Miracle-dz/UniFAR-FTUs huggingface dataset:
Inter-context control-flow and data-flow test adequacy criteria for nesC applications

NesC is a programming language for applications that run on top of networked sensor nodes. Such an application mainly uses an interrupt to trigger a sequence of operations, known as contexts, to perform its actions. However, a high degree of inter-context interleaving in an application can cause it to be error-prone. For instance, a context may mistakenly alter another context's data kept at a shared variable. Existing concurrency testing techniques target testing programs written in general-purpose programming languages, where a small scale of inter-context interleaving between program executions may make these techniques inapplicable. We observe that nesC blocks new context interleaving when handling interrupts, and this feature significantly restricts the scale of inter-context interleaving that may occur in a nesC application. This paper models how operations on different contexts may interleave as inter-context flow graphs. Based on these graphs, it proposes two test adequacy criteria, one on inter-context data-flows and another on inter-context control-flows. It evaluates the proposal by a real-life open-source nesC application. The empirical results show that the new criteria detect significantly more failures than their conventional counterparts.
Optimal demand response using mechanism design in the smart grid

Demand side management is considered to be a key component in the future smart grid that can help to achieve an efficient utilization of energy. In this paper we consider a residential power network, where consumers are asked to report their information about power usage to service provider, then the provider determines the optimal power allocations and charges for each user based on social welfare maximization. The benefit of each user is related to demand for electricity and the quantity of power allocated. Assuming consumers are strategic and selfish, we proposed an efficient pricing algorithm with which consumers cannot achieve greater benefit by mis-reporting and social welfare maximization can be achieved. Finally we present simulation results to show that our proposed method can benefit both of the service provider and consumers.
Formal Verification of a Superscalar Execution Unit 1

Abstract. Many modern systems are designed as a set of interconnected reactive subsystems. The subsystem verification task is to verify an implementation of the subsystem against the simple deterministic high-level specification of the entire system. Our verification methodology, based on Symbolic Trajectory Evaluation, is able to bridge the wide gap between the abstract specification and the implementation specific details of the subsystem. This paper presents a detailed description of an industrial application of this methodology to the fixed point execution unit of the PowerPC processor. We were able to verify a representative instruction under all possible stall, bypass, pipeline conditions and under all possible timings for interface to other functional units in the processor.
Active Learning and the Total Cost of Annotation

Active learning (AL) promises to reduce the cost of annotating labeled datasets for trainable human language technologies. Contrary to expectations, when creating labeled training material for HPSG parse selection and later reusing it with other models, gains from AL may be negligible or even negative. This has serious implications for using AL, showing that additional cost-saving strategies may need to be adopted. We explore one such strategy: using a model during annotation to automate some of the decisions. Our best results show an 80% reduction in annotation cost compared with labeling randomly selected data with a single model.
Constructing Behavioral State Machine using Interface Protocol Specification

A behavior of an embedded system is designed by a state machine, which receives input events from externals through the interface, and sends output actions to externals through the interface. Thus the interface specification becomes major concerns in the system design. This paper describes a design method that defines the interface of a component by protocol state machines, and then systematically constructs a behavioral state machine of the component using the interface protocol state machines. The design support system developed to realize the method, which provides enough guidance for designing behavior state machine by using protocol specification, is also described.
Fault isolation for device drivers

This work explores the principles and practice of isolating low-level device drivers in order to improve OS dependability. In particular, we explore the operations drivers can perform and how fault propagation in the event a bug is triggered can be prevented. We have prototyped our ideas in an open-source multiserver OS (MINIX 3) that isolates drivers by strictly enforcing least authority and iteratively refined our isolation techniques using a pragmatic approach based on extensive software-implemented fault-injection (SWIFI) testing. In the end, out of 3,400,000 common faults injected randomly into 4 different Ethernet drivers using both programmed I/O and DMA, no fault was able to break our protection mechanisms and crash the OS. In total, we experienced only one hang, but this appears to be caused by buggy hardware.
Improving the infra-red of holographic descriptions of QCD

