gebhart/patrepeval huggingface dataset:
A Clinical Technique for Prevention of Spasm and Preservation of Endothelium in Saphenous Vein Grafts (1984)

Spasm and endothelial injury during harvesting of saphenous vein grafts can be prevented by a protocol that involves perivenous infiltration with 37 degrees C papaverine hydrochloride solution prior to skin incision, initial distention of the vein with the same warm papaverine solution, storage of the distended vein graft in a cold papaverine solution, and maintenance of the vein in the distended state throughout the operative procedure. This technique preserves endothelial integrity in human reversed saphenous vein grafts.
Use of phage display for isolation and characterization of single‐chain variable fragments against dihydroflavonol 4‐reductase from Petunia hybrida (1997)

To isolate specific single-chain variable (scFv) fragments against dihydroflavonol 4-reductase (DFR) from Petunia hybrida the phage display technology was used. DFR was overproduced in Escherichia coli, purified and used for immunization. From DFR-immunized mice, a phage display library was made starting from spleen mRNA using an optimized set of primers for V(H) and V(L) amplification. Several rounds of panning against recombinant DFR yielded five different scFv fragments, confirmed by subsequent DNA sequencing. They all specifically bound to recombinant DFR in ELISA and DFR in flower extracts on Western blot. These results show that phage display is a promising technology in plant molecular biology to obtain specific recombinant antibodies not only for ELISA and Western blot but also for in vivo applications in the long run.
Organic-Inorganic Hybrid Materials as Semiconducting Channels in Thin-Film Field-Effect Transistors (1999)

Organic-inorganic hybrid materials promise both the superior carrier mobility of inorganic semiconductors and the processability of organic materials. A thin-film field-effect transistor having an organic-inorganic hybrid material as the semiconducting channel was demonstrated. Hybrids based on the perovskite structure crystallize from solution to form oriented molecular-scale composites of alternating organic and inorganic sheets. Spin-coated thin films of the semiconducting perovskite (C(6)H(5)C(2)H(4)NH(3))(2)SnI(4) form the conducting channel, with field-effect mobilities of 0.6 square centimeters per volt-second and current modulation greater than 10(4). Molecular engineering of the organic and inorganic components of the hybrids is expected to further improve device performance for low-cost thin-film transistors.
Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors (2005)

Histone deacetylase inhibitors (HDACis) inhibit tumor cell growth and survival, possibly through their ability to regulate the expression of specific proliferative and/or apoptotic genes. However, the HDACi-regulated genes necessary and/or sufficient for their biological effects remain undefined. We demonstrate that the HDACis suberoylanilide hydroxamic acid (SAHA) and depsipeptide regulate a highly overlapping gene set with at least 22% of genes showing altered expression over a 16-h culture period. SAHA and depsipeptide coordinately regulated the expression of several genes within distinct apoptosis and cell cycle pathways. Multiple genes within the Myc, type beta TGF, cyclin/cyclin-dependent kinase, TNF, Bcl-2, and caspase pathways were regulated in a manner that favored induction of apoptosis and decreased cellular proliferation. APAF-1, a gene central to the intrinsic apoptotic pathway, was induced by SAHA and depsipeptide and shown to be important, but not essential, for HDACi-induced cell death. Overexpression of p16(INK4A) and arrest of cells in G(1) can suppress HDACi-mediated apoptosis. Although p16(INK4A) did not affect the genome-wide transcription changes mediated by SAHA, a small number of apoptotic genes, including BCLXL and B-MYB, were differentially regulated in a manner consistent with attenuated HDACi-mediated apoptosis in arrested cells. We demonstrate that different HDACi alter transcription of a large and common set of genes that control diverse molecular pathways important for cell survival and proliferation. The ability of HDACi to target multiple apoptotic and cell proliferation pathways may provide a competitive advantage over other chemotherapeutic agents because suppression/loss of a single pathway may not confer resistance to these agents.
Engineering Exon-Skipping Vectors Expressing U7 snRNA Constructs for Duchenne Muscular Dystrophy Gene Therapy (2010)

Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disorder caused by mutations in the dystrophin gene. In most cases, the open-reading frame is disrupted which results in the absence of a functional protein. Antisense-mediated exon skipping is one of the most promising approaches for the treatment of DMD and has recently been shown to correct the reading frame and restore dystrophin expression in vitro and in vivo. Specific exon skipping can be achieved using synthetic oligonucleotides or viral -vectors encoding modified snRNAs, by masking important splicing sites. We have recently demonstrated that enhanced exon skipping can be induced by a U7 snRNA carrying binding sites for the heterogeneous ribonucleoprotein A1. In DMD patient cells, bifunctional U7 snRNAs harboring silencer motifs induce complete skipping of exon 51 and thus restore dystrophin expression to near wild-type levels. Furthermore, we have confirmed the efficacy of these constructs in vivo in transgenic mice carrying the entire human DMD locus after intramuscular injection of AAV vectors encoding the bifunctional U7 snRNA. These new constructs are very promising for the optimization of therapeutic exon skipping for DMD, but also offer powerful and versatile tools to modulate pre-mRNA splicing in a wide range of applications. Here, we outline the design of these U7 snRNA constructs to achieve efficient exon skipping of the dystrophin gene. We also describe methods to evaluate the efficiency of such U7 snRNA constructs in vitro in DMD patient cells and in vivo in the transgenic hDMD mouse model, using lentiviral and recombinant adeno-associated viral vectors, respectively.
Structural Basis for the Recognition of Lewis Antigens by Genogroup I Norovirus (2012)

Noroviruses (NoVs) bind to histo-blood group antigens, namely, ABH antigens and Lewis antigens. We previously showed the NoVs GI/2, GI/3, GI/4, and GI/8 were able to strongly bind to Lewis a (Le(a)) antigen, which is expressed by individuals who are nonsecretors. In this study, to investigate how Lewis antigens interact with GI NoV virion protein 1 (VP1), we determined the crystal structures of the P domain of the VP1 protein from the Funabashi 258 (FUV258) strain (GI/2) in complexes with Le(a), Le(b), H type 1, or A type 1 antigens. The structures were compared with those of the NV/68 strain (GI/1), which does not bind to the Le(a) antigen. The four loop structures, loop P, loop S, loop A, and loop B, continuously deviated by more than 2 Å in length between the Cα atoms of the corresponding residues of the FUV258 and NV/68 P domains. The most pronounced differences between the two VP1 proteins were observed in the structures of loop P. In the FUV258 P domain, loop P protruded toward the next protomer, forming a Le(a) antigen-binding site. The Gln389 residue make a significant contribution to the binding of the Le(a) antigen through the stabilization of loop P as well as through direct interactions with the α4-fucosyl residue (α4Fuc) of the Le(a) antigen. Mutation of the Gln389 residue dramatically affected the degree of binding of the Lewis antigens. Collectively, these results suggest that loop P and the amino acid residue at position 389 affect Lewis antigen binding.
Yield Effects of Genetically Modified Crops in Developing Countries (2003)

Onfarm field trials carried out with Bacillus thuringiensis (Bt) cotton in different states of India show that the technology substantially reduces pest damage and increases yields. The yield gains are much higher than what has been reported for other countries where genetically modified crops were used mostly to replace and enhance chemical pest control. In many developing countries, small-scale farmers especially suffer big pest-related yield losses because of technical and economic constraints. Pest-resistant genetically modified crops can contribute to increased yields and agricultural growth in those situations, as the case of Bt cotton in India demonstrates.
Increased Levels of Soluble P-Selectin in Hypercholesterolemic Patients (1998)

Hypercholesterolemia is associated with elevated plasmatic P-selectin. Altered oxidative processes leading to endothelial dysfunction and persistent platelet activation may contribute to increased soluble P-selectin levels. P-selectin may be proposed as a marker of endothelial dysfunction in hypercholesterolemic patients.
Characterization of a membrane-based gradient generator for use in cell-signaling studies (2006)

This paper describes a method to create stable chemical gradients without requiring fluid flow. The absence of fluid flow makes this device amenable to cell signaling applications where soluble factors can impact cell behavior. This device consists of a membrane-covered source region and a large volume sink region connected by a microfluidic channel. The high fluidic resistance of the membrane limits fluid flow caused by pressure differences in the system, but allows diffusive transport of a chemical species through the membrane and into the channel. The large volume sink region at the end of the microfluidic channel helps to maintain spatial and temporal stability of the gradient. The chemical gradient in a 0.5 mm region near the sink region experiences a maximum of 10 percent change between the 6 and 24 h data points. We present the theory, design, and characterization of this device and provide an example of neutrophil chemotaxis as proof of concept for future quantitative cell-signaling applications.
An Active Site Substitution, F87V, Converts Cytochrome P450 BM-3 into a Regio- and Stereoselective (14S,15R)-Arachidonic Acid Epoxygenase (1997)

