gebhart/patrepeval huggingface dataset:
Biochemical and Immunologic Properties of the Nonstructural Proteins of the Hepatitis C Virus: Implications for Development of Antiviral Agents and Vaccines (2000)

Infection with the hepatitis C virus (HCV) is the major cause of non-A, non-B hepatitis worldwide. The viral genome, a positive-sense, single-stranded, 9.6-kb long RNA molecule, is translated into a single polyprotein of about 3,000 amino acids. The viral polyprotein is proteoytically processed to yield all the mature viral gene products. The genomic order of HCV has been determined to be C-->E1-->E2-->p7-->NS2-->NS3-->NS4A-->NS4B-->NS5A++ +-->NS5B. C, E1, and E2 are the virion structural proteins. Whereas the function of p7 is currently unknown, NS2 to NS5B are thought to be the nonstructural proteins. Generation of the mature nonstructural proteins relies on the activity of viral proteinases. Cleavage at the NS2-NS3 junction is accomplished by a metal-dependent autocatalytic proteinase encoded within NS2 and the N-terminus of NS3. The remaining downstream cleavages are effected by a serine proteinase contained also within the N-terminal region of NS3. NS3, in addition, contains an RNA helicase domain at its C-terminus. NS3 forms a heterodimeric complex with NS4A. The latter is a membrane protein that acts as a cofactor of the proteinase. Although no function has yet been attributed to NS4B, NS5A has been recently suggested to be involved in mediating the resistance of the HCV to the action of interferon. Finally, the NS5B protein has been shown to be the viral RNA-dependent RNA polymerase. This article reviews the current understanding of the structure and the function of the various HCV nonstructural proteins with particular emphasis on their potential as targets for the development of novel antiviral agents and vaccines.
CD13+CD4+CD25hiregulatory T cells exhibit higher suppressive function and increase with tumor stage in non-small cell lung cancer patients (2009)

Regulatory T cells (Tregs) in peripheral blood and tumor infiltrating lymphocytes (TILs) play crucial roles in suppressing anti-tumor immune responses in cancer patients, and correlate with clinical outcomes. We identified an important subpopulation, CD13+CD4+CD25hiTreg cells, among CD4+CD25hiTreg cells in the peripheral blood of non-small cell lung cancer (NSCLC) patients. Peripheral blood mononuclear cells (PBMCs) were isolated from patients with NSCLC (n = 72) or from healthy donors (n = 30). Flow cytometric analyses were performed to study the expression of cell-surface or intracellular markers on the CD4+CD25hiTreg cells. The immune suppressive function of CD13+CD4+CD25hiTreg cells was evaluated by co-culturing with CD4+CD25-T cells that were activated by PHA. Our data showed that, compared with CD4+CD25(Low/-)T cells, CD13 expression was enriched on CD4+CD25hiTreg cells. The CD13+CD4+CD25hiTreg cells also expressed higher levels of Foxp3, CTLA-4, membrane-bound transforming growth factor beta1 (mTGFbeta1) and B7-H1, and are more suppressive to CD25 expression and proliferation of CD4+CD25-T cells. Additionally, we showed that the expression of Foxp3, CTLA-4, B7-H1, mTGFbeta1 and the secretion of TGFbeta1 and IL-10 on CD13+CD4+CD25hiTreg cells was significantly suppressed by anti-CD13 mAb (WM15), and the ability of these cells to suppress CD25 expression and proliferation of CD4+CD25-T cells was inhibited by WM15 as well. Interestingly, the percentage of CD13+CD4+CD25hiTreg cells among the CD4+CD25hiTreg population increased significantly and correlated with pathological stage in NSCLC: healthy donor (9.84% +/- 2.23%) <stage I (21.64% +/- 2.78%) <stage II (31.86% +/- 3.01%) <stage III (45.64% +/- 6.12%) <stage IV (58.78% +/- 12.89%). Moreover, the percentage of CD13+CD4+CD25hiTreg cells decreased dramatically after surgical removal of tumors. CD13 is a new surface molecule for identifying a CD4+CD25hiTreg cell subpopulation with higher suppressive ability. The percentage of CD13+CD4+CD25hiTreg cells among the CD4+CD25hiTreg cell population correlated with the pathological stage in NSCLC and tumor burden. CD13 represents a potential target to suppress Treg cells in anti-tumor therapy.
Induction of Heme Oxygenase-1 Expression in Vascular Smooth Muscle Cells (1997)

