Developing interpretable models with optimized set reduction for identifying high risk software components

Applying equal testing and verification effort to all parts of a software system is not very efficient, especially when resources are limited and scheduling is tight. Therefore, one needs to be able to differentiate low/high fault frequency components so that testing/verification effort can be concentrated where needed. Such a strategy is expected to detect more faults and thus improve the resulting reliability of the overall system. This paper presents the Optimized Set Reduction approach for constructing such models, intended to fulfill specific software engineering needs. Our approach to classification is to measure the software system and build multivariate stochastic models for predicting high risk system components. We present experimental results obtained by classifying Ada components into two classes: is or is not likely to generate faults during system and acceptance test. Also, we evaluate the accuracy of the model and the insights it provides into the error making process

Membrane Tension Orchestrates Rear Retraction in Matrix-Directed Cell Migration

In development, wound healing, and cancer metastasis, vertebrate cells move through 3D interstitial matrix, responding to chemical and physical guidance cues. Protrusion at the cell front has been extensively studied, but the retraction phase of the migration cycle is not well understood. Here, we show that fast-moving cells guided by matrix cues establish positive feedback control of rear retraction by sensing membrane tension. We reveal a mechanism of rear retraction in 3D matrix and durotaxis controlled by caveolae, which form in response to low membrane tension at the cell rear. Caveolae activate RhoA-ROCK1/PKN2 signaling via the RhoA guanidine nucleotide exchange factor (GEF) Ect2 to control local F-actin organization and contractility in this subcellular region and promote translocation of the cell rear. A positive feedback loop between cytoskeletal signaling and membrane tension leads to rapid retraction to complete the migration cycle in fast-moving cells, providing directional memory to drive persistent cell migration in complex matrices. © 2019 The AuthorsCell migration through 3D matrix is critical to developmental and disease processes, but the mechanisms that control rear retraction are poorly understood. Hetmanski et al. show that differential membrane tension allows caveolae to form at the rear of migrating cells and activate the contractile actin cytoskeleton to promote rapid retraction. © 2019 The Author

Graphene oxide activates canonical TGFβ signalling in a human chondrocyte cell line <i>via</i> increased plasma membrane tension

Data availability: No new data. Data sharing not applicable to this article as no datasets were generated or analysed during the current study.Footnote: Electronic supplementary information (ESI) available. See doi: https://doi.org/10.1039/d3nr06033k .Graphene Oxide (GO) has been shown to increase the expression of key cartilage genes and matrix components within 3D scaffolds. Understanding the mechanisms behind the chondroinductive ability of GO is critical for developing articular cartilage regeneration therapies but remains poorly understood. The objectives of this work were to elucidate the effects of GO on the key chondrogenic signalling pathway – TGFβ and identify the mechanism through which signal activation is achieved in human chondrocytes. Activation of canonical signalling was validated through GO-induced SMAD-2 phosphorylation and upregulation of known TGFβ response genes, while the use of a TGFβ signalling reporter assay allowed us to identify the onset of GO-induced signal activation which has not been previously reported. Importantly, we investigate the cell–material interactions and molecular mechanisms behind these effects, establishing a novel link between GO, the plasma membrane and intracellular signalling. By leveraging fluorescent lifetime imaging (FLIM) and a membrane tension probe, we reveal GO-mediated increases in plasma membrane tension, in real-time for the first time. Furthermore, we report the activation of mechanosensory pathways which are known to be regulated by changes in plasma membrane tension and reveal the activation of endogenous latent TGFβ in the presence of GO, providing a mechanism for signal activation. The data presented here are critical to understanding the chondroinductive properties of GO and are important for the implementation of GO in regenerative medicine.The authors acknowledge financial support to LO from the UKRI Engineering and Physical Sciences Research Council (EPSRC) Centre for Doctoral Training (CDT) in Advanced Biomedical Materials (EP/S022201/1). Additional support to SW from Medical Research Council (Grant MR/S002553/1). A. K. acknowledges the studentship from the UK Research and Innovation (UKRI) Engineering and Physical Sciences Research Council (EPSRC) Centre for Doctoral Training programme (Graphene NOWNANO CDT; EP/L01548X/1). The authors acknowledge the Manchester Collaborative Centre for Inflammation Research (MCCIR) as the funding source for the FACSVerse. The ICN2 has been supported by the Severo Ochoa Centres of Excellence programme [SEV-2017-0706] and is currently supported by the Severo Ochoa Centres of Excellence programme, Grant CEX2021-001214-S, both funded by MCIN/AEI/10.13039.501100011033

