gebhart/patrepeval huggingface dataset:
Peptide-Retargeted Adenovirus Encoding a Tissue Inhibitor of Metalloproteinase-1 Decreases Restenosis after Intravascular Gene Transfer (2002)

In this study we have attached cyclic targeting peptides by way of a poly-lysine spacer on the surface of an adenovirus using a transglutaminase enzymatic reaction to enhance transduction efficiency and to modify tissue tropism in vivo. Nuclear targeted lacZ- and TIMP-1-encoding adenoviruses were coupled to a peptide-motif (HWGF) that can bind to matrix metalloproteinase (MMP)-2 and MMP-9. Modified viruses were used to evaluate gene transfer efficiency, biodistribution, and the effect on neointima formation following balloon denudation injury. In vitro, both rabbit aortic smooth muscle cells and human endothelial hybridoma cells demonstrated significantly increased reporter gene expression with HWGF-modified adenoviruses (AdlacZ(HWGF)) compared with control (AdlacZ) or mismatch peptide-modified (AdlacZ(MM)) adenoviruses. However, in human hepatocellular Hep-G2 cells, both AdlacZ(HWGF) and AdlacZ(MM) produced significantly lower transgene expression compared with the respective control viruses. In vivo, local intravascular catheter-mediated gene transfer of a HWGF-targeted TIMP-1-encoding adenovirus (AdTIMP-1(HWGF)) significantly reduced intimal thickening in a rabbit aortic balloon denudation model (P < 0.05) compared with the control adenovirus. X-Gal staining and biodistribution analyses with TaqMan RT-PCR revealed that the cyclic peptides altered vector tropism and, in particular, reduced transduction of the liver. We found that the HWGF peptide modification increased transduction efficiency of the adenovirus-mediated gene transfer in smooth muscle cells and endothelial cells in in vitro and enhanced gene transfer to the arterial wall in vivo; that peptide modification of adenoviruses beneficially modulated tissue tropism in vivo; and that efficient TIMP-1 gene transfer reduced intimal thickening in an established restenosis model in rabbits.
Expression of a hybrid complement regulatory protein, membrane cofactor protein decay accelerating factor on Chinese hamster ovary. Comparison of its regulatory effect with those of decay accelerating factor and membrane cofactor protein. (1994)

C activation on the cell surface is supposedly regulated by membrane cofactor protein (MCP) and decay accelerating factor (DAF). These are complementary in function: MCP acts as a cofactor in factor I-mediated C3b and C4b inactivation, thus preventing the assembly of C3 convertases, whereas DAF accelerates spontaneous decay of the assembled C3 convertase. In this report, a hybrid MCP-DAF was expressed on Chinese hamster ovary cells by transfecting cDNA, and its regulatory activity was compared with those of MCP and DAF transfectants and with a transfectant expressing both MCP and DAF (MCP + DAF). The C3 deposition on sensitized CHO cells through activation of the classical pathway was blocked to a different degree with these transfectants, the order being MCP + DAF > DAF > hybrid MCP-DAF > MCP. Likewise, the C3 deposition via the alternative pathway was blocked efficiently in the order hybrid > MCP + DAF > MCP. The C-mediated cytolysis of CHO cells virtually reflected the degree of C3 fragment deposition. The MCP-DAF transfectant acquired additive protective activity against alternative pathway-mediated C3 deposition and cytolysis but was less potent in circumventing classical pathway attack than cells that expressed DAF alone or DAF + MCP. Hybrid MCP-DAF may be useful for alleviating C-mediated cell damage, especially via the alternative pathway.
An empirical approach for thermal stability (Tm) prediction of PNA/DNA duplexes (2004)

To predict the Tm value of PNA/DNA duplex, we performed to determine the melting temperature of several PNA oligomers. For Tm calculation model building, we searched the correlativity of measured Tm value and each base contents of PNA oligomer. Here, We propose a novel formula for thermal stability (Tm) prediction of PNA/DNA duplexes.
Expression, Secretion, and Processing of Rice α-Amylase in the Yeast Yarrowia lipolytica (1997)

