Miracle-dz/UniFAR-FTUs huggingface dataset:
Visual exploration of function call graphs for feature location in complex software systems

Maintenance, reengineering, and refactoring processes of software systems are typically driven and organized in terms of features. Feature change requests need to be translated into changes in source code, which is a highly cost intensive and time consuming task when complex legacy software systems are concerned; their documentation is likely to be outdated and incomplete. In this paper, we propose a prototype tool that supports users in locating and understanding feature implementation in large (>1 MLOC) C/C++ systems. A combination of static and dynamic analysis allows extracting of the function call graph during feature execution and interpreting it within the static architecture of the system. An interactive multi-view visualization enables users to explore that graph. An effective 2 1/2D visualization provides various visual cues that facilitate finding those paths in the function call graph that are essential for understanding feature functionality. Additionally to source code aspects, the dynamic metric of function execution times is exploited, which gives significant hints to feature-implementing functions. Furthermore, information on functions is extended by architectural aspects, thereby supporting users in remaining oriented during their analysis and exploration task as they can give priority to selected architectural components and thereby hide insignificant function calls.
The Discodermia calyx Toxin Calyculin A Enhances Cyclin D1 Phosphorylation and Degradation, and Arrests Cell Cycle Progression in Human Breast Cancer Cells

Cyclin D1 is a key regulator of the cell cycle that is over expressed in more than half of breast cancer patients. The levels of cyclin D1 are controlled primarily through post-translational mechanisms and phosphorylation of cyclin D1 at T286 induces its proteasomal degradation. To date, no studies have explored the involvement of phosphatases in this process. Here we treated human breast cancer cells with the structurally distinct toxins calyculin A, okadaic acid, and cantharidin, which are known to inhibit Ser/Thr phosphatases of the PPP family. At low nanomolar concentrations calyculin A induced T286 phosphorylation and degradation of cyclin D1 via the proteosome in MDA-MB-468 and MDA-MB-231 cells. Cyclin D1 degradation also was dose-dependently induced by okadaic acid and catharidin, implicating a negative regulatory role for type-2A phosphatases. These effects occurred without increasing phosphorylation of p70S6K, cyclin D3, or myosin light chain that were used as endogenous reporters of cellular PP2A and PP1 activity. A reverse phase phosphoprotein array analysis revealed increased phosphorylation of only 6 out of 33 Ser/Thr phosphosites, indicating selective inhibition of phosphatases by calyculin A. Calyculin A treatment induced cell cycle arrest in MDA-MB-468 and MCF-7 breast cancer cells. These findings suggest that a specific pool of type-2A phosphatase is inhibited by calyculin A leading to the degradation of cyclin D1 in human breast cancer cells. The results highlight the utility of toxins as pharmacological probes and points to the T286 cyclin D1 phosphatase inhibited by calyculin A as a possible target for chemotherapy to treat triple negative breast cancer.
Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

Virus-Enhanced Sulfur Oxidation How do microbial viruses affect subsurface microbial communities? Anantharaman et al. (p. 757, published online 1 May) investigated the interactions between ubiquitous marine lithotrophs found at hydrothermal vents and their viruses. The genes for sulfur oxidation in viruses that infect abundant marine chemosynthetic sulfur-oxidizing bacteria enhanced sulfur oxidation, thereby influencing the biogeochemical sulfur cycle. Host-derived viral auxiliary metabolic genes for sulfur oxidation play a key biogeochemical role in the dark ocean. Viruses are the most abundant biological entities in the oceans and a pervasive cause of mortality of microorganisms that drive biogeochemical cycles. Although the ecological and evolutionary effects of viruses on marine phototrophs are well recognized, little is known about their impact on ubiquitous marine lithotrophs. Here, we report 18 genome sequences of double-stranded DNA viruses that putatively infect widespread sulfur-oxidizing bacteria. Fifteen of these viral genomes contain auxiliary metabolic genes for the α and γ subunits of reverse dissimilatory sulfite reductase (rdsr). This enzyme oxidizes elemental sulfur, which is abundant in the hydrothermal plumes studied here. Our findings implicate viruses as a key agent in the sulfur cycle and as a reservoir of genetic diversity for bacterial enzymes that underpin chemosynthesis in the deep oceans.
Hardware Strengthening a Distributed Logging Scheme

