Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining Software Repositories for Defect Categorization

Early detection of software defects is very important to decrease the software cost and subsequently increase the software quality. Success of software industries not only depends on gaining knowledge about software defects, but largely reflects from the manner in which information about defect is collected and used. In software industries, individuals at different levels from customers to engineers apply diverse mechanisms to detect the allocation of defects to a particular class. Categorizing bugs based on their characteristics helps the Software Development team take appropriate actions to reduce similar defects that might get reported in future releases. Classification, if performed manually, will consume more time and effort. Human resource having expert testing skills & domain knowledge will be required for labeling the data. Therefore, the need of automatic classification of software defect is high. This work attempts to categorize defects by proposing an algorithm called Software Defect CLustering (SDCL). It aims at mining the existing online bug repositories like Eclipse, Bugzilla and JIRA for analyzing the defect description and its categorization. The proposed algorithm is designed by using text clustering and works with three major modules to find out the class to which the defect should be assigned. Software bug repositories hold software defect data with attributes like defect description, status, defect open and close date. Defect extraction module extracts the defect description from various bug repositories and converts it into unified format for further processing. Unnecessary and irrelevant texts are removed from defect data using data preprocessing module. Finally grouping of defect data into clusters of similar defect is done using clustering technique. The algorithm provides classification accuracy more than 80% in all of the three above mentioned repositories.
Quantitation of glucosamine sulfate in plasma by HPLC-MS/MS after administration of powder for oral solution formulation.

A rapid method for the quantification of glucosamine in human plasma using high-performance liquid chromatography coupled to tandem mass spectrometry was developed and validated. The sample preparation includes a simple deproteinization step, using D-[1-¹³C] glucosamine hydrochloride as an internal standard. Chromatographic separation was performed on an ACE Ciano column using isocratic elution with acetonitrile and aqueous 2 mM ammonium acetate containing 0.025% formic acid (80:20). Selected reaction monitoring was performed using the transitions m/z 180.1 → m/z 72.1 and m/z 181.0 → m/z 74.6 to quantify glucosamine and internal standard, respectively. The method was validated and proved to be linear, accurate and precise over the range 50-5000 ng/mL of glucosamine. Recovery rates higher than 90% were obtained for both glucosamine and internal standard. No matrix effect was detected in the samples. The validated method was successfully applied to a pharmacokinetic study after oral administration of a powder for oral solution formulation containing glucosamine sulfate.
Implication Networks from Large Gene-expression Datasets

We present a new algorithm for building Boolean networks f rom very large amounts of gene expression data. The resulting networks include not only symmetric relationships between genes, such as co-expression, but also asymmetr ic relations that represent if-then rules. The approach is conceptually simple and fast eno ugh that it can build a complete gene network using 3 billion gene pairs with more than 9,500 e xpression values per genepair in less than 3 hours on an ordinary office computer. The algorithm was applied to publicly available data from thousands of microarrays fo r humans, mice, and fruit flies (for a total of 365 million Affymetrix probeset expression levels). The resulting network consists of hundreds of millions of relationships between genes, and contains biologically meaningful information about gender differences, tissue d iff rences, development, differentiation and co-expression. We also examine re lationships that are conserved between humans, mice, and fruit flies. The full Bool ean relationships are available for exploration at http://gourd.stanford. edu/~sahoo/recomb07/ .
Zero-Moment Point - Thirty Five Years of its Life

This paper is devoted to the permanence of the concept of Zero-Moment Point, widelyknown by the acronym ZMP. Thirty-five years have elapsed since its implicit presentation (actually before being named ZMP) to the scientific community and thirty-three years since it was explicitly introduced and clearly elaborated, initially in the leading journals published in English. Its first practical demonstration took place in Japan in 1984, at Waseda University, Laboratory of Ichiro Kato, in the first dynamically balanced robot WL-10RD of the robotic family WABOT. The paper gives an in-depth discussion of source results concerning ZMP, paying particular attention to some delicate issues that may lead to confusion if this method is applied in a mechanistic manner onto irregular cases of artificial gait, i.e. in the case of loss of dynamic balance of a humanoid robot. After a short survey of the history of the origin of ZMP a very detailed elaboration of ZMP notion is given, with a special review concerning “boundary cases” when the ZMP is close to the edge of the support polygon and “fictious cases” when the ZMP should be outside the support polygon. In addition, the difference between ZMP and the center of pressure is pointed out. Finally, some unresolved or insufficiently treated phenomena that may yield a significant improvement in robot performance are considered.
ERCC1 C118T associates with response to FOLFOX4 chemotherapy in colorectal cancer patients in Han Chinese.

