Theory of Single Charge Exchange Heavy Ion Reactions

The theory of heavy ion single charge exchange reactions is reformulated. In momentum space the reaction amplitude factorizes into a product of projectile and target transition form factors, folded with the nucleon-nucleon isovector interaction and a distortion coefficient which accounts for initial and final state ion-ion elastic interactions. The multipole structure of the transition form factors is studied in detail for Fermi-type non-spin flip and Gamow-Teller-type spin flip transitions, also serving to establish the connection to nuclear beta decay. The reaction kernel is evaluated for central and rank-2 tensor interactions. Initial and final state elastic ion-ion interaction are shown to be dominated by the imaginary part of the optical potential allowing to evaluate the reaction coefficients in the strong absorption limit, realized by the black disk approximation. In that limit the distortion coefficient is evaluated in closed form, revealing the relation to the total reaction cross section and the geometry of the transition form factors. It is shown that at small momentum transfer distortion effects reduce to a simple scaling factor, allowing to define reduced forward-angle cross section which is given by nuclear matrix elements of beta decay-type. The response function formalism is used to describe nuclear charge changing transitions. Spectral distributions obtained by a self-consistent HFB and QRPA approach are discussed for $\tau_\pm$ excitations of $^{18}O$ and $^{40}Ca$, respectively, and compared to spectroscopic data. The interplay of nuclear structure and reaction dynamics is illustrated for the single charge exchange reaction $^{18}O+^{40}Ca \to ^{18}F+^{40}K$ at $T_{lab}=270$ MeV

Ambulatory Care Pharmacy Resident

Objectives: 1. Review the background, epidemiology, and diagnostic criteria for the antiphospholipid syndrome 2. List clinical manifestations associated with antiphospholipid syndrome 3. Describe the pathophysiology of thrombosis in the antiphospholipid syndrome 4. Evaluate the evidence for the different intensities of oral anticoagulation in the 1. Background 1-3 i. Antiphospholipid syndrome (APS) is an autoimmune disease characterized by the presence of antiphospholipid antibodies (aPL)

Successful ATAC-Seq From Snap-Frozen Equine Tissues

An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin to characterize tissue specificity of genome function for prioritized tissues have been performed. Due to the logistics of tissue collection and storage, extracting nuclei from a large number of tissues for ATAC-seq at the time of collection is not always practical. To assess the feasibility of using stored frozen tissues for ATAC-seq and to provide a guideline for the equine FAANG project, we compared ATAC-seq results from nuclei isolated from frozen tissue to cryopreserved nuclei (CN) isolated at the time of tissue harvest in liver, a highly cellular homogenous tissue, and lamina, a relatively acellular tissue unique to the horse. We identified 20,000– 33,000 accessible chromatin regions in lamina and 22–61,000 in liver, with consistently more peaks identified using CN isolated at time of tissue collection. Our results suggest that frozen tissues are an acceptable substitute when CN are not available. For more challenging tissues such as lamina, nuclei extraction at the time of tissue collection is still preferred for optimal results. Therefore, tissue type and accessibility to intact nuclei should be considered when designing ATAC-seq experiments

Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq.

One of the primary aims of the Functional Annotation of ANimal Genomes (FAANG) initiative is to characterize tissue-specific regulation within animal genomes. To this end, we used chromatin immunoprecipitation followed by sequencing (ChIP-Seq) to map four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) in eight prioritized tissues collected as part of the FAANG equine biobank from two thoroughbred mares. Data were generated according to optimized experimental parameters developed during quality control testing. To ensure that we obtained sufficient ChIP and successful peak-calling, data and peak-calls were assessed using six quality metrics, replicate comparisons, and site-specific evaluations. Tissue specificity was explored by identifying binding motifs within unique active regions, and motifs were further characterized by gene ontology (GO) and protein-protein interaction analyses. The histone marks identified in this study represent some of the first resources for tissue-specific regulation within the equine genome. As such, these publicly available annotation data can be used to advance equine studies investigating health, performance, reproduction, and other traits of economic interest in the horse

Decoding the Equine Genome: Lessons from ENCODE

The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era

GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.</p