In the online world, service providers allow users to upload data to be stored or processed. In some cases, privacy will become an essential feature. Sensitive content can be the data provided to or the services used at the service provider. Logging of the actions of the service providers can therefore also generate privacy-sensitive content. However, to enhance transparency towards users, logging can be a very useful tool. In this paper, we build upon the concept of distributed privacy-preserving log trails. The trust in such a system lies in the storage of a vector in a certain register stored in software. With a piece of malicious software, a hacker or curious user could misuse this register to learn about a certain process or to learn for whom a service is performed, although the scheme ensures forward-unlinkability and forward-integrity. In this paper, we strengthen the conventional software approach by implementing the vector in external hardware. This hardens the scheme further, and reduces the level to which the log server has to be trusted, at the cost of additional but solvable security threats.
Advanced Technologies for Infrared Wireless Indoor Local Area Networks 1

The main degrading factor of infrared communication systems is the shot noise due to ambient light. Due to the directional nature of both signal and noise, the signal-to-noise ratio (SNR) at the receiver can vary significantly. In order to minimise these SNR fluctuation effects, this paper discusses some advanced techniques for the design of non-directed wireless infrared communication systems that can produce interesting performance improvements. The first technique, angle diversity, makes use of the directional nature of the SNR at the receiver. The second technique adapts system data rate to environment conditions considering three different methods: i) adaptive filtering, ii) repetition coding, and iii) binary convolutional coding. Design challenges and solutions for implementing these techniques will be also mentioned.
Dynamic Learning and Context-Dependence in Sequential, Attribute-Based, Stated-Preference Valuation Questions

A hybrid stated-preference model is presented that combines the referendum contingent valuation response format with an experimentally designed set of attributes. A sequence of valuation questions is asked to a random sample in a mail-out mail-back format. Econometric analysis shows greater discrimination between alternatives in the final choice in the sequence, and the vector of preference parameters shifts. Lead and lag choice sets have a structural influence on current choices and unobserved factors induce positive correlation across the responses. These results indicate that people learn about their preferences for attribute-based environmental goods by comparing attribute levels across choice sets. (JEL Q23, Q26)
Change Bursts as Defect Predictors

In software development, every change induces a risk. What happens if code changes again and again in some period of time? In an empirical study on Windows Vista, we found that the features of such change bursts have the highest predictive power for defect-prone components. With precision and recall values well above 90%, change bursts significantly improve upon earlier predictors such as complexity metrics, code churn, or organizational structure. As they only rely on version history and a controlled change process, change bursts are straight-forward to detect and deploy.
Primitive communication of humanoid robot with human via hierarchical mimesis model on the proto symbol space

Communication is defined as a process of information exchange between individuals through some common systems such as symbols, signs, languages, or gestures. This communication skill is important for social robots which interact with humans. Especially primitive communication consists of interaction patterns between 2 humans. In this paper we propose a mimetic communication model, which is a hierarchical model based on mimesis model that integrates motion recognition with motion generation by hidden Markov models (HMMs). HMMs in the lower layer abstract the motion patterns and HMMs in the upper layer represent the interaction patterns through the lower proto symbols. We also demonstrate the validity of this model through several experiments on a humanoid robot
An aggregated multi-cut decomposition algorithm for two-stage transmission expansion planning problems

The L-shaped method is a decomposition algorithm that is commonly used to solve large-scale two-stage stochastic programming problems. The classic single-cut L-shaped method usually suffer the performance issue because only a single optimality cut is applied at each major iteration. This paper presents an aggregated multi-cut version of the L-shaped method for solving two-stage transmission expansion planning (TEP) problems. This algorithm allows the user to control the aggregation level of the optimality cuts so that the overall computational performance can be improved. Simulation results show that the proposed algorithm is computationally more efficient than the classical L-shaped method.
Molecular Identification and Description of the Female of Nothoaspis reddelli (Ixodida: Argasidae) from A Cave in Southeastern Mexico

