gebhart/patrepeval huggingface dataset:
Essential Role of Cyclophilin A for Hepatitis C Virus Replication and Virus Production and Possible Link to Polyprotein Cleavage Kinetics (2009)

Viruses are obligate intracellular parasites and therefore their replication completely depends on host cell factors. In case of the hepatitis C virus (HCV), a positive-strand RNA virus that in the majority of infections establishes persistence, cyclophilins are considered to play an important role in RNA replication. Subsequent to the observation that cyclosporines, known to sequester cyclophilins by direct binding, profoundly block HCV replication in cultured human hepatoma cells, conflicting results were obtained as to the particular cyclophilin (Cyp) required for viral RNA replication and the underlying possible mode of action. By using a set of cell lines with stable knock-down of CypA or CypB, we demonstrate in the present work that replication of subgenomic HCV replicons of different genotypes is reduced by CypA depletion up to 1,000-fold whereas knock-down of CypB had no effect. Inhibition of replication was rescued by over-expression of wild type CypA, but not by a mutant lacking isomerase activity. Replication of JFH1-derived full length genomes was even more sensitive to CypA depletion as compared to subgenomic replicons and virus production was completely blocked. These results argue that CypA may target an additional viral factor outside of the minimal replicase contributing to RNA amplification and assembly, presumably nonstructural protein 2. By selecting for resistance against the cyclosporine analogue DEBIO-025 that targets CypA in a dose-dependent manner, we identified two mutations (V2440A and V2440L) close to the cleavage site between nonstructural protein 5A and the RNA-dependent RNA polymerase in nonstructural protein 5B that slow down cleavage kinetics at this site and reduce CypA dependence of viral replication. Further amino acid substitutions at the same cleavage site accelerating processing increase CypA dependence. Our results thus identify an unexpected correlation between HCV polyprotein processing and CypA dependence of HCV replication.
Cross-reactions between engineered xylose and galactose pathways in recombinant Saccharomyces cerevisiae (2010)

PGM2 overexpression was shown to benefit xylose and galactose fermentation, alone and in combination. In contrast, galactose fermentation was impaired in the engineered xylose-utilizing strain harbouring extra copies of the non-ox PPP genes and a deletion of the GRE3 gene, unless PGM2 was overexpressed. These cross-reactions are of particular relevance for the fermentation of mixed sugars from lignocellulosic feedstock.
Severe community-acquired pneumonia: current outcomes, epidemiology, etiology, and therapy (2001)

Severe community-acquired pneumonia is a clinical diagnosis with a significant impact on healthcare management around the world, with the highest morbidity and mortality of all of the forms of community-acquired pneumonia. Patients with severe pneumonia usually require intensive care unit management, including vasopressors or mechanical ventilation. Early clinical suspicion and prompt empiric antimicrobial therapies are mandatory in patients with severe pneumonia. A number of recent studies and guidelines addressing these issues have been published, and they will be reviewed in this article.
Structure and Functional Expression of an ω-Conotoxin-Sensitive Human N-Type Calcium Channel (1992)

N-type calcium channels are omega-conotoxin (omega-CgTx)-sensitive, voltage-dependent ion channels involved in the control of neurotransmitter release from neurons. Multiple subtypes of voltage-dependent calcium channel complexes exist, and it is the alpha 1 subunit of the complex that forms the pore through which calcium enters the cell. The primary structures of human neuronal calcium channel alpha 1B subunits were deduced by the characterization of overlapping complementary DNAs. Two forms (alpha 1B-1 and alpha 1B-2) were identified in human neuroblastoma (IMR32) cells and in the central nervous system, but not in skeletal muscle or aorta tissues. The alpha 1B-1 subunit directs the recombinant expression of N-type calcium channel activity when it is transiently co-expressed with human neuronal beta 2 and alpha 2b subunits in mammalian HEK293 cells. The recombinant channel was irreversibly blocked by omega-CgTx but was insensitive to dihydropyridines. The alpha 1B-1 alpha 2b beta 2-transfected cells displayed a single class of saturable, high-affinity (dissociation constant = 55 pM) omega-CgTx binding sites. Co-expression of the beta 2 subunit was necessary for N-type channel activity, whereas the alpha 2b subunit appeared to modulate the expression of the channel. The heterogeneity of alpha 1B subunits, along with the heterogeneity of alpha 2 and beta subunits, is consistent with multiple, biophysically distinct N-type calcium channels.
Wafer-Level Package With Simultaneous TSV Connection and Cavity Hermetic Sealing by Solder Bonding for MEMS Device (2009)