The gene encoding rice alpha-amylase in Oryza sativa was expressed in the yeast Yarrowia lipolytica, which is a potential host system for heterologous protein expression. For efficient secretion, the strong and inducible XPR2 promoter was used in the construction of four kinds of expression vectors with the following configurations between the XPR2 promoter and terminator: 1) XPR2 prepro-region-rice alpha-amylase coding sequence, 2) rice alpha-amylase signal peptide-rice alpha-amylase coding sequence, 3) XPR2 signal peptide-rice alpha-amylase coding sequence, and 4) XPR2 signal peptide-dipeptide stretch-rice alpha-amylase coding sequence. Secretion of active recombinant rice alpha-amylase into the culture medium was achieved only in the first two cases, demonstrating that the XPR2 signal peptide is not sufficient to direct the secretion of heterologous protein. Furthermore, our study shows that the XPR2 prepro-region causes imprecise processing (after Pro150-Ala151 or Val135-Leu136 instead of Lys156-Arg157) and leads to N-terminal amino acid sequences that differ from that of native rice alpha-amylase. Secondary structure analysis proposed that the structural form in the vicinity of the KEX2-like endopeptidase processing site in the XPR2 pro-region might play a critical role in the processing of heterologous proteins. These results suggest that the XPR2 pro-region is dispensable for obtaining the precise N-terminal amino acid in heterologous protein secretion. In contrast, utilizing the rice alpha-amylase signal peptide was sufficient in directing secretion of recombinant protein with the expected N-terminal sequence, indicating that the signal peptide of rice alpha-amylase was effectively recognized and processed by the Y. lipolytica secretory pathway.
Expression of glycans linked to natural killer cell inhibition on the human zona pellucida (1997)

Protection of the gametes from potential immune responses is a primary function in human reproduction. The primary cell type responsible for the innate immune response in the uterus is the natural killer (NK) cell. NK cells normally recognize Class I major histocompatibility (MHC) molecules on potential target cells. Since both human spermatozoa and human oocytes do not express Class I MHC molecules on their surfaces, the appropriate cell surface signal that abrogates potential NK cell-mediated responses directed against these gametes is unknown. Recent evidence indicates that surface expression of bisecting-type N-linked glycans protects cells sensitive to NK cell-mediated lysis. We report that the zona pellucida of the human egg and plasma membranes of human spermatozoa potentially bind a lectin probe specific for bisecting type glycans in a carbohydrate-dependent manner. Since the innate immune response in the uterus is primarily mediated by NK cells, our results indicate that human gametes may be protected from this response by expressing bisecting type N-linked glycans on their surfaces.
Guided-mode resonance filters of finite aperture (1995)

The operation of optical narrowband reflection filters based on resonance anomalies of waveguide gratings is well established for gratings of infinite extent. We investigate the properties of finite-aperture waveguide-grating resonance filters by means of rigorous electromagnetic theory and an approximate model. The rigorous approach illustrates the scattering of optical energy from the guided mode at and near the edges of the element, which leads to a reduced diffraction efficiency into the backward-diffracted zeroth order. The approximate approach provides an optical-engineering model for the estimation of the minimum grating size required to achieve a high resonance-wavelength reflectivity.
Mutations in Soybean Microsomal Omega‐3 Fatty Acid Desaturase Genes Reduce Linolenic Acid Concentration in Soybean Seeds (2005)

One major locus ( Fan ) and several minor loci have been shown to contribute to the linolenic acid level in soybean [ Glycine max (L.) Merr.] seeds. The Fan gene encodes a microsomal omega‐3 fatty acid desaturase ( Arabidopsis FAD3 homolog), and soybeans contain three FAD3 genes. The objective of this work was to characterize candidate soybean FAD3 genes from low linolenic acid soybean lines and associate those alleles with the trait. Mutations in two of the three soybean FAD3 genes were identified, and genotypes with the mutant alleles conferred a reduction of over two thirds of the linolenic acid present in the seed. The two mutant genes contributed unequally but additively to the phenotype. The results demonstrated that the mutant genotype can be identified with mutation‐specific molecular markers in the F 2 generation, and the low linolenic acid trait will be stably inherited in subsequent generations.
Designing for mass transit railways within freeway medians (2006)

