Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success

Background Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of ‘putative’ SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. Results Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. Conclusions Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future studies of non-model organisms

Relativistic Proton Production During the 14 July 2000 Solar Event: The Case for Multiple Source Mechanisms

Protons accelerated to relativistic energies by transient solar and interplanetary phenomena caused a ground-level cosmic ray enhancement on 14 July 2000, Bastille Day. Near-Earth spacecraft measured the proton flux directly and ground-based observatories measured the secondary responses to higher energy protons. We have modelled the arrival of these relativistic protons at Earth using a technique which deduces the spectrum, arrival direction and anisotropy of the high-energy protons that produce increased responses in neutron monitors. To investigate the acceleration processes involved we have employed theoretical shock and stochastic acceleration spectral forms in our fits to spacecraft and neutron monitor data. During the rising phase of the event (10:45 UT and 10:50 UT) we find that the spectrum between 140 MeV and 4 GeV is best fitted by a shock acceleration spectrum. In contrast, the spectrum at the peak (10:55 UT and 11:00 UT) and in the declining phase (11:40 UT) is best fitted with a stochastic acceleration spectrum. We propose that at least two acceleration processes were responsible for the production of relativistic protons during the Bastille Day solar event: (1) protons were accelerated to relativistic energies by a shock, presumably a coronal mass ejection (CME). (2) protons were also accelerated to relativistic energies by stochastic processes initiated by magnetohydrodynamic (MHD) turbulence.Comment: 38 pages, 9 figures, accepted for publication in the Astrophysical Journal, January, 200

An Improved Model for Relativistic Solar Proton Acceleration applied to the 2005 January 20 and Earlier Events

This paper presents results on modelling the ground level response of the higher energy protons for the 2005 January 20 ground level enhancement (GLE). This event, known as GLE 69, produced the highest intensity of relativistic solar particles since the famous event on 1956 February 23. The location of recent X-ray and gamma-ray emission (N14 W61) was near to Sun-Earth connecting magnetic field lines, thus providing the opportunity to directly observe the acceleration source from Earth. We restrict our analysis to protons of energy greater than 450 MeV to avoid complications arising from transport processes that can affect the propagation of low energy protons. In light of this revised approach we have reinvestigated two previous GLEs: those of 2000 July 14 (GLE 59) and 2001 April 15 (GLE 60). Within the limitations of the spectral forms employed, we find that from the peak (06:55 UT) to the decline (07:30 UT) phases of GLE 69, neutron monitor observations from 450 MeV to 10 GeV are best fitted by the Gallegos-Cruz & Perez-Peraza stochastic acceleration model. In contrast, the Ellison & Ramaty spectra did not fit the neutron monitor observations as well. This result suggests that for GLE 69, a stochastic process cannot be discounted as a mechanism for relativistic particle acceleration, particularly during the initial stages of this solar event. For GLE 59 we find evidence that more than one acceleration mechanism was present, consistent with both shock and stochastic acceleration processes dominating at different times of the event. For GLE 60 we find that Ellison & Ramaty spectra better represent the neutron monitor observations compared to stochastic acceleration spectra. The results for GLEs 59 and 60 are in agreement with our previous work.Comment: 42 pages, 10 figures, 10 tables, published in ApJ, August 200

Mental Health First Aid USA: The Implementation of a Mental Health First Aid Training Program in a Rural Healthcare Setting

Nearly one-quarter of adults in the United States suffer from a documented mental disorder. Consequently, anyone could encounter a person with symptoms of mental illness at some point as they carry out their daily life activities. Although laypersons may accurately identify physical illnesses, they may lack necessary skills to identify symptoms of mental disorders, or know how to adequately respond to persons in a mental health crisis. Mental Health First Aid USA is an evidence-based certification program designed to teach lay citizens to recognize certain symptoms of common mental illnesses, offer and provide first aid assistance, and guide a person toward appropriate services and other support. The program targets a broad audience, from teachers, police officers, clergy members, and healthcare professionals to the average citizen volunteer. This practice note describes a pilot implementation of Mental Health First Aid USA by a social worker at a rural hospital in Central California. The process and results of program implementation are discussed as well as implications for social work practice in rural healthcare settings

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

Configuration Smells in Continuous Delivery Pipelines: A Linter and a Six-Month Study on GitLab

An effective and efficient application of Continuous Integration (CI) and Delivery (CD) requires software projects to follow certain principles and good practices. Configuring such a CI/CD pipeline is challenging and error-prone. Therefore, automated linters have been proposed to detect errors in the pipeline. While existing linters identify syntactic errors, detect security vulnerabilities or misuse of the features provided by build servers, they do not support developers that want to prevent common misconfigurations of a CD pipeline that potentially violate CD principles (“CD smells”). To this end, we propose CD-Linter, a semantic linter that can automatically identify four different smells in pipeline configuration files. We have evaluated our approach through a large-scale and long-term study that consists of (i) monitoring 145 issues (opened in as many open-source projects) over a period of 6 months, (ii) manually validating the detection precision and recall on a representative sample of issues, and (iii) assessing the magnitude of the observed smells on 5,312 open-source projects on GitLab. Our results show that CD smells are accepted and fixed by most of the developers and our linter achieves a precision of 87% and a recall of 94%. Those smells can be frequently observed in the wild, as 31% of projects with long configurations are affected by at least one smell

RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding

Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization

Iconic dishes, culture and identity: the Christmas pudding and its hundred years’ journey in the USA, Australia, New Zealand and India

Asserting that recipes are textual evidences reflecting the society that produced them, this article explores the evolution of the recipes of the iconic Christmas pudding in the United States, Australia, New Zealand and India between the mid-nineteenth and the mid-twentieth centuries. Combining a micro-analysis of the recipes and the cookbook that provided them with contemporary testimonies, the article observes the dynamics revealed by the preparation and consumption of the pudding in these different societies. The findings demonstrate the relevance of national iconic dishes to the study of notions of home, migration and colonization, as well as the development of a new society and identity. They reveal how the preservation, transformation and even rejection of a traditional dish can be representative of the complex and sometimes conflicting relationships between colonists, migrants or new citizens and the places they live in