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ContextSoftware selection in large-scale software development continues to be ad hoc and ill-structured. Previous proposals for software component selection tend to be technology-specific and/or do not consider business or ecosystem concerns.ObjectiveOur main aim is to develop an industrially relevant technology-agnostic method that can support practitioners in making informed decisions when selecting software components for use in tools or in products based on a holistic perspective of the overall environment.MethodWe used method engineering to iteratively develop a software selection method for Ericsson AB based on a combination of published research and practitioner insights. We used interactive rapid reviews to systematically identify and analyse scientific literature and to support close cooperation and co-design with practitioners from Ericsson. The model has been validated through a focus group and by practical use at the case company.ResultsThe model consists of a high-level selection process and a wide range of criteria for assessing and for evaluating software to include in business products and tools.ConclusionsWe have developed an industrially relevant model for component selection through active engagement from a company. Co-designing the model based on previous knowledge demonstrates a viable approach to industry-academia collaboration and provides a practical solution that can support practitioners in making informed decisions based on a holistic analysis of business, organisation and technical factors.

Background Genetic influence on DNA methylation is potentially an important mechanism affecting individual differences in humans. We use next-generation sequencing to assay blood DNA methylation at approximately 4.5 million loci, each comprising 2.9 CpGs on average, in 697 normal subjects. Methylation measures at each locus are tested for association with approximately 4.5 million single nucleotide polymorphisms (SNPs) to exhaustively screen for methylation quantitative trait loci (meQTLs). Results Using stringent false discovery rate control, 15 % of methylation sites show genetic influence. Most meQTLs are local, where the associated SNP and methylation site are in close genomic proximity. Distant meQTLs and those spanning different chromosomes are less common. Most local meQTLs encompass common SNPs that alter CpG sites (CpG-SNPs). Local meQTLs encompassing CpG-SNPs are enriched in regions of inactive chromatin in blood cells. In contrast, local meQTLs lacking CpG-SNPs are enriched in regions of active chromatin and transcription factor binding sites. Of 393 local meQTLs that overlap disease-associated regions from genome-wide studies, a high percentage encompass common CpG-SNPs. These meQTLs overlap active enhancers, differentiating them from CpG-SNP meQTLs in inactive chromatin. Conclusions Genetic influence on the human blood methylome is common, involves several heterogeneous processes and is predominantly dependent on local sequence context at the meQTL site. Most meQTLs involve CpG-SNPs, while sequence-dependent effects on chromatin binding are also important in regions of active chromatin. An abundance of local meQTLs resulting from methylation of CpG-SNPs in inactive chromatin suggests that many meQTLs lack functional consequence. Integrating meQTL and Roadmap Epigenomics data could assist fine-mapping efforts.

The aspartate‐to‐alanine aminotransferase ratio (AAR) is associated with liver fibrosis, but its predictive performance is suboptimal. We hypothesized that the association between AAR and liver disease depends on absolute transaminase levels and developed and validated a model to predict liver‐related outcomes in the general population. A Cox regression model based on age, AAR, and alanine aminotransferase (ALT) level (dynamic AAR [dAAR]) using restricted cubic splines was developed in Finnish population‐based health‐examination surveys (FINRISK, 2002‐2012; n = 18,067) with linked registry data for incident liver‐related hospitalizations, hepatocellular carcinoma, or liver death. The model was externally validated for liver‐related outcomes in a Swedish population cohort (Swedish Apolipoprotein Mortality Risk [AMORIS] subcohort; n = 126,941) and for predicting outcomes and/or prevalent fibrosis/cirrhosis in biopsied patients with nonalcoholic fatty liver disease (NAFLD), chronic hepatitis C, or alcohol‐related liver disease (ALD). The dynamic AAR model predicted liver‐related outcomes both overall (optimism‐corrected C‐statistic, 0.81) and in subgroup analyses of the FINRISK cohort and identified persons with >10% risk for liver‐related outcomes within 10 years. In independent cohorts, the C‐statistic for predicting liver‐related outcomes up to a 10‐year follow‐up was 0.72 in the AMORIS cohort, 0.81 in NAFLD, and 0.75 in ALD. Area‐under‐the‐curve (AUC) for detecting prevalent cirrhosis was 0.80‐0.83 in NAFLD, 0.80 in hepatitis C, but only 0.71 in ALD. In ALD, model performance improved when using aspartate aminotransferase instead of ALT in the model (C‐statistic, 0.84 for outcome; AUC, 0.82 for prevalent cirrhosis). Conclusion: A dAAR score provides prospective predictions for the risk of incident severe liver outcomes in the general population and helps detect advanced liver fibrosis/cirrhosis. The dAAR score could potentially be used for screening the unselected general population and as a trigger for further liver evaluations.

