Miracle-dz/UniFAR-FTUs huggingface dataset:
MODEL-DRIVEN REVERSE ENGINEERING AND PROGRAM COMPREHENSION: AN EXAMPLE

En este articulo se presenta un ejemplo que describe como la Ingenieria Dirigida por Modelos (IDM) puede ser aplicada al desarrollo de herramientas para la ingenieria reversa y comprension de programas. Se selecciono como caso de estudio la herramienta CodeCrawler, especificamente la funcionalidad denominada polymetric view, desarrollada mediante tecnologias y tecnicas de la IDM. Para ello, se emplearon dos metamodelos (entrada y salida) y transformaciones a nivel de los metamodelos que permiten generar la informacion de un polymetric view asociado a un proyecto de software, utilizando la informacion extraida del codigo fuente. Las tecnologias utilizadas para el desarrollo del ejemplo, las relacionadas con el Eclipse Modeling Project, especificamente el lenguaje de transformacion ATL y el lenguaje KM3. El enfoque seguido para obtener la implementacion resultante puede ser utilizado para desarrollar una herramienta de ingenieria reversa y comprension de software mediante tecnicas de la IDM, incorporando el vocabulario del dominio en la implementacion
A Parallel Platform for Big Data Analytics: A Design Science Approach

Following a Design Science approach, at the core of this paper we propose a technically innovative parallel platform for Big Data analytics. The design of the proposed platform allows for analyzing and filtering billions of records, querying data structures with 1,000s of columns, getting answers in milliseconds without cubes, continuously importing data with low latency, and executing 1,000s of concurrent queries. Deploying the platform has empowered organizations across many industries to capture new business opportunities from better analytic quality of very large, close to real-time data. With our single platform design project, we hope to provide an interim attempt at theorizing about achieving data quality and business opportunities from Big Data analytics.
Dynamics aware 3D occupancy grid map with semantic information

In many modern robotics applications the agents are expected to produce accurate representations of dynamic environments. Most mapping algorithms, however, assume the world to be static. Furthermore, these applications may also require semantic information about the environment. Most popular approaches add extra information as additional layers on top of the map used for navigation, leading to complex, decoupled systems. In this paper we present a probabilistic grid-based approach for modeling changing environments which can also incorporate augmented information right in the core of the map. Our method represents both, the dynamic of the cells and the objects contained in each of them by the state transition probabilities of a Hidden Markov Model. We evaluated the map in different use cases, proving its usefulness for modern robotics applications. The framework is available as a new, open source, mapping software.
Face recognition based on facial feature training

The detection and extraction of characteristic features of the human face are primordial tasks in any given approach for face recognition. Within this context, the present paper will present a comprehensive list of steps that can help obtain the major discriminative features of the human face with the abstraction of the fuzzy data that are influenced by several external factors, notably light conditions, which often disrupt the results obtained by classifiers for human face recognition.
Evidence that the Linker between the Methyltransferase and Helicase Domains of Potato Virus X Replicase Is Involved in Homologous RNA Recombination

ABSTRACT Recombination in RNA viruses, one of the main factors contributing to their genetic variability and evolution, is a widespread phenomenon. In this study, an in vivo assay to characterize RNA recombination in potato virus X (PVX), under high selection pressure, was established. Agrobacterium tumefaciens was used to express in Nicotiana benthamiana leaf tissue both a PVX isolate labeled with green fluorescent protein (GFP) containing a coat protein deletion mutation (ΔCP) and a transcript encoding a functional coat protein +3′-ntr. Coexpression of the constructs led to virus movement and systemic infection; reconstituted recombinants were observed in 92% of inoculated plants. Similar results were obtained using particle bombardment, demonstrating that recombination mediated by A. tumefaciens was not responsible for the occurrence of PXC recombinants. The speed of recombination could be estimated by agroinfection of two PVX mutants lacking the 3′ and 5′ halves of the genome, respectively, with an overlap in the triple gene block 1 gene, allowing GFP expression only in the case of recombination. Ten different pentapeptide insertion scanning replicase mutants with replication abilities comparable to wild-type virus were applied in the different recombination assays. Two neighboring mutants affecting the linker between the methyltransferase and helicase domains were shown to be strongly debilitated in their ability to recombine. The possible functional separation of replication and recombination in the replicase molecule supports the model that RNA recombination represents a distinct function of this protein, although the underlying mechanism still needs to be investigated.
Immunobiography and the Heterogeneity of Immune Responses in the Elderly: A Focus on Inflammaging and Trained Immunity

