Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying wasted effort in the field via developer interaction data

During software projects, several parts of the source code are usually re-written due to imperfect solutions before the code is released. This wasted effort is of central interest to the project management to assure on-time delivery. Although the amount of thrown-away code can be measured from version control systems, stakeholders are more interested in productivity dynamics that reflect the constant change in a software project. In this paper we present a field study of measuring the productivity of a medium-sized J2EE project. We propose a productivity analysis method where productivity is expressed through dynamic profiles - the so-called Micro-Productivity Profiles (MPPs). They can be used to characterize various constituents of software projects such as components, phases and teams. We collected detailed traces of developers' actions using an Eclipse IDE plug-in for seven months of software development throughout two milestones. We present and evaluate profiles of two important axes of the development process: by milestone and by application layers. MPPs can be an aid to take project control actions and help in planning future projects. Based on the experiments, project stakeholders identified several points to improve the development process. It is also acknowledged, that profiles show additional information compared to a naive diff-based approach.
Predicting Protein-Protein Interactions from Protein Sequences Using Phylogenetic Profiles

—In this study, a high accuracy protein-protein interaction prediction method is developed. The importance of the proposed method is that it only uses sequence information of proteins while predicting interaction. The method extracts phylogenetic proﬁles of proteins by using their sequence information. Combining the phylogenetic proﬁles of two proteins by checking existence of homologs in different species and ﬁtting this combined proﬁle into a statistical model, it is possible to make predictions about the interaction status of two proteins. For this purpose, we apply a collection of pattern recognition techniques on the dataset of combined phylogenetic proﬁles of protein pairs. Support Vector Machines, Feature Extraction using ReliefF, Naive Bayes Classiﬁcation, K-Nearest Neighborhood Classiﬁcation, Decision Trees, and Random Forest Classiﬁcation are the methods we applied for ﬁnding the classiﬁcation method that best predicts the interaction status of protein pairs. Random Forest Classiﬁcation outperformed all other methods with a prediction accuracy of 76.93%.
Abdul Rani Shankar Chelliah Muhammad Nazri Bin Abdul Halim

There is an increasing awareness of environmental and safe-products for international businesses. Environmental, sustainability and green management provides opportunities to Malaysian SMEs to explore the international market and find new customer segment. Eco-centric and techno-centric paradigms allow for the discussion of green management and highlight business management theory for environmental segments. © 2014 AESS Publications. All Rights Reserved.
Tetrahydrobiopterin: important endothelial mediator independent of endothelial nitric oxide synthase.

See related article, pp 287–294 Tetrahydrobiopterin (BH4), an essential cofactor for diverse cellular processes, is present in almost every cell or tissue of higher organisms. BH4 has well-defined functions in terms of enzymatic activities (BH4 is a crucial cofactor for the aromatic amino acid hydroxylases and all isoforms of nitric oxide synthase [NOS]) but has other less-defined functions in cells. BH4 is a growth or proliferation factor for various mammalian cells, including hematopoietic and endothelial cells.1,2 Epidermal growth factor and nerve growth factor act to increase proliferation of rat PC12 cells by elevating BH4 levels.3 However, BH4 is also a powerful antioxidant4 and has scavenging capabilities, reacting with superoxide anion radicals peroxynitrite and hydrogen peroxide.5 BH4 bioavailability is, thus, potently influenced by oxidative stress in cells. GTP cyclohydrolase I (GTPCH), 6-pyruvoyltetrahydropterin synthase, and sepiapterin reductase act in sequence to generate BH4 de novo in endothelial cells.5 The first enzyme, GTPCH, is thought to be the rate-controlling enzyme. GTPCH activity can be controlled at the transcriptional level by a number of mediators, including nutritional (phenylalanine and arginine), hormonal (insulin and estrogen), immunologic (inflammatory cytokines including interleukin1, interferon-γ, and tumor necrosis factor-α), therapeutic (statins and cyclosporin A), and endothelium-derived (basic fibroblast growth factor and H2O2) factors.5 These agonists act via different mechanisms but all lead to the increased generation of BH4. BH4 regulates NO synthesis in both mature endothelial cells and endothelial progenitor cells (EPCs). Bone marrow–derived EPCs have the potential to give rise to circulating vascular …
Analytical review on object segmentation and recognition

