bluuebunny/crossref_metadata_2025_split huggingface dataset:
ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome
Authors: Hirsch Pascal , Tagirdzhanov Azat , Kushnareva Aleksandra , Olkhovskii Ilia , Graf Simon , Schmartz Georges P. , Hegemann Julian , Bozhüyük Kenan , Rolf Müller , Keller Andreas , Gurevich Alexey 
Published: September 2023

ABSTRACTThe human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19,218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible athttps://www.ccb.uni-saarland.de/abc_humi/.GRAPHICAL ABSTRACT
Effect of ethanolic extract of Cyperus rotundus reduces the surgical induced secondary lymphedema and oxidative stress in adult mice tail
Authors: Pandey Nikhil , Mishra Priyanka 
Published: September 2023

AbstractBackgroundLymphedema is clinically manifested as swelling in the extremities due to abnormal accumulation of protein rich in the extravascular interstitial space resulting in irreversible structural changes to the limb (s). The aim of this explorative work was to evaluate the effect ofCyperus rotundusroot (CRR) ethanolic extract in a mouse tail model of secondary lymphedema. Method: Mice were temporally anaesthetised under sterile condition and the skin from the tail was removed from distal part of the trunk after leaving 1cm of distance. The animals were divided into Experimental control (EC) andCyperus rotundusroot (CRR) 80 mg/kg b.w. /day) treated groups. Change in tail volume and circumference were monitored for 20 days. TNFα, SOD and catalase were estimated from blood obtained through retro-orbital at day 0, 5, 10 and 15. Further TS of upper part of the tail skin was stained with H&E stain to document histological changes mRNA level of COX-2 was estimated from the skin.RESULTSEC group showed gradual rise in tail oedema post-surgery (PS), elevated inflammation, oxidative stress and histopathological alterations. However in CRR (80 mg/kg b.w./day) treated group shown the reduced tail oedema after post-surgery. TNFα, SOD and catalase levels were significantly less in CRR then EC group supporting anti-inflammatory potential. CRR protected the tail from structural damage. It also down regulated the expression of COX-2 in comparison to EC group. Conclusions: CRR ethanolic extract significantly attenuated secondary lymphedema indicating it potential for therapeutic use.Graphical abstract
Immunization Staff Training Needs Assessment: An Overview Of Findings From Cameroon
Authors: Adidja Amani , Nchinjoh Sangwe Clovis , Gu Jessica , Lekeumo Cheuyem Fabrice Zobel , Edwige Nadege Nnang , Vouking Marius , Muteh Jude Nkwain , Agbor Valirie Ndip , Mvalo Mbanga Clarence , Bernard Nsah , Ngenge Budzi Michael , Ndoula Shalom Tchokfe , Njoh Andreas Ateke , Mattei Pietro Di , Tonga Calvin , Saidu Yauba 
Published: September 2023

AbstractBackgroundIn recent years, Cameroon’s Expanded Program on Immunization (EPI) has witnessed a sizable decline in its performance. Many stakeholders have cited weaknesses in human resources as one of the major drivers for the observed trend. In a bid to better understand and redress this situation, the EPI and its partners conducted a Training Needs Assessment (TNA) among central, regional, and district staff. The assessment aimed to quantify and characterize core capability gaps and leverage the findings to design an evidence-based capacity-building plan.MethodsA descriptive cross-sectional study was conducted using aggregated data from a survey carried out among EPI staff from May to September 2016 across Cameroon’s health pyramid - central, regional, and district levels; and analysis was done using Microsoft Office Excel 2016.ResultsOver half of EPI staff had worked for less than three years in their current post, and roughly three-third of them did not receive pre-service training on vaccination. Additionally, about half of them had not received any form of in-service training on immunization. Supportive supervision was the most frequently cited topic for training, with a surprisingly higher need at the central level (80%). Financial incentive was not a primary motivating factor for learning. Approximately half of the respondents at all levels were not aware of onboarding materials. Most of the respondents identified multiple meetings, high staff turnover, and competing priorities as major barriers to learning. Only about half of surveyed staff reported participating in performance reviews, with nearly half of these reviews conducted when an opportunity arose.ConclusionThere are still many gaps challenging the EPI goal achievement in Cameroon. Sustainably addressing these issues will require a comprehensive framing of capability-building activities. High-quality EPI human resources will boost the country’s vaccination performance and contribute to the reduction of infant mortality in the country.
Factor XI localization in human deep venous thrombus and function of activated factor XI on venous thrombus formation and hemostasis in rabbit
Authors: Oguri Nobuyuki , Gi Toshihiro , Nakamura Eriko , Maekawa Kazunari , Furukoji Eiji , Okawa Hoshimi , Kouyama Sho , Horiuchi Saki , Sakae Tatefumi , Azuma Minako , Asada Yujiro , Yamashita Atsushi 
Published: September 2023