The City of Perth in Western Australia has one of the highest car usages in the world, with only three other cities having higher car ownership per capita. In searching for an alternative to the unsustainable dependence on private car commuting in the metropolitan area, finding continuous rights of way for railway mass transit was extremely difficult. There were many constraints. Consequently, the medians of the major freeway systems had to be seriously considered and were adopted. Railways once preceded the development of other major infrastructure and this allowed total separation with generous buffers. Today, urban passenger railways must be integrated with existing infrastructure and the environment. There is a general lack of regulatory and industry guidelines for locating mass transit railways in the median of major road arteries, both in Australia and overseas. This is a major challenge for engineers, operators and regulators. Road and rail engineers in Perth have now developed standard minimum reserve widths. In the absence of other guidelines, design must be based on the codes of railway engineering practice of the time. New standards may have to be developed. The whole process must be subject to risk analysis. Perth's Northern Suburbs Railway (NSR) was built within the median of the Mitchell Freeway for the majority of its route. Its success has been outstanding and today it carries the equivalent of between three and four freeway lanes of traffic in the morning peak rush hour. In the planning and design of the Southern Suburbs Railway (SSR), a review of the Northern Suburbs experience and overseas practises showed that a railway can be located within more narrow freeway medians than was available for the Northern Suburbs. The design of that section of the SSR within the median of the Kwinana Freeway showed that the greatest risk to safety is from vehicle or debris fouling the path of an oncoming train. This paper describes the background issues, constraints, design standards, outcomes of risk analysis, different barrier types, final outcomes, operating parameters and conclusions appertaining to a railway in the median of a freeway.
Coadministration of Angiopoietin-1 and Vascular Endothelial Growth Factor Enhances Collateral Vascularization (2000)

Using growth factors to induce vasculogenesis is a promising approach in the treatment of ischemic legs and myocardium. Because the vasculogenesis requires a cascade of growth factors, their receptors, and intracellular signals, such therapies may require the application of more than a single growth factor. We examined the effect of 2 endothelial cell-specific growth factors, angiopoietin-1 (Ang1) and vascular endothelial growth factor (VEGF), on primary cultured porcine coronary artery endothelial cells. VEGF, but not Ang1, increased DNA synthesis and cell number. Ang1 or VEGF induced migration and sprouting activity, increased plasmin and matrix metalloproteinase-2 secretion, and decreased tissue inhibitors of metalloproteinase type 2 secretion. A combination of the submaximal doses of Ang1 and VEGF enhanced these effects and was more potent than the maximal dose of either alone. In a rabbit ischemic hindlimb model, a combination of Ang1 and VEGF gene delivery produced an enhanced effect on resting and maximal blood flow and capillary formation that was greater than that of either factor alone. Angiographic analyses revealed that larger blood vessels were formed after gene delivery of Ang1 or Ang1 plus VEGF than after VEGF gene delivery. These results suggest that combined treatment of Ang1 and VEGF could be used to produce therapeutic vascularization.
Direct Continuous Method for Monitoring Biofilm Infection in a Mouse Model (2003)

We have developed a rapid, continuous method for real-time monitoring of biofilms, both in vitro and in a mouse infection model, through noninvasive imaging of bioluminescent bacteria colonized on Teflon catheters. Two important biofilm-forming bacterial pathogens, Staphylococcus aureus and Pseudomonas aeruginosa, were made bioluminescent by insertion of a complete lux operon. These bacteria produced significant bioluminescent signals for both in vitro studies and the development of an in vivo model, allowing effective real-time assessment of the physiological state of the biofilms. In vitro viable counts and light output were parallel and highly correlated (S. aureus r = 0.98; P. aeruginosa r = 0.99) and could be maintained for 10 days or longer, provided that growth medium was replenished every 12 h. In the murine model, subcutaneous implantation of the catheters (precolonized or postimplant infected) was well tolerated. An infecting dose of 10 (3) to 10 (5) CFU/catheter for S. aureus and P. aeruginosa resulted in a reproducible, localized infection surrounding the catheter that persisted until the termination of the experiment on day 20. Recovery of the bacteria from the catheters of infected animals showed that the bioluminescent signal corresponded to the CFU and that the lux constructs were highly stable even after many days in vivo. Since the metabolic activity of viable cells could be detected directly on the support matrix, nondestructively, and noninvasively, this method is especially appealing for the study of chronic biofilm infections and drug efficacy studies in vivo.
Molecular mechanisms underlying nutrient detection by incretin-secreting cells (2009)

