gebhart/patrepeval huggingface dataset:
Decoupled DIMM (2009)

The widespread use of multicore processors has dramatically increased the demands on high bandwidth and large capacity from memory systems. In a conventional DDR2/DDR3 DRAM memory system, the memory bus and DRAM devices run at the same data rate. To improve memory bandwidth, we propose a new memory system design called decoupled DIMM that allows the memory bus to operate at a data rate much higher than that of the DRAM devices. In the design, a synchronization buffer is added to relay data between the slow DRAM devices and the fast memory bus; and memory access scheduling is revised to avoid access conflicts on memory ranks. The design not only improves memory bandwidth beyond what can be supported by current memory devices, but also improves reliability, power efficiency, and cost effectiveness by using relatively slow memory devices. The idea of decoupling, precisely the decoupling of bandwidth match between memory bus and a single rank of devices, can also be applied to other types of memory systems including FB-DIMM. Our experimental results show that a decoupled DIMM system of 2667MT/s bus data rate and 1333MT/s device data rate improves the performance of memory-intensive workloads by 51% on average over a conventional memory system of 1333MT/s data rate. Alternatively, a decoupled DIMM system of 1600MT/s bus data rate and 800MT/s device data rate incurs only 8% performance loss when compared with a conventional system of 1600MT/s data rate, with 16% reduction on the memory power consumption and 9% saving on memory energy.
Matrix Metalloproteinase-2 and −9 Differentially Regulate Smooth Muscle Cell Migration and Cell-Mediated Collagen Organization (2003)

MMP-2 and MMP-9 genetic deficiency decreased by 81% and 65%, respectively (P<0.01), SMC invasion in vitro and decreased formation of intimal hyperplasia in vivo (P<0.01). However, we found that MMP-9, but not MMP-2, was necessary for organization of collagen by SMCs. Likewise, we found that MMP-9 deficiency resulted in a 50% reduction of SMC attachment to gelatin (P<0.01), indicating that SMCs may use MMP-9 as a bridge between the cell surface and matrix. Furthermore, we found that the hyaluronan receptor, CD44, assists in attachment and utilization of MMP-9 by SMCs. Understanding the specific roles of these MMPs, generally thought to be similar, could improve the design of therapeutic interventions aimed at controlling vascular remodeling.
Cytokine Expression and Accelerated Tooth Movement (2010)

It has been shown that inhibiting the expression of certain cytokines decreases the rate of tooth movement. Here, we hypothesized that stimulating the expression of inflammatory cytokines, through small perforations of cortical bone, increases the rate of bone remodeling and tooth movement. Forty-eight rats were divided into 4 groups: 50-cN force applied to the maxillary first molar (O), force application plus soft tissue flap (OF), force application plus flap plus 3 small perforations of the cortical plate (OFP), and a control group (C). From the 92 cytokines studied, the expression of 37 cytokines increased significantly in all experimental groups, with 21 cytokines showing the highest levels in the OFP group. After 28 days, micro-computed tomography, light and fluorescent microscopy, and immunohistochemistry demonstrated higher numbers of osteoclasts and bone remodeling activity in the OFP group, accompanied by generalized osteoporosity and increased rate of tooth movement.
A Method for Automatic Fall Detection of Elderly People Using Floor Vibrations and Sound—Proof of Concept on Human Mimicking Doll Falls (2009)

Falls are a major risk for the elderly people living independently. Rapid detection of fall events can reduce the rate of mortality and raise the chances to survive the event and return to independent living. In the last two decades, several technological solutions for detection of falls were published, but most of them suffer from critical limitations. In this paper, we present a proof of concept to an automatic fall detection system for elderly people. The system is based on floor vibration and sound sensing, and uses signal processing and pattern recognition algorithm to discriminate between fall events and other events. The classification is based on special features like shock response spectrum and mel frequency ceptral coefficients. For the simulation of human falls, we have used a human mimicking doll: "Rescue Randy." The proposed solution is unique, reliable, and does not require the person to wear anything. It is designed to detect fall events in critical cases in which the person is unconscious or in a stress condition. From the preliminary research, the proposed system can detect human mimicking dolls falls with a sensitivity of 97.5% and specificity of 98.6%.
High‐temperature kinetics of the homogeneous reverse water–gas shift reaction (2004)

