gebhart/patrepeval huggingface dataset:
Test case selection and prioritization in continuous integration environment (2019)

It is beneficial for continuous integration (CI), that building and testing a software happens as quickly as possible. Sometimes, when a test suite grows large during the lifecycle of the software, testing becomes slow and inefficient. It is a good idea to parallelize test executions to speed up testing, but in addition to that, test case selection and prioritization can be used. In this case study, we use incremental machine learning techniques to predict failing and passing tests in the test suite of existing software from the space industry and execute only test cases that are predicted failing. We apply such test case selection techniques to 35 source code modifying commits of the software and compare their performances to traditional coverage based selection techniques and other heuristics. Secondly, we apply different incremental machine learning techniques in test case prioritization and compare their performances to traditional coverage based prioritization techniques. We combine features that have been used successfully in previous studies, such as code coverage, test history, test durations and text similarity to separate passing and failing tests with machine learning. The results suggest, that certain test case selection and prioritization techniques can enhance testing remarkably, providing significantly better results compared to random selection and prioritization. Additionally, incremental machine learning techniques require a learning period of approximately 20 source code modifying commits to produce equal or better results than the comparison techniques in test case selection. Test case prioritization techniques with incremental machine learning perform significantly better than the traditional coverage based techniques, and they can outweigh the traditional techniques in the weighted average of faults detected (APFD) values immediately after initial training. We show that machine learning does not need a rigorous amount of training to outperform traditional approaches in test case selection and prioritization. Therefore, incremental machine learning suits test case selection and prioritization well, when initial training data does not exist.
Aromatase and Its Inhibitors: Significance for Breast Cancer Therapy (2002)

Endocrine adjuvant therapy for breast cancer in recent years has focussed primarily on the use of tamoxifen to inhibit the action of estrogen in the breast. The use of aromatase inhibitors has found much less favor due to poor efficacy and unsustainable side effects. Now, however, the situation is changing rapidly with the introduction of the so-called phase III inhibitors, which display high affinity and specificity towards aromatase. These compounds have been tested in a number of clinical settings and, almost without exception, are proving to be more effective than tamoxifen. They are being approved as first-line therapy for elderly women with advanced disease. In the future, they may well be used not only to treat young, postmenopausal women with early-onset disease but also in the chemoprevention setting. However, since these compounds inhibit the catalytic activity of aromatase, in principle, they will inhibit estrogen biosynthesis in every tissue location of aromatase, leading to fears of bone loss and possibly loss of cognitive function in these younger women. The concept of tissue-specific inhibition of aromatase expression is made possible by the fact that, in postmenopausal women when the ovaries cease to produce estrogen, estrogen functions primarily as a local paracrine and intracrine factor. Furthermore, due to the unique organization of tissue-specific promoters, regulation in each tissue site of expression is controlled by a unique set of regulatory factors. These factors are potential targets for the design of selective aromatase modulators, which could selectively inhibit aromatase expression in breast with the same efficacy as the phase III inhibitors of activity but leave expression in other local sites such as bone and brain untouched.
Growth and characterization of electrodeposited Cu<sub>2</sub>O thin films (2013)

This work demonstrates the electrodeposition of cuprous oxide (Cu2O) thin films onto a fluorine-doped tin oxide (FTO)-coated conducting glass substrates from Cu(II) sulfate solution with C6H8O7 chelating agent. During cyclic voltammetry experiences, the potential interval where the electrodeposition of Cu2O is carried out was established. The thin films were obtained potentiostatically and were characterized through different techniques. From the Mott-Schottky measurements, the flat-band potential and the acceptor density for the Cu2O thin films are determined. All the films showed a p-type semiconductor character with a carrier density varying between 2.41 x 10(18) cm(-3) and 5.38 x 10(18) cm(-3). This little difference is attributed to the increase of the stoichiometric defects in the films with the deposition potential. Atomic force microscopy analysis showed that the Cu2O thin films obtained at high potential are more homogenous in appearance and present lower crystallites size. X-ray diffraction measurements indicate a cubic structure with good crystallization state and the deposition potential was found to have an influence on the size of the crystallites. The optical measurements show a direct band gap between 2.07-2.49 eV depending on the applied potential.
Small bowel gastrointestinal stromaltumor (GIST) arising in a jejunal diverticulum. (2009)

In this report, we present a very rare case of a small bowel GIST arising in a true jejunal diverticulum in a 56-year-old woman.
The Use of a Combination Skin Hook and Tissue Forceps: A New Instrument for Dermatologic Surgery (“Frankel‐Adson Forceps”*) (1988)

The dermatologic surgeon frequently uses both skin hook and tissue forceps to accomplish atraumatic wound closure. Since this requires the surgeon to change instruments frequently during the course of the procedure, a combination skin hook and tissue forceps has been developed to make possible the simultaneous use of these two instruments. In addition, using a new technique that combines the two capabilities of this instrument, the surgeon can further reduce the risk of tissue trauma during surgery. The instrument and this technique are described.
Vivaldi Antennas for Single Beam Integrated Receivers (1982)

