gebhart/patrepeval huggingface dataset:
Anomaly-based bug prediction, isolation, and validation (2009)

Software defects, commonly known as bugs, present a serious challenge for system reliability and dependability. Once a program failure is observed, the debugging activities to locate the defects are typically nontrivial and time consuming. In this paper, we propose a novel automated approach to pin-point the root-causes of software failures. Our proposed approach consists of three steps. The first step is bug prediction, which leverages the existing work on anomaly-based bug detection as exceptional behavior during program execution has been shown to frequently point to the root cause of a software failure. The second step is bug isolation, which eliminates false-positive bug predictions by checking whether the dynamic forward slices of bug predictions lead to the observed program failure. The last step is bug validation, in which the isolated anomalies are validated by dynamically nullifying their effects and observing if the program still fails. The whole bug prediction, isolation and validation process is fully automated and can be implemented with efficient architectural support. Our experiments with 6 programs and 7 bugs, including a real bug in the gcc 2.95.2 compiler, show that our approach is highly effective at isolating only the relevant anomalies. Compared to state-of-art debugging techniques, our proposed approach pinpoints the defect locations more accurately and presents the user with a much smaller code set to analyze.
Tissue Engineering of Nearly Transparent Corneal Stroma (2005)

We determined whether a polyglycolic acid (PGA) scaffold bearing an adherent corneal stromal cell insert could be integrated into the ultrastructure of rabbit corneal stroma without compromising tissue transparency. Stromal cells were isolated from 10 newborn rabbits and expanded by tissue culture. After reaching confluence, the cells were harvested and mixed with nonwoven PGA fibers to form cell-scaffold constructs. After 1 week of culturing, they were implanted into the corneal stroma of female rabbit recipients. Green fluorescent protein (GFP) expression in transplanted corneal stromal cells was monitored at the protein level to determine cellular origin in the reconstructed stroma. Eight weeks after implantation, transmission electron microscopy and histological evaluation were performed on stromal tissue. Insertion of PGA scaffold alone served as a sham control. After stromal implantation, implants gradually became transparent over an 8-week period. During this time stromal histology was gradually restored, as collagen fibril organization approached that of their normal counterpart. GFP-labeled corneal stromal cells were preponderant in the regions bearing inserted scaffolds, suggesting that they were derived from the implants rather than from neighboring corneal stromal cells. No reconstructed stroma developed in regions where naked PGA was implanted instead. We conclude that intrastromal implantation of PGA fiber scaffold implants bearing corneal stromal cells is a useful procedure for corneal stromal tissue reconstruction because, over an 8-week period, the implants become progressively more transparent. Marked losses of translucence during this period combined with restoration of ultrastructure indicate that the implants provide the functions needed for deturgescing initially swollen stroma.
The Impact of Deep Hierarchical Discourse Structures in the Evaluation of Text Coherence (2014)

Previous work by Lin et al. (2011) demonstrated the effectiveness of using discourse relations for evaluating text coherence. However, their work was based on discourse relations annotated in accordance with the Penn Discourse Treebank (PDTB) (Prasad et al., 2008), which encodes only very shallow discourse structures; therefore, they cannot capture long-distance discourse dependencies. In this paper, we study the impact of deep discourse structures for the task of co-herence evaluation, using two approaches: (1) We compare a model with features derived from discourse relations in the style of Rhetorical Structure Theory (RST) (Mann and Thompson, 1988), which annotate the full hierarchical discourse structure, against our re-implementation of Lin et al.’s model; (2) We compare a model encoded using only shallow RST-style discourse relations, against the one encoded using the complete set of RST-style discourse relations. With an evaluation on two tasks, we show that deep discourse structures are truly useful for better dif-ferentiation of text coherence, and in general, RST-style encoding is more powerful than PDTB-style encoding in these settings. 1
The relative contributions of stereo, lighting, and background scenes in promoting 3D depth visualization (1999)

