gebhart/patrepeval huggingface dataset:
KLEE: unassisted and automatic generation of high-coverage tests for complex systems programs (2008)

We present a new symbolic execution tool, KLEE, capable of automatically generating tests that achieve high coverage on a diverse set of complex and environmentally-intensive programs. We used KLEE to thoroughly check all 89 stand-alone programs in the GNU COREUTILS utility suite, which form the core user-level environment installed on millions of Unix systems, and arguably are the single most heavily tested set of open-source programs in existence. KLEE-generated tests achieve high line coverage -- on average over 90% per tool (median: over 94%) -- and significantly beat the coverage of the developers' own hand-written test suite. When we did the same for 75 equivalent tools in the BUSYBOX embedded system suite, results were even better, including 100% coverage on 31 of them.We also used KLEE as a bug finding tool, applying it to 452 applications (over 430K total lines of code), where it found 56 serious bugs, including three in COREUTILS that had been missed for over 15 years. Finally, we used KLEE to crosscheck purportedly identical BUSYBOX and COREUTILS utilities, finding functional correctness errors and a myriad of inconsistencies.
Tissue Transglutaminase Facilitates the Polymerization of Insulin-like Growth Factor-binding Protein-1 (IGFBP-1) and Leads to Loss of IGFBP-1's Ability to Inhibit Insulin-like Growth Factor-I-stimulated Protein Synthesis (2001)

Insulin-like growth factor-binding protein-1 (IGFBP-1) binds to insulin-like growth factors (IGFs) and has been shown to inhibit or stimulate cellular responses to IGF-I in vitro. This capacity of IGFBP-1 to inhibit or stimulate IGF-I actions correlates with its ability to form stable high molecular weight multimers. Since the ability of some proteins to polymerize is dependent upon transglutamination, we determined if tissue transglutaminase could catalyze this reaction and the effect of polymerization of IGFBP-1 upon IGF-I action. Following incubation with pure tissue transglutaminase (Tg), IGFBP-1 formed covalently linked multimers that were stable during SDS-polyacrylamide gel electrophoresis using reducing conditions. Dephosphorylated IGFBP-1 polymerized more rapidly and to a greater extent compared with native (phosphorylated) IGFBP-1. Exposure to IGF-I stimulated transglutamination of IGFBP-1 in vitro. An IGFBP-1 mutant in which Gln(66)-Gln(67) had been altered to Ala(66)-Ala(67) (Q66A/Q67A) was relatively resistant to polymerization by Tg compared with native IGFBP-1. Tg localized in fibroblast membranes was also shown to catalyze the formation of native IGFBP-1 multimers, however, Q66A/Q67A IGFBP-1 failed to polymerize. Although the mutant IGFBP-1 potently inhibited IGF-I stimulated protein synthesis in pSMC cultures, the same concentration of native IGFBP-1 had no inhibitory effect. The addition of higher concentrations of native IGFBP-1 did inhibit the protein synthesis response, and this degree of inhibition correlated with the amount of monomeric IGFBP-1 that was present. In conclusion, IGFBP-1 is a substrate for tissue transglutaminase and Tg leads to the formation of high molecular weight covalently linked multimers. Polymerization is an important post-translational modification of IGFBP-1 that regulates cellular responses to IGF-I.
Long-term Branched-chain Amino Acid Supplementation Improves Glucose Tolerance in Patients with Nonalcoholic Steatohepatitis-related Cirrhosis (2012)

Branched-chain amino acid (BCAA) supplements have mainly been administered as a nutritional intervention for decompensated liver cirrhosis. Several studies have shown that short-term BCAA supplementation improves insulin and glucose tolerance in patients with liver cirrhosis. However, the long-term effects of BCAA supplementation on glucose tolerance and in patients with nonalcoholic steatohepatitis (NASH)-related liver cirrhosis are unknown. Herein, we report 2 cases of NASH-related liver cirrhosis in which long-term BCAA supplementation improved glycemic control. We conclude that in the absence of an effective conventional therapy for NASH-related liver cirrhosis, BCAA supplementation should be considered as an alternative treatment.
Fc-mediated immune precipitation. IV. Antigen dependency and specificity. (1983)

