Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comprehensive Evaluation of Software Reliability Modeling Based on Marshall-Olkin Type Fault-Detection Time Distribution

Marshall-Olkin type distribution is defined as a maximum or minimum value distribution of N i.i. d. (secondary) random variables, where N is a geometric distributed random variable. Gopal, and Damondaran (2011) and Xiao (2015) considered the special cases where the underlying random variables are exponentially and Weibull distributed, respectively, and investigated an applicability of these specific Marshall-Olkin type distributions to software reliability modeling with non-homogeneous Poisson process. In this paper, we further generalize the existing software reliability growth model (SRGM) to more general ones by assuming that the secondary probability distribution is given by one of eleven representative distributions with positive support. For these new SRGMs, we develop efficient parameter estimation algorithms based on the EM (Expectation-Maximization) principle, and provide two stable statistical inference schemes in the respective cases where the software fault-detection time and its grouped data are available, respectively. In numerical examples with sixteen data sets (eight for each of detection time data or grouped data), the resulting Marshall-Olkin type SRGMs are compared with the existing eleven SRGMs in terms of goodness-of-fit performance, and reliability prediction.
Neuropsychological characteristics of adolescent boys differing in risk for high blood pressure

Background: Individuals with established hypertension have been found to display deficits in a number of neuropsychological abilities. In general, these are probably due to structural changes in the brain produced by sustained high blood pressure. However, a potentially important line of research suggests that some of these deficits may extend to younger individuals with less severe elevations of blood pressure, perhaps even children, and thus be related more to risk for hypertension than hypertension per se.Purpose: The objective was to examine the relationships between neuropsychological function and risk for hypertension in children.Methods: Measurements of blood pressure and parental history of hypertension were obtained in 88 French-Canadian 14-year-old boys and used to predict performance on a neuropsychological battery.Results: Boys at greater risk of hypertension by virtue of having a parental history of high blood pressure and normatively elevated systolic blood pressure had significantly lower scores on a verbal learning factor score compared to boys at lower risk. Boys with normatively elevated systolic blood pressure also had significantly lower scores on a spatial learning and memory factor score compared to boys with lower blood pressure. The results could not be attributed to differences in family socioeconomic status.Conclusions: Using a younger sample than typically employed in the area, the results support previous suggestions that some of the neuropsychological characteristics displayed by hypertensive individuals may predate the development of clinically elevated blood pressure and could be associated with risk for the disorder.
Clustering Weekly Patterns of Human Mobility Through Mobile Phone Data

With the rapid growth of cell phone networks during the last decades, call detail records (CDR) have been used as approximate indicators for large scale studies on human and urban mobility. Although coarse and limited, CDR are a real marker of human presence. In this paper, we use more than 800 million CDR to identify weekly patterns of human mobility through mobile phone data. Our methodology is based on the classification of individuals into six distinct presence profiles where we focus on the inherent temporal and geographical characteristics of each profile within a territory. Then, we use an event-based algorithm to cluster individuals and we identify 12 weekly patterns. We leverage these results to analyze population estimates adjustment processes and as a result, we propose new indicators to characterize the dynamics of a territory. Our model has been applied to real data coming from more than 1.6 million individuals and demonstrates its relevance. The product of our work can be used by local authorities for human mobility analysis and urban planning.
Saccadic suppression as a perceptual consequence of efficient sensorimotor estimation

Humans perform saccadic eye movements two to three times per second. When doing so, the nervous system strongly suppresses sensory feedback for extended periods of time in comparison with the movement time. Why does the brain discard so much visual information? Here we suggest that perceptual suppression may arise from efficient sensorimotor computations, assuming that perception and control are fundamentally linked. More precisely, we show that a Bayesian estimator should reduce the weight of sensory information around the time of saccades, as a result of signal dependent noise and of sensorimotor delays. Such reduction parallels the behavioral suppression occurring prior to and during saccades, and the reduction in neural responses to visual stimuli observed across the visual hierarchy. We suggest that saccadic suppression originates from efficient sensorimotor processing, indicating that the brain shares neural resources for perception and control.
PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database