More powerful contemporary computer hardware has enabled the development and exploration of a wide variety of techniques to depict spatial characteristics of computer-generated objects in three-dimensional (3D) space. Particularly, the role of stereoscopic viewing and the use of object motion to reflect the position and size of objects in 3D space have been extensively studied. However, the effective use of computer-rendered object shadows to provide spatial information about the relative position and size of objects in virtual space has not. Subjects perform two tasks with 3D geometric patterns of objects presented on a computer screen: (1) positioning the object to complete a symmetrical geometric figure and (2) resizing the object to match the size of other objects. Performance accuracy and speed are recorded under the following conditions: (1) objects casting shadows on and off, (2) shadows from one or two light sources (nested within the shadows-on condition), (3) stereoscopic and monoscopic viewing, and (4) different scene backgrounds: flat plane (i.e., floor), "stair-step" floor with no walls, and floor with walls (i.e., room). The use of object shadows as depth cues enhances the accuracy (but not the speed) of object positioning, but does not enhance either the accuracy or the speed of object resizing. Moreover, the object shadows are not as effective as stereoscopic viewing in facilitating both positioning-task and resizing-task performances. Furthermore, task performances degrade with the stair-step scene background and when the number of shadowing light sources increases from one to two.
Optimizing delayed branches (1982)

Delayed branches are commonly found in micro-architectures. A compiler or assembler can exploit delayed branches. This is achieved by moving code from one of several points to the positions following the branch instruction. We present several strategies for moving code to utilize the branch delay, and discuss the requirements and benefits of these strategies. An algorithm for processing branch delays has been implemented and we give empirical results. The performance data show that a reasonable percentage of these delays can be avoided.
Is Fluoride Bonded to Two Pd Acceptors Still Basic? Three CH2Cl2 Molecules Encapsulating a Pd2(μ-F)2 Square and New Implications for Catalysis (2002)

The unexpectedly high basicity of bridging fluoride ions in novel dinuclear Pd complexes is manifested by intramolecular CH⋅⋅⋅F interactions and the unprecedented hydrogen bonding of three CH2Cl2 molecules to the Pd2F2 framework (see scheme). Novel deprotonation of a coordinated (alkyl)3P ligand to produce a bifluoride is reported.
Discontinuation of Secondary Prophylaxis for Cryptococcal Meningitis in Human Immunodeficiency Virus–Infected Patients Treated with Highly Active Antiretroviral Therapy: A Prospective, Multicenter, Randomized Study (2003)

A prospective, multicenter, randomized study was conducted with human immunodeficiency virus (HIV)-infected patients who were successfully treated for acute cryptococcal meningitis, were receiving secondary prophylaxis, and were naive for antiretroviral therapy. Patients were randomized to continue or discontinue secondary prophylaxis when the CD4 cell count had increased to >100 cells/microL and an undetectable HIV RNA level had been sustained for 3 months. At a median of 48 weeks after randomization, there were no episodes of cryptococcal meningitis in either group.
Mammalian transglutaminases (2005)

Transglutaminases form a large family of intracellular and extracellular enzymes that catalyse the Ca2+-dependent post-translational modification of proteins. Despite significant advances in our understanding of the biological role of most mammalian transglutaminase isoforms, recent findings suggest new scenarios, most notably for the ubiquitous tissue transglutaminase. It is becoming apparent that some transglutaminases, normally expressed at low levels in many tissue types, are activated and/or overexpressed in a variety of diseases, thereby resulting in enhanced concentrations of cross-linked proteins. As applies to all enzymes that exert their metabolic function by modifying the properties of target proteins, the identification and characterization of the modified proteins will cast light on the functions of transglutaminases and their involvement in human diseases. In this paper we review data on the properties of mammalian transglutaminases, particularly as regards their protein substrates and the relevance of transglutaminase-catalysed reactions in physiological and disease conditions.
The wheat wcs120 promoter is cold‐inducible in both monocotyledonous and dicotyledonous species (1998)