Abstract The high‐temperature rate of reaction of the homogeneous, reverse water–gas shift reaction (rWGSR) has been evaluated in quartz reactors with rapid feed preheating under both low‐ and high‐pressure conditions. The form of the power‐law rate expression was consistent with the Bradford mechanism. The Arrhenius expressions for the reaction rate constant, corresponding to the empty reactor, were in very good agreement with the low‐pressure results of Graven and Long, but yielded rate constants roughly four times greater than those obtained in our packed reactor and those reported by Kochubei and Moin and by Tingey. Reactor geometry was not responsible for these differences because computational fluid dynamics simulations revealed similar residence time distributions and comparable conversions when the same kinetic expression was used to model the rWGSR in each reactor. Most likely, the empty NETL reactor and the Graven and Long reactor did not attain an invariant value of the concentration of the chain carrier (H) at low reaction times, which led to an overestimation of the rate constant. Conversions attained in an Inconel® 600 reactor operating at comparable conditions were approximately two orders of magnitude greater than those realized in the quartz reactor. This dramatic increase in conversion suggests that the Inconel® 600 surfaces, which were depleted of nickel during the reaction, catalyzed the rWGSR. © 2004 American Institute of Chemical Engineers AIChE J, 50: 1028–1041, 2004
Carbohydrate deficient serum transferrin in a new systemic hereditary syndrome. (1990)

Four patients with a new, inherited, complex developmental deficiency syndrome were studied. The syndrome affects the central and peripheral nervous system, and also the retina, liver, bone, adipose tissue, and genital organs. Abnormalities of glycoproteins, glycopeptide hormones, and lipids have been found in serum from these patients, the most pronounced being increased cathodal forms of transferrin. Isoforms of serum transferrin were therefore analysed qualitatively and quantitatively by isoelectric focusing and isocratic anion exchange chromatography, and the carbohydrate composition was determined in transferrin isolated by immune affinity chromatography. All the patients had about tenfold raised serum concentrations of isotransferrins with higher isoelectric points than normal. Similar findings, though less pronounced, were made in all the fathers and in one of the mothers. Half the transferrin in the patients was constantly present in two principal abnormal cathodal forms in approximately equal amounts. Carbohydrate determinations in purified transferrin showed quantitatively similar deficiencies of sialic acid, galactose, and N-acetylglucosamine, the mannose content being normal. The results suggest that either two or all of the normally four terminal trisaccharides in transferrin may be missing. A defect in the synthesis or catabolism, or both, of this trisaccharide, which is common to many secretory glyco-conjugates, is likely. Apart from providing a quantitative diagnostic method, the present findings may serve as a basis for further studies of the metabolic deficiency in this syndrome.
Advances and Future Challenges in Adenoviral Vector Pharmacology and Targeting (2011)

Adenovirus is a robust vector for therapeutic applications, but its use is limited by our understanding of its complex in vivo pharmacology. In this review we describe the necessity of identifying its natural, widespread, and multifaceted interactions with the host since this information will be crucial for efficiently redirecting virus into target cells. In the rational design of vectors, the notion of overcoming a sequence of viral "sinks" must be combined with re-targeting to target populations with capsid as well as shielding the vectors from pre-existing or toxic immune responses. It must also be noted that most known adenoviral pharmacology is deduced from the most commonly used serotypes, Ad5 and Ad2. However, these serotypes may not represent all adenoviruses, and may not even represent the most useful vectors for all purposes. Chimeras between Ad serotypes may become useful in engineering vectors that can selectively evade substantial viral traps, such as Kupffer cells, while retaining the robust qualities of Ad5. Similarly, vectorizing other Ad serotypes may become useful in avoiding immunity against Ad5 altogether. Taken together, this research on basic adenovirus biology will be necessary in developing vectors that interact more strategically with the host for the most optimal therapeutic effect.
Protein-S-S-Glutathione Mixed Disulfides as Models of Unfolded Proteins (1994)