Slot line antennas intended for rnm-wave single beam applications as well as for imaging systems are experimentally investigated. In particular the Vivaldi antenna is investigated, and it is found that a 3 dB beam width of typically 30° is obtained and a 10 dB beam width of about 60° can be achieved. The 10 dB beam efficiency as defined in the text can be made about 60% as compared to 70% for a corrugated scalar horn.
Micro Grid Techniques (continued) and Their Contribution to Specimen Preparation Techniques for High Resolution Work<xref ref-type="fn" rid="fn1"><sup>†</sup></xref> (1972)

On the basis of the preparation method of the plastic micro grid already published, two kinds of micro grid techniques have been developed. One is a preparing technique of the micro grid which has large holes of 10– 100μ. The other is a technique for making various kinds of metal or carbon micro grids based on the plastic micro grids. These many types of micro grids are mainly contributed to the specimen preparation techniques for high resolution work. Detailed explanations of the techniques are given concerning the significance of using the micro grid, concrete operation methods and other related techniques. It is a favorable merit that this specimen techniques have a possibility to minimize the specimen drift caused by the electron irradiation in the electron microscope. The quantities of specimen drift were measured experimentally and compared, for the different supporting membranes and supporting processes.
Evidence for the Metabolism of Maleic Acid in Dogs and Human Beings (1958)

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Mechanism of increased conversion of branched chain keto acid dehydrogenase from inactive to active form by a medium chain fatty acid (octanoate) in skeletal muscle. (1992)

We and others have previously shown that octanoate increases the oxidation of branched chain amino acids (BCAA) in skeletal muscle. The present study was designed to investigate the mechanism of this increased oxidation. Studies were performed with rat hind limbs perfused with 0.50 mM L-[1-14C]leucine with or without octanoate. The flux through branched chain keto acid (BCKA) dehydrogenase was measured, and the basal and total activity of BCKA dehydrogenase in skeletal muscle was determined. The rate of flux through BCKA dehydrogenase increased by 37, 119, and 297% with 0.5, 1.0, and 2.0 mM octanoate, respectively. This increase in flux was not due to a change in BCAA aminotransferase activity but was due to an increase in the basal activity of BCKA dehydrogenase. There was a strong correlation (r = 0.96) between increases in flux through BCKA dehydrogenase and increases in the basal activities of BCKA dehydrogenase. Preincubation of BCKA dehydrogenase with Mg2+ caused full activation of this enzyme, but preincubation with octanoate did not activate this enzyme. On the other hand, octanoate completely prevented the ATP-dependent inactivation of fully activated BCKA dehydrogenase. We conclude that octanoate increases the oxidation of leucine in skeletal muscle by increasing the activation of BCKA dehydrogenase. The mechanism of this activation is the inhibition of BCKA dehydrogenase kinase rather than the stimulation of a specific or nonspecific protein phosphatase.
The libstdc++ parallel mode: Software engineering considerations (2008)

The C++ Standard Library implementation provided with the free GNU C++ compiler, libstdc++, provides a “parallel mode ” as of version 4.3. Using this mode enables existing serial code to take advantage of many parallelized STL algorithms, an approach to making use of multi-core processors which are now or will soon will be ubiquitous. This paper describes the goals, the design choices and the software engineering issues discovered during design and implementation, and the results of user testing, presenting possible solutions to outstanding issues. We adress standards compliance, influencing algorithm and parameter choices at compile and run time, and the interplay between execution speed, the executable size and the compilation time.
Deciphering the Roles of the Histone H2B N-Terminal Domain in Genome-Wide Transcription (2006)

Histone N-terminal domains are frequent targets of posttranslational modifications. Multiple acetylated lysine residues have been identified in the N-terminal domain of H2B (K6, K11, K16, K17, K21, and K22), but little is known about how these modifications regulate transcription. We systematically mutated the N-terminal domain of histone H2B, both at known sites of lysine acetylation and elsewhere, and characterized the resulting changes in genome-wide expression in each mutant strain. Our results indicate that known sites of lysine acetylation in this domain are required for gene-specific transcriptional activation. However, the entire H2B N-terminal domain is principally required for the transcriptional repression of a large subset of the yeast genome. We find that the histone H2B repression (HBR) domain, comprised of residues 30 to 37, is necessary and sufficient for this repression. Many of the genes repressed by the HBR domain are located adjacent to telomeres or function in vitamin and carbohydrate metabolism. Deletion of the HBR domain also confers an increased sensitivity to DNA damage by UV irradiation. We mapped the critical residues in the HBR domain required for its repression function. Finally, comparisons of these data with previous studies reveal that a surprising number of genes are coregulated by the N-terminal domains of histone H2B, H3, and H4.
Modeling the sleep mode for cellular digital packet data (1999)

