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

Investigating the causes of patient anxiety at induction of anaesthesia: A mixed methods study

Aim: To investigate patient anxiety at anaesthetic induction and whether this is affected by anaesthetic room interventions. Methods: A mixed methods study was carried out: pre-induction interventions were directly observed. Patient anxiety was assessed quantitatively with cardiovascular changes, the visual analogue scale and the state-trait anxiety inventory. Interviews allowed qualitative assessment. Results: Patient-reported anxiety did not correlate with cardiovascular changes. Anaesthetic room interventions were not predictive of anxiety. Postoperative interviews identified five sources of anxiety, mostly related to preparation for surgery. Staff responses to anxiety were also highlighted. Discussion: Patient-reported anxiety and its biological response are not correlated. Pre-induction interventions do not contribute to anxiety. Anxiety levels at induction are similar to or lower than earlier in the preoperative period. Conclusions: On induction of anaesthesia, patients have little control over their situation but are actively reassured and distracted by theatre staff. Our data suggest staff are good at this. More could still be done to reduce preoperative sources of anxiety

Modelling GTPase dynamics to understand rhoa-driven cancer cell invasion

Metastasis, initially driven by cells migrating and invading through the local environment, leads to most cancer-associated deaths. Cells can use a variety of modes to move in vitro, all of which depend on Rho GTPases at some level. While traditionally it was thought that Rac1 activity drives protrusive lamellipodia at the leading edge of a polarised cell while RhoA drives rear retraction, more recent work in 3D microenvironments has revealed a much more complicated picture of GTPase dynamics. In particular, RhoA activity can dominate the leading edge polymerisation of actin to form filopodial actinspike protrusions that drive more invasive cell migration. We recently described a potential mechanism to abrogate this pro-invasive localised leading edge Rac1 to RhoA switch via manipulation of a negative feedback loop that was revealed by adopting a logical modelling approach. Both challenging dogma and taking a formal, mathematical approach to understanding signalling involved in motility may be vital to harnessing harmful cell migration and preventing metastasis in future research

Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER

BACKGROUND: We compare two new software packages for linkage analysis, LODPAL and GENEFINDER. Both allow for covariate adjustment. Replicates 1 to 3 of Genetic Analysis Workshop 13 simulated data sets were used for the analyses. We described the results of searching for evidence of loci contributing to a simulated quantitative trait related to systolic blood pressure (SBP). Individuals with SBP greater than 130 mm Hg were defined as affected individuals, and all others as unaffected. Total cholesterol was treated as a covariate. RESULTS: Using LODPAL, the power of detecting one of the three major genes related to SBP is 44.4% when a LOD score of 1 is used as the cut-off point. The power of GENEFINDER is lower than that of LODPAL. It is 22.2%. CONCLUSIONS: Based on the limited comparison, LODPAL provided the more reasonable power to detect linkage compared to GENEFINDER. After adjusting for the total cholesterol covariate, the current version of both programs appeared to give a high number of false positives

A MAPK-Driven Feedback Loop Suppresses Rac Activity to Promote RhoA-Driven Cancer Cell Invasion

Data Availability: All relevant data are within the paper and its Supporting Information files.Supporting Information is available online at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004909#sec024 .Cell migration in 3D microenvironments is fundamental to development, homeostasis and the pathobiology of diseases such as cancer. Rab-coupling protein (RCP) dependent co-trafficking of α5β1 and EGFR1 promotes cancer cell invasion into fibronectin (FN) containing extracellular matrix (ECM), by potentiating EGFR1 signalling at the front of invasive cells. This promotes a switch in RhoGTPase signalling to inhibit Rac1 and activate a RhoA-ROCK-Formin homology domain-containing 3 (FHOD3) pathway and generate filopodial actin-spike protrusions which drive invasion. To further understand the signalling network that drives RCP-driven invasive migration, we generated a Boolean logical model based on existing network pathways/models, where each node can be interrogated by computational simulation. The model predicted an unanticipated feedback loop, whereby Raf/MEK/ERK signalling maintains suppression of Rac1 by inhibiting the Rac-activating Sos1-Eps8-Abi1 complex, allowing RhoA activity to predominate in invasive protrusions. MEK inhibition was sufficient to promote lamellipodia formation and oppose filopodial actin-spike formation, and led to activation of Rac and inactivation of RhoA at the leading edge of cells moving in 3D matrix. Furthermore, MEK inhibition abrogated RCP/α5β1/EGFR1-driven invasive migration. However, upon knockdown of Eps8 (to suppress the Sos1-Abi1-Eps8 complex), MEK inhibition had no effect on RhoGTPase activity and did not oppose invasive migration, suggesting that MEK-ERK signalling suppresses the Rac-activating Sos1-Abi1-Eps8 complex to maintain RhoA activity and promote filopodial actin-spike formation and invasive migration. Our study highlights the predictive potential of mathematical modelling approaches, and demonstrates that a simple intervention (MEK-inhibition) could be of therapeutic benefit in preventing invasive migration and metastasis.JHRH is supported by a University of Manchester President’s Doctoral Scholarship and BBSRC-DTP (BB/J014478/1). This work was supported by the Wellcome Trust (090453/Z/09/Z and 090453/Z/09/A to PTC)