MOTIVATION To fully understand how a protein kinase regulates biological processes, it is imperative to first identify its substrate(s) and interacting protein(s). However, of the 518 known human serine/threonine/tyrosine kinases, 35% of these have known substrates, while 14% of the kinases have identified substrate recognition motifs. In contrast, 85% of the kinases have protein-protein interaction (PPI) datasets, raising the possibility that we might reveal potential kinase-substrate pairs from these PPIs. RESULTS PhosphoPOINT, a comprehensive human kinase interactome and phospho-protein database, is a collection of 4195 phospho-proteins with a total of 15 738 phosphorylation sites. PhosphoPOINT annotates the interactions among kinases, with their down-stream substrates and with interacting (phospho)-proteins to modulate the kinase-substrate pairs. PhosphoPOINT implements various gene expression profiles and Gene Ontology cellular component information to evaluate each kinase and their interacting (phospho)-proteins/substrates. Integration of cSNPs that cause amino acids change with the proteins with the phosphoprotein dataset reveals that 64 phosphorylation sites result in a disease phenotypes when changed; the linked phenotypes include schizophrenia and hypertension. PhosphoPOINT also provides a search function for all phospho-peptides using about 300 known kinase/phosphatase substrate/binding motifs. Altogether, PhosphoPOINT provides robust annotation for kinases, their downstream substrates and their interaction (phospho)-proteins and this should accelerate the functional characterization of kinomemediated signaling. AVAILABILITY PhosphoPOINT can be freely accessed in http://kinase. bioinformatics.tw/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Behavioural salinity preference of juvenile yellow perch Perca flavescens.

The present study determined the behavioural salinity preference of a freshwater stock of juvenile yellow perch Perca flavescens acclimated to salinities of 0 and 10. The preferred salinities ranged between 7·3 and 13·0 (mean ± s.d. = 10·4 ± 1·7; n = 13) with no significant effect of acclimation salinity. The results showed that juvenile P. flavescens prefers near isoosmotic salinities, which could be due to a lowered energetic cost of osmoregulation.
A Passive PEEC-Based Micromodeling Circuit for High-Speed Interconnection Problems

A passive partial element equivalent circuit (PEEC)-based micromodeling circuit is proposed for time-domain simulation of a high-speed interconnection problem. This physics-based model order reduction method derives a concise and physically meaningful circuit model from the PEEC model by absorbing its insignificant nodes. To maintain high fidelity of the original electromagnetic PEEC model, the concept of pseudoinductor is introduced to the node-absorbing process. The derivation process does not involve any matrix inversion or decomposition and is highly suitable for GPU parallel computations. Passivity of the micromodeling circuit is ensured by a new passivity checking and enforcement method proposed for the first time. As the scale of the micromodeling circuit can be one order of magnitude smaller than that of the original PEEC model, the time-domain simulation can be three orders of magnitude faster. Two practical examples are given to demonstrate the high fidelity, scalability, and accuracy of the proposed micromodeling circuit, showing excellent applicability to high-speed interconnection problems.
AMPK Inhibits ULK1-Dependent Autophagosome Formation and Lysosomal Acidification via Distinct Mechanisms

