bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Serodiagnosis ofTrypanosoma vivaxInfections in Cattle Reveals Higher Infection Rates in the Livestock Regions of Argentina
Authors: Bontempi Iván , Arias Diego G. , Castro Graciela V. , Peverengo Luz , Díaz Genaro , Allassia Martín , Greif Gonzalo , Marcipar Iván 
Published: February 2024

AbstractBovine trypanosomiasis, caused by Trypanosoma vivax, currently affects cattle, resulting in significant economic consequences in sub-Saharan Africa and South America. The development of new diagnostic antigens is crucial for improving and refining existing methods. Our study assessed the effectiveness of two recombinant antigens in detecting specific antibodies in cattle. These antigens are derivatives of an invariant surface glycoprotein (ISG) from T. vivax. We evaluated a fraction of an antigen previously described (TvY486_0045500), referred to as TvISGAf, from an African strain, and identified a new ISG antigen from an American isolate, TvISGAm. ELISA evaluation using these antigens was conducted on 212 samples from cattle. The diagnostic performance was enhanced when utilizing a combination of both antigens (denominated TvISG-based ELISA), achieving a sensitivity of 89.6% and specificity of 93.8%. Following validation of the TvISG-based ELISA, we determined the seroprevalence of T. vivax infection in 892 field samples from cattle in the central region of Argentina. The average seroprevalence of T. vivax was 53%, with variation across the six surveyed departments ranging from 21% to 69%. These results support the use of the TvISG ELISA as a valuable serological tool for detecting and monitoring T. vivax infection in cattle. They also reported for the first time T. vivax seroprevalence in Argentina, highlighting the widespread endemic nature of the disease in the region. To effectively manage the increasing spread of T. vivax in the vast livestock production areas of South America, we support the need for consistent surveillance programs and implementation of preventive strategies.
Differential cell type-specific function of the aryl hydrocarbon receptor and its repressor in diet-induced obesity and fibrosis
Authors: Graelmann Frederike J. , Gondorf Fabian , Majlesain Yasmin , Niemann Birte , Klepac Katarina , Gottschalk Marlene , Mayer Michelle , Iriady Irina , Hatzfeld Philip , Lindenberg Sophie K. , Wunderling Klaus , Thiele Christoph , Abdullah Zeinab , He Wei , Hiller Karsten , Händler Kristian , Beyer Marc D. , Ulas Thomas , Pfeifer Alexander , Esser Charlotte , Weighardt Heike , Förster Irmgard , Reverte-Salisa Laia 
Published: February 2024

AbstractThe aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor regulating xenobiotic responses as well as physiological metabolism. Dietary AhR ligands activate the AhR signaling axis in the intestine and throughout the organism, whereas AhR activation is negatively regulated by the AhR repressor (AhRR). While AhR-deficient mice are known to be resistant to diet-induced obesity (DIO), we here demonstrate that AhRR deficiency also leads to a robust, but not as profound protection from DIO and hepatosteatosis. Under conditions of DIO, AhRR-/-mice did not accumulate TCA cycle intermediates in the circulation in contrast to wild-type (WT) mice, indicating protection from metabolic dysfunction. This effect could be mimicked by dietary supplementation of AhR ligands in WT mice. Because of the predominant expression of the AhRR in myeloid cells, AhRR-deficient macrophages were analyzed for changes in metabolism and showed major metabolic alterations regarding oxidative phosphorylation and mitochondrial activity as well as increased expression of genes involved inde novolipogenesis and mitochondrial biogenesis. Mice with a genetic deficiency of the AhRR in myeloid cells did not show alterations in weight gain after high fat diet (HFD) but demonstrated ameliorated liver damage compared to control mice. Further, deficiency of the AhR in myeloid cells also did not affect weight gain but led to enhanced liver damage and adipose tissue fibrosis compared to controls. Although conditional ablation of either the AhR or AhRR in myeloid cells did not recapitulate the phenotype of the global knockout, our findings suggest that enhanced AhR signaling in myeloid cells deficient for AhRR protects from diet-induced liver damage and fibrosis, whereas myeloid cell-specific AhR deficiency is detrimental.
Evolution and inhibition of the FIKK effector kinase family inP. falciparum
Authors: Belda Hugo , Bradley David , Christodoulou Evangelos , Nofal Stephanie D. , Broncel Malgorzata , Jones David , Davies Heledd , Bertran M. Teresa , Purkiss Andrew G. , Ogrodowicz Roksana W. , Joshi Dhira , O’Reilly Nicola , Walport Louise , Claessens Antoine , Powell Andrew , House David , Kjaer Svend , Landry Christian R. , Treeck Moritz 
Published: February 2024

