bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiota Predict Infections and Acute Graft-Versus-Host Disease after Pediatric Allogeneic Hematopoietic Stem Cell Transplantation
Authors: Margolis Elisa B , Alfaro Gabriela Maron , Sun Yilun , Dallas Ronald H , Allison Kim J , Ferrolino Jose , Ross Hailey S , Davis Amy E , Jia Qidong , Turner Paige , Mackay Victoria , Morin Cara E. , Triplett Brandon M , Tang Li , Hayden Randall T 
Published: February 2023

AbstractDespite intensive prophylactic and pre-emptive measures, infections remain an important cause of morbidity and mortality in pediatric recipients of allogeneic hematopoietic cell transplantation (allo-HCT). Disruption of the gut microbiota has been linked to clinical outcomes after adult allo-HCT. The objective was to evaluate whether these or differing microbiota disruptions or signatures were associated with risk of infection in pediatric allo-HCT.In a prospective observational study, fecal samples from 74 children were collected prior to conditioning and at the time of neutrophil recovery and profiled by means of 16S ribosomal rRNA sequencing. The associations between microbiome signatures and infections or acute graft-versus-host disease (aGVHD) were examined using Cox proportional-hazards analysis.Previously associated indices of microbiome disruption in adults, including diversity and butyrate producer frequency, did not predict infection risk in pediatric allo-HCT. Unique microbiota signatures were associated with different infections or aGVHD. A ratio of strict and facultative anaerobes (e.g.Lachnoclostridium, Parabacteroides, Clostridium spp.) prior to conditioning predicted likelihood of bacteremia (cox hazards ratio 3.89) in first year post HCT. A distinct ratio of oral (e.g.Rothia, Veillonellaspp.) to colonic anaerobes (e.g.Anaerobutyricum, Dorea, Romboutsiaspp.) at neutrophil recovery predicted likelihood of bacterial infections (cox hazards ratio 1.81) and viral enterocolitis (cox hazards ratio 1.96) through first year post transplant.Interactions between medical interventions, pediatric hosts and microbial communities may be responsible for these consistent microbiota signatures that predict infections. A future multi-center investigation will be needed to demonstrate whether these ratios can be generalized to other pediatric cohorts.Key Points(1 or 2, <140 characters): Gut microbial communities can predict which children after HCT will have infections or acute graft versus host disease. These ratios of gut community members can be used to focus prevention and treatment on children at highest risks for complications.
Prevalence and Factors Associated with Renal Disease Among HIV Infected Children on Antiretroviral Therapy Attending Joint Clinical Research Center, Lubowa, Kampala
Authors: Bagoloire Lynn Kolosi , Sheilla Ansiima , Kalyango Joan , Mugerwa Henry , Bruhan Kaggwa , Waiswa Peter , Barungi Nicolette Nabukeera , Musiime Victor 
Published: February 2023

AbstractIntroductionRenal disease is asymptomatic in its early stages but on progression into advanced stage is expensive to manage requiring renal replacement therapy. Monitoring of children’s renal functionality is not routinely done but only on a doctor’s request. However, there is currently no published study on renal disease prevalence among children living with HIV in Uganda and the associated factors.ObjectiveTo determine the prevalence of renal disease and its associated factors among HIV positive children on ART at the Joint Clinical Research Center (JCRC) Pediatric clinic.MethodsWe conducted a cross sectional study from JCRC Pediatrics Clinic. Children attending the clinic between January and August, 2020 were recruited using consecutive sampling. Information on age, sex, z sore for age, Blood pressure, route of transmission, clinical stage of the disease, ART regimen, duration on ART, non-ART drugs, Viral load and comorbidities was obtained. Blood and urine samples were also collected from the participants and sent to the laboratory for analysis. Renal disease was diagnosed using either proteinuria on urine dipstick or reduced estimated Glomerular Filtration Rate, (eGFR).ResultsThe study participants were 261, of which 51% were female and 49% male, with a median age of 12 years. The prevalence of renal diseases was 21.5% as proteinuria and 9.6% with low eGFR. Factors associated with proteinuria were; age (p-value =0.01), clinical stage of the disease (p=0.035) and diastolic blood pressure (DBP, p = 0.001) and with low eGFR were; DBP (p < 0.001) and clinical stage of disease (p < 0.001).ConclusionThe prevalence of proteinuria was high (21.5%) and that of low eGFR was (9.1%). Early screening for renal disease when still asymptomatic as a preventive strategy for renal disease should be considered, especially using affordable yet effective methods like urinalysis. This is because all the participants were asymptomatic at the time of enrollment.
Identification of circulating apolipoprotein M as a new determinant of insulin sensitivity and relationship with adiponectin
Authors: Frances Laurie , Croyal Mikaël , Ruidavets Jean-Bernard , Maraninchi Marie , Combes Guillaume , Raffin Jérémy , de Souto Barreto Philippe , Ferrières Jean , Blaak Ellen E. , Perret Bertrand , Moro Cédric , Valéro René , Martinez Laurent O. , Viguerie Nathalie 
Published: February 2023

