gebhart/patrepeval huggingface dataset:
Efficient synonym filtering and scalable delayed translation for hybrid virtual caching (2016)

Conventional translation look-aside buffers (TLBs) are required to complete address translation with short latencies, as the address translation is on the critical path of all memory accesses even for L1 cache hits. Such strict TLB latency restrictions limit the TLB capacity, as the latency increase with large TLBs may lower the overall performance even with potential TLB miss reductions. Furthermore, TLBs consume a significant amount of energy as they are accessed for every instruction fetch and data access. To avoid the latency restriction and reduce the energy consumption, virtual caching techniques have been proposed to defer translation to after L1 cache misses. However, an efficient solution for the synonym problem has been a critical issue hindering the wide adoption of virtual caching. Based on the virtual caching concept, this study proposes a hybrid virtual memory architecture extending virtual caching to the entire cache hierarchy, aiming to improve both performance and energy consumption. The hybrid virtual caching uses virtual addresses augmented with address space identifiers (ASID) in the cache hierarchy for common non-synonym addresses. For such non-synonyms, the address translation occurs only after last-level cache (LLC) misses. For uncommon synonym addresses, the addresses are translated to physical addresses with conventional TLBs before L1 cache accesses. To support such hybrid translation, we propose an efficient synonym detection mechanism based on Bloom filters which can identify synonym candidates with few false positives. For large memory applications, delayed translation alone cannot solve the address translation problem, as fixed-granularity delayed TLBs may not scale with the increasing memory requirements. To mitigate the translation scalability problem, this study proposes a delayed many segment translation designed for the hybrid virtual caching. The experimental results show that our approach effectively lowers accesses to the TLBs, leading to significant power savings. In addition, the approach provides performance improvement with scalable delayed translation with variable length segments.
Development of a monoclonal antibody specific for beta/A4 amyloid in Alzheimer's disease brain for application to in vivo imaging of amyloid angiopathy. (1992)

We evaluated the efficacy of murine monoclonal antibodies (Mabs) targeted to beta/A4 amyloid for development of procedures for the in vivo identification of amyloid angiopathy (AA) in Alzheimer's disease (AD). Mabs to beta/A4 amyloid were prepared and screened for effectiveness in visualizing AA and senile plaques in postmortem AD brain sections. They were assessed again after enzymatic cleavage to produce Fab fragments and after labeling with 99mTc using a diamide dimercaptide ligand system. Modified and radiolabeled Fab fragments retained activity and specificity towards amyloid-laden blood vessels and senile plaques. A highly specific murine Mab, 10H3, was identified and characterized that fulfills criteria necessary for the development of a diagnostic imaging agent. Expansion and adaptation of these strategies may provide the methods and materials for the noninvasive analysis of AA in living patients, and permit assessment of the contribution of AA to the clinical and pathological features of AD.
Microcomputer Programs for Prediction and Comparative Evaluation of Protein Secondary Structure From Nucleotide Sequence Data: Application to Ribulose-l,5-Bisphosphate Carboxylase Sequences (1985)

Apple II PASCAL computer programs are described for routine evaluation of protein secondary structures predicted from DNA or amino acid sequence data. The programs predict protein secondary structure using the directional information algorithm of Garnier et al. (1978), and calculate hydrophobicity (Kyte and Doolittle, 1982), hydrophilicity (Hopp and Woods, 1981), hydrophobic moment (Eisenberg et al., 1984b), and secondary structure propensity profiles. The novel feature of these programs is the application of numeric and graphic methods, designed to facilitate detection and characterization of structural similarities/divergences using the aforementioned structural parameters. The use of the programs is demonstrated on a set of sequences from the large and small subunits of ribulose-1,5-bisphosphate carboxylase.
A Bacillus cereus cytolytic determinant, cereolysin AB, which comprises the phospholipase C and sphingomyelinase genes: nucleotide sequence and genetic linkage (1989)