Cytochrome P450 BM-3 catalyzes the high turnover regio- and stereoselective metabolism of arachidonic and eicosapentaenoic acids. To map structural determinants of productive active site fatty acid binding, we mutated two amino acid residues, arginine 47 and phenylalanine 87, which flank the surface and heme ends of the enzyme's substrate access channel, respectively. Replacement of arginine 47 with glutamic acid resulted in a catalytically inactive mutant. Replacement of arginine 47 with alanine yielded a protein with reduced substrate binding affinity and arachidonate sp3 carbon hydroxylation activity (72% of control wild type). On the other hand, arachidonic and eicosapentaenoic acid epoxidation was significantly enhanced (154 and 137%, of control wild type, respectively). As with wild type, the alanine 47 mutant generated (18R)-hydroxyeicosatetraenoic, (14S,15R)-epoxyeicosatrienoic, and (17S,18R)-epoxyeicosatetraenoic acids nearly enantiomerically pure. Replacement of phenylalanine 87 with valine converted cytochrome P450 BM-3 into a regio- and stereoselective arachidonic acid epoxygenase ((14S,15R)epoxyeicosatrienoic acid, 99% of total products). Conversely, metabolism of eicosapentaenoic acid by the valine 87 mutant yielded a mixture of (14S,15R)- and (17S,18R)-epoxyeicosatetraenoic acids (26 and 69% of total, 94 and 96% optical purity, respectively). Finally, replacement of phenylalanine 87 with tyrosine yielded an inactive protein. We propose that: (a) fatty acid oxidation by P450 BM-3 is incompatible with the presence of residues with negatively charged side chains at the surface opening of the substrate access channel or a polar aromatic side chain in the vicinity of the heme iron; (b) the high turnover regio- and stereoselective metabolism of arachidonic and eicosapentaenoic acids involves charge-dependent anchoring of the fatty acids at the mouth of the access channel by arginine 47, as well as steric gating of the heme-bound oxidant by phenylalanine 87; and (c) substrate binding coordinates, as opposed to oxygen chemistries, are the determining factors responsible for reaction rates, product chemistry, and, thus, catalytic outcome.
Regioselective Carboxylation of 9-Xanthenones with Manganese(III) Acetate (1983)

Abstract Seven 9-xanthenones were oxidized with manganese(III) acetate to give carboxy-, dicarboxy-, (acetoxymethyl)(carboxy)-, (carboxy)(hydroxymethyl)-, and acetoxymethyl-9-xanthenones, and to yield small amounts of (carboxymethyl)(carboxy)-, carboxymethyl-, (acetoxymethyl)(carboxymethyl)-, bis(acetoxymethyl)-, and diacetoxymethyl-9-xanthenones. The carboxyl group was preferentially introduced into the peri positions and the acetoxymethyl groups were located at positions ortho to the methoxyl or methyl group. The regioselectivity and mechanism of the carboxylation reaction is discussed briefly.
Adaptive mixed-initiative dialogue management (2002)

This paper describes an architecture that supports adaptive mixed-initiative dialogue. It is based on a generalisation of the form-filling paradigm. Rather than a flat slot structure, we use a hierarchy that contains slots at various levels of abstraction. Along with the slot hierarchy, a question hierarchy is defined that allows for adaptive mixed-initiative dialogue. Depending on the success or failure of certain questions, the system can zoom-in to more detailed questions, or zoom-out to higher-level questions. The distribution of initiative in dialogue is closely related to the granularity of the information that is asked for. To determine the right granularity level for system questions we have to take into account the influences on user freedom, predictability and the knowledge of the user. Giving the user initiative is suitable in situations where the user knows what to do. In such cases, the user may give all relevant information in one turn. However, giving the user more initiative tends to make his behaviour less predictable and therefore increases the chance on speech-understanding errors. The system should switch to lower-level questions when higher-level ones fail, and when the user supplies unsolicited information, the system can switch to higher-level questions.
Lidocaine increases the anti‐inflammatory cytokine IL‐10 following mechanical ventilation in healthy mice (2014)