AbstractBackgroundAdiponectin and apolipoprotein M (apoM) are adipokines indicatives of healthy adipose tissue and down-regulated with obesity. We compared circulating apoM with adiponectin regarding their relationship with metabolic parameters and insulin sensitivity and examined their gene expression patterns in adipocytes and in the adipose tissue.MethodsCirculating apoM and adiponectin were examined in 169 men with overweight in a cross-sectional study, and 13 patients with obesity during a surgery-induced slimming program. Correlations with clinical parameters including the insulin resistance index (HOMA-IR) were analyzed. Multiple regression analyses were performed on HOMA-IR. TheAPOMandADIPOQgene expression were measured in the adipose tissue from 267 individuals with obesity and a human adipocyte cell line.ResultsParticipants with type 2 diabetes had lower circulating adiponectin and apoM, while apoM was higher in individuals with dyslipidemia. Similar to adiponectin, apoM showed negative associations with HOMA-IR and hs-CRP (r>-0.2), and positive correlations with HDL markers (HDL-C and apoA-I, r>0.3). Unlike adiponectin, apoM was positively associated with LDL markers (LDL-C and apoB100, r< 0.20) and negatively correlated with insulin and age (r>-0.2). The apoM was the sole negative determinant of HOMA-IR in multiple regression models, while adiponectin not contributing significantly. After surgery, the change in HOMA-IR was negatively associated with the change in circulating apoM (r=-0.71), but not with the change in adiponectin. TheAPOMandADIPOQgene expression positively correlated in adipose tissue (r>0.44) as well as in adipocytes (r>0.81). In adipocytes,APOMwas downregulated by inflammatory factors and upregulated by adiponectin.ConclusionsThe apoM rises as a new partner of adiponectin regarding insulin sensitivity. At the adipose tissue level, the adiponectin may be supported by apoM to promote a healthy adipose tissue.
Reconstructing colonization dynamics to establish how human activities transformed island biodiversity
Authors: Tomlinson Sean , Lomolino Mark , Haythorne Sean , Anderson Atholl , Austin Jeremy J. , Brown Stuart , Perry George , Wilmshurst Janet , Wood Jamie R. , Fordham Damien A. 
Published: February 2023

