23 research outputs found
Author Correction: Multi-ancestry meta-analysis of genome-wide association studies discovers 67 new loci associated with chronic back pain
No full textBiconed graphs, weighted forests, and h-vectors of matroid complexes
No full textA well-known conjecture of Richard Stanley posits that the -vector of the
independence complex of a matroid is a pure -sequence. The
conjecture has been established for various classes but is open for graphic
matroids. A biconed graph is a graph with two specified `coning vertices', such
that every vertex of the graph is connected to at least one coning vertex. The
class of biconed graphs includes coned graphs, Ferrers graphs, and complete
multipartite graphs. We study the -vectors of graphic matroids arising from
biconed graphs, providing a combinatorial interpretation of their entries in
terms of `-weighted forests' of the underlying graph. This generalizes
constructions of Kook and Lee who studied the M\"obius coinvariant (the last
nonzero entry of the -vector) of graphic matroids of complete bipartite
graphs. We show that allowing for partially -weighted forests gives rise to
a pure multicomplex whose face count recovers the -vector, establishing
Stanley's conjecture for this class of matroids. We also discuss how our
constructions relate to a combinatorial strengthening of Stanley's Conjecture
(due to Klee and Samper) for this class of matroids.Comment: 15 pages, 3 figures; V2: added omitted author to metadata; V3: added
Section 5 involving a worked example, added Section 6 connecting our work to
that of Klee and Samper, small change to title, other corrections and edits
as suggested by referee
Using machine learning to improve risk prediction in durable left ventricular assist devices.
No full textRisk models have historically displayed only moderate predictive performance in estimating mortality risk in left ventricular assist device therapy. This study evaluated whether machine learning can improve risk prediction for left ventricular assist devices. Primary durable left ventricular assist devices reported in the Interagency Registry for Mechanically Assisted Circulatory Support between March 1, 2006 and December 31, 2016 were included. The study cohort was randomly divided 3:1 into training and testing sets. Logistic regression and machine learning models (extreme gradient boosting) were created in the training set for 90-day and 1-year mortality and their performance was evaluated after bootstrapping with 1000 replications in the testing set. Differences in model performance were also evaluated in cases of concordance versus discordance in predicted risk between logistic regression and extreme gradient boosting as defined by equal size patient tertiles. A total of 16,120 patients were included. Calibration metrics were comparable between logistic regression and extreme gradient boosting. C-index was improved with extreme gradient boosting (90-day: 0.707 [0.683-0.730] versus 0.740 [0.717-0.762] and 1-year: 0.691 [0.673-0.710] versus 0.714 [0.695-0.734]; each p<0.001). Net reclassification index analysis similarly demonstrated an improvement of 48.8% and 36.9% for 90-day and 1-year mortality, respectively, with extreme gradient boosting (each p<0.001). Concordance in predicted risk between logistic regression and extreme gradient boosting resulted in substantially improved c-index for both logistic regression and extreme gradient boosting (90-day logistic regression 0.536 versus 0.752, 1-year logistic regression 0.555 versus 0.726, 90-day extreme gradient boosting 0.623 versus 0.772, 1-year extreme gradient boosting 0.613 versus 0.742, each p<0.001). These results demonstrate that machine learning can improve risk model performance for durable left ventricular assist devices, both independently and as an adjunct to logistic regression
Genome-Wide Association Study of Chronic Dizziness in the Elderly Identifies Loci Implicating MLLT10, BPTF, LINC01224, and ROS1
No full textMulti-ancestry meta-analysis of genome-wide association studies discovers 67 new loci associated with chronic back pain.
No full textThis multi-ancestry meta-analysis of genome-wide association studies (GWAS) investigated the genetic factors underlying chronic back pain (CBP) in a sample from the Million Veteran Program comprised of 553,601 Veterans of African (19.2%), European (72.6%), and Hispanic (8.2%) ancestry. The results revealed novel (N = 67) and known (N = 20) genome-wide significant loci associated with CBP, with 43 independent variants replicating in a non-overlapping contemporary meta-GWAS of the spinal pain dorsalgia phenotype. The most significant novel variant was rs12533005 (chr7:114416000, p = 1.61 × 10-20, OR = 0.96 (95% CI: 0.95-0.97), EA = C, EAF = 0.39), in an intron of the FOXP2 gene. In silico functional characterization revealed enrichment in brain and pituitary tissues. Mendelian randomization analysis of 62 variants for CBP-MVP revealed 48 with causal links to dorsalgia. Notably, four genes (INPP5B, DRD2, HTT, SLC30A6) associated with these variants are targets of existing drugs. Our findings more than double the number of previously reported genetic predictors across all spinal pain phenotypes
Disentangling non-random assortment, indirect effects, and joint plasticity as causes of phenotypic (dis)similarity between social partners
No full textClass B, Araya-Ajoy Y, Dingemans NJ, et al. Disentangling non-random assortment, indirect effects, and joint plasticity as causes of phenotypic (dis)similarity between social partners. Journal of Evolutionary Biology . 