gebhart/patrepeval huggingface dataset:
Automated task distribution in multicore network processors using statistical analysis (2007)

Chip multiprocessor designs are the most common types of architectures seen in Network Processors. As the Network Processors are used to implement increasingly complicated applications, task distribution among the cores is becoming an important problem. In this paper, we propose a new task allocation scheme for such architectures. This scheme relies on the inherent modular nature of the networking applications and intelligently distributes modules among different execution cores. Additionally, we selectively replicate modules to parallelize execution of tasks having longer processing time. We have developed a technique that uses the probability distribution of the execution times of different modules in the networking applications. The proposed schemes result in resource utilization of up to 95%, 89%, and 84% on average for the processors with 2, 4, and 8 cores, respectively. The schemes are highly scalable and can improve the throughput by 6.72 times for 8 core processors, aggregated over four representative applications. The combination of selective replication of modules and variation-aware task allocation result in up to 12.5% (9.9% on average) performance improvement as compared to a scheme based on just mean processing time.
Improvements to parallel plate flow chambers to reduce reagent and cellular requirements (2001)

These modifications are simple and easily implemented so that study of rare leukocyte subsets using scarce or expensive reagents can occur.
Selective Inhibition of Matrix Metalloproteinase-13 Increases Collagen Content of Established Mouse Atherosclerosis (2011)

Pharmacological MMP-13 inhibition yields collagen accumulation in plaques (a feature associated in humans with resistance to rupture), even in established plaques. This study, of considerable clinical relevance, furnishes new mechanistic insight into regulation of the plaque's extracellular matrix and validates molecular imaging for studying plaque biology.
Tumorigenicity of simian virus 40-hepatocyte cell lines: effect of in vitro and in vivo passage on expression of liver-specific genes and oncogenes. (1988)

Five simian virus 40 (SV40)-hepatocyte cell lines were examined for tumorigenicity and the effect of in vitro passage on the expression of four liver-specific genes (albumin, transferrin, alpha 1-antitrypsin, and phosphoenolpyruvate carboxykinase), two oncogenes (c-Ha-ras and c-raf), and two genes associated with hepatocarcinogenesis (alpha-fetoprotein and placental-type glutathione-S-transferase). At low passage (12 to 22), all five cell lines expressed the four liver-specific genes at levels similar to those in the liver and were not tumorigenic or were weakly tumorigenic. At high passage (33 to 61), the cell lines formed carcinomas, and four out of five cell lines produced primary tumors that metastasized. At least two cell lines produced well-differentiated hepatocellular carcinomas that expressed liver-specific RNAs. Levels of expression of liver-specific genes changed with time in culture. Some of the changes in liver-specific gene expression in the tumor tissue (such as for the phosphoenolpyruvate carboxykinase gene) paralleled those that occurred with in vitro passage, while other changes (such as for the albumin gene) did not parallel those that occurred with in vitro passage. Correlations between enhanced expression of c-Ha-ras and tumorigenic potential and between the process of SV40 immortalization and induced expression of c-raf and glutathione-S-transferase-P were observed. Induction of alpha-fetoprotein was detected with in vitro and in vivo passage only in the CWSV14 cell line and was paralleled by diminished albumin expression. In conclusion, we developed a model system with five SV40-hepatocyte cell lines, tumors induced by them, and tumor cell lines to examine changes in gene expression that accompany the progression from a normal cell to a hepatocellular carcinoma. Because the SV40-hepatocyte cell lines and tumor cell lines remain highly differentiated and vary in the magnitude of expression of specific genes, they can be used to study the molecular mechanisms regulating gene expression, in particular those regulating specific genes associated with differentiation.
The Use of Zwittergent 3-14 in the Purification of Recombinant Human Interferon-β Ser 17 (Betaseron) (1995)