The prime objective of this review is to analyze popular techniques used for object segmentation and recognition. In this paper various existing object segmentation and recognition methodologies have been systematically analyzed and presented. The importance of object segmentation can be in identifying the object in a video. It is majorly used in video surveillance system, in human activity recognition, in shadow detection which includes both static and moving objects. The object recognition also has various applications in the field of video stabilization, cell counting in bio-imaging and in automated vehicle parking system. Google's driverless car and Microsoft's Kinect System also uses object recognition methodologies for its implementation. We have concluded our findings with the various pros and cons of the existing methods and with the possibility of future research in this area.
Contact/impact Problems, Energy Conservation and Planetary Gears

A discretization scheme for contact/impact problems related to the modeling of gears is presented. The problem is rst discretized in time and then a variational formulation for the resulted one step problem is developed. A Finite Element discretization completes the discretization process. Although drived in the slightly di rent manner, discretization is just a special case of Laursen and Chavla algorithm specialized to the case of a rigid body motion with superimposed small elastic deformation. The scheme conserves precisely linear momentum and the total energy. The angular momentum is conserved up to a linearization in the rotation angle. L. Demkowicz, A. Bajer
Effectiveness of rapid rail transit system in Beijing

The effectiveness of rapid rail transit system is analyzed using tools of complex network for the first time. We evaluated the effectiveness of the system in Beijing quantitatively from different perspectives, including descriptive statistics analysis, bridging property, centrality property, ability of connecting different part of the system and ability of disease spreading. The results showed that the public transport of Beijing does benefit from the rapid rail transit lines, and the benefit of different regions from RRTS is gradually decreased from the north to the south. The paper concluded with some policy suggestions regarding how to promote the system. This study offered significant insight that can help understand the public transportation better. The methodology can be easily applied to analyze other urban public systems, such as electricity grid, water system, to develop more livable cities.
Hidden Markov tree model applied to the detection of micro-calcification clusters in mammograms

This paper is concerned to the application of a relatively new image texture segmentation algorithm named Hidden Markov Tree (HMT) to the detection of micro-calcification clusters in mammograms. The HMT is a wavelet-based tree-structured probabilistic graph that can capture the statistical properties of the coefficients of the wavelet transform. The aim of this approach is, on the one hand, to take advantage of the wavelet coefficients in the characterization of different textures, and on the other hand, to link these coefficients by a tree structure enabling texture change to be detected. The application of the method was evaluated using the Digital Database for Screening Mammography (DDSM) for training purposes and a sample of the Nijmegen database for testing purposes.
Studies of Neurological Transmission Analysis using Hierarchical Bayesian Mixture Models

Hierarchically structured mixture models are studied in the context of data analysis and inference on neural synaptic transmission characteristics in mammalian, and other, central nervous systems. Mixture structures arise due to uncertainties about the stochastic mechanisms governing the responses to electro-chemical stimulation of individual neurotransmitter release sites at nerve junctions. Models attempt to capture scienti c features such as the sensitivity of individual synaptic transmission sites to electro-chemical stimuli, and the extent of their electro-chemical responses when stimulated. This is done via suitably structured classes of prior distributions for parameters describing these features. Such priors may be structured to permit assessment of currently topical scienti c hypotheses about fundamental neural function. Posterior analysis is implemented via stochastic simulation. Several data analyses are described to illustrate the approach, with resulting neurophysiological insights in some recently generated experimental contexts. Further developments and open questions, both neurophysiological and statistical, are noted.
HPV16 E7 Protein and hTERT Proteins Defective for Telomere Maintenance Cooperate to Immortalize Human Keratinocytes

