gebhart/patrepeval huggingface dataset:
An API for Runtime Code Patching (2000)

The authors present a postcompiler program manipulation tool called Dyninst, which provides a C++ class library for program instrumentation. Using this library, it is possible to instrument and modify application programs during execution. A unique feature of this library is that it permits machine-independent binary instrumentation programs to be written. The authors describe the interface that a tool sees when using this library. They also discuss three simple tools built using this interface: a utility to count the number of times a function is called, a program to capture the output of an already running program to a file, and an implementation of conditional breakpoints. For the conditional breakpoint example, the authors show that by using their interface compared with gdb, they are able to execute a program with conditional breakpoints up to 900 times faster.
Biodegradation Kinetics of Phenanthrene Partitioned into the Micellar Phase of Nonionic Surfactants (1996)

Surfactants above their critical micelle concentration can solubilize hydrophobic contaminants into their micelles. This process enhances the apparent solubility of contaminants such as hydrocarbons and, therefore, also their desorption from soils. Conceivably, in the absence of any inhibitory effects, such surfactants may enhance the biodegradation of the hydrocarbon. Through a set of screening experiments, a series of nonionic surfactants were identified that do not inhibit the biodegradation of phenanthrene. A mathematical model was formulated to describe the interaction of the biomass−contaminant−water−surfactant system. Assumptions that the model formulation is based on are that the phenanthrene in solution, partitioned into the micellar phase and sorbed onto the biomass and other solid surfaces,is at equilibrium and that these equilibria can be described by simple partition coefficients. It was also assumed that the presence of the surfactant does not affect the biochemical characteristics of the biomass. An effective bioavailable micellar-phase concentration of phenanthrene was defined. The model simulates experimental data well, indicating that a fraction of the micellar-phase phenanthrene is directly bioavailable. For three of the surfactants tested (Triton N101, Triton X100, and Brij 30), the micellar-phase bioavailable fraction of phenanthrene decreased with an increasing surfactant concentration. For Brij 35, it was found that the fraction of the phenanthrene associated with the micellar phase was not directly bioavailable.
Natural Splice Variant of MHC Class I Cytoplasmic Tail Enhances Dendritic Cell-Induced CD8+ T-Cell Responses and Boosts Anti-Tumor Immunity (2011)

Dendritic cell (DC)-mediated presentation of MHC class I (MHC-I)/peptide complexes is a crucial first step in the priming of CTL responses, and the cytoplasmic tail of MHC-I plays an important role in modulating this process. Several species express a splice variant of the MHC-I tail that deletes exon 7-encoding amino acids (Δ7), including a conserved serine phosphorylation site. Previously, it has been shown that Δ7 MHC-I molecules demonstrate extended DC surface half-lives, and that mice expressing Δ7-K(b) generate significantly augmented CTL responses to viral challenge. Herein, we show that Δ7-D(b)-expressing DCs stimulated significantly more proliferation and much higher cytokine secretion by melanoma antigen-specific (Pmel-1) T cells. Moreover, in combination with adoptive Pmel-1 T-cell transfer, Δ7-D(b) DCs were superior to WT-D(b) DCs at stimulating anti-tumor responses against established B16 melanoma tumors, significantly extending mouse survival. Human DCs engineered to express Δ7-HLA-A*0201 showed similarly enhanced CTL stimulatory capacity. Further studies demonstrated impaired lateral membrane movement and clustering of human Δ7-MHC-I/peptide complexes, resulting in significantly increased bioavailability of MHC-I/peptide complexes for specific CD8+ T cells. Collectively, these data suggest that targeting exon 7-encoded MHC-I cytoplasmic determinants in DC vaccines has the potential to increase CD8+ T-cell stimulatory capacity and substantially improve their clinical efficacy.
Inferential Structure Determination (2005)

Macromolecular structures calculated from nuclear magnetic resonance data are not fully determined by experimental data but depend on subjective choices in data treatment and parameter settings. This makes it difficult to objectively judge the precision of the structures. We used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision. This probability distribution also determines additional unknowns, such as theory parameters, that previously had to be chosen empirically. We implemented this approach by using Markov chain Monte Carlo techniques. Our method provides an objective figure of merit and improves structural quality.
Developmental- and differentiation-specific patterns of human γ- and β-globin promoter DNA methylation (2007)