AbstractAmong the ∼200Plasmodiumspecies that infect vertebrates, six infect humans. Of these,P. falciparumcauses >95% of all ∼500,000 annual fatalities. Phylogenetically,P. falciparumbelongs to theLaveraniasubgenus, a group ofPlasmodiumspecies that infect great apes. Common toLaveraniaspecies is the family of FIKK kinases. One million years ago, a single FIKK kinase conserved in allPlasmodiumspecies gained an export element in theLaveraniasubgenus and expanded into the family of ∼20 atypical FIKK kinases, most of which are exported into the host cell. Thefikkgenes are conserved in syntenic loci across theLaverania, arguing for a rapid expansion controlling important functions in host cell remodelling and pathogenesis. We provide evidence that the FIKK paralogues evolved specific and mutually exclusive phosphorylation motif preferences, conserved across theirLaveraniaorthologues, in a short evolutionary timeframe. Surprisingly, we find that FIKK13 has evolved exclusive tyrosine-phosphorylation preference, which was thought to be absent inPlasmodiumspecies. Combining a crystal structure with AlphaFold2 predictions, we identify residues that determine kinase-specificity within the FIKK family in a fast-evolving flexible loop. Finally, we show that all expressed members of the FIKK kinase family can be chemically inhibitedin vitrousing a single compound. Such a pan-specific inhibitor of this kinase family important for virulence could reduce the ability of the parasite to gain escape-mutations and resistance.
Molecular, Cellular, and Developmental Organization of the Mouse Vomeronasal organ at Single Cell Resolution
Authors: Hills Max , Ma Limei , Fang Ai , Chiremba Thelma , Malloy Seth , Scott Allison , Perera Anoja , Yu C. Ron 
Published: February 2024

SUMMARYWe have generated single cell transcriptomic atlases of vomeronasal organs (VNO) from juvenile and adult mice. Combined with spatial molecular imaging, we uncover a distinct, previously unidentified class of cells that express the vomeronasal receptors and a population of canonical olfactory sensory neurons in the VNO. High resolution trajectory and cluster analyses reveal the lineage relationship, spatial distribution of cell types, and a putative cascade of molecular events that specify the V1r, V2r, and OR lineages from a common stem cell population. The expression of vomeronasal and olfactory receptors follow power law distributions, but there is high variability in average expression levels between individual receptor and cell types. Substantial co-expression is found between receptors across clades, from different classes, and between olfactory and vomeronasal receptors, with nearly half from pairs located on the same chromosome. Interestingly, the expression of V2r, but not V1r, genes is associated with various transcription factors, suggesting distinct mechanisms of receptor choice associated with the two cell types. We identify association between transcription factors, surface axon guidance molecules, and individual VRs, thereby uncovering a molecular code that guides the specification of the vomeronasal circuitry. Our study provides a wealth of data on the development and organization of the accessory olfactory system at both cellular and molecular levels to enable a deeper understanding of vomeronasal system function.
The Origins of ATP Dependence in Biological Nitrogen Fixation
Authors: Harris Derek F. , Rucker Holly R. , Garcia Amanda K. , Yang Zhi-Yong , Chang Scott D. , Feinsilber Hannah , Kaçar Betül , Seefeldt Lance C. 
Published: February 2024

AbstractLife depends on a conserved set of chemical energy currencies that are relics of early biochemistry. One of these is ATP, a molecule that, when paired with a divalent metal ion such as Mg2+, can be hydrolyzed to support numerous cellular and molecular processes. Despite its centrality to extant biochemistry, it is unclear whether ATP supported the function of ancient enzymes. We investigate the evolutionary necessity of ATP by experimentally reconstructing an ancestral variant of the key N2-reducing enzyme nitrogenase. We show that the ancestor has a strict requirement for ATP and its hydrolysis is coupled to electron transfer for N2reduction. Our results provide direct laboratory evidence of ATP usage by an ancient enzyme, and underscore how biomolecular constraints can entirely decouple cofactor selection from environmental availability.
Genome-wide analysis of TFIIB’s role in termination of transcription
Authors: O’Brien Michael J. , Schrader Jared , Ansari Athar 
Published: February 2024