Abstract: Nothoaspis reddelli Keirans and Clifford, 1975, was described from 3 males collected in Grutas de Xtacumbilxunaán, Campeche, Mexico, although females have remained undescribed for 37 yr. Recently adult females of this species were collected from Cueva de Villa Luz ( = Cueva de las Sardinas, Cueva del Azufre), in Tapijulapa, Tabasco, Mexico. Here we present a morphological description of the female stage, together with 16S rDNA sequences that confirm the conspecificity of our female, male, and nymphal specimens. The female integument of the anterior portion of the dorsal surface is smooth (nothoaspis), appearing to consist of 3 large “subunits,” 1 anterior and 2 posterior, each with a small sublateral “subunit” on either side. The remaining dorsal covered integument is a cell-like configuration. The hood is large and bluntly rounded, and visible dorsally. The spiracular plate is oval. It possesses 1 pair of posthypostomal setae. The palpal trochanter has 1 pair of setae and a 5/5 hypostome decreasing to 4/4 at the apex. There is a single central pore at the base of the hypostome.
Prevalence of a Polymorphism of the Phosphatidylinositol 3-Kinase p85α Regulatory Subunit (Codon 326Met→ile) in Japanese NIDDM Patients

Phosphatidylinositol 3-kinase is a heterodimeric enzyme composed of an 85-kDa regulatory subunit (p85), containing two SH2 and one SH3 domain, and a 110-kDa catalytic subunit (pi 10) (1,2). This kinase has been shown to be important for insulin-stimulated glucose transport in insulin sensitive cells (3-5). Recently, Andersen et al. (6) identified a missense mutation at nucleotide 1020 (G-»A) changing Met to He (codon 326Met̂ ik) i n fat p85a regulatory subunit of phosphatidylinositol 3-kinase. Thus, we examined the prevalence of a polymorphism of codon 326~* of the p85a subunit of PI 3-kinase, using the double mismatched polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis (Fig. 1) to understand the contribution of this mutation to the development of NIDDM in Japanese patients. The diagnosis of NIDDM and the definition of normal glucose tolerance were established, following a 75-g oral glucose tolerance test, based on the guidelines of the World Health Organization. We examined 260 normal control subjects (mean age, 57.0 ± 10.5 years; BMI, 22.6 ± 2.6 kg/m) and 200 Japanese NIDDM patients (mean age, 56.8 ± 13.7 years; BMI, 24.9 ± 5.2 kg/m). In agreement with the results of Andersen et al. (6), there was no significant difference between the normal subjects and the NIDDM patients in the distribution of the wildtype, heterozygote, and homozygote genotypes (198, 57, and 5 in normal subjects vs. 150, 43, and 7 in NIDDM patients, respectively) or in the allelic frequency (12.9% in normal subjects vs. 14.3% in NIDDM patients, respectively). We also compared the clinical characteristics of each genotype (wild-type, heterozygote, and homozygote) among the NIDDM patients and found that several parameters, including BMI (25.3 ± 4.7, 23.9 ± 6.8, and 26.2 ± 3.6 kg/m), fasting glucose (143.2 ± 39.9, 156.7 ± 53.8, and 157.0 ± 111.7 mg/dl), and age at onset of diabetes (46.1 ± 15.0, 47.1 ± 11.4, and 47.5 ± 10.8 years) were not statistically different among the three genotypes.
Produktivitas tanaman dan kehilangan hasil tanaman padi (Oryza sativa L.) kultivar Ciherang pada kombinasi jarak tanam dengan frekuensi penyiangan berbeda