Previous studies have shown that wild-type human telomerase reverse transcriptase (hTERT) protein can functionally replace the human papillomavirus type 16 (HPV-16) E6 protein, which cooperates with the viral E7 protein in the immortalization of primary keratinocytes. In the current study, we made the surprising finding that catalytically inactive hTERT (hTERT-D868A), elongation-defective hTERT (hTERT-HA), and telomere recruitment-defective hTERT (hTERT N+T) also cooperate with E7 in mediating bypass of the senescence blockade and effecting cell immortalization. This suggests that hTERT has activities independent of its telomere maintenance functions that mediate transit across this restriction point. Since hTERT has been shown to have a role in gene activation, we performed microarray studies and discovered that E6, hTERT and mutant hTERT proteins altered the expression of highly overlapping sets of cellular genes. Most important, the E6 and hTERT proteins induced mRNA and protein levels of Bmi1, the core subunit of the Polycomb Group (PcG) complex 1. We show further that Bmi1 substitutes for E6 or hTERT in cell immortalization. Finally, tissue array studies demonstrated that expression of Bmi1 increased with the severity of cervical dysplasia, suggesting a potential role in the progression of cervical cancer. Together, these data demonstrate that hTERT has extra-telomeric activities that facilitate cell immortalization and that its induction of Bmi1 is one potential mechanism for mediating this activity.
Pain Perception Within Consciousness

As a psychological state, pain is perceived by the affected individual and it corresponds to a form of conscious awareness as a subjective conscious experience mediated in part by beliefs or emotions. Regardless of its 'physical' origins, pain, like all other perceptions, is a mental experience at different degrees of consciousness. The experience of pain requiring a stimulus, a feeling or emotion, and an effect or result, consists of an intermingling of chemical, biological, psychological, physiologic, socioeconomic, cultural, ethnic backgrounds, emotional, and cognitive factors. Not only the activation but also the connections are involved in conscious pain perception. Moreover, interconnectivity between the periaqueductal matter and orbitofrontal cortex is the key to cognitive-emotional responses associated with pain. Thus, the central pain control processes arising from interactions among the cognitive-evaluative, motivational-affective, and sensory-discriminative systems characterize the pain response, being also influenced by both noxious input and cognitive self-regulation. Neuroimaging studies (Davis et al., 2015) in healthy volunteers showed that pain cannot be localized in an isolated “pain center” in the brain, but it rather encompasses a neural circuitry.
Stability of walking in a multilegged robot suffering leg loss

This article describes: tests of fault tolerance of the eight-legged walking robot SCORMON in the event of leg loss. It evaluates different gaits, which are based on biological research on insect and arachnid walking and concludes with a discussion, what the best gait for the SCORPION system is, when 2 legs are lost It also includes a short introduction to the SCORPION robot and its biomimetic software approach and its performance in different terrain.
Dissecting molecular stress networks: identifying nodes of divergence between life‐history phenotypes

The complex molecular network that underlies physiological stress response is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose connections span cells, tissues and organs. Variable nodes are points in the network upon which natural selection may act. Thus, identifying variable nodes will reveal how this molecular stress network may evolve among populations in different habitats and how it might impact life‐history evolution. Here, we use physiological and genetic assays to test whether laboratory‐born juveniles from natural populations of garter snakes (Thamnophis elegans), which have diverged in their life‐history phenotypes, vary concomitantly at candidate nodes of the stress response network, (i) under unstressed conditions and (ii) in response to an induced stress. We found that two common measures of stress (plasma corticosterone and liver gene expression of heat shock proteins) increased under stress in both life‐history phenotypes. In contrast, the phenotypes diverged at four nodes both under unstressed conditions and in response to stress: circulating levels of reactive oxygen species (superoxide, H2O2); liver gene expression of GPX1 and erythrocyte DNA damage. Additionally, allele frequencies for SOD2 diverge from neutral markers, suggesting diversifying selection on SOD2 alleles. This study supports the hypothesis that these life‐history phenotypes have diverged at the molecular level in how they respond to stress, particularly in nodes regulating oxidative stress. Furthermore, the differences between the life‐history phenotypes were more pronounced in females. We discuss the responses to stress in the context of the associated life‐history phenotype and the evolutionary pressures thought to be responsible for divergence between the phenotypes.
XTENSIONS OF C OMBINATORIAL S TRUCTURES