Owing to its memory and plasticity, the immune system (IS) is capable of recording all the immunological experiences and stimuli it was exposed to. The combination of type, dose, intensity, and temporal sequence of antigenic stimuli that each individual is exposed to has been named “immunobiography. ” This immunological history induces a lifelong continuous adaptation of the IS, which is responsible for the capability to mount strong, weak or no response to specific antigens, thus determining the large heterogeneity of immunological responses. In the last years, it is becoming clear that memory is not solely a feature of adaptive immunity, as it has been observed that also innate immune cells are provided with a sort of memory, dubbed “trained immunity. ” In this review, we discuss the main characteristics of trained immunity as a possible contributor to inflammaging within the perspective of immunobiography, with particular attention to the phenotypic changes of the cell populations known to be involved in trained immunity. In conclusion, immunobiography emerges as a pervasive and comprehensive concept that could help in understanding and interpret the individual heterogeneity of immune responses (to infections and vaccinations) that becomes particularly evident at old age and could affect immunosenescence and inflammaging.
Duplicate Detection for Identifying Social Spam in Microblogs

As an important kind of social media, microblog has become an important source of opinion mining and collective behavior study. However, social spams may affect the analytical results greatly. This paper focuses on the problem of identifying potential social spammers who copy pieces of information from others. An improved locality-sensitive hashing based method is used for detecting duplicated tweets. Intensive empirical study over a real-life microblog dataset crawled from Sina Weibo, one of the most popular microblogging services, is conducted. The characteristics of potential spammers and their behaviors are analyzed.
Physical geometric algorithms for structural molecular biology

This paper surveys our recent work in three key areas, using a physical geometric algorithm approach to data interpretation, experiment planning, and drug design: 1) data-directed computational protocols for high-throughput protein structure determination; 2) an experiment planning and data interpretation algorithms for reducing mass degeneracy in mass spectrometry; and 3) computer-aided drug design tools and applying them to the design of an inhibitor for the core-binding factor-/spl beta/ on-coprotein (CBF/spl beta/-MYII11), a fusion protein involved in some forms of acute myclomonocytic leukemia. Our long-range goal is the structural and functional understanding of biopolymer interactions in systems of significant biochemical as well as pharmacological interest. The research overviewed here represents a set of important steps towards that goal.
Viscoplastic Constitutive Equation for Computer Simulation of Hot Working Processing

The newly developed viscoplastic mechanical model based upon the viscoplastic model of the Chaboche type is proposed. The points of proposition are (i). Dimensional ambiguity existing in the Chaboche type’s equation is extinguished. (ii) Dependence of yield stress on strain rate is made clear and installed into the model. Its validity is verified by simulating the torsional test data on the steel performed by C. Rossard and P. Blain at elevated temperature using the proposed model. Furthermore, the six viscoplastic material parameters contained in the model are identified by the simulation involving coefficient of viscosity. © 2008 ASME
Src Catalytic but Not Scaffolding Function Is Needed for Integrin-Regulated Tyrosine Phosphorylation, Cell Migration, and Cell Spreading