A cloned cytolytic determinant from the genome of Bacillus cereus GP-4 has been characterized at the molecular level. Nucleotide sequence determination revealed the presence of two open reading frames. Both open reading frames were found by deletion and complementation analysis to be necessary for expression of the hemolytic phenotype by Bacillus subtilis and Escherichia coli hosts. The 5' open reading frame was found to be nearly identical to a recently reported phospholipase C gene derived from a mutant B. cereus strain which overexpresses the respective protein, and it conferred a lecithinase-positive phenotype to the B. subtilis host. The 3' open reading frame encoded a sphingomyelinase. The two tandemly encoded activities, phospholipase C and sphingomyelinase, constitute a biologically functional cytolytic determinant of B. cereus termed cereolysin AB.
An Introduction to Dermatological Surgery (1996)

Introduction. Equipment. Sterilization of surgical equipment. Local anaesthetics. Haemostasis. Suture materials, suturing and knot tying. Pre-operative assessment and preparation. Anatomy and danger areas. Curretage. Snip excision. Cautery and electrodesiccation. Shave excision. Elliptical excision, punch biopsy and dog ear repairs. Epidermoid cysts, milia and lipomas. Nail avulsion and ingrown toenail. Treatment of viral warts. Cryotherapy in general practice. Treatment of skin tumours. Management of complications. Legal aspects of surgery in general practice. Histological interpretation. Nursing perspective. Index
Self-limiting growth of tantalum oxide thin films by pulsed plasma-enhanced chemical vapor deposition (2007)

Ta 2 O 5 thin films were fabricated by pulsed plasma-enhanced chemical vapor deposition (PECVD) with simultaneous delivery of O2 and the metal precursor. By appropriately controlling the gas-phase environment self-limiting deposition at controllable rates (∼1Å/pulse) was obtained. The process was insensitive to substrate temperature, with a constant deposition rate observed from 90to350°C. As-deposited Ta2O5 films under these conditions displayed good dielectric properties. Performance improvements correlate strongly with film density and composition as measured by spectroscopic ellipsometry and Fourier transform infrared spectroscopy. Pulsed PECVD eliminates the need for gas actuation and inert purge steps required by atomic layer deposition.
The Virion of Mengovirus Contains Anti-Interferon Activity (1993)

Many viruses are resistant to the antiviral state induced by interferon (IFN) in certain cell lines because they produce factors having anti-IFN activity (AIA). We show here that is+, a mengovirus strain resistant to low concentrations of IFN, also produces an AIA, but that an IFN-sensitive mutant (is-1) does not. This activity was detected when is+ rescued is-1 from the antiviral state induced in mouse L cells by mouse IFN. The mengovirus AIA was found in cell lysates prepared from cells infected with is+, and in the virions of purified, inactivated is+ but not in lysates prepared from is-1-infected cells or in the is-1 virion. Also the pentameric subunits that make up the viral capsid contained AIA, whereas the individual monomeric subunits that constitute the pentamers did not. We also describe an assay system for detecting and quantitating the mengovirus AIA.
Correlation of histological localization of tumor-associated macrophages with clinicopathological features in endometrial cancer. (2004)

Our findings demonstrate that the histological location of infiltrated TAMs may be taken into account in the clinical evaluation of endometrial cancer.
Quantitative Proteomics: Comparison of the Macular Bruch Membrane/Choroid Complex from Age-related Macular Degeneration and Normal Eyes (2010)

A quantitative proteomics analysis of the macular Bruch membrane/choroid complex was pursued for insights into the molecular mechanisms of age-related macular degeneration (AMD). Protein in trephine samples from the macular region of 10 early/mid-stage dry AMD, six advanced dry AMD, eight wet AMD, and 25 normal control post-mortem eyes was analyzed by LC MS/MS iTRAQ (isobaric tags for relative and absolute quantitation) technology. A total of 901 proteins was quantified, including 556 proteins from > or =3 AMD samples. Most proteins differed little in amount between AMD and control samples and therefore reflect the proteome of normal macular tissues of average age 81. A total of 56 proteins were found to be elevated and 43 were found to be reduced in AMD tissues relative to controls. Analysis by category of disease progression revealed up to 16 proteins elevated or decreased in each category. About 60% of the elevated proteins are involved in immune response and host defense, including many complement proteins and damage-associated molecular pattern proteins such as alpha-defensins 1-3, protein S100s, crystallins, histones, and galectin-3. Four retinoid processing proteins were elevated only in early/mid-stage AMD, supporting a role for retinoids in AMD initiation. Proteins uniquely decreased in early/mid-stage AMD implicate hematologic malfunctions and weakened extracellular matrix integrity and cellular interactions. Galectin-3, a receptor for advanced glycation end products, was the most significantly elevated protein in advanced dry AMD, supporting a role for advanced glycation end products in dry AMD progression. The results endorse inflammatory processes in both early and advanced AMD pathology, implicate different pathways of progression to advanced dry and wet AMD, and provide a new database for hypothesis-driven and discovery-based studies of AMD.
The renal handling of low molecular weight proteins (1972)