Mixed disulfides between glutathione and the reduced forms of disulfide-bonded proteins were generated and characterized to explore their suitability as models of the unfolded state of newly-synthesized secretory proteins. RNase T1 and alpha-lactalbumin were reduced and converted to mixed disulfide derivatives, named GS-RNase T1 and GS-alpha-lactalbumin, in good yield; the molecular masses of the derivatives were confirmed by electrospray mass spectrometry. The intrinsic fluorescence of the derivatives and the binding of the hydrophobic fluorescent dye ANS were characteristic of fully unfolded proteins. Fluorescence studies and enzyme activity data indicated that GS-RNase T1 could be refolded to a nativelike state at NaCl concentrations greater than 1.5 M, as was previously demonstrated for the reduced, carboxymethylated derivative of this protein. The [NaCl]-dependent folding/unfolding equilibrium for GS-RNase T1 was reversible and could be influenced by urea. Fluorescence studies indicated that GS-alpha-lactalbumin showed a [NaCl]-dependent partial shift toward a more nativelike state, which was enhanced by the presence of Ca2+ ions. Both of the GS derivatives stimulated the ATPase activity of BiP, with apparent affinities in the range 0.1-1.0 mM. The results indicate that these GS-S-protein mixed disulfide derivatives are ideal model unfolded proteins that can be used as substrates for detailed studies on secretory protein folding in vitro and on the interactions between unfolded proteins and facilitators of protein folding.
Effect of Loop Sequence and Loop Length on the Intrinsic Fluorescence of G-Quadruplexes (2013)

Guanine quadruplex structures (GQSs) exhibit unique spectroscopic features, including an inverse melting profile at 295 nm, distinctive circular dichroism features, and intrinsic fluorescence. Herein, we investigate effects of loop sequence and loop length on the intrinsic fluorescence of 13 DNA GQSs. We report label-free fluorescence enhancements upon intramolecular GQS formation of up to 16-fold and a shift in the emission maximum to the visible portion of the spectrum. Effects can be understood in the context of available nuclear magnetic resonance GQS structures. The intrinsic fluorescence of GQSs may be useful for nucleic acid studies and for the development of label-free detection methods.
Evaluation of Chemical Amendments to Reduce Ammonia Volatilization from Poultry Litter (1996)

Ammonia volatilization from poultry litter often causes high levels of atmospheric ammonia in poultry houses, which is detrimental to both farm workers and birds. Ammonia emissions from houses also aggravate environmental problems, such as acid rain, and result in a loss of fertilizer nitrogen. The objectives of this study were to determine the effect of litter amendments on ammonia volatilization and to determine the effect of these amendments on nitrogen and phosphorus content in litter. The results of this research indicate that alum [Al2(SO4)3.18H2O], ferrous sulfate (FeSO4.7H2O), and phosphoric acid (H3PO4) dramatically reduce ammonia volatilization form litter. The amount of ammonia lost from litter treated with sodium bisulfate (NaHSO4) and a proprietory product made of Ca-Fe silicate with a phosphoric acid coating was not different from the control (untreated litter). Aluminum sulfate (alum) and ferrous sulfate also reduced water soluble P concentrations in litter, whereas phosphoric acid greatly increased water-soluble P levels. The most effective compound evaluated with respect to reducing both ammonia loss and P solubility was alum.
Conservation of Glycoprotein H (gH) in Herpesviruses: Nucleotide Sequence of the gH Gene from Herpesvirus Saimiri (1988)

