DNA recombination using bridge RNAs, and archaeal/eukaryotic Nop5-family proteins, which promote RNA-guided RNA 2’-O-methylation using C/D-box snoRNAs. Based on conservation in the protein primary sequence, domain architecture, and three-dimensional structure, as well as common architectural features of the non-coding RNA components, we propose that programmable RNA modification emerged via exaptation of components derived from IS110-like transposons. Alongside recent studies highlighting the origins of CRISPR-Cas9 and Cas12 in IS605-family transposons, these findings underscore how recurrent domestication events of transposable elements gave rise to complex RNA-guided biological mechanisms.
Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery
Authors: Kumar Anuj , Roth Jennifer , Kim Hyunho , Saura Patricia , Bohn Stefan , Reif-Trauttmansdorff Tristan , Schubert Anja , Kaila Ville R. I. , Schuller Jan M. , Müller Volker 
Published: June 2024

AbstractThe Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD+and pumps sodium ions (Na+) across a membrane, powering ATP synthesis. Rnf is widespread in primordial organisms and the evolutionary predecessor of the Na+-pumping NADH-quinone oxidoreductase (Nqr)1. By running in reverse, Rnf reduces ferredoxin with NADH as reductant at the expense of the transmembrane electrochemical ion gradient and provides low potential electrons for nitrogenases as well as CO2reductases. Yet, the molecular principles that couple the long-range electron transfer to the Na+translocation across the membrane remain elusive. Here we resolve key functional states along the electron transfer pathway using redox-controlled cryo-electron microscopy (cryo-EM) that, in combination with biochemical functional assays and atomistic molecular simulations, provide key insight into the redox-driven Na+pumping mechanism. We show that the reduction of the unique membrane-embedded [2Fe2S] cluster in the vestibule between the RnfA/E subunits electrostatically attracts the sodium ions, and in turn, triggers aninward/outwardtransition with alternating membrane access driving the Na+pump and the reduction of NAD+. Our study unveils an ancient mechanism for redox-driven ion pumping, and provides key understanding of the fundamental principles governing energy conversion in biological systems.
Immune correlates of early clearance ofMycobacterium tuberculosisamong tuberculosis household contacts in Indonesia
Authors: Setiabudiawan Todia P. , Apriani Lika , Verrall Ayesha J. , Utami Fitria , Schneider Marion , Indrati Agnes R. , Halim Pauline P. , Kaplonek Paulina , Malca Hadar , Lee Jessica Shih-Lu , Moorlag Simone J.C.F.M. , de Bree L. Charlotte J. , Mourits Vera P. , Joosten Leo A.B. , Netea Mihai G. , Alisjahbana Bachti , McNamara Ryan P. , Alter Galit , van Laarhoven Arjan , Ussher James E. , Sharples Katrina , Koeken Valerie A. C. M. , Hill Philip C. , van Crevel Reinout 
Published: June 2024

AbstractSome individuals, even when heavily exposed to an infectious tuberculosis patient, do not develop a specific T-cell response as measured by interferon-gamma release assay (IGRA). This could be explained by an IFN-γ-independent adaptive immune response, or an effective innate host response clearingMycobacterium tuberculosis (Mtb)without adaptive immunity. In heavily exposed Indonesian tuberculosis household contacts (n=1347), a persistently IGRA negative status was associated with presence of a BCG scar, and - especially among BCG-vaccinated individuals - with altered innate immune cells dynamics, higher heterologous (Escherichia coli-induced) proinflammatory cytokine production, and higher inflammatory proteins in the IGRA mitogen tube. Neither circulating concentrations ofMtb-specific antibodies nor functional antibody activity associated with IGRA status at baseline or follow-up. In a cohort of adults in a low tuberculosis incidence setting, BCG vaccination induced heterologous innate cytokine production, but only marginally affectedMtb-specific antibody profiles. Our findings suggest that a more efficient host innate immune response, rather than a humoral response, mediates early clearance ofMtb. The protective effect of BCG vaccination againstMtbinfection may be linked to innate immune priming, also termed ‘trained immunity’.
PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways
Authors: Vande Moortele Tibo , Verschaffelt Pieter , Huang Qingyao , T. Doncheva Nadezhda , Holstein Tanja , Jachmann Caroline , Dawyndt Peter , Martens Lennart , Mesuere Bart , Van Den Bossche Tim 
Published: June 2024

AbstractBackgroundMetaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data.ResultsThis manuscript introduces PathwayPilot, a user-friendly web application for exploring and visualizing metabolic pathways. PathwayPilot can compare functional annotations across different samples or organisms within a sample. A case study on the impact of caloric restriction on gut microbiota demonstrated the tool’s efficacy in deciphering complex metaproteomic data. The re-analysis revealed significant shifts in enzyme expressions related to short-chain fatty acid biosynthesis, aligning with existing research findings and showcasing PathwayPilot’s capability for accurate functional annotation and comparison across different microbial communities.ConclusionsPathwayPilot represents a significant advancement in metaproteomic data analysis, offering a user-friendly interface for exploring and visualizing metabolic pathways. This study not only validates the tool’s applicability in real-world scenarios but also highlights its potential for broader research implications in microbial ecology and health sciences.
The silicon transporters (SITs) gene was found inSynechococcussp. XM24
Authors: Han Yabo , Sun Jun 
Published: June 2024

AbstractSilicate serves as a crucial nutrient for diatoms, which are capable of absorbing dissolved silicon from their surroundings through silicon transporters (SITs), thus playing a significant role in the global ocean’s silicon cycle. Recent studies have indicated that marine single-celledSynechococcusalso has the ability to accumulate silicon. Given that the evolution ofSynechococcuspredates that of diatoms, it is postulated thatSynechococcusmay utilize transporters such as SITs found in diatoms, to absorb dissolved silicon in the ocean. This research delves into the silicon accumulation inSynechococcussp. XM24, particularly focusing on two key aspects. Firstly, the study investigates the potential presence of SITs inSynechococcussp. XM24 under the condition of Depleted-Repleted silicate. Subsequently, two gene sequences suspected to encodeSITs, were identified, and their protein sequences and functions were successfully predicted, shedding light on their involvement in membrane transport processes.
Pre- and postnatal maternal depressive symptoms associate with local connectivity of the left amygdala in 5-year-olds
Authors: Vartiainen Elena , Copeland Anni , Pulli Elmo P. , Kumpulainen Venla , Silver Eero , Rajasilta Olli , Jolly Ashmeet , Luotonen Silja , Audah Hilyatushalihah K. , Hashempour Niloofar , Bano Wajiha , Suuronen Ilkka , Saukko Ekaterina , Häkkinen Suvi , Karlsson Hasse , Karlsson Linnea , Tuulari Jetro J. 
Published: June 2024

AbstractBackgroundMaternal depressive symptoms can influence brain development in offspring, prenatally through intrauterine programming, and postnatally through caregiving related mother–child interaction.MethodsThe participants were 5-year-old mother-child dyads from the FinnBrain Birth Cohort Study (N = 68; 28 boys, 40 girls). Maternal depressive symptoms were assessed with the Edinburgh Postnatal Depression Scale (EPDS) at gestational week 24, 3 months, 6 months, and 12 months postnatal. Children’s brain imaging data were acquired with task-free functional magnetic resonance imaging (fMRI) at the age of 5 years in 7 min scans while watching theInscapesmovie. The derived brain metrics included whole brain regional homogeneity (ReHo) and seed-based connectivity maps of the bilateral amygdalae.ResultsWe found that maternal depressive symptoms were positively associated with ReHo values of the left amygdala. The association was highly localised and strongest with the maternal depressive symptoms at three months postnatal. Seed-based connectivity analysis did not reveal associations between distal connectivity of the left amygdala region and maternal depressive symptoms.ConclusionsThese results suggest that maternal depressive symptoms soon after birth may influence offspring’s neurodevelopment in the local functional coherence in the left amygdala. They underline the potential relevance of postnatal maternal distress exposure on neurodevelopment that has received much less attention than prenatal exposures. These results offer a possible thus far understudied pathway of intergenerational effects of perinatal depression that should be further explored in future studies.
Isolation and characterization ofSporomusa carbonissp. nov., a carboxydotrophic hydrogenogen in the genus ofSporomusaisolated from a charcoal burning pile
Authors: Böer Tim , Rosenbaum Florian P. , Eysell Lena , Müller Volker , Daniel Rolf , Poehlein Anja 
Published: June 2024