A new method for purifying human interferon-beta SER17 from E. coli-derived inclusion bodies has been developed. This procedure eliminates the need for strong denaturants, such as sodium dodecyl sulfate or chaotropes. The procedure makes use of a nondenaturing detergent and a brief incubation at pH 12 to solubilize interferon-beta Ser17 from inclusion bodies. The detergent used was Zwittergent 3-14 (nonionic and pH-insensitive), which is included in the class of sulfobetaines (RN+ (CH3)2(CH2)xSO3-). Zwittergent 3-14 was used in combination with urea to produce a urea/Zwittergent 3-14 washed inclusion body preparation enriched in human interferon-beta Ser17 (Betaseron). Solubilization of inclusion bodies was accomplished by employing a brief (1 minute) shift to pH 12 in the presence of 2.5% Zwittergent 3-14 followed by rapid adjustment to pH 8.0. Solubilization was complete, and the solution could be rapidly adjusted to pH 8 without any observable precipitation of protein. The resultant supernatant could be successfully subjected to a number of chromatographic and analytic procedures, many of which are not compatible with strong anionic detergents, such as SDS. Betaseron was purified from Zwittergent 3-14 solubilized inclusion body lysates using both ion-exchange and size-exclusion chromatography. Purified Betaseron retained bioactivity and could be refolded by simple dialysis against a nonreducing buffer. This method represents a novel procedure for purifying Betaseron from inclusion bodies using a nondenaturing detergent and ion-exchange chromatography.
An overview of intelligent vehicle highway systems (IVHS) (2002)

The national IVHS program consists of six interrelated application areas: (1) advanced traffic management systems (ATMS), (2) advanced traveler information systems (ATIS), (3) advanced public transportation systems (APTS), (4) advanced vehicle control systems (AVCS), (5) advanced rural transportation systems (ARTS), and (6) commercial vehicle operations (CVO). These diverse applications anticipate a wide range of new technologies and a remarkable variety of commercial opportunities. IVHS applications will require both the development of brand new systems and products, as well as the innovative adaptation of existing systems and products from other applications. This paper presents an overview of the national IVHS program, and describes general commercial opportunities in each of the IVHS application areas.
Characteristics of Human Rheumatoid Synovial and Normal Blood Dendritic Cells (1987)

Dendritic cells (DC) were isolated from synovial tissue and synovial fluids of patients with rheumatoid arthritis and from peripheral blood of healthy donors. The cells were analysed for various surface antigens in indirect immunofluorescence by means of monoclonal antibodies. Surface antigen expression and accessory activity of the DC during short-term cultures were also investigated. Both the rheumatoid synovial and the normal blood DC were strongly positive for panleucocyte antigen and class II major histocompatibility complex (MHC) antigens (HLA-DP, HLA-DQ, and HLA-DR). The DC suspensions (purity approximately 80-85%) showed very low percentage of cells staining for various other cell membrane markers, including B cell, T cell, natural killer (NK) cell, and various monocyte/macrophage markers as well as markers specific for dendritic reticulum cells and Reed Sternberg cells. Moreover, neither rheumatoid nor normal DC reacted with the RFD1 monoclonal antibody, which is specific for interdigitating cells of human thymus. In contrast to Langerhans' cells, the DC lacked the thymocyte (T6) marker. The various DC expressed neither complement receptors (CR1, CR3), transferrin receptors, nor Fc receptors. They also lacked enzyme markers like peroxidase and nonspecific esterase. The DC formed clusters with autologous T cells. Cluster formation was readily inhibited by anti-HLA-DR and anti-CD2 (T11) monoclonal antibodies. After 3 to 5 days in culture the DC still expressed class II MHC antigens and were potent stimulators in allogeneic mixed lymphocyte reactions (MLR). Only a small number of cells in the DC suspensions from synovial tissue expressed fibroblast antigens before and after culture.
Increased frequency ofATM mutations in breast carcinoma patients with early onset disease and positive family history (2001)

ATM mutations, specifically missense mutations, are more common in breast carcinoma cases selected for first-degree family history and early age at diagnosis.
Advances in pancreatic cancer research: Moving towards early detection (2014)