In this paper, a wafer-level package with simultaneous through silicon via (TSV) connection and cavity hermetic sealing by low-temperature solder bonding for microelectromechanical system (MEMS) device such as resonator is presented. Wet etching technique combined with dry etching technique is utilized to achieve a ldquoY-shapedrdquo through wafer interconnection structure to shorten the TSV in order to reduce cost. Ansoft HFSS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> 3-D electromagnetic simulator is used to assess the transition properties of signal with frequency of the new interconnection structure. Sn solder bonding is utilized to achieve simultaneous TSV connection and cavity hermetic sealing. Average shear strength of 19.5 Mpa and excellent leak rate of around 1.9 times 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> atm cc/s have been achieved, which meet the requirements of MIL-STD-883E. Kevin structure is also fabricated to measure the resistance of the metallized TSV, the resistance of the ldquoY-shapedrdquo through wafer interconnection and the contact resistance of the Cu/Sn IMC bond joint.
Truthful mechanisms for one-parameter agents (2001)

The authors show how to design truthful (dominant strategy) mechanisms for several combinatorial problems where each agent's secret data is naturally expressed by a single positive real number. The goal of the mechanisms we consider is to allocate loads placed on the agents, and an agent's secret data is the cost she incurs per unit load. We give an exact characterization for the algorithms that can be used to design truthful mechanisms for such load balancing problems using appropriate side payments. We use our characterization to design polynomial time truthful mechanisms for several problems in combinatorial optimization to which the celebrated VCG mechanism does not apply. For scheduling related parallel machines (Q/spl par/C/sub max/), we give a 3-approximation mechanism based on randomized rounding of the optimal fractional solution. This problem is NP-complete, and the standard approximation algorithms (greedy load-balancing or the PTAS) cannot be used in truthful mechanisms. We show our mechanism to be frugal, in that the total payment needed is only a logarithmic factor more than the actual costs incurred by the machines, unless one machine dominates the total processing power. We also give truthful mechanisms for maximum flow, Q/spl par//spl Sigma/C/sub j/ (scheduling related machines to minimize the sum of completion times), optimizing an affine function over a fixed set, and special cases of uncapacitated facility location. In addition, for Q/spl par//spl Sigma/w/sub j/C/sub j/ (minimizing the weighted sum of completion times), we prove a lower bound of 2//spl radic/3 for the best approximation ratio achievable by truthful mechanism.
Thrombin specificity (1985)

alpha-Thrombin cleavage of 30 polypeptide hormones and their derivatives were analysed by quantitative amino-terminal analysis. The polypeptides included secretin, vasoactive intestinal polypeptide, cholecystokinin fragment, dynorphin A, somatostatins, gastrin-releasing peptide, calcitonins and human parathyroid hormone fragment. Most of them were selected mainly on the ground that they contain sequence structures homologous to the well known tripeptide substrates of alpha-thrombin. All selected polypeptides have one single major cleavage site and both Arg-Xaa and Lys-Xaa bonds were found to be selectively cleaved by alpha-thrombin. Under fixed conditions (1 nmol polypeptide/0.5 NIH unit alpha-thrombin in 20 microliters of 50 mM ammonium bicarbonate at 25 degrees C), the time required for 50% cleavage ranges from less than 1 min to longer than 24 h. Heparin invariably enhanced thrombin cleavage on all polypeptide analysed. The optimum cleavage site for alpha-thrombin has the structures of (a) P4-P3-Pro-Arg-P1'-P2', where P3 and P4 are hydrophobic amino acid and P1', P2' are nonacidic amino acids and (b) P2-Arg-P1', where P2 or P1' are Gly. The requirement for hydrophobic P3 and P4 was further demonstrated by the drastic decrease of thrombin cleavage rates in both gastrin-releasing peptide and calcitonins after chemical removal of hydrophobic P3 and P4 residues. The requirement for nonacidic P1' and P2' residues was demonstrated by the drastic increase of thrombin cleavage rates in both calcitonin and parathyroid hormone fragments, after specific chemical modification of acidic P1' and P2' residues. These findings confirm the importance of hydrophobic P2-P4 residues for thrombin specificity and provide new evidence to indicate that apolar P1' and P2' residues are also crucial for thrombin specificity. It is concluded that specific cleavage of polypeptides by alpha-thrombin can be reasonably predicted and that chemical modification can be a useful tool in enhancing thrombin cleavage.
Reduction of Macrophage Infiltration and Chemoattractant Gene Expression Changes in White Adipose Tissue of Morbidly Obese Subjects After Surgery-Induced Weight Loss (2005)