Intravenously administered lidocaine increases levels of plasma IL-10 with infusion from 2, 4, and 8 mg/kg/h and pulmonary levels of IL-10 with 8 mg/kg/h in a murine mechanical ventilation model. Intravenously administered lidocaine appears to reduce anesthetic need in mice.
Persistent Colonization by Haemophilus influenzae in Chronic Obstructive Pulmonary Disease (2004)

Nontypeable Haemophilus influenzae colonizes the respiratory tract of adults with chronic obstructive pulmonary disease (COPD) and causes intermittent exacerbations. Isolates of H. influenzae collected monthly in a prospective study were subjected to molecular typing. During a 7-year study spanning 345 patient-months of observation, 122 episodes of negative cultures lasting 1 month or more, and that were preceded and followed by isolation of an apparently identical strain of H. influenzae, were found. Seventeen such episodes of negative cultures, lasting 6 months or more and spanning 203 patient-months, were studied in detail to test the hypothesis that these periods of negative cultures represented continuous colonization by the same strain of H. influenzae. Molecular typing by three independent methods established that the strains preceding and following the episodes of negative cultures were indeed identical. Strain-specific H. influenzae DNA was detected in some of the sputum samples that had yielded negative cultures. These results indicate that some patients with COPD are persistently colonized with H. influenzae and that sputum cultures underestimate the frequency of colonization of the respiratory tract by H. influenzae in COPD. This observation has a significant impact on understanding bacterial colonization in COPD.
Variable mercaptopurine metabolism and treatment outcome in childhood lymphoblastic leukemia. (1989)

Intracellular thioguanine nucleotides (6-TGN) are the major cytotoxic metabolites of mercaptopurine (6-MP). Red blood cell (RBC) 6-TGN concentrations were measured in a group of 120 consecutive children with lymphoblastic leukemia (ALL) to assess interpatient variability and its clinical importance. Assays were performed after at least 2 months 6-MP maintanance chemotherapy and a minimum 7 days unattenuated protocol dose of 75 mg/m2. Observed 6-TGN concentrations ranged from 126 to 832 pmol/8 x 10(8) RBCs (median, 275). There was a correlation between 6-TGN and neutropenia 14 days postassay (rs = .51; P less than .0005), and an inverse correlation between 6-TGN and the length of time uninterrupted full protocol dose was tolerated without neutropenia (rs = -.3; P less than .01). After a median follow-up of 49 months, 19 children had relapsed, of whom 17 (89%) had 6-TGN concentrations below the group median (log-rank chi 2 = 11.9; P less than .001). Multivariate analysis using Cox's proportional hazards regression showed the 6-TGN effect on disease control to be independent of diagnostic WBC count, sex, age, immunological cell type, French-American-British (FAB) type, variation in other antineoplastic therapy, and duration of remission at the time of 6-TGN assay. Children with ALL taking the same dose of 6-MP show great variability in its measurable cytotoxic effect, and this variability is apparently important in predicting treatment outcome.
Proton Transfer Pathways in Bacteriorhodopsin at 2.3 Angstrom Resolution (1998)

Photoisomerization of the retinal of bacteriorhodopsin initiates a cyclic reaction in which a proton is translocated across the membrane. Studies of this protein promise a better understanding of how ion pumps function. Together with a large amount of spectroscopic and mutational data, the atomic structure of bacteriorhodopsin, determined in the last decade at increasing resolutions, has suggested plausible but often contradictory mechanisms. X-ray diffraction of bacteriorhodopsin crystals grown in cubic lipid phase revealed unexpected two-fold symmetries that indicate merohedral twinning along the crystallographic c axis. The structure, refined to 2.3 angstroms taking this twinning into account, is different from earlier models, including that most recently reported. One of the carboxyl oxygen atoms of the proton acceptor Asp85 is connected to the proton donor, the retinal Schiff base, through a hydrogen-bonded water and forms a second hydrogen bond with another water. The other carboxyl oxygen atom of Asp85 accepts a hydrogen bond from Thr89. This structure forms the active site. The nearby Arg82 is the center of a network of numerous hydrogen-bonded residues and an ordered water molecule. This network defines the pathway of the proton from the buried Schiff base to the extracellular surface.
Neutrophils responsive to endogenous IFN-β regulate tumor angiogenesis and growth in a mouse tumor model (2010)