The antigen dependency of Fc-mediated immune precipitation was investigated by comparing the immune precipitation of three different protein antigens (bovine serum albumin, BSA, human plasma transferrin, HPT, and human fibrinogen, HFg) using specific intact rabbit IgG antibodies and isomolar solutions of the corresponding F(ab')2 fragments. We found that this precipitin mechanism is highly antigen-dependent both quantitatively and qualitatively. Sucrose density gradient ultracentrifugation was used for the identification of Fc-precipitating immune complexes, and we demonstrated that different types of complexes take part in Fc-mediated immune precipitation in the different antigen-antibody systems. Thus, only small complexes are involved in the HFg system, whereas small as well as large complexes precipitate by this mechanism in the BSA and the HPT systems. The specificity of Fc-mediated immune precipitation was studied by mixing human serum albumin (HSA)-anti-HSA IgG complexes with either HPT-anti-HPT IgG or HFg-anti-HFg IgG complexes. These investigations show that Fc-mediated immune precipitation is a specific process due to the preferential binding of homologous complexes.
Le capital en agriculture. Les données macro-économiques et leur évolution (1987)

Capital in agriculture : macroeconomic datas and their evolution - National Accounts give a macroeconomic measurement of Gross Invesment in Fixed Capital. For agriculture, a method more detailed than the one used for other sectors is applied to come closer to corporeal investment. According to specificities of macroeconomic approaches various hypothesies were made which limit some figures and conclusions but were difficult to avoid. After introducing those problems as they set in the National Accounts based on 1971, the paper deals with the main features of Gross Investment in Fixed Capital since 1959 and its main components. Beyond movements which are specific to the various types of investment, different periods appear and noti- cingly, for the very last years, a fall of corporeal investment in all its components. Agriculture appears to be more strongly hit by those problems than other sectors, a situation than seems preoccupying.
Wisconsin Electric Power Company load management experiment (1976)

On August 1, 1973, the Wisconsin Electric Power Company management established a task force to investigate the feasibility of installing a load management program (defined as direct control only). The implementation of Phase I began in July 1975. The first phase calls for the installation of equipment to remotely control 500 residential and farm water heaters and remotely read meters on two full meter reading routes of approximately 750 customers. If Phase I is successful, Phase II will offer water heater control to the remainder of the 173,000 water heating customers. Completion of Phase II is scheduled for the summer of 1978. This system provides the capability to shed loads in planned increments, as well as large blocks, thereby defining the need for new generating capacity while simultaneously providing equivalent spinning reserve for sudden outages. (MCW)
Theory and optimization of lens ducts (1996)

Lens ducts are simple optical devices that have found application in the coupling of pump radiation from extended two-dimensional semiconductor laser diode arrays into solid-state laser gain media. The operation of these devices relies on the combined effects of lensing at their curved input surface and channeling by total internal reflection off their canted planar sides, to contain and couple semiconductor diode laser light efficiently to the input face of a solid-state laser crystal or glass. The lens duct provides a robust method for amplifying the irradiance of laser diode array pump sources and has made possible a scalable diode end-pumping architecture that offers the opportunity to expand significantly the number of ions and transitions that can be practically engaged in diode-pumped solid-state laser systems. An analytic model that describes the transfer efficiency of lens ducts and aids in the optimization of their design is presented.
Interaction between hepatitis C virus core protein and E1 envelope protein (1996)

Hepatitis C virus has three structural genes named C, E1, and E2. The C gene encodes the core (capsid) protein and the E1 and E2 genes encode the envelope proteins. In an immunoprecipitation experiment, the E1 protein was found to be precipitated by an anti-core antibody in the presence but not in the absence of the core protein, indicating that the E1 protein can interact with the core protein. This interaction is independent of whether the E1 and the C genes are linked in cis or separated in different DNA constructs for expression. The interaction between the core and the E1 proteins is confirmed by the observation that a hybrid protein derived from the core protein and the tissue plasminogen activator is localized in the nucleus in the absence of the E1 protein and in the perinuclear region in the presence of the E1 protein. Deletion-mapping studies indicate that the carboxy-terminal sequences of both the core and the E1 proteins are important for their interaction. Since little E1 sequence is exposed on the cytosolic side of the membrane of the endoplasmic reticulum, the interaction between the core and the E1 proteins most likely takes place in the endoplasmic reticulum membrane. The E2 protein could not be coprecipitated with the core protein by the anti-core antibody in a similar assay and likely does not interact with the core protein. The implications of these findings on the morphogenesis of the hepatitis C virus virion are discussed.
Platelets and Thrombin Generation (2002)