Cellular digital packet data (CDPD) utilizes sleep mode mechanism to conserve the power of mobile end systems (M-ESs). A timer called T203 determines how quick an M-ES enters the sleep mode, and another timer called T204 determines how often the M-ES wakes up. A large T204 value and a small T203 value can effectively reduce the power consumption at the cost of degrading the frame transmission performance, i.e., more lost frames, longer frame waiting times, and larger waiting variance. When the power consumption budget is determined in a CDPD system design, our study provides guidelines to determine the timer values as well as the buffer size to optimize the frame transmission performance.
Clustering Approaches to Identifying Gene Expression Patterns from DNA Microarray Data (2008)

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.
Prediction of vesico‐ureteric reflux in childhood urinary tract infection: a multivariate approach (2000)

A prediction rule based on age, gender, family history, CRP and US results is useful in assessing the probability of VUR in the individual child with a first UTI and may help the physician to make decisions about performing additional imaging techniques. Prospective validation of the model in future patients, however, will be necessary before applying the rule in practice.
Neutralization of transforming growth factor-beta 1 in a mouse model of immune-induced lung fibrosis. (1994)

We examined the contribution of the cytokine transforming growth factor beta 1 (TGF-beta 1) in the inflammatory response and fibrotic reaction in a mouse model of immune-induced lung fibrosis caused by repeated intranasal exposure to heat-killed bacillus Calmette-Guérin (BCG). Mice received 200 micrograms of BCG 3 days/week for 4 weeks, and simultaneous intraperitoneal injections of a monospecific rabbit antiserum against mouse TGF-beta 1 or a preimmune serum (normal rabbit globulin). BCG instillations generated a copious release of antigenic TGF-beta 1 in the lungs at 1, 2, 3 and 4 weeks (up to 15 ng/lungs/mouse). Treatment with anti-TGF-beta 1 antiserum significantly diminished the number of free lung cells recovered by bronchoalveolar lavage (BAL), although the BAL cellular profile was not affected. Moreover, anti-TGF-beta 1 treatment of challenged mice diminished very significantly the total levels of interleukin-1 beta (IL-1 beta) and tumour necrosis factor-alpha (TNF-alpha) in the lungs of animals challenged with BCG. Histological examination and morphometric analysis of Masson's Trichrome-stained sections and measurements of total lung hydroxyproline levels showed a substantial decrease in lung fibrosis and granulomatous response of challenged mice given anti-TGF-beta 1. These data argue for a role for TGF-beta 1 in inducing inflammation and lung fibrosis in response to an immune stimulus.
Protection of Hamsters by Venezuelan Equine Encephalitis Virus Candidate Vaccine V3526 against Lethal Challenge by Mosquito Bite and Intraperitoneal Injection (2008)

In an attempt to improve the current live, attenuated vaccine (TC-83) for Venezuelan equine encephalitis virus (VEEV), specific mutations associated with attenuation of VEEV in rodent models were inserted into a full-length cDNA clone of the Trinidad donkey strain of VEEV by site-directed mutagenesis. Because some viruses have been reported to be more pathogenic when introduced by mosquito bite than the same virus introduced by needle inoculation, there were concerns that the presence of mosquito saliva, or changes in the virus caused by replication in a mosquito, might allow the virus to overcome the protective effects of prior vaccination with V3526. Therefore, we determined if hamsters vaccinated with V3526 were protected from challenge with the virulent Trinidad donkey strain of VEEV. All non-vaccinated hamsters died after intraperitoneal challenge or after being fed on by VEEV-inoculated Aedes taeniorhynchus. In contrast, hamsters vaccinated with V3526 were resistant to intraperitoneal challenge and infection by VEEV-infected Ae. taeniorhynchus. Therefore, the V3526 candidate vaccine elicits protection against VEEV infection by mosquito bite.
Structural observation of photochromism (2006)

The reversible formation of a long-lived, coloured F-centre has been observed in small structural changes delineated by neutron diffraction.
Activation of neuromedin B-preferring bombesin receptors on rat glioblastoma C-6 cells increases cellular Ca2+ and phosphoinositides (1992)