The hormones glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) are secreted postprandially from intestinal K- and L-cells, respectively. As incretins, these hormones stimulate insulin secretion from the pancreatic beta-cell, and have independently been implicated in the control of food intake and lipid metabolism. Whilst the enteroendocrine cells producing GIP and GLP-1 are therefore attractive targets for the treatment of diabetes and obesity, our understanding of their physiology is fairly limited. The mechanisms employed to sense the arrival of carbohydrate, fat and protein in the gut lumen have been investigated using organ perfusion techniques, primary epithelial cultures and cell line models. The recent development of mice with fluorescently labeled GIP or GLP-1-expressing cells is now enabling the use of single cell techniques to investigate stimulus-secretion coupling mechanisms. This review will focus on the current knowledge of the molecular machinery underlying nutrient sensing within K- and L-cells.
Transcranial magnetic stimulation during PET: reaching and verifying the target site. (1998)

Transcranial magnetic stimulation (TMS) during positron emission tomography (PET) is a novel technique for in vivo measurements of connectivity and excitability of the human cerebral cortex. Here we describe tools that allow investigators to position the stimulating coil over a target region and to verify the actual position of the coil after the study. The former is achieved by coregistering the head of the subject with an MR image of his/her brain using frameless stereotaxy. The latter is accomplished by identifying the coil on a transmission scan and coregistering it, e.g., with a model of the electrical field induced in the brain.
Electrohydrodynamic pumping and flow measurement (1991)

A micromachined electrohydrodynamic (EHD) injection pump with improved characteristics and a novel method for flow measurement with the same structure are presented. Based on the structure of the EHD injection pump, an improved design with grid distances in the range between 10 mu m and 60 mu m was achieved, yielding a reduction in the required driving voltage. Grid areas of 2.5*2.5 mm/sup 2/ and 1*1 mm/sup 2/ were accomplished. The outer dimensions of the smallest pumps are 3*3*1.0 mm/sup 3/. One of the grids is etched back from the frontside and mounted upside down on the lower grid in order to reduce the grid distance. The two grids are bounded together by anodic bonding. The pump is mounted in a ceramic housing with two fluid ports. Based on this structure, a novel method for the measurement of fluid flow and velocity was developed. This technique is well suited for small flow rates below 100 mL/min down to some mu L/min. Volumetric flow rates down to 8 mu L/min were measured with a 2.5*2.5 mm/sup 2/ grid area.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evidence for Two Subtypes of Ebola Virus Based on Oligonucleotide Mapping of RNA (1983)

Ebola viruses isolated during outbreaks of acute hemorrhagic fever in Africa from 1976 to 1979 were examined by T1 oligonucleotide mapping of virion RNA. Two Ebola virus subtypes distinguishable by their oligonucleotide patterns were involved in the outbreaks of the disease during this three-year period. The first type was isolated in Zaire in 1976 and again in 1977; the second type caused outbreaks in Sudan in 1976 and again in 1979. Oligonucleotide patterns of the two groups of Ebola viruses (Zaire and Sudan) were remarkably similar within the group but differed between groups by approximately 60 oligonucleotides. We can conclude from this study (1) that the outbreaks of hemorrhagic fever which occurred concurrently in 1976 in Zaire and Sudan were caused by viruses that are genetically distinct; (2) that compared with other RNA viruses there was an unusually high genetic stability among viruses within Zaire and Sudan over two- and three-year periods, respectively; and (3) that the two genetic subtypes probably evolved from a common ancestor since they share common oligonucleotides.
Structurally Diverse Dendritic Libraries:  A Highly Efficient Functionalization Approach Using Click Chemistry (2005)