BACKGROUND Genetic variations influence treatment outcomes in cancer patients treated with chemotherapy. Detection of pharmacogenetic markers associated with treatment response may enable doctor to plan more precise and effective treatment tailoring to individual cancer patients. METHODS A novel oligonucleotide microarray was developed to genotype 13 variations (DPYD*2, DPYD*5, DPYD*9, TYMS 6 bp Ins/Del, UGT1A1*6, UGT1A1*27, UGT1A1*28, GSTP1 Ile105Val, XRCC1 Arg399Gln, MTHFR C677T, MDR1 C3435T/A, MDR1 G2677A/T and ERCC1 C118T). The accuracy of genotypes obtained by microarray was assessed by independent sequencing. 73 patients first diagnosed with colorectal cancer (CRC) were treated with FOLFOX4 chemotherapy. RESULTS All genotypes were successfully called by microarray, and were consistent with those identified by independent sequencing except two TYMS 6 bp Ins/Del genotypes. Patients with CT or TT genotype exhibited a higher probability of response to treatment than those with CC genotype. No other SNP was found to be associated with treatment response. Furthermore, these SNPs showed no associations with gastrointestinal, hematological or neurological toxicity. CONCLUSIONS ERCC1 C118T may be a predictive marker of treatment response to 5-FU/platinum chemotherapy for CRC. The microarray can significantly facilitate the process of detecting genetic variations and may help doctor plan more effective medication for individual cancer patient.
Social and Environmental Predictors of Plasma HIV RNA Rebound Among Injection Drug Users Treated With Antiretroviral Therapy

IntroductionEvidence is needed to improve HIV treatment outcomes for individuals who use injection drugs (IDU). Although studies have suggested higher rates of plasma viral load (PVL) rebound among IDU on antiretroviral therapy (ART), risk factors for rebound have not been thoroughly investigated. MethodsWe used data from a long-running community-recruited prospective cohort of IDU in Vancouver, Canada, linked to comprehensive ART and clinical monitoring records. Using proportional hazards methods, we modeled the time to confirmed PVL rebound above 1000 copies per milliliter among IDU on ART with sustained viral suppression, defined as 2 consecutive undetectable PVL measures. ResultsBetween 1996 and 2009, 277 individuals had sustained viral suppression. Over a median follow-up of 32 months, 125 participants (45.1%) experienced at least 1 episode of virologic failure for an incidence of 12.6 [95% confidence interval (CI): 10.5 to 15.0] per 100 person-years. In a multivariate model, PVL rebound was independently associated with sex-trade involvement [adjusted hazard ratio (AHR) = 1.40, 95% CI: 1.08 to 1.82) and recent incarceration (AHR = 1.83, 95% CI: 1.33 to 2.52). Methadone maintenance therapy (AHR = 0.79, 95% CI: 0.66 to 0.94) was protective. No measure of illicit drug use was predictive. ConclusionsIn this setting of free ART, several social and environmental factors predicted higher risks of viral rebound among IDU, including sex-trade involvement and incarceration. These findings should help inform efforts to identify individuals at risk of viral rebound and targeted interventions to treat and retain individuals in effective ART.
Source localization in an ocean waveguide using supervised machine learning