AbstractAimThe drivers and dynamics of initial human migrations across individual islands and archipelagos are poorly understood, affecting assessments of human-modification of island biodiversity. Here, we describe and test a process-explicit approach for reconstructing human arrival and expansion on islands, which combines archaeological and climate records with high-resolution spatial population models. Using Polynesian colonisation of New Zealand as an example, we show that our new method can generate information crucial for assessing how humans affected biodiversity on islands.InnovationThe transition of islands from prehuman to human dominated ecosystems has typically been assessed by comparing biodiversity before and after time of first arrival, without considering the potential importance of the spatiotemporal dynamics of the human expansion event. Our new approach, which uses pattern-oriented modelling methods to combine inferences of human colonisation dynamics from dated archaeological material with spatially explicit population models, produces validated reconstructions of the pattern and pace of human migration across islands at high spatiotemporal resolutions. From these reconstructions, demographic and environmental drivers of human colonization can be identified, and the role that people had on biodiversity established. Using this technique, we show that closely reconciling inferences of Polynesian colonisation of New Zealand requires there to have been a single founding population of approximately 500 people, arriving between 1233 and 1257 AD, settling multiple areas, and expanding quickly over both North and South islands. The resultant maps of Māori colonisation dynamics provide new opportunities to better determine how human activities transformed biodiversity of New Zealand in space and time.Main conclusionsProcess-explicit models can reconstruct human migration across large islands, producing validated, high resolution spatiotemporal projections of human occupancy and abundance that account for dispersal and population dynamics. This modelling framework should prove effective across any islands and archipelagos where climate and archaeological records are available.
Structural-Functional Brain Network Coupling Predicts Human Cognitive Ability
Authors: Popp Johanna L. , Thiele Jonas A. , Faskowitz Joshua , Seguin Caio , Sporns Olaf , Hilger Kirsten 
Published: February 2023

AbstractIndividual differences in general cognitive ability (GCA) have a biological basis within the structure and function of the human brain. Network neuroscience investigations revealed neural correlates of GCA in structural as well as in functional brain networks. However, whether the relationship between structural and functional networks, the structural-functional brain network coupling (SC-FC coupling), is related to individual differences in GCA remains an open question. We used data from 1030 adults of the Human Connectome Project, derived structural connectivity from diffusion weighted imaging, functional connectivity from resting-state fMRI, and assessed GCA as a latentg-factor from 12 cognitive tasks. Two similarity measures and six communication measures were used to model possible functional interactions arising from structural brain networks. SC-FC coupling was estimated as the degree to which these measures align with the actual functional connectivity, providing insights into different neural communication strategies. At the whole-brain level, higher GCA was associated with higher SC-FC coupling, but only when considering path transitivity as neural communication strategy. Taking region-specific variations in the SC-FC coupling strategy into account and differentiating between positive and negative associations with GCA, allows for prediction of individual cognitive ability scores in a cross-validated prediction framework (correlation between predicted and observed scores:r= .25,p< .001). The same model also predicts GCA scores in a completely independent sample (N= 567,r= .19,p< .001). Our results propose structural-functional brain network coupling as a neurobiological correlate of GCA and suggest brain region-specific coupling strategies as neural basis of efficient information processing predictive of cognitive ability.
Multivariate adaptive shrinkage improves cross-population transcriptome prediction for transcriptome-wide association studies in underrepresented populations
Authors: Araujo Daniel S. , Nguyen Chris , Hu Xiaowei , Mikhaylova Anna V. , Gignoux Chris , Ardlie Kristin , Taylor Kent D. , Durda Peter , Liu Yongmei , Papanicolaou George , Cho Michael H. , Rich Stephen S. , Rotter Jerome I. ,   NHLBI TOPMed Consortium, Im Hae Kyung , Manichaikul Ani , Wheeler Heather E. 
Published: February 2023

AbstractTranscriptome prediction models built with data from European-descent individuals are less accurate when applied to different populations because of differences in linkage disequilibrium patterns and allele frequencies. We hypothesized methods that leverage shared regulatory effects across different conditions, in this case, across different populations may improve cross-population transcriptome prediction. To test this hypothesis, we made transcriptome prediction models for use in transcriptome-wide association studies (TWAS) using different methods (Elastic Net, Joint-Tissue Imputation (JTI), Matrix eQTL, Multivariate Adaptive Shrinkage in R (MASHR), and Transcriptome-Integrated Genetic Association Resource (TIGAR)) and tested their out-of-sample transcriptome prediction accuracy in population-matched and cross-population scenarios. Additionally, to evaluate model applicability in TWAS, we integrated publicly available multi-ethnic genome-wide association study (GWAS) summary statistics from the Population Architecture using Genomics and Epidemiology Study (PAGE) and Pan-UK Biobank with our developed transcriptome prediction models. In regard to transcriptome prediction accuracy, MASHR models performed better or the same as other methods in both population-matched and cross-population transcriptome predictions. Furthermore, in multi-ethnic TWAS, MASHR models yielded more discoveries that replicate in both PAGE and PanUKBB across all methods analyzed, including loci previously mapped in GWAS and new loci previously not found in GWAS. Overall, our study demonstrates the importance of using methods that benefit from different populations’ effect size estimates in order to improve TWAS for multi-ethnic or underrepresented populations.
Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology
Authors: Qi Qin , Ghaly Timothy M , Penesyan Anahit , Rajabal Vaheesan , Stacey Jeremy AC , Tetu Sasha G , Gillings Michael R 
Published: February 2023

AbstractHorizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of epicPCR (emulsion,pairedisolation andconcatenationpolymerasechainreaction) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified theRhizobactergenus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR.SynopsisWe present a novel single-cell genomic surveillance technology for identifying environmental bacterial hosts of a class of mobile genetic elements that are linked to anthropogenic pollution and contribute to the dissemination of antimicrobial resistance.
Chemoresistome Mapping in Individual Breast Cancer Patients Unravels Diversity in Dynamic Transcriptional Adaptation
Authors: Dadiani Maya , Friedlander Gilgi , Perry Gili , Balint-Lahat Nora , Gilad Shlomit , Morzaev-Sulzbach Dana , Shenoy Anjana , Ben-Moshe Noa Bossel , Pavlovsky Anya , Domany Eytan , Barshack Iris , Geiger Tamar , Kaufman Bella , Gal-Yam Einav Nili 
Published: February 2023

AbstractEmerging evidence reinforce the role of non-genetic adaptive resistance to chemotherapy, that involves rewiring of transcriptional programs in surviving tumors. We combined longitudinal transcriptomics with temporal pattern analysis to dissect patient-specific emergence of resistance in breast cancer. Matched triplets of tumor biopsies (pre-treatment, post-treatment and adjacent normal) were collected from breast cancer patients who received neo-adjuvant chemotherapy. Full transcriptome was analyzed by longitudinal pattern classification to follow patient-specific expression modulations. We found that dynamics of gene expression dictates resistance-related modulations. The results unraveled important principles in emergence of adaptive resistance: 1. Genes with resistance patterns are already dysregulated in the primary tumor, supporting a primed drug-tolerant state. 2. In each patient, multiple resistance-related genes are rewired but converge into few dysregulated modules. 3. Rewiring of diverse genes and pathway dysregulation vary among individuals who receive the same treatments. Patient-specific chemoresistome maps disclosed tumors’ acquired resistance and exposed their vulnerabilities.Mapping the complexity of dysregulated pathways in individual patients revealed important insights on adaptive resistance mechanisms. To survive the toxic drug effect, tumor cells either sustain a drug-tolerant state or intensify it, specifically bypassing the drug’s interference. Depicting an individual road map to resistance can offer personalized therapeutic strategies.
Cholesteryl hemiazelate Identified in Cardiovascular Disease Patients Causesin vitroandin vivoInflammation
Authors: Domingues Neuza , Gaifem Joana , Matthiesen Rune , Saraiva Diana P. , Bento Luís , Marques André R.A. , Soares Maria I. L. , Sampaio Julio , Klose Christian , Surma Michal A. , Almeida Manuel S. , Rodrigues Gustavo , Gonçalves Pedro Araújo , Ferreira Jorge , Gouveia e Melo Ryan , Pedro Luís Mendes , Simons Kai , Pinho e Melo Teresa M. V. D. , Cabral M. Guadalupe , Jacinto Antonio , Silvestre Ricardo , Vaz Winchil , Vieira Otília V. 
Published: February 2023

