gebhart/patrepeval huggingface dataset:
A Novel Approach Based on Gestalt Psychology for Abstracting the Content of Large Execution Traces for Program Comprehension (2011)

The analysis of execution traces can reveal important information about the behavioral aspects of complex software systems, hence reducing the time and effort it takes to understand and maintain them. Traces, however, tend to be considerably large which hinders their effective analysis. Existing traces analysis tools rely on some sort of visualization techniques to help software engineers make sense of trace content. Many of these techniques have been studied and found to be limited in many ways. In this paper, we present a novel trace analysis technique that automatically divides the content of a large trace into meaningful segments that correspond to the program's main execution phases such as initializing variables, performing a specific computation, etc. These phases can simplify significantly the exploration of large traces by allowing software engineers to first understand the content of a trace at a high-level before they decide to dig into the details. Our phase detection method is inspired by Gestalt laws that characterize the proximity, similarity, and continuity of the elements of a data space. We model these concepts in the context of execution traces and show how they can be used as gravitational forces that yield the formation of dense groups of trace elements, which indicate candidate phases. We applied our approach to two software systems. The results are very promising.
Altitude correction for hemoglobin. (1994)

The striking parallelism between the hypoxia-induced hemoglobin increase with altitude in young children (girls and boys) and that in male adults strongly suggests that the proposed correction factors for Hb are applicable for all ages and possibly both genders, at least in the Andes.
Applied inter-working in DRiVE: a next generation multi-access approach (2005)

During the last few years a tremendous increase in the number of mobile computers, in conjunction with the growth of wireless services, makes supporting Internet mobility important. Mobile users need to switch between networks in different administrative domains and between different types of access system as they move around the network. By introducing the DRiVE/sup /spl phi// system, a generic IPv6 backbone, based on Mobile IPv6 (MIPv6), extended to Hierarchical Mobile IPv6 (HMIPv6) improves the interworking connectivity. DRiVE is a hybrid system that integrates different access technologies into a common IPv6 network. The objectives of the DRiVE project are to develop and co-ordinate dynamic spectrum allocation, asymmetric usage of traffic and interworking of different radio access systems. The extension of MIPv6 to HMIPv6 opens a new path for reducing user signalling, minimising frequent address allocation and decreasing the number of "observable" inter-system handovers. The HMIPv6 introduces a new function, the so-called mobility anchor point (MAP). The MAP operates as a "virtual" home agent (HA), ie, intercepts packets addressed to the MAP destined to the mobile node's home address, encapsulates them, and tunnels them over the interconnected access system to the mobile node's registered care-of address. This paper describes several topics covered in the DRiVE system of which two scenarios: (1) registration, and (2) traffic routing are emphasised.
PchR, a regulator of ferripyochelin receptor gene (fptA) expression in Pseudomonas aeruginosa, functions both as an activator and as a repressor (1996)

The product of the pchR gene, an AraC-like regulatory protein, is required for production of the FptA ferric pyochelin receptor in response to iron limitation and pyochelin (D. E. Heinrichs and K. Poole, J. Bacteriol. 175:5882-5889, 1993). The influence of iron, pyochelin, PchR, and FptA on fptA and pchR gene expression was assessed with fptA-lacZ and pchR-lacZ transcriptional fusions. As was expected, the expression of fptA decreased dramatically following the inactivation of pchR by the insertion of an OmegaHg cartridge, although the effect (> 10-fold) was not as dramatic as that of pyochelin deficiency, which obviated fptA gene expression. Insertional inactivation of pchR in a pyochelin-deficient (Pch-) background restored fptA expression to levels observed in the pyochelin-producing (Pch+) PchR- strain, suggesting that PchR represses fptA expression in the absence of pyochelin. Consistent with this, the cloned gene caused a five-fold decrease in the expression of the fptA-lacZ fusion in Escherichia coli. pchR gene expression was inducible by iron limitation, a result in agreement with the previous identification of a Fur box upstream of the gene, although the magnitude of the induction was less than that observed for fptA in response to iron limitation. Expression of pchR was effectively absent in a pyochelin-deficient strain, and insertional inactivation of pchR in a Pch+ or Pch- background caused an increase in pchR gene expression. PchR, thus, negatively regulates its own expression. Two related heptameric sequences, CGAGGAA and CGTGGAT, were identified upstream of the putative -35 region of both fptA and pchR and may function as a binding site for PchR. Insertional inactivation of fptA caused a marked decrease in fptA expression in a Pch+ background and obviated the apparent repression of fptA expression in a Pch- background, reminiscent of the effect of a pchR mutation. The fptA mutant did not, however, exhibit a defect in pchR expression. Interestingly, fptA mutants were unable to grow in the presence of pyochelin, suggesting that FptA is the sole outer membrane receptor for ferric pyochelin. These data indicate that PchR functions as both an activator and a repressor in controlling the expression of fptA and pchR. The involvement of FptA in this control is unclear, although it may be important in mediating the pyochelin effect on fptA expression, possibly by modulating PchR activity.
Renal expression of IL-6 and TNFα genes in lupus nephritis (1998)