The mechanisms underlying the human fetal-to-adult beta-globin gene switch remain to be determined. While there is substantial experimental evidence to suggest that promoter DNA methylation is involved in this process, most data come from studies in nonhuman systems. We have evaluated human gamma- and beta-globin promoter methylation in primary human fetal liver (FL) and adult bone marrow (ABM) erythroid cells. Our results show that, in general, promoter methylation and gene expression are inversely related. However, CpGs at -162 of the gamma promoter and -126 of the beta promoter are hypomethylated in ABM and FL, respectively. We also studied gamma-globin promoter methylation during in vitro differentiation of erythroid cells. The gamma promoters are initially hypermethylated in CD34(+) cells. The upstream gamma promoter CpGs become hypomethylated during the preerythroid phase of differentiation and are then remethylated later, during erythropoiesis. The period of promoter hypomethylation correlates with transient gamma-globin gene expression and may explain the previously observed fetal hemoglobin production that occurs during early adult erythropoiesis. These results provide the first comprehensive survey of developmental changes in human gamma- and beta-globin promoter methylation and support the hypothesis that promoter methylation plays a role in human beta-globin locus gene switching.
Identification of a Protein That Purifies with the Scrapie Prion (1982)

Purification of prions from scrapie-infected hamster brain yielded a protein that was not found in a similar fraction from uninfected brain. The protein migrated with an apparent molecular size of 27,000 to 30,000 daltons in sodium dodecyl sulfate polyacrylamide gels. The resistance of this protein to digestion by proteinase K distinguished it from proteins of similar molecular weight found in normal hamster brain. Initial results suggest that the amount of this protein correlates with the titer of the agent.
Fountain codes (2005)

Fountain codes are record-breaking sparse-graph codes for channels with erasures, such as the internet, where files are transmitted in multiple small packets, each of which is either received without error or not received. Standard file transfer protocols simply chop a file up into K packet-sized pieces, then repeatedly transmit each packet until it is successfully received. A back channel is required for the transmitter to find out which packets need retransmitting. In contrast, fountain codes make packets that are random functions of the whole file. The transmitter sprays packets at the receiver without any knowledge of which packets are received. Once the receiver has received any N packets, where N is just slightly greater than the original file size K, the whole file can be recovered. In the paper random linear fountain codes, LT codes, and raptor codes are reviewed. The computational costs of the best fountain codes are astonishingly small, scaling linearly with the file size.
Methylglyoxal induces apoptosis in Jurkat leukemia T cells by activating c-Jun N-Terminal kinase (2000)

Methylglyoxal (MG) is a physiological metabolite, but it is known to be toxic, inducing stress in cells and causing apoptosis. This study examines molecular mechanisms in the MG-induced signal transduction leading to apoptosis, focusing particularly on the role of JNK activation. We first confirmed that MG caused apoptosis in Jurkat cells and that it was cell type dependent because it failed to induce apoptosis in MOLT-4, HeLa, or COS-7 cells. A caspase inhibitor, Z-DEVD-fmk, completely blocked MG-induced poly(ADP-ribose)polymerase (PARP) cleavage and apoptosis, showing the critical role of caspase activation. Inhibition of JNK activity by a JNK inhibitor, curcumin, remarkably reduced MG-induced caspase-3 activation, PARP cleavage, and apoptosis. Stable expression of the dominant negative mutant of JNK also protected cells against apoptosis notably, although not completely. Correspondingly, loss of the mitochondrial membrane potential induced by MG was decreased by the dominant negative JNK. These results confirmed a crucial role of JNK working upstream of caspases, as well as an involvement of JNK in affecting the mitochondrial membrane potential.
Asynchronous BVH construction for ray tracing dynamic scenes on parallel multi-core architectures (2007)