The present study was directed toward determining the role of the kidney in the metabolism of various classes of serum proteins and to define the urinary protein excretion patterns and the pathogenesis of disorders of protein metabolism in patients with proteinuria. To this end, the metabolic fates of a small protein, lambda-L chain (mol wt 44,000), and a protein of intermediate size, IgG (mol wt 160,000), were studied in controls and patients with renal disease. Controls metabolized 0.28%/hr of circulating IgG and 22.3%/hr of circulating lambda-L chain. All the IgG and 99% of the lambda-L chain was catabolized with the remaining lambda-L chain lost intact into the urine. The kidney was shown to be the major site of catabolism for small serum proteins. Three distinct disorders of protein metabolism were noted in patients with renal tubular disease and tubular proteinuria, glomerular disease (the nephrotic syndrome), and disease involving the entire nephrons (uremia), respectively. Patients with renal tubular disease had a 50-fold increase in the daily urinary excretion of 15-40,000 molecular weight proteins such as lysozyme and lambda-L chains. Serum IgG and lambda-L chain survivals were normal; however, the fraction of the over-all lambda-L chain metabolism accounted for by proteinuria was increased 40-fold whereas endogenous catabolism was correspondingly decreased. Thus, tubular proteinuria results from a failure of proximal tubular uptake and catabolism of small proteins that are normally filtered through the glomerulus. Patients with the nephrotic syndrome had a slight increase in lambda-L chain survival whereas IgG survival was decreased and the fraction of IgG lost in the urine was markedly increased. Here, abnormal glomerular permeability to proteins of intermediate size is the basic abnormality. Patients with uremia had a normal IgG survival but a four to 10-fold prolongation of lambda-L chain survival due to loss of entire nephrons, the major site of metabolism of these proteins. This results in an increase (up to 10-fold) in the serum concentration of lambda-L chain, lysozyme, and other small biologically active proteins, a phenomenon that may be of importance in causing some of the manifestations of the uremic syndrome.
Ultra-short-acting .beta.-adrenergic receptor blocking agents. 3. Ethylenediamine derivatives of (aryloxy)propanolamines having esters on the aryl function (1983)

Various ethylenediamine derivatives have been incorporated into the nitrogen substituent of certain short-acting (aryloxy)propanolamine systems that contain esters on their aryl functions. Although several of these compounds showed durations of action comparable to their prototypes, most of the nitrogen substituents significantly prolonged the duration of beta-adrenergic blockade. Similarly, while one of the compounds showed appreciable cardioselectivity in vitro, generally, little enhancement of cardioselectivity was obtained. A brief discussion of structure-activity relationships observed for the ethylenediamine derivatives is presented.
Laser ablation cell sorting in scanning cytometry (2001)