A surprisingly good holographic description of QCD can be obtained from naive five dimensional gauge theory on a truncated AdS space. We seek to improve the infra-red description of QCD in such models by using a more sophisticated metric and an action derived from string theory duals of chiral symmetry breaking. Our metric is smooth into the infra-red and the chiral condensate is a prediction of the dynamics. The theory reproduces QCD meson data at the 10% level.
Low-Temperature Sol–Gel Autocombustion Synthesis and Magnetic Properties of Magnetite

Using citric acid, ferric nitrate, and ammonia as starting materials, magnetite (Fe3O4) powders were successfully synthesized through a low-temperature sol-gel autocombustion method. The molar ratios Φ of citric acid to ferric nitrate were adjusted from 0.1:1 to 1.5:1. The combustions were activated at a temperature as low as 300 °C. The X-ray diffraction was used in the determination of the phases of the prepared samples. The results illustrate that some of the as-prepared samples have pure Fe3O4 phase. Magnetite can be synthesized within a large range of molar ratio of citric acid to ferric nitrate. Scanning electron microscopy studies show us porous characteristics of the prepared samples. The results of vibrating sample magnetometer studies show us ferrimagnetic properties of the as-prepared magnetite products at room temperature with a maximum saturation magnetization as high as 91 emu/g. The magnetic hysteresis loops reveal soft magnetic properties of these materials. The saturation magnetization value of the sample of Φ = 0.5 is about 99% of the corresponding bulk value, which indicates that Φ = 0.5 is the most suitable molar ratio for the experiment.
The Mathematical Modelling of the Effects of Thin Layer Drying of Groundnut (Kerstigiella geocarpa harms)

DOI: 10.15580/GJSETR.2018. 3.062818070 A research was done on the effects of mathematical modelling of the thin layer drying of groundnuts (Kerstigiella geocarpa harms) at 67% Moisture Content (% dry basis ) and varying air temperatures of 45, 55 and 65C, at air velocities of 0.6, 1.0 and 1.5 m/s. In order to select the most suitable form of the drying curve, 5 different thin layer semi-theoretical drying models were fitted to experimental data and the moisture diffusivity was calculated from Fick’s second law as the major equation. The highest value of coefficient of determination (R), the low values of errors from the Sum of Square Error (SSE) and Root Mean Square Error (RMSE) indicates that the Two-Term model can satisfactorily describe the drying curve of groundnuts (Kerstigiella geocarpa harms) for drying air velocity of 1.5 m/s and temperature of 55oC. According to the results, the calculated value of effective moisture diffusivity varied from 1.33 to 4.11×10m/s and the value of activation energy varied from 26.29 to 30.57 kJ/mol. Submitted: 17/06/2018 Accepted: 22/06/2018 Published: 27/07/2018
Non-Coding RNAs in Retinal Development

Retinal development is dependent on an accurately functioning network of transcriptional and translational regulators. Among the diverse classes of molecules involved, non-coding RNAs (ncRNAs) play a significant role. Members of this family are present in the cell as transcripts, but are not translated into proteins. MicroRNAs (miRNAs) are small ncRNAs that act as post-transcriptional regulators. During the last decade, they have been implicated in a variety of biological processes, including the development of the nervous system. On the other hand, long-ncRNAs (lncRNAs) represent a different class of ncRNAs that act mainly through processes involving chromatin remodeling and epigenetic mechanisms. The visual system is a prominent model to investigate the molecular mechanisms underlying neurogenesis or circuit formation and function, including the differentiation of retinal progenitor cells to generate the seven principal cell classes in the retina, pathfinding decisions of retinal ganglion cell axons in order to establish the correct connectivity from the eye to the brain proper, and activity-dependent mechanisms for the functionality of visual circuits. Recent findings have associated ncRNAs in several of these processes and uncovered a new level of complexity for the existing regulatory mechanisms. This review summarizes and highlights the impact of ncRNAs during the development of the vertebrate visual system, with a specific focus on the role of miRNAs and a synopsis regarding recent findings on lncRNAs in the retina.
The Bricklayer Ecosystem - Art, Math, and Code

