gebhart/patrepeval huggingface dataset:
Non-Detrimental Web Application Security Scanning (2005)

The World Wide Web has become a sophisticated platform capable of delivering a broad range of applications. However, its rapid growth has resulted in numerous security problems that current technologies cannot address. Researchers from both academic and private sector are devoting a considerable amount of resources to the development of Web application security scanners (i.e., automated software testing platforms for Web application security auditing) with some success. However, little is known about their potential side effects. It is possible for an auditing process to induce permanent changes in an application's state. Due to this potential, we have so far avoided large-scale empirical evaluations of our Web Application Vulnerability and Error Scanner (WAVES). we introduce a testing methodology that allows for harmless auditing, define three testing modes - heavy, relaxed, and safe modes, and report our results from two experiments. In the first, we compared the coverage and side effects of the three scanning modes using 5 real-world Web applications chosen from the 38 found vulnerable in a previous static verification effort. In the second, we used the relaxed mode to conduct a 48-hour test involving 1120 random Web sites, of which 55 were found to be vulnerable.
Pulse Shape Discrimination With Selected Elpasolite Crystals (2012)

In recent years, a number of materials from the elpasolite crystal family have been under development for either or both gamma ray and neutron detection. The scintillators show good energy resolution and thermal neutron detection efficiency. The latter is achieved due to the fact, that the selected compositions contain Li-6 ions. In order to effectively and reliably register both types of radiation, it is necessary to separate them through particle identification schemes. This can be accomplished using either pulse height or/and pulse shape discrimination, with the latter being more reliable. In this paper, we summarize our work and provide current status of pulse shape discrimination in the selected elpasolite scintillators. These include Cs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> LiYCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> (CLYC), Cs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> LiLaCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> (CLLC), Cs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> LiLaBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> (CLLB), and Cs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> LiYBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> (CLYB).
Superluminescent diodes with bent waveguide (1996)

Superluminescent diodes are fabricated with a bent waveguide to prevent optical feedback. The bent ridge waveguide is formed with one end normal to the cleaved facet and the other angled at 7/spl deg/ from the facet normal. The spectral ripple of these devices is around 10% at 6 mW output power. The farfield pattern emitted from the angled facet is crescent-shaped. As the device is set up in an external-cavity configuration, lasing operation is observed regardless of the additional 10.8 dB bending loss introduced by the bent waveguide.
Cholecystokinin antagonists. Synthesis and biological evaluation of 3-substituted benzolactams (1989)

A series of 1,3-substituted benzolactams are reported that are potent nonpeptidal antagonists of the peptide hormone cholecystokinin (CCK). Design considerations were based upon the natural product CCK antagonist asperlicin and the potent benzodiazepine antagonist series exemplified by L-364,718 (1). Compound 19, the most potent compound in the benzolactam series, had an IC50 = 3 nM for inhibition of binding of 125I-CCK-8 to CCK receptors in rat pancreatic tissue, and its racemic analogue 8 was found to be orally active in inhibiting CCK-induced gastric emptying in mice, with an ED50 = 2.6 mg/kg po. The effects of ring size, substitution at positions 1 and 3, and stereochemistry at position 3 are discussed. Conformational studies of compound 19 and L-364,718 have delineated similarities that these molecules share in their core conformations and substituent orientations.
Surface display of proteins by gram-negative bacterial autotransporters. (2006)

Expressing proteins of interest as fusions to proteins of the bacterial envelope is a powerful technique with many biotechnological and medical applications. Autotransporters have recently emerged as a good tool for bacterial surface display. These proteins are composed of an N-terminal signal peptide, followed by a passenger domain and a translocator domain that mediates the outer membrane translocation of the passenger. The natural passenger domain of autotransporters can be replaced by heterologous proteins that become displayed at the bacterial surface by the translocator domain. The simplicity and versatility of this system has made it very attractive and it has been used to display functional enzymes, vaccine antigens as well as polypeptides libraries. The recent advances in the study of the translocation mechanism of autotransporters have raised several controversial issues with implications for their use as display systems. These issues include the requirement for the displayed polypeptides to remain in a translocation-competent state in the periplasm, the requirement for specific signal sequences and "autochaperone" domains, and the influence of the genetic background of the expression host strain. It is therefore important to better understand the mechanism of translocation of autotransporters in order to employ them to their full potential. This review will focus on the recent advances in the study of the translocation mechanism of autotransporters and describe practical considerations regarding their use for bacterial surface display.
A transgenic mouse model of steatosis and hepatocellular carcinoma associated with chronic hepatitis C virus infection in humans. (2000)