ABSTRACT Autophagy maintains metabolism in response to starvation, but each nutrient is sensed distinctly. Amino acid deficiency suppresses mechanistic target of rapamycin complex 1 (MTORC1), while glucose deficiency promotes AMP-activated protein kinase (AMPK). The MTORC1 and AMPK signaling pathways converge onto the ULK1/2 autophagy initiation complex. Here, we show that amino acid starvation promoted formation of ULK1- and sequestosome 1/p62-positive early autophagosomes. Autophagosome initiation was controlled by MTORC1 sensing glutamine, leucine, and arginine levels together. In contrast, glucose starvation promoted AMPK activity, phosphorylation of ULK1 Ser555, and LC3-II accumulation, but with dynamics consistent with a block in autophagy flux. We studied the flux pathway and found that starvation of amino acid but not of glucose activated lysosomal acidification, which occurred independently of autophagy and ULK1. In addition to lack of activation, glucose starvation inhibited the ability of amino acid starvation to activate both autophagosome formation and the lysosome. Activation of AMPK and phosphorylation of ULK1 were determined to specifically inhibit autophagosome formation. AMPK activation also was sufficient to prevent lysosome acidification. These results indicate concerted but distinct AMPK-dependent mechanisms to suppress early and late phases of autophagy.
Stable High‐Index Faceted Pt Skin on Zigzag‐Like PtFe Nanowires Enhances Oxygen Reduction Catalysis

Selectively exposing active surfaces and judiciously tuning the near‐surface composition of electrode materials represent two prominent means of promoting electrocatalytic performance. Here, a new class of Pt3Fe zigzag‐like nanowires (Pt‐skin Pt3Fe z‐NWs) with stable high‐index facets (HIFs) and nanosegregated Pt‐skin structure is reported, which are capable of substantially boosting electrocatalysis in fuel cells. These unique structural features endow the Pt‐skin Pt3Fe z‐NWs with a mass activity of 2.11 A mg−1 and a specifc activity of 4.34 mA cm−2 for the oxygen reduction reaction (ORR) at 0.9 V versus reversible hydrogen electrode, which are the highest in all reported PtFe‐based ORR catalysts. Density function theory calculations reveal a combination of exposed HIFs and formation of Pt‐skin structure, leading to an optimal oxygen adsorption energy due to the ligand and strain effects, which is responsible for the much enhanced ORR activities. In contrast to previously reported HIFs‐based catalysts, the Pt‐skin Pt3Fe z‐NWs maintain ultrahigh durability with little activity decay and negligible structure transformation after 50 000 potential cycles. Overcoming a key technical barrier in electrocatalysis, this work successfully extends the nanosegregated Pt‐skin structure to nanocatalysts with HIFs, heralding the exciting prospects of high‐effcient Pt‐based catalysts in fuel cells.
Resistance Monitoring of Four Insecticides and a Description of an Artificial Diet Incorporation Method for Chilo suppressalis (Lepidoptera: Crambidae)

Abstract Chilo suppressalis (Walker; Lepidoptera: Crambidae) is one of the most damaging rice pests in China. Insecticides play a major role in its management. We describe how we monitored the resistance of C. suppressalis to four insecticides in seven field populations from Jiangxi, Hubei, and Hunan Provinces, China, in 2014–2016.The topical application method for resistance monitoring was suitable for triazophos, monosultap, and abamectin. The conventional rice seedling dipping method proved ineffective for testing chlorantraniliprole so the new artificial diet incorporation method was substituted. This new method provided more consistent results than the other methods, once baseline toxicity data had been established. All populations had moderate to high resistance to triazophos from 2014 to 2016. Monosultap resistance in two populations increased from low in 2014 to moderate in 2016 and the other five populations showed moderate to high-level resistance throughout. Abamectin resistance in three populations increased from sensitive or low in 2014 to moderate in 2015–2016, and the other populations had moderate to high levels of resistance. Resistance to chlorantraniliprole increased from sensitive or low in 2014 to moderate to high in 2016.These results suggested that resistance management strategies should be developed according to the needs of a specific location. It was suggested that, in these localities, organophosphate insecticides should be prohibited, the application of nereistoxin, macrolide antibiotic, and diamide insecticides should be limited, and other insecticides, including spinetoram and methoxyfenozide, that exhibited no resistance should be used rationally and in rotation to delay resistance development.
Epidemiology of Transient Ischemic Attacks Using Time- or Tissue-Based Definitions: A Population-Based Study