AbstractBackgroundNovel anticoagulants targeting coagulation factor XI (FXI)/activated FXI (FXIa) are under development. However, whether FXI is present in human deep vein thrombosis (DVT) and whether FXIa and activated factor X (FXa) play different roles in venous thrombus formation and hemostasis remain unclear. This study aimed to determine the presence of FXI in DVT and the effects of direct oral FXIa and FXa inhibitors on venous thrombus formation and hemostasis in rabbits and mural thrombus formation in flow chamber system.MethodsWe immunohistochemically assessed FXI localization in human aspirated DVT (n=15). Additionally, we compared thrombus formation induced by endothelial denudation and stenosis in jugular vein, and skin bleeding time and volume between rabbits treated with direct FXIa inhibitors (ONO-1600586) and FXa inhibitors (rivaroxaban).Ex vivorabbit and human blood were perfused on a flow chamber under low shear rates (70/s).ResultFXI was localized in all DVT, predominantly in fibrin-rich areas. The FXI-immunopositive area in the non-organizing area was greater than that in the organizing area. Although FXIa and FXa inhibitors comparably inhibited venous thrombus formation, FXIa inhibitors did not affect bleeding time or volume in rabbits. FXIa or FXa inhibitors mildly or strongly inhibited fibrin formation at low shear rates respectively. Furthermore, the FXIa inhibitor suppressed human FXIa activity, thrombin generation, and fibrin formation during perfusion.ConclusionThe pathological findings of human DVT suggest FXI’s role in human DVT. FXIa inhibitors may inhibit less fibrin formation than FXa inhibitors, and may explain the minor role of FXIa in hemostasis.EssentialPresence of factor XI (FXI) in venous thrombus and less bleeding in its inhibition are unclear.We assessed FXI localization in deep vein thrombosis (DVT) and function of FXIa in rabbit.FXI localized in human DVT that provide a rationale for FXI inhibition in human DVT.FXIa inhibitor inhibited less fibrin formation than factor Xa inhibitor under low-shear rate.
Effects of Data Transformation and Model Selection on Feature Importance in Microbiome Classification Data
Authors: Karwowska Zuzanna , Aasmets Oliver ,   Estonian Biobank research team, Kosciolek Tomasz , Org Elin 
Published: September 2023

AbstractAccurate classification of host phenotypes from microbiome data is essential for future therapies in microbiome-based medicine and machine learning approaches have proved to be an effective solution for the task. The complex nature of the gut microbiome, data sparsity, compositionality and population-specificity however remain challenging, which highlights the critical need for standardized methodologies to improve the accuracy and reproducibility of the results. Microbiome data transformations can alleviate some of the aforementioned challenges, but their usage in machine learning tasks has largely been unexplored. Our aim was to assess the impact of various data transformations on the accuracy, generalizability and feature selection by analysis using more than 8,500 samples from 24 shotgun metagenomic datasets. Our findings demonstrate the feasibility of distinguishing between healthy and diseased individuals using microbiome data with minimal dependence on the algorithm and transformation selection. Remarkably, presence-absence transformation performed comparably well to abundance-based transformations, and only a small subset of predictors is crucial for accurate classification. However, while different transformations resulted in comparable classification performance, the most important features varied significantly, which highlight the need to reevaluate machine-learning based biomarker detection. Our research provides valuable guidance for applying machine learning on microbiome data, offering novel insights and highlighting important areas for future research.
The Chordate Origins of Heart Regeneration
Authors: Schuster Keaton J. , Christiaen Lionel 
Published: September 2023

