gebhart/patrepeval huggingface dataset:
Distributed application development for three-tier architectures: Microsoft on Windows DNA (1998)

The organizational boundaries that have traditionally constrained applications are giving way to the opportunities inherent in electronic commerce and networked operations. Today, the geography of an application can extend far beyond an organization's boundaries, literally into consumers' homes. It is possible to think of an Internet application needing to handle literally millions of users. The argument for responding to these changes with three-tiered component computing is deceptively simple: partitioning applications cleanly into presentation, application logic and data components enhances scalability, reusability, security and manageability. Yet, even with new Web front ends, most companies have not taken full advantage of multi-tiered architectures. The Windows DNA (Distributed interNet Applications) architecture creates a seamless environment for developing multi-tier distributed computing applications. Windows DNA does this by unifying PC, client-server and Web-based application development around a common, component-based application architecture. Large and small organizations alike can improve their effectiveness by creating a new class of business solutions. Unless such an architecture is ubiquitous and accessible to virtually any organization, a broad shift to three-tier Web-enabled computing cannot occur.
Construction of a normalized cDNA library by introduction of a semi-solid mRNA-cDNA hybridization system (1994)

We report a novel procedure to construct a normalized (equalized) cDNA library. By introduction of the highly efficient self-hybridization system between a whole mRNA population and their corresponding cDNA immobilized on latex beads, which involves relatively simple manipulations, we were able to generate an mRNA population in which the copy number of abundant species was reduced while that of rare species was enriched. In a typical experiment, after several cycles of self-hybridization on the beads, the ratio of the most to the least abundant marker mRNA species dropped by a factor of 300 (from 10,000 to 30) while the complexity and length of mRNAs in the population remained unchanged. The procedure should provide a potent tool for the expression cloning of cDNA and also facilitate the construction of whole cDNA catalogs from specific tissues (or cell types) from higher organisms.
An 80 Kb P1 clone from chromosome 3p21.3 suppresses tumor growth in vivo. (1996)

High frequencies of allelic loss on the short arm of chromosome 3 in small cell lung cancer (SCLC) and a number of other tumors suggest the existence of a tumor suppressor gene(s) within the deleted regions. Two small cell lung cancer lines, NCI H740 and GLC20, have been described which have homozygous deletions in the region 3p21.3. The deleted region overlaps with a 2 Mb fragment of human DNA present in the interspecies hybrid HA(3)BB9F, that suppresses tumor formation by mouse A9 fibrosarcoma cells. Human sequences from this cell hybrid were isolated using inter Alu PCR. From this starting point, a P1 contig was developed for the region of 450 Kb that is common to the homozygous deletions seen in the SCLC lines NCI H740 and GLC20 and is also present in HA(3)BB9F, the suppressed A9 hybrid. Individual P1 clones were assayed for their ability to suppress the tumorigenicity of the mouse fibrosarcoma cell line A9 as assayed by injection of transfected A9 cells into athymic nude mice. The introduction of one of the P1 clones into A9 cells resulted in suppression of tumor growth whereas two other P1 clones from the contig failed to suppress tumor formation in athymic nude mice. These data functionally delimit a tumor suppressor locus to a region of 80 kb within a P1 clone at 3p21.3.
Chemical and stochastic modeling of lignin hydrodeoxygenation (1987)

An a priori Monte Carlo simulation of the product spectrum resulting from the thermal and catalytic depolymerization of lignin has been developed. The simulation combines model compound reaction pathways and kinetics, deactivation parameters, and stochastic models of polymer diffusion into a Markov-chain based simulation of the reaction of lignin polymers. Predicted product class ratios of single-ring phenolics were in reasonable agreement with experimental data pertaining to lignin liquefaction, especially as regards neat pyrolysis. The advantage of catalytic liquefaction was suggested by the increase in single-ring product yields, especially those of phenols and hydrocarbons, relative to pyrolysis.
Multicast in SMDS over an ATM network (2003)

It is shown that an asynchronous transfer mode (ATM) network architecture equipped with connectionless servers at the ATM switches is suitable for switched multimegabit data service (SMDS) support. A multicast tree computation scheme based on the underlying routing procedure is proposed. Two different address handling methods-encapsulation and nonencapsulation-are considered, and their effectiveness in providing multicast service is compared.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Complement 4 Locus II Gene Deletion and DQA1*0301 Gene: Genetic Risk Factors for IgA Nephropathy and Henoch-Schönlein Nephritis (1996)