Endotoxic shock is a life-threatening consequence of severe Gram-negative infection characterized by vascular smooth muscle cell relaxation and severe hypotension. The production of nitric oxide (NO), through the inducible NO synthase pathway, has been implicated as a major contributor in this process. We now demonstrate that heme oxygenase (HO), an enzyme that generates carbon monoxide (CO) in the course of heme metabolism, may also be involved in the hemodynamic compromise of endotoxic shock. Inducible HO (HO-1) mRNA levels are dramatically increased in aortic tissue from rats receiving endotoxin, and this increase in vascular HO-1 message is associated with an 8.9-fold increase in HO enzyme activity in vivo. Immunocytochemical staining localizes an increase in HO-1 protein within smooth muscle cells of both large (aorta) and small (arterioles) blood vessels. Furthermore, zinc protoporphyrin IX, an inhibitor of HO activity, abrogates endotoxin-induced hypotension in rats. Studies performed in rat vascular smooth muscle cells in vitro show that the induction of HO-1 mRNA is regulated at the level of gene transcription, and this induction is independent of NO production. Taken together, these studies suggest that the up-regulation of HO-1, and the subsequent production of CO, contributes to the reduction in vascular tone during endotoxic shock.
Comparison of IgE‐binding antigens in horse dander and a mixture of horse hair and skin scrapings (1993)

Extracts of horse dander (HD) and horse hair and skin scrapings (HHSS) have been compared with respect to their content of proteins and carbohydrates. The protein content of HD is more than double that of HHSS, while the carbohydrate content is of the same order. SDS-PAGE and IEF, both combined with immunoblotting, and CIE/CRIE showed the IgE-binding ability of the proteins/glycoproteins present in the two extracts. SDS-PAGE/immunoblotting showed the presence of mainly the same IgE-binding bands in the two extracts. Nine were detected in HD, and seven in HHSS. Four of these were glycoproteins. The most important allergen was a glycoprotein with molecular mass of 27 kDa showing IgE-binding ability to the 16 patient sera available. Another important allergen with molecular mass of 67 kDa is probably horse albumin. IEF/immunoblotting showed the presence of a glycoprotein with IgE-binding ability at pH 3.2 in both extracts. Tandem CRIE showed that both extracts contained the same four allergens as major allergens. In addition, as we observed when analyzing both extracts in CRIE against 16 different patient sera, each extract contained allergens not present in the other extract. We may conclude from this investigation that commercial allergen extracts to be used in diagnosis and immunotherapy should include both horse dander and horse hair and skin scrapings in the starting material for the preparation of extracts. If not, allergens which may be of importance for some patients will be missing.
Electrophysiologic Testing to Identify Patients with Coronary Artery Disease Who Are at Risk for Sudden Death (2000)

Patients with coronary artery disease, left ventricular dysfunction, and asymptomatic, unsustained ventricular tachycardia in whom sustained ventricular tachyarrhythmias cannot be induced have a significantly lower risk of sudden death or cardiac arrest and lower overall mortality than similar patients with inducible sustained tachyarrhythmias.
Cinchona Alkaloid-Lewis Acid Catalyst Systems for Enantioselective Ketene−Aldehyde Cycloadditions (2004)

Asymmetric cinchona alkaloid-catalyzed acid chloride-aldehyde cyclocondensation (AAC) reactions afford enantioenriched 4-substituted and 3,4-disubstituted beta-lactones with near perfect absolute and relative stereocontrol. These reactions are characterized by the operational simplicity derived from using commercially available or easily obtained (one-step) reaction catalysts and in situ ketene generation from acid chlorides. The range of aldehyde substrates that serve as effective AAC substrates include sterically hindered aldehydes such as cyclohexanecarboxaldehyde and pivaldehyde.
Seeding of Vascular Grafts with an Immortalized Human Dermal Microvascular Endothelial Cell Line (1995)

