Miracle-dz/UniFAR-FTUs huggingface dataset:
Random testing: from the classical approach to a global view and full test automation

Research has brought a number of different methods for automated test and test data generation in the last decades. These methods range from simple applications such as random testing, to complex analysis systems, such as constraint-based methods. While research on these methods has been extensive, industrial application to large-scale systems is still seldom. One of the reasons may be that the simple methods fail - e.g. in terms of achieved coverage -- for complex systems-under-test, while the complex methods are difficult to implement and often have limitations in terms of the language scope they can be applied to. This paper aims to present practical experience with a number of different methods based on random testing in various fields of application, ranging from automated unit tests to automated system and integration tests. This experience led to strategic combination of different methods, which shall be described and discussed based on actual results.
Pain in U.S. nursing homes: validating a pain scale for the minimum data set.

PURPOSE The aim of this study was to validate a pain scale for the Minimum Data Set (MDS) assessment instrument and examine prevalence of pain in major nursing home subpopulations, including type of admission and cognitive status. DESIGN AND METHODS This study considered validation of the MDS pain items and derivation of scale performed against the Visual Analogue Scale (VAS), using Automatic Interaction Detection. The derivation data describe 95 postacute care nursing home patients who are able to communicate. The scale is then used in retrospective analysis of 34,675 Michigan nursing home residents. RESULTS A four-group scale was highly predictive of VAS pain scores (variance explanation 56%) and therefore quite valid in detecting pain. In the prevalence sample, only 47% of postacute patients compared to 63% of postadmission patients reported no pain, and these percentages rose with increasing cognitive impairment. IMPLICATIONS Pain is prevalent in nursing home residents, especially in those with cognitive dysfunction, and often untreated.
CASE REUSE BY MODEL-BASED INTERPRETATION

For applying case-basedreasoning to design, adaptation and combination are essential. They require adaptation knowledge defining the parts of a case that can be changed without compromising its function. We have investigated model-based interpretations for providing this knowledge. An interpretation is a functional model given by the user to explain the structure given by a case. It defines the intended functions and provides constraints on the structure which avoid violating them. Since the interpretation may be different from that used in the design of the case, creative reuse of cases is also possible. This paper reports on the results of this investigation with two case-based design programs: FAMING for mechanism part shapes and CADRE for buildings.
Palindromic polynomials, time-reversible systems, and conserved quantities

The roots of palindromic and antipalindromic polynomials appear in pairs (lambda,1/lambda). A polynomial with such roots is antipalindromic if and only if in addition, it has a root at 1 of an odd multiplicity. The result has applications in system theory: 1) any kernel representation of a discrete-time, time-reversible, scalar, autonomous LTI system is either palindromic or antipalindromic. (Similar statement holds for systems with inputs.) 2) LTI systems with palindromic or antipalindromic kernel representations have nontrivial conserved quantities.
Adaptive insertion policies for high performance caching

The commonly used LRU replacement policy is susceptible to thrashing for memory-intensive workloads that have a working set greater than the available cache size. For such applications, the majority of lines traverse from the MRU position to the LRU position without receiving any cache hits, resulting in inefficient use of cache space. Cache performance can be improved if some fraction of the working set is retained in the cache so that at least that fraction of the working set can contribute to cache hits. We show that simple changes to the insertion policy can significantly reduce cache misses for memory-intensive workloads. We propose the LRU Insertion Policy (LIP) which places the incoming line in the LRU position instead of the MRU position. LIP protects the cache from thrashing and results in close to optimal hitrate for applications that have a cyclic reference pattern. We also propose the Bimodal Insertion Policy (BIP) as an enhancement of LIP that adapts to changes in the working set while maintaining the thrashing protection of LIP. We finally propose a Dynamic Insertion Policy (DIP) to choose between BIP and the traditional LRU policy depending on which policy incurs fewer misses. The proposed insertion policies do not require any change to the existing cache structure, are trivial to implement, and have a storage requirement of less than two bytes. We show that DIP reduces the average MPKI of the baseline 1MB 16-way L2 cache by 21%, bridging two-thirds of the gap between LRU and OPT.
Leptin’s Pro-Angiogenic Signature in Breast Cancer