These studies were carried out to examine the presence of the inflammatory cytokines IL-6 and TNFalpha in kidneys of patients with lupus nephritis as an indicator of their possible role in its pathogenesis. A total of 19 kidney biopsies from patients with type III or IV lupus nephritis were processed by direct immunofluorescence using monoclonal anti-IL-6 and TNFalpha antibodies. Local expression of these genes was demonstrated both by in situ hybridization and by reverse transcriptase-PCR amplification of total RNA isolated from kidney tissue. Fifty-two percent of the biopsies exhibited IL-6 and TNFalpha deposited along the glomeruli and tubules; in situ expression of these cytokines was demonstrated in 6 biopsies with type IV, and 1 with type III nephritis. Inflammatory cytokines are actively synthesized in the kidneys of patients with lupus nephritis and therefore, may play a role in its pathogenesis.
Test suite reduction for fault detection and localization: A combined approach (2014)

The relation of test suites and actual faults in a software is of critical importance for timely product release. There are two particularily critical properties of test suites to this end: fault localization capability, to characterize the effort of finding the actually defective program elements, and fault detection capability which measures how probable is their manifestation and detection in the first place. While there are well established methods to predict fault detection capability (by measuring code coverage, for instance), characterization of fault localization is an emerging research topic. In this work, we investigate the effect of different test reduction methods on the performance of fault localization and detection techniques. We also provide new combined methods that incorporate both localization and detection aspects. We empirically evaluate the methods first by measuring detection and localization metrics of test suites with various reduction sizes, followed by how reduced test suites perform with actual faults. We experiment with SIR programs traditionally used in fault localization research, and extend the case study with large industrial software systems including GCC and WebKit.
Efficient Opportunistic Sensing using Mobile Collaborative Platform MOSDEN (2013)

Mobile devices are rapidly becoming the primary computing device in people’s lives. Application delivery platforms like Google Play, Apple App Store have transformed mobile phones into intelligent computing devices by the means of applications that can be downloaded and installed instantly. Many of
Intragenic<i>GNAS</i>Deletion Involving Exon A/B in Pseudohypoparathyroidism Type 1A Resulting in an Apparent Loss of Exon A/B Methylation: Potential for Misdiagnosis of Pseudohypoparathyroidism Type 1B (2009)

We discovered a novel multiexonic GNAS deletion transmitted to our patient from her mother who is mosaic for this mutation. The deletion led to different phenotypic manifestations in the two generation and appeared, in the patient, as loss of GNAS imprinting.
Efficient SERS substrates made by electroless silver deposition into patterned silicon structures (2004)

A nano fabrication process using caesium chloride in an island lithography scheme has been used to make wells in a silicon dioxide layer on silicon. Silver structures have been made in these wells using an electroless process that involves the reduction of silver ions and oxidation of silicon in the presence of fluoride ions. The silver deposition process is found to be diffusion controlled. The "electroless" solution composition determines the structure of the deposited silver. Thus structures can be generated that resemble a torus or a pillar or a small set of spheres. The torus structure was found to give SERS signals for pyridine about 100 times higher than other reported structures. The stability of the torus structure in pure water is limited, and it is therefore necessary to store these structures in alkaline media or with an adsorbate layer as a protector, so making long-term active substrate storage possible. The free energy difference that drives the conversion of tori to pillars has its origin in the excess surface energy, determined by the surface curvature.
Malignant Mixed Müllerian Tumor of the Uterus. Features Favoring its Origin from a Common Cell Clone and an Epithelial-to-Mesenchymal Transformation Mechanism of Histogenesis (1998)

A similar immunoreactivity for p53 in both carcinomatous and sarcomatous components, expression of epithelial markers in the sarcomatous cells, and disruption of the basement membrane profile in areas of transition between carcinomatous and sarcomatous tissue, would all suggest, as has been postulated for extragenital sarcomatoid carcinomas, an origin from a common epithelial clone and an epithelial-to-mesenchymal transformation-based mechanism of development for this MMMT. In addition, these findings provide further analogies between these categories of tumors, supporting a unifying nosological concept for MMMTs and sarcomatoid carcinomas of non-genital tract origin.
Collapse and Burst Test Methods for Sand Screens (2008)