The wcs120 gene is specifically induced by low temperature (LT) and encodes a protein that is thought to play an important role in the cold acclimation process in wheat. To identify the regulatory elements involved in its LT responsiveness, the transient expression activity of different promoter regions was determined using the luciferase reporter gene. The data indicate the involvement of putative enhancer elements, negative and positive regulatory regions in the transcriptional regulation of this gene. The promoter was found to be cold-inducible in different freezing-tolerant and -sensitive monocot and dicot species, suggesting that universal transcription factors responsive to LT may be present in all plants. This promoter could be used to drive the genes needed for LT tolerance in sensitive species.
Vibrating-mesh nebulization of liposomes generated using an ethanol-based proliposome technology (2010)

This is the first study that evaluates the influence of the compartmental design of the micropump Aeroneb Go nebulizer and the viscosity of a proliposome hydration medium on vibrating-mesh aerosolization of liposomes. Ethanol-based proliposomes comprising soya phosphatidylcholine and cholesterol (1:1 mole ratio) were hydrated by using isotonic NaCl (0.9%) or sucrose (9.25%) solutions to generate liposomes that entrapped approximately 61% of the hydrophilic drug, salbutamol sulphate. Liposomes were aerosolized by the nebulizer to a two-stage impinger. For both formulations, the aerosol mass output was higher than the phospholipid output, indicating some accumulation of large liposomes or liposome aggregate within the nebulizer. Using NaCl (0.9%) solution as the dispersion medium, aerosol droplet size was much smaller and aerosol mass and phospholipid outputs were higher. This was attributed to the lower viscosity of the NaCl solution, resulting in a reduced retention of the aerosols in the "trap" of the nebulizer. For the entrapped salbutamol sulphate, although the "fine particle fraction" was relatively high (57.44%), size reduction of the liposomes during nebulization caused marked losses of the drug originally entrapped. Overall, liposomes generated from proliposomes when using this nebulizer showed high nebulization output and small droplet size. However, further work is required to reduce the losses of the originally entrapped drug from liposomes.
269. Integrated CD28 and 4-1BB Signals Strongly Potentiate CD8+ T Cell Mediated radication of Metastatic Prostate Cancer (2006)

Immune-mediated tumor eradication requires the adequate expansion, trafficking and intra-tumoral activation of tumor antigen- specific T cells. Suboptimal T cell activation results in anergy and apoptosis, thereby aborting effective tumor immunity. To avoid these pitfalls, tumor-specific T cells must be given optimal activating signals at the time of antigen priming and restimulation. It is not clear, however, what costimulatory ligands or combinations thereof are best suited to achieve tumor eradication, what activating mechanisms are redundant, antagonistic or additive, nor how to most effectively provide T cell costimulation in a clinically relevant fashion.
Neurospora wc-1 and wc-2 : Transcription, Photoresponses, and the Origins of Circadian Rhythmicity (1997)

Circadian rhythmicity is universally associated with the ability to perceive light, and the oscillators ("clocks") giving rise to these rhythms, which are feedback loops based on transcription and translation, are reset by light. Although such loops must contain elements of positive and negative regulation, the clock genes analyzed to date-frq in Neurospora and per and tim in Drosophila-are associated only with negative feedback and their biochemical functions are largely inferred. The white collar-1 and white collar-2 genes, both global regulators of photoresponses in Neurospora, encode DNA binding proteins that contain PAS domains and are believed to act as transcriptional activators. Data shown here suggest that wc-1 is a clock-associated gene and wc-2 is a clock component; both play essential roles in the assembly or operation of the Neurospora circadian oscillator. Thus DNA binding and transcriptional activation can now be associated with a clock gene that may provide a positive element in the feedback loop. In addition, similarities between the PAS-domain regions of molecules involved in light perception and circadian rhythmicity in several organisms suggest an evolutionary link between ancient photoreceptor proteins and more modern proteins required for circadian oscillation.
Cystic fibrosis: progress in mapping the disease locus using polymorphic DNA markers. I. (1985)