Obesity is linked to increased incidence of breast cancer. The precise causes and mechanisms of these morbid relationships are unknown. Contradictory data on leptin angiogenic actions have been published. However, accumulating evidence would suggest that leptin’s pro-angiogenic effects in cancer play an essential role in the disease. Leptin, the main adipokine secreted by adipose tissue, is also abnormally expressed together with its receptor (OB-R) by breast cancer cells. Leptin induces proliferation and angiogenic differentiation of endothelial cells upregulates VEGF/VEGFR2 and transactivates VEGFR2 independent of VEGF. Leptin induces two angiogenic factors: IL-1 and Notch that can increase VEGF expression. Additionally, leptin induces the secretion and synthesis of proteases and adhesion molecules needed for the development of angiogenesis. Leptin’s paracrine actions can further affect stromal cells and tumor associated macrophages, which express OB-R and secrete VEGF and IL-1, respectively. A complex crosstalk between leptin, Notch and IL-1 (NILCO) that induces VEGF/VEGFR2 is found in breast cancer. Leptin actions in tumor angiogenesis could amplify, be redundant and/or compensatory to VEGF signaling. Current failure of breast cancer anti-angiogenic therapies emphasizes the necessity of targeting the contribution of other pro-angiogenic factors in breast cancer. Leptin’s impact on tumor angiogenesis could be a novel target for breast cancer, especially in obese patients. However, more research is needed to establish the importance of leptin in tumor angiogenesis. This review is focused on updated information on how leptin could contribute to tumor angiogenesis.
Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories

Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology.
Thioacetamide-Induced Acute Hepatic Encephalopathy in Rat: Behavioral, Biochemical and Histological Changes

Background As a serious neuropsychiatric disease, hepatic encephalopathy (HE) is a clinical condition with several types regarding chronicity and clinical diversity that can develop as a complication of both acute and chronic liver failure. This study evaluates changes in thioacetamide (TAA)-induced acute hepatic encephalopathy (AHE) in rat as an animal model. Methods Both genders of C57BL6, BALB/C mice and Sprague Dawley rats; (10 animals in each group) were compared for induction of AHE to clarify which animal and gender were appropriate. The animals (10 male rats in each group) were categorized in 4 groups according to the dose of the TAA administered (200, 300 and 400 mg/kg of TAA at 24 h intervals for 4 days). A control group was treated with solvent of TAA which was water (5 ml/kg/day). The behavioral, biochemical markers of hepatic failure and histological aspects of thioacetamide (TAA) induced AHE and the correlation between the clinical severity and liver failure biomarkers were evaluated. Results Rat was shown to be an animal model of choice for AHE while the optimum dosage of TAA to induce AHE was 300 mg/kg/day at 24 h intervals for 4 days. The behavioral score was partially correlated with the rising of some biomarkers and pathological findings. Conclusion Rat can be introduced as the animal of choice for AHE to study the pathophysiology, pharmacology and the survival rate of disease in liver transplant patients.
NADH Oxidase Activity of Rat Cardiac Sarcoplasmic Reticulum Regulates Calcium-Induced Calcium Release