Abstract This paper will review the test methods advocated in the draft of the ISO Sand Control Screens (SCS) that is scheduled to go to ballot in 2009. In early 2004, a task group was formed to develop the initial ISO SCS standard that covers the use of conventional screens in oil/gas wells. A key part of the draft is two test methods developed to determine the performance rating for the collapse or burst resistance of a conventional sand screen assembly. Included in the draft are definitions of product design families, and the scaling methods that can be used. While the draft was being formed, the service companies have conducted periodic collapse or burst tests to provide performance ratings on specific products. Many of these tests were conducted using the methods outlined in the draft. The test methods are valid approaches to simulate a collapse or burst load that can be applied to a sand screen during well development or production. This paper will present test results of over sixty collapses and burst tests, and will summarize lessons learned about the test methods. Many applications for oil/gas wells may require high collapse or burst ratings for the screens. Even in seemingly low pressure applications, completion problems many require higher collapse or burst resistance than anticipated, and the screen must not fail or the well could be lost. The ISO SCS draft establishes test methods for conventional sand screens that will provide the operators with reliable ratings for collapse and burst resistance.
The chicken lysozyme chromatin domain contains a second, widely expressed gene (2002)

The chicken lysozyme (cLys) locus has been shown to contain all of the cis-elements necessary for position-independent and tissue-specific expression entirely within a 24-kb region defined by general DNase I sensitivity and flanked by matrix attachment regions. As such, it has been viewed as an example of a functional chromatin domain, which is structurally and functionally isolated from neighbouring chromatin. We report here the identification and characterisation of the chicken glioma-amplified sequence (cGas41) locus, which though widely expressed, is contained entirely within the lysozyme chromatin domain. The cGas41 transcript encodes a putative transcription factor, starts 207 bp downstream of the cLys polyadenylation site and is preceded by a CpG island with proposed dual promoter/origin function. The location and differential expression of cGas41 compels re-evaluation of the accumulated literature on the lysozyme domain, and represents an example of two unrelated, differentially expressed vertebrate genes coexisting in the same functional chromatin domain.
Experimental Studies on the Selective β-C–H Halogenation of Enones (2015)

Here we describe the realization of a one-pot protocol for the β-C-H halogenation of cyclic enones via umpolung of the β-carbon. The developed method includes hydrazone formation and selective β-halogenation (bromination, chlorination) with N-bromosuccinimide and Palau'chlor (2-chloro-1,3-bis(methoxycarbonyl)guanidine) followed by hydrolysis of the hydrazone moiety. Using the optimized conditions, we were able to effectively β-brominate and β-chlorinate for the first time cyclic enones with different substitution patterns and various functional groups in one flask, whereas previous methods for this transformation required several steps. Additionally, the utility of the method was demonstrated in a short synthesis of the core structure of the Aspidosperma alkaloid jerantinine E.
Relief mapping of non-height-field surface details (2006)

The ability to represent non-height-field mesostructure details is of great importance for rendering complex surface patterns, such as weave and multilayer structures. Currently, such representations are based on the use of 3D textures or large datasets of sampled data. While some of the 3D-texture-based approaches can achieve interactive performance, all these approaches require large amounts of memory. We present a technique for mapping non-height-field structures onto arbitrary polygonal models in real time, which has low memory requirements. It generalizes the notion of relief mapping to support multiple layers. This technique can be used to render realistic impostors of 3D objects that can be viewed from close proximity and from a wide angular range. Contrary to traditional impostors, these new one-polygon representations can be observed from both sides, producing correct parallax and views that are consistent with the observation of the 3D geometry they represent.
Triglyceride-lowering Effect of Dietary Vitamin E in Streptozocin-induced Diabetic Rats: Increased Lipoprotein Lipase Activity in Livers of Diabetic Rats Fed High Dietary Vitamin E (1986)

High vitamin E supplementation in the diets of streptozocin-induced diabetic rats eliminates accumulation of lipid peroxides in the plasma and the liver, returns the plasma triglycerides toward normal levels, and increases the activity of lipoprotein lipase. Vitamin E has no effect on the levels of insulin or glucose. These findings suggest that vitamin E increases the total hepatic triglyceride lipase activity by increasing the lipoprotein lipase activity possibly by protecting the membrane-bound lipase against peroxidative damage.
Isolation of animal cell mutants deficient in plasmalogen biosynthesis and peroxisome assembly. (1986)

