Kronos: a workflow assembler for genome analytics and informatics.

BackgroundThe field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.ResultsWe present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows.ConclusionsThe Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos

Academic, socioeconomic and interpersonal consequences of cannabis use : a narrative review

This article reviews the literature on the association between cannabis use (CU) and psychosocial functioning, operationalized here as academic achievement, economic prospects, social relationships and quality of life. So far, study results have been inconsistent. To clarify whether CU has an impact on psychosocial functioning, this article mainly reviewed prospective and longitudinal studies published since 2000 and examined whether studies controlled for confounding factors (e.g. socio-demographics, other substance use, psychopathology, social environment). The review suggested that when confounding variables are controlled for, the association between CU and psychosocial outcomes is generally small or non-significant. When significant associations remain, they are for chronic, dependent or early onset CU specifically, suggesting that the frequency of use and age of onset may be necessary elements to detect persistent, however small, psychosocial consequences. These results illustrate the importance of controlling for intra- and inter-individual differences to examine the link between CU and later psychosocial functioning. Results also suggest that policy and prevention efforts should consider targeting the individual and environmental factors (e.g. early academic and cognitive functioning, social disadvantage, family functioning, personality, smoking) that account for much of the association between CU and later psychosocial problems, rather than, or in addition to, CU itself

Molecular profiling in diffuse large B‐cell lymphoma: why so many types of subtypes?

Funder: Michael Smith Foundation for Health Research; Id: http://dx.doi.org/10.13039/501100000245Summary: The term diffuse large B‐cell lymphoma (DLBCL) includes a heterogeneous collection of biologically distinct tumours. This heterogeneity currently presents a barrier to the successful deployment of novel, biologically targeted therapies. Molecular profiling studies have recently proposed new molecular classification systems. These have the potential to resolve the biological heterogeneity of DLBCL into manageable subgroups of tumours that rely on shared oncogenic programmes. In many cases these biological programmes straddle the boundaries of our existing systems for classifying B‐cell lymphomas. Here we review the findings from these major molecular profiling studies with a specific focus on those that propose new genetic subgroups of DLBCL. We highlight the areas of consensus and discordance between these studies and discuss the implications for current clinical practice and for clinical trials. Finally, we address the outstanding challenges and solutions to the introduction of genomic subtyping and precision medicine in DLBCL

Pemanfaatan Teknologi Digital untuk Meningkatkan Pemasaran UMKM Pada Kedai Joglo Bolo Seno

Usaha Mikro, Kecil dan Menengah (UMKM) merupakan kegiatan ekonomi rakyat yang berskala kecil dan menengah. Data UMKM di Kota Yogyakarta menunjukan adanya empat puluh delapan ribu UMKM. Faktor keberhasilan UMKM di antaranya adalah promosi melalui media sosial dan mengikuti event atau pameran. Salah satu teknologi yang dapat dimanfaatkan UMKM untuk mempromosikan produknya adalah media sosial, seperti Instagram. Pengabdian ini dilakukan guna untuk meningkatkan pemasaran UMKM pada kedai Joglo Bolo Seno dengan memberikan pemahaman dan pelatihan media sosial, serta e-commerce sebagai media pemasaran. Metode yang digunakan pada pengabdian ini terdapat 3 tahapan metode yaitu pelatihan menggunakan e-commerce, pelatihan menggunakan media sosial Instagram, dan pelatihan menggunakan aplikasi canva. Hasil dari pengabdian ini berupa akun Instagram, akun Shopee-Food, akun Go-Food, dan pelatihan menggunakan aplikasi canva untuk membuat desain konten media sosial. Dari pengabdian ini diharapkan UMKM Joglo Bolo Seno dapat berkembang dengan adanya modernisasi bisnis

A longitudinal analysis of motivation profiles at work

This paper examines the multidimensional nature of workplace motivation and the importance of a continuum structure in self-determination theory through application of complementary variable- and person-centered approaches. This approach is taken to simultaneously model the complexity of motivation and highlight interactions between motivational factors. Additionally, this study represents an initial test of the temporal stability of work motivation profiles. A sample of 510 full-time employees were recruited from a range of occupations. Results support the central importance of a general factor representing self-determination as the most influential factor in an employee’s motivation profile. However, smaller effects associated with the motivation subscales, especially identified regulation, were also noticed. Importantly, motivation profiles were found to be highly stable over the 4-month duration of this study. Results lend support to the theoretical position that while general self-determination is an essential component of motivation, it alone does not fully describe an employee’s motivation

Indigenous Sex-selective Salmon Harvesting Demonstrates Pre-contact Marine Resource Management in Burrard Inlet, British Columbia, Canada

To gain insight into pre-contact Coast Salish fishing practices, we used new palaeogenetic analytical techniques to assign sex identifications to salmonid bones from four archaeological sites in Burrard Inlet (Tsleil-Waut), British Columbia, Canada, dating between about 2300–1000 BP (ca. 400 BCE–CE 1200). Our results indicate that male chum salmon (Oncorhynchus keta) were preferentially targeted at two of the four sampled archaeological sites. Because a single male salmon can mate with several females, selectively harvesting male salmon can increase a fishery’s maximum sustainable harvest. We suggest such selective harvesting of visually distinctive male spawning chum salmon was a common practice, most effectively undertaken at wooden weirs spanning small salmon rivers and streams. We argue that this selective harvesting of males is indicative of an ancient and probably geographically widespread practice for ensuring sustainable salmon populations. The archaeological data presented here confirms earlier ethnographic accounts describing the selective harvest of male salmon

The Influence of Overweight and Obesity on Longitudinal Trends in Maternal Serum Leptin Levels During Pregnancy

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/93689/1/oby.2010.172.pd

Genetic heterogeneity in primary and relapsed mantle cell lymphomas : impact of recurrent CARD11 mutations

The genetic mechanisms underlying disease progression, relapse and therapy resistance in mantle cell lymphoma (MCL) remain largely unknown. Whole-exome sequencing was performed in 27 MCL samples from 13 patients, representing the largest analyzed series of consecutive biopsies obtained at diagnosis and/or relapse for this type of lymphoma. Eighteen genes were found to be recurrently mutated in these samples, including known (ATM, MEF2B and MLL2) and novel mutation targets (S1PR1 and CARD11). CARD11, a scaffold protein required for B-cell receptor (BCR)-induced NF-κB activation, was subsequently screened in an additional 173 MCL samples and mutations were observed in 5.5% of cases. Based on in vitro cell line-based experiments, overexpression of CARD11 mutants were demonstrated to confer resistance to the BCR-inhibitor ibrutinib and NF-κB-inhibitor lenalidomide. Genetic alterations acquired in the relapse samples were found to be largely non-recurrent, in line with the branched evolutionary pattern of clonal evolution observed in most cases. In summary, this study highlights the genetic heterogeneity in MCL, in particular at relapse, and provides for the first time genetic evidence of BCR/NF-κB activation in a subset of MCL

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

Motivation: Next-generation sequencing (NGS) has enabled whole genome and transcriptome single nucleotide variant (SNV) discovery in cancer. NGS produces millions of short sequence reads that, once aligned to a reference genome sequence, can be interpreted for the presence of SNVs. Although tools exist for SNV discovery from NGS data, none are specifically suited to work with data from tumors, where altered ploidy and tumor cellularity impact the statistical expectations of SNV discovery