gebhart/patrepeval huggingface dataset:
Converting Path Structures Into Block Structures Using Eigenvalue Decompositions Of Self-Similarity Matrices. (2013)

[TODO] Add abstract here.
High molecular weight kininogen binds to laminin – characterization and kinetic analysis (2009)

High molecular weight kininogen (HK) is an abundant plasma protein that plays a central role for the function of the kallikrein/kinin/kininogen system. Thus, cleavage of HK by kallikrein liberates bradykinin, which stimulates vascular repair and a two-chain protein, activated HK (HKa), which induces apoptosis in proliferating endothelial cells. The localization of these events remains obscure, although the basement membrane may be of importance. Analyzing the interaction between HK and HKa and selected basement membrane proteins, we observed that they bound to the major noncollageneous proteins laminin, but not to vitronectin or fibronectin coated on microtiter plates. The binding to laminin was Zn2+ independent. However, at low but not at high concentrations of albumin, Zn2+ increased the affinity for the binding by abolishing an inhibitory effect of Ca2+. Recombinant human kininostatin encompassing the amino acid sequence, Arg439-Ser532 but not the endothelial cell binding peptide sequence (His479-His498; HKH20) within kininostatin inhibited the binding of HKa to laminin. This established that the amino acid sequence Arg439-Lys478 in domain 5 of HK is of importance for its binding to laminin. Extensive proteolytic cleavage of HK and HKa with kallikrein abolished the binding to laminin, releasing a 12 kDa anti-kininostatin reacting peptide. On the basis of these results, we propose that the binding of HK to laminin is a primary event, which secures proper localization of the cleavage products for subsequent interaction with the endothelium to promote inflammatory and pro- and anti-angiogenic activities.
Long-term supplementation with n-3 fatty acids, II: effect on neutrophil and monocyte chemotaxis (1992)

The effect of a daily supplement with 4 g of n-3 polyunsaturated fatty acids (PUFA) for 9 months to 24 healthy volunteers on neutrophil and monocyte chemotaxis was studied using the under-agarose technique. Autologous serum and n-formyl-methionyl-leucyl-phenylalanine were used as chemoattractants. The effect after 9 months of supplementation with n-3 PUFA was also compared to results after short-term supplementation with n-3 PUFA for 6 weeks. Monocyte chemotaxis was reduced after 9 months of supplementation with n-3 PUFA to the same extent as after 6 weeks supplement. Neutrophil-directed migration towards chemoattractants was reduced after 9 months on fish oil, and this decrease was significantly greater than the decrease obtained after 6 weeks of supplementation. The spontaneous migration of neutrophils was significantly attenuated after 9 months compared to baseline and to 6 weeks. These findings lend support to a role for n-3 PUFA in the management of chronic inflammatory and atherosclerotic vascular diseases.
Gastrin receptors on isolated canine parietal cells. (1984)

The receptors in the fundic mucosa that mediate gastrin stimulation of acid secretion have been studied. Synthetic human gastrin-17-I (G17) with a leucine substitution in the 15th position ( [Leu15]-G17) was iodinated by chloramine T; high saturable binding was found to enzyme-dispersed canine fundic mucosal cells. 127I-[Leu15]-G17, but not 127I-G17, retained binding potency and biological activity comparable with uniodinated G17. Fundic mucosal cells were separated by size by using an elutriator rotor, and specific 125I-[Leu-15]-G17 binding in the larger cell fractions was highly correlated with the distribution of parietal cells. There was, however, specific gastrin binding in the small cell fractions, not accounted for by parietal cells. Using sequential elutriation and stepwise density gradients, highly enriched parietal and chief cell fractions were prepared; 125I-[Leu15]-G17 binding correlated positively with the parietal cell (r = 0.98) and negatively with chief cell content (r = -0.96). In fractions enriched to 45-65% parietal cells, specific 125I-[Leu15]-G17 binding was rapid, reaching a steady state at 37 degrees C within 30 min. Dissociation was also rapid, with the rate similar after 100-fold dilution or dilution plus excess pentagastrin. At a tracer concentration from 10 to 30 pM, saturable binding was 7.8 +/- 0.8% per 10(6) cells (mean +/- SE) and binding in the presence of excess pentagastrin accounted for 11% of total binding. G17 and carboxyl terminal octapeptide of cholecystokinin (26-33) were equipotent in displacing tracer binding and in stimulating parietal cell function ( [14C]aminopyrine accumulation), whereas the tetrapeptide of gastrin (14-17) had a much lower potency. Proglumide inhibited gastrin binding and selectively inhibited gastrin stimulation of parietal cell function. Canine parietal cells have specific receptors for gastrin that mediate stimulation of parietal cell function. Gastrin receptors were undetectable on chief cells, and yet present on another smaller mucosal cell(s).
The expression and role of BAMBI in pancreatic cancer (2015)

Objective
To investigate the expression of BAMBI in pancreatic carcinoma tissue and its clinical value.


Methods
Expression of BAMBI was detected by immunohistochemistry in 69 cases of pancreatic cancer and 15 normal pancreatic samples. The survival and its association with clinicopathologic parameters were analyzed.