AbstractApart from its well-established role in initiation of transcription, the general transcription factor TFIIB has been implicated in the termination step as well. The ubiquity of TFIIB involvement in termination as well as mechanistic details of its termination function, however, remains largely unexplored. To determine the prevalence of TFIIB’s role in termination, we performed GRO-seq analyses insua7-1mutant (TFIIBsua7-1) and the isogenic wild type (TFIIBWT) strains of yeast. Almost a three-fold increase in readthrough of the poly(A)-termination signal was observed in TFIIBsua7-1mutant compared to the TFIIBWTcells. Of all genes analyzed in this study, nearly 74% genes exhibited a statistically significant increase in terminator readthrough in the mutant. To gain an understanding of the mechanistic basis of TFIIB involvement in termination, we performed mass spectrometry of TFIIB, affinity purified from chromatin and soluble cellular fractions, from TFIIBsua7-1and TFIIBWTcells. TFIIB purified from the chromatin fraction of TFIIBWTcells exhibited significant enrichment of CF1A and Rat1 termination complexes. There was, however, a drastic decrease in TFIIB interaction with both CF1A and Rat1 termination complexes in TFIIBsua7-1mutant. ChIP assay revealed that the recruitment of Pta1 subunit of CPF complex, Rna15 subunit of CF1 complex and Rat1 subunit of Rat1 complex registered nearly 90% decline in the mutant over wild type cells. The overall conclusion of these results is that TFIIB affects termination of transcription on a genome-wide scale, and TFIIB-termination factor interaction may play a crucial role in the process.
Modularity in the evolution of visual signals associated with aggressive displays
Authors: Fialko Kristina , Price Trevor D. 
Published: February 2024

ABSTRACTInteractions between conspecifics commonly involve the use of stereotyped display movements, which can vary markedly between species. Theoretically, sexual selection by female choice can lead to large differences between species, but sexual selection by male competition may result in more limited diversification. Here, we evaluate display evolution in the aggressive signals of 10 leaf warbler species. Using high-speed videography of territorial behavior, we quantify differences in wing motion intensity and form. We find that both the rate of wing motion and the form of the display remain similar across species, which we attribute to an effective signal maintained through multiple speciation events. Differences among species arise though discrete additions to the behavioral repertoire (three species), loss of display (one species) and the presence of a pale patch on the wing. While some habitats differ discretely and dramatically in light intensity, this cannot account for all the differences in display behavior. We conclude that display evolution proceeds largely in a modular fashion. The basic conventional signal is maintained across species, enabling modifications to appear without loss of efficacy.
Stability of the Wheat Seed Mycobiome Across North Carolina’s Longitudinal Gradient
Authors: Becker Lindsey E. , Hawkes Christine V. , Heiniger Ryan , Cubeta Marc A. 
Published: February 2024

ABSTRACTImproving wheat yield and performance involves selecting varieties that are well adapted for a regional area. Although host genotype and environment are major factors that impact crop performance and resilience, less is known about the relative contribution and occurrence of wheat seed endophytic fungal communities across spatial and temporal scales. An increased understanding of composition and assembly of beneficial endophytic fungal communities across regional scales provides valuable insight into the stability of the endophytic seed mycobiome. Our aim in this study was to examine the relative contribution and impact of latitude and longitude gradients within North Carolina (NC) on wheat seed fungal community structure of two regionally adapted soft red winter wheat cultivars, Hilliard and USG 3640. We examined the endophytic wheat seed microbiome of the two winter wheat cultivars planted in official variety trials at five geographic locations across NC in 2021 and two geographic locations in 2022. ITS1 sequence-based analysis of surface disinfested wheat seeds was conducted to determine alpha and beta diversity. Species richness is influenced by geographical location, however wheat seed mycobiome community structure is stable across cultivars and years. Latitude and longitude contributed to the observed variation in wheat seed mycobiome structure, in addition to yield, seed moisture, and leaf nutrients. When surveying taxa present within all cultivars, geographical sites and years,AlternariaandEpicoccumspp. exhibited high relative abundance in the wheat seed mycobiome. Our results provide a comprehensive catalog of core fungal taxa well-adapted to diverse environments and conserved across wheat cultivars.
MetaWorm: An Integrative Data-Driven Model SimulatingC. elegansBrain, Body and Environment Interactions
Authors: Zhao Mengdi , Wang Ning , Jiang Xinrui , Ma Xiaoyang , Ma Haixin , He Gan , Du Kai , Ma Lei , Huang Tiejun 
Published: February 2024

