gebhart/patrepeval huggingface dataset:
Expression of human dopamine β-hydroxylase in Drosophila Schneider 2 cells (1996)

Human dopamine beta-hydroxylase (DBH) has been expressed in transformed Drosophila Schneider 2 (S2) cells with yields of > 16 mg/l. Most of the activity was found in the culture fluid. Similarly, human neuroblastoma cells also secrete native DBH into the medium, but at a much lower level than recombinant Drosophila cells. We have purified native and recombinant human DBH by a modified purification procedure using SP-Sepharose, lentil lectin-Sepharose and gel-filtration chromatography and carried out studies to compare the two enzymes. Two variants of human DBH that differ by a single amino acid (either serine or alanine) at position 304 were expressed in Drosophila cells, purified, and found to have no significant difference in enzyme activity. The molecular mass of human DBH monomer has been determined from SDS/PAGE to be 73 kDa, but the recombinant DBH from Drosophila is smaller at 66 kDa. The difference may be due to glycosylation as deglycosylated enzymes from both sources are identical in size (61 kDa). The Km of tyramine for native and recombinant human enzymes are virtually the same but higher than bovine DBH by about 3-fold. Likewise, the inhibition of native and recombinant human DBH by fusaric acid and SKF102698 is not significantly different but IC50 values are 2-3-fold higher than that for the bovine enzyme. These results strongly support the conclusion that recombinant human DBH from Drosophila S2 cells can be used in place of human neuroblastoma-derived DBH for drug screening, characterization of the enzyme's physicochemical properties, and determination of structure-function relationships. The Drosophila expression system has thus provided a convenient source for large quantities of human DBH enzyme.
The Recognition of Collagen and Triple-helical Toolkit Peptides by MMP-13 (2014)

Remodeling of collagen by matrix metalloproteinases (MMPs) is crucial to tissue homeostasis and repair. MMP-13 is a collagenase with a substrate preference for collagen II over collagens I and III. It recognizes a specific, well-known site in the tropocollagen molecule where its binding locally perturbs the triple helix, allowing the catalytic domain of the active enzyme to cleave the collagen α chains sequentially, at Gly(775)-Leu(776) in collagen II. However, the specific residues upon which collagen recognition depends within and surrounding this locus have not been systematically mapped. Using our triple-helical peptide Collagen Toolkit libraries in solid-phase binding assays, we found that MMP-13 shows little affinity for Collagen Toolkit III, but binds selectively to two triple-helical peptides of Toolkit II. We have identified the residues required for the adhesion of both proMMP-13 and MMP-13 to one of these, Toolkit peptide II-44, which contains the canonical collagenase cleavage site. MMP-13 was unable to bind to a linear peptide of the same sequence as II-44. We also discovered a second binding site near the N terminus of collagen II (starting at helix residue 127) in Toolkit peptide II-8. The pattern of binding of the free hemopexin domain of MMP-13 was similar to that of the full-length enzyme, but the free catalytic subunit bound none of our peptides. The susceptibility of Toolkit peptides to proteolysis in solution was independent of the very specific recognition of immobilized peptides by MMP-13; the enzyme proved able to cleave a range of dissolved collagen peptides.
A wide range PLL for 64X speed CD-ROM & 10X speed DVD-ROM (2002)

We propose a wide range PLL (phase locked loop) for 64X speed CD-ROM and 10X speed DVD-ROM. The proposed PLL has a locking range of 75 MHz-370 MHz. A new V-I converter and a differential delay cell are used in a 3-stage ring VCO to reduce jitter. In addition, we propose a new charge pump which has perfect current matching characteristics for sourcing/sinking currents. This new charge pump improves the locking time and the locking range of the PLL. Implemented in a 0.25 /spl mu/m, 1-poly 5-metal CMOS process, the wide range PLL consumes less than 100 mW with a single 2.5 V power supply. It occupies an active area of 1.9 mm by 1.1 mm.
Multivirus-Specific T Cell Immunotherapy To Prevent Or Treat Infections Of Allogeneic Stem Cell Transplant Recipients (2010)