Angiogenesis is a hallmark of malignant neoplasias, as the formation of new blood vessels is required for tumors to acquire oxygen and nutrients essential for their continued growth and metastasis. However, the signaling pathways leading to tumor vascularization are not fully understood. Here, using a transplantable mouse tumor model, we have demonstrated that endogenous IFN-beta inhibits tumor angiogenesis through repression of genes encoding proangiogenic and homing factors in tumor-infiltrating neutrophils. We determined that IFN-beta-deficient mice injected with B16F10 melanoma or MCA205 fibrosarcoma cells developed faster-growing tumors with better-developed blood vessels than did syngeneic control mice. These tumors displayed enhanced infiltration by CD11b+Gr1+ neutrophils expressing elevated levels of the genes encoding the proangiogenic factors VEGF and MMP9 and the homing receptor CXCR4. They also expressed higher levels of the transcription factors c-myc and STAT3, known regulators of VEGF, MMP9, and CXCR4. In vitro, treatment of these tumor-infiltrating neutrophils with low levels of IFN-beta restored expression of proangiogenic factors to control levels. Moreover, depletion of these neutrophils inhibited tumor growth in both control and IFN-beta-deficient mice. We therefore suggest that constitutively produced endogenous IFN-beta is an important mediator of innate tumor surveillance. Further, we believe our data help to explain the therapeutic effect of IFN treatment during the early stages of cancer development.
N-end Rule Specificity within the Ubiquitin/Proteasome Pathway Is Not an Affinity Effect (2001)

The N-end rule relates the amino terminus to the rate of degradation through the ubiquitin/26 S proteasome pathway. Proteins bearing basic (type 1) or large hydrophobic (type 2) amino termini are assumed to be targeted through this pathway by their higher affinity for binding to the responsible E3 ligase compared with proteins bearing other residues (type 3). Paradoxically, a significant fraction of eukaryotic protein degradation occurs through the N-end rule pathway, although the majority of cellular proteins are type 3 substrates. We have exploited specific interactions between ubiquitin carrier proteins (E2/Ubc) and their cognate E3 ligases to purify for the first time the mammalian N-end rule ligase E3alpha/Ubr1 to near homogeneity. In vitro studies show that E3alpha forms lysine 48-linked polyubiquitin degradation signals on type 1-3 substrates and is absolutely dependent on Ubc2/Rad6 orthologs. Biochemically defined kinetic studies show that the basis of N-end rule specificity is a k(cat) rather than the K(m) effect originally proposed, since all three substrate classes show similar binding affinities (K(m) approximately 5 microm) but V(max) values that are 100- and 50-fold greater for type 1 and 2 versus type 3 model substrates, respectively. In addition, the N-end rule dipeptides lysylalanine and phenylalanylalanine are general noncompetitive inhibitors for E3alpha-catalyzed ubiquitination of type 1-3 substrates rather than type-specific competitive inhibitors as predicted. These observations are consistent with a model in which the N-end rule effect reflects substrate binding-induced transitions in E3alpha to a catalytically competent conformer, the equilibrium for which depends on the identity of the amino terminus or the presence of basic or hydrophobic surface features. The model reconciles conflicts between specific predictions and empirical observations relating N-end rule targeting in addition to explicating the efficacy of selected dipeptides as potent in vivo inhibitors of this pathway.
Swelling, Strain, and Radiation Damage of He+ Implanted GaP (1986)

Swelling, strain, and damage density are measured as a function of fluence and post-bombardment annealing temperature on (111) GaP single crystals bombarded with 0.6 and 1.0 MeV He+ ions in the range of fluences till 5 × 1017 cm−2. It is demonstrated that after an initial saturating behaviour of damage density, strain, and swelling in the region near the surface, strong disorder of the whole implanted layer can be reached due to the fluence dependent broadening of the damage peak towards the surface. An (111) GaP-Einkristallen, die mit 0,6- und 1,0 MeV-He+-Ionen bestrahlt wurden, wurden die Volumenausdehnung, Änderung der Netzebenenabstände und die Defektdichte in Abhängigkeit von der implantierten Dosis und der Ausheiltemperatur im Dosisbereich bis 5 × 1017 cm−2 ge-messen. Es wird gezeigt, daß nach einem anfänglichen Sättigungsverhalten dieser Größen im oberflächennahen Bereich bei höheren Dosiswerten durch die Verbreiterung der vergrabenen stark geschädigten Schicht in Richtung Oberfläche ein Übergang zu einer starken Schädigung der gesamten durchstrahlten Schicht erreicht wird.