Abstract— NADH and Ca2+ have important regulatory functions in cardiomyocytes related to excitation-contraction coupling and ATP production. To elucidate elements of these functions, we examined the effect of NADH on sarcoplasmic reticulum (SR) Ca2+ release and the mechanisms of this regulation. Physiological concentrations of cytosolic NADH inhibited ryanodine receptor type 2 (RyR2)–mediated Ca2+-induced Ca2+ release (CICR) from SR membranes (IC50=120 &mgr;mol/L) and significantly lowered single channel open probability. In permeabilized single ventricular cardiomyocytes, NADH significantly inhibited the amplitude and frequency of spontaneous Ca2+ release. Blockers of electron transport prevented the inhibitory effect of NADH on CICR in isolated membranes and permeabilized cells, as well as on the activity of RyR2 channels reconstituted in lipid bilayer. An endogenous NADH oxidase activity from rat heart copurified with SR enriched with RyR2. A significant contribution by mitochondria was excluded as NADH oxidation by SR exhibited >9-fold higher catalytic activity (8.8 &mgr;mol/mg protein per minute) in the absence of exogenous mitochondrial complex I (ubiquinone) or complex III (cytochrome c) electron acceptors, but was inhibited by rotenone and pyridaben (IC50=2 to 3 nmol/L), antimycin A (IC50=13 nmol/L), and diphenyleneiodonium (IC50=28 &mgr;mol/L). Cardiac junctional SR treated with [3H](trifluoromethyl)diazirinyl-pyridaben specifically labeled a single 23-kDa PSST-like protein. These data indicate that NADH oxidation is tightly linked to, and essential for, negative regulation of the RyR2 complex and is a likely component of an important physiological negative-feedback mechanism coupling SR Ca2+ fluxes and mitochondrial energy production.
The Role of Action Research in the Investigation and Diffusion of Innovations in Health Care: The PRIDE Project

In this article, the authors discuss the role of action research in relation to the investigation and practical implementation of innovations in health care. The diffusion of innovations is an essential component of the modernization of health services worldwide. However, the literature shows that it is not an easy process to research. A paradox is noted that although action research has much to offer, it has had only a limited impact in the innovation field. Drawing on an example of a project in the United Kingdom, the authors discuss whether action research is a valuable method in the study of the diffusion of innovations. They analyze its strengths and limitations as a “whole systems approach” that combines researching with developing and diffusing innovations. They argue that it is best suited to the study of innovation diffusion where there is a need for high level of adaptation in each new setting.
Obstacle avoidance and formation regrouping strategy and control for UAV formation flight

Obstacle avoidance (OA) and formation regrouping (FR) are very important issues for implementation of automatic UAVs formation flight. In this paper, the OA strategy and control for UAV leader is investigated first. Then, it is followed by investigation of the OA strategy and control for UAV follower. In the process of OA, in order to conduct OA reasonably and efficiently, the formation is split first and then all the UAVs regroup to fly in the original formation after OA process is completed. To this end, formation splitting and regrouping strategies in four OA scenarios are presented for UAV formation flight. Simulation experimental results demonstrate that the presented OA and FR strategies and control are effective.
Under Consideration for Publication in J. Functional Programming Transparent Fault Tolerance for Scalable Functional Computation

Reliability is set to become a major concern on emergent large-scale architectures. While there are many parallel languages, and indeed many parallel functional languages, very few address reliability. The notable exception is the widely emulated Erlang distributed actor model that provides explicit supervision and recovery of actors with isolated state. We investigate scalable transparent fault tolerant functional computation with automatic supervision and recovery of tasks. We do so by developing HdpH-RS, a variant of the Haskell distributed parallel Haskell (HdpH) DSL with Reliable Scheduling. Extending the distributed work stealing protocol of HdpH for task supervision and recovery is challenging. To eliminate elusive concurrency bugs, we validate the HdpH-RS work stealing protocol using the SPIN model checker. HdpH-RS differs from the actor model in that its principal entities are tasks, i.e. independent stateless computations, rather than isolated stateful actors. Thanks to statelessness, fault recovery can be performed automatically and entirely hidden in the HdpH-RS runtime system. Statelessness is also key for proving a crucial property of the semantics of HdpH-RS: fault recovery does not change the result of the program, akin to deterministic parallelism. HdpH-RS provides a simple distributed fork/join-style programming model, with minimal exposure of fault tolerance at the language level, and a library of higher level abstractions such as algorithmic skeletons. In fact, the HdpH-RS DSL is exactly the same as the HdpH DSL, hence users can opt in or out of fault tolerant execution without any refactoring. Computations in HdpH-RS are always as reliable as the root node, no matter how many nodes and cores are actually used. We benchmark HdpH-RS on conventional clusters and an HPC platform: all benchmarks survive Chaos Monkey random fault injection; the system scales well e.g. up to 1400 cores on the HPC; reliability and recovery overheads are consistently low even at scale.
Evaluation of MODIS LAI/FPAR Product Collection 6. Part 2: Validation and Intercomparison

