Principles of Antifragile Software

The goal of this paper is to study and define the concept of "antifragile software". For this, I start from Taleb's statement that antifragile systems love errors, and discuss whether traditional software dependability fits into this class. The answer is somewhat negative, although adaptive fault tolerance is antifragile: the system learns something when an error happens, and always imrpoves. Automatic runtime bug fixing is changing the code in response to errors, fault injection in production means injecting errors in business critical software. I claim that both correspond to antifragility. Finally, I hypothesize that antifragile development processes are better at producing antifragile software systems.Comment: see https://refuses.github.io

On the mean value of the energy for resonant states

In this work we discuss possible definitions of the mean value of the energy for a resonant (Gamow) state. The mathematical and physical aspects of the formalism are reviewed. The concept of rigged Hilbert space is used as a supportive tool in dealing with Gamow-resonances.Comment: 9 page

EMMIE and engineering: What works as evidence to improve decisions?

While written by a proponent of realism, this article argues in favour of a pragmatic approach to evaluation. It argues that multiple sources of evidence collected using diverse research methods can be useful in conducting informative evaluations of programmes, practices and policies. It argues in particular that methods, even if their assumptions appear incommensurable with one another, should be chosen to meet the evidence needs of decision-makers. These evidence needs are captured in the acronym, EMMIE, which refers to Effect size, Mechanism, Moderator (or context), Implementation and Economic impact. Finally the article questions evidence hierarchies that are inspired by clinical trials, and suggests instead that, notwithstanding the clear differences in the physical and social worlds, engineering may provide a superior model for evaluators to try to emulate. And engineering is, above all, a pragmatic field

A Generic Platform for Cellular Screening Against Ubiquitin Ligases

Ubiquitin signalling regulates most aspects of cellular life, thus deregulation of ubiquitylation has been linked with a number of diseases. E3 ubiquitin ligases provide substrate selectivity in ubiquitylation cascades and are therefore considered to be attractive targets for developing therapeutic molecules. In contrast to established drug target classes, such as protein kinases, GPCRs, hormone receptors and ion channels, ubiquitin drug discovery is in its early stages. This is, in part, due to the complexity of the ubiquitylation pathways and the lack of robust quantitative technologies that allow high-throughput screening of inhibitors. Here we report the development of a Ubiquitin Ligase Profiling system, which is a novel and generic cellular technology designed to facilitate identification of selective inhibitors against RING type E3 ubiquitin ligases. Utilization of this system requires a single co-transfection of cells with assay vectors, thereby enabling readout of E3 ubiquitin ligase catalytic activity within the cellular environment. Therefore, our robust high-throughput screening platform offers novel opportunities for the development of inhibitors against this difficult-to-target E3 ligase enzyme class

RNAi screen for NRF2 inducers identifies targets that rescue primary lung epithelial cells from cigarette smoke induced radical stress

Chronic Obstructive Pulmonary Disease (COPD) is a highly prevalent condition characterized by inflammation and progressive obstruction of the airways. At present, there is no treatment that suppresses the chronic inflammation of the disease, and COPD patients often succumb to the condition. Excessive oxidative stress caused by smoke inhalation is a major driving force of the disease. The transcription factor NRF2 is a critical player in the battle against oxidative stress and its function is impaired in COPD. Increasing NRF2 activity may therefore be a viable therapeutic option for COPD treatment. We show that down regulation of KEAP1, a NRF2 inhibitor, protects primary human lung epithelial cells from cigarette-smoke-extract (CSE) induced cell death in an established in vitro model of radical stress. To identify new potential drug targets with a similar effect, we performed a siRNA screen of the 'druggable' genome using a NRF2 transcriptional reporter cell line. This screen identified multiple genes that when down regulated increased NRF2 transcriptional activity and provided a survival benefit in the in vitro model. Our results suggest that inhibiting components of the ubiquitin-proteasome system will have the strongest effects on NRF2 transcriptional activity by increasing NRF2 levels. We also find that down regulation of the small GTPase Rab28 or the Estrogen Receptor ESRRA provide a survival benefit. Rab28 knockdown increased NRF2 protein levels, indicating that Rab28 may regulate NRF2 proteolysis. Conversely ESRRA down regulation increased NRF2 transcriptional activity without affecting NRF2 levels, suggesting a proteasome-independent mechanism

Epidemiology of Abdominal Obesity among Adolescents from a Brazilian State Capital

The objective of this study was to investigate the effects of socioeconomic, demographic and lifestyle factors on abdominal obesity in adolescents from a Brazilian state capital. In this cross-sectional study, 656 high school students (423 girls and 233 boys) from public schools, ranging in age from 14 to 19 yr, were evaluated. Abdominal obesity was identified based on waist circumference. Socioeconomic data (socioeconomic status, household head's education, and school grade), demographic data (gender and age), and information regarding lifestyle (physical activity, eating habits, aerobic fitness, and nutritional status) were collected. Logistic regression was used for multivariate analysis. The prevalence of abdominal obesity was 6.6% (95% confidence interval [CI]: 4.6-8.4). Being in the second (odds ratio [OR] = 0.41; 95% CI: 0.19-0.88) or third year (OR = 0.18; 95% CI: 0.06-0.59) of high school was a protective factor against abdominal obesity. In addition, students presenting low aerobic fitness (OR = 4.10; 95% CI: 1.62-10.4) and those with excess weight (OR = 208.6; 95% CI: 47.7-911.7) had a higher probability of abdominal obesity. In conclusion, demographic factors such as school grade, lifestyle habits, low aerobic fitness and excess weight are associated with central obesity