AbstractThe human heart is infamous for not healing after infarction in adults, prompting biomedical interest in species that can regenerate damaged hearts. In such animals as zebrafish and neonatal mice, cardiac repair relies on remaining heart tissue supporting cardiomyocyte proliferation. Naturalde novocardiogenesis in post-embryonic stages thus remains elusive. Here we show that the tunicateCiona, an ascidian among the closest living relatives to the vertebrates, can survive complete chemogenetic ablation of the heart and loss of cardiac function, and recover both cardiac tissue and contractility. As in vertebrates, Ciona heart regeneration relies on Bone Morphogenetic Protein (BMP) signaling-dependent proliferation of cardiomyocytes, providing insights into the evolutionary origins of regenerative cardiogenesis in chordates. Remarkably, prospective lineage tracing by photoconversion of the fluorescent protein Kaede suggested that new cardiomyocytes can emerge from endodermal lineages in post-metamorphic animals, providing an unprecedented case of regenerativede novocardiogenesis. Finally, while embryos cannot compensate for early losses of the cardiogenic lineage, forming heartless juveniles, developing animals gain their regenerative ability during metamorphosis, uncovering a fundamental transition between deterministic embryogenesis and regulative post-embryonic development.
The interactome of histone deacetylase HDA19 in dark-grown Arabidopsis seedlings
Authors: Vélez-Bermúdez Isabel Cristina , Schmidt Wolfgang 
Published: September 2023

AbstractHere, we describe a data set derived from an immunoprecipitation (IP)-based analysis of the histone deacetylase HDA19 interactome in etiolated Arabidopsis seedlings. HISTONE DEACETYLASE 19 (HDA19) belongs to the class 1 of the Reduced Potassium Dependence3/Histone Deacetylase-1 (RPD3/HDA1) superfamily and is possibly the most intensively studied HDA. Here, we describe a data set derived from an immunoprecipitation (IP)-based analysis of the histone deacetylase HDA19 interactome in etiolated Arabidopsis seedlings. We believe that this data set presented here provides a valuable resource for follow-up research on novel interacting partners of this central protein.
Dose-Response Relationships between Physical Exercises and Mental Health during Early Adolescence: an Investigation of the Underlying Neural and Genetic Mechanisms from the ABCD Study
Authors: Yu Gechang , Wu Xinran , Liu Zhaowen , Shi Mai , Fan Huaxin , Liu Yu , Kuang Nanyu , Peng Songjun , Lian Zhengxu , Chen Jingyang , Yang Senyou , Huang Chuiguo , Wu Hongjiang , Fan Baoqi , Feng Jianfeng , Cheng Wei , Sahakian Barbara J. , Robbins Trevor W. , Becker Benjamin , Zhang Jie 
Published: September 2023