An interval in a combinatorial structure R is a set I of points which are related to every point in R \ I in the same way. A structure is simple if it has no proper intervals. Every combinatorial structure can be expressed as an inflation of a simple structure by structures of smaller sizes — this is called the substitution (or modular) decomposition. In this paper we prove several results of the following type: An arbitrary structure S of size n belonging to a class C can be embedded into a simple structure from C by adding at most f (n) elements. We prove such results when C is the class of all tournaments, graphs, permutations, posets, digraphs, oriented graphs and general relational structures containing a relation of arity greater than 2. The function f (n) in these cases is 2, ⌈log2(n + 1)⌉, ⌈(n + 1)/2⌉, ⌈(n + 1)/2⌉, ⌈log4(n + 1)⌉, ⌈log3(n + 1)⌉ and 1, respectively. In each case these bounds are best possible.
Tyrosine phosphorylation and cytoskeletal tension regulate the release of fibroblast adhesions

We have investigated the mechanisms by which fibroblasts release their adhesions to the extracellular matrix substrata using a permeabilized cell system in which the adhesions remain relatively stable. A large number of different molecules were assayed for their effect on focal adhesion stability using immunofluorescence with antibodies against different focal adhesion constituents. ATP uniquely stimulates a rapid breakdown of focal adhesions, and at high ATP concentrations (> 5 mM), many cells are released from the dish. The remaining cells appear contracted with talin, alpha-actinin, and vinculin localized diffusely throughout the cell. Integrin containing tracks of variable intensity outline the regions where cells had resided before they detached from the substratum. At lower ATP concentrations (0.5-5 mM) the cells remain spread; however the focal adhesion components, including integrin, show an array of phenotypes ranging from diffusely localized throughout the cell to a localization in small, thin focal adhesions. Okadaic acid, a serine, threonine phosphatase inhibitor, enhances the contracted phenotype, even at low concentrations (0.5 mM) of ATP. The localization of focal adhesion components is different in okadaic acid-treated cells. In highly contracted cells, integrin is present in tracks where the cells resided before the contraction; however focal adhesions are no longer apparent. Talin, vinculin, and alpha-actinin localize in trabecular networks toward the periphery of the cell. Interestingly, phosphotyrosine staining as well as nascent, intracellular integrin precedes the recruitment of focal adhesion constituents into the trabecular network. The ATP-stimulated focal adhesion breakdown appears to operate through two mechanisms. First, ATP stimulates the tyrosine phosphorylation of several cytoskeletally associated proteins. These tyrosine phosphorylations correlated well with focal adhesion breakdown. Furthermore, addition of a recombinant, constitutively active tyrosine phosphatase inhibits both the tyrosine phosphorylations and the breakdown of the focal adhesions. None of the major tyrosine phosphoproteins are FAK, integrin, tensin, paxillin, or other phosphoproteins implicated in focal adhesion assembly. The second mechanism is cell contraction. High ATP concentrations, or lower ATP concentrations in the presence of okadaic acid induce cell contraction. Inhibiting the contraction by addition of a heptapeptide IRICRKG, which blocks the actin-myosin interaction, also inhibits focal adhesion breakdown. Neither the peptide nor the phosphatase inhibits focal adhesion breakdown under all conditions suggesting that both tension and tyrosine phosphorylations mediate the release of adhesions.
General D-branes solutions from string theory