Viral infections cause morbidity and mortality in allogeneic HSCT recipients. We and others have successfully generated and infused adoptive T-cell lines specific for EBV, CMV and Adenovirus using monocytes and EBV-transformed lymphoblastoid cell (EBV-LCL) gene-modified with an adenovector as antigen presenting cells (APCs). We have shown that as few as 2×105/kg trivirus-specific cytotoxic T lymphocytes (CTL) proliferated by several logs post-infusion and appeared to prevent and treat even severe viral disease resistant to other available therapies. Despite the encouraging clinical results, broader implementation of this "trispecific" CTL approach is limited by high production costs, complexity of manufacture and the prolonged time (4-6 weeks for EBV-LCL generation, and 6-8 weeks for CTL manufacture – total 10-14 weeks) for preparation. To overcome these manufacturing limitations we have developed new, GMP-compliant strategies. In place of adenovectors we now use DCs nucleofected with non-viral DNA plasmids encoding LMP2 and BZLF1 (EBV), Hexon and Penton (Adv), pp65 (CMV) and Large T antigen (BK virus) to stimulate T-cells. Furthermore, by pooling nucleofected DCs prior to PBMC stimulation, we can reproducibly generate multivirus-specific CTL lines reactive against all the stimulating antigens, without discernible antigenic competition. Secondly, we have demonstrated that the culture of activated T-cells in the presence of IL-4 (1,000U/ml) and IL-7 (10ng/ml) promotes the survival of both high and low frequency antigen-specific CTL and sustains the breadth of reactivity in our lines. Finally, we have replaced traditional plastic cultureware with a new, gas permeable culture device (G-Rex) which promotes the expansion and survival of large cell numbers in a closed system with minimal technician intervention. By implementing these changes we can now produce multispecific CTL targeting EBV, CMV, Ad, and BK virus at a cost per 106 cells that is reduced by >90%, and in just 10 days rather than 10 weeks using an approach that may be extended to additional protective viral antigens. Our approach should be of value for prophylactic and treatment applications for high risk allogeneic HSCT recipients.
Where zeolites and oxides merge: semi-condensed tetrahedral frameworks (2000)

The synthesis of new inorganic materials constructed with extended lattices has taken place mainly in two areas, complex oxides and porous framework structures. In the former case the drive has been towards controlling electronic and magnetic properties while in the latter domain porosity and the ability to enclathrate small organic or inorganic units has been paramount. Semi-condensed framework materials, whose compositions and structures place them at the borderline of these two classes, are described in this article, such compound types include the sodalite, cancrinite, analcime, zeloites ABW and JBW and scapolite structures. In each case recent chemistry and developments are described particularly with respect to advances made at The University of Southampton. The potential for merging the properties and structures of these two classes of compounds are also discussed.
Effect of nonionic detergents on lipoxygenase catalysis (1994)

In many studies on lipoxygenase catalysis, nonionic detergents are used to obtain an optically transparent solution of the fatty acid substrate. In order to resolve some controversies that exist with regard to the interpretation of kinetic data obtained with solutions containing nonionic detergents, a systematic investigation was undertaken into the effects of Lubrol, Tween-20 and Triton X-100 (0-0.8 g/L) on the kinetics of linoleate (2.5-110 microM) dioxygenation, catalyzed by lipoxygenase-1 or lipoxygenase-2 from soybean, at pH 9 or 10, at 25 degrees C. Under most conditions, it was found that the detergents slowed down the reaction. However, at high linoleate concentrations, where substrate inhibition of lipoxygenase is significant, small amounts of detergent increased the dioxygenation rate. In a quantitative analysis of the results, a kinetic model in which the incorporation of linoleate in the detergent micelles is formulated as a simple reversible equilibrium, and in which both lipoxygenase-1 and -2 interact with free linoleate, but not with linoleate incorporated in the micelles, appeared to be sufficient to predict experimental results over a wide range of experimental conditions. According to this model, the changes in the dioxygenation kinetics caused by the presence of nonionic detergents are similar (but not equal) to those caused by competitive inhibitors. The conclusions that monomeric, nonmicellar linoleate is the preferred substrate for lipoxygenase and that the observed inhibition and stimulation are solely due to changes in the effective linoleate concentration strongly corroborate the earlier observations by Galpin and Allen [Biochim. Biophys. Acta 488 (1977), 392-401].
Mitochondrial Iron Metabolism and Its Role in Neurodegeneration (2010)

