Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding software evolution: the maisqual ant data set

Software engineering is a maturing discipline which has seen many drastic advances in the last years. However, some studies still point to the lack of rigorous and mathematically grounded methods to raise the field to a new emerging science, with proper and reproducible foundations to build upon. Indeed, mathematicians and statisticians do not necessarily have software engineering knowledge, while software engineers and practitioners do not necessarily have a mathematical background. The Maisqual research project intends to fill the gap between both fields by proposing a controlled and peer-reviewed data set series ready to use and study. These data sets feature metrics from different repositories, from source code to mail activity and configuration management meta data. Metrics are described and commented, and all the steps followed for their extraction and treatment are described with contextual information about the data and its meaning. This article introduces the Apache Ant weekly data set, featuring 636 extracts of the project over 12 years at different levels of artefacts – application, files, functions. By associating community and process related information to code extracts, this data set unveils interesting perspectives on the evolution of one of the great success stories of open source.
Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening

Olfactory receptors (ORs) belong to the class A G-Protein Coupled Receptor superfamily of proteins. Unlike G-Protein Coupled Receptors, ORs exhibit a combinatorial response to odors/ligands. ORs display an affinity towards a range of odor molecules rather than binding to a specific set of ligands and conversely a single odorant molecule may bind to a number of olfactory receptors with varying affinities. The diversity in odor recognition is linked to the highly variable transmembrane domains of these receptors. The purpose of this study is to decode the odor-olfactory receptor interactions using in silico docking studies. In this study, a ligand (odor molecules) dataset of 125 molecules was used to carry out in silico docking using the GLIDE docking tool (SCHRODINGER Inc Pvt LTD). Previous studies, with smaller datasets of ligands, have shown that orthologous olfactory receptors respond to similarly-tuned ligands, but are dramatically different in their efficacy and potency. Ligand docking results were applied on homologous pairs (with varying sequence identity) of ORs from human and mouse genomes and ligand binding residues and the ligand profile differed among such related olfactory receptor sequences. This study revealed that homologous sequences with high sequence identity need not bind to the same/ similar ligand with a given affinity. A ligand profile has been obtained for each of the 20 receptors in this analysis which will be useful for expression and mutation studies on these receptors.
Mutations of genes in synthesis of the carotenoid precursors of ABA lead to pre-harvest sprouting and photo-oxidation in rice

Pre-harvest sprouting (PHS) or vivipary in cereals is an important agronomic trait that results in significant economic loss. A considerable number of mutations that cause PHS have been identified in several species. However, relatively few viviparous mutants in rice (Oryza sativa L.) have been reported. To explore the mechanism of PHS in rice, we carried out an extensive genetic screening and identified 12 PHS mutants (phs). Based on their phenotypes, these phs mutants were classified into three groups. Here we characterize in detail one of these groups, which contains mutations in genes encoding major enzymes of the carotenoid biosynthesis pathway, including phytoene desaturase (OsPDS), ζ-carotene desaturase (OsZDS), carotenoid isomerase (OsCRTISO) and lycopene β-cyclase (β-OsLCY), which are essential for the biosynthesis of carotenoid precursors of ABA. As expected, the amount of ABA was reduced in all four phs mutants compared with that in the wild type. Chlorophyll fluorescence analysis revealed the occurrence of photoinhibition in the photosystem and decreased capacity for eliminating excess energy by thermal dissipation. The greatly increased activities of reactive oxygen species (ROS) scavenging enzymes, and reduced photosystem (PS) II core proteins CP43, CP47 and D1 in leaves of the Oscrtiso/phs3-1 mutant and OsLCY RNAi transgenic rice indicated that photo-oxidative damage occurred in PS II, consistent with the accumulation of ROS in these plants. These results suggest that the impairment of carotenoid biosynthesis causes photo-oxidation and ABA-deficiency phenotypes, of which the latter is a major factor controlling the PHS trait in rice.
Human Vascular Smooth Muscle Cells From Restenosis or In-Stent Stenosis Sites Demonstrate Enhanced Responses to p53: Implications for Brachytherapy and Drug Treatment for Restenosis