Clinically actionable secondary findings in 130 triads from sub-Saharan African families with non-syndromic orofacial clefts

Abstract Introduction The frequency and implications of secondary findings (SFs) from genomic testing data have been extensively researched. However, little is known about the frequency or reporting of SFs in Africans, who are underrepresented in large‐scale population genomic studies. The availability of data from the first whole‐genome sequencing for orofacial clefts in an African population motivated this investigation. Methods In total, 130 case‐parent trios were analyzed for SFs within the ACMG SFv.3.0 list genes. Additionally, we filtered for four more genes (HBB, HSD32B, G6PD and ACADM). Results We identified 246 unique variants in 55 genes; five variants in four genes were classified as pathogenic or likely pathogenic (P/LP). The P/LP variants were seen in 2.3% (9/390) of the subjects, a frequency higher than ~1% reported for diverse ethnicities. On the ACMG list, pathogenic variants were observed in PRKAG (p. Glu183Lys). Variants in the PALB2 (p. Glu159Ter), RYR1 (p. Arg2163Leu) and LDLR (p. Asn564Ser) genes were predicted to be LP. Conclusion This study provides information on the frequency and pathogenicity of SFs in an African cohort. Early risk detection will help reduce disease burden and contribute to efforts to increase knowledge of the distribution and impact of actionable genomic variants in diverse populations

Evidence of gene-environment interaction for two genes on chromosome 4 and environmental tobacco smoke in controlling the risk of nonsyndromic cleft palate

Nonsyndromic cleft palate (CP) is one of the most common human birth defects and both genetic and environmental risk factors contribute to its etiology. We conducted a genome-wide association study (GWAS) using 550 CP case-parent trios ascertained in an international consortium. Stratified analysis among trios with different ancestries was performed to test for GxE interactions with common maternal exposures using conditional logistic regression models. While no single nucleotide polymorphism (SNP) achieved genome-wide significance when considered alone, markers in SLC2A9 and the neighboring WDR1 on chromosome 4p16.1 gave suggestive evidence of gene-environment interaction with environmental tobacco smoke (ETS) among 259 Asian trios when the models included a term for GxE interaction. Multiple SNPs in these two genes were associated with increased risk of nonsyndromic CP if the mother was exposed to ETS during the peri-conceptual period (3 months prior to conception through the first trimester). When maternal ETS was considered, fifteen of 135 SNPs mapping to SLC2A9 and 9 of 59 SNPs in WDR1 gave P values approaching genome-wide significance (10-6<P<10-4) in a test for GxETS interaction. SNPs rs3733585 and rs12508991 in SLC2A9 yielded P = 2.26×10-7 in a test for GxETS interaction. SNPs rs6820756 and rs7699512 in WDR1 also yielded P = 1.79×10-7 and P = 1.98×10-7 in a 1 df test for GxE interaction. Although further replication studies are critical to confirming these findings, these results illustrate how genetic associations for nonsyndromic CP can be missed if potential GxE interaction is not taken into account, and this study suggest SLC2A9 and WDR1 should be considered as candidate genes for CP. © 2014 Wu et al

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p 10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10−392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group

Non-emphysematous chronic obstructive pulmonary disease is associated with diabetes mellitus