Small-caliber vascular grafts (&lt; 6 mm) for arterial bypass frequently fail owing either to acute thrombosis or long-term fibrosis. One strategy to enhance patency is the coverage ("seeding") of luminal polymeric graft surfaces with endothelial cells (EC), which may in themselves be thromboresistant and antiproliferative, or which could be transfected with genes whose products are thrombolytic or growth-inhibitory. Advances in understanding of EC-biomaterial interaction have led to improvements in cell coverage and retention, but the sources of EC for such procedures have been limited to large vessels (autologous veins) and microvascular endothelium isolated from autologous adipose tissue. Before the practice of graft seeding can gain widespread clinical acceptance, the practical constraints of EC harvest, EC culture, and quick access to the seeded prosthesis for the surgical procedure must be overcome. Ideally, an EC line with a high proliferative capacity could be preestablished on the grafts, which could then be cryopreserved and made available as needed. The authors have seeded Dacron graft material with an immortalized human dermal microvascular EC line, HMEC-1. These cells were initially transfected with simian virus 40A large T antigen and have been passaged more than 100 times without signs of senescence. They also express von Willebrand factor, take up acetylated low density lipoproteins, and rapidly form tubes when cultured on matrigel. Confluent coverage of Dacron graft segments, either untreated or coated with gelatin, was achieved in two weeks. The cells formed a monolayer over topographically elevated regions or appeared to be &gt; one layer thick in other areas. Cells were also shown to remain viable after freezing. These results suggest a potential practical method for enhancement of small- caliber vascular graft biocompatibility in humans.
The gamma subunit of DNA polymerase III holoenzyme of Escherichia coli is produced by ribosomal frameshifting. (1990)

The tau and gamma subunits of DNA polymerase III holoenzyme are both products of the dnaX gene. Since tau and gamma are required as stoichiometric components of the replicative complex, a mechanism must exist for the cell to coordinate their synthesis and ensure that both subunits are present in an adequate quantity and ratio for assembly. We have proposed that gamma is produced by a translational frameshift event. In this report, we describe the use of dnaX-lacZ fusions in all three reading frames to demonstrate that gamma, the shorter product of dnaX, is generated by ribosomal frameshifting to the -1 reading frame of the mRNA within an oligo(A) sequence that is followed by a sequence predicted to form a stable secondary structure. Immediately after frameshifting a stop codon is encountered, leading to translational termination. Mutagenesis of the oligo(A) sequence abolishes frameshifting, and partial disruption of the predicted distal secondary structure severely impairs the efficiency. Comparison of the expression of lacZ fused to dnaX distal to the site of frameshifting in the -1 and 0 reading frames indicates that the efficiency of frameshifting is approximately 40%.
Manufacture of liposomes - a review (2011)

A brief introduction to liposomes and the methods of their preparation is presented. Various laboratory-scale and large-scale methods of preparation of liposomes are reviewed. They include some of the recent techniques like the 'bubble' method, microencapsulation, microfluidization, LLC method, ethanol injection, freon injection and detergent dialysis and the traditional methods like hydration, sonication and reverse phase evaporation. This paper also discusses the crucial problems like stability and quality control in the commercialization of liposomes and the methods (such as lyophilization and the various characterization techniques like electron microscopy and gel permeation chromatography) to overcome them, Also discussed is the mechanism of vesicle formation.
Codon and mRNA Sequence Optimization of Microdystrophin Transgenes Improves Expression and Physiological Outcome in Dystrophic mdx Mice Following AAV2/8 Gene Transfer (2008)