Chronic hepatitis C is a necroinflammatory disease of the liver that is caused by infection with hepatitis C virus (HCV) (1). Uniquely adapted to establish persistent infections within the human liver, the major pathologic hallmark of this flavivirus infection is the insidious progression of hepatic fibrosis and loss of functioning hepatocyte mass (2-4). Typically, this occurs against a background of chronic hepatic inflammation and associated macroand microvesicular steatosis. A significant proportion of infected persons ultimately develop cirrhosis, hepatic failure, or hepatocellular carcinoma (HCC) (5-7). These lethal manifestations of hepatitis C are currently thought to result in approximately 8,000-10,000 deaths annually among the 3.9 million Americans infected with this virus (8). This makes hepatitis C the single most common cause of clinically significant liver disease in the United States today. Despite this, little is known about the molecular mechanisms underlying the chronic hepatic changes that are associated with this viral infection. However, it is generally believed that most if not all of the pathologic consequences of hepatitis C arise as a result of the cellular immune response to the infection, and that the infection itself is likely to be noncytopathic. Existing therapies for chronic hepatitis C include recombinant human interferon, either alone or in combination with ribavirin (9,10). These antiviral therapies are only partially effective, leading to the
Detecting software modularity violations (2011)

This paper presents Clio, an approach that detects modularity violations, which can cause software defects, modularity decay, or expensive refactorings. Clio computes the discrepancies between how components should change together based on the modular structure, and how components actually change together as revealed in version history. We evaluated Clio using 15 releases of Hadoop Common and 10 releases of Eclipse JDT. The results show that hundreds of violations identified using Clio were indeed recognized as design problems or refactored by the developers in later versions. The identified violations exhibit multiple symptoms of poor design, some of which are not easily detectable using existing approaches.
Selectively increased expression and functions of chemokine receptor CCR9 on CD4+ T cells from patients with T-cell lineage acute lymphocytic leukemia. (2003)

In a total of 38 typical T-cell lineage acute lymphocytic leukemia (T-ALL) and T-cell lineage chronic lymphocytic leukemia (T-CLL) cases investigated, we found that CC chemokine receptor CCR9 was selectively and frequently expressed on T-ALL CD4+ T cells, was moderately expressed on T-CLL CD4+ T cells, and was rarely expressed on normal CD4+ T cells. These findings were demonstrated at protein and mRNA levels using flow cytometry and real-time quantitative reverse transcription-PCR technique and were verified by digital confocal microscopy and Northern blotting. Thymus-expressed chemokine, a ligand for CCR9, selectively induced T-ALL CD4+ T-cell chemotaxis and adhesion. Interleukin (IL)-2 and IL-4, together, down-regulated the expression and functions of CCR9 in T-ALL CD4+ T cells including chemotaxis and adhesion. It was also demonstrated that IL-2 and IL-4, together, internalized CCR9 on T-ALL CD4+ T cells and subsequently inhibited functions of CCR9 in these cells. Thymus-expressed chemokine mRNA was highly expressed in CD4+ T cells, involving lymph node and skin in T-ALL patients, and was expressed at moderate levels in lymph node and skin tissues in T-CLL patients. Our findings may provide new clues to understanding various aspects of T-ALL CD4+ T cells, such as functional expression of CCR9-thymus-expressed chemokine receptor-ligand pairs as well as the effects of IL-2 and IL-4, which may be especially important in cytokine/chemokine environment for the pathophysiological events of T-ALL CD4+ T-cell trafficking.
Recent developments in CCR2 antagonists (2009)