There have been several reports suggesting that the deficiency of complement 4 (C4) and/or deletion of C4 genes are the genetic risk factors in patients with IgA nephropathy (IgAN) and Henoch-Schönlein nephritis (HSN). In the current study, we tried to clarify the genetic structure of deleted C4 genes as well as the isotype deficiency of the patients. Also, we investigated the DQB and DRB genes which are located near the C4 genes to identify a possible linkage and to find the associated allele. Our results showed that locus II deletion of C4, not the C4B sequence loss, is a risk factor for these diseases and the deleted gene can be either C4A or C4B. There was no specific isotype deficiency or specific allotype which was significantly increased or decreased in the patients. But, there was an increased frequency of DQA1*0301 gene in the patient group (corrected p = 0.04), which suggests that DQA1*0301 as well as C4 gene deletion could be genetic risk factors for these diseases.
Metal-backed acetabular cups in total hip arthroplasty. (1990)

Metal backing for the acetabular component of a total hip replacement, initially designed to allow replacement of the polyethylene liner, has since been universally accepted as a means of decreasing peak stresses at the interfaces of bone and cement. We studied the results of 238 total hip replacements that had been performed between 1980 and 1983 and that differed only in that 138 of the acetabular components had a metal backing and 100 were made of polyethylene only. Kaplan-Meier survival analysis, with three different modes of failure (radiolucency, loosening, and revision), showed a significant increase in the rate of failure of the metal-backed acetabular cup compared with the all-polyethylene cup: radiolucency, 39 compared with 23 per cent (p less than 0.0001); loosening, 4 compared with 2 per cent (p less than 0.0001); and revision, 6 compared with 2 per cent (p less than 0.0034). It was concluded that metal backing cannot be recommended for a cemented acetabular component of a total hip-replacement system.
Peripheral Blood Platelets Express VEGF-C and VEGF which Are Released during Platelet Activation (1998)

VEGF-C is a recently characterised endothelial growth factor structurally related to vascular endothelial growth factor (VEGF). We studied the expression of VEGF-C and VEGF in the cells of peripheral blood and in the umbilical cord blood CD 34+ cells, representing haematopoietic progenitor cells. Expression of VEGF-C was detected in the CD34+ cells. In peripheral blood VEGF-C mRNA was restricted to platelets and T-cells. In contrast to the expression pattern of VEGF-C, VEGF mRNA was detected in all peripheral blood cell fractions studied, and also in CD34+ cells. VEGF-C mRNA was also detected in fresh bone marrow samples of acute leukaemia patients, but the expression did not show lineage specificity. VEGF-C and VEGF polypeptides were present in platelets and they were released from activated platelets together with the release of beta-thromboglobulin, suggesting that VEGF-C and VEGF reside in the alpha-granules of platelets. VEGF-C and VEGF, released from activated platelets, may have a role in angiogenesis during wound healing, and possibly also in other pathological conditions, such as atherosclerosis, tumour growth, and metastasis formation.
Agonistic and antagonistic activities of bacterially derived Rhodobacter sphaeroides lipid A: comparison with activities of synthetic material of the proposed structure and analogs (1995)

