Continuous Deployment Transitions at Scale

Predictable, rapid, and data-driven feature rollout; lightning-fast; and automated fix deployment are some of the benefits most large software organizations worldwide are striving for. In the process, they are transitioning toward the use of continuous deployment practices. Continuous deployment enables companies to make hundreds or thousands of software changes to live computing infrastructure every day while maintaining service to millions of customers. Such ultra-fast changes create a new reality in software development. Over the past four years, the Continuous Deployment Summit, hosted at Facebook, Netflix, Google, and Twitter has been held. Representatives from companies like Cisco, Facebook, Google, IBM, Microsoft, Netflix, and Twitter have shared the triumphs and struggles of their transition to continuous deployment practices—each year the companies press on, getting ever faster. In this chapter, the authors share the common strategies and practices used by continuous deployment pioneers and adopted by newcomers as they transition and use continuous deployment practices at scale

Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm

Citation: Boyles, R. E., Cooper, E. A., Myers, M. T., Brenton, Z., Rauh, B. L., Morris, G. P., & Kresovich, S. (2016). Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm. Plant Genome, 9(2), 17. doi:10.3835/plantgenome2015.09.0091Grain yield and its primary determinants, grain number and weight, are important traits in cereal crops that have been well studied; however, the genetic basis of and interactions between these traits remain poorly understood. Characterization of grain yield per primary panicle (YPP), grain number per primary panicle (GNP), and 1000-grain weight (TGW) in sorghum [Sorghum bicolor (L.) Moench], a hardy C-4 cereal with a genome size of similar to 730 Mb, was implemented in a diversity panel containing 390 accessions. These accessions were genotyped to obtain 268,830 single-nucleotide polymorphisms (SNPs). Genome-wide association studies (GWAS) were performed to identify loci associated with each grain yield component and understand the genetic interactions between these traits. Genome-wide association studies identified associations across the genome with YPP, GNP, and TGW that were located within previously mapped sorghum QTL for panicle weight, grain yield, and seed size, respectively. There were no significant associations between GNP and TGW that were within 100 kb, much greater than the average linkage disequilibrium (LD) in sorghum. The identification of nonoverlapping loci for grain number and weight suggests these traits may be manipulated independently to increase the grain yield of sorghum. Following GWAS, genomic regions surrounding each associated SNP were mined for candidate genes. Previously published expression data indicated several TGW candidate genes, including an ethylene receptor homolog, were primarily expressed within developing seed tissues to support GWAS. Furthermore, maize (Zea mays L.) homologs of identified TGW candidates were differentially expressed within the seed between small- and large-kernel lines from a segregating maize population

Near Resonant Spatial Images of Confined Bose-Einstein Condensates in the '4D' Magnetic Bottle

We present quantitative measurements of the spatial density profile of Bose-Einstein condensates of sodium atoms confined in a new '4D' magnetic bottle. The condensates are imaged in transmission with near resonant laser light. We demonstrate that the Thomas-Fermi surface of a condensate can be determined to better than 1%. More generally, we obtain excellent agreement with mean-field theory. We conclude that precision measurements of atomic scattering lengths and interactions between phase separated cold atoms in a harmonic trap can be measured with high precision using this method.Comment: 15 pages, 3 figures. Submitted 10/30/97, accepted for publication in Phys. Rev. A Rapid Com

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Moderate (2%, v/v) Ethanol Feeding Alters Hepatic Wound Healing after Acute Carbon Tetrachloride Exposure in Mice

Wound healing consists of three overlapping phases: inflammation, proliferation, and matrix synthesis and remodeling. Prolonged alcohol abuse can cause liver fibrosis due to deregulated matrix remodeling. Previous studies demonstrated that moderate ethanol feeding enhances liver fibrogenic markers and frank fibrosis independent of differences in CCl4-induced liver injury. Our objective was to determine whether or not other phases of the hepatic wound healing response were affected by moderate ethanol after CCl4 exposure. Mice were fed moderate ethanol (2% v/v) for two days and then were exposed to CCl4 and euthanized 24–96 h later. Liver injury was not different between pair- and ethanol-fed mice; however, removal of necrotic tissue was delayed after CCl4-induced liver injury in ethanol-fed mice. Inflammation, measured by TNFα mRNA and protein and hepatic Ly6c transcript accumulation, was reduced and associated with enhanced hepatocyte apoptosis after ethanol feeding. Hepatocytes entered the cell cycle equivalently in pair- and ethanol-fed mice after CCl4 exposure, but hepatocyte proliferation was prolonged in livers from ethanol-fed mice. CCl4-induced hepatic stellate cell activation was increased and matrix remodeling was prolonged in ethanol-fed mice compared to controls. Taken together, moderate ethanol affected each phase of the wound healing response to CCl4. These data highlight previously unknown effects of moderate ethanol exposure on hepatic wound healing after acute hepatotoxicant exposure

PSI4 1.4 : Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.Peer reviewe

Range-wide conservation genetics of Buff-breasted Sandpipers (Tryngites subruficollis)

Range-wide monitoring of shorebirds (Aves: Charadriiformes) suggests that many species are declining. For most species, it is unknown whether distinct population units exist, which makes management and conservation difficult. One shorebird of conservation concern, the Buff-breasted Sandpiper (Tryngites subruficollis), is a New World migrant that breeds at Arctic latitudes in North America and Russia and winters in southeastern South America. We conducted a molecular survey of samples representing each of three migratory regions (breeding, migration, and wintering) using nine polymorphic microsatellite loci and 1.5 kb of highly variable mitochondrial DNA (mtDNA) from the cytochrome b gene and mtDNA control region. We analyzed contemporary population structure, demographic trends, and phylogeographic patterns. Overall, microsatellite and mtDNA analyses revealed that Buff-breasted Sandpipers are panmictic both regionally and at a global scale, with no signal of a recent genetic bottleneck. The mtDNA analyses revealed a pattern of haplotype diversity consistent with an expansion from a single refugium (Tajima's D: -2.27, P < 0.01; Fu's F[subscript s]: -30.6, P < 0.0001), after the height of the Wisconsinan glaciation (8,400–45,000 years before present). Overall, our molecular analyses suggest that Buff-breasted Sandpipers should be treated as a single conservation unit, and management efforts for this species should focus on limiting future declines to ensure that genetic viability is maintained