Monocyte chemoattractant protein-1 (MCP-1) is a major chemoattractant for monocytes and memory T cells by means of their binding to its specific cell-surface receptor, CC-chemokine receptor-2 (CCR2). CCR2 belongs to the G-protein-coupled seven-transmembrane receptor superfamily. The evidence in favor of CCR2 and MCP-1 having dominant roles in monocyte chemotaxis and chronic inflammation was provided by CCR2 and MCP-1 knockout mice. It has been recognized that CCR2 antagonists are potential therapeutic agents in preventing, treating, or ameliorating a CCR2-mediated inflammatory syndrome or disease such as psoriasis, uveitis, rheumatoid arthritis, multiple sclerosis, asthma, obesity, and chronic obstructive pulmonary disease. This review summarizes recent developments in small-molecule CCR2 antagonists disclosed by patent applications published between 2005 and 2008 and related publications.
Independent Circadian and Sleep/Wake Regulation of Adipokines and Glucose in Humans (2005)

Leptin and adiponectin play important physiological roles in regulating appetite, food intake, and energy balance and have pathophysiological roles in obesity and anorexia nervosa. To assess the relative contributions of day/night patterns in behaviors (sleep/wake cycle and food intake) and of the endogenous circadian pacemaker on observed day/night patterns of adipokines, in six healthy subjects we measured circulating leptin, soluble leptin receptor, adiponectin, glucose, and insulin levels throughout a constant routine protocol (38 h of wakefulness with constant posture, temperature, and dim light, as well as identical snacks every 2 h) and throughout sleep and fasting periods before and after the constant routine. There were significant endogenous circadian rhythms in leptin, glucose, and insulin, with peaks around the usual time of awakening. Sleep/fasting resulted in additional systematic decreases in leptin, glucose, and insulin, whereas wakefulness/food intake resulted in a systematic increase in leptin. Thus, the day/night pattern in leptin is likely caused by combined effects from the endogenous circadian pacemaker and day/night patterns in behaviors. Our data imply that alterations in the sleep/wake schedule would lead to an increased daily range in circulating leptin, with lowest leptin upon awakening, which, by influencing food intake and energy balance, could be implicated in the increased prevalence of obesity in the shift work population.
In vitro susceptibility of Bartonella species to 17 antimicrobial compounds: comparison of Etest and agar dilution (2006)

Telithromycin, macrolides, doxycycline and rifampicin were the most effective agents against Bartonella spp. Our data confirm that Etest may be a reliable method for determining susceptibility of Bartonella spp.
Blocking anthrax lethal toxin at the protective antigen channel by using structure-inspired drug design (2005)

Bacillus anthracis secretes three polypeptides: protective antigen (PA), lethal factor (LF), and edema factor (EF), which interact at the surface of mammalian cells to form toxic complexes. LF and EF are enzymes that target substrates within the cytosol; PA provides a heptameric pore to facilitate LF and EF transport into the cytosol. Other than administration of antibiotics shortly after exposure, there is currently no approved effective treatment for inhalational anthrax. Here we demonstrate an approach to disabling the toxin: high-affinity blockage of the PA pore by a rationally designed low-molecular weight compound that prevents LF and EF entry into cells. Guided by the sevenfold symmetry and predominantly negative charge of the PA pore, we synthesized small cyclic molecules of sevenfold symmetry, beta-cyclodextrins chemically modified to add seven positive charges. By channel reconstitution and high-resolution conductance recording, we show that per-6-(3-aminopropylthio)-beta-cyclodextrin interacts strongly with the PA pore lumen, blocking PA-induced transport at subnanomolar concentrations (in 0.1 M KCl). The compound protected RAW 264.7 mouse macrophages from cytotoxicity of anthrax lethal toxin (= PA + LF). More importantly, it completely protected the highly susceptible Fischer F344 rats from lethal toxin. We anticipate that this approach will serve as the basis for a structure-directed drug discovery program to find new and effective treatments for anthrax.
0.1 μm-rule MRAM development using double-layered hard mask (2002)