This paper describes the Bricklayer Ecosystem - a freely-available online educational ecosystem created for people of all ages and coding backgrounds. Bricklayer is designed in accordance with a "low-threshold infinite ceiling" philosophy and has been successfully used to teach coding to primary school students, middle school students, university freshmen, and in-service secondary math teachers. Bricklayer programs are written in the functional programming language SML and, when executed, create 2D and 3D artifacts. These artifacts can be viewed using a variety of third-party tools such as LEGO Digital Designer (LDD), LDraw, Minecraft clients, Brickr, as well as STereoLithography viewers.
β-Catenin activity in the dermal papilla of the hair follicle regulates pigment-type switching

The switch between black and yellow pigment is mediated by the interaction between Melanocortin receptor 1 (Mc1r) and its antagonist Agouti, but the genetic and developmental mechanisms that modify this interaction to obtain different coat color in distinct environments are poorly understood. Here, the role of Wnt/β-catenin signaling in the regulation of pigment-type switching was studied. Loss and gain of function of β-catenin in the dermal papilla (DP) of the hair follicle results in yellow and black animals, respectively. β-Catenin activity in the DP suppresses Agouti expression and activates Corin, a negative regulator of Agouti activity. In addition, β-catenin activity in the DP regulates melanocyte activity by a mechanism that is independent of both Agouti and Corin. The coordinate and inverse regulation of Agouti and Corin renders pelage pigmentation sensitive to changes in β-catenin activity in the DP that do not alter pelage structure. As a result, the signals that specify two biologically distinct quantitative traits are partially uncoupled despite their common regulation by the β-catenin pathway in the same cells.
Inhibition of nonsense-mediated mRNA decay (NMD) by a new chemical molecule reveals the dynamic of NMD factors in P-bodies

In mammals, nonsense-mediated mRNA decay (NMD) is a quality-control mechanism that degrades mRNA harboring a premature termination codon to prevent the synthesis of truncated proteins. To gain insight into the NMD mechanism, we identified NMD inhibitor 1 (NMDI 1) as a small molecule inhibitor of the NMD pathway. We characterized the mode of action of this compound and demonstrated that it acts upstream of hUPF1. NMDI 1 induced the loss of interactions between hSMG5 and hUPF1 and the stabilization of hyperphosphorylated isoforms of hUPF1. Incubation of cells with NMDI 1 allowed us to demonstrate that NMD factors and mRNAs subject to NMD transit through processing bodies (P-bodies), as is the case in yeast. The results suggest a model in which mRNA and NMD factors are sequentially recruited to P-bodies.
Children's Use of Electronic Games: Choices of Game Mode and Challenge Levels

Introduction. Interactive electronic games are popular and are believed to contribute to physical activity accrual. The purpose of this study was to examine children's electronic game use during conditions in which they had free access to selecting interactive and seated screen-based versions of electronic games and during the interactive versions had free choice in making adjustments to the activity intensity. Methods. We systematically observed 60 Hong Kong primary school children during two 60-minute game sessions while simultaneously recording their game mode choices and physical activity levels using SOFIT (System for Observing Fitness Instruction Time). Results. When given free choice, children spent more than half of their available time participating in interactive versions of games. These versions of games provided significantly more moderate-to-vigorous physical activity and greater energy expenditure than the computer screen versions. Children with the opportunity to modify intensity levels spent more time playing the interactive versions and accrued more physical activity. Conclusions. The tenets of behavioral choice theory were supported. Access to new-generation interactive games, particularly those with modifiable intensity levels, may facilitate children's participation in physical activity.
Clitic-hood as a PhonologicalCorrelate of Phase-Head Status