Recent developments have produced several techniques for interactive ray tracing of dynamic scenes. In particular, bounding volume hierarchies (BVHs) are efficient acceleration structures that handle complex triangle distributions and can accommodate deformable scenes by updating (refitting) the bounding primitive without restructuring the entire tree. Unfortunately, updating only the bounding primitive can result in a degradation of the quality of the BVH, and in some scenes will result in a dramatic deterioration of rendering performance. The typical method to avoid this degradation is to rebuild the BVH when a heuristic determines the tree is no longer efficient, but this rebuild results in a disruption of interactive system response.We present a method that removes this gradual decline in performance while enabling consistently fast BVH performance. We accomplish this by asynchronously rebuilding the BVH concurrently with rendering and animation, allowing the BVH to be restructured within a handful of frames.
Snake Venom Disintegrin: An Effective Inhibitor of Breast Cancer Growth and Dissemination (1999)

Contortrostatin, a 13.5 kDa disulfide-linked, homodimeric polypeptide possessing an Arg-Gly-Asp sequence, was isolated from venom of the southern copperhead snake. Contortrostatin binds to integrins and blocks the adhesion of human breast cancer cells (MDA-MB-435) to extracellular matrix proteins including fibronectin and vitronectin. Contortrostatin also inhibits invasion of MDA-MB-435 cells. Daily intratumor injection of contortrostatin (5 μg/mouse/day) into MDA-MB-435 tumor, established in an orthotopic xenograft nude mouse model, significantly inhibits growth of the tumor and reduces the occurrence of pulmonary metastasis. Contortrostatin is not cytotoxic to MDA-MB-435 cells in vitro. Integrin αvβ3, which mediates cell motility and tumor invasion, is one of the binding sites for contortrostatin on MDA-MB-435 cells. On the chick embryo chorioallantoic membrane, contortrostatin inhibited angiogenesis induced by growth factors and by MDA-MB-435 cells. Contortrostatin effectively blocked adhesion of human umbilical vein endothelial cells (HUVEC) to immobilized vitronectin and significantly inhibited invasion of HUVEC. Integrin αvβ3 is one of the binding sites for contortrostatin on HUVEC. Detachment of HUVEC from vitronectin by contortrostatin induced apoptosis. It is concluded that contortrostatin blocks avβ3, and perhaps other integrins on breast cancer and vascular endothelial cells, and thus inhibits in vivo progression by a combination of anti-tumor and anti-angiogenic activities.
High Constitutive Signaling of the Ghrelin Receptor—Identification of a Potent Inverse Agonist (2003)

Ghrelin is a GH-releasing peptide that also has an important role as an orexigenic hormone-stimulating food intake. By measuring inositol phosphate turnover or by using a reporter assay for transcriptional activity controlled by cAMP-responsive elements, the ghrelin receptor showed strong, ligand-independent signaling in transfected COS-7 or human embryonic kidney 293 cells. Ghrelin and a number of the known nonpeptide GH secretagogues acted as agonists stimulating inositol phosphate turnover further. In contrast, the low potency ghrelin antagonist, [D-Arg1,D-Phe5,D-Trp7,9,Leu11]-substance P was surprisingly found to be a high potency (EC50 = 5.2 nm) full inverse agonist as it decreased the constitutive signaling of the ghrelin receptor down to that observed in untransfected cells. The homologous motilin receptor functioned as a negative control as it did not display any sign of constitutive activity; however, upon agonist stimulation the motilin receptor signaled as strongly as the unstimulated ghrelin receptor. It is concluded that the ghrelin receptor is highly constitutively active and that this activity could be of physiological importance in its role as a regulator of both GH secretion and appetite control. It is suggested that inverse agonists for the ghrelin receptor could be particularly interesting for the treatment of obesity.
Multicenter Evaluation of the Performance Characteristics of the Bayer VERSANT HCV RNA 3.0 Assay (bDNA) (2004)