0.1 /spl mu/m rule magnetic random access memory (MRAM) was developed using double-layered hard mask of SiO/sub 2//metal. 30% magnetoresistance ratio under switching operation, read and write characteristics for MRAM cell with 0.1/spl times/0.6 /spl mu/m/sup 2/ were observed using current induced magnetic field. It is found that switching current of tunneling magnetoresistance (TMR) device with 0.1 /spl mu/m length can be reduced by thinning free layer and reduction of TMR aspect ratio.
Patient with 13 Chromosome Deletion: Evidence That the Retinoblastoma Gene Is a Recessive Cancer Gene (1983)

Although a constitutional chromosomal deletion including 13q14 has been found to date in all retinoblastoma patients whose esterase D activity is 50 percent of normal, one female patient has been found who has 50 percent esterase D activity in all normal cells examined but no deletion of 13q14 at the 550-band level. Therefore, she has the smallest constitutional chromosomal deletion within 13q14 that is associated with susceptibility to retinoblastoma. Two stem lines were identified in a retinoblastoma from this patient, and each one had a missing 13 chromosome. No detectable esterase D activity was found in the tumor, indicating that the normal nondeleted 13 chromosome was lost in both stem lines. Thus the data from this patient not only show that there is a total loss of genetic information at the location of the retinoblastoma gene within the tumor, but also imply that recessive genes may play an important role in the development of certain human tumors including retinoblastoma.
Use of a lipophilic cation for determination of membrane potential in neuroblastoma-glioma hybrid cell suspensions (1979)

Neuroblastoma-glioma hybrid cells (NG108-15) in suspension accumulate the permeant lipophilic cation [(3)H]tetraphenylphosphonium (TPP(+)) against a concentration gradient. The steady-state level of TPP(+) accumulation is about twice as great in physiological media of low K(+) concentration (i.e., 5 mM K(+)/135 mM Na(+)) than in a medium of high K(+) concentration (i.e., 121 mM K(+)/13.5 mM Na(+)). The latter manipulation depolarizes the NG108-15 plasma membrane and indicates that the resting membrane potential (DeltaPsi) is due primarily to a K(+) diffusion gradient (K(in) (+) --> K(out) (+)). TPP(+) accumulation is time and temperature dependent, achieving a steady state in 15-20 min at 37 degrees C, and is a linear function of cell number and TPP(+) concentration (i.e., the concentration gradient is constant). The difference in TPP(+) accumulation in low and high K(+) media under various conditions has been used to calculate mean (+/-SD) DeltaPsi values of -56 +/- 3, -63 +/- 4, and -66 +/- 5 mV at 26, 33, and 37 degrees C, respectively. Importantly, these values are virtually identical to those obtained by direct electrophysiological measurements made under the same conditions. TPP(+) accumulation is abolished by the protonophore carbonylcyanide-m-chlorophenylhydrazone, whereas the neurotoxic alkaloid veratridine diminishes uptake to the same level as that observed in high K(+) media. In addition, the effect of veratridine is dependent upon the presence of external Na(+) and is blocked by tetrodotoxin. The steady-state level of TPP(+) accumulation is enhanced by monensin, indicating that this ionophore induces hyperpolarization under appropriate conditions. Finally, ouabain has essentially no effect on the steady-state level of TPP(+) accumulation in short-term experiments, suggesting that Na(+),K(+)-ATPase activity makes little contribution to the resting potential in these cells. Because many of these observations are corroborated by intracellular recording techniques, it is concluded that TPP(+) distribution measurements can provide a biochemical method for determining membrane potentials in populations of cultured neuronal cells.
Thermal managerment of high power memory module for server platforms (2008)