In human obesity, the stroma vascular fraction (SVF) of white adipose tissue (WAT) is enriched in macrophages. These cells may contribute to low-grade inflammation and to its metabolic complications. Little is known about the effect of weight loss on macrophages and genes involved in macrophage attraction. We examined subcutaneous WAT (scWAT) of 7 lean and 17 morbidly obese subjects before and 3 months after bypass surgery. Immunomorphological changes of the number of scWAT-infiltrating macrophages were evaluated, along with concomitant changes in expression of SVF-overexpressed genes. The number of scWAT-infiltrating macrophages before surgery was higher in obese than in lean subjects (HAM56+/CD68+; 22.6 +/- 4.3 vs. 1.4 +/- 0.6%, P < 0.001). Typical "crowns" of macrophages were observed around adipocytes. Drastic weight loss resulted in a significant decrease in macrophage number (-11.63 +/- 2.3%, P < 0.001), and remaining macrophages stained positive for the anti-inflammatory protein interleukin 10. Genes involved in macrophage attraction (monocyte chemotactic protein [MCP]-1, plasminogen activator urokinase receptor [PLAUR], and colony-stimulating factor [CSF]-3) and hypoxia (hypoxia-inducible factor-1alpha [HIF-1alpha]), expression of which increases in obesity and decreases after surgery, were predominantly expressed in the SVF. We show that improvement of the inflammatory profile after weight loss is related to a reduced number of macrophages in scWAT. MCP-1, PLAUR, CSF-3, and HIF-1alpha may play roles in the attraction of macrophages in scWAT.
Relationship Between Periodontal Condition and Plasma Reactive Oxygen Metabolites in Patients in the Maintenance Phase of Periodontal Treatment (2008)

A positive association was found between plasma oxidative status and CAL in patients in the maintenance phase of periodontal therapy. A systemic increase in oxidative stress may influence the rate of progression of periodontal disease.
Construction of a Cultivation System of a Yeast Single Cell in a Cell Chip Microchamber (2006)

A novel single cell screening system was constructed using a yeast cell chip in combination with the yeast cell surface engineering [NanoBiotechnology 2005, 1, 105-111]. Enzymes or functional proteins displayed on a yeast cell surface can be used as a protein cluster. To achieve high-throughput screening of protein libraries on the cell surface, a catalytic reaction by a single cell-surface-engineered yeast cell was successfully carried out in the microchamber on the yeast cell chip. After screening, to replicate a target cell for use in measuring of activity, DNA sequencing, and preservation, a novel single cell cultivation system in the yeast cell chip was constructed. To avoid damage of the rapid dry up of medium in the microchamber array, the yeast cell chip was modified with a protection sheet, so that the modified chip was like a micro-culture tank constructed on the yeast cell chip microchamber. As a result, single yeast cell cultivation in the yeast cell chip microchamber was observed, and the modified yeast cell chip was evaluated to be good for a single cell selection. The improvement showed that the single cell screening system coupled with the single cell cultivation using the modified yeast cell chip may be superior to that by a cell sorter for the isolation of a target cell and its practical use.
Effects of intravenous iron on fibroblast growth factor 23 (FGF23) in haemodialysis patients: a randomized controlled trial (2016)