Flow cytometry has been an important tool for automated cells sorting. However, the lack of good sensitivity prevents it from being used for rare events sorting; furthermore, fragile cells, anchorage-dependent cells, and clump forming cells cannot be sorted this way. A fully automated, high-speed scanning cytometer with autofocus and image segmentation is capable of accurately locating contaminant cells in a monolayer cell population. A laser ablation system was incorporated into the cytometer to negatively sort out the unwanted cells by applying a focused, ultra-short laser pulse (sub-micron diameter, pulse duration = 4 nsec, wavelength - 500 nm) to each targeted cell. Due to the high power density (approximately 10<SUP>10</SUP> W/cm<SUP>2</SUP>) that was present at the focal point, disruptive mechanical forces were generated and were responsible for the kill. Fluorescently stained NIH-3T3 fibroblast cells were used as a model contaminant target ells in an unstained NIH-3T3 population to determine the identification-kill effectiveness. The contaminant cells were stained with the fluorochrome CellTracker Blue CMAC, whereas the background cells were left intact. Ablation pulses were applied in frame-by-frame increment batches to the cell culture on the microscope. The negative sorting effectiveness was analyzed by automatically re-scanning the post-ablation cell culture in phase contrast and propidium iodide stained epi fluorescent fields to verify cell death.
Fucoidan Reduces Secretion and Expression of Vascular Endothelial Growth Factor in the Retinal Pigment Epithelium and Reduces Angiogenesis In Vitro (2014)

Fucoidan is a polysaccharide isolated from brown algae which is of current interest for anti-tumor therapy. In this study, we investigated the effect of fucoidan on the retinal pigment epithelium (RPE), looking at physiology, vascular endothelial growth factor (VEGF) secretion, and angiogenesis, thus investigating a potential use of fucoidan for the treatment of exudative age-related macular degeneration. For this study, human RPE cell line ARPE-19 and primary porcine RPE cells were used, as well as RPE/choroid perfusion organ cultures. The effect of fucoidan on RPE cells was investigated with methyl thiazolyl tetrazolium--assay, trypan blue exclusion assay, phagocytosis assay and a wound healing assay. VEGF expression was evaluated in immunocytochemistry and Western blot, VEGF secretion was evaluated in ELISA. The effect of fucoidan on angiogenesis was tested in a Matrigel assay using calcein-AM vital staining, evaluated by confocal laser scanning microcopy and quantitative image analysis. Fucoidan displays no toxicity and does not diminish proliferation or phagocytosis, but reduces wound healing in RPE cells. Fucoidan decreases VEGF secretion in RPE/choroid explants and RPE cells. Furthermore, it diminishes VEGF expression in RPE cells even when co-applied with bevacizumab. Furthermore, fucoidan reduces RPE-supernatant- and VEGF-induced angiogenesis of peripheral endothelial cells. In conclusion, fucoidan is a non-toxic agent that reduces VEGF expression and angiogenesis in vitro and may be of interest for further studies as a potential therapy against exudative age-related macular degeneration.
Interaction between nutrition and gastrointestinal parasitism in sheep (2001)

Effects of gastrointestinal nematode infection on metabolism and nutrient utilisation in sheep are reviewed. Infection induces protein deficiency by increasing the demand for amino acids in the alimentary tract while reducing supply through depression of appetite. Mechanisms through which improved protein nutrition could improve the performance of the host are then discussed. Opportunities for capitalising on such effects are limited by our rudimentary understanding of the cell-mediated immune response in gastrointestinal epithelial tissue. Both resistance of the animal to larval establishment and performance in the face of larval challenge can be enhanced by improved protein nutrition. However, enhanced immune responses may not necessarily be synonymous with improved productivity except at luxurious levels of protein intake, because of apparently competing demands for protein. Such levels of protein nutrition are difficult to achieve in pasture-based systems, because of the protein limiting role of the rumen. Work with proteinprotecting tannins to overcome this limitation is discussed. The much more limited evidence for effect of mineral nutrition, particularly copper (Cu), molybdenum (Mo), cobalt (Co) and phosphorus (P), on outcome of larval challenge is also reviewed.
Community Awareness and Attitudes towards Influenza Outbreak and Prevention in Serian, Sarawak (1999)

Our results suggest that cathepsin A may participate in the pathogenesis of absolute glaucoma and that proteolysis may play a significant role in local destruction of the retina and the optic nerve.
Evidence for the Mitochondrial Lactate Oxidation Complex in Rat Neurons: Demonstration of an Essential Component of Brain Lactate Shuttles (2008)