We present the nucleotide sequence of the glycoprotein H (gH) gene of herpesvirus saimiri (HVS), a representative of the T lymphotropic herpesviruses of New World monkeys, and compare the predicted amino acid sequence with sequences of homologous proteins from four human herpesviruses. The HVS gH gene is located within a block of genes encoding products conserved in all herpesvirus subgroups as represented by the human herpesviruses herpes simplex virus, varicella-zoster virus, cytomegalovirus and Epstein-Barr virus. In agreement with the biological grouping of HVS as a lymphotropic gammaherpesvirus, its gH amino acid sequence shows greatest similarity to that of the B lymphotropic Epstein-Barr virus, although the nucleotide sequences of their respective gH genes show little similarity given different G + C compositions of 31% and 54%. The similarity observed between the gH amino acid sequences of the two representative gammaherpesviruses is greater than that between the two human alphaherpesviruses varicella-zoster virus and herpes simplex virus. The members of the gH family range in size from 706 to 743 amino acid residues for the beta- and gammaherpesviruses, to 838 to 841 for the alphaherpesviruses, giving non-glycosylated precursors with Mr values of 78,322 to 93,651. The difference in size is due to heterogeneity in the poorly conserved N-terminal regions of the larger alphaherpesviruses compared to the smaller beta- and gammaherpesvirus molecules. Greatest similarity is observed in the C-terminal halves of the proteins including residues surrounding four conserved cysteine residues, a conserved N-linked glycosylation site (within the sequence NGTV) 13 to 18 residues proximal to the membrane-spanning sequences, and a short cytoplasmic domain of seven or eight residues for the beta- and gammaherpesviruses' and 14 or 15 residues for the alphaherpesviruses' gH. Thus, the representatives of all subgroups of herpesviruses, including those with a non-human host, encode gH homologues. Together with the observation that gH of these viruses are major targets for virus neutralization by antibody, this suggests that this glycoprotein family is essential among all herpesviruses and represents a major component involved in herpesvirus infectivity.
ACC/AHA Guidelines for the Management of Patients With Unstable Angina and Non–ST-Segment Elevation Myocardial Infarction: Executive Summary and Recommendations (2000)

I 1. The initial evaluation of the patient with suspected ACS should include a search for noncoronary causes that could explain the development of symptoms. (Level of Evidence: C)
<title>Photodetection of early cancer in the upper aerodigestive tract and the bronchi using photofrin II and colorectal adenocarcinoma with fluoresceinated monoclonal antibodies</title> (1991)

The performance of a fluorescence endoscope for the detection of early cancer is clinically evaluated. the apparatus is based on the imaging of the laser-induced fluorescence (LIF) of a dye which localizes in the tumor after IV injection with a higher concentration than in the surrounding normal tissue. The tests are carried out in several of the hollow organs, such as the upper aerodigestive tract, the bronchi, and the colon. In the two former cases the dye used is photofrin II, whereas in the latter case conjugates between monoclonal antibodies (Mab) directed against carcinoembrionic antigen (CEA) and fluorescein molecules are injected. The fluorescence contrast between tumor and surrounding tissue is enhanced by real-time image processing which eliminates most of the tissue autofluorescence as well as the fluorescence due to the relatively small amount of dye localized in the normal tissue. This is done by recording the fluorescence image in two spectral domains, after which these two images are digitized and manipulated with a mathematical operator (lookup-table). The sources of false positives and false negatives are evaluated in terms of the fluorescent dye and tissue optical properties.
Specific Residues of the Influenza A Virus Hemagglutinin Viral RNA Are Important for Efficient Packaging into Budding Virions (2007)

A final step in the influenza virus replication cycle is the assembly of the viral structural proteins and the packaging of the eight segments of viral RNA (vRNA) into a fully infectious virion. The process by which the RNA genome is packaged efficiently remains poorly understood. In an approach to analyze how vRNA is packaged, we rescued a seven-segmented virus lacking the hemagglutinin (HA) vRNA (deltaHA virus). This virus could be passaged in cells constitutively expressing HA protein, but it was attenuated in comparison to wild-type A/WSN/33 virus. Supplementing the deltaHA virus with an artificial segment containing green fluorescent protein (GFP) or red fluorescent protein (RFP) with HA packaging regions (45 3' and 80 5' nucleotides) partially restored the growth of this virus to wild-type levels. The absence of the HA vRNA in the deltaHA virus resulted in a 40 to 60% reduction in the packaging of the PA, NP, NA, M, and NS vRNAs, as measured by quantitative PCR (qPCR), and the packaging of these vRNAs was partially restored in the presence of GFP/RFP packaging constructs. To further define nucleotides of the HA coding sequence which are important for vRNA packaging, synonymous mutations were introduced into the full-length HA cDNA of influenza A/WSN/33 and A/Puerto Rico/8/34 viruses, and mutant viruses were rescued. qPCR analysis of vRNAs packaged in these mutant viruses identified a key region of the open reading frame (nucleotides 1659 to 1671) that is critical for the efficient packaging of an influenza virus H1 HA segment.
Isolation and characterization of single‐chain Fv genes encoding antibodies specific for Drosophila Poxn protein (1998)

