358 research outputs found
Data From: Selecting optimal partitioning schemes for phylogenomic datasets.
No full text<p>This collection includes all of the input files, results, and scripts to generate the figures found in this paper: Selecting optimal partitioning schemes for phylogenomic datasets. Robert Lanfear, Brett Calcott, David Kainer, Christoph Mayer, Alexandros Statmatakis Which is accepted at BMC Evolutionary Biology</p
Reproduction Files for: Inequalities in Exposure to Firearm Violence by Race, Sex, and Birth Cohort from Childhood to Age 40 Years, 1995-2021.
No full textThis dataverse contains reproduction files for: Charles C. Lanfear, Rebecca Bucci, David S. Kirk, and Robert J. Sampson. "Inequalities in Exposure to Firearm Violence by Race, Sex, and Birth Cohort from Childhood to Age 40 Years, 1995-2021,” JAMA Network Open. 2023;6(5):e2312465.doi:10.1001/jamanetworkopen.2023.12465.
The restricted PHDCN+ data required for reproducing the paper are available through a Data Use Agreement (DUA). To access these data, users must complete and sign the DUA included in the reproducibility files and return it to [email protected]. Users agree not to use the data other than for reproducibility purposes and in no case shall any attempts to be made to link other sources of information or to use combinations of variables to identify individuals
Gun Carrying from Adolescence to Adulthood: Initiation, Continuity, and Exposure to Gun Violence across the Life Course
No full textThis project is a continuation of the following OSF preregistration:
Lanfear, C. C., Kirk, D., Sampson, R., & Bucci, R. (2022, June 16). The changing risks of exposure to gun violence among multiple cohorts of children living in Chicago in the mid 1990s and followed over a 25-year period. https://doi.org/10.17605/OSF.IO/4K2AM
That preregistration resulted in the following publication:
Lanfear, C. C., Bucci, R., Kirk, D., & Sampson, R. (2023). Inequalities in Exposure to Firearm Violence by Race, Sex, and Birth Cohort From Childhood to Age 40 Years, 1995-2021. JAMA Network Open, 6(5):e2312465. https://doi.org/10.1001/jamanetworkopen.2023.12465
The initial preregistration focused on both exposure to gun violence and gun behaviors, i.e., carrying and use, but these outcomes were separated to produce more focused and cohesive papers. Lanfear et al. (2023) examined exposure to gun violence. The present project examines gun carrying and gun use. Accordingly, relevant material from the initial preregistration completed June 16th, 2022 is reused or edited. Where relevant, it is noted when analyses were conducted in relation to the initial or current preregistration plan.
This study is a descriptive analysis of patterns in onset of concealed gun carrying using data from the PHDCN+ (where onset is defined as the first instance of carrying a concealed weapon, whether legally or illegally): five survey waves on four birth cohorts living in Chicago in 1995 separated in age by 15 years who were studied from 1995 through 2021—including those who moved out of Chicago. We leverage the multicohort design of the PHDCN+ to examine differences in timing of onset across demographic groups and how timing of onset is related to prior exposure to gun violence, recent gun carrying, and onset of gun use. We use survival models and logistic regression to estimate age-specific probabilities of ever carrying a concealed gun
Pharmacogenetics of ophthalmic topical β-blockers
No full textGlaucoma is the second leading cause of blindness worldwide. The primary glaucoma risk factor is elevated intraocular pressure. Topical β-blockers are affordable and widely used to lower intraocular pressure. Genetic variability has been postulated to contribute to interpersonal differences in efficacy and safety of topical β-blockers. This review summarizes clinically significant polymorphisms that have been identified in the β-adrenergic receptors (ADRB1, ADRB2 and ADRB3). The implications of polymorphisms in CYP2D6 are also discussed. Although the candidate-gene approach has facilitated significant progress in our understanding of the genetic basis of glaucoma treatment response, most drug responses involve a large number of genes, each containing multiple polymorphisms. Genome-wide association studies may yield a more comprehensive set of polymorphisms associated with glaucoma outcomes. An understanding of the genetic mechanisms associated with variability in individual responses to topical β-blockers may advance individualized treatment at a lower cost
Are the deuterostome posterior Hox genes a fast-evolving class?