Duchenne muscular dystrophy is a fatal muscle-wasting disorder. Lack of dystrophin compromises the integrity of the sarcolemma and results in myofibers that are highly prone to contraction-induced injury. Recombinant adeno-associated virus (rAAV)-mediated dystrophin gene transfer strategies to muscle for the treatment of Duchenne muscular dystrophy (DMD) have been limited by the small cloning capacity of rAAV vectors and high titers necessary to achieve efficient systemic gene transfer. In this study, we assess the impact of codon optimization on microdystrophin (DeltaAB/R3-R18/DeltaCT) expression and function in the mdx mouse and compare the function of two different configurations of codon-optimized microdystrophin genes (DeltaAB/R3-R18/DeltaCT and DeltaR4-R23/DeltaCT) under the control of a muscle-restrictive promoter (Spc5-12). Codon optimization of microdystrophin significantly increases levels of microdystrophin mRNA and protein after intramuscular and systemic administration of plasmid DNA or rAAV2/8. Physiological assessment demonstrates that codon optimization of DeltaAB/R3-R18/DeltaCT results in significant improvement in specific force, but does not improve resistance to eccentric contractions compared with noncodon-optimized DeltaAB/R3-R18/DeltaCT. However, codon-optimized microdystrophin DeltaR4-R23/DeltaCT completely restored specific force generation and provided substantial protection from contraction-induced injury. These results demonstrate that codon optimization of microdystrophin under the control of a muscle-specific promoter can significantly improve expression levels such that reduced titers of rAAV vectors will be required for efficient systemic administration.
Phase Defect Repair Method for Alternating Phase Shift Masks Conjugate Twin-Shifter Method (1992)

Phase shift masks (PSMs) enable current optical exposure systems to provide significantly higher resolution in effective depth of focus (DOF). Localized phase errors, or other transparent defects in the mask phase shifter elements, can cause loss of DOF and degradation of image contrast. Transparent defects of this type have prevented PSMs from becoming practical for large-scale production of integrated circuits containing deep submicrometer features. This paper describes a new technique that is useful for repairing Alternating PSMs containing transparent defects in the phase shifter elements.
Tests and estimates of allelic association in complex inheritance (1998)

Family-based procedures such as the transmission disequilibrium test (TDT) were motivated by concern that sample-based methods to map disease genes by allelic association are not robust to population stratification, migration, and admixture. Other factors to consider in designing a study of allelic association are specification of gene action in a weakly parametric model, efficiency, diagnostic reliability for hypernormal individuals, interest in linkage and imprinting, and sibship composition. Family-based samples lend themselves to the TDT despite its inefficiency compared with cases and unrelated normal controls. The TDT has an efficiency of 1/2 for parent-offspring pairs and 2/3 for father-mother-child trios. Against cases and hypernormal controls, the efficiency is only 1/6 on the null hypothesis. Although dependent on marker gene frequency and other factors, efficiency for hypernormal controls is always greater than for random controls. Efficiency of the TDT is increased in multiplex families and by inclusion of normal sibs, approaching a case-control design with normal but not hypernormal controls. Isolated cases favor unrelated controls, and only in exceptional populations would avoidance of stratification justify a family-based design to map disease genes by allelic association.
The repertoire of glycan determinants in the human glycome (2009)

The number of glycan determinants that comprise the human glycome is not known. This uncertainty arises from limited knowledge of the total number of distinct glycans and glycan structures in the human glycome, as well as limited information about the glycan determinants recognized by glycan-binding proteins (GBPs), which include lectins, receptors, toxins, microbial adhesins, antibodies, and enzymes. Available evidence indicates that GBP binding sites may accommodate glycan determinants made up of 2 to 6 linear monosaccharides, together with their potential side chains containing other sugars and modifications, such as sulfation, phosphorylation, and acetylation. Glycosaminoglycans, including heparin and heparan sulfate, comprise repeating disaccharide motifs, where a linear sequence of 5 to 6 monosaccharides may be required for recognition. Based on our current knowledge of the composition of the glycome and the size of GBP binding sites, glycoproteins and glycolipids may contain approximately 3000 glycan determinants with an additional approximately 4000 theoretical pentasaccharide sequences in glycosaminoglycans. These numbers provide an achievable target for new chemical and/or enzymatic syntheses, and raise new challenges for defining the total glycome and the determinants recognized by GBPs.
Occurrence and Growth of Lactic Acid Bacteria in Wine: A Review (1985)

The growth of lactic acid bacteria in wine is of considerable significance to red and white wine quality. Malolactic fermentation and spoilage are two important consequences of the growth of lactic acid bacteria in wines. This review discusses the ecology, growth, and survival of lactic acid bacteria in wines along with the changes they cause to wine composition. Two hundred eight references are cited.
Enhanced Forward Explicit Congestion Notification (E-FECN) scheme for datacenter Ethernet networks (2008)