AbstractThe behavior of an organism is profoundly influenced by the complex interplay between its brain, body, and environment. Existing data-driven models focusing on either the brain or the body-environment separately. A model that integrates these two components is yet to be developed. Here, we present MetaWorm, an integrative data-driven model of a widely studied organism,C. elegans. This model consists of two sub-models: the brain model and the body & environment model. The brain model was built by multi-compartment models with realistic morphology, connectome, and neural population dynamics based on experimental data. Simultaneously, the body & environment model employed a lifelike body and a 3D physical environment, facilitating easy behavior quantification. Through the closed-loop interaction between two sub-models, MetaWorm faithfully reproduced the realistic zigzag movement towards attractors observed inC. elegans. Notably, MetaWorm is the first model to achieve seamless integration of detailed brain, body, and environment simulations, enabling unprecedented insights into the intricate relationships between neural structures, neural activities, and behaviors. Leveraging this model, we investigated the impact of neural system structure on both neural activities and behaviors. Consequently, MetaWorm can enhance our understanding of how the brain controls the body to interact with its surrounding environment.
Melting curve analysis reveals false-positive norovirus detection in a molecular syndromic panel
Authors: Matic Nancy , Lawson Tanya , Young Matthew , Jang Willson , Bilawka Jennifer , Gowland Leah , Ritchie Gordon , Leung Victor , Payne Michael , Stefanovic Aleksandra , Romney Marc G. , Lowe Christopher F. 
Published: February 2024

AbstractBackgroundMolecular syndromic panels can improve rapidity of results and ease clinical laboratory workflow, although caution has been raised for potential false-positive results. Upon implementation of a new panel for infectious diarrhea (BioFire® FilmArray® Gastrointestinal [GI] Panel, bioMérieux) in our clinical laboratory, a high number of stool samples with norovirus were detected.ObjectivesTo investigate positive percent agreement and the false-positive rate of norovirus detected by the multiplex Biofire GI panel compared to a singleplex commercial assay.Study designFrom October 2023 to January 2024, all prospective stool samples with a positive norovirus result by BioFire had melting curves reviewed manually using the BioFire FilmArray Torch System. Stool samples further underwent testing by a supplementary real-time RT-PCR assay (Xpert® Norovirus, Cepheid) for comparative analysis.ResultsOf the 50 stool samples with norovirus detected by BioFire, 18 (36%) tested negative by Xpert (deemed “false-positives”). Melting curve analysis revealed nearly all of these samples had atypical melting curve morphologies for the “Noro-1” target on BioFire (16/18, 89%), which was statistically significant (Odds Ratio 173.2, 95% CI [22.2, 5326.9],p<0.0001). Stool samples with multiple pathogens including norovirus detected by BioFire were not more likely to produce false-positive norovirus results (Odds Ratio 1, 95% CI [0.3, 3.3],p=1).ConclusionsAlthough not described in the manufacturer’sInstructions for Use, we propose routine manual review of melting curves for the BioFire GI panel prior to reporting, to avoid potential false-positive norovirus results.
Student and staff experiences of a novel curriculum-based peer support intervention (“study groups”) to support the mental health and wellbeing of postgraduate taught students
Authors: McCloud Tayla , James Tiffeny , Rowe Sarah , Huntley Jonathan , Lewis Gemma , Callender Claire , Johnson Sonia , Billings Jo 
Published: February 2024