No full textThere has been a great deal of interest in analysing the molecular evolution of the Hox cluster using both bioinformatic and experimental approaches. The posterior Hox genes have been of particular interest to both groups of biologists for a number of reasons: they appear to be associated with the evolution of a number of morphological novelties; the protostomes appear to be have lost a highly-conserved and functionally important amino acid motif (the hexapeptide motif) from their posterior Hox genes; and deuterostome posterior Hox genes seem to be evolving more quickly than all other Hox genes. In this chapter I will discuss the last of these points. The idea that Deuterostome posterior Hox genes were evolving more quickly than other Hox genes was first suggested by David Ferrier and colleagues. In this chapter, I start by introducing the posterior Hox genes--their distribution among the animal phyla and the likely sequence of duplications that led to this distribution. I then introduce the idea of 'deuterostome posterior flexibility' and examine this hypothesis in light of more recent phylogenetic and genomic work on the Hox cluster. Finally, I discuss some new approaches that could be used to test directly for differential rates of evolution among Hox genes and to assess what might underlie these differences.12 page(s
Pharmacogenomics of the Natriuretic Peptide System in Heart Failure
No full textPURPOSE OF REVIEW: Heart failure (HF) continues to be a public health burden despite advances in therapy, and the natriuretic peptide (NP) system is clearly of critical importance in this setting, spawning valuable diagnostic and prognostic testing, such as B-type natriuretic peptide (BNP) and N-terminal pro-BNP (NT-proBNP), as well as current and future therapeutics, including recombinant natriuretic peptides (e.g., carperitide, nesiritide) and recently sacubitril, which inhibits the key clearance mechanism for NPs. This article intends to summarize the existing evidence for the role of NP system genetic variation on cardiovascular phenotypes relevant to HF with particular focus on the potential impact on pharmacologic therapies.
RECENT FINDINGS: Several genes in NP system have been interrogated, in many cases genetic variation impacting protein quantity and function or related disease states. Recent data supports genetic variants potentially impacting pharmacokinetics or dynamics of medications targeting the pathway. Growing evidence indicates the importance of genetic variation to the functioning of the NP system and its pharmacologic manipulation
Pharmacogenomics in heart failure: where are we now and how can we reach clinical application?
No full textHeart failure is becoming increasingly prevalent in the United States and is a significant cause of morbidity and mortality. Several therapies are currently available to treat this chronic illness; however, clinical response to these treatment options exhibit significant interpatient variation. It is now clearly understood that genetics is a key contributor to diversity in therapeutic response, and evidence that genetic polymorphisms alter the pharmacokinetics, pharmacodynamics, and clinical response of heart failure drugs continues to accumulate. This suggests that pharmacogenomics has the potential to help clinicians improve the management of heart failure by choosing the safest and most effective medications and doses. Unfortunately, despite much supportive data, pharmacogenetic optimization of heart failure treatment regimens is not yet a reality. In order to attenuate the rising burden of heart failure, particularly in the context of the recent paucity of new effective interventions, there is an urgent need to extend pharmacogenetic knowledge and leverage these associations in order to enhance the effectiveness of existing heart failure therapies. This review focuses on the current state of pharmacogenomics in heart failure and provides a glimpse of the aforementioned future needs
Pharmacogenetic Risk Scores for Perindopril Clinical and Cost Effectiveness in Stable Coronary Artery Disease: When Are We Ready to Implement?
No full textMOESM1 of Molecular differentiation of the Murraya paniculata Complex (Rutaceae: Aurantioideae: Aurantieae)
No full textAdditional file 1 Table S1. List of accessions of Murraya and Merrillia used for molecular phylogenetic analyses and the locations from which they were sourced. Table S2. GenBank accession numbers for the regions used to determine the monophyly and dating of divergence of the Murraya accessions. Figure S1. Phylogenetic analysis of the combined sequences of six chloroplastal regions from accessions of Murraya and Merrillia. Figure S2. 50% majority-rule bootstrap consensus tree based on the indels of six chloroplastal regions from accessions of Murraya and Merrillia derived from maximum parsimony analysis. Figure S3. Phylogenetic analysis by of the ITS regions of accessions of Murraya. Figure S4. Bayesian inference tree based on the 6 chloroplastal regions combined with the ITS region of accessions of Murraya and Merrillia following partitioning and model selection using PartitionFinder 2 (Lanfear et al. 2016) using the greedy algorthim (Lanfear et al. 2012)
- …