Pancreatic ductal adenocarcinoma(PDAC) is one of the most lethal forms of cancer. Substantial progress has been made in the understanding of the biology of pancreatic cancer, and advances in patient management have been significant. However, most patients(nearly80%) who present with locally advanced or metastatic disease have an extremely poor prognosis. Survival is better for those with malignant disease localized to the pancreas, because surgical resection at present offers the only chance of cure. Therefore, the early detection of pancreatic cancer may benefit patients with PDAC.However, its low rate of incidence and the limitations of current screening strategies make early detection difficult. Recent advances in the understanding of the pathogenesis of PDAC suggest that it is possible to detect PDAC in early stages and even identify precursor lesions. The presence of new-onset diabetes mellitus in the early phase of pancreatic cancer may provide cluesfor its early diagnosis. Advances in the identification of novel circulating biomarkers including serological signatures, autoantibodies, epigenetic markers, circulating tumor cells and microRNAs suggest that they can be used as potential tools for the screening of precursors and early stage PDAC in the future. However, proper screening strategies based on effective screening methodologies need to be tested for clinical application.
Therapies for Hepatitis C Infection: Targeting the Non-Structural Proteins of HCV (2002)

The hepatitis C virus infects an estimated 1-3% of the world population. A large proportion of individuals afflicted by this rapidly spreading epidemic eventually progress to chronic liver disorders. Liver failures associated with chronic hepatitis C infections are the leading cause for liver transplantations in the US. Currently, the backbone of anti-HCV therapy, consisting of various forms of interferon in combination with broad-spectrum antivirals such as ribavirin, has only met with limited success. This review will provide coverage of recent efforts towards the development of novel antiviral strategies that target inhibition of essential enzymatic functions encoded by the non-structural region of the HCV genome. These include principally, inhibition of the NS3 protease and helicase, and of the NS5B RNA-dependent RNA polymerase. Keywords: Hepatitis c infection, Non-structural proteins, Hepatitis c virus, Ns3 protease, Benzimidazole-containing inhibitors, Inhibition of ns3 helicase, Ns5b polymerase
Synthesis of 2’-Modified Nucleotides (2000)

We show in this work the development of modified building blocks for the synthesis of nuclease resistant hammerhead ribozymes. These modified monomers retain the 2’-OH which is essential for the activity of these molecules. Our final goal is to generate a catalytic antisense approach with potential application in gene therapy.
GaAs-AlAs monolithic microresonator arrays (1987)

Monolithic optical logic devices 1.5–5 μm across are defined by ion-beam assisted etching through a GaAs/AlAs Fabry–Perot structure grown by molecular beam epitaxy. They show reduced energy requirements (more than an order of magnitude smaller than the unetched heterostructure), uniform response over small arrays, negligible crosstalk at 3 μm center-center spacing, ∼150 ps recovery time, and thermal stability at 82 MHz operating frequency. All experiments were performed at room temperature.
A rapid screening assay for antioxidant potential of natural and synthetic agents in vitro (2002)

There are literally thousands of known agents with potential chemopreventive and antioxidant activity; however, the expanding list of natural and synthetic compounds makes it difficult to test every agent in the widely accepted 2-year animal bioassay and human clinical trials. Therefore, short-term screening assays are needed to sort out the most efficacious compounds for long-term animal studies. In the present study, the identification of chemopreventive agents with efficacious antioxidant potential was explored with a Cu2+-mediated Fenton-type reaction, coupled with oxidative DNA lesion detection by 32P-postlabeling. Several agents inhibited the formation of 8-oxo-2'-deoxyguanosine (8-oxodG), a benchmark oxidative DNA lesion, but ellagic acid, a polyphenol found in berries, offered maximal (>80%) inhibition of 8-oxodG formation. However, a well-known tea polyphenol, epigallocatechin gallate, along with silymarin and D,L-sulforaphane, exhibited a pro-oxidant effect, with 50-70% increase in 8-oxodG induction. In general, our results agree with the reported antioxidant - pro-oxidant activities of the compounds, rendering this in vitro screening assay to be useful in determining the antioxidant potential of compounds rapidly and cost-effectively.
Scaffold optimization in discontinuous epitope containing protein mimics of gp120 using smart libraries (2013)

A diversity of protein surface discontinuous epitope mimics is now rapidly and efficiently accessible. Despite the important role of protein-protein interactions involving discontinuous epitopes in a wide range of diseases, mimicry of discontinuous epitopes using peptide-based molecules remains a major challenge. Using copper(I) catalyzed azide-alkyne cycloaddition (CuAAC), we have developed a general and efficient method for the synthesis of collections of discontinuous epitope mimics. Up to three different cyclic peptides, representing discontinuous epitopes in HIV-gp120, were conjugated to a selection of scaffold molecules. Variation of the scaffold molecule, optimization of the ring size of the cyclic peptides and screening of the resulting libraries for successful protein mimics led to an HIV gp120 mimic with an IC50 value of 1.7 μM. The approach described here provides rapid and highly reproducible access to clean, smart libraries of very complex bio-molecular constructs representing protein mimics for use as synthetic vaccines and beyond.
The kinetics of antibody binding to membrane antigens in solution and at the cell surface (1980)

