Protocol-based verification of message-passing parallel programs

© 2015 ACM.We present ParTypes, a type-based methodology for the verification of Message Passing Interface (MPI) programs written in the C programming language. The aim is to statically verify programs against protocol specifications, enforcing properties such as fidelity and absence of deadlocks. We develop a protocol language based on a dependent type system for message-passing parallel programs, which includes various communication operators, such as point-to-point messages, broadcast, reduce, array scatter and gather. For the verification of a program against a given protocol, the protocol is first translated into a representation read by VCC, a software verifier for C. We successfully verified several MPI programs in a running time that is independent of the number of processes or other input parameters. This contrasts with alternative techniques, notably model checking and runtime verification, that suffer from the state-explosion problem or that otherwise depend on parameters to the program itself. We experimentally evaluated our approach against state-of-the-art tools for MPI to conclude that our approach offers a scalable solution

Fact sheet: Field considerations for measuring evapotranspiration with the Eddy Covariance Method.

In semi-arid ponderosa pine forests of the southwestern US, up to 90% of the annual water budget is re-turned to the atmosphere through evapotranspiration (ET). Accurate measurements of this component of the water budget are, therefore, critical to assess hydrological responses to planned forest restoration. The eddy covariance (EC) method is an atmospheric measurement technique that yields accurate ET measurements. The EC method calculates vertical turbulent fluxes within an atmospheric boundary layer over natural ecosystems and agricultural systems to determine gas exchange rates (e.g., water vapor concentration, carbon dioxide (CO2) concentration) (Burba 2013). Both natural and human-mediated processes affect forest gas exchange. Recent studies of both wildfire and forest restoration treatments in stands of ponderosa pine show a reduction of ET compared to an undisturbed forest site (Dore et al. 2010). Application of EC to investigate CO2 and water fluxes in ponderosa pine forest improves understanding of CO2 and water flux exchange patterns. This fact sheet describes installation of an EC system, including flux tower placement requirements and maintenance of scientific instruments

Classifying the Degree of Bark Beetle-Induced Damage on Fir (Abies mariesii) Forests, from UAV-Acquired RGB Images

Bark beetle outbreaks are responsible for the loss of large areas of forests and in recent years they appear to be increasing in frequency and magnitude as a result of climate change. The aim of this study is to develop a new standardized methodology for the automatic detection of the degree of damage on single fir trees caused by bark beetle attacks using a simple GIS-based model. The classification approach is based on the degree of tree canopy defoliation observed (white pixels) in the UAV-acquired very high resolution RGB orthophotos. We defined six degrees (categories) of damage (healthy, four infested levels and dead) based on the ratio of white pixel to the total number of pixels of a given tree canopy. Category 1: 75% (dead). The definition of “white pixel” is crucial, since light conditions during image acquisition drastically affect pixel values. Thus, whiteness was defined as the ratio of red pixel value to the blue pixel value of every single pixel in relation to the ratio of the mean red and mean blue value of the whole orthomosaic. The results show that in an area of 4 ha, out of the 1376 trees, 277 were healthy, 948 were infested (Cat 2, 628; Cat 3, 244; Cat 4, 64; Cat 5, 12), and 151 were dead (Cat 6). The validation led to an average precision of 62%, with Cat 1 and Cat 6 reaching a precision of 73% and 94%, respectively. © 2022 by the authors. Licensee MDPI, Basel, Switzerland

The transglutaminase type 2 and pyruvate kinase isoenzyme M2 interplay in autophagy regulation

Autophagy is a self-degradative physiological process by which the cell removes worn-out or damaged components. Constant at basal level it may become highly active in response to cellular stress. The type 2 transglutaminase (TG2), which accumulates under stressful cell conditions, plays an important role in the regulation of autophagy and cells lacking this enzyme display impaired autophagy/mitophagy and a consequent shift their metabolism to glycolysis. To further define the molecular partners of TG2 involved in these cellular processes, we analysed the TG2 interactome under normal and starved conditions discovering that TG2 interacts with various proteins belonging to different functional categories. Herein we show that TG2 interacts with pyruvate kinase M2 (PKM2), a rate limiting enzyme of glycolysis which is responsible for maintaining a glycolytic phenotype in malignant cells and displays non metabolic functions, including transcriptional co-activation and protein kinase activity. Interestingly, the ablation of PKM2 led to the decrease of intracellular TG2's transamidating activity paralleled by an increase of its tyrosine phosphorylation. Along with this, a significant decrease of ULK1 and Beclin1 was also recorded, thus suggesting a block in the upstream regulation of autophagosome formation. These data suggest that the PKM2/TG2 interplay plays an important role in the regulation of autophagy in particular under cellular stressful conditions such as those displayed by cancer cells

A giant comet-like cloud of hydrogen escaping the warm Neptune-mass exoplanet GJ 436b