Background and Purpose— Transient ischemic attack (TIA) epidemiology may have changed in recent years as a consequence of improved identification and treatment of vascular risk factors. Our aim was to provide updated information about TIA epidemiology in Italy. Methods— Cases of first-ever TIA were ascertained from January 1, 2011, until December 31, 2012, in a population-based prospective registry. All residents in the L’Aquila district with an incident TIA were included and followed up to 2 years after the event. Outcome events were recurrent TIA, nonfatal and fatal stroke, nonfatal and fatal myocardial infarction, and all-cause mortality. Results— A total of 210 patients with a TIA according to the traditional time-based definition were included (51.4% women); 151 patients (71.9%) with transient symptoms and negative brain neuroimaging were broadly considered as tissue-based TIA, 29 patients (13.8%) had transient symptoms and evidence of a congruous acute ischemic lesion, and 30 patients (14.3%) had an acute neurovascular syndrome. The crude annual incidence rate for traditional time-based TIA was 35.2 per 100 000 (95% confidence interval, 30.6–40.3) and 28.6 per 100 000 (95% confidence interval, 24.1–33.5) when standardized to the 2011 European population. The incidence peaked in subjects aged ≥85 years, in both sexes. At 2 years, outcome events occurred in 50 patients (23.8%) including 15 patients (7.1%) with nonfatal or fatal strokes. Conclusions— Our population-based study found a low annual TIA incidence rate and a fair TIA prognosis confirming the effectiveness of preventive strategies for cardiovascular diseases. We also proved the nonfitting applicability of the tissue-based definition in our district.
RNAi-mediated silencing of estrogen receptor α in the ventromedial nucleus of hypothalamus abolishes female sexual behaviors

Estrogen receptor α (ERα) plays a major role in the regulation of neuroendocrine functions and behaviors by estrogens. Although the generation of ERα knockout mice advanced our knowledge of ERα functions, gene deletion using this method is global and potentially confounded by developmental consequences. To achieve a site-specific knockdown of ERα in the normally developed adult brain, we have generated an adeno-associated virus vector expressing a small hairpin RNA targeting ERα. After bilateral injection of this vector into the hypothalamic ventromedial nucleus in ovariectomized female mice, expression levels of ERα as well as the estrogen-inducible progesterone receptor were profoundly reduced despite the continued presence of this receptor elsewhere in the brain. Functionally, silencing of ERα in the ventromedial nucleus abolished female proceptive and receptive sexual behaviors while enhancing rejection behavior. These results provide evidence that adeno-associated virus-mediated long-term knockdown of genes can be used to delineate their effects on complex behaviors in discrete brain regions.
Optimal Warping Paths are unique for almost every pair of Time Series

Update rules for learning in dynamic time warping spaces are based on optimal warping paths between parameter and input time series. In general, optimal warping paths are not unique resulting in adverse effects in theory and practice. Under the assumption of squared error local costs, we show that no two warping paths have identical costs almost everywhere in a measure-theoretic sense. Two direct consequences of this result are: (i) optimal warping paths are unique almost everywhere, and (ii) the set of all pairs of time series with multiple equal-cost warping paths coincides with the union of exponentially many zero sets of quadratic forms. One implication of the proposed results is that typical distance-based cost functions such as the k-means objective are differentiable almost everywhere and can be minimized by subgradient methods.
LifeSim: A lifetime reliability simulator for manycore systems