We give the general solution for the elementary and solitonic D-brane configurations as a result of a reinterpretation of the already known p-branes. These solutions are found by means of a relevant conformal transformation on the string inspired action and its dual form. From this point of view, the nature of the electric and magnetic charge is clearer and the elementary and solitonic behaviour dependence on the initial lagrangian set. We give a complete characterisation of the spacetime defined by these solutions. The dual pair of instanton and 7-brane solution is presented as an example.
Bi-alphabetism: A window on phonological processing

In Serbian, lexical decision latencies to words composed of letters that exist in both the Roman and Cyrillic alphabets (some of which have different phonemic interpretations in each) are slower than for the unique alphabet transcription of those same words. In this study, we use the effect of phonological ambiguity to explore the time course of semantic facilitation. Targets are either the phonologically ambiguous forms (e.g., PETAK meaning “Friday” when pronounced as a Roman string /petak/ but without meaning when pronounced in Cyrillic as /retak/) or the unique alphabet transcription of the same word (ПETAK). We manipulate alphabet match and semantic relatedness of prime to target. In addition to replicating slowing due to phonological ambiguity, we show 1) greater alphabet switch cost for bivalent then for unambiguous targets as well as for unrelated then for related prime-target pairs and 2) greater semantic facilitation as the number of shared common letters between prime and target increases. Results reveal the interaction of phonological and semantic processes in Serbian. The findings are discussed in terms of a triangle model of language processing, which hypothesizes a division of labor between an orthography-to-semantics, and an orthographyto-phonology-to-semantics route and their simultaneous contribution to activation of meaning.
Estimating Relative Density on a Metric Space

Let X1 , X2 , . , be stationary and ergodic random variables with values in a metric space M with distance d, let P(A) = P(Xn in A) and let S(x,r)) > 0 if r > 0, and suppose also that for x in M0 , P(S(s,r)) is continuous in x and is differentiable in r for r >= 0, and with a positive derivative for all r in a neighborhood of 0. Consider the set M* of pairs (x,y) such that both x and y are in M0 and limr->0 P(S(x,y)) exists and is a finite positive number R(x,y). Then R(x,y) is called the relative density of P for the pair x,y. The differentiability condition is essentially the same as required for P to have a positive density in the Euclidean case. Note there may be pairs of elements (x,y) such that limr->0 P(S(x,r))/P(S(y,r)) fails to exist, is zero, or is positive infinity. For example, if P on the square [0,1]X[0,1] concentrates a total probability of . 5 uniformly on the line x = y, 0 <= x,y <= 1, and distributes probability uniformly on the square excepting this line, then the line of pairs x = y is in M* and so is the square excepting the line. But a pair with one element on the line and the other gives a limit of 0 or positive infinity depending which element appears in the numerator (or denominator). This kinds of measures may be of considerable interest and examples where they arise can be given.
Grouped Bees Algorithm: A Grouped Version of the Bees Algorithm

In many non-deterministic search algorithms, particularly those analogous to complex biological systems, there are a number of inherent difficulties, and the Bees Algorithm (BA) is no exception. The BA is a population-based metaheuristic search algorithm inspired by bees seeking nectar/pollen. Basic versions and variations of the BA have their own drawbacks. Some of these drawbacks are a large number of parameters to be set, lack of methodology for parameter setting and computational complexity. This paper describes a Grouped version of the Bees Algorithm (GBA) addressing these issues. Unlike its conventional version, in this algorithm bees are grouped to search different sites with different neighbourhood sizes rather than just discovering two types of sites, namely elite and selected. Following a description of the GBA, the results gained for 12 well-known benchmark functions are presented and compared with those of the basic BA, enhanced BA, standard BA and modified BA to demonstrate the efficacy of the proposed algorithm. Compared to the conventional implementations of the BA, the proposed version requires setting of fewer parameters, while producing the optimum solutions much more quickly.