The high fidelity and efficiency of Click chemistry are exploited in the synthesis of a library of chain end functionalized dendritic macromolecules. In this example, the selectivity of the Cu-catalyzed [3 + 2π] cycloaddition reaction of azides with terminal acetylenes, coupled with mild reaction conditions, permits unprecedented functional group tolerance during the derivatization of dendrimeric and hyperbranched scaffolds. The resulting dendritic libraries are structurally diverse, encompassing a variety of backbones/surface functional groups, and are prepared in almost quantitative yields under very mild conditions. The robust and simple nature of this procedure, combined with its applicability to many aspects of polymer synthesis and materials chemistry, demonstrates an evolving synergy between advanced organic chemistry and functional materials.
Insulin-like Growth Factor (IGF)-binding Protein-3 (IGFBP-3) Functions as an IGF-reversible Inhibitor of IGFBP-4 Proteolysis (1995)

Previous studies have shown that insulin-like growth factor (IGF)-binding protein-4 (IGFBP-4) is degraded only in the presence of exogenous IGFs; however, we found that cation-dependent proteinase activity present in conditioned medium of MC3T3-E1 osteoblasts degrades 125I-recombinant human (rh)IGFBP-4 in the absence of IGFs. Addition of IGF-I, IGF-II, or insulin to conditioned medium had little affect on 125I-rhIGFBP-4 proteolysis, while extraction of IGFs resulted in only a approximately 10% reduction in proteinase activity. Since factors other than IGFs appeared to be involved in regulating IGFBP-4 proteolysis, we hypothesized that IGFBP-3, an IGFBP produced by many cell lines, but not MC3T3-E1 cells, might function as an inhibitor of IGFBP-4 proteolysis. Addition of rhIGFBP-3 to conditioned media inhibited 125I-rhIGFBP-4 proteolysis by 90%, while IGF-I and IGF-II reversed the inhibitory effects of rhIGFBP-3 in a dose-dependent manner. 125I-rhIGFBP-4 proteolysis was not inhibited by N-terminal rhIGFBP-3 fragments that bind IGFs, but was inhibited by two synthetic peptides corresponding to sequences contained in the mid-region or C-terminal region of IGFBP-3. Both inhibitory peptides contain highly basic, putative heparin-binding domains and heparin partially reversed the inhibitory effects of rhIGFBP-3 on 125I-rhIGFBP-4 proteolysis. These data demonstrate that rhIGFBP-3 inhibits IGFBP-4-degrading proteinase activity and binding of IGFs or glycosaminoglycans to IGFBP-3 may induce conformational changes in the binding protein, causing disinhibition of the proteinase.
Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family (2014)

WRKY proteins comprise a large family of transcription factors that play important roles in plant defence regulatory networks, including responses to various biotic and abiotic stresses. To date, no large-scale study of WRKY genes has been undertaken in grape (Vitis vinifera L.). In this study, a total of 59 putative grape WRKY genes (VvWRKY) were identified and renamed on the basis of their respective chromosome distribution. A multiple sequence alignment analysis using all predicted grape WRKY genes coding sequences, together with those from Arabidopsis thaliana and tomato (Solanum lycopersicum), indicated that the 59 VvWRKY genes can be classified into three main groups (I-III). An evaluation of the duplication events suggested that several WRKY genes arose before the divergence of the grape and Arabidopsis lineages. Moreover, expression profiles derived from semiquantitative PCR and real-time quantitative PCR analyses showed distinct expression patterns in various tissues and in response to different treatments. Four VvWRKY genes showed a significantly higher expression in roots or leaves, 55 responded to varying degrees to at least one abiotic stress treatment, and the expression of 38 were altered following powdery mildew (Erysiphe necator) infection. Most VvWRKY genes were downregulated in response to abscisic acid or salicylic acid treatments, while the expression of a subset was upregulated by methyl jasmonate or ethylene treatments.
Draft genome sequence of Streptomyces coelicoflavus ZG0656 reveals the putative biosynthetic gene cluster of acarviostatin family α-amylase inhibitors (2012)

To our knowledge, S. coelicoflavus ZG0656 is the first strain in this species for which a genome sequence has been reported. The analysis of sct-cluster provided important insights into the biosynthesis of acarviostatins. This work will be a platform for producing novel variants and yield improvement.