AbstractAdolescence is a critical developmental with increased vulnerability to mental disorders. While the positive impact of physical exercise on adult mental health is well-established, dose-response relationships and the underlying neural and genetic mechanisms in adolescents remain elusive. Leveraging data from >11,000 pre-adolescents (9-10 years, ABCD Study) we examined associations between seven different measures of exercise dosage across 15 exercises and psychopathology, and the roles of brain function and structure and psychiatric genetic risks. Five specific exercises (basketball, baseball/softball, soccer, football, and skiing) were associated with better mental health while the beneficial effects varied with exercise types, dosage measures and dimensions of psychopathology. Interestingly, more exercise does not always translate to better mental health whilst earlier initiation was consistently advantageous. Communication between attention and default-mode brain networks mediated the beneficial effect of playing football. Crucially, exercise mitigates the detrimental effects of psychiatric genetic risks on mental health. We offer a nuanced understanding of exercise effects on adolescent mental health to promote personalized exercise-based interventions in youth.
Structural neurodevelopment at the individual level - a life-course investigation using ABCD, IMAGEN and UK Biobank data
Authors: Shi Runye , Xiang Shitong , Jia Tianye , Robbins Trevor W. , Kang Jujiao , Banaschewski Tobias , Barker Gareth J. , Bokde Arun L.W. , Desrivières Sylvane , Flor Herta , Grigis Antoine , Garavan Hugh , Gowland Penny , Heinz Andreas , Brühl Rüdiger , Martinot Jean-Luc , Martinot Marie-Laure Paillère , Artiges Eric , Nees Frauke , Orfanos Dimitri Papadopoulos , Paus Tomáš , Poustka Luise , Hohmann Sarah , Millenet Sabina , Fröhner Juliane H. , Smolka Michael N. , Vaidya Nilakshi , Walter Henrik , Whelan Robert , Schumann Gunter , Lin Xiaolei , Sahakian Barbara J. , Feng Jianfeng ,   IMAGEN Consortium
Published: September 2023

AbstractAdolescents exhibit remarkable heterogeneity in the structural architecture of brain development. However, due to the lack of large-scale longitudinal neuroimaging studies, existing research has largely focused on population averages and the neurobiological basis underlying individual heterogeneity remains poorly understood. Using structural magnetic resonance imaging from the IMAGEN cohort (n=1,543), we show that adolescents can be clustered into three groups defined by distinct developmental patterns of whole-brain gray matter volume (GMV). Genetic and epigenetic determinants of group clustering and long-term impacts of neurodevelopment in mid-to-late adulthood were investigated using data from the ABCD, IMAGEN and UK Biobank cohorts. Group 1, characterized by continuously decreasing GMV, showed generally the best neurocognitive performances during adolescence. Compared to Group 1, Group 2 exhibited a slower rate of GMV decrease and worsened neurocognitive development, which was associated with epigenetic changes and greater environmental burden. Further, Group 3 showed increasing GMV and delayed neurocognitive development during adolescence due to a genetic variation, while these disadvantages were attenuated in mid-to-late adulthood. In summary, our study revealed novel clusters of adolescent structural neurodevelopment and suggested that genetically-predicted delayed neurodevelopment has limited long-term effects on mental well-being and socio-economic outcomes later in life. Our results could inform future research on policy interventions aimed at reducing the financial and emotional burden of mental illness.
Mechanisms of type I interferon production by chicken TLR21
Authors: Guabiraba Rodrigo , Rodrigues Damaris Ribeiro , Manna Paul T. , Chollot Mélanie , Saint-Martin Vincent , Trapp Sascha , Oliveira Marisa , Bryant Clare E , Ferguson Brian J 
Published: September 2023

AbstractThe innate immune response relies on the ability of host cells to rapidly detect and respond to microbial nucleic acids. Toll-like receptors (TLRs), a class of pattern recognition receptors (PRRs), play a fundamental role in distinguishing self from non-self at the molecular level. In this study, we focused on TLR21, an avian TLR that recognizes DNA motifs commonly found in bacterial genomic DNA, specifically unmethylated CpG motifs. TLR21 is believed to act as a functional homologue to mammalian TLR9. By analysing TLR21 signalling in chickens, we sought to elucidate avian TLR21 activation outputs in parallel to that of other nucleic acid species. Our analyses revealed that chicken TLR21 (chTLR21) triggers the activation of NF-κB and induces a potent type-I interferon response in chicken macrophages, similar to the signalling cascades observed in mammalian TLR9 activation. Notably, the transcription of interferon beta (IFNB) by chTLR21 was found to be dependent on both NF-κB and IRF7 signalling, but independent of the TBK1 kinase, a distinctive feature of mammalian TLR9 signalling. These findings highlight the conservation of critical signalling components and downstream responses between avian TLR21 and mammalian TLR9, despite their divergent evolutionary origins. These insights into the evolutionarily conserved mechanisms of nucleic acid sensing contribute to the broader understanding of host-pathogen interactions across species.
When the heart meets the mind Exploring the brain-heart interaction during time perception
Authors: Khoshnoud Shiva , Leitritz David , Bozdağ Meltem Çinar , Igarzábal Federico Alvarez , Noreika Valdas , Wittmann Marc 
Published: September 2023