The aim of this paper is to assess the latest version of the MODIS LAI/FPAR product (MOD15A2H), namely Collection 6 (C6). We comprehensively evaluate this product through three approaches: validation with field measurements, intercomparison with other LAI/FPAR products and comparison with climate variables. Comparisons between ground measurements and C6, as well as C5 LAI/FPAR indicate: (1) MODIS LAI is closer to true LAI than effective LAI; (2) the C6 product is considerably better than C5 with RMSE decreasing from 0.80 down to 0.66; (3) both C5 and C6 products overestimate FPAR over sparsely-vegetated areas. Intercomparisons with three existing global LAI/FPAR products (GLASS, CYCLOPES and GEOV1) are carried out at site, continental and global scales. MODIS and GLASS (CYCLOPES and GEOV1) agree better with each other. This is expected because the surface reflectances, from which these products were derived, were obtained from the same instrument. Considering all biome types, the RMSE of LAI (FPAR) derived from any two products ranges between 0.36 (0.05) and 0.56 (0.09). Temporal comparisons over seven sites for the 2001–2004 period indicate that all products properly capture the seasonality in different biomes, except evergreen broadleaf forests, where infrequent observations due to cloud contamination induce unrealistic variations. Thirteen years of C6 LAI, temperature and precipitation time series data are used to assess the degree of correspondence between their variations. The statistically-significant associations between C6 LAI and climate variables indicate that C6 LAI has the potential to provide reliable biophysical information about the land surface when diagnosing climate-driven vegetation responses.
The European Hepatitis C Virus database

As no efficient culture system for Hepatitis C Virus (HCV) is currently available, most of the research against this virus is driven by analysis of its genomic sequences. Thus, a database that allows researchers to study genetic variability of all available sequences could play an important role in helping drugs and vaccine design and in providing additional insight into the basic biology, immunology and evolution of the virus. In this paper, we describe the European Hepatitis C Virus database (euHCVdb, http://euhcvdb.ibcp.fr) and its website that offers access to HCV public sequences automatically annotated and a set of tools for analysis. The euHCVdb database focuses on HCV protein sequence, structure and function analysis.
Association of Leukocyte Mitochondrial DNA Copy Number with Colorectal Cancer Risk: Results from the Shanghai Women's Health Study

Background: Mitochondria play an important role in cellular energy metabolism, free radical production, and apoptosis, and thus may be involved in cancer development. Methods: We evaluated mitochondrial DNA (mtDNA) copy number in peripheral leukocytes in relation to colorectal cancer risk in a case–control study of 444 colorectal cancer cases and 1,423 controls nested in the Shanghai Women's Health Study, a population-based, prospective cohort study. Relative mtDNA copy number was determined by a quantitative real-time PCR assay using peripheral leukocyte DNA samples collected at the time of study enrollment, before cancer diagnosis. Results: We found that baseline mtDNA copy number was lower among women who subsequently developed colorectal cancer [geometric mean, 0.277; 95% confidence interval (CI), 0.269–0.285] than among women who remained cancer-free (geometric mean, 0.288; 95% CI, 0.284–0.293; P = 0.0153). Multivariate adjusted ORs were 1.26 (95% CI, 0.93–1.70) and 1.44 (95% CI, 1.06–1.94) for the middle and lower tertiles of mtDNA copy number, respectively, compared with the upper tertile (highest mtDNA copy number; Ptrend = 0.0204). The association varied little by the interval between blood collection and cancer diagnosis. Conclusions: Our data suggest that mtDNA copy number measured in peripheral leukocytes may be a potential biomarker useful for colorectal cancer risk assessment. Impact: If confirmed, mtDNA copy number measured in peripheral leukocytes may be a biomarker useful for colorectal cancer risk assessment. Cancer Epidemiol Biomarkers Prev; 23(11); 2357–65. ©2014 AACR.
Anaerobic Metabolism at Thermal Extremes: A Metabolomic Test of the Oxygen Limitation Hypothesis in an Aquatic Insect