This review examines the evidence that platelets play a major role in localizing and controlling the burst of thrombin generation leading to fibrin clot formation. From the first functional description of platelets, it has been recognized that platelets supply factors that support the activation of prothrombin. Studies have demonstrated that on activation, the amount of one specific lipid, phosphatidylserine, is significantly increased on the outer leaflet of platelet membranes. When it was found that phosphatidylserine containing lipid extracts could be substituted for platelets in clotting assays, this suggested the possibility that changes in platelet lipid composition were necessary and sufficient to account for platelet surface thrombin generation. Because a growing body of data suggest that platelet-binding proteins provide much of the specificity for platelet thrombin generation, we review in this report data suggesting that changes in lipid composition are necessary but not sufficient to account for platelet surface regulation of thrombin generation. Also, we review data suggesting that platelets from different individuals differ in their capacity to generate thrombin, whereas platelets from a single subject support thrombin generation in a reproducible manner. Individual differences in platelet thrombin generation might be accounted for by differences in platelet-binding proteins.
Origin of ‘‘residual’’ persistent photoconductivity in selectively doped GaAs/AlxGa1−xAs heterojunctions (1986)

We present experimental results which clearly separate the various physical mechanisms which cause persistent photoconductivity in GaAs/AlxGa1−xAs heterojunctions. For high Al mole fraction the major contribution is from the donor-related DX center. This contribution is eliminated by reducing the Al mole fraction x, but we observe a ‘‘residual’’ effect for x≲0.2. We show that this is due to the persistent photovoltage developed between channel and semi-insulating substrate. Charge trapping in the epitaxial GaAs buffer layer contributes negligibly, contrary to the assumptions of other workers. This is demonstrated by fabricating modulation-doped field-effect transistors of low Al mole fraction on conductive substrates. In these devices persistent photoconductivity is eliminated as long as the substrate (back gate) potential is fixed with respect to the channel.
Pharmacological Innovations for Posttraumatic Stress Disorder and Medication- Enhanced Psychotherapy (2012)

Posttraumatic stress disorder (PTSD) is a common condition for which existing treatments are ineffective for many patients. Recent discoveries in the neurobiology of learning and memory, along with expanding knowledge of how those systems are impacted by the biology of the stress response, have opened new arenas for potential medication treatments for PTSD. We conducted a review of registered clinical trials investigating the efficacy of new agents for PTSD. The glucocoritcoid and adrenergic signaling systems are the most frequent targets of these investigational approaches to the prevention and treatment of PTSD. Additional trials are evaluating modulation of other CNS targets, including neurosteroids, glutamate, gamma-amino butyric acid, endocannabinoids, oxytocin, neurokinin/Substance P, and dopamine. A particularly exciting area of research is studies examining Medication-Enhanced Psychotherapy (MEP). Medications provided before or after exposure therapy for PTSD can enhance outcomes by: 1) strengthening learning and memory of fear extinction; 2) disrupting reconsolidation, thereby weakening fear memories; or 3) facilitating engagement in psychotherapy by reducing fear and enhancing openness to experience. The next few years promise to produce insight into the neurobiology and clinical efficacy of several novel approaches in the pharmacologic treatment and prevention of PTSD.
A Method for the Determination of Tobacco-specific Nitrosamines (TSNA), Nitrate and Nitrite in Tobacco Leaves and Processed Tobacco (1989)