The p53 tumor suppressor gene regulates growth arrest and apoptosis after DNA damage. Recent studies suggest that p53 is inactive in vascular smooth muscle cells (VSMCs) in human angioplasty restenosis, promoting VSMC accumulation and vessel stenosis. In contrast, the success of irradiation (brachytherapy) for in-stent restenosis argues that DNA-damage p53 responses are intact. We examined p53 expression and function in human VSMCs from normal vessels (n-VSMCs) and angioplasty/in-stent restenosis sites (r-VSMCs). p53 expression was uniformly low in all VSMCs and was induced by DNA damage. However, p53 induced profoundly different biological effects in r-VSMCs versus n-VSMCs, causing growth arrest and apoptosis in r-VSMCs only. In addition, dominant-negative p53 promoted cell proliferation and apoptosis in r-VSMCs but not n-VSMCs. Cytotoxic drug– or irradiation-induced growth arrest and apoptosis in both cell types was mediated only partly by p53. In contrast, cyclin D degradation in response to DNA damage, a critical early mediator of growth arrest, was impaired in r-VSMCs, an effect that required p53. We conclude that p53 expression and function are normal or increased in r-VSMCs and may underlie the success of brachytherapy. We also identify a restenosis VSMC-specific defect in cyclin D degradation induced by DNA damage.
Modeling Quantum Entanglements in Quantum Language Models

Recently, a Quantum Language Model (QLM) was proposed to model term dependencies upon Quantum Theory (QT) framework and successively applied in Information Retrieval (IR). Nevertheless, QLM's dependency is based on co-occurrences of terms and has not yet taken into account the Quantum Entanglement (QE), which is a key quantum concept and has a significant cognitive implication. In QT, an entangled state can provide a more complete description for the nature of realities, and determine intrinsic correlations of considered objects globally, rather than those co-occurrences on the surface. It is, however, a real challenge to decide and measure QE using the classical statistics of texts in a post-measurement configuration. In order to circumvent this problem, we theoretically prove the connection between QE and statistically Unconditional Pure Dependence (UPD). Since UPD has an implementable deciding algorithm, we can in turn characterize QE by extracting the UPD patterns from texts. This leads to a measurable QE, based on which we further advance the existing QLM framework. We empirically compare our model with related models, and the results demonstrate the effectiveness of our model.
HEMODYNAMIC AND IMMUNE CONSEQUENCES OF OPIATE ANALGESIA AFTER TRAUMA/HEMORRHAGE

The regulation of compensatory hemodynamic, inflammatory, and metabolic counter-regulatory responses to traumatic injury (trauma/hemorrhage [tx/hem]) and subsequent inflammatory challenges during the post-tx/hem period relies on balanced activation of neuroendocrine and opioid pathways. Pharmacological interventions during the rescue period as well as during the early post-tx/hem period that target these regulatory pathways can potentially affect the activation or efficacy of compensatory mechanisms. Their impact on mechanisms involved in these responses has not been well defined. We examined the impact of morphine and ketamine on immediate hemodynamic responses to tx/hem as well as on the integrity of host defense mechanisms at day 5 post-tx/hem. Morphine (10 mg/kg), ketamine (18 mg/kg), or saline (0.3 ml) were injected intraperitoneally at 15 min post-tx/hem (soft tissue injury and fixed pressure hemorrhage, 40 mmHg, 60 min) and 15 min before lactated Ringer’s fluid resuscitation (LRFR, 2.4× total blood volume removed). Morphine, but not ketamine, produced effective and sustained analgesia. Morphine and ketamine impaired the rise in mean arterial blood pressure (MABP) during LRFR and increased 48-h mortality (2- to 3-fold). Morphine and ketamine markedly (40%-80%) attenuated the systemic LPS- (100 μg/100 g body weight) induced TNF response at day 5 post-tx/hem. Morphine attenuated LPS-induced lung and spleen TNF expression, whereas ketamine enhanced spleen TNF expression but did not alter lung responses. Subsequent studies demonstrated that the morphine-induced impairment of the response was not due to altered cytokine responses during the early post-tx/hem period but that they could be restored and 24 h mortality could be reduced by increasing the volume of LRFR (2-fold). These results indicate that morphine and ketamine analgesia compromise the hemodynamic and host defense responses after tx/hem, directly affecting mortality and morbidity during the recovery period.
Fault‐tolerant timestamp‐based two‐phase commit protocol for RESTful services