Lipid A from the photosynthetic bacterium Rhodobacter sphaeroides (RSLA) has been previously shown to antagonize many of the effects of endotoxins from more pathogenic gram-negative bacteria. We have reported on the synthesis of the proposed structure of RSLA and determined that bacterially derived RSLA is not identical to its proposed structure (W.J. Christ, P. D. McGuinness, O. Asano, Y. Wang, M. A. Mullarkey, M. Perez, L. D. Hawkins, T. A. Blythe, G. R. Dubuc, and A. L. Robidoux, J. Am. Chem. Soc. 116:3637-3638, 1994). Here we report results of analyzing the antagonistic and agonistic activities of bacterially derived RSLA in comparison with the activities of chemically synthesized material of the proposed structure of RSLA and analogs. Results indicated that all compounds were approximately equally potent at inhibiting endotoxin-induced release of tumor necrosis factor alpha from human monocytes and human whole blood as well as endotoxin-induced generation of nitric oxide in murine macrophages. In addition, all compounds were of equivalent potencies at inhibiting the binding of 125I-labelled lipopolysaccharide derivatized with 2-(p-azido-salicylamido) ethyl-1-3'-dithiopropionate to murine macrophages. Higher concentrations of bacterially derived RSLA (10 to 100 microM) were agonistic in human and murine assays. In gamma interferon-treated murine macrophages, agonism was exhibited at concentrations as low as 100 nM. In contrast, all synthetic materials were either dramatically less agonistic or devoid of agonistic activity when tested at concentrations as high as 100 microM. It is possible either that bacterially derived RSLA contains a small amount of a highly agonistic impurity or that the agonistic activity of RSLA is intrinsic to its molecular structure. In either case, these biological results support our previous report concluding that biologically derived RSLA is not identical to synthetic material of its proposed structure.
Focal Adhesion Kinase Facilitates Platelet-derived Growth Factor-BB-stimulated ERK2 Activation Required for Chemotaxis Migration of Vascular Smooth Muscle Cells (2000)

The focal adhesion (FAK) non-receptor protein-tyrosine kinase (PTK) links both extracellular matrix/integrin and growth factor stimulation to intracellular signals promoting cell migration. Here we show that both transient and stable overexpression of the FAK C-terminal domain termed FRNK (FAK-related non-kinase) inhibits serum and platelet-derived growth factor (PDGF)-BB-induced vascular smooth muscle cell (SMC) migration in wound healing and in vitro Boyden Chamber chemotaxis assays, respectively. Expression of FRNK, but not a point mutant of FRNK (FRNK L1034S), disrupted the formation of a complex containing both FAK and the activated PDGF-beta receptor and resulted in reduced tyrosine phosphorylation of endogenous FAK at the Tyr-397 binding site for Src family PTKs. As demonstrated using FAK-deficient and FAK-reconstituted fibroblasts, FAK positively contributed to PDGF-BB-stimulated ERK2/MAP kinase activity, and in SMCs, ERK2/MAP kinase activity was required for PDGF-BB-stimulated chemotaxis. Stable expression of FRNK but not FRNK L1034S expression in SMCs lowered the extent and duration of stimulated ERK2/MAP kinase activation at low but not at high PDGF-BB concentrations. Importantly, stable expression of FRNK in SMCs did not affect SMC morphology or proliferation in culture. Because the increased migration of vascular SMCs in response to extracellular matrix proteins and growth factors contributes to neointima formation, our results show that FAK inhibition by FRNK expression may provide a novel approach to regulate abnormal vascular SMC migration in vivo.
Mouse Models for miRNA Expression: The ROSA26 Locus (2010)

In 1991, Soriano and coworkers isolated the ROSA26 locus in a gene-trap mutagenesis screening performed in mouse embryonic stem (ES) cells. The ubiquitous expression of ROSA26 in embryonic and adult tissues, together with the high frequency of gene-targeting events observed at this locus in murine ES cells has led to the establishment in the past 10 years of over 130 knock-in lines expressing successfully from the ROSA26 locus a variety of transgenes including reporters, site-specific recombinases and, recently, noncoding RNAs. Different strategies can be employed to drive transgene expression from the ROSA26 locus. This chapter provides an overview of the current methodologies used to generate ROSA26 knock-in lines and describes different approaches that exploit the ROSA26 gene to control expression of transgenes, including miRNAs, in a temporal, cell-type, and stage-specific fashion.
Long-term inhibition of dipeptidyl peptidase IV improves glucose tolerance and preserves islet function in mice (2002)

Long-term DPPIV inhibition improves glucose tolerance in both normal and glucose-intolerant mice through improved islet function as judged by increased GLUT-2 expression, increased insulin secretion and protection from increased islet size in insulin resistance.
A regulatory element in the promoter of the human granulocyte-macrophage colony-stimulating factor gene that has related sequences in other T-cell-expressed cytokine genes. (1995)

Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a cytokine with a broad spectrum of cell-differentiating and colony-stimulating activities. It is expressed by several undifferentiated (bone marrow stromal cells, fibroblasts) and fully differentiated (T cells, macrophages, and endothelial cells) cells. Its expression in T cells is activation dependent. We have found a regulatory element in the promoter of the GM-CSF gene which contains two symmetrically nested inverted repeats (-192 CTTGGAAAGGTTCATTAATGAAAACCCCCAAG -161). In transfection assays with the human GM-CSF promoter, this element has a strong positive effect on the expression of a reporter gene by the human T-cell line Jurkat J6 upon stimulation with phorbol dibutyrate and ionomycin or anti-CD3 antibody. This element also acts as an enhancer when inserted into a minimal promoter vector. In DNA band-retardation assays this sequence produces six specific bands that involve one or the other of the inverted repeats. We have also shown that a DNA-protein complex can be formed involving both repeats and probably more than one protein. The external inverted repeat contains a core sequence CTTGG...CCAAG, which is also present in the promoters of several other T-cell-expressed human cytokines (interleukins 4, 5, and 13). The corresponding elements in GM-CSF and interleukin 5 promoters compete for the same proteins in band-retardation assays. The palindromic elements in these genes are larger than the core sequence, suggesting that some of the interacting proteins may be different for different genes. Considering the strong positive regulatory effect and their presence in several T-cell-expressed cytokine genes, these elements may be involved in the coordinated expression of these cytokines in T-helper cells.
Localization of Susceptibility to Familial Idiopathic Scoliosis (2000)

These data indicate a limited number of genetic loci predisposing to idiopathic scoliosis.
Enhancement of antifungal chemotherapy by interferon-gamma in experimental systemic cryptococcosis (2000)

The possible enhancement, using immunotherapy with interferon-gamma (IFN-gamma), combined with conventional antifungal therapy, was studied in a murine model of systemic cryptococcosis. Four weeks after intravenous challenge, infection was quantified in brains and livers of survivors. Groups received IFN-gamma every other day beginning 7 days before (prophylaxis), or after infection (14 doses), or amphotericin B post-infection, or combinations of these regimens. IFN-gamma alone was modestly effective, but impressively and significantly potentiated amphotericin in reducing infection in the most important site of infection, the brain. The efficacy was seen after lethal and non-lethal challenges, and when IFN-gamma was given by the intravenous or subcutaneous routes. In non-lethal infection, only the combination amphotericin-IFN-gamma resulted in sterilization of the central nervous system. Potentiation of fluconazole was less impressive. Adding prophylactic IFN-gamma doses to IFN-gamma therapy did not consistently enhance the therapeutic effect. These results suggest IFN-gamma may have a role in potentiating conventional antifungal therapy of cryptococcosis.
Mutations of the microsomal triglyceride-transfer-protein gene in abetalipoproteinemia. (1995)

Elevated plasma levels of apolipoprotein B (apoB)-containing lipoproteins constitute a major risk factor for the development of coronary heart disease. In the rare recessively inherited disorder abetalipoproteinemia (ABL) the production of apoB-containing lipoproteins is abolished, despite no abnormality of the apoB gene. In the current study we have characterized the gene encoding a microsomal triglyceride-transfer protein (MTP), localized to chromosome 4q22-24, and have identified a mutation of the MTP gene in both alleles of all individuals in a cohort of eight patients with classical ABL. Each mutant allele is predicted to encode a truncated form of MTP with a variable number of aberrant amino acids at its C-terminal end. Expression of genetically engineered forms of MTP in Cos-1 cells indicates that the C-terminal portion of MTP is necessary for triglyceride-transfer activity. Deletion of 20 amino acids from the carboxyl terminus of the 894-amino-acid protein and a missense mutation of cysteine 878 to serine both abolished activity. These results establish that defects of the MTP gene are the predominant, if not sole, cause of hereditary ABL and that an intact carboxyl terminus is necessary for activity.
Crystal structure of human parathyroid hormone 1-34 at 0.9-A resolution. (2000)

The N-terminal fragment 1-34 of parathyroid hormone (PTH), administered intermittently, results in increased bone formation in patients with osteoporosis. PTH and a related molecule, parathyroid hormone-related peptide (PTHrP), act on cells via a common PTH/PTHrP receptor. To define more precisely the ligand-receptor interactions, we have crystallized human PTH (hPTH)-(1-34) and determined the structure to 0.9-A resolution. hPTH-(1-34) crystallizes as a slightly bent, long helical dimer. Analysis reveals that the extended helical conformation of hPTH-(1-34) is the likely bioactive conformation. We have developed molecular models for the interaction of hPTH-(1-34) and hPTHrP-(1-34) with the PTH/PTHrP receptor. A receptor binding pocket for the N terminus of hPTH-(1-34) and a hydrophobic interface with the receptor for the C terminus of hPTH-(1-34) are proposed.
Identification of fibronectin neoepitopes present in human osteoarthritic cartilage (2006)