ABSTRACT Src family kinases (SFKs) are crucial for signaling through a variety of cell surface receptors, including integrins. There is evidence that integrin activation induces focal adhesion kinase (FAK) autophosphorylation at Y397 and that Src binds to and is activated by FAK to carry out subsequent phosphorylation events. However, it has also been suggested that Src functions as a scaffolding molecule through its SH2 and SH3 domains and that its kinase activity is not necessary. To examine the role of SFKs in integrin signaling, we have expressed various Src molecules in fibroblasts lacking other SFKs. In cells plated on fibronectin, FAK could indeed autophosphorylate at Y397 independently of Src but with lower efficiency than when Src was present. This step was promoted by kinase-inactive Src, but Src kinase activity was required for full rescue. Src kinase activity was also required for phosphorylation of additional sites on FAK and for other integrin-directed functions, including cell migration and spreading on fibronectin. In contrast, Src mutations in the SH2 or SH3 domain greatly reduced binding to FAK, Cas, and paxillin but had little effect on tyrosine phosphorylation or biological assays. Furthermore, our indirect evidence indicates that Src kinase activity does not need to be regulated to promote cell migration and FAK phosphorylation. Although Src clearly plays important roles in integrin signaling, it was not concentrated in focal adhesions. These results indicate that the primary role of Src in integrin signaling is as a kinase. Indirect models for Src function are proposed.
A Differential Evolution Based Algorithm to Optimize the Radio Network Design Problem

In this paper we present a Differential Evolution based algorithm used to solve the Radio Network Design (RND) problem. This problem consists in determining the optimal locations for base station transmitters in order to get a maximum coverage area with a minimum number of transmitters. Because of the very high amount of possible solutions, this problem is suitable to be tackled with evolutionary techniques, so in our work it has been developed an algorithm inspired on the well-known Differential Evolution algorithm, obtaining good results.
Towards the Assessment of Stress and Emotional Responses of a Salutogenesis-Enhanced Software Tool Using Psychophysiological Measurements

Software development is intellectual, based on collaboration, and performed in a highly demanding economic market. As such, it is dominated by time pressure, stress, and emotional trauma. While studies of affect are emerging in software engineering research, stress has yet to find its place in the literature despite that it is highly related to affect. In this paper, we study stress coping with the affect-laden framework of Salutogenesis, which is a validated psychological framework for enhancing mental health through a feeling of coherence. We propose a controlled experiment for testing our hypotheses that a static analysis tool enhanced with the Salutogenesis model will bring 1) a higher number of fixed quality issues, 2) reduced cognitive load, 3) reduction of the overall stress, and 4) positive affect induction effects to developers. The experiment will make use of validated physiological measurements of stress as proxied by cortisol and alpha-amylase levels in saliva samples, a psychometrically validated measurement of mood and affect disposition, and stress inductors such as a cognitive load task. Our hypotheses, if empirically supported, will lead to the creation of environments, methods, and tools that alleviate stress among developers while enhancing affect on the job and task performance.
Implementation of System Model Applied to Wearable Device Platform for the User's Gesture Recognition in Vehicular Environment

Recently it is issued that the interaction technology for driver's gesture recognition in vehicular environment. Drivers want to control the multimedia system, air conditioning system and other applications which are equipped in head unit on dash board through the simple hands motion. But, limited under the safety driving condition, gesture cognition while being in car has many problems due to specific condition on road. In car, according to vehicle status such as forward and backward moving or horizontal tilting, data errors of the motion sensors are caused and unexpected driver's motion will be registered. In this paper, it is proposed the system model for the gesture interaction between users and vehicle are defined and the data processing process including specific hardware structure is adopted in order to reduce the motion sensing errors.
Regulation of intracellular signaling and function by caveolin