Thermal limits in ectotherms may arise through a mismatch between supply and demand of oxygen. At higher temperatures, the ability of their cardiac and ventilatory activities to supply oxygen becomes insufficient to meet their elevated oxygen demand. Consequently, higher levels of oxygen in the environment are predicted to enhance tolerance of heat, whereas reductions in oxygen are expected to reduce thermal limits. Here, we extend previous research on thermal limits and oxygen limitation in aquatic insect larvae and directly test the hypothesis of increased anaerobic metabolism and lower energy status at thermal extremes. We quantified metabolite profiles in stonefly nymphs under varying temperatures and oxygen levels. Under normoxia, the concept of oxygen limitation applies to the insects studied. Shifts in the metabolome of heat-stressed stonefly nymphs clearly indicate the onset of anaerobic metabolism (e.g., accumulation of lactate, acetate, and alanine), a perturbation of the tricarboxylic acid cycle (e.g., accumulation of succinate and malate), and a decrease in energy status (e.g., ATP), with corresponding decreases in their ability to survive heat stress. These shifts were more pronounced under hypoxic conditions, and negated by hyperoxia, which also improved heat tolerance. Perturbations of metabolic pathways in response to either heat stress or hypoxia were found to be somewhat similar but not identical. Under hypoxia, energy status was greatly compromised at thermal extremes, but energy shortage and anaerobic metabolism could not be conclusively identified as the sole cause underlying thermal limits under hyperoxia. Metabolomics proved useful for suggesting a range of possible mechanisms to explore in future investigations, such as the involvement of leaking membranes or free radicals. In doing so, metabolomics provided a more complete picture of changes in metabolism under hypoxia and heat stress.
Differential cross section results from NuTeV

The NuTeV experiment has collected high statistics, high energy samples of $\nu$ and $\bar{\nu}$ charged-current interactions using the sign-selected Fermilab neutrino beam. NuTeV has extracted $\nu$ and $\bar{\nu}$ differential cross sections for DIS single-muon production at moderate $x>0.015$ and average $Q^2\sim 15$ GeV$^2$. Differential cross sections and structure function results are presented. The NuTeV measurement has improved systematic precision and includes data over an expanded kinematic range up to high inelasticity.
When cell biology meets theory

Cell biologists now have tools and knowledge to generate useful quantitative data. But how can we make sense of these data, and are we measuring the correct parameters? Moreover, how can we test hypotheses quantitatively? To answer these questions, the theory of physics is required and is essential to the future of quantitative cell biology.
Integration of multiple-baseline color stereo vision with focus and defocus analysis for 3D shape measurement

A 3D vision system named SVIS is developed for 3D shape measurement that integrates three methods: (i) multiple- baseline, multiple-resolution Stereo Image Analysis (SIA) that uses colore image data, (ii) Image Defocus Analysis (IDA), and (iii) Image Focus Analysis (IFA). IDA and IFA are less accurate than stereo but they do not suffer from the correspondence problem associated with stereo. A rough 3D shape is first obtained using IDA and then IFA is used to obtain an improved estimate. The result is then used in SIA to solve the correspondence problem and obtain an accurate measurement of 3D shape. SIA is implemented using color images recorded at multiple-baselines. Color images provide more information than monochrome images for stereo matching. Therefore matching errors are reduced and accuracy of 3D shape is improved. Further improvements are obtained through multiple-baseline stereo analysis. First short baseline images are analyzed to obtain an initial estimate of 3D shape. In this step, stereo matching errors are low and computation is fast since a shorter baseline result in lower disparities. The initial estimate of 3D shape is used to match longer baseline stereo images. This yields more accurate estimation of 3D shape. The stereo matching step is implemented using a multiple-resolution matching approach to reduce computation. First lower resolution images are matched and the result are used in matching higher resolution images. This paper presented the algorithms and the experimental result of 3D shape measurements on SVIS for several objects. These results suggest a practical vision system for 3D shape measurement.