AbstractIt has been hypothesized that time estimation relies on bodily rhythms and interoceptive signals, such as heartbeats. Extending previous research demonstrating this connection, we provided further electrophysiological evidence that the brain registers heartbeats while tracking time intervals. We evaluated the heartbeat-evoked potential (HEP) and the contingent negative variation (CNV) during an auditory duration-reproduction task with intervals lasting 4, 8, and 12 seconds and a control reaction-time task employing the exact durations. The (interoceptive) Self-Awareness Questionnaire (SAQ) and the heartbeat-counting task (HCT) were administered. The SAQ, but not the HCT scores, correlated with the mean reproduced durations for 4s, 8s, and 12s intervals: the higher the SAQ score (a stronger awareness of bodily signals), the longer the duration reproductions and the more accurate the timing behavior. The HEP amplitude within 130-270 ms (HEP1) and 470-520 ms (HEP2) after the R peak was smaller for the 4s interval than for the 8s and 12s intervals. This is a timing-specific effect, as the HEP amplitude did not differ for intervals in the reaction-time task. A ramp-like increase in HEP2 amplitudes was significant for the duration-encoding phase of the timing task, but not for the control reaction-time task. The HEP2 increase within the reproduction phase of the timing task correlated significantly with the reproduced durations for the 8s and the 12s intervals. The larger the registered increase in the HEP2, the greater the under-reproduction of the estimated duration. The initial and late CNV components were significantly more negative during the encoding phase than during the reaction-time task. Given the link between these components with attention modulation and temporal memory, we interpret the CNV findings as indicating greater executive resources oriented towards time. We conclude that interoceptive awareness (SAQ) and state-like cortical responses to the heartbeat (HEP) predict duration reproductions, emphasizing the notion of the embodiment of time.
An analytical derivation of the distribution of distances between heterozygous sites in diploid species to efficiently infer demographic history
Authors: Arndt Peter F. , Massip Florian , Sheinman Michael 
Published: September 2023

AbstractHeterozygous sites are not uniformly distributed along a diploid genome. Rather, their density varies as a result of recombination events, and their local density reflects the time to the last common ancestor of the maternal and paternal copies of a genomic region. The distribution of the density of heterozygous sites therefore carries information about the history of the population size. Despite previous efforts, an exact derivation of the distribution of heterozygous sites is still lacking. As a consequence, the estimation of population size variation is difficult and requires several simplifying assumptions. Using a novel theoretical framework, we are able to derive an analytical formula for the distribution of distances between heterozygous sites. Our theory can account for arbitrary demographic histories, including bottlenecks. In the case of a constant population size the distribution follows a simple function and exhibits a power-law tail proportional torαwithα=−3, whereris the distance between heterozygous sites. This prediction is accurately validated when considering heterozygous sites in individuals of African descent. Other populations migrated out of Africa and underwent at least one bottleneck which left a distinct mark on their interval distribution between heterozygous sites, i.e., an overrepresentation of intervals between 10 and 100 kbp in length. Our analytical theory for non-constant population sizes reproduces this behavior and can be used to study historical changes in population size with high accuracy. The simplicity of our approach facilitates the analysis of demographic histories for diploid species, requiring only a single unphased genome.