To evaluate the presence of components of a putative Intracellular Lactate Shuttle (ILS) in neurons, we attempted to determine if monocarboxylate (e.g. lactate) transporter isoforms (MCT1 and -2) and lactate dehydrogenase (LDH) are coexpressed in neuronal mitochondria of rat brains. Immunohistochemical analyses of rat brain cross-sections showed MCT1, MCT2, and LDH to colocalize with the mitochondrial inner membrane marker cytochrome oxidase (COX) in cortical, hippocampal, and thalamic neurons. Immunoblotting after immunoprecipitation (IP) of mitochondria from brain homogenates supported the histochemical observations by demonstrating that COX coprecipitated MCT1, MCT2, and LDH. Additionally, using primary cultures from rat cortex and hippocampus as well as immunohistochemistry and immunocoprecipitation techniques, we demonstrated that MCT2 and LDH are coexpressed in mitochondria of cultured neurons. These findings can be interpreted to mean that, as in skeletal muscle, neurons contain a mitochondrial lactate oxidation complex (mLOC) that has the potential to facilitate both intracellular and cell-cell lactate shuttles in brain.
Tumor growth inhibition by synthetic and expressed siRNA targeting focal adhesion kinase (2008)

Focal adhesion kinase (FAK) was first identified as a viral Src substrate, and substantial experimental data have significantly correlated the elevated FAK expression in human tumor cells with an increased cell adhesion and invasion potential. However, studies investigating the role of FAK in cell proliferation have been limited. Recently, a technique known as RNA interference (RNAi) was successfully adapted to mammalian cells to decrease specifically the expression of targeted cellular genes. In this study, we investigated the role of FAK in cell proliferation, adhesion, and migration by using small interfering RNA (siRNA) technique. Firstly, we constructed a plasmid library expressing short hairpin RNAs (shRNAs) targeting FAK and selected clones substantially suppressing FAK expression in HeLa and HT1080 cells. We then studied the function of FAK in the highly invasive human prostate cancer cell line, PC3M, and mouse breast cancer cell line 4T1, by using selected shRNA clones (#40 and #42) and siRNAs chemically synthesized following the target sequences of #40 and #42. We demonstrated that the decrease of FAK protein expression by treatment with shRNA/siRNA targeting FAK inhibited cell adhesion on a fibronectin/laminin-coated plate, cell migration in a haptotactic migration assay, and cell proliferation in vitro. Furthermore, it suppressed tumor growth in vivo in heterotopic/orthotopic mice models. These results support our hypothesis that FAK plays a crucial role in tumor formation and growth in vivo by regulation of cell adhesion and proliferation by FAK-dependent signals.
Protein Import and Routing Systems of Chloroplasts (1999)

Plastids are ubiquitous plant cell organelles that perform many essential functions. Chloroplasts are the most complex type of plastid, both structurally and functionally, containing six distinct compartments and performing essential processes, such as fatty acid and amino acid biosynthesis in
Hepatitis C virus RNA replication is regulated by host geranylgeranylation and fatty acids (2005)

Hepatitis C virus (HCV) infection is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Our laboratory has previously demonstrated that high-level HCV replication during acute infection of chimpanzees is associated with the modulation of multiple genes involved in lipid metabolism, and that drugs that regulate cholesterol and fatty acid biosynthesis regulate the replication of the subgenomic HCV replicon in Huh-7 cells. In this article, we demonstrate that Huh-7 cells harboring replicating, full-length HCV RNAs express elevated levels of ATP citrate lyase and acetyl-CoA synthetase genes, both of which are involved in cholesterol and fatty acid biosynthesis. Further, we confirm that the cholesterol-biosynthetic pathway controls HCV RNA replication by regulating the cellular levels of geranylgeranyl pyrophosphate, we demonstrate that the impact of geranylgeranylation depends on the fatty acid content of the cell, and we show that fatty acids can either stimulate or inhibit HCV replication, depending on their degree of saturation. These results illustrate a complex cellular-regulatory network that controls HCV RNA replication, presumably by modulating the trafficking and association of cellular and/or viral proteins with cellular membranes, suggesting that pharmacologic manipulation of these pathways may have a therapeutic effect in chronic HCV infection.