In this multicenter evaluation, the VERSANT HCV RNA 3.0 Assay (bDNA) (Bayer Diagnostics, Tarrytown, N.Y.) was shown to have excellent reproducibility, linearity, and analytical sensitivity across specimen collection matrices (serum, EDTA, ACD-A), and hepatitis C virus (HCV) genotypes 1 to 6. The VERSANT HCV bDNA Assay has a reportable range of 615 to 7690000 (7.69 x 10(6)) IU/ml. The total coefficient of variation (CV) ranged from 32.4% at 615 IU/ml to 17% at 6.8 x 10(6) IU/ml. The assay was linear across the reportable range. Analytical specificity of 98.8% was determined by testing 999 specimens from volunteer blood donors. Evaluation of HCV genotypes using RNA transcripts of representative clones of 1a, 1b, 2a, 2b, 2c, 3a, 4a, 5a, and 6a and patient specimens showed that the largest difference between genotype 1, upon which the assay is standardized, and non-1 genotypes was within 1.5-fold. Testing of potentially interfering endogenous substances and exogenous substances and conditions found no interference in HCV-positive or HCV-negative specimens except for unconjugated bilirubin at concentrations of >or=20 mg/dl and protein at concentrations of >or=9 g/dl. Biological variability was estimated from 29 clinically stable individuals not on HCV therapy who were tested weekly over an 8-week period. The combined estimate of total (biologic plus assay) variability was 0.15 log(10) standard deviation (CV, 36.1%), a fold change of 2.6. Thus, the observed fold change between any two consecutive HCV RNA measures is expected to be less than 2.6-fold (equivalent to 0.41 log(10) IU/ml) 95% of the time in clinically stable individuals.
Diphenylpropionic Acids as New AT1 Selective Angiotensin II Antagonists (1996)

The synthesis and pharmacological evaluation of a new series of potent AT1 selective diphenylpropionic acid nonpeptide angiotensin II receptor antagonists are reported. The new compounds were evaluated for in vitro AT1 (rat liver) and AT2 (rat adrenal) binding affinity as well as for in vivo inhibition of angiotensin II-induced increase in mean arterial blood pressure in pithed rats. Unsaturation of the diphenylpropionic acids as well as substitution or replacement by alkyl groups of the pendant phenyl ring resulted in a decrease of potency. On the other hand, the presence of small alkyl groups in the alpha-position to the carboxylic acid was important for activity, with one of the resultant diastereoisomers (R*,R*) being ca. 10-fold more active than the other (R*,S*). Oral evaluation of the most active compounds in a furosemide-treated sodium-depleted rat model showed that compound 36g (UR-7198) reduced blood pressure dose dependently. This compound showed in vitro and iv potencies similar to that of the reference compound losartan but faster onset of action and somewhat greater oral activity, presumably due to its improved bioavailability.
Excitatory Connections Made by Presynaptic Cortico-Cortical Pyramidal Cells in Layer 6 of the Neocortex (2005)

Paired intracellular recordings with biocytin labelling were made in slices of adult rat somatosensory and visual cortex and in cat visual cortex to examine the properties of synaptic connections made by layer 6 pyramidal cells, to determine whether cortico-cortical pyramids more commonly provide input to other layer 6 pyramids than cortico-thalamic cells, and whether these connections exhibit paired pulse and brief train depression. Pyramidal cells with cortico-cortical like morphology were 2-4 times more likely to innervate other pyramidal cells than were cortico-thalamic like cells, but less likely to innervate inhibitory interneurons. The excitatory postsynaptic potentials elicited by presynaptic, phasically firing cortico-cortical pyramids in all classes of postsynaptic infragranular layer pyramidal cells exhibited strong, presynaptically mediated paired pulse and brief train depression. Those with larger paired pulse ratios also exhibited post-tetanic potentiation, but this was accompanied by stronger paired pulse and brief train depression. Both the firing characteristics and the outputs of cortico-cortical pyramidal cells display pronounced phasic characteristics, indicating that these cells respond most effectively to and preferentially pass on information related to novelty.
Fault Tolerance in Distributed Neural Computing (2015)

With the increasing complexity of computing systems, complete hardware reliability can no longer be guaranteed. We need, however, to ensure overall system reliability. One of the most important features of artificial neural networks is their intrinsic fault-tolerance. The aim of this work is to investigate whether such networks have features that can be applied to wider computational systems. This paper presents an analysis, in both the learning and operational phases, of a distributed feed-forward neural network with decentralised event-driven time management, which is insensitive to intermittent faults caused by unreliable communication or faulty hardware components. The learning rules used in the model are local in space and time, which allows efficient scalable distributed implementation. We investigate the overhead caused by injected faults and analyse the sensitivity to limited failures in the computational hardware in different areas of the network.
Interleukin-6 in the Bone Marrow Microenvironment Promotes the Growth and Survival of Neuroblastoma Cells (2008)