Joint testing of genotypic and gene-environment interaction identified novel association for BMP4 with non-syndromic CL/P in an Asian population using data from an International Cleft Consortium

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common disorder with complex etiology. The Bone Morphogenetic Protein 4 gene (BMP4) has been considered a prime candidate gene with evidence accumulated from animal experimental studies, human linkage studies, as well as candidate gene association studies. The aim of the current study is to test for linkage and association between BMP4 and NSCL/P that could be missed in genome-wide association studies (GWAS) when genotypic (G) main effects alone were considered.We performed the analysis considering G and interactions with multiple maternal environmental exposures using additive conditional logistic regression models in 895 Asian and 681 European complete NSCL/P trios. Single nucleotide polymorphisms (SNPs) that passed the quality control criteria among 122 genotyped and 25 imputed single nucleotide variants in and around the gene were used in analysis. Selected maternal environmental exposures during 3 months prior to and through the first trimester of pregnancy included any personal tobacco smoking, any environmental tobacco smoke in home, work place or any nearby places, any alcohol consumption and any use of multivitamin supplements. A novel significant association held for rs7156227 among Asian NSCL/P and non-syndromic cleft lip and palate (NSCLP) trios after Bonferroni correction which was not seen when G main effects alone were considered in either allelic or genotypic transmission disequilibrium tests. Odds ratios for carrying one copy of the minor allele without maternal exposure to any of the four environmental exposures were 0.58 (95%CI = 0.44, 0.75) and 0.54 (95%CI = 0.40, 0.73) for Asian NSCL/P and NSCLP trios, respectively. The Bonferroni P values corrected for the total number of 117 tested SNPs were 0.0051 (asymptotic P = 4.39*10(-5)) and 0.0065 (asymptotic P = 5.54*10(-5)), accordingly. In European trios, no significant association was seen for any SNPs after Bonferroni corrections for the total number of 120 tested SNPs.Our findings add evidence from GWAS to support the role of BMP4 in susceptibility to NSCL/P originally identified in linkage and candidate gene association studies

Racial disparity in long-term mortality rate after hospitalization for myocardial infarction: the Atherosclerosis Risk in Communities study

BACKGROUND: The underlying reasons why African American patients have a significantly higher mortality rate than European American patients after a myocardial infarction (MI) remain unclear. This study examined the racial disparity in mortality rates after MI and possible explanatory factors. METHODS: A prospective analysis was conducted within the Atherosclerosis Risk in Communities (ARIC) study, a community-based study of 15,792 middle-aged adults. From 1987 to 1998, 642 patients (471 European American and 171 African American) hospitalized for MI without prior history of MI were identified. Of these 642 patients, 129 (82 European American and 47 African American) died during follow-up. RESULTS: Cox proportional hazard models were used to analyze the racial difference in mortality rate after MI. After adjusting for age and sex, the relative hazard (RH) comparing African American patients to European American patients was 1.80 (95% CI, 1.24-2.61). The RH decreased after adjusting for vascular risk factors (1.29; 95% CI, 0.83-2.00), socioeconomic position (1.31; 95% CI, 0.83-2.09), severity of MI (1.60; 95% CI, 1.05-2.45), and treatment (1.36; 95% CI, 0.92-2.00). In the final model, which included all factors aforementioned, the RH for race was 1.00 (95% CI, 0.56-1.77). CONCLUSIONS: Our findings suggested that vascular risk factors, socioeconomic position, and treatment play major roles in the racial disparity in mortality rate after MI.http://deepblue.lib.umich.edu/bitstream/2027.42/78990/1/DingDiezRoux2003_AmHeartJ.pd

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

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