Recent cloning studies confirm the presence of two subtypes of bombesin (Bn) receptors. In contrast to the gastrin-releasing peptide (GRP)-preferring subtype, which has been widely studied, nothing is known about the cellular mechanisms of the neuromedin B (NMB)-preferring subtype, which occurs widely in the central nervous system and gastrointestinal tissues, partially because of the lack of a cell line with functional receptors. In the present study we have investigated Bn receptors on the rat glioblastoma cell line C-6, reported to contain mRNA of the NMB receptor subtype. Binding of 125I-[D-Tyr0]NMB to these cells was time- and temperature-dependent, saturable, reversible, and only inhibited by Bn receptor agonists or antagonists. For Bn receptor agonists the relative potencies were: NMB (1.7 nM) approximately equal to litorin (3 nM) greater than ranatensin (8 nM) greater than Bn (19 nM) greater than neuromedin C (NMC) (210 nM) greater than GRP (500 nM). These relative affinities were almost identical to those for the NMB receptor subtype on rat oesophageal tissue and for Balb 3T3 cells stably transfected with the NMB receptor subtype. These potencies differed from those for the GRP receptor subtype on rat pancreatic acini [Bn approximately equal to litorin (4 nM) greater than ranatensin, NMC, GRP (15-20 nM) much greater than NMB (351 nM)]. The relative potencies of four different classes of Bn receptor antagonists were compared. Results from C-6 tumour cells agreed closely with those for binding to the NMB receptor subtype on rat oesophageal tissue and in Balb 3T3 cells stably transfected with this receptor, and differed markedly from those for binding to the GRP receptor subtype on rat pancreatic acini. Four Bn receptor antagonists had a higher affinity for the GRP subtype ([D-Phe6]Bn-(6-13)ethyl ester (500 x), [D-Phe6][psi 13-14,Cpa14]Bn- (6-14) (70 x) (where psi 13-14 refers to the replacement of the -CONH- peptide bond between Leu13 and Met14 by -CH2NH2) [psi 13-14,Leu14]Bn, [D-Phe6]Bn-(6-13) propylamide (30 x)] and two had a higher affinity for the NMB subtype on C-6 cells and transfected cells ([D-Pro4,D-Trp7,9,10] substance P-(4-11) (9 x) and [Tyr4,D-Phe12]Bn (18 x)]. In C-6 tumour cells, Bn receptor agonists caused an increase in cytosolic Ca2+ and the generation of inositol phosphates. For both responses, NMB was more than 50-fold more potent than GRP. Neither NMB nor GRP increased cyclic AMP. These results demonstrate that the rat glioblastoma cell line C-6 possesses functional NMB-preferring Bn receptors, and agonist occupation activates phospholipase C, thus increasing cytosolic Ca2+ and inositol phosphate formation. Because the interaction of Bn-related peptides with C-6 cell receptors is identical with that reported in other tissues containing the mRNA for the NMB subtype, this cell line should prove useful in exploring further the cellular basis of action of the peptides that interact with this receptor in the central nervous system and various other tissues.
Genetic analysis of a temperature-sensitive Salmonella typhimurium rho mutant with an altered rho-associated polycytidylate-dependent adenosine triphosphatase activity (1981)

A conditional-lethal rho mutant of Salmonella typhimurium LT2 has been isolated. The mutation was selected as a suppressor of the polarity of an insertion sequence (IS)2-induced mutation (gal3) carried on an F' plasmid. In addition to suppression of IS2-induced polarity, the rho-111 mutation suppressed nonsense and frameshift polarity. The rho-associated polycytidylic acid-dependent adenosine triphosphatase activity in the mutant strain was elevated 15-fold above that in the parental strain, and the mutant rho protein was thermally unstable. A temperature-resistant revertant of the mutant strain did not suppress polarity and contained normal levels of polycytidylic acid-dependent adenosine triphosphatase, suggesting that the phenotype of the rho-111-bearing strain is the consequence of a single mutation. The rho-111 mutation was located on the S. typhimurium linkage map midway between the ilv and cya loci by phage P22 cotransduction studies. F' plasmid maintenance was not impaired in the mutant strain, and the mutation was recessive to the wild-type allele. The rho-111 mutation did not alter in vivo expression of either the tryptophan or histidine operons.
Lung perfusion measured using magnetic resonance imaging: New tools for physiological insights into the pulmonary circulation (2010)

Since the lung receives the entire cardiac output, sophisticated imaging techniques are not required in order to measure total organ perfusion. However, for many years studying lung function has required physiologists to consider the lung as a single entity: in imaging terms as a single voxel. Since imaging, and in particular functional imaging, allows the acquisition of spatial information important for studying lung function, these techniques provide considerable promise and are of great interest for pulmonary physiologists. In particular, despite the challenges of low proton density and short T2* in the lung, noncontrast MRI techniques to measure pulmonary perfusion have several advantages including high reliability and the ability to make repeated measurements under a number of physiologic conditions. This brief review focuses on the application of a particular arterial spin labeling (ASL) technique, ASL-FAIRER (flow sensitive inversion recovery with an extra radiofrequency pulse), to answer physiologic questions related to pulmonary function in health and disease. The associated measurement of regional proton density to correct for gravitational-based lung deformation (the "Slinky" effect (Slinky is a registered trademark of Pauf-Slinky incorporated)) and issues related to absolute quantification are also discussed.