The conventional approach to the identification of the affected gene in inherited diseases is through the demonstration of specific biochemical abnormalities in patients, their tissues, or cells. This approach has, unfortunately, been unsuccessful in the case of cystic fibrosis (CF), the most common severe autosomal recessive disorder in Causasians. An alternative approach is to locate the CF gene by linkage studies with chromosomal markers. We report here our results of testing 39 DNA restriction fragment length polymorphic (RFLP) markers using a panel of 45 two-generation Canadian families each with two or more affected children. The probability of linkage between each marker and CF was analyzed by the lod score method using the LIPED program. The results of these analyses show that none of the markers tested is closely linked to the disease locus.
The Pseudomonas syringae pv. syringae 61 hrpH product, an envelope protein required for elicitation of the hypersensitive response in plants (1992)

Pseudomonas syringae pv. syringae 61 contains a 25-kb cluster of hrp genes that are required for elicitation of the hypersensitive response (HR) in tobacco. TnphoA mutagenesis of cosmid pHIR11, which contains the hrp cluster, revealed two genes encoding exported or inner-membrane-spanning proteins (H.-C. Huang, S. W. Hutcheson, and A. Collmer, Mol. Plant-Microbe Interact. 4:469-476, 1991). The gene in complementation group X, designated hrpH, was subcloned on a 3.1-kb SalI fragment into pCPP30, a broad-host-range, mobilizable vector. The subclone restored the ability of hrpH mutant P. syringae pv. syringae 61-2089 to elicit the HR in tobacco. DNA sequence analysis of the 3.1-kb SalI fragment revealed a single open reading frame encoding an 81,956-Da preprotein with a typical amino-terminal signal peptide and no likely inner-membrane-spanning hydrophobic regions. hrpH was expressed in the presence of [35S]methionine by using the T7 RNA polymerase-promoter system and vector pT7-3 in Escherichia coli and was shown to encode a protein with an apparent molecular weight of 83,000 on sodium dodecyl sulfate-polyacrylamide gels. The HrpH protein in E. coli was located in the membrane fraction and was absent from the periplasm and cytoplasm. The HrpH protein possessed similarity with several outer membrane proteins that are known to be involved in protein or phage secretion, including the Klebsiella oxytoca PulD protein, the Yersinia enterocolitica YscC protein, and the pIV protein of filamentous coliphages. All of these proteins possess a possible secretion motif, GG(X)12VP(L/F)LXXIPXIGXL(F/L), near the carboxyl terminus, and they lack a carboxyl-terminal phenylalanine, in contrast to other outer membrane proteins with no known secretion function. These results suggest that the P. syringae pv. syringae HrpH protein is involved in the secretion of a proteinaceous HR elicitor.
Chronic Stimulation of Glucose Transporter Gene Expression in L6 Myocytes Mediated via the Insulin-like Growth Factor-1 Receptor (1989)

We have used differentiated L6 myocytes to investigate the regulation of glucose transporter gene expression by insulin and insulin-like growth factor-1 (IGF-1). Chronic exposure to insulin (1 microM) or IGF-1 (10 nm) resulted in a 2- to 5-fold stimulation of 3H-2-deoxy-D-glucose uptake and a corresponding increase in the expression of rat brain/HepG2-type glucose transporter mRNA (GTmRNA) and immunoreactive transporter protein. The dose responses to both insulin and IGF-1 for stimulation of glucose uptake were paralleled by the expression of GTmRNA. Glucose uptake and GTmRNA levels were half maximally stimulated by 350 and 100 nM insulin, respectively, or by 2 nM IGF-1. Comparison of receptor occupancy with stimulation of glucose uptake and GTmRNA expression suggests that insulin exerts its effects through the IGF-1 receptor. Fibroblast growth factor, epidermal growth factor, platelet-derived growth factor, and phorbol ester had little or no effect on GTmRNA expression. These results demonstrate that the IGF-1 receptor mediates chronic regulation of transporter mRNA expression and protein synthesis and activity in cultured rat muscle cells.
Gremlin is a novel agonist of the major proangiogenic receptor VEGFR2 (2010)