Service‐oriented architecture provides interoperability and weak coupling features for software development. Representational state transfer (REST) is an architectural style that has attracted attention in the SOA domain as it allows the development of Web services based on original principles of the World Wide Web. Unlike Web service specifications, which are based on Simple Object Access Protocol and Web Services Description Language, REST does not provide ‘official’ standards to address non‐functional requirements of services, such as security, reliability, and transaction control. The timestamp‐based two‐phase commit protocol for RESTful service (TS2PC4RS) algorithm specifies concurrency control of RESTful services during a transaction. An extension of the TS2PC4RS specifies the concurrency control of the Web services considering the update operation to meet some business rules. However, neither algorithm addresses transaction control when failures occur. In long‐term transactions, failures can occur and compromise the success of Web service applications. Two common failures traditionally considered in the analysis of protocols are host and connection failures. The aim of this paper is to address fault tolerance for TS2PC4RS and its extension. A fault‐tolerant protocol based on timeout and log records is proposed. The fault‐tolerant protocol provides support for the host and connection failures that may occur during a transaction execution. The fault‐tolerant mechanisms are used to meet the application domain business rules that guide the behavior of RESTful services. We describe the protocol using scenarios when failures occur. Copyright © 2012 John Wiley & Sons, Ltd.
Measuring wing kinematics, flight trajectory and body attitude during forward flight and turning maneuvers in dragonflies

SUMMARY A robust technique for determining the wing kinematics, body position and attitude of a free-flight dragonfly is described. The new method is based on a projected comb-fringe technique combined with the natural landmarks on a dragonfly, allowing us to establish the local body-centered coordinate system with high accuracy, and to measure the body attitude at any instant. The kinematic parameters, including wingbeat frequency, flapping angle, angle of attack, torsional angle and camber deformation, required no assumptions to be made with respect to wing geometry, deformability (except the assumption of rigid leading edges) or bilateral wing symmetry. Two typical flight behaviors, forward flight and turning maneuvers, of dragonflies Polycanthagyna melanictera Selys were measured and analyzed.
Performance of Different Projectile Nose Shapes in Normal Penetrating Armor Targets

Based on the cavity expansion theory, an analysis model of normal penetration of slender nose projectile into armor targets was established, and the variation relation curve of penetration depth and initial velocity when initial velocity is below ballistic limit was obtained. By carrying out ballistic impact test using 85mm smoothbore gun, various projectile nose shapes and armor target thickness and their effect on damage were considered. The research results have indicated that the damage of target is mainly ductile reaming and the shape of crater is almost the same as the projectile nose embedded in the target. Within a relatively low velocity range, nose shape has a greater influence on penetration depth. In contrast, within a relatively high velocity range, the target thickness has a greater influence on penetration depth. It can provide theoretical basis for the design of projectile noses and analysis of anti-penetration performance of armor targets.
Human endothelial cells grow poorly on vitronectin: Role of PAI‐1