ABSTRACTOxidation of polyunsaturated fatty acids (PUFA) in low-density lipoproteins (LDL) trapped in the arterial intima plays a critical role in atherosclerosis. Though there have been many studies on the atherogenicity of oxidized derivatives of unsaturated fatty acid esters of cholesterol, the effects of the oxidation end-products of these esters has been ignored in the literature.Through lipidomics analyses of the plasma of cardiovascular disease patients and human endarterectomy specimens we identified and quantified cholesteryl hemiesters (ChE), end-products of oxidation of polyunsaturated-fatty acid esters of cholesterol. Cholesteryl hemiazelate (ChA) was the most prevalent ChE identified. Importantly human monocytes, monocyte-derived macrophages (MDM) and neutrophils exhibit inflammatory features when exposed to sub-toxic concentrations of ChAin vitro. ChA increases the secretion of proinflammatory cytokines such as IL-1β and IL-6 and modulates the surface markers profile of monocytes and MDM.In vivo, when zebrafish larvae were fed with a ChA-enriched diet they exhibited neutrophil and macrophage accumulation in the vasculature in a caspase 1- and cathepsin B-dependent manner. ChA also triggered lipid accumulation at the bifurcation sites of the vasculature of the zebrafish larvae and negatively impacted their life expectancy.We conclude that ChA has pro-atherogenic properties and can be considered part of a damage-associated molecular pattern (DAMP) in the development of atherosclerosis.
New to Ehretiaceae:Keraunea. Re-evaluation of a genus of climbers from Brazil
Authors: Cheek Martin , Lombardi Julio A. , Simões Ana Rita G. , Zuntini Alexandre R. 
Published: February 2023

AbstractWe definitively placeKeraunea, a genus of showy forest climbers from remnants of the Mata Atlântica of Brazil, in Ehretiaceae. PreviouslyKerauneahad been ascribed to Convolvulaceae based on morphology, or divided between Malpighiaceae and Ehretiaceae based on molecular analyses (polyphyletic).Kerauneais morphologically anomalous in the Ehretiaceae, having fruits which are held in the centre of a large wing-like bract by adnation of the pedicel, and due the stem-twining habit of some species. However, morphologicallyKerauneashares two apomorphies with monotypicCortesiaCav., halophytic shrubs of Argentina: 1) “two parted endocarps” (the fruit contains two endocarps each with two 1-seeded cells, while four 1-seeded endocarps are plesiomorphic in Ehretiaceae) and 2) a large bract that subtends the flower (absence of bracts is plesiomorphic in Ehretiaceae). A combined tree using four markers (ITS,trnL-F,rbcL andmatK) places the three species ofKerauneasampled unambiguously in a clade withEhretia+Cortesia+Halganiaand monophyly forKerauneais shown with high support. In an ITS treeKerauneais sister toCortesiawith low support.We expand the generic description ofKerauneaincluding the first account of the internal fruit structures and the seed, and present new data on the vegetative architecture including variation within the genus, some species being stem twiners while one species at least, is described as a scandent shrub.Keraunea lombardiana, previously included withinK. brasiliensis, is formally described from Minas Gerais and Bahia as the third species of the genus and both these species are described. In all five species are recognised but two, known to us only from digital images, are not formally described because sufficiently detailed descriptions cannot be made. All five species are mapped, and provisional conservation assessments are recorded, of either Endangered or Critically Endangered. The state of Bahia, with three species, has the highest species diversity, mainly in dry forest. Three species appear confined to moist coastal forest, extending southwards from Bahia to the state of Rio de Janeiro.Keraunearemains incompletely known. Not one of the species has both anthetic flowers and fruits described. Studies on pollen, germination, anatomy, embryology and phytochemisty are entirely lacking. Field observations of pollination, seed dispersal and phenology are also required. However, the most urgent requirement is undoubtedly a formal taxonomic revision based on a full herbarium search and targeted fieldwork, with full IUCN 2012 extinction risk assessments for each taxon. This is urgent because it seems that all the taxa that we present in this paper (and more that can be expected to be found) appear to be highly range restricted and generally not to occur in protected areas, and so appear to be highly threatened.