Australian and New Zealand Clinical Trials Register ACTRN12614000548639 . Registered 22 May 2014 (retrospectively registered).
An increased prevalence of Epstein-Barr virus infection in young patients suggests a possible etiology for systemic lupus erythematosus. (1997)

An unknown environmental agent has been suspected to induce systemic lupus erythematosus (lupus) in man. Prompted by our recent immunochemical findings, we sought evidence for an association between Epstein-Barr virus infection and lupus. Because the vast majority of adults have been infected with Epstein-Barr virus, we chose to study children and young adults. Virtually all (116 of 117, or 99%) of these young patients had seroconverted against Epstein-Barr virus, as compared with only 70% (107 of 153) of their controls (odds ratio 49.9, 95% confidence interval 9.3-1025, P < 0. 00000000001). The difference in the rate of Epstein-Barr virus seroconversion could not be explained by serum IgG level or by cross-reacting anti-Sm/nRNP autoantibodies. No similar difference was found in the seroconversion rates against four other herpes viruses. An assay for Epstein-Barr viral DNA in peripheral blood lymphocytes established Epstein-Barr virus infection in the peripheral blood of all 32 of the lupus patients tested, while only 23 of the 32 matched controls were infected (odds ratio > 10, 95% confidence interval 2.53-infinity, P < 0.002). When considered with other evidence supporting a relationship between Epstein-Barr virus and lupus, these data are consistent with, but do not in themselves establish, Epstein-Barr virus infection as an etiologic factor in lupus.
Internet Media Type message/sipfrag (2002)

This document registers the message/sipfrag Multipurpose Internet Mail Extensions (MIME) media type. This type is similar to message/sip, but allows certain subsets of well formed Session Initiation Protocol (SIP) messages to be represented instead of requiring a complete SIP message. In addition to end-to-end security uses, message/sipfrag is used with the REFER method to convey information about the status of a referenced request.
On dense pattern mining in graph streams (2010)

Many massive web and communication network applications create data which can be represented as a massive sequential stream of edges. For example, conversations in a telecommunication network or messages in a social network can be represented as a massive stream of edges. Such streams are typically very large, because of the large amount of underlying activity in such networks. An important application in these domains is to determine frequently occurring dense structures in the underlying graph stream. In general, we would like to determine frequent and dense patterns in the underlying interactions. We introduce a model for dense pattern mining and propose probabilistic algorithms for determining such structural patterns effectively and efficiently. The purpose of the probabilistic approach is to create a summarization of the graph stream, which can be used for further pattern mining. We show that this summarization approach leads to effective and efficient results for stream pattern mining over a number of real and synthetic data sets.
Transfection of a differentiated human hepatoma cell line (Huh7) with in vitro-transcribed hepatitis C virus (HCV) RNA and establishment of a long-term culture persistently infected with HCV (1995)

T7 RNA polymerase transcripts of a putative full-length cDNA clone of hepatitis C virus type 1 (HCV-1) were used to transfect a differentiated human hepatoma cell line, Huh7. The transfected genome replicated in cells, as evidenced by the appearance of progeny HCV RNA, detection of negative-strand viral RNA, and incorporation of [3H]uridine into the viral genome. Incubation of naive Huh7 cells with conditioned medium from transfected cells resulted in a new HCV infection, suggesting the production of biologically active virus in the inoculum. Maintenance of the transfected cells under serum-free culture conditions resulted in the selection of persistently infected cells which displayed a distinctive cellular morphology. This is the first demonstration that HCV RNA produced from cloned HCV cDNA is infectious and replication competent. This approach should provide a valuable system for studying HCV replication, persistence, and pathogenicity.
Photocontrolled Degradation of Stimuli-Responsive Poly(ethyl glyoxylate): Differentiating Features and Traceless Ambient Depolymerization (2016)