Abstract A method for the simultaneous determination of tobacco-specific nitrosamines [TSNA], N'-nitrosonornicotine [NNN], 4-(methylnitrosamino)1-(3-pyridyl)-1-butanone [NNK], N'-nitrosoanabasine [NAB] and N'-nitrosoanatabine [NAT], as well as nitrate and nitrite in tobacco leaves and processed tobacco was developed. The analytical procedure included aqueous extraction of tobacco leaves and processed tobacco respectively under alkaline conditions in the presence of an antibacterial agent and, for TSNA analysis, a further clean-up of the aqueous extract by liquid-liquid partition extraction (kieselguhr column extraction), removal of nicotine, and determination of the nitrosamines by gas chromatography In combination with chemiluminescence detection. It is demonstrated that N'-nitrosopentylpicolylamine [NPePicA] as well as N-nitrosodibenzylamine [NDBenzA] can be used for internal standardization. For clean-up two different extraction procedures can be utilized: alkaline extraction on kieselguhr / ascorbic acid extraction columns or acidic extraction on kieselguhr including prior destruction of nitrite with sodium azide. The recoveries of the internal standards were in a similar range (73-96 %) as those of the TSNA. The analysis of nitrite and nitrate was carried out according to standard analytical procedures using the alkaline aqueous extract. The determination of nitrate and nitrite showed high accuracy and reproducibility. It is demonstrated that, under the conditions described, artifact formation did not occur even when nitrite was present. The method described is specifically applicable for the simultaneous determination of TSNA and nitrate/nitrite in tobacco leaves.
Immunological activity of a 14-kilodalton recombinant protein of Mycobacterium tuberculosis H37Rv (1987)

A 14-kilodalton peptide antigen from Mycobacterium tuberculosis was isolated from an Escherichia coli lambda gt 11 recombinant DNA clone and was identified by Western blotting (immunoblotting) with monoclonal antibody TB68. Immunization of mice and guinea pigs with the recombinant peptide (rTB68) induced in vitro lymphoproliferative responses in draining lymph node lymphocyte cultures as well as in vivo delayed-type hypersensitivity reactions. Moreover, rTB68 was found both to induce and to cross-react with Mycobacterium leprae immune lymphocytes, but did not generate protective effects against live M. leprae challenge in mice. These findings showed that a 14-kilodalton peptide which has been characterized as specific for M. tuberculosis on the basis of B-cell recognition was capable of generating cell-mediated immune responses and moreover contained T-cell epitopes which were cross-reactive with M. leprae antigens.
Fate of the Sperm Mitochondria, and the Incorporation, Conversion, and Disassembly of the Sperm Tail Structures during Bovine Fertilization1 (1996)

Sperm incorporation and the conversion of the sperm-derived components into zygotic structures during in vitro fertilization of bovine oocytes was explored by combining ultrastructural studies with observations of the fertilizing sperm tagged with a mitochondrion-specific vital dye MitoTracker green FM. The zygotes fertilized by the MitoTracker-labeled sperm were fixed at various times after fertilization and then processed for immunocytochemistry to examine the distribution of DNA, microtubules, and sperm tail components, including the fibrous sheath and axonemal microtubules. We show here that the complete incorporation of the sperm, but not sperm-oocyte binding and oocyte activation, depends upon the integrity of oocyte microfilaments and is inhibited by the microfilament disrupter cytochalasin B. After sperm incorporation, the mitochondria are displaced from the sperm's connecting piece, and the sperm centriole is exposed to the egg cytoplasm. This event is followed by the formation of the microtubule-based sperm aster, which is responsible for the union of male and female pronuclei. Concomitantly, the major structure of the sperm principal piece, the fibrous sheath, disappears. After the first mitosis, the compact mitochondrial sheath can be seen in one of the blastomeres. An aggregate of the sperm mitochondria is observed at the entry of the second mitosis, although they remain in the vicinity of the nucleus and can later be seen at one pole of the metaphase spindle. The mitochondrial cluster is occasionally found in one of the blastomeres in the early-stage four-cell embryos, but it is no longer detected by the beginning of the third mitotic cycle. These data suggest that the disassembly of the sperm tail during bovine fertilization occurs as a series of precisely orchestrated events involving the destruction (fibrous sheath and mitochondrial sheath) and transformation (DNA, sperm centriole) of particular sperm structures into zygotic and embryonic components.
Electroporation-mediated interleukin-12 gene therapy for hepatocellular carcinoma in the mice model. (2001)