The usefulness of intrabodies as specific inhibitors of gene function has been extensively demonstrated in cell culture assays. However, very few experiments have been conducted with intrabodies expressed in whole organisms. To evaluate the intrabody technology in Drosophila, we focused on poxn protein, since its effects can be easily studied. We purified the recombinant poxn protein. We next isolated three single-chain variable fragments (scFv) which specifically recognize poxn protein. Two scFvs, designated alpha-Poxn2 and alpha-Poxn4, react with both denatured and native Poxn with half maximal inhibition values of 100 nM and 40 nM, respectively. The alpha-Poxn5 scFv also recognizes denatured Poxn but either does not recognize native Poxn or its half maximal inhibition value for native Poxn is high.
A beta-glucan inhibitable receptor on human monocytes: its identity with the phagocytic receptor for particulate activators of the alternative complement pathway. (1985)

The ligand specificity of the human monocyte receptor that mediates phagocytosis of particulate activators of the human alternative complement pathway was defined by inhibiting the phagocytic response with glycans known to be present in zymosan. When monocytes in monolayers were preincubated with 100 micrograms/ml of beta-glucan and then incubated with 1.25 to 2.5 X 10(6) zymosan particles, the percentage of cells that exhibited phagocytosis was inhibited in a time-dependent manner; maximal inhibition occurred within 20 min of preincubation. beta-Glucan inhibited monocyte phagocytosis of zymosan and rabbit erythrocytes (Er) in a similar dose-dependent fashion and at 100 micrograms/ml reduced monocyte ingestion of 5 X 10(6)/ml zymosan and 2 X 10(8)/ml Er by 63 +/- 8% and 68 +/- 16% (mean +/- SD, n = 3), respectively. The other glycan constituent of zymosan, mannan, was less than 1% as active, and 10 mg/ml of mannan reduced the number of monocytes ingesting zymosan and Er by 56 +/- 12% and 26 +/- 11%, respectively. At concentrations as high as 500 micrograms/ml, beta-glucan had no effect on monocyte Fc, C3b, or fibronectin receptor-mediated functions. Enzymatic hydrolysis of beta-glucan and alpha-mannan with beta-glucosidase or beta-glucanase before their incubation with monocytes abrogated their inhibitory capacity, whereas hydrolysis with alpha-mannosidase or alpha-glucosidase did not. Neither of the two alpha-glucans tested (dextran T-70 and nigeran) affected monocyte ingestion of zymosan particles or sheep erythrocytes (Es) sensitized with rabbit 7S anti-Es (EsIgG) at concentrations as high as 2 mg/ml. In contrast, a number of beta-glucans were active against zymosan but not EsIgG ingestion with a 75% reduction in the number of monocytes ingesting zymosan occurring with 100 micrograms/ml laminarin, 500 micrograms/ml soluble pachyman, and 900 micrograms/ml of soluble pustulan. The galactan, agarose, either in suspensions at 2 mg/ml or in a soluble portion at 600 micrograms/ml failed to affect monocyte ingestion of zymosan particles or Er. Thus, the monocyte receptor for particulate activators that is specifically inhibited by beta-glucan at a rate compatible with a phagocytic process and that recognizes beta-glucans but not alpha-glucans, mannan, or galactan is a beta-glucan receptor.
Synthesis and Biological Activity of New 3-Hydroxy-3-methylglutaryl-CoA Synthase Inhibitors: 2-Oxetanones with a Side Chain Mimicking the Extended Structure of 1233A. (1994)

Structural analogs of 1233A, a microbial metabolite inhibiting 3-hydroxy-3- methylglutaryl coenzyme A (HMG-CoA) synthase, were designed and synthesized. The 2-oxetanone moiety was left intact. All analogs prepared were tested for inhibition of HMG-CoA synthase activity and sterol synthesis in mouse liver and for effect on serum triglyceride levels. Of these analogs, trans-4-[2-[3-(7-carboxy-2- naphthyl)phenyl]ethyl]-3-hydroxymethyl-2-oxetanone (4a) showed the highest inhibitory activity in vitro, and also had in vivo inhibitory activity without causing any increase in triglyceride level.