2025.Social partners frequently resemble each other. These correlations between the phenotypes of interacting individuals (e.g. social partners, group members, etc.) can be caused by multiple processes. These processes include joint plasticity in response to shared environments, plasticity in response to partner phenotype, and genetic similarity arising from non-random assortment due to clustered relatives, spatiotemporal stratification, and partner choice. Although social plasticity and non-random assortment can influence evolutionary dynamics, these two processes have most often been studied separately and disentangling the causes of partner resemblance in observational datasets can be challenging. Furthermore, standard statistical models of social plasticity do not allow for potential social feedback between partners' phenotypes and estimating joint plasticity to shared environmental effects requires environmental data that is rarely available. In this study, we investigated the performance of various statistical models to estimate non-random assortment and social plasticity in observational datasets. We simulated data for a socially monogamous species in which non-random mating, social plasticity (with or without feedback) and joint plastic responses to unknown environmental factors occurred alone or simultaneously. Commonly used 'variance-partitioning approaches' retrieved biased estimates except when the process they aimed to estimate occurred on its own. By contrast, a recently proposed statistical model explicitly including social plasticity as a dynamic process generating feedback between partners' phenotypes (the so-called social animal model) performed best even in scenarios with multiple co-occurring processes. While we recommend empiricists use this latter approach, we also highlight the importance of appropriate sampling designs given the study question and system, and using simulations to assess model performance in realistic scenarios. © The Author(s) 2025. Published by Oxford University Press on behalf of the European Society of Evolutionary Biology. All rights reserved. For commercial re-use, please contact [email protected] for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site-for further information please contact [email protected]
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Genome-Wide Association Study of Chronic Dizziness in the Elderly Identifies Loci Implicating MLLT10, BPTF, LINC01224, and ROS1
No full textPurposeChronic age-related imbalance is a common cause of falls and subsequent death in the elderly and can arise from dysfunction of the vestibular system, an elegant neuroanatomical group of pathways that mediates human perception of acceleration, gravity, and angular head motion. Studies indicate that 27-46% of the risk of age-related chronic imbalance is genetic; nevertheless, the underlying genes remain unknown.MethodsThe cohort consisted of 50,339 cases and 366,900 controls in the Million Veteran Program. The phenotype comprised cases with two ICD diagnoses of vertigo or dizziness at least 6 months apart, excluding acute or recurrent vertiginous syndromes and other non-vestibular disorders. Genome-wide association studies were performed as individual logistic regressions on European, African American, and Hispanic ancestries followed by trans-ancestry meta-analysis. Downstream analysis included case-case-GWAS, fine mapping, probabilistic colocalization of significant variants and genes with eQTLs, and functional analysis of significant hits.ResultsTwo significant loci were identified in Europeans, another in the Hispanic population, and two additional in trans-ancestry meta-analysis, including three novel loci. Fine mapping revealed credible sets of intronic single nucleotide polymorphisms (SNPs) in MLLT10 - a histone methyl transferase cofactor, BPTF - a subunit of a nucleosome remodeling complex implicated in neurodevelopment, and LINC01224 - a proto-oncogene receptor tyrosine kinase.ConclusionDespite the difficulties of phenotyping the nature of chronic imbalance, we replicated two loci from previous vertigo GWAS studies and identified three novel loci. Findings suggest candidates for further study and ultimate treatment of this common elderly disorder
Casanovas are liars : behavioral syndromes, sperm competition risk, and the evolution of deceptive male mating behavior in live-bearing fishes [version 2; referees: 2 approved, 1 approved with reservations]
No full textMale reproductive biology can by characterized through competition over mates as well as mate choice. Multiple mating and male mate choice copying, especially in internally fertilizing species, set the stage for increased sperm competition, i.e., sperm of two or more males can compete for fertilization of the female’s ova. In the internally fertilizing fish Poecilia mexicana, males respond to the presence of rivals with reduced expression of mating preferences (audience effect), thereby lowering the risk of by-standing rivals copying their mate choice. Also, males interact initially more with a non-preferred female when observed by a rival, which has been interpreted in previous studies as a strategy to mislead rivals, again reducing sperm competition risk (SCR). Nevertheless, species might differ consistently in their expression of aggressive and reproductive behaviors, possibly due to varying levels of SCR. In the current study, we present a unique data set comprising ten poeciliid species (in two cases including multiple populations) and ask whether species can be characterized through consistent differences in the expression of aggression, sexual activity and changes in mate choice under increased SCR. We found consistent species-specific differences in aggressive behavior, sexual activity as well as in the level of misleading behavior, while decreased preference expression under increased SCR was a general feature of all but one species examined. Furthermore, mean sexual activity correlated positively with the occurrence of potentially misleading behavior. An alternative explanation for audience effects would be that males attempt to avoid aggressive encounters, which would predict stronger audience effects in more aggressive species. We demonstrate a positive correlation between mean aggressiveness and sexual activity (suggesting a hormonal link as a mechanistic explanation), but did not detect a correlation between aggressiveness and audience effects. Suites of correlated behavioral tendencies are termed behavioral syndromes, and our present study provides correlational evidence for the evolutionary significance of SCR in shaping a behavioral syndrome at the species level across poeciliid taxa
Allele frequencies for allele <i>CYP2D6*5</i> (whole gene deletion) in different HARE groups.
No full textIn addition, we show allele frequencies in the three components of the HARE HIS group (EUR, AFR, AMR) calculated using individuals ancestry-homozygous at CYP2D6.</p
CYP2D6 allele frequencies for three MVP HARE groups, MVP Local Ancestry Inference (LAI) and two publicly available data sets: 1000 genome project and gnomAD.
No full textOnly consensus Tier 1 alleles [9] are shown. We note that we did not perform LAI in HARE EUR samples. Thus LAI frequencies are identical by default to HARE EUR frequencies. For HARE HIS, LAI corresponds to the AMR track allele frequencies (3-way deconvolution). We estimate imputation quality per site and ethnicity. We do not present allele frequencies for poorly imputed sites.</p