In addition to their well-established role in providing the cell with ATP, mitochondria are the source of iron-sulfur clusters (ISCs) and heme - prosthetic groups that are utilized by proteins throughout the cell in various critical processes. The post-transcriptional system that mammalian cells use to regulate intracellular iron homeostasis depends, in part, upon the synthesis of ISCs in mitochondria. Thus, proper mitochondrial function is crucial to cellular iron homeostasis. Many neurodegenerative diseases are marked by mitochondrial impairment, brain iron accumulation, and oxidative stress - pathologies that are inter-related. This review discusses the physiological role that mitochondria play in cellular iron homeostasis and, in so doing, attempts to clarify how mitochondrial dysfunction may initiate and/or contribute to iron dysregulation in the context of neurodegenerative disease. We review what is currently known about the entry of iron into mitochondria, the ways in which iron is utilized therein, and how mitochondria are integrated into the system of iron homeostasis in mammalian cells. Lastly, we turn to recent advances in our understanding of iron dysregulation in two neurodegenerative diseases (Alzheimer's disease and Parkinson's disease), and discuss the use of iron chelation as a potential therapeutic approach to neurodegenerative disease.
Enigmatic, ultrasmall, uncultivated Archaea (2010)

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete approximately 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher coding density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3:159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.
Identification of a novel <scp>BET</scp> bromodomain inhibitor‐sensitive, gene regulatory circuit that controls Rituximab response and tumour growth in aggressive lymphoid cancers (2013)

Immuno-chemotherapy elicit high response rates in B-cell non-Hodgkin lymphoma but heterogeneity in response duration is observed, with some patients achieving cure and others showing refractory disease or relapse. Using a transcriptome-powered targeted proteomics screen, we discovered a gene regulatory circuit involving the nuclear factor CYCLON which characterizes aggressive disease and resistance to the anti-CD20 monoclonal antibody, Rituximab, in high-risk B-cell lymphoma. CYCLON knockdown was found to inhibit the aggressivity of MYC-overexpressing tumours in mice and to modulate gene expression programs of biological relevance to lymphoma. Furthermore, CYCLON knockdown increased the sensitivity of human lymphoma B cells to Rituximab in vitro and in vivo. Strikingly, this effect could be mimicked by in vitro treatment of lymphoma B cells with a small molecule inhibitor for BET bromodomain proteins (JQ1). In summary, this work has identified CYCLON as a new MYC cooperating factor that autonomously drives aggressive tumour growth and Rituximab resistance in lymphoma. This resistance mechanism is amenable to next-generation epigenetic therapy by BET bromodomain inhibition, thereby providing a new combination therapy rationale for high-risk lymphoma.
Multi-label informed feature selection (2016)