This paper demonstrates an approach for thermal solution development of high power memory module for computer system platforms. A lumped thermal resistance equation is adopted to consider the coupling between register/buffer and DRAMs. Comprehensive thermal analysis is done to characterize the thermal resistances under various memory thermal conditions in different system configurations. Memory thermal gap is identified and addressed with efficient and low cost thermal solutions such as full DIMM heat spreader (FDHS). Structural consideration is further discussed to address FDHS air gap risk related to height differences between DRAM and register/buffer packages. The thermal solution development approach is applicable to memory modules such as registered DIMM (RDIMM) or fully buffered DIMM (FBD).
Mechanisms of multidrug transporters (1997)

Drug resistance, mediated by various mechanisms, plays a crucial role in the failure of the drug-based treatment of various infectious diseases. As a result, these infectious diseases re-emerge rapidly and cause many victims every year. Another serious threat is imposed by the development of multidrug resistance (MDR) in eukaryotic (tumor) cells, where many different drugs fail to perform their therapeutic function. One of the causes of the occurrence of MDR in these cells is the action of transmembrane transport proteins that catalyze the active extrusion of a large number of structurally and functionally unrelated compounds out of the cell. The mode of action of these MDR transporters and their apparent lack of substrate specificity is poorly understood and has been subject to many speculations. In this review we will summarize our current knowledge about the occurrence, mechanism and molecular basis of (multi-)drug resistance especially as found in bacteria.
Myocardial ischaemia and the cardiac nervous system (1999)

The intrinsic cardiac nervous system has been classically considered to contain only parasympathetic efferent postganglionic neurones which receive inputs from medullary parasympathetic efferent preganglionic neurones. In such a view, intrinsic cardiac ganglia act as simple relay stations of parasympathetic efferent neuronal input to the heart, the major autonomic control of the heart purported to reside solely in the brainstem and spinal cord. Data collected over the past two decades indicate that processing occurs within the mammalian intrinsic cardiac nervous system which involves afferent neurones, local circuit neurones (interconnecting neurones) as well as both sympathetic and parasympathetic efferent postganglionic neurones. As such, intrinsic cardiac ganglionic interactions represent the organ component of the hierarchy of intrathoracic nested feedback control loops which provide rapid and appropriate reflex coordination of efferent autonomic neuronal outflow to the heart. In such a concept, the intrinsic cardiac nervous system acts as a distributive processor, integrating parasympathetic and sympathetic efferent centrifugal information to the heart in addition to centripetal information arising from cardiac sensory neurites. A number of neurochemicals have been shown to influence the interneuronal interactions which occur within the intrathoracic cardiac nervous system. For instance, pharmacological interventions that modify beta-adrenergic or angiotensin II receptors affect cardiomyocyte function not only directly, but indirectly by influencing the capacity of intrathoracic neurones to regulate cardiomyocytes. Thus, current pharmacological management of heart disease may influence cardiomyocyte function directly as well as indirectly secondary to modifying the cardiac nervous system. This review presents a brief summary of developing concepts about the role of the cardiac nervous system in regulating the normal heart. In addition, it provides some tentative ideas concerning the importance of this nervous system in cardiac disease states with a view to stimulating further interest in neural control of the heart so that appropriate neurocardiological strategies can be devised for the management of heart disease.
Perceived Exertion: Subjectivity and Objectivity in Work Intensity Assessment (1986)

For several years I have argued that the Borg (15-point scale) RPE-scale (Borg, 1973) is a valuable tool in assessing the work intensity of adults (Burke, 1979). In my experience there are two common, if fallacious, criticisms of the scale as a measure of work intensity. The first one sounds something like: "the scale is too subjective". The second one sounds something like: "I've tried it but it doesn't work … when I multiply by 10 it never equals heart rate". This paper will attempt to argue that these so called criticisms really miss the point. Those who make the first criticism fail to understand that subjectivity is an advantage as a measure of work intensity in the presence of objectivity. The second criticism is fallacious in that heart rate is not the most important measure of work intensity. Heart rate like RPE is a predictor of work intensity.