A rapid autoradiographic screening procedure has been developed for identifying Chinese hamster ovary cell mutants defective in the peroxisomal enzyme dihydroxyacetonephosphate (DHAP) acyltransferase. Ten mutants were found among 60,000 colonies grown from a stock of mutagen-treated cells, and 3 have been characterized with respect to their enzymology and phospholipid biosynthesis. All three contain 3% (or less) of the parental DHAP acyltransferase activity measured at pH 5.5, the optimum for the peroxisomal enzyme. When measured at pH 7.4, all three contained 70-85% of the wild-type activity, but it was sensitive to N-ethylmaleimide. Glycerol-3-phosphate acyltransferase activities were identical in mutant and parent strains. Two other peroxisomal enzymes, alkyl-DHAP synthase and particulate catalase, were also reduced by factors of 5-10 in all three mutants, suggesting that these strains are deficient in some aspect of peroxisome assembly, possibly like cells from patients with Zellweger syndrome. Short-term and long-term labeling with 32Pi revealed that these mutants are grossly deficient in the de novo synthesis and content of plasmalogens. In parental cells the plasmalogen form of phosphatidylethanolamine constitutes 7.1% of the total phospholipid, but it is reduced to 0.7% in the mutants. This decrease is accompanied by a compensatory increase in the diacyl form of phosphatidylethanolamine. The results presented here support the view that there are two DHAP acyltransferases in animal cells and that the peroxisome is essential for the biosynthesis of plasmalogens.
Isolation of a New Homeobox Gene Belonging to the Pitx/Rieg Family: Expression During Lens Development and Mapping to the Aphakia Region on Mouse Chromosome 19 (1997)

We recently reported the positional cloning of a homeobox gene involved in the pathogenesis of Rieger syndrome, RIEG1 , and its mouse homolog, Rieg1 . Rieg1 (also independently described as Pitx2) is highly homologous to the Ptx1/Potx gene product, suggesting that there may be additional members of this novel Pitx family. The Pitx genes play an important role in eye, tooth, pituitary and umbilical region development as evidenced by Rieger syndrome and iris hypoplasia phenotypes, resulting from mutations in the RIEG1 gene and by expression studies. In order to characterize further the Pitx gene family we searched mouse cDNA libraries to identify additional members. A new gene was isolated which encodes a homeoprotein with strong homology to the other Pitx proteins and 97-100% identity in the homeodomain itself, suggesting that this is a third member of the family, Pitx3 . In whole mount in situ hybridization on mouse embryos ranging from 8.5 to 11.5 days post-coitum (d.p.c.), Pitx3 mRNA was seen only in the developing lens starting at day 11. Hybridization on cross-sections revealed strong signals in the lens vesicle in 11 d.p.c. embryos and throughout the lens, particularly in the anterior epithelium and equator region in 15 d.p.c. embryos. Pitx3 was mapped close to aphakia on mouse chromosome 19. The aphakia homozygous mouse is characterized by small eyes lacking a lens, which fail to develop beyond 11 d.p.c. These data make Pitx3 a strong candidate gene for the aphakia phenotype in the mouse and suggest a role for the human homolog in congenital lens malformations.
Reversible Fiber-Optic Fluorosensing of Lower Alcohols (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReversible Fiber-Optic Fluorosensing of Lower AlcoholsGuillermo. Orellana, Ana M. Gomez-Carneros, Cesar. de Dios, Ana A. Garcia-Martinez, and Maria C. Moreno-BondiCite this: Anal. Chem. 1995, 67, 13, 2231–2238Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://pubs.acs.org/doi/10.1021/ac00109a050https://doi.org/10.1021/ac00109a050research-articleACS PublicationsRequest reuse permissionsArticle Views213Altmetric-Citations42LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cloning and characterization of a gene (UVR3) required for photorepair of 6-4 photoproducts in Arabidopsis thaliana (1998)

UV radiation induces two major classes of pyrimidine dimers: the pyrimidine [6-4] pyrimidone photoproduct (6-4 product) and the cyclobutane pyrimidine dimer (CPD). Many organisms produce enzymes, termed photolyases, that specifically bind to these damage products and split them via a UV-A/blue light-dependent mechanism, thereby reversing the damage. These photolyases are specific for either CPDs or 6-4 products. A gene that expresses a protein with 6-4 photolyase activity in vitro was recently cloned from Drosophila melanogaster and Xenopus laevis. We report here the isolation of a homolog of this gene, cloned on the basis of sequence similarity, from the higher plant Arabidopsis thaliana. This cloned gene produces a protein with 6-4 photolyase activity when expressed in Escherichia coli. We also find that a previously described mutant of Arabidopsis (uvr3) that is defective in photoreactivation of 6-4 products carries a nonsense mutation in this 6-4 photolyase homolog. We have therefore termed this gene UVR3. Although homologs of this gene have previously been shown to produce a functional 6-4 photolyase when expressed in heterologous systems, this is the first demonstration of a requirement for this gene for photoreactivation of 6-4 products in vivo.
Neovascularization in Tissue Engineering (2012)

A prerequisite for successful tissue engineering is adequate vascularization that would allow tissue engineering constructs to survive and grow. Angiogenic growth factors, alone and in combination, have been used to achieve this, and gene therapy has been used as a tool to enable sustained release of these angiogenic proteins. Cell-based therapy using endothelial cells and their precursors presents an alternative approach to tackling this challenge. These studies have occurred on a background of advancements in scaffold design and assays for assessing neovascularization. Finally, several studies have already attempted to translate research in neovascularization to clinical use in the blossoming field of therapeutic angiogenesis.