Multi-label learning has been extensively studied in the area of bioinformatics, information retrieval, multimedia annotation, etc. In multi-label learning, each instance is associated with multiple interdependent class labels, the label information can be noisy and incomplete. In addition, multilabeled data often has noisy, irrelevant and redundant features of high dimensionality. As an effective data preprocessing step, feature selection has shown its effectiveness to prepare high-dimensional data for numerous data mining and machine learning tasks. Most of existing multi-label feature selection algorithms either boil down to solving multiple single-labeled feature selection problems or directly make use of imperfect labels. Therefore, they may not be able to find discriminative features that are shared by multiple labels. In this paper, we propose a novel multi-label informed feature selection framework MIFS, which exploits label correlations to select discriminative features across multiple labels. Specifically, to reduce the negative effects of imperfect label information in finding label correlations, we decompose the multi-label information into a low-dimensional space and then employ the reduced space to steer the feature selection process. Empirical studies on real-world datasets demonstrate the effectiveness and efficiency of the proposed framework.
A green method for the preparation of anode materials for lithium ion batteries (2001)

Here we demonstrate for the first time that an anode material for lithium ion batteries can be satisfactorily prepared by a green method. By selecting benign and easily recycled oxidants, solutions of H2O2 and Ce(SO4)2, the electrochemical performance of a natural graphite anode material can be markedly improved. Through thermogravimetric analysis, differential thermal analysis, X-ray photoelectron spectroscopy, high resolution electron microscopy and measurements of lithium capacity it was found that the surface structure of the natural graphite was modified with a dense layer of oxides, which could prevent the co-intercalation of solvent molecules. In addition, the stability of the graphite crystal was improved and the decomposition of electrolyte molecules was prohibited. Furthermore, a large number of nano-channels were introduced by oxidation, which favored lithium intercalation and de-intercalation. The reversible lithium capacity was enhanced from 251 to >330 mA h g−1, and no capacity fading was observed in the first 10 cycles. This green method is also highly efficient and economical, the process can be performed below 60 °C.
Carbon Dioxide as Cushion Gas for Natural Gas Storage (2002)

Natural gas storage is used to smooth the natural gas supply to meet high peak demand. In natural gas storage, the working gas (methane) is injected and produced seasonally while a cushion gas that is not extracted is used to provide pressure support. In the case of depleted gas reservoirs being used for gas storage, the cushion gas is commonly leftover native gas (methane). Another approach is to produce most of the methane from the reservoir since it can be sold for profit and inject a cheap inert gas for use as the cushion gas. Carbon dioxide injection during carbon sequestration with enhanced gas recovery can be carried out to produce the methane while simultaneously filling the reservoir with carbon dioxide. Carbon dioxide undergoes a large change in density near its critical pressure, an advantageous feature if used as a cushion gas. Furthermore, the injection of carbon dioxide into the ground may in the future be economically favorable through carbon credits or tax advantages offerred to encourage carbon sequestration. Reservoir simulations of methane injection into a model gas storage reservoir with carbon dioxide as cushion gas demonstrate that 30% more methane can be stored relative to a native gas cushion. Along with economic considerations of carbon dioxide and natural gas prices, the critical issue for the use of carbon dioxide as a cushion gas is limiting the rate of mixing between methane and carbon dioxide through careful reservoir selection and operations.
EXTRACELLULAR ENZYMES FROM STRAINS OF SORANGIUM (1965)

Soil organisms belonging to the myxobacter group and predatory on molds, yeasts, nematodes, and streptomycetes as well as on a wide range of bacteria elaborate at least two extracellular enzymes: a protease and a lysin. The protease hydrolyzes casein and haemoglobin and is inactive against bacterial cell walls while the lysin hydrolyzes bacterial cell walls but is inactive on proteins. These enzymes have been separated on hydroxylapatite columns and some of their properties are described. The predatory action of many of the isolates may be explained by the secretion and subsequent action of these two enzymes.
Low-frequency ultradian insulin rhythms are coupled to cardiovascular, autonomic, and neuroendocrine rhythms (1997)