Acoustic source localization is classically addressed with Matched-field processing (MFP). However, since MFP is necessarily based on accurately modeled ocean environment, it may not be well adapted as realistic ocean environment is far more complex and unpredictable. In this paper, the potential of applying machine learning techniques is explored regarding the source localization with unstable and fluctuating ocean acoustic signals. The sound pressure is preprocessed to a normalized sample covariance matrix as input data. Machine learning methods, such as feedforward neural network (FNN), support vector machines (SVM) and random forests (RF), are proposed to be experimented. Both classification and regression are performed to address the range estimation problem. The performance for all methods is evaluated with mean absolute percentage error (MAPE), and the lowest MAPE of 2.31 % is obtained from SVM.
Surgical adjuvant therapy of rectal carcinoma: a controlled evaluation of leucovorin, 5-fluorouracil and radiation therapy with or without interferon-alpha2b.

BACKGROUND The aim of this study was to determine whether the efficacy of the combination of 5-fluorouracil (5-FU), leucovorin (LV) and radiation therapy (RT) could be improved by the addition of interferon-alpha2b (IFN-alpha) in patients who have had a 'curative' resection, for rectal adenocarcinoma (Dukes' B2/C; T3 N0, T4 N0, N1-3). PATIENTS AND METHODS A total of 207 eligible patients with a performance status of 0 or 1 were randomized postoperatively between days 21 and 70 to one of the two treatment groups: group A, LV 20 mg/m2 i.v. bolus and 5-FU 425 mg/m2 i.v. days 1-5 and 29-33, LV 20 mg/m2 and 5-FU 400 mg/m2 days 57-60 and 85-88, LV 20 mg/m2 and 5-FU 380 mg/m2 days 1-5 and 29-33 with the second day 1 occurring 28 days after the completion of RT (45 Gy); group B, LV, 5-FU and RT as in group A, and IFN-alpha 5 x 10(6) IU s.c. three times during each week chemotherapy is given. RESULTS 104 patients were randomized into group A and 103 into group B. There was no statistically significant difference in either disease-free survival or overall survival between the two groups. Toxicity was also the same, except for the flu-like syndrome associated with the IFN-alpha administration. CONCLUSIONS There was no difference in efficacy between the two combinations. Toxicity was greater with the LV + 5-FU + IFN-alpha regimen because of the flu-like syndrome.
ASSORTMENT OF ONTOLOGIES USEFUL IN NATURAL LANGUAGE PROCESSING

Since the field of NLP has a long history, the literature in this field is growing fast through the recent years. Different knowledge bases or ontologies are available that help us capture different aspects of natural language. There is a huge variety of ontologies that are available either freely or are licensed. Each of these has some new information to offer. But to the very core, each ontology offer a certain kind of knowledge supporting its underlying principle like common sense knowledge, knowledge about purpose of an artifact etc. In this paper, we have tried to collate different ontologies that offer us such diversified knowledge with varied underlying principle which have proved to be helpful in understanding the natural language.
Prophylactic cancer vaccination by targeting functional non-self

Abstract Despite the monumental success of childhood prophylactic vaccination, there is no similar program designed to provide protection as we age against adult onset diseases like breast cancer. Instead, the predominant focus of current cancer vaccine strategy is to vaccinate after the tumors become established. This strategy has at best provided incremental improvement in overall survival. We propose the development of an adult vaccination program modeled on the childhood program that provides protection against diseases we confront as we enter our middle age. Since most cases of adult cancers are not associated with definitive etiopathogenic viruses, we propose extending our selection of vaccine targets to tissue-specific self proteins that are over-expressed in developing tumors but are no longer expressed in normal tissues (‘retired or former self’), are expressed in normal tissues under readily avoidable conditions (‘conditional self’), or are incapable of targeting any clinically significant autoimmune complications (‘irrelevant self’). By extending prophylactic vaccination to such “functional non-self” targets, prophylactic vaccination against adult onset diseases like breast cancer may occur safely in the absence of any autoimmune inflammatory complications and may potentially reduce disease incidence in a manner that mimics the impact of childhood vaccination on diseases like measles and polio.
POSSIBLE STELLAR STREAMS IN THE EDGE-ON SPIRAL NGC 891 DISCOVERED FROM KINEMATICS OF PLANETARY NEBULAE