AbstractBackgroundIn recent years there has been increasing concern for the wellbeing of higher education students, and institutions are under pressure to act. Loneliness and social isolation appear common among students, particularly postgraduate taught (PGT) students, and are linked to adverse outcomes such as depression and abandoning studies. We have in place a novel curriculum-based peer support intervention (“study groups”) that may help support the mental health and wellbeing of postgraduate taught students.AimThis study aimed to explore student and staff experiences of the study groups and their perceptions of how they may influence social cohesion, loneliness and wellbeing.MethodsQualitative semi-structured interviews were conducted with students and staff to explore their experiences and views of the study groups intervention. Transcripts of the interviews were analysed by the study authors following the principles of reflexive thematic analysis.ResultsWe completed interviews with 20 students and five staff members. We found that students valued the study groups as a way to make friends, improve feelings of connectedness and cohesion, and receive emotional support. The shared experience of group members was key, although completing joint assignments could be a stressor for some.ConclusionsThis research suggests that this is a promising intervention to support the mental health and wellbeing of higher education students, and to reduce loneliness and improve social cohesion.
Factors associated with commuting stress among tertiary education employees in Georgetown, Guyana
Authors: Van-Veen Davon , Jamme Hue-Tam , Ross Heather , Chhetri Netra 
Published: February 2024

AbstractThe aim of this study was to identify factors associated with commuting stress using symptomatology among tertiary education employees in Georgetown Guyana. A cross sectional survey was conducted among 427 (100 male, 317 female) participants, with a mean age of 29.6(sd=8.7) years. Data about their demographic characteristics, psychosocial measures (perceived stress, coping and resilience), characteristics about their commute (length, mode, and satisfaction with commute infrastructure), and how often they experienced selected symptoms associated with stress on the daily commute was collected using a self administered questionnaire. A commuting stress score was calculated for each participant and this was followed by regression analysis. The results showed that after controlling for resiliency, coping, perception of job, total life stress, income levels and education all of which can contribute to how persons perceive hassles in their lives, the regression model demonstrated that females, persons who used public transportation, persons who have longer commute times and persons who are less satisfied with the commute infrastructure are more likely to report that they experience symptoms associated with stress while engaged in the daily commute compared to males, persons who use private transportation, persons who have shorter commute times and persons who are more satisfied with the commute infrastructure respectively. Once all controlled variables were accounted for, it appears that for this study population, age, where they live and whether or not they actively or passively commuted did not have any meaningful impact on whether they would report if they experienced stress associated symptoms while engaged in the daily commute. he results suggest the need for a multi-pronged approach to address commuting stress, involving individual healthcare, mental-health-centric urban transport design, improved commute infrastructure, and increased employer engagement. Future studies employing qualitative and experimental methods are recommended.
Identifying temporal patterns in the progression of neurodegenerative disease using unsupervised clustering
Authors: Giannoula Alexia , De Paepe Audrey E. , Sanz Ferran , Furlong Laura I. , Camara Estela 
Published: February 2024

AbstractObjectivesOne of the principal goals of Precision Medicine is to stratify patients by accounting for individual variability. However, extracting meaningful information from Real-World Data, such as Electronic Health Records, still remains challenging due to methodological and computational issues.Materials & methodsA Dynamic Time Warping-based unsupervised-clustering methodology is presented in this paper for the clustering of patient trajectories of multi-modal health data on the basis of shared temporal characteristics. Building on an earlier methodology, a new dimension of time-varying numerical clinical and imaging features (six in total) is incorporated, through an adapted cost-minimization algorithm for clustering on different, possibly overlapping, feature subsets. A cluster evaluation process is also implemented, by admitting two user-defined parameters (granularity threshold and feature contribution). The model disease chosen is Huntington’s disease (HD), characterized by progressive neurodegeneration.ResultsFrom a wide range of examined user-defined parameters, four case examples are highlighted to exemplify the combined effects of feature weights and granularity threshold in the stratification of HD trajectories in homogeneous clusters. For each identified cluster, polynomial fits that describe the temporal behavior of the assessed features are provided for an informative comparison, together with their averaged values.DiscussionThe proposed data-mining methodology permits the stratification of distinct time patterns of multi-modal health data in individuals that share a diagnosis or future diagnosis, employing user-customized criteria beyond the current clinical practice.ConclusionsThis work bears implications for better analysis of individual variability in disease progression, opening doors to personalized preventative, diagnostic and therapeutic strategies.