Tujuan penelitian ini adalah untuk menge-tahui pengaruh kombinasi jarak tanam dan frekuensi penyiangan gulma yang berbeda terhadap produktivitas dan kehilangan hasil padi sawah kultivar Ciherang. Percobaan ini dilak-sanakan di lahan sawah Sanggar Penelitian Latihan dan Pengembangan Pertanian (SPLPP) Fakultas Pertanian Universitas Padjadjaran unit Ciparay dari bulan November 2010 sampai Februari 2011. Rancangan percobaan yang digunakan adalah Rancangan Acak Kelompok (RAK) terdiri dari dua belas perlakuan, dengan tiga kali ulangan. Adapun perlakuan yang digunakan adalah sebagai berikut : A (jarak tanam 25 x 25 cm dengan tanpa penyiangan), B (jarak tanam 25 x 25 cm dengan disiang satu kali), C (jarak tanam 25 x 25 cm dengan, disiang dua kali), D (jarak tanam 25 x 25 cm dengan disiang tiga kali), E (jarak tanam 28 x 28 cm dengan tanpa penyiangan), F (jarak tanam 28 x 28 cm dengan disiang satu kali), G (jarak tanam 28 x 28 cm dengan disiang dua kali), H (jarak tanam 28 x 28 cm dengan disiang tiga kali), I (jarak tanam 30 x 30 cm dengan tanpa penyiangan), J (jarak tanam 30 x 30 cm dengan disiang satu kali), K (jarak tanam 30 x 30 cm dengan disiang dua kali), L (jarak tanam 30 x 30 cm dengan disiang tiga kali). Hasil per-cobaan menunjukkan bahwa dengan jarak tanam 30 x 30 cm, disiang tiga kali akan memberikan hasil yang paling baik terhadap hasil panen padi kultivar Ciherang dan akan meningkatkan hasil panen dibanding dengan jarak tanam standar, yaitu 25 cm x 25 cm, disiang tiga kali. Kehilangan hasil tertinggi diperoleh pada perlakuan jarak tanam 30 x 30 cm dengan tanpa penyiangan. Kata kunci : Produktivitas padi ∙ Kehilangan hasil ∙ Kultivar Ciherang ∙ Jarak tanam ∙ Prekuensi penyiangan
Constructing Flexible Scheduling Systems for Decision Support

Scheduling often involves, in addition to optimization, continuous decision making where continuity in the solutions produced is important. Furthermore, substantial diversity in the nature of different scheduling problems exists. In this paper we present a view of scheduling as decision support for continuous planning, and introduce a system for rapid delivery of large-scale scheduling applications.1
Nitric Oxide Inhibition of Homocysteine-induced Human Endothelial Cell Apoptosis by Down-regulation of p53-dependent Noxa Expression through the Formation of S-Nitrosohomocysteine*

Hyperhomocysteinemia is believed to induce endothelial dysfunction and promote atherosclerosis; however, the pathogenic mechanism has not been clearly elucidated. In this study, we examined the molecular mechanism by which homocysteine (HCy) causes endothelial cell apoptosis and by which nitric oxide (NO) affects HCy-induced apoptosis. Our data demonstrated that HCy caused caspase-dependent apoptosis in cultured human umbilical vein endothelial cells, as determined by cell viability, nuclear condensation, and caspase-3 activation and activity. These apoptotic characteristics were correlated with reactive oxygen species (ROS) production, lipid peroxidation, p53 and Noxa expression, and mitochondrial cytochrome c release following HCy treatment. HCy also induced p53 and Noxa expression and apoptosis in endothelial cells from wild type mice but not in the p53-deficient cells. The NO donor S-nitroso-N-acetylpenicillamine, adenoviral transfer of inducible NO synthase gene, and antioxidants (α-tocopherol and superoxide dismutase plus catalase) but not oxidized SNAP, 8-Br-cGMP, nitrite, and nitrate, suppressed ROS production, p53-dependent Noxa expression, and apoptosis induced by HCy. The cytotoxic effect of HCy was decreased by small interfering RNA-mediated suppression of Noxa expression, indicating that Noxa up-regulation plays an important role in HCy-induced endothelial cell apoptosis. Overexpression of inducible NO synthase increased the formation of S-nitroso-HCy, which was inhibited by the NO synthase inhibitor N-monomethyl-l-arginine. Moreover, S-nitroso-HCy did not increase ROS generation, p53-dependent Noxa expression, and apoptosis. These results suggest that up-regulation of p53-dependent Noxa expression may play an important role in the pathogenesis of atherosclerosis induced by HCy and that an increase in vascular NO production may prevent HCy-induced endothelial dysfunction by S-nitrosylation.
Distributed real-time sentiment analysis for big data social streams