Caveolae, flask‐like invaginations of the plasma membrane, were discovered nearly 60 years ago. Originally regarded as fixation artifacts of electron microscopy, the functional role for these structures has taken decades to unravel. The discovery of the caveolin protein in 1992 (by the late Richard G.W. Anderson) accelerated progress in defining the contribution of caveolae to cellular physiology and pathophysiology. The three isoforms of caveolin (caveolin‐1, ‐2, and ‐3) are caveolae‐resident structural and scaffolding proteins that are critical for the formation of caveolae and their localization of signaling entities. A PubMed search for “caveolae” reveals ~280 publications from their discovery in the 1950s to the early 1990s, whereas a search for “caveolae or caveolin” after 1990, identifies ~7000 entries. Most work on the regulation of biological responses by caveolae and caveolin since 1990 has focused on caveolae as plasma membrane microdomains and the function of caveolin proteins at the plasma membrane. By contrast, our recent work and that of others has explored the localization of caveolins in multiple cellular membrane compartments and in the regulation of intracellular signaling. Cellular organelles that contain caveolin include mitochondria, nuclei and the endoplasmic reticulum. Such intracellular localization allows for a complexity of responses to extracellular stimuli by caveolin and the possibility of novel organelle‐targeted therapeutics. This review focuses on the impact of intracellular localization of caveolin on signal transduction and cell regulation. —Fridolfsson, H. N. , Roth, D. M. , Insel, P. A. , Patel, H. H. Regulation of intracellular signaling and function by caveolin. FASEB J. 28, 3823‐3831 (2014). www.fasebj. org
Efficient estimation of 3D Euclidean distance fields from 2D range images

Several existing algorithms for reconstructing 3D models from range data first approximate the object's 3D distance field to provide an implicit representation of the scanned object and then construct a surface model of the object using this distance field. In these existing approaches, computing and storing 3D distance values from range data contribute significantly to the computational and storage requirements. This paper presents an efficient method for estimating the 3D Euclidean distance field from 2D range images that can be used by any of these algorithms. The proposed method uses Adaptively Sampled Distance Fields to minimize the number of distance evaluations and significantly reduce storage requirements of the sampled distance field. The method is fast because much of the computation required to convert the line-of-sight range distances to Euclidean distances can be done during a pre-processing step in the 2D coordinate space of each range image.
Generation of Functional CLL-Specific Cord Blood CTL Using CD40-Ligated CLL APC

Though remissions have been observed following allo-HSCT for the treatment of CLL, many CLL patients are ineligible for transplant due to the lack of HLA-compatible donors. The use of umbilical cord blood (UCB) permits transplantation of many patients who lack HLA-compatible donors due to reduced requirements for stringent HLA matching between graft and recipient; however, disease relapse remains a concern with this modality. The generation of CLL-specific CTL from UCB T-cells, primed and expanded against the leukemic clone, might enhance the GVL effect and improve outcomes with UCB transplantation. Here we report the generation of functional, CLL-specific CTL using CD40-ligated CLL cells to prime partially-HLA matched UCB T-cells. Functionality and specificity were demonstrated by immune synapse assay, IFN-γ ELISpot, multi-parametric intracellular cytokine flow cytometry, and 51Cr release assay. The use of patient-specific, non-CLL controls demonstrated the generation of both alloantigen and CLL-specific responses. Subsequently, we developed a clinically-applicable procedure permitting separation of alloreactive CTL from leukemia-specific CTL. Leukemia-specific CTL were able to mediate in vivo killing of CLL in humanized mice without concurrent or subsequent development of xenoGVHD. Our results demonstrate that generation of CLL-specific effectors from UCB is feasible and practical, and the results support further exploration of this strategy as a treatment modality for CLL.
Characterization of chylomicron remnant binding to rat liver membranes.

The binding of chylomicron remnants to rat liver membranes was investigated using radioiodinated lipoproteins. The specific activity of binding increased in parallel with increased enrichment in plasma membrane markers. The yield of receptor activity, however, decreased with enrichment. Accordingly, a partially purified plasma membrane preparation was used for routine studies. Binding was saturable, with half maximal binding achieved at 4.6 micro g tetramethylurea-precipitable protein per ml. The rate of binding was time- and temperature-dependent. It could be inhibited only moderately by 10 mM EDTA. Chylomicron remnants appeared to bind to the membrane as a unit. The bound particle was richer in apoproteins of 20,000-50,000 molecular weight relative to low molecular weight apoproteins than the particles that were not bound. Lipoprotein particles containing only human apoB did not bind to liver membranes nor did they compete for the remnant binding site. Rat lipoproteins of d 1.019-1.063 g/ml did compete for remnant binding. When they were separated into apoB-rich (LDL) or apoE-rich (HDL(c)) fractions by block electrophoresis, the apoE-rich fraction was a more potent competitor. ApoE purified and reconstituted into dimyristoyl phosphatidylcholine vesicles was a potent competitor for the remnant binding site. Vesicles containing (125)I-labeled apoE bound to the membranes, and they could be displaced by unlabeled remnants. Dimyristoyl phosphatidylcholine vesicles themselves did not compete with either remnants or apoE-phospholipid vesicles. These results offer strong support for the hypothesis that the liver membrane chylomicron remnant receptor recognizes apoE with a high affinity, and this initiates the rapid removal of lipoproteins that contain this apoprotein. -Cooper, A. D. , S. K. Erickson, R. Nutik, and M. A. Shrewsbury. Characterization of chylomicron remnant binding to rat liver membranes.
Drought-induced forest decline: causes, scope and implications

