Assessment of OvineSNP50 in Nigerian and Kenyan sheep populations

Deciphering genomic information requires markers that are polymorphic and sufficient enough to capture its vast array of genetic data. Polymorphic loci can differ greatly between breeds of the same species and the exclusion of the Nigerian and some African sheep breeds during the development of the OvineSNP50 chip necessitated the validation of SNPs included on the chip to allow for genomic applications of the excluded breeds. A total of sixty sheep samples were genotyped [10 each of the Balami, Uda, West African Dwarf and Yankasa from Nigeria, Dorper and Red Maasai from Kenya (East Africa)] using the Ovine 50k Illumina SNP bead chip. Results revealed that 33,994 SNPs (97.47%) of the called 34,876 SNPs were validated for downstream analysis. Mean heterozygosity values of 0.154 and 0.153 were obtained for polymorphic SNPs on sex and autosomal chromosomes respectively, while the values of 0.662 and 0.054 were obtained on the sex and autosomal chromosomes respectively for the mean identity-bystate (IBS). Six and three individuals violated the per ID and identity-by-state (IBS) thresholds, respectively. It was observed that the Ovine 50k Illumina SNP bead chip wasinformative in the Nigerian and East African sheep that were studied, and should be useful in examining the underlying genetic variation.Keywords: Sheep, OvineSNP50, genome-wide, call rate, minor allele frequenc

The position of graptolites within Lower Palaeozoic planktic ecosystems.

An integrated approach has been used to assess the palaeoecology of graptolites both as a discrete group and also as a part of the biota present within Ordovician and Silurian planktic realms. Study of the functional morphology of graptolites and comparisons with recent ecological analogues demonstrates that graptolites most probably filled a variety of niches as primary consumers, with modes of life related to the colony morphotype. Graptolite coloniality was extremely ordered, lacking any close morphological analogues in Recent faunas. To obtain maximum functional efficiency, graptolites would have needed varying degrees of coordinated automobility. A change in lifestyle related to ontogenetic changes was prevalent within many graptolite groups. Differing lifestyle was reflected by differing reproductive strategies, with synrhabdosomes most likely being a method for rapid asexual reproduction. Direct evidence in the form of graptolithophage 'coprolitic' bodies, as well as indirect evidence in the form of probable defensive adaptations, indicate that graptolites comprised a food item for a variety of predators. Graptolites were also hosts to a variety of parasitic organisms and provided an important nutrient source for scavenging organisms

Nuclear Skins and Halos in the Mean-Field Theory

Nuclei with large neutron-to-proton ratios have neutron skins, which manifest themselves in an excess of neutrons at distances greater than the radius of the proton distribution. In addition, some drip-line nuclei develop very extended halo structures. The neutron halo is a threshold effect; it appears when the valence neutrons occupy weakly bound orbits. In this study, nuclear skins and halos are analyzed within the self-consistent Skyrme-Hartree-Fock-Bogoliubov and relativistic Hartree-Bogoliubov theories for spherical shapes. It is demonstrated that skins, halos, and surface thickness can be analyzed in a model-independent way in terms of nucleonic density form factors. Such an analysis allows for defining a quantitative measure of the halo size. The systematic behavior of skins, halos, and surface thickness in even-even nuclei is discussed.Comment: 22 RevTeX pages, 22 EPS figures included, submitted to Physical Review

Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program

Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs

Dexamethasone intravitreal implant in previously treated patients with diabetic macular edema : Subgroup analysis of the MEAD study

Background: Dexamethasone intravitreal implant 0.7 mg (DEX 0.7) was approved for treatment of diabetic macular edema (DME) after demonstration of its efficacy and safety in the MEAD registration trials. We performed subgroup analysis of MEAD study results to evaluate the efficacy and safety of DEX 0.7 treatment in patients with previously treated DME. Methods: Three-year, randomized, sham-controlled phase 3 study in patients with DME, best-corrected visual acuity (BCVA) of 34.68 Early Treatment Diabetic Retinopathy Study letters (20/200.20/50 Snellen equivalent), and central retinal thickness (CRT) 65300 \u3bcm measured by time-domain optical coherence tomography. Patients were randomized to 1 of 2 doses of DEX (0.7 mg or 0.35 mg), or to sham procedure, with retreatment no more than every 6 months. The primary endpoint was 6515-letter gain in BCVA at study end. Average change in BCVA and CRT from baseline during the study (area-under-the-curve approach) and adverse events were also evaluated. The present subgroup analysis evaluated outcomes in patients randomized to DEX 0.7 (marketed dose) or sham based on prior treatment for DME at study entry. Results: Baseline characteristics of previously treated DEX 0.7 (n = 247) and sham (n=261) patients were similar. In the previously treated subgroup, mean number of treatments over 3 years was 4.1 for DEX 0.7 and 3.2 for sham, 21.5 % of DEX 0.7 patients versus 11.1 % of sham had 6515-letter BCVA gain from baseline at study end (P = 0.002), mean average BCVA change from baseline was +3.2 letters with DEX 0.7 versus +1.5 letters with sham (P = 0.024), and mean average CRT change from baseline was -126.1 \u3bcm with DEX 0.7 versus -39.0 \u3bcm with sham(P < 0.001). Cataract-related adverse events were reported in 70.3 % of baseline phakic patients in the previously treated DEX 0.7 subgroup; vision gains were restored following cataract surgery. Conclusions: DEX 0.7 significantly improved visual and anatomic outcomes in patients with DME previously treated with laser, intravitreal anti-vascular endothelial growth factor, intravitreal triamcinolone acetonide, or a combination of these therapies. The safety profile of DEX 0.7 in previously treated patients was similar to its safety profile in the total study population