The reaction kinetics of 125I-labelled mouse monoclonal antibodies binding to three cell-surface antigens of rat thymocytes (Thy-1.1, W3/25) were studied. The differences between bivalent and univalent interactions were determined by using antibody in the F(ab')2 or Fab' form and by using antigen in polymeric or monomeric forms. Association rate constants (k+1), dissociation rate constants (k-1) and equilibrium constants were determined. Also, the dissociation kinetics of rabbit antibodies against rat Thy-1 antigen were studied. The major findings were as follows. (i) With F(ab')2 antibody there was no simple relationship between antigen density at the cell surface and extent of bivalent binding. Extensive univalent binding was observed unless the antibody had a high k-1 for the univalent interaction, in which case all binding was bivalent. (ii) k+1 values were similar for F(ab')2 or Fab' antibody, and for the different antibodies were in the range 0.8 x 10(5)--1.1 x 10(6) M-1.s-1. These differences were sufficient to affect the interpretation of serological assays with the different antibodies. (iii) Antibody bound bivalently dissociated much more slowly than that bound univalently. However, the k-1 values for the univalently bound antibody were sufficiently low in most cases that the lifetime of the univalent complex was similar to or greater than the time needed for the assay. Thus the results could be interpreted on the basis of irreversible reactions. The overall conclusion from the study is that for an understanding of the binding of antibody to cell-surface antigens the kinetics of the interaction are of major importance and theories based on equilibrium binding are inappropriate.
Efficacy and safety of pemafibrate (K-877), a selective peroxisome proliferator-activated receptor α modulator, in patients with dyslipidemia: Results from a 24-week, randomized, double blind, active-controlled, phase 3 trial (2017)

Pemafibrate was superior to fenofibrate in terms of serum TG-lowering effect and hepatic and renal safety.
Procedure for isolation of bacterial lipopolysaccharides from both smooth and rough Pseudomonas aeruginosa and Salmonella typhimurium strains (1983)

Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. It is now well established that within a single organism, size heterogeneity of this molecule can exist. We have developed a LPS isolation procedure which is effective in extracting both smooth and rough LPS in high yields (51 to 81% of the LPS present in whole cells as quantitated by using hydroxy fatty acid, heptose, and 2-keto-3-deoxyoctonate yields) and with a high degree of purity. The contamination by protein (0.1% by weight of LPS), nucleic acids (1%), lipids (2 to 5%), and other bacterial products was low. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the LPS demonstrated the presence of a high degree of size heterogeneity in the isolated smooth LPS as well as the presence of significant amounts of rough-type LPS. The Pseudomonas aeruginosa LPS interacted well with a monoclonal antibody in a variety of immunochemical analyses. The usefulness of the procedure was demonstrated by comparing LPS preparations obtained from wild-type and mutant strains of P. aeruginosa and Salmonella typhimurium. For example, it was shown that the LPS of an antibiotic supersusceptible mutant Z61 of P. aeruginosa, which was previously characterized as identical to wild type with respect to the ratio of smooth to rough LPS molecules isolated by the phenol-water procedure, actually contained only a small proportion of O-antigenic side chains.
A macrophage colony-stimulating factor receptor–green fluorescent protein transgene is expressed throughout the mononuclear phagocyte system of the mouse (2003)