A large number of episodes of forest mortality associated with drought and heat stress have been detected worldwide in recent decades, suggesting that some of the world's forested ecosystems may be already responding to climate change. Here, we summarize a special session titled ‘Drought-induced forest decline: causes, scope and implications’ within the 12th European Ecological Federation Congress, held in Ávila (Spain) from 25 to 29 September 2011. The session focused on the interacting causes and impacts of die-off episodes at the community and ecosystem levels, and highlighted recent events of drought- and heat-related tree decline, advances in understanding mechanisms and in predicting mortality events, and diverse consequences of forest decline. Talks and subsequent discussion noted a potentially important role of carbon that may be interrelated with plant hydraulics in the multi-faceted process leading to drought-induced mortality; a substantial and yet understudied capacity of many forests to cope with extreme climatic events; and the difficulty of separating climate effects from other anthropogenic changes currently shaping forest dynamics in many regions of the Earth. The need for standard protocols and multi-level monitoring programmes to track the spatio-temporal scope of forest decline globally was emphasized as critical for addressing this emerging environmental issue.
Early allograft dysfunction: Causes, recognition, and management

1. Early allograft dysfunction (EAD) defines grafts with marginal function early after liver transplantation. It has been validated in the Model for EndStage Liver Disease era. 2. EAD is an important cause of morbidity and mortality after liver transplantation. 3. Both donor and recipient risk factors are associated with the development of EAD. 4. The use of statistical models has helped to predict EAD for given donor-recipient matches. 5. The identification of cytokine profiles associated with EAD may help to define potential interventions in the future.
New biological activity of Rhinacanthus nasutus extracts.

BACKGROUND The MeOH extracts from aerial part and roots of Rhinacanthus nasutus were investigated for new biological activities. MATERIALS AND METHODS The MeOH extract of the root was stepwise separated by organic solvents into n-hexane, EtOAc, n-BuOH and H(2)O layer fractions. Cytotoxic activity against human tumor and normal cells was determined by the MTT method. Nitric oxide (NO) was determined by the Griess method. Osteoclastogenesis was monitored by tartrate-resistant acid phosphatase (TRAP) activity. RESULTS The MeOH extract of the root showed much higher tumor-specific cytotoxicity than that of the aerial part. The EtOAc fraction of the root showed the highest tumor-specific cytotoxicity, followed by the n-BuOH, n-hexane and H(2)O fractions. None of the four fractions protected the cells from the cytotoxicity of UV irradiation. The n-BuOH fraction not only stimulated NO production by mouse macrophage-like RAW264.7 cells, but also inhibited the lipopolysaccharide (LPS)-stimulated NO production. The EtOAc fraction inhibited the receptor activator for nuclear factor-κB ligand (RANKL)-stimulated osteoclastogenesis of the RAW264.7 cells most potently, followed by the n-hexane, n-BuOH and H(2)O fractions. The n-BuOH fraction slightly, but significantly stimulated osteoclastogenesis. CONCLUSION Antitumor and macrophage/osteoclast-modulating substances are enriched in EtOAc and n-BuOH fractions of MeOH extract of R. nasutus roots.