We have found 125 planetary nebulae (PNs) in NGC 891, using an [O iii] λ5007 on-band/off-band filter technique with the Faint Object Camera and Spectrograph (FOCAS) at the Cassegrain focus of the Subaru telescope, Mauna Kea. Radial velocities were measured for all detected sources, using a method of slitless spectroscopy which we briefly describe. The radial velocities allow us to study the motions of different stellar populations in NGC 891. The PN kinematics show rotation at large distances from the galactic plane. Of particular interest is the strong asymmetry of PN distribution at large height, which we interpret as two possible stellar streams that could be orbiting the galaxy at large angles to the main structure. These streams, if real, are probably remnants of a previous minor merging episode. This idea finds support in recent reports of clump-like, incompletely mixed structures from deep HST/ACS images of this galaxy.
Nonlinear behavioral modeling of power amplifiers using radial-basis function neural networks

A radial-basis function neural network (RBFNN) is proposed for modeling the dynamic nonlinear behavior of RF power amplifiers. In the model the signal's envelope is used. The model requires less training than a model using both IQ-data. Sampled input and output signals from a power amplifier for 3G were used in the identification and validation. The RBFNN is compared with a parallel Hammerstein model. For a memory depth of one sample the RBFNN gives a better model, in- and out-of-band; for three samples the RBFNN reduces the in-band error more while the Hammerstein model reduces the error out-of-band more.
MASS/LENGTH RESIDUALS: MEASURES OF BODY CONDITION OR GENERATORS OF SPURIOUS RESULTS?

In studies of animal ecology, it is fashionable to use the residuals from an ordinary least squares (OLS) linear regression of body mass against a linear measure of size (the body size indicator, BSI) as an index of body condition. These residual indices are used to study the relationship between condition and reproductive investment, survi- vorship, habitat use, and other parameters. I identify a series of key assumptions underlying the use of this method, each of which is likely to be violated in some or all studies. These assumptions are: (1) that the functional relationship between mass and BSI is linear; (2) that condition is independent of BSI length; (3) that BSI length accurately indicates struc- tural size; (4) that there is no correlation between the size of BSI relative to other structural components (i.e., shape) and the parameter against which the residuals are analyzed; (5) that BSI length is strictly independent of mass; and (6) that BSI length is not subjected to error. Violations of these assumptions place the results of some studies in question and explain the poor relationship observed between OLS residuals and more direct measures of condition. I use avian morphometric data to illustrate how OLS methods can easily lead to Type I and Type II errors through violations of assumptions (5) and (6). Significant relationships reported between OLS residual indices and parameters correlating with body size (e.g., size of sexual ornaments or egg size) are at particular risk of being spurious when the correlation coefficient between mass and BSI is low. Residual indices of condition are often likely to be more reliable when calculated with alternative methods such as nonparametric or model II regression. However, whatever the method used to produce them, residual indices are not suitable for studying the heritability of condition.
Relative risk estimated from the ratio of two median unbiased estimates

Summary. Clinical trials often include binary end points. In some cases, no successes are observed and the usual large sample estimates of relative risk are undefined. The paper proposes an estimator for relative risk based on the median unbiased estimator. The relative risk estimator proposed is well defined and performs satisfactorily for a wide range of data configurations. To facilitate the use of the estimator, a deterministic bootstrap confidence interval is also proposed, and an SAS macro is available to perform the necessary calculations. An on‐going randomized clinical trial motivated the development of the estimator and is used to illustrate the approach.
Detecting Sarcasm on Twitter : A Behavior Modeling Approach

Sarcasm is a nuanced form of language where usually, the speaker explicitly states the opposite of what is implied. Imbued with intentional ambiguity and subtlety, detecting sarcasm is a difficult task, even for humans. Current works approach this challenging problem primarily from a linguistic perspective, focussing on the lexical and syntactic aspects of sarcasm. In this thesis, I explore the possibility of using behavior traits intrinsic to users of sarcasm to detect sarcastic tweets. First, I theorize the core forms of sarcasm using findings from the psychological and behavioral sciences, and some observations on Twitter users. Then, I develop computational features to model the manifestations of these forms of sarcasm using the user’s profile information and tweets. Finally, I combine these features to train a supervised learning model to detect sarcastic tweets. I perform experiments to extensively evaluate the proposed behavior modeling approach and compare with the state-of-the-art.
Molecular analysis of the seedlessness character in grape using RAPD markers