The trend of an exponential increase in prediabetes and type 2 diabetes (T2D) is projected to continue rising worldwide. Physical activity could help prevent T2D and the progression and complications of the disease. Therefore, we need to create opportunities for individuals to acquire the necessary knowledge and skills to self-manage their chronic condition through physical activity. eHealth is a potential resource that could facilitate self-management and thus improve population health. However, there is limited research on users' perception of eHealth in promoting physical activity in primary care settings. This study aims to explore the perspectives of health care professionals and individuals with prediabetes and T2D on eHealth to promote physical activity in primary care. A qualitative approach was applied using focus group discussions among individuals with prediabetes or T2D (14 participants in four groups) and health care professionals (10 participants in two groups). The discussions were audio-recorded and transcribed verbatim. Qualitative content analysis was used inductively to code the data. Three main categories emerged: utility, adoption process, and accountability. The utility of eHealth was described as a motivational, entertaining, and stimulating tool. Registration of daily medical measurements and lifestyle parameters in a cohesive digital platform was recognized as a potential resource for strengthening self-management skills. The adoption process includes eHealth to increase the accessibility of care and personalize the support of physical activity. However, participants stated that digital technology might only suit some and could increase health care providers' administrative burden. Accountability refers to the knowledge and skills to optimize eHealth and ensure data integrity and security. People with prediabetes and T2D and health care professionals positively viewed an integration of eHealth technology in primary care to promote physical activity. A cohesive platform using personal metrics, goal-setting, and social support to promote physical activity was suggested. This study identified eHealth illiteracy, inequality, privacy, confidentiality, and an increased workload on health care professionals as factors of concern when integrating eHealth into primary care. Continuous development of eHealth competence was reported as necessary to optimize the implementation of eHealth technology in primary care.

Background In methylome-wide association studies (MWAS) there are many possible differences between cases and controls (e.g. related to life style, diet, and medication use) that may affect the methylome and produce false positive findings. An effective approach to control for these confounders is to first capture the major sources of variation in the methylation data and then regress out these components in the association analyses. This approach is, however, computationally very challenging due to the extremely large number of methylation sites in the human genome. Result We introduce MethylPCA that is specifically designed to control for potential confounders in studies where the number of methylation sites is extremely large. MethylPCA offers a complete and flexible data analysis including 1) an adaptive method that performs data reduction prior to PCA by empirically combining methylation data of neighboring sites, 2) an efficient algorithm that performs a principal component analysis (PCA) on the ultra high-dimensional data matrix, and 3) association tests. To accomplish this MethylPCA allows for parallel execution of tasks, uses C++ for CPU and I/O intensive calculations, and stores intermediate results to avoid computing the same statistics multiple times or keeping results in memory. Through simulations and an analysis of a real whole methylome MBD-seq study of 1,500 subjects we show that MethylPCA effectively controls for potential confounders. Conclusions MethylPCA provides users a convenient tool to perform MWAS. The software effectively handles the challenge in memory and speed to perform tasks that would be impossible to accomplish using existing software when millions of sites are interrogated with the sample sizes required for MWAS.

Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methylation association studies in scenarios where no cell-type proportions are available. As their recommendation was mainly based on simulated data, we sought to replicate findings in two large-scale empirical studies. In our empirical data, SVA did not fully correct for cell-type effects, its performance was somewhat unstable, and it carried a risk of missing true signals caused by removing variation that might be linked to actual disease processes. By contrast, a reference-based correction method performed well and did not show these limitations. A disadvantage of this approach is that if reference methylomes are not (publicly) available, they will need to be generated once for a small set of samples. However, given the notable risk we observed for cell-type confounding, we argue that, to avoid introducing false-positive findings into the literature, it could be well worth making this investment. Please see related Correspondence article: https://genomebiology.biomedcentral.com/articles/10/1186/s13059-017-1149-7 and related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0935-y

Recent genome-wide association studies (GWAS) have made substantial progress in identifying disease loci. The next logical step is to design functional experiments to identify disease mechanisms. This step, however, is often hampered by the large size of loci identified in GWAS that is caused by linkage disequilibrium between SNPs. In this study, we demonstrate how integrating methylome-wide association study (MWAS) results with GWAS findings can narrow down the location for a subset of the putative casual sites. We use the disease schizophrenia as an example. To handle “data analytic” variation, we first combined our MWAS results with two GWAS meta-analyses ( N  = 32,143 and 21,953), that had largely overlapping samples but different data analysis pipelines, separately. Permutation tests showed significant overlapping association signals between GWAS and MWAS findings. This significant overlap justified prioritizing loci based on the concordance principle. To further ensure that the methylation signal was not driven by chance, we successfully replicated the top three methylation findings near genes SDCCAG8 , CREB1 and ATXN7 in an independent sample using targeted pyrosequencing. In contrast to the SNPs in the selected region, the methylation sites were largely uncorrelated explaining why the methylation signals implicated much smaller regions (median size 78 bp). The refined loci showed considerable enrichment of genomic elements of possible functional importance and suggested specific hypotheses about schizophrenia etiology. Several hypotheses involved possible variation in transcription factor-binding efficiencies.

We studied the use of methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq) as a cost-effective screening tool for methylome-wide association studies (MWAS). Because MBD-seq has not yet been applied on a large scale, we first developed and tested a pipeline for data processing using 1500 schizophrenia cases and controls plus 75 technical replicates with an average of 68 million reads per sample. This involved the use of technical replicates to optimize quality control for multi- and duplicate-reads, an experiment to identify CpGs in loci with alignment problems, CpG coverage calculations based on multiparametric estimates of the fragment size distribution, a two-stage adaptive algorithm to combine data from correlated adjacent CpG sites, principal component analyses to control for confounders and new software tailored to handle the large data set. We replicated MWAS findings in independent samples using a different technology that provided single base resolution. In an MWAS of age-related methylation changes, one of our top findings was a previously reported robust association involving . Our results also suggested that owing to the many confounding effects, a considerable challenge in MWAS is to identify those effects that are informative about disease processes. This study showed the potential of MBD-seq as a cost-effective tool in large-scale disease studies.

Comprehensive understanding and early detection of drug-induced lung toxicity remain critical challenges in respiratory drug development. In this study, we propose a multi-omics framework that integrates spatial and temporal tissue-specific transcriptomic signatures with proteomics from minimally invasive biofluids to understand mechanisms and identify safety biomarkers associated with lung toxicity. Using this framework, we identified a panel of candidate biomarkers in bronchoalveolar lavage fluid and plasma, including LCN2/NGAL, RETNLA, SP-D, SPP1/osteopontin, and MMP7, that correlate with histopathological features (e.g., inflammation and epithelial remodeling). We confirmed that these molecular biomarkers were consistently dysregulated across a range of inhaled lung toxicants, human disease (IPF), and environmental exposures (smoke, Alternaria), demonstrating broad applicability across different toxic exposures and translatability. Collectively, this study establishes a robust workflow for mechanism-guided biomarker discovery and proposes a panel of candidates for monitoring drug-induced lung injury in humans.

We generalize the adiabatic approximation to the case of open quantum systems, in the joint limit of slow change and weak open system disturbances. We show that the approximation is ``physically reasonable'' as under wide conditions it leads to a completely positive evolution, if the original master equation can be written on a time-dependent Lindblad form. We demonstrate the approximation for a non-Abelian holonomic implementation of the Hadamard gate, disturbed by a decoherence process. We compare the resulting approximate evolution with numerical simulations of the exact equation.