Results
The expression of BAMBI in the cancer tissue was much higher than that in the normal tissues (56.5% vs 16.7%, P<0.01). The expression of BAMBI was not associated with age, sex and tumor size, differentiation, but expression of BAMBI in patient with lymph node metastasis was higher than that in patient without lymph node metastasis (67.4% vs 38.5%, P=0.019), the expression of BAMBI in TNM stage Ⅲ was higher than that in stage Ⅰ+ Ⅱ (75.0% vs 31.0%, P=0.001). The median survival of BAMBI-positive group (6 months) was lower than that of BAMBI-negative group (10 months).


Conclusions
BAMBI is over-expressed in pancreatic carcinoma, and its expression is associated with lymph node metastasis, TNM staging, differentiation and prognosis.


Key words: 
Pancreatic neoplasms; BMP and activin membrane-bound inhibitor; Immunohistochemistry
Immunotherapy with allotumour mRNA-transfected dendritic cells in androgen-resistant prostate cancer patients (2005)

Here, we present results from a clinical trial employing a new vaccination method using dendritic cells (DCs) transfected with mRNA from allogeneic prostate cancer cell lines (DU145, LNCaP and PC-3). In all, 20 patients were enrolled and 19 have completed vaccination. Each patient received at least four weekly injections with 2 x 10(7) transfected DCs either intranodally or intradermally. Safety and feasibility of vaccination were determined. Immune responses were measured as delayed-type hypersensitivity and by in vitro immunoassays including ELISPOT and T-cell proliferation in pre- and postvaccination peripheral blood samples. Serum prostate-specific antigen (PSA) levels and bone scans were monitored. No toxicity or serious adverse events related to vaccinations were observed. A total of 12 patients developed a specific immune response to tumour mRNA-transfected DCs. In total, 13 patients showed a decrease in log slope PSA. This effect was strengthened by booster vaccinations. Clinical outcome was significantly related to immune responses (n = 19, P = 0.002, r = 0.68). Vaccination with mRNA-transfected DCs is safe and results in cellular immune responses specific for antigens encoded by mRNA derived from the prostate cancer cell lines. The observation that in some patients vaccination affected the PSA level suggests that this approach may become useful as a treatment modality for prostate cancer patients.
Non‐Aqueous Synthesis of High‐Purity Metal Oxide Nanopowders Using an Ether Elimination Process (2004)

A soft-chemistry route to (impurity free) Ta2O5 and HfO2 nanopowders (see Figure) based upon a synthesis protocol that involves the reaction of metal alkoxides with benzyl alcohol is presented. The formation of HfO2 proceeds via an unprecedented ether-elimination process and extends the available non-aqueous reaction methodologies in addition to the well-known ester and alkyl halide eliminations.
Randomized Phase II Trial of Chemoradiotherapy Followed by Either Dose-Dense or Metronomic Temozolomide for Newly Diagnosed Glioblastoma (2009)

Both dose-dense and metronomic temozolomide regimens were well tolerated with modest toxicity. The dose-dense regimen appears promising, with 1-year survival of 80%.
Diphtheria Toxin and Related Proteins (1973)

Abstract The kinetic data of entry of Fragment A from diphtheria toxin and Fragment A176 derived from the serologically related protein of reduced toxicity, cross-reacting material 176, across the living HeLa cell membrane have been studied by following the rate of inactivation of the HeLa cell protein-synthesizing system. Similar kinetic studies have been carried out on the competition between toxin and the two nontoxic, serologically related proteins, cross-reacting materials 197 and 228. It is suggested that there are entry sites on the HeLa cell membrane that specifically interact with the Fragment B part of the molecule. It is concluded that Fragment A from toxin and related mutant proteins is crossing the cell membrane continuously to reach a steady state level in which the rate of entry is balanced by the rate of degradation in the cytoplasm. A maximum intracellular level is reached when all of the entry sites become saturated. Saturation of sites is approached at toxin concentrations of 5 x 10-7 m or higher.
The Influence of GLP-1 on Glucose-Stimulated Insulin Secretion (2003)

The intestinally derived hormone glucagon-like peptide 1 (GLP-1) (7-36 amide) has potent effects on glucose-mediated insulin secretion, insulin gene expression, and beta-cell growth and differentiation. It is, therefore, considered a potential therapeutic agent for the treatment of type 2 diabetes. However, the dose-response relationship between GLP-1 and basal and glucose-stimulated prehepatic insulin secretion rate (ISR) is currently not known. Seven patients with type 2 diabetes and seven matched nondiabetic control subjects were studied. ISR was determined during a graded glucose infusion of 2, 4, 6, 8, and 12 mg x kg(-1) x min(-1) over 150 min on four occasions with infusion of saline or GLP-1 at 0.5, 1.0, and 2.0 pmol x kg(-1) x min(-1). GLP-1 enhanced ISR in a dose-dependent manner during the graded glucose infusion from 332 +/- 51 to 975 +/- 198 pmol/kg in the patients with type 2 diabetes and from 711 +/- 123 to 2,415 +/- 243 pmol/kg in the control subjects. The beta-cell responsiveness to glucose, expressed as the slope of the linear relation between ISR and the glucose concentration, increased in proportion to the GLP-1 dose to 6 times relative to saline at the highest GLP-1 dose in the patients and 11 times in the control subjects, but it was 3 to 5 times lower in the patients with type 2 diabetes compared with healthy subjects at the same GLP-1 dose. During infusion of GLP-1 at 0.5 pmol x kg(-1) x min(-1) in the patients