Neuroblastoma, the second most common solid tumor in children, frequently metastasizes to the bone marrow and the bone. Neuroblastoma cells present in the bone marrow stimulate the expression of interleukin-6 (IL-6) by bone marrow stromal cells (BMSC) to activate osteoclasts. Here we have examined whether stromal-derived IL-6 also has a paracrine effect on neuroblastoma cells. An analysis of the expression of IL-6 and its receptor, IL-6R, in 11 neuroblastoma cell lines indicated the expression of IL-6 in 4 cell lines and of IL-6R in 9 cell lines. Treatment of IL-6R-positive cells with recombinant human IL-6 resulted in signal transducer and activator of transcription-3 and extracellular signal-regulated kinase-1/2 activation. Culturing IL-6R-positive neuroblastoma cells in the presence of BMSC or recombinant human IL-6 increased proliferation and protected tumor cells from etoposide-induced apoptosis, whereas it had no effect on IL-6R-negative tumor cells. In vivo, neuroblastoma tumors grew faster in the presence of a paracrine source of IL-6. IL-6 induced the expression of cyclooxygenase-2 in neuroblastoma cells with concomitant release of prostaglandin-E2, which increased the expression of IL-6 by BMSC. Supporting a role for stromal-derived IL-6 in patients with neuroblastoma bone metastasis, we observed elevated levels of IL-6 in the serum and bone marrow of 16 patients with neuroblastoma bone metastasis and in BMSC derived from these patients. Altogether, the data indicate that stromal-derived IL-6 contributes to the formation of a bone marrow microenvironment favorable to the progression of metastatic neuroblastoma.
Blue up-conversion laser in Tm&gt;sup&lt;3&gt;/sup&lt;+doped ZBLAN glass fiber (2006)

An 1120nm Raman fiber laser pumped Tm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> +-doped ZBLAN fiber up-conversion laser was demonstrated with blue output power levels up to 116mW. The effects of the reflectivity of the output coupler mirrors on blue laser were investigated. Based on our experimental results, we also found that there exists a competition between photodegradation and photocuring in the operation of blue fiber laser, which can affect the maximum output power of blue fiber laser greatly.
Descriptor Matching with Convolutional Neural Networks: a Comparison to SIFT (2014)

Latest results indicate that features learned via convolutional neural networks outperform previous descriptors on classification tasks by a large margin. It has been shown that these networks still work well when they are applied to datasets or recognition tasks different from those they were trained on. However, descriptors like SIFT are not only used in recognition but also for many correspondence problems that rely on descriptor matching. In this paper we compare features from various layers of convolutional neural nets to standard SIFT descriptors. We consider a network that was trained on ImageNet and another one that was trained without supervision. Surprisingly, convolutional neural networks clearly outperform SIFT on descriptor matching. This paper has been merged with arXiv:1406.6909
Specific transcription factors prognostic for prostate cancer progression. (1998)

We have previously identified (M. Wang et al., Oncol. Res., in press, 1998) an enhancer element [human tissue inhibitor of metalloproteinase-1 enhancer-1 (HTE)] for the human tissue inhibitor of metalloproteinase-1 promoter that binds a novel zinc finger, cysteine-rich transcription factor (CRTF). In this study, we have used electrophoretic mobility shift assays to examine the relative level of expression of CRTF, jun/fos, and IFN-gamma responsive signal transducer activators of transcription (STATs) that bind specific HTE, activator protein, and IFN-gamma (Fcy and interferon regulatory factor) response motifs in tumor lines and human prostate tissue [i.e., normal (n = 3); benign prostatic hyperplasia (BPH; n = 12); high grade prostate intraepithelial neoplasia (PIN; n = 10); and prostate cancer adenocarcinoma (PCA; n = 61) plus seminal vesicle (n = 10) tissues]. The data showed that CRTF was overexpressed in PCA (Gleason's score, 10>8>6>5>4) compared with BPH, PIN, seminal vesicle, and normal tissues. To a much lesser degree, jun/fos and STAT 1 were also elevated in PCA compared to BPH, PIN, and normal tissues. In addition, blinded studies showed that CRTF and jun/fos were present at low levels in organ-confined specimens but at significantly elevated levels (P < 0.001) in samples exhibiting capsular penetration and localized spread, which indicated that CRTF and perhaps jun/fos were markers for cancer progression.