AbstractA Gram-negative bacterial strain, designated ACPtT, was isolated from the covering top soil of an active charcoal burning pile. Cells of ACPtTwere strictly anaerobic, rod-shaped and grew optimally at 40°C and pH 7. The substrates ribose, glucose, sucrose, raffinose, melezitose, pyruvate, vanillate, syringate, methanol and CO were utilized for growth. Phylogenomic analysis of the 4.1 Mb genome showed that strain ACPt represented a novel species of the genusSporomusa. The most closely related species to ACPtTwasSporomusa malonicawith an average amino acid identity of 80.1%. The genome of ACPtTencoded cytochromes, ubiquinones, the Wood-Ljungdahl gene cluster and an Rnf complex, which were identified as common features allSporomusatype strains. However, strain ACPt did not ferment H2+ CO2via acetogenesis as otherSporomusaspecies, but employed the metabolism of a carboxydotrophic hydrogenogen converting CO to H2+ CO2. Based on the genomic, morphological and physiological features presented in this study, strain ACPtTis proposed as a novel species in the genusSporomusawith the nameSporomusa carbonissp. nov. (DSM 116159Tand CCOS 2105T).
RecombiCraft Library construction: A novel method for DNA Library cloning and expansion using non-enzymatic single-step DNA recombination and liquid culture
Authors: Kawai-Harada Yuki , Mardikoraem Mehrsa , Lauro Katherine , Nimmagadda Vasudha , Tong Quynh , Bello Kayla , Woldring Daniel , Harada Masako 
Published: June 2024

AbstractIn this study, we introduceRecombiCraft, an innovative, rapid, and cost-efficient method for constructing DNA libraries inE. coli. This method uses seamless ligation cloning extract (SLiCE) coupled with liquid culture amplification to effectively minimize sequence biases. The technique capitalizes on the natural homologous recombination capabilities ofE. colicell lysates, eliminating the need for multiple purified enzymes and reducing costs. We first synthesized the library backbone and inserts via PCR, employing high-fidelity polymerase to minimize sequence bias. The SLiCE technique was then used to assemble the DNA fragments introduced intoE. colithrough electroporation. To ensure the integrity of the library, we optimized culture times based on next-generation sequencing analysis which confirmed the minimal sequence bias. The RecombiCraft method demonstrates that this approach is economical and maintains the library’s uniformity. It is a promising tool for genetic research and biotechnological applications with a significantly shorter library generation period.
Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex
Authors: Patel Amun C. , Sinha Souvik , Arantes Pablo R. , Palermo Giulia 
Published: June 2024

AbstractTheVibrio choleraeCascade-TniQ complex unveiled a new paradigm in biology, demonstrating that CRISPR-associated proteins can direct DNA transposition. Despite the tremendous potential of “knocking in” genes at desired sites, the mechanisms underlying DNA binding and transposition remain elusive. In this system, a conformational change of the Cas8 protein is essential for DNA binding, yet how it occurs is unclear. Here, structural modeling and free energy simulations reconstruct the Cas8 helical bundle and reveal an open-to-close conformational transition at key steps of the complex’s function. We show that when Cascade-TniQ binds RNA, the Cas8 bundle changes conformation mediated by the interaction with the Cas7.1 protein. This interaction alleviates unfavorable contacts and synchronizes Cas8’s shift with neighboring subunits, lowering the barrier for the transition to the open state, a critical requirement for DNA binding. As DNA fully pairs with RNA, the open state becomes increasingly accessible, favoring interactions with DNA and aiding the formation of an R-loop. These outcomes provide the first dynamic representation of a critical conformational change in one of the largest CRISPR systems and illustrate its role at critical steps of the Cascade-TniQ biophysical function, advancing our understanding of nucleic acid binding and transposition mechanisms.
Flagellar Motility is Mutagenic
Authors: Bhattacharyya Souvik , Lopez Shelby , Singh Abhyudai , Harshey Rasika M. 
Published: June 2024

AbstractFlagella are highly complex rotary molecular machines that enable bacteria to not only migrate to optimal environments but to also promote range expansion, competitiveness, virulence, and antibiotic survival. Flagellar motility is an energy-demanding process, where the sum of its production (biosynthesis) and operation (rotation) costs has been estimated to total ∼10% of the entire energy budget of anE. colicell. The acquisition of such a costly adaptation process is expected to secure short-term benefits by increasing competitiveness and survival, as well as long-term evolutionary fitness gains. While the role of flagellar motility in bacterial survival has been widely reported, its direct influence on the rate of evolution remains unclear. We show here that both production and operation costs contribute to elevated mutation frequencies. Our findings suggest that flagellar movement may be an important player in tuning the rate of bacterial evolution.
Compositionally unique mitochondria in filopodia support cellular migration
Authors: Marlar-Pavey Madeleine , Tapias-Gomez Daniel , Mettlen Marcel , Friedman Jonathan R. 
Published: June 2024