Big data trend has enforced the data-centric systems to have continuous fast data streams. In recent years, real-time analytics on stream data has formed into a new research field, which aims to answer queries about “what-is-happening-now” with a negligible delay. The real challenge with real-time stream data processing is that it is impossible to store instances of data, and therefore online analytical algorithms are utilized. To perform real-time analytics, pre-processing of data should be performed in a way that only a short summary of stream is stored in main memory. In addition, due to high speed of arrival, average processing time for each instance of data should be in such a way that incoming instances are not lost without being captured. Lastly, the learner needs to provide high analytical accuracy measures. Sentinel is a distributed system written in Java that aims to solve this challenge by enforcing both the processing and learning process to be done in distributed form. Sentinel is built on top of Apache Storm, a distributed computing platform. Sentinel's learner, Vertical Hoeffding Tree, is a parallel decision tree-learning algorithm based on the VFDT, with ability of enabling parallel classification in distributed environments. Sentinel also uses SpaceSaving to keep a summary of the data stream and stores its summary in a synopsis data structure. Application of Sentinel on Twitter Public Stream API is shown and the results are discussed.
Spatial and temporal dissection of immediate and early events following cadherin-mediated epithelial cell adhesion

Cell-cell adhesion is at the top of a molecular cascade of protein interactions that leads to the remodeling of epithelial cell structure and function. The earliest events that initiate this cascade are poorly understood. Using high resolution differential interference contrast microscopy and retrospective immunohistochemistry, we observed that cell-cell contact in MDCK epithelial cells consists of distinct stages that correlate with specific changes in the interaction of E-cadherin with the cytoskeleton. We show that formation of a stable contact is preceded by numerous, transient contacts. During this time and immediately following formation of a stable contact, there are no detectable changes in the distribution, relative amount, or Triton X- 100 insolubility of E-cadherin at the contact. After a lag period of approximately 10 min, there is a rapid acquisition of Triton X-100 insolubility of E-cadherin localized to the stable contact. Significantly, the total amount of E-cadherin at the contact remains unchanged during this time. The increase in the Triton X-100 insoluble pool of E-cadherin does not correlate with changes in the distribution of actin or fodrin, suggesting that the acquisition of the Triton X-100 insolubility is due to changes in E-cadherin itself, or closely associated proteins such as the catenins. The 10 minute lag period, and subsequent prompt and localized nature of E-cadherin reorganization indicate a form of signaling is occurring.
Probabilistic Relational PCA

One crucial assumption made by both principal component analysis (PCA) and probabilistic PCA (PPCA) is that the instances are independent and identically distributed (i.i.d.). However, this common i.i. d. assumption is unreasonable for relational data. In this paper, by explicitly modeling covariance between instances as derived from the relational information, we propose a novel probabilistic dimensionality reduction method, called probabilistic relational PCA (PRPCA), for relational data analysis. Although the i.i. d. assumption is no longer adopted in PRPCA, the learning algorithms for PRPCA can still be devised easily like those for PPCA which makes explicit use of the i.i. d. assumption. Experiments on real-world data sets show that PRPCA can effectively utilize the relational information to dramatically outperform PCA and achieve state-of-the-art performance.
Binomial congestion control algorithms

This paper introduces and analyzes a class of nonlinear congestion control algorithms called binomial algorithms, motivated in part by the needs of streaming audio and video applications for which a drastic reduction in transmission rate upon each congestion indication (or loss) is problematic. Binomial algorithms generalize TCP-style additive-increase by increasing inversely proportional to a power k of the current window (for TCP, k=0); they generalize TCP-style multiplicative decrease by decreasing proportional to a power l of the current window (for TCP, l=1). We show that there are an infinite number of deployable TCP-compatible binomial algorithms, those which satisfy k+1=1, and that all binomial algorithms converge to fairness under a synchronized-feedback assumption provided k+l>0; k, l/spl ges/0. Our simulation results show that binomial algorithms interact well with TCP across a RED gateway. We focus on two particular algorithms, IIAD (k=1, l=0) and SQRT (k=l=0.5), showing that they are well-suited to applications that do not react well to large TCP-style window reductions.
An Analytical Comparison of Approaches to Personalizing PageRank

PageRank, the popular link-analysis algorithm for ranking web pages, assigns a query and user independent estimate of "importance" to web pages. Query and user sensitive extensions of PageRank, which use a basis set of biased PageRank vectors, have been proposed in order to personalize the ranking function in a tractable way. We analytically compare three recent approaches to personalizing PageRank and discuss the tradeoffs of each one.