Controlling the stereochemistry and regularity of butanethiol self-assembled monolayers on Au(111)

© 2014 American Chemical Society. The rich stereochemistry of the self-assembled monolayers (SAMs) of four butanethiols on Au(111) is described, the SAMs containing up to 12 individual C, S, or Au chiral centers per surface unit cell. This is facilitated by synthesis of enantiomerically pure 2-butanethiol (the smallest unsubstituted chiral alkanethiol), followed by in situ scanning tunneling microscopy (STM) imaging combined with density functional theory molecular dynamics STM image simulations. Even though butanethiol SAMs manifest strong headgroup interactions, steric interactions are shown to dominate SAM structure and chirality. Indeed, steric interactions are shown to dictate the nature of the headgroup itself, whether it takes on the adatom-bound motif RS•Au(0)S•R or involves direct binding of RS• to face-centered-cubic or hexagonal-close-packed sites. Binding as RS• produces large, organizationally chiral domains even when R is achiral, while adatom binding leads to rectangular plane groups that suppress long-range expression of chirality. Binding as RS• also inhibits the pitting intrinsically associated with adatom binding, desirably producing more regularly structured SAMs

Semiochemical-based alternatives to synthetic toxicant insecticides for pollen beetle management

There is an urgent need to develop sustainable pest management systems to protect arable crops in order to replace the current over-reliance on synthetic insecticides. Semiochemicals are insect- or plant-derived chemicals that are used by organisms as information signals. Integrated pest management tools are currently in development that utilise semiochemicals to manipulate the behaviour of pest insects and their natural enemies to provide effective control of pests within the crop. These innovative tools usually require fewer inputs and can involve multiple elements therefore reducing the likelihood of resistance developing compared with use of synthetic toxicants. We review here the life cycle of the pollen beetle Brassicogethes aeneus (previously known as Meligethes aeneus) which is a pest insect of oilseed rape (Brassica napus) and describe the current knowledge of any behaviour mediated by semiochemicals in this species. We discuss the behavioural processes where semiochemical-based control approaches may be appropriate and consider how these approaches could be integrated into an integrated pest management strategy for this important arable crop

Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCF^Slmb degron

Spinal muscular atrophy (SMA) is caused by homozygous mutations in human SMN1. Expression of a duplicate gene (SMN2) primarily results in skipping of exon 7 and production of an unstable protein isoform, SMNΔ7. Although SMN2 exon skipping is the principal contributor to SMA severity, mechanisms governing stability of survival motor neuron (SMN) isoforms are poorly understood. We used a Drosophila model system and label-free proteomics to identify the SCFSlmb ubiquitin E3 ligase complex as a novel SMN binding partner. SCFSlmb interacts with a phosphor degron embedded within the human and fruitfly SMN YG-box oligomerization domains. Substitution of a conserved serine (S270A) interferes with SCFSlmb binding and stabilizes SMNΔ7. SMA-causing missense mutations that block multimerization of full-length SMN are also stabilized in the degron mutant background. Overexpression of SMNΔ7S270A, but not wild-type (WT) SMNΔ7, provides a protective effect in SMA model mice and human motor neuron cell culture systems. Our findings support a model wherein the degron is exposed when SMN is monomeric and sequestered when SMN forms higher-order multimers

Homo-PROTACs:bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation

E3 ubiquitin ligases are key enzymes within the ubiquitin proteasome system which catalyze the ubiquitination of proteins, targeting them for proteasomal degradation. E3 ligases are gaining importance as targets to small molecules, both for direct inhibition and to be hijacked to induce the degradation of non-native neo-substrates using bivalent compounds known as PROTACs (for 'proteolysis-targeting chimeras'). We describe Homo-PROTACs as an approach to dimerize an E3 ligase to trigger its suicide-type chemical knockdown inside cells. We provide proof-of-concept of Homo-PROTACs using diverse molecules composed of two instances of a ligand for the von Hippel-Lindau (VHL) E3 ligase. The most active compound, CM11, dimerizes VHL with high avidity in vitro and induces potent, rapid and proteasome-dependent self-degradation of VHL in different cell lines, in a highly isoform-selective fashion and without triggering a hypoxic response. This approach offers a novel chemical probe for selective VHL knockdown, and demonstrates the potential for a new modality of chemical intervention on E3 ligases.Targeting the ubiquitin proteasome system to modulate protein homeostasis using small molecules has promising therapeutic potential. Here the authors describe Homo-PROTACS: small molecules that can induce the homo-dimerization of E3 ubiquitin ligases and cause their proteasome-dependent degradation