Forty-eight polymorphic RAPD primers were used to study the genetic similarity of eight grapevine (Vitis spp.) accessions: Italia, Seyve Villard 12327, Seyve Villard 12375, Crimson Seedless, CG 87746, A 1976, Gota de Ouro and CNPUV 154-27. Gota de Ouro, the only Vitis labrusca cultivar, was the most distant cultivar from the others. The population CNPUV 154 (Seyve Villard 12327 x CG 87746) was evaluated for fresh and dry seed weight. Four phenotypic classes were considered for dry matter percentage (DM%): 1 (DM > 55), 2 (45 < DM < 55), 3 (35 < DM < 45) and 4 (DM < 35). The observed frequencies for the classes 1, 2, 3, and 4 were 37, 27, 53, and 9 individuals, respectively. Of the 500 RAPD screened primers, 111 were selected as polymorphic. According to BSA, markers generated by OPK02, OPM16, OPS03, and OPU13 primers could be related to the region that controls seedlessness
Étude de mesures de testabilité de systèmes logiques

Ce memoire est consacre a l'etude de mesures de testabilite de systemes logiques et a l'introduction de ces mesures dans un outil de generation de programmes de test. Un etat de l'art sur la testabilite est fait, ainsi qu'une analyse critique des principaux programmes operationnels : TMEAS, CAMELOT et SCOAP. Une description d'un systeme operationnel d'aide a la specification automatique de programmes de test : CATA, est donnee. Nous formalisons des mesures de controlabilite, observabilite et testabilite. Puis nous nous interessons a la determination d'une strategie de test, definissant un ensemble minimal et ordonne d'ecoulements permettant le test complet d'un systeme, au vu des mesures definies.
Resistance of cold- and starvation-stressed Vibrio vulnificus to heat and freeze-thaw exposure.

The effects of cold storage and starvation on the subsequent heat resistance and freeze-thaw resistance of Vibrio vulnificus were studied. Three strains of V. vulnificus were evaluated. Cold stress had no effect on freeze-thaw resistance (P > 0.05). Starvation enhanced freeze-thaw resistance for one strain compared to controls (P < 0.05). V. vulnificus was not heat resistant; control populations were inactivated within 12 min at 47 degrees C. Starvation increased heat tolerance for one strain, but differences were small from a processing perspective (P < 0.05). Cold stress had no effect on heat resistance (P > 0.05). Cold adaptation (holding 4 h at 15 degrees C) enhanced cold temperature (5 degrees C) tolerance. This information will be helpful in the development of methods to minimize V. vulnificus risk.
CRISPR Technology Reveals RAD(51)-ical Mechanisms of Repair in Roundworms: An Educational Primer for Use with “Promotion of Homologous Recombination by SWS-1 in Complex with RAD-51 Paralogs in Caenorhabditis elegans”

The mechanisms cells use to maintain genetic fidelity via DNA repair and the accuracy of these processes have garnered interest from scientists engaged in basic research to clinicians seeking improved treatment for cancer patients. Despite the continued advances, many details of DNA repair are still incompletely understood. In addition, the inherent complexity of DNA repair processes, even at the most fundamental level, makes it a challenging topic. This primer is meant to assist both educators and students in using a recent paper, “Promotion of homologous recombination by SWS-1 in complex with RAD-51 paralogs in Caenorhabditis elegans,” to understand mechanisms of DNA repair. The goals of this primer are to highlight and clarify several key techniques utilized, with special emphasis on the clustered, regularly interspaced, short palindromic repeats technique and the ways in which it has revolutionized genetics research, as well as to provide questions for deeper in-class discussion.