The increasing demand for high-performance applications along with the advancement of technology, leading to power hungry manycore processors and rising chip temperature, have made the devices increasingly susceptible to wearout and aging resulting in early failure of the processing cores. The systemlevel analysis and optimization techniques offer a holistic view and ample opportunities to address lifetime reliability challenges, that can be explored and evaluated with the help of a fast and accurate simulation environment. This paper presents LifeSim, a simulation tool that integrates i) a state-of-the-art manycore simulator, ii) a thermal simulator and iii) a lifetime reliability analyzer. The simulation tool is easily configurable without any code modification and compilation, with the help of a configuration file. To facilitate the development of solutions to mitigate aging and improve lifetime reliability, we enhanced the simulator with scheduling and frequency control features. It offers both preemptive and non-preemptive scheduling along with an interface for dynamic voltage frequency scaling (DVFS). Further, it logs statistics such as power, temperature, aging, and mean time to failure (MTTF) and also generates graphs for visualization and easy comparison of the performance of the solution adopted by the user.
A Sinorhizobium meliloti RpoH-Regulated Gene Is Involved in Iron-Sulfur Protein Metabolism and Effective Plant Symbiosis under Intrinsic Iron Limitation

ABSTRACT In Sinorhizobium meliloti, RpoH-type sigma factors have a global impact on gene expression during heat shock and play an essential role in symbiosis with leguminous plants. Using mutational analysis of a set of genes showing highly RpoH-dependent expression during heat shock, we identified a gene indispensable for effective symbiosis. This gene, designated sufT, was located downstream of the sufBCDS homologs that specify the iron-sulfur (Fe/S) cluster assembly pathway. The identified transcription start site was preceded by an RpoH-dependent promoter consensus sequence. SufT was related to a conserved protein family of unknown molecular function, of which some members are involved in Fe/S cluster metabolism in diverse organisms. A sufT mutation decreased bacterial growth in both rich and minimal media, tolerance to stresses such as iron starvation, and activities of some Fe/S cluster-dependent enzymes. These results support the involvement of SufT in SUF (sulfur mobilization) system-mediated Fe/S protein metabolism. Furthermore, we isolated spontaneous pseudorevertants of the sufT mutant with partially recovered growth; each of them had a mutation in rirA. This gene encodes a global iron regulator whose loss increases the intracellular iron content. Deletion of rirA in the original sufT mutant improved growth and restored Fe/S enzyme activities and effective symbiosis. These results suggest that enhanced iron availability compensates for the lack of SufT in the maintenance of Fe/S proteins. IMPORTANCE Although RpoH-type sigma factors of the RNA polymerase are present in diverse proteobacteria, their role as global regulators of protein homeostasis has been studied mainly in the enteric gammaproteobacterium Escherichia coli. In the soil alphaproteobacterium Sinorhizobium meliloti, the rpoH mutations have a strong impact on symbiosis with leguminous plants. We found that sufT is a unique member of the S. meliloti RpoH regulon; sufT contributes to Fe/S protein metabolism and effective symbiosis under intrinsic iron limitation exerted by RirA, a global iron regulator. Our study provides insights into the RpoH regulon function in diverse proteobacteria adapted to particular ecological niches and into the mechanism of conserved Fe/S protein biogenesis.
Who talks to whom about what? How interdisciplinary communication and knowledge of expertise distribution improve in integrated R&D labs

Abstract Although several studies have examined the impact of open workspaces, there is still an on-going debate about its advantages and disadvantages. Our paper contributes to this debate by shedding light on three issues: the effect of open workspaces on (1) the flow of communication along and across hierarchical lines; (2) the content of communication; and (3) the specificities of open integrated laboratories. Our findings derive from a longitudinal case in a large pharmaceutical company that has relocated some R&D teams from enclosed to multi-space offices and labs. The relocation has resulted in (a) increased interdisciplinary communication, particularly at lower hierarchical levels, (b) a shift of the location of discussions and the content of conversations and (c) an improved knowledge about expertise distribution. Practitioner Summary: Communication is essential in knowledge-driven organisations. This article examines the impact of a relocation of R&D employees from enclosed to multi-space offices and labs on communication patterns. We explain how the new environment fosters interdisciplinary communication, shifts the location of discussions and increases the knowledge of expertise distribution.