Plasma insulin levels were assayed to compare with earlier reported rhythms of the cardiovascular, autonomic, and neuroendocrine systems in 10 resting normal adults over 5-6 h. Our earlier report included time-series analysis for impedance cardiography measures of stroke volume, heart rate, cardiac output, thoracic fluid index, ejection velocity index, and ventricular ejection time; automated cuff measures of systolic, diastolic, and mean arterial pressures; the nasal cycle as a marker of lateralized autonomic tone; and indwelling venous catheters for sampling blood every 7.5 min to assay for adrenocorticotropic hormone, luteinizing hormone, epinephrine, and norepinephrine. Insulin was later assayed from the same plasma samples. Time-series analysis using the fast orthogonal search method of Korenberg detected insulin periodicities at ranges of 220-340, 115-145, 70-100, and 40-65, with significance across subjects at ranges of 115-145, 70-100, and 40-65 min. Significant periods for the other parameters were reported earlier at 220-340, 170-215, 115-145, 70-100, and 40-65 min, with periods at 115-145, 70-100, and 40-65 min dominating across parameters. These results suggest that insulin secretion has a common pacemaker (the hypothalamus) or a mutually entrained pacemaker with the autonomic, cardiovascular, and neuroendocrine systems.
Exploiting half precision arithmetic in Nvidia GPUs (2017)

With the growing importance of deep learning and energy-saving approximate computing, half precision floating point arithmetic (FP16) is fast gaining popularity. Nvidia's recent Pascal architecture was the first GPU that offered FP16 support. However, when actual products were shipped, programmers soon realized that a naïve replacement of single precision (FP32) code with half precision led to disappointing performance results, even if they are willing to tolerate the increase in error precision reduction brings. In this paper, we developed an automated conversion framework to help users migrate their CUDA code to better exploit Pascal's half precision capability. Using our tools and techniques, we successfully convert many benchmarks from single precision arithmetic to half precision equivalent, and achieved significant speedup improvement in many cases. In the best case, a 3× speedup over the FP32 version was achieved. We shall also discuss some new issues and opportunities that the Pascal GPUs brought.
Neutralizing Antibodies after Infection with Dengue 1 Virus (2007)

Severity of disease is markedly increased when infection with dengue virus type 2 (DENV-2) follows infection with DENV-1 at an interval of 20 years. Studies have shown that heterologous neutralizing antibody titers are inversely correlated with severity of a second infection. If this mechanism controlled disease severity in Cuba, heterotypic antibody titers should have declined over time. To determine whether phenotypic changes in dengue antibodies occur over time, we analyzed serum samples collected 4-8 and 20-22 years after DENV-1 infection. We found a significant increase in mean titer of homologous DENV-1 neutralizing antibodies and a significant decrease in heterologous antibodies to 1 of 2 genotypes of DENV-2 virus (the American genotype). Asian DENV-2 viruses were not neutralized during either interval; however, the American genotype underwent phenotypic changes in heterotypic viral neutralizing antibodies in the predicted direction. This finding may be related to the time-dependent changes in severity of disease found with secondary dengue infection.
Properties of Gain-shifted EDFA (1580 nm-band EDFA) Cascades in WDM Transmission Systems (2006)

Over the past year, the 1580 nm-band WDM transmission experiments using gain-shifted EDFA (GS-EDFA : 1580-nm-band EDFA) have achived the results which confirm that the performance is almost comparable with that obtained with the conventional 1550 nm-band systems under the same fiber dispersion [1][2].
Generalization of the Subspace-Based Array Shape Estimations (2004)

This work describes a nonplane wave signal model for array shape estimation in ocean environments. Though existing array shape estimation methods, which utilize reference sources, show good performance in the environment where plane wave assumption is satisfied, their performances are degraded significantly in more realistic nonplane wave situation. The proposed subspace-based array shape estimation method, which generalizes the conventional subspace fitting method, works very well for both plane wave and nonplane wave environments. The Cramer-Rao lower bound is investigated to analyze the theoretical lower bound of the variance of the estimation. The simulation results indicate that the proposed method correctly estimates the shape of perturbed array regardless of reference source location.