This paper presents evidence supporting an expectation generated by the conjunction of two logically independent claims about the derivation: first, that a phase-head triggers its complement’s spellout (Chomsky 2001), and second, that spelled-out material tendsto preserveitsphonological makeup, Dobler et al. (2009). Theexpectation is that phase-headsshould havetheprosodic statusof “cliti cs” , defined as adjuncts to a certain prosodic domain, Selkirk (1996). I show that this expectation is borne out in the Mainland North Germanic languages where whether or not a suffixal determiner behaves as a phonological cliti c perfectly correlates with the presence in a language of the “double DP” structure. This fact is naturally accounted for assuming that what is at stake is the phase-head status of the head realized by the suffixal determiner. Descriptively, definite expressions without modifiers in Norwegian, Swedish, and Danish consist of a nominal stem followed by a suffixal determiner, (1). Another shared feature is that if there is a prenominal modifier in a definite expression, the free-standing determiner appears in front of the modifier.1 However, in this case in Norwegian and Swedish the suffixal determiner is retained on the noun, whereas in Danish it is obligatorily absent, as illustrated in (2)–(3). This has been widely known in the literature as the “double definiteness” or “double determination” contrast.
Contribution of MS-Based Proteomics to the Understanding of Herpes Simplex Virus Type 1 Interaction with Host Cells

Like other DNA viruses, herpes simplex virus type 1 (HSV-1) replicates and proliferates in host cells continuously modulating the host molecular environment. Following a sophisticated temporal expression pattern, HSV-1 encodes at least 89 multifunctional proteins that interplay with and modify the host cell proteome. During the last decade, advances in mass spectrometry applications coupled to the development of proteomic separation methods have allowed to partially monitor the impact of HSV-1 infection in human cells. In this review, we discuss the current use of different proteome fractionation strategies to define HSV-1 targets in two major application areas: (i) viral-protein interactomics to decipher viral-protein interactions in host cells and (ii) differential quantitative proteomics to analyze the virally induced changes in the cellular proteome. Moreover, we will also discuss the potential application of high-throughput proteomic approaches to study global proteome dynamics and also post-translational modifications in HSV-1-infected cells that will greatly improve our molecular knowledge of HSV-1 infection.
On diagonal loading for minimum variance beamformers

Minimum variance beamformers are usually complemented with diagonal loading techniques in order to provide robust ness against finite sample size effects. In spite of its usefulness and popularity, some of the insights of this interesting technique have remained inconspicuous for decades. This work presents a new asymptotic performance study that will shed some light on the finite sample size behavior of this spatial filter. The asymptotic description establishes the existence of an optimum loading factor, which can be estimated from the received data.
Online submillimeter three dimensional imaging of magnetic and paramagnetic contaminants flow rate in multiphase flow pipelines using magnetic particle imaging technique

In this paper, submillimeter three dimensional tomography imaging of paramagnetic contaminants flow rate in multiphase flow pipelines is presented. The device, which is based on Magnetic Particle Imaging (MPI), consists of an array of twelve coils and a pair of permanent magnets and is not influenced with the other phases that constitute the crude oil (e.g. oil, water, sand, and gas) and which are mainly diamagnetic materials. The concentration of the paramagnetic particles can be measured in a three dimensional volumetric space with high spatial and temporal sensitivities which are proportional to the strength of the applied magnetic field. This is also influenced by the size and distribution of the particles and the anisotropy of the permanent magnet. To increase the sensitivity and improve the spatio- encoding field, a two dimensional Linear Field Scanning (LFS) technique coupled with a two dimensional excitation field is proposed. The results demonstrate that the technique would constitute a breakthrough in the area of solid flow measurements and imaging.
Transfer learning for collaborative filtering via a rating-matrix generative model

Cross-domain collaborative filtering solves the sparsity problem by transferring rating knowledge across multiple domains. In this paper, we propose a rating-matrix generative model (RMGM) for effective cross-domain collaborative filtering. We first show that the relatedness across multiple rating matrices can be established by finding a shared implicit cluster-level rating matrix, which is next extended to a cluster-level rating model. Consequently, a rating matrix of any related task can be viewed as drawing a set of users and items from a user-item joint mixture model as well as drawing the corresponding ratings from the cluster-level rating model. The combination of these two models gives the RMGM, which can be used to fill the missing ratings for both existing and new users. A major advantage of RMGM is that it can share the knowledge by pooling the rating data from multiple tasks even when the users and items of these tasks do not overlap. We evaluate the RMGM empirically on three real-world collaborative filtering data sets to show that RMGM can outperform the individual models trained separately.
Investigating the Evolutionary Importance of Denisovan Introgressions in Papua New Guineans and Australians