Human OA cartilage contains fibronectin fragments with catabolic activity and a major cleavage site within fibronectin. This study is the first to characterize fibronectin neoepitopes in OA cartilage, suggesting that they may represent a novel biomarker of arthritis.
Rheology of Gastric Mucin Exhibits a pH-Dependent Sol−Gel Transition (2007)

Gastric mucin, a high molecular weight glycoprotein, is responsible for providing the gel-forming properties and protective function of the gastric mucus layer. Bulk rheology measurements in the linear viscoelastic regime show that gastric mucin undergoes a pH-dependent sol-gel transition from a viscoelastic solution at neutral pH to a soft viscoelastic gel in acidic conditions, with the transition occurring near pH 4. In addition to pH-dependent gelation behavior in this system, further rheological studies under nonlinear deformations reveal shear thinning and an apparent yield stress in this material which are also highly influenced by pH.
The splice variants of vascular endothelial growth factor (VEGF) and their receptors (2001)

Vascular endothelial growth factor (VEGF) is a secreted mitogen highly specific for cultured endothelial cells. In vivo VEGF induces microvascular permeability and plays a central role in both angiogenesis and vasculogenesis. VEGF is a promising target for therapeutic intervention in certain pathological conditions that are angiogenesis dependent, most notably the neovascularisation of growing tumours. Through alternative mRNA splicing, a single gene gives rise to several distinct isoforms of VEGF, which differ in their expression patterns as well as their biochemical and biological properties. Two VEGF receptor tyrosine kinases (VEGFRs) have been identified, VEGFR-1 (Flt-1) and VEGFR-2 (KDR/Flk-1). VEGFR-2 seems to mediate almost all observed endothelial cell responses to VEGF, whereas roles for VEGFR-1 are more elusive. VEGFR-1 might act predominantly as a ligand-binding molecule, sequestering VEGF from VEGFR-2 signalling. Several isoform-specific VEGF receptors exist that modulate VEGF activity. Neuropilin-1 acts as a co-receptor for VEGF(165), enhancing its binding to VEGFR-2 and its bioactivity. Heparan sulphate proteoglycans (HSPGs), as well as binding certain VEGF isoforms, interact with both VEGFR-1 and VEGFR-2. HSPGs have a wide variety of functions, such as the ability to partially restore lost function to damaged VEGF(165) and thereby prolonging its biological activity.
Tolerances in microlens fabrication by multilevel etching and mass-transport smoothing (1994)

A method is developed for the quantitative assessment of microlens deficiencies caused by inaccuracies in the multistep mesa fabrication or by incomplete mass-transport smoothing. Analytical expressions are obtained and tolerable imperfections are deduced for the practical effort-saving fabrication of highperformance micro-optical elements.
Delineation of the human hematolymphoid system: potential applications of defined cell populations in cellular therapy (1997)

Hematopoietic stem cells (HSC) have the capacity to reconstitute all the blood cells in the body. HSC are rare, representing on average 0.05% of the mononuclear cells present in healthy human bone marrow. Due to their capacity for self-renewal and their pluripotent, long-term reconstituting potential, HSC are considered ideal for transplantation to reconstitute the hematopoietic system after treatment for various hematologic disorders or as a target for the delivery of therapeutic genes. Human HSC also have potential applications in restoring the immune system in autoimmune diseases and in the induction of tolerance for allogeneic solid organ transplantation. With the increased interest in human HSC for clinical applications, technology for the isolation of candidate HSC and knowledge of human hematopoiesis have been growing rapidly. In this article, we discuss the functional characterization of a human CD34+Thy-1+ HSC population which is essentially free of residual disease, our efforts to generate alternate monoclonal antibodies for the isolation of clinically useful stem or progenitor cell populations, and the identification of a novel lymphoid progenitor as part of an exploration towards defining progenitors with potential application as adjuncts to HSC-based cellular therapy.