Applications of nonviral vectors for gene transfer into tumors in vivo have been limited by the relatively low expression levels of the transferred gene. The aim of this study is to evaluate the efficacy of electroporation-mediated interleukin-12 (IL-12) gene therapy for hepatocellular carcinoma (HCC). First, we investigated the optimal conditions of electric pulses (voltage, pulsing duration, numbers of shocks) of in vivo electroporation for gene transfer into HCC established by s.c. implantation of MH134 cells to C3H mice. This process made use of plasmid DNA that express the luciferase gene. We concluded that the optimal conditions for the electric pulses are as follows: voltage at 150 V; pulsing duration at 50 ms; nonpulsing duration at 950 ms; and the number of shocks at 10. Second, we tried to treat s.c. HCC by electroporation using plasmid DNA that expresses the murine interleukin-12 (mlL-12) gene. Intratumoral administration of the mIL-12 vector elevated serum IL-12 and IFN-gamma and significantly inhibited the growth not only of HCC into which the mIL-12 vector had been directly transferred, but also of the distant HCC. In addition, intratumoral administration of the mIL-12 vector inhibited spontaneous lung metastasis and delayed establishment of HCC injected 3 days after mIL-12 gene therapy. The IL-12 gene therapy induced more lymphocyte infiltration by NK cells, CD3+ cells, and Mac-1 positive cells into the tumor and reduced the number of microvessels. Therefore, more terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling-positive tumor cells were found. These results demonstrate that gene therapy for HCC by electroporation in vivo using IL-12 is very efficient and is thus promising for further clinical trial.
Multiscale Entropy Analysis of Complex Physiologic Time Series (2002)

There has been considerable interest in quantifying the complexity of physiologic time series, such as heart rate. However, traditional algorithms indicate higher complexity for certain pathologic processes associated with random outputs than for healthy dynamics exhibiting long-range correlations. This paradox may be due to the fact that conventional algorithms fail to account for the multiple time scales inherent in healthy physiologic dynamics. We introduce a method to calculate multiscale entropy (MSE) for complex time series. We find that MSE robustly separates healthy and pathologic groups and consistently yields higher values for simulated long-range correlated noise compared to uncorrelated noise.
Shape Classification Using the Inner-Distance (2007)

Part structure and articulation are of fundamental importance in computer and human vision. We propose using the inner-distance to build shape descriptors that are robust to articulation and capture part structure. The inner-distance is defined as the length of the shortest path between landmark points within the shape silhouette. We show that it is articulation insensitive and more effective at capturing part structures than the Euclidean distance. This suggests that the inner-distance can be used as a replacement for the Euclidean distance to build more accurate descriptors for complex shapes, especially for those with articulated parts. In addition, texture information along the shortest path can be used to further improve shape classification. With this idea, we propose three approaches to using the inner-distance. The first method combines the inner-distance and multidimensional scaling (MDS) to build articulation invariant signatures for articulated shapes. The second method uses the inner-distance to build a new shape descriptor based on shape contexts. The third one extends the second one by considering the texture information along shortest paths. The proposed approaches have been tested on a variety of shape databases, including an articulated shape data set, MPEG7 CE-Shape-1, Kimia silhouettes, the ETH-80 data set, two leaf data sets, and a human motion silhouette data set. In all the experiments, our methods demonstrate effective performance compared with other algorithms.
Nuclear Transplantation in Mouse Embryos: Assessment of Recipient Cell Stage1 (1986)

Enucleated zygotes were compared with enucleated two-cell embryos as recipients for donor nuclei from eight-cell embryos. Only one or two cleavage divisions were observed when eight-cell nuclei were transplanted to enucleated zygotes. Development of enucleated two-cell embryos containing a transplanted eight-cell nucleus was appreciably better with 51% (45/89) of the embryos forming blastocysts in vitro and 42% (25/60) initiating implantation. Of these, eleven implantation sites on Day 10 of gestation were examined histologically and two contained normally developing embryos. No development was observed beyond Day 12 of gestation. These observations indicate that a major transition occurs between the zygote and two-cell stage that results in the two-cell recipient being more compatible with the eight-cell nucleus than with the zygote.