AbstractLocal metabolic demand within cells varies widely and the extent to which individual mitochondria can be specialized to meet these functional needs is unclear. We examined the subcellular distribution of MICOS, a spatial and functional organizer of mitochondria, and discovered that it dynamically enriches at the tip of a minor population of mitochondria in the cell periphery that we term “METEORs”. METEORs have a unique composition; MICOS enrichment sites are depleted of mtDNA and matrix proteins and contain high levels of the Ca2+uniporter MCU, suggesting a functional specialization. METEORs are also enriched for the myosin MYO19, which promotes their trafficking to a small subset of filopodia. We identify a positive correlation between the length of filopodia and the presence of METEORs and show that elimination of mitochondria from filopodia impairs cellular motility. Our data reveal a novel type of mitochondrial heterogeneity and suggest compositionally specialized mitochondria support cell migration.
Evaluating USDA’s farm balance sheet forecasts
Authors: Díaz Cachay Pedro Antonio , Kuethe Todd 
Published: June 2024

PurposeThe United States Department of Agriculture Farm Balance Sheet forecasts provide important, timely information on the financial assets and debt in the U.S. farm sector. Despite their prominent role in policy and decision making, the forecasts have not been rigorously evaluated. This research examines the degree to which the USDA’s Farm Balance Forecasts are optimal predictors of subsequent official estimates.Design/methodology/approachFollowing prior studies of USDA’s farm income forecasts, archived asset and debt forecasts from 1986 through 2021 are used in regression-based tests of bias and efficiency.FindingsForecasts from 1986–2021 are found to be unbiased but inefficient. The forecasts have a tendency to over-react to new information early in the revision process.Originality/valueThese findings can be helpful for forecast users in adjusting their expectations and for forecasters in adjusting the current forecasting methods.
Effect of external corporate factors on takaful performance
Authors: Sallemi Nourhen , Zouari Ghazi 
Published: June 2024

PurposeThis study examines the impact of external corporate factors (external auditors, insured satisfaction and corporate social responsibility) on the performance (ROA, ROE, ROI) of takaful providers of distinguishable Muamalah contracts (wakalah and Hybrid).Design/methodology/approachThe full sample includes 30 Takaful insurance companies listed in Southeast Asia (SEA) and Gulf Cooperation Council (GCC) countries over the period 2011–2021. We use the FGLS method for data analysis.FindingsOur results reveal that Takaful insurance, which holds one of the Big Four with qualified Shariah members as external auditors, leads to improved performance (ROA, ROE and ROI). In addition, our findings show that Takaful insurance should be concerned with insured satisfaction to determine its success and generate higher performance for both the wakalah and hybrid contracts (ROA, ROE and ROI). Furthermore, Corporate Social Responsibility is considered a source of efficiency that enhances Takaful’s performance for the two types of wakalah and hybrid models (ROA, ROE and ROI).Practical implicationsSome suggestions may be useful for Takaful insurance regulatory authorities to intensify CSR activities, hold one of the Big Four as an external auditor and realize insured satisfaction.Originality/valueThis study highlights that it is beneficial for policymakers, insurers and investors to explore external factors that influence financial performance (return on assets, ROA; return on equity, ROE; return on investment,) in the Takaful insurance market, which uses wakalah and hybrid contracts.
A hybrid tool wear prediction model based on JDA
Authors: Huang Hua , Yu Weiwei , Yao Jiajing , Yang Peidong 
Published: June 2024

PurposeAiming at solving the problems of low prediction accuracy and poor generalization caused by the difference in tool wear data distribution and the fixation of single global model parameters, a hybrid prediction modeling method for tool wear based on joint distribution adaptation (JDA) is proposed.Design/methodology/approachFirstly, JDA is exploited to adapt the data features with different data distributions. Then, the adapted data features are identified by the KNN classifier. Finally, according to the tool state classification results, different regression prediction models are assigned to different wear stages to complete the whole tool wear prediction task.FindingsThe results of milling experiments show that the maximum prediction accuracy of this method is 95.13%, and it has good recognition accuracy and generalization performance. Through the application of the tool wear hybrid prediction modeling method, the prediction accuracy and generalization performance of the model are improved and the tool monitoring is realized.Originality/valueThe research results can provide solutions and a theoretical basis for the application of tool wear monitoring technology in practical industrial applications.