The cell adhesive protein vitronectin is a common component of interstitial extracellular matrix and circulates in plasma. It competes effectively with other plasma proteins to adsorb to certain biomaterial surfaces, and is likely to represent an important cell adhesion mediator on the luminal surface of vascular grafts. It is also found associated with certain vascular pathologies. We have shown previously that human endothelial cells grow poorly on a vitronectin surface compared with other extracellular matrix molecules. In this paper we show that endothelial cells seeded on vitronectin and fibronectin produced substantially different profiles of extracellular matrix molecules. The most outstanding difference was in the amount of matrix‐localised plasminogen activator‐inhibitor‐1 which was high on vitronectin and negligible on fibronectin. This was correlated with a small but significant inhibition of cell adhesion to vitronectin compared with fibronectin, and very significant interference with dissociation of cell: extracellular matrix contacts, resulting either from direct inhibition of the proteolytic activity of urokinase, or from interference with urokinase‐receptor signaling and consequent focal adhesion turnover. Such interference would inhibit cell proliferation by disabling the cells from loosening their matrix contacts in order to proceed through mitosis. This would seriously compromise endothelial recovery in cases of damage to the vascular wall and placement of stents or grafts, where the presence of surface‐adsorbed vitronectin is likely to modulate the tissue response. J. Cell. Biochem. 82: 98–109, 2001. © 2001 Wiley‐Liss, Inc.
Natural Projections for the Synthesis of Non-Conflicting Supervisory Controllers

Abstract A common strategy in the design of discrete-event systems is to apply synthesis algorithms not to the actual plant model but to an Abstraction that is realised on a significantly smaller state set. Depending on the control objectives, certain conditions are imposed on the plant and on the Abstraction, in order to end up with an appropriate controller. A well known result from the literature is that Abstractions obtained by a so called natural observer can be used for the purpose of non-blocking supervisory control. Despite additional favourable properties of natural observers regarding state count and composed plants, as a condition for non-blocking supervisory control it is restrictive, i.e., sufficient but not necessary. This contrasts the sufficient and necessary condition developed in this paper.
Neutron-induced soft error rate estimation for SRAM using PHITS

This paper presents a novel neutron-induced soft-error-rate (SER) estimation tool with a particle transport code: PHITS. The proposed tool can calculate the SER according to various data patterns and the layout of the memory cells in an SRAM. As layouts, two kinds of an NMOS-PMOS-NMOS 6T and an inside-out PMOS-NMOS-PMOS versions are considered. The proposed tool distinguishes a single-event-upset (SEU) SER, a horizontal multiple-cell-upset (MCU) SER, and a vertical MCU SER using an extracting function. The horizontal MCU SER in the inside-out version of the PMOS-NMOS-PMOS 6T SRAM cell layout was expected to be 26-41% less than that of the general NMOS-PMOS-NMOS 6T cell layout.
Incorporation Rate of Leucine into Proteins in Human Liver Slices

Abstract. The rate of incorporation of leucine into hepatic proteins in liver slices from 42 patients was studied. Zero order kinetics for the incorporation of leucine in relation to the incubation time and to the amount of incubated proteins were obtained, provided that the medium contained a complete amino acid mixture with a concentration 4 times that of normal human serum. – Inulin space and water content of the preparation were of the same magnitude as reported for rat liver. The presence of fructose (5.5 mM) in the medium caused an inhibition of the rate of incorporation of leucine into pro teins. Insulin in the medium, however, stimulated tho incorporation rate. – Assuming that the rate of incorporation of leucine into hepatic proteins is representative of protein synthesis, the half‐life of liver proteins can be calculated to be 35 days for subjects below 60 years of age. For those who were older than 60 years, the protein turnover rate was approximately 30% higher.
Optimization of a QoS-aware channel assignment for cognitive radio networks

The channel assignment problem is an important issue in cognitive radio networks because the conventional fixed spectrum allocation mechanism leads to significant spectrum underutilization. In this paper, the QoS-aware channel assignment is formulated as an optimization problem. The objective is to maximize the utilization of spectrum opportunities and fairness among secondary users (SUs) subject to constraints of different SUs demands, spectrum levels of the QoS and channel availabilities for each SU. Designing the QoS-Aware channel assignment scheme is based on genetic algorithm (GA) and quantum genetic algorithm (QGA). Two different objective functions are proposed as the network utilization and fairness indexes. Simulation results are provided to show the efficiency of the proposed method.
Voiced/unvoiced decision algorithm for HMM-based speech synthesis