Previous research reported that Papua New Guineans (PNG) and Australians contain introgressions from Denisovans. Here we present a genome-wide analysis of Denisovan introgressions in PNG and Australians. We firstly developed a two-phase method to detect Denisovan introgressions from whole-genome sequencing data. This method has relatively high detection power (79.74%) and low false positive rate (2.44%) based on simulations. Using this method, we identified 1.34 Gb of Denisovan introgressions from sixteen PNG and four Australian genomes, in which we identified 38,877 Denisovan introgressive alleles (DIAs). We found that 78 Denisovan introgressions were under positive selection. Genes located in the 78 introgressions are related to evolutionarily important functions, such as spermatogenesis, fertilization, cold acclimation, circadian rhythm, development of brain, neural tube, face, and olfactory pit, immunity, etc. We also found that 121 DIAs are missense. Genes harboring the 121 missense DIAs are also related to evolutionarily important functions, such as female pregnancy, development of face, lung, heart, skin, nervous system, and male gonad, visual and smell perception, response to heat, pain, hypoxia, and UV, lipid transport, metabolism, blood coagulation, wound healing, aging, etc. Taken together, this study suggests that Denisovan introgressions in PNG and Australians are evolutionarily important, and may help PNG and Australians in local adaptation. In this study, we also proposed a method that could efficiently identify archaic hominin introgressions in modern non-African genomes.
Deletion of SIRT1 from hepatocytes in mice disrupts lipin-1 signaling and aggravates alcoholic fatty liver.

BACKGROUND & AIMS Sirtuin (SIRT1) is a nicotinamide adenine dinucleotide-dependent protein deacetylase that regulates hepatic lipid metabolism by modifying histones and transcription factors. Ethanol exposure disrupts SIRT1 activity and contributes to alcoholic liver disease in rodents, but the exact pathogenic mechanism is not clear. We compared mice with liver-specific deletion of Sirt1 (Sirt1LKO) mice with their LOX littermates (controls). METHODS We induced alcoholic liver injury in male Sirt1LKO and control mice, placing them on Lieber-DeCarli ethanol-containing diets for 10 days and then administering a single dose of ethanol (5 g/kg body weight) via gavage. Liver and serum samples were collected. We also measured messenger RNA levels of SIRT1, SFRS10, and lipin-1β and lipin-1α in liver samples from patients with alcoholic hepatitis and individuals without alcoholic hepatitis (controls). RESULTS On the ethanol-containing diet, livers of Sirt1LKO mice accumulated larger amounts of hepatic lipid and expressed higher levels of inflammatory cytokines than control mice; serum of Sirt1LKO mice had increased levels of alanine aminotransferase and aspartate aminotransferase. Hepatic deletion of SIRT1 exacerbated ethanol-mediated defects in lipid metabolism, mainly by altering the function of lipin-1, a transcriptional regulator of lipid metabolism. In cultured mouse AML-12 hepatocytes, transgenic expression of SIRT1 prevented fat accumulation in response to ethanol exposure, largely by reversing the aberrations in lipin-1 signaling induced by ethanol. Liver samples from patients with alcoholic hepatitis had reduced levels of SIRT1 and a higher ratio of Lpin1β/α messenger RNAs than controls. CONCLUSIONS In mice, hepatic deletion of Sirt1 promotes steatosis, inflammation, and fibrosis in response to ethanol challenge. Ethanol-mediated impairment of hepatic SIRT1 signaling via lipin-1 contributes to development of alcoholic steatosis and inflammation. Reagents designed to increase SIRT1 regulation of lipin-1 can be developed to treat patients with alcoholic fatty liver disease.