The bone morphogenic protein antagonist gremlin is expressed during embryonic development and under different pathologic conditions, including cancer. Gremlin is a proangiogenic protein belonging to the cystine-knot superfamily that includes transforming growth factor-β proteins and the angiogenic vascular endothelial growth factors (VEGFs). Here, we demonstrate that gremlin binds VEGF receptor-2 (VEGFR2), the main transducer of VEGF-mediated angiogenic signals, in a bone morphogenic protein-independent manner. Similar to VEGF-A, gremlin activates VEGFR2 in endothelial cells, leading to VEGFR2-dependent angiogenic responses in vitro and in vivo. Gremlin thus represents a novel proangiogenic VEGFR2 agonist distinct from the VEGF family ligands with implications in vascular development, angiogenesis-dependent diseases, and tumor neovascularization.
Degeneration of germ cells in normal, hypophysectomized and hormone treated hypophysectomized rats (1977)

In normal adult rats some germ cells degenerate at several vulnerable steps of spermatogenesis. These are the type A spermatogonia, midpachytene spermatocytes, primary and secondary spermatocytes which degenerate during their respective maturation divisions and step 7 and 19 spermatitids. In the present study, these degenerating cells were examined under the electron microscope, and their frequency was determined in toluidine blue stained semithin sections of testes from normal, hypophysectomized (at 5.5 days after operation) and hypophysectomized rats injected with FSH and LH separately or in combination. With the exception of the step 19 spermatids, the degenerating germ cells underwent necrosis in vacuolated spaces delimited by Sertoli cells. In the case of the affected step 19 spermatids, an apical cytoplasmic process of the Sertoli cell initially ensheathed a long segment of their flagellum, and then each degeneration cell was drawn deep in the seminiferous epithelium where it was phagocytozed by the Sertoli cell. Soon after hypophysectomy the incidence of degenerating mid-pachytene spermatocytes, step 7 and 19 spermatids which are present in stages VII or VIII of the cycle of the seminiferous epithelium, increased significantly. In contrast the number of degenerating primary or secondary spermatocytes during the meiotic divisions seen in stage XIV of the cycle or of any other germinal cell was not significantly modified. While the injection of FSH alone had no influence on the number of degenerating cells in hypophysectomized rats, injections of LH at the two doses administered (0.7 microng or 20 microng) reduced significantly the number of degenerating cells seen in stages VII-VIII of the cycle; combined injections of FSH and LH (20 microng) reduced the number of these degenerating cells to the normal low values. Thus it appeared that the mid-pachytene spermatocytes and the step 7 and 19 spermatids, all present in the adluminal compartment of the seminiferous epithelium in stages VII or VIII of the cycle, were more sensitive to the presence of absence of gonadotropic hormones than the other germ cells present in the seminiferous epithelium.
Distribution of radioactive and nonradioactive vitamin B 12 in normal and malignant tissues of an infant with neuroblastoma. (1972)

An infant with disseminated neuroblastoma was given radioactive vitamin B12 30, 21, and 9 days before he succumbed to the disease. The retention of radioactive vitamin B12 was determined by scanning the external hepatic area for radioactivity. At autopsy, the organs and tumors were obtained, cleaned, and weighed, and either the whole organ or a section was taken for analysis. The normal and malignant tissues were assayed for radioactivity and microbiologically for vitamin B12. Tumors associated with the liver, pancreas, and adrenals had considerably lower vitamin B12 concentrations and radioactivity retention than did adjacent normal tissue. Two large mediastinal tumors were also uniformly low in vitamin B12 concentration and radioactivity. Neuroblastoma cells can proliferate rapidly and presumably synthesize nucleic acids in the presence of low concentrations of vitamin B12. Results of the assays also revealed that normal liver contained by far the highest vitamin B12 concentration, the highest total vitamin B12 content, and the greatest retention of radioactivity of the organs studied. The liver contained 82.6 and 80.8%, respectively, of the total vitamin B12 and radioactivity recovered in the organs of the infant with neuroblastoma. The liver also contained 42% of the radioactive vitamin B12 retained by the infant. The distribution of this vitamin among the organs of this child differed considerably from that in most laboratory animals.