This paper introduces a novel method to improve the U/V decision method in HMM-based speech synthesis. In the conventional method, the U/V decision of each state is independently made, and a state in the middle of a vowel may be decided as unvoiced. In this paper, we propose to utilize the constraints of natural speech to improve the U/V decision inside a unit, such as syllable or phone. We use a GMM-based U/V change time model to select the best U/V change time in one unit, and refine the U/V decision of all states in that unit based on the selected change time. The result of a perceptual evaluation demonstrates that the proposed method can significantly improve the naturalness of the synthetic speech.
Optimal Two-stage Designs for Single-arm Phase II Oncology Trials with Two Binary Endpoints

Summary Objectives: In phase II clinical trials in oncology, the potential efficacy of a new treatment regimen is assessed in terms of anticancer activity. The standard approach consists of a single-arm two-stage design where a single binary endpoint is compared to a specified target value. However, a new drug would still be considered promising if it showed a lower tumor response rate than the target level but would lead, for example, to disease stabilization. Methods: We present an analytical solution for the calculation of the type I and type II error rate for a two-stage design where the hypothesis test considers two endpoints and provide optimal and minimax solutions. Furthermore, the problem of inference about the two single endpoints following rejection of the global null hypothesis is addressed by deriving a multiple test procedure that controls the experimentwise type I error rate in the strong sense. Results: The proposed methods are illustrated with a real data example, and the new design is tabulated for a wide range of parameter values. Similar to two-stage designs with a single endpoint, the characteristics of optimal and minimax designs with two endpoints with respect to expected and maximum sample size can be quite different. Therefore, the choice of an admissible design may be a valuable compromise. Conclusions: The new procedure extends Simon’s two-stage design to two endpoints. This approach allows a more comprehensive assessment of the overall picture of antitumor efficacy of a new treatment than restriction to a single outcome.
Climate of Illinois and Central United States: Comparison of Model Simulations of the Current Climate, Comparison of Model Sensitivity to Enhanced Greenhouse Gas Forcing, and Regional Climate Model Simulations

3 Introduction . 4 Background . 5 Data . 5 Results . 7 Discussion . 18 Conclusions . 22 Future Work . 23 Acknowledgements . 23 References . 23 Table 1 . 25 Table 2 . 27 Figures . 28
Identification of the best stimulation parameters to measure in situ the comunication between muscle and nerve in mouse Tibialis muscle

Investigating the path functionality of the nerve stimulation signal and the muscle contraction is of primary importance in the study of a wide variety of pathologic conditions: neuromuscular diseases like Amyotrophic Lateral Sclerosis and Duchenne Muscular Dystrophy, as well as acute denervation and aging. Alterations of coupling between motor neuron conduction and muscle contraction can be studied in mice, comparing the muscle contraction elicited by two alternating stimulation paradigms: direct stimulation on the membrane and indirect stimulation through the nerve. The fundamental assumption behind this approach is that in a healthy model the two stimulations should lead to the same contractile response of the muscle. In this work we have searched for the pulse stimulation parameters that better resemble the physiological action potential. Applying these optimized stimulations it is then possible to design new final protocols to evaluate all the contractile parameters of muscle tissue in a wide variety of pathological models.
Power Control of a Nonpitchable PMSG-Based Marine Current Turbine at Overrated Current Speed With Flux-Weakening Strategy

This paper deals with power control strategies for a fixed-pitch direct-drive marine current turbine (MCT) when the marine current speed exceeds the rated value corresponding to the MCT nominal power. At overrated marine current speed, the MCT control strategy is supposed to be changed from maximum power point tracking (MPPT) stage to constant power stage. In this paper, flux-weakening strategy is investigated to realize appropriate power control strategies at high marine current speeds. During flux-weakening operations, the generator can be controlled to produce nominal or overnominal power for a specific speed range (constant power range). These two power control modes are compared, and the constant power range is calculated. The relationship between the expected constant power range and generator parameter requirements [stator inductance, permanent magnet (PM) flux, and nominal power coefficient] is analyzed. A Torque-based control with a robust feedback flux-weakening strategy is then carried out in the simulation. The proposed control strategies are tested in both high tidal speed and swell wave cases; the results validate the analysis and show the feasibility of the proposed control method.