Ethernet is replacing the traditional storage networking technologies like Fiber Channel and Infiniband in Datacenters. The key feature of these traditional technologies that make them suitable for datacenter is their low-loss low-delay operation. Consequently IEEE 802.1 standards committee is developing new specification for congestion management for Ethernet in datacenter networks. Backward Congestion Notification (BCN) and Forward Explicit Congestion Notification (FECN) are two proposals. Each of the proposals has its own advantages and disadvantages. FECN outperforms BCN in fairness and response time while BCN is able to respond to sudden increases in load in less than a round trip time. In this paper, we propose an enhanced version of FECN that takes the best of both proposals and adds BCN if there is a sudden severe congestion. It is shown that E-FECN performs better than the previous proposals. 1.
Electrically Conductive Epoxy Adhesives (2011)

Conductive adhesives are widely used in electronic packaging applications such as die attachment and solderless interconnections, component repair, display interconnections, and heat dissipation. The effects of film thickness as functions of filler volume fraction, conductive filler size, shape, as well as uncured adhesive matrix viscosity on the electrical conduction behavior of epoxy-based adhesives are presented in this work. For this purpose, epoxy-based adhesives were prepared using conductive fillers of different size, shape, and types, including Ni powder, flakes, and filaments, Ag powder, and Cu powder. The filaments were 20 μm in diameter, and 160 or 260 μm in length. HCl and H3PO4 acid solutions were used to etch and remove the surface oxide layers from the fillers. The plane resistance of filled adhesive films was measured using the four-point method. In all cases of conductive filler addition, the planar resistivity levels for the composite adhesive films increased when the film thickness was reduced. The shape of resistivity-thickness curves was negative exponential decaying type and was modeled using a mathematical relation. The relationships between the conductive film resistivities and the filler volume fractions were also derived mathematically based on the experimental data. Thus, the effects of surface treatment of filler particles, the type, size, shape of fillers, and the uncured epoxy viscosity could be included empirically by using these mathematical relations based on the experimental data. By utilizing the relations we proposed to model thickness-dependent and volume fraction-dependent conduction behaviors separately, we were able to describe the combined and coupled volume fraction-film thickness relationship mathematically based on our experimental data.
First-in-Human Case Study: Pregnancy in Women With Crohn's Perianal Fistula Treated With Adipose-Derived Stem Cells: A Safety Study (2015)

Local treatment with mesenchymal stem cells derived from adipose tissue seems not to affect the ability to conceive, the course of pregnancy, pregnancy outcomes, or newborns' health in female patients. This is the first publication about pregnancy outcome in women with perianal fistula and Crohn's disease treated with stem cell therapy, and could be of interest for doctors working in cell therapy. This is a very important question for patients, and there was no answer for them until now.
“Second Generation” Ruthenium Carbene Complexes with a cis-Dichloro Arrangement (2004)

The synthesis, characterization, and catalytic activity of a series of unprecedented ruthenium-based metathesis catalysts bearing a cis-dichloro arrangement, an N-heterocyclic carbene, and a chelating carbene ligand derived from 2-vinylbenzaldehyde or 2-vinylbenzoic acid ester are presented.
Pre‐Metalation Structural Insights into the Use of Alkali‐Metal‐Mediated Zincation for Directed ortho‐Metalation of a Tertiary Aromatic Amide (2006)

The predator meets its prey in the structure of [{(iPr)2NC(Ph)(O)}Li(μ-tmp)(μ-tBu)Zn(tBu)] which reveals an aromatic amide–alkali metal zincate “precomplex” for directed ortho-metalation (DoM) that exists prior to the devouring (ortho-zincation) of the amide by the zincate. tmp=2,2,6,6-tetramethylpiperidide.
Simplified production and concentration of lentiviral vectors to achieve high transduction in primary human T cells (2013)

The optimised protocol described here is easy to implement and should facilitate the production of high-titre lentivirus with superior transduction efficiency in primary human T cells without the need for further purification methods.