The depolymerization of coatings prepared from a 6-nitroveratryl carbonate end-capped poly(ethyl glyoxylate) (PEtG) self-immolative polymer was studied. This polymer undergoes end-to-end depolymerization following cleavage of the end-cap by UV light. Several important fundamental differences between this class of polymers and conventional degradable polymers were revealed. For example, polymer backbone cleavage and depolymerization exhibited different dependencies on pH, emphasizing the decoupling of these processes. Probing of the coating erosion mechanism illustrated an interesting combination of features from surface erosion and bulk degradation mechanisms that arise from the end-to-end depolymerization mechanism and further differentiate these polymers from convention degradable polymers. It was also demonstrated that, unlike backbone cleavage, PEtG depolymerization did not exhibit a dependence on water and that PEtG could depolymerize back to the volatile monomer ethyl glyoxylate at ambient temperature and pressure. This unusual feature was utilized to perform facile polymer reprogramming/recycling via an irradiation–trapping–repolymerization sequence as well as polymer patterning by a simple irradiation–evaporation sequence.
Factors that affect Li mobility in layered lithium transition metal oxides (2006)

The diffusion constant of Li in electrode materials is a key aspect of the rate capability of rechargeable Li batteries. The factors that affect Li mobility in layered lithium transition metal oxides are systematically studied in this paper by means of first-principles calculations. In close packed oxides octahedral ions diffuse by migrating through intermediate tetrahedral sites. Our results indicate that the activation barrier for Li hopping is strongly affected by the size of the tetrahedral site and the electrostatic interaction between ${\mathrm{Li}}^{+}$ in that site and the cation in the octahedron that shares a face with it. The size of the tetrahedral site is determined by the $c$-lattice parameter which has a remarkably strong effect on the activation barrier for Li migration. The effect of other factors such as cation mixing and doping with nontransition metal ions can be interpreted quantitatively in terms of the size and electrostatic effect. A general strategy to design high rate electrode materials is discussed.
Biodegradation of trichloroethylene by Methylosinus trichosporium OB3b (1989)

The methanotroph Methylosinus trichosporium OB3b, a type II methanotroph, degraded trichloroethylene at rates exceeding 1.2 mmol/h per g (dry weight) following the appearance of soluble methane monooxygenase in continuous and batch cultures. Cells capable oxidizing trichloroethylene contained components of soluble methane monooxygenase as demonstrated by Western blot (immunoblot) analysis with antibodies prepared against the purified enzyme. Growth of cultures in a medium containing 0.25 microM or less copper sulfate caused derepression of the synthesis of soluble methane monooxygenase. In these cultures, the specific rates of methane and methanol oxidation did not change during growth, while trichloroethylene oxidation increased with the appearance of soluble methane monooxygenase. M. trichosporium OB3b cells that contained soluble methane monooxygenase also degraded vinyl chloride, 1,1-dichloroethylene, cis-1,2-dichloroethylene, and trans-1,2-dichloroethylene.
AWG-Based Non-Blocking Clos Networks (2014)

The three-stage Clos networks remain the most popular solution to many practical switching systems to date. The aim of this paper is to show that the modular structure of Clos networks is invariant with respect to the technological changes. Due to the wavelength routing property of arrayed-waveguide gratings (AWGs), non-blocking and contention-free wavelength-division-multiplexing (WDM) switches require that two calls carried by the same wavelength must be connected by separated links; otherwise, they must be carried by different wavelengths. Thus, in addition to the non-blocking condition, the challenge of the design of AWG-based multistage switching networks is to scale down the wavelength granularity and to reduce the conversion range of tunable wavelength converters (TWCs). We devise a logic scheme to partition the WDM switch network into wavelength autonomous cells and show that the wavelength scalability problem can be solved by recursively reusing similar, but smaller, set of wavelengths in different cells. Furthermore, we prove that the rearrangeably non-blocking (RNB) condition and route assignments in these AWG-based three-stage networks are consistent with that of classical Clos networks. Thus, the optimal AWG-based non-blocking Clos networks also can achieve 100% utilization when all input and output wavelength channels are busy.