Background: Chronic obstructive pulmonary disease (COPD) has been classically divided into blue bloaters and pink puffers. The utility of these clinical subtypes is unclear. However, the broader distinction between airway-predominant and emphysema-predominant COPD may be clinically relevant. The objective was to define clinical features of emphysema-predominant and non-emphysematous COPD patients. Methods: Current and former smokers from the Genetic Epidemiology of COPD Study (COPDGene) had chest computed tomography (CT) scans with quantitative image analysis. Emphysema-predominant COPD was defined by low attenuation area at -950 Hounsfield Units (LAA-950) ≥10%. Non-emphysematous COPD was defined by airflow obstruction with minimal to no emphysema (LAA-950 < 5%). Results: Out of 4197 COPD subjects, 1687 were classified as emphysema-predominant and 1817 as non-emphysematous; 693 had LAA-950 between 5-10% and were not categorized. Subjects with emphysema-predominant COPD were older (65.6 vs 60.6 years, p < 0.0001) with more severe COPD based on airflow obstruction (FEV1 44.5 vs 68.4%, p < 0.0001), greater exercise limitation (6-minute walk distance 1138 vs 1331 ft, p < 0.0001) and reduced quality of life (St. George's Respiratory Questionnaire score 43 vs 31, p < 0.0001). Self-reported diabetes was more frequent in non-emphysematous COPD (OR 2.13, p < 0.001), which was also confirmed using a strict definition of diabetes based on medication use. The association between diabetes and non-emphysematous COPD was replicated in the ECLIPSE study. Conclusions: Non-emphysematous COPD, defined by airflow obstruction with a paucity of emphysema on chest CT scan, is associated with an increased risk of diabetes. COPD patients without emphysema may warrant closer monitoring for diabetes, hypertension, and hyperlipidemia and vice versa

Stres oksydacyjny i oksydacyjna modyfikacja białek pod wpływem ołowiu i kadmu u gołębi z różnych środowisk północnej Polski

The aim of this study was to compare ecophysiological basis for developing feral pigeons (Columba livia f. urbana) in various environments of Northern Poland. We examined heavy metals contents, lipid and protein peroxidation, antioxidant enzymes activity in individuals growing and feeding in the different polluted regions. Pigeons from urban area possessed high maintenance of cadmium in the blood, but low lead in comparison to birds from rural area. Our results suggest that increased level of heavy metals (Pb and Cd) in the blood of pigeons from different regions of Northern Poland tended to affect negatively initiate lipid peroxidation and increased oxidative modified protein content. Our results suggest that increased level of oxidative stress in birds is dependent upon environmental pollution. Statistical analysis (ANOVA and GLM) has shown that colony localization (urban or rural areas) modified antioxidative defense system, level of lipid and protein peroxidation, and blood total antioxidant activity.Celem badań była analiza ekofizjologiczna postaw rozwoju dzikich gołębi (Columba livia f. urbana) w różnych środowiskach północnej Polski. Przebadaliśmy zawartość metali ciężkich, poziom procesów lipoperoksydacji, oksydacyjnej modyfikacji białek oraz aktywność enzymów antykoksydacyjnych u gołębi rozwijających się w środowiskach o różnym stopniu antropopresji. Krew gołębi pochodzących z miejskiego obszaru charakteryzowała się zwiększoną zawartością kadmu, a obszarów wiejskich – ołowiu. Wyniki naszych badań sugerują, że zwiększenie poziomu metali ciężkich ↑ (Pb i Cd) we krwi gołębi różnych regionów północnej Polski prowadzi do intensyfikacji procesów lipoperoksydacji, oksydacyjnej modyfikacji białek i zależy od stopnia zanieczyszczenia środowiska. Statystyczna analiza (ANOVA i GLM) wykazała, że lokalizacja kolonii (miejskie albo wiejskie obszary) wpływa na zmiany parametrów funkcjonowania systemu pro- i antyutleniania, modyfikuje mechanizmy obrony antyoksydacyjnej – całkowitą zdolność antyoksydacyjną