The c-fms gene encodes the receptor for macrophage colony-stimulating factor (CSF-1). The gene is expressed selectively in the macrophage and trophoblast cell lineages. Previous studies have indicated that sequences in intron 2 control transcript elongation in tissue-specific and regulated expression of c-fms. In humans, an alternative promoter was implicated in expression of the gene in trophoblasts. We show that in mice, c-fms transcripts in trophoblasts initiate from multiple points within the 2-kilobase (kb) region flanking the first coding exon. A reporter gene construct containing 3.5 kb of 5' flanking sequence and the downstream intron 2 directed expression of enhanced green fluorescent protein (EGFP) to both trophoblasts and macrophages. EGFP was detected in trophoblasts from the earliest stage of implantation examined at embryonic day 7.5. During embryonic development, EGFP highlighted the large numbers of c-fms-positive macrophages, including those that originate from the yolk sac. In adult mice, EGFP location was consistent with known F4/80-positive macrophage populations, including Langerhans cells of the skin, and permitted convenient sorting of isolated tissue macrophages from disaggregated tissue. Expression of EGFP in transgenic mice was dependent on intron 2 as no lines with detectable EGFP expression were obtained where either all of intron 2 or a conserved enhancer element FIRE (the Fms intronic regulatory element) was removed. We have therefore defined the elements required to generate myeloid- and trophoblast-specific transgenes as well as a model system for the study of mononuclear phagocyte development and function.
An 8MHz 75&#x00B5;A/MHz zero-leakage non-volatile logic-based Cortex-M0 MCU SoC exhibiting 100% digital state retention at V<inf>DD</inf>=0V with &lt;400ns wakeup and sleep transitions (2013)

We demonstrate a non-volatile logic (NVL)-based SoC that backs up its working state (all flip-flops) upon receiving a power interrupt, has zero leakage in sleep mode, and needs less than 400ns to restore the system state upon power-up. Without NVL, a chip would either have to keep all flip-flops powered resulting in high standby power, or waste energy and time rebooting after power-up. For energy harvesting applications, NVL is a “must have” because there is no constant power source available to keep flip-flops (FFs) alive, and even when the intermittent power source is available, boot-up code alone may consume all of the harvested energy. For handheld devices with limited cooling and battery capacity, zero-leakage IC's with “instant-on” capability are ideal.
A micro cell culture analog (µCCA) with 3-D hydrogel culture of multiple cell lines to assess metabolism-dependent cytotoxicity of anti-cancer drugs (2009)

A microfluidic device with 3-D hydrogel cell cultures has been developed to test the cytotoxicity of anti-cancer drugs while reproducing multi-organ interactions. In this device, a micro cell culture analog (microCCA), cells embedded in 3-D hydrogels are cultured in separate chambers representing the liver, tumor, and marrow, which are connected by channels mimicking blood flow. While the microfluidic network provides a platform for mimicking the pharmacokinetic and pharmacodynamic profiles of a drug in humans, the 3-D hydrogel provides a more physiologically realistic environment to mimic the tissue than monolayer culture. Colon cancer cells (HCT-116) and hepatoma cells (HepG2/C3A) were encapsulated in Matrigel and cultured in the tumor and the liver chamber in a microCCA, respectively. Myeloblasts (Kasumi-1) were encapsulated in alginate in the marrow chamber; a stiffer hydrogel was necessary to prevent cell migration out of the matrix. The cytotoxic effect of Tegafur, an oral prodrug of 5-fluorouracil (5-FU), on each cell line was tested using the microCCA with cell-embedded hydrogel. The comparison of experimental results using a 96-well microtiter plate and a microCCA demonstrated that the microCCA was able to reproduce the metabolism of Tegafur to 5-FU in the liver and consequent death of cells by 5-FU, while the cultures in a 96-well microtiter plate were unable to do so. The microCCA utilizing 3-D hydrogel cell cultures has potential as a platform for pharmacokinetic-based drug screening in a more physiologically realistic environment.
Double minute chromosomes can be produced from precursors derived from a chromosomal deletion. (1988)

Recent experiments have shown that gene amplification can be mediated by submicroscopic, autonomously replicating, circular extrachromosomal molecules. We refer to those molecules as episomes (S. Carroll, P. Gaudray, M. L. DeRose, J. F. Emery, J. L. Meinkoth, E. Nakkim, M. Subler, D. D. Von Hoff, and G. M. Wahl, Mol. Cell. Biol. 7:1740-1750, 1987). The experiments reported in this paper explore the way episomes are formed and their fate in the cell over time. The data reveal that in our system the episomes are initially 250 kilobases, but gradually enlarge until they become double minute chromosomes. In addition, we show that episomes or double minute chromosomes can integrate into chromosomes. Our results also suggest that episomes can be produced by deletion of the corresponding sequences from the chromosome.