Exoplanets orbiting close to their parent stars could lose some fraction of their atmospheres because of the extreme irradiation. Atmospheric mass loss primarily affects low-mass exoplanets, leading to suggest that hot rocky planets might have begun as Neptune-like, but subsequently lost all of their atmospheres; however, no confident measurements have hitherto been available. The signature of this loss could be observed in the ultraviolet spectrum, when the planet and its escaping atmosphere transit the star, giving rise to deeper and longer transit signatures than in the optical spectrum. Here we report that in the ultraviolet the Neptune-mass exoplanet GJ 436b (also known as Gliese 436b) has transit depths of 56.3 +/- 3.5% (1 sigma), far beyond the 0.69% optical transit depth. The ultraviolet transits repeatedly start ~2 h before, and end >3 h after the ~1 h optical transit, which is substantially different from one previous claim (based on an inaccurate ephemeris). We infer from this that the planet is surrounded and trailed by a large exospheric cloud composed mainly of hydrogen atoms. We estimate a mass-loss rate in the range of ~10^8-10^9 g/s, which today is far too small to deplete the atmosphere of a Neptune-like planet in the lifetime of the parent star, but would have been much greater in the past.Comment: Published in Nature on 25 June 2015. Preprint is 28 pages, 12 figures, 2 table

Plasticity and dystonia: a hypothesis shrouded in variability.

Studying plasticity mechanisms with Professor John Rothwell was a shared highlight of our careers. In this article, we discuss non-invasive brain stimulation techniques which aim to induce and quantify plasticity, the mechanisms and nature of their inherent variability and use such observations to review the idea that excessive and abnormal plasticity is a pathophysiological substrate of dystonia. We have tried to define the tone of our review by a couple of Professor John Rothwell's many inspiring characteristics; his endless curiosity to refine knowledge and disease models by scientific exploration and his wise yet humble readiness to revise scientific doctrines when the evidence is supportive. We conclude that high variability of response to non-invasive brain stimulation plasticity protocols significantly clouds the interpretation of historical findings in dystonia research. There is an opportunity to wipe the slate clean of assumptions and armed with an informative literature in health, re-evaluate whether excessive plasticity has a causal role in the pathophysiology of dystonia

Impact of metabolic comorbidity on the association between body mass index and heatlh-related quality of life: a Scotland-wide cross-sectional study of 5,608 participants

<p/>Background: The prevalence of obesity is rising in Scotland and globally. Overall, obesity is associated with increased morbidity, mortality and reduced health-related quality of life. Studies suggest that "healthy obesity" (obesity without metabolic comorbidity) may not be associated with morbidity or mortality. Its impact on health-related quality of life is unknown. <p/>Methods: We extracted data from the Scottish Health Survey on self-reported health-related quality of life, body mass index (BMI), demographic information and comorbidity. SF-12 responses were converted into an overall health utility score. Linear regression analyses were used to explore the association between BMI and health utility, stratified by the presence or absence of metabolic comorbidity (diabetes, hypertension, hypercholesterolemia or cardiovascular disease), and adjusted for potential confounders (age, sex and deprivation quintile). <p/>Results: Of the 5,608 individuals, 3,744 (66.8%) were either overweight or obese and 921 (16.4%) had metabolic comorbidity. There was an inverted U-shaped relationship whereby health utility was highest among overweight individuals and fell with increasing BMI. There was a significant interaction with metabolic comorbidity (p = 0.007). Individuals with metabolic comorbidty had lower utility scores and a steeper decline in utility with increasing BMI (morbidly obese, adjusted coefficient: -0.064, 95% CI -0.115, -0.012, p = 0.015 for metabolic comorbidity versus -0.042, 95% CI -0.067, -0.018, p = 0.001 for no metabolic comorbidity). <p/>Conclusions: The adverse impact of obesity on health-related quality of life is greater among individuals with metabolic comorbidity. However, increased BMI is associated with reduced health-related quality of life even in the absence of metabolic comorbidity, casting doubt on the notion of "healthy obesity"

The Role of Innate APOBEC3G and Adaptive AID Immune Responses in HLA-HIV/SIV Immunized SHIV Infected Macaques

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Integration of decision support systems to improve decision support performance

Decision support system (DSS) is a well-established research and development area. Traditional isolated, stand-alone DSS has been recently facing new challenges. In order to improve the performance of DSS to meet the challenges, research has been actively carried out to develop integrated decision support systems (IDSS). This paper reviews the current research efforts with regard to the development of IDSS. The focus of the paper is on the integration aspect for IDSS through multiple perspectives, and the technologies that support this integration. More than 100 papers and software systems are discussed. Current research efforts and the development status of IDSS are explained, compared and classified. In addition, future trends and challenges in integration are outlined. The paper concludes that by addressing integration, better support will be provided to decision makers, with the expectation of both better decisions and improved decision making processes

Can disordered mobile phone use be considered a behavioral addiction? An update on current evidence and a comprehensive model for future research

Despite the many positive outcomes, excessive mobile phone use is now often associated with potentially harmful and/or disturbing behaviors (e.g., symptoms of deregulated use, negative impact on various aspects of daily life such as relationship problems, and work intrusion). Problematic mobile phone use (PMPU) has generally been considered as a behavioral addiction that shares many features with more established drug addictions. In light of the most recent data, the current paper reviews the validity of the behavioral addiction model when applied to PMPU. On the whole, it is argued that the evidence supporting PMPU as an addictive behavior is scarce. In particular, it lacks studies that definitively show behavioral and neurobiological similarities between mobile phone addiction and other types of legitimate addictive behaviors. Given this context, an integrative pathway model is proposed that aims to provide a theoretical framework to guide future research in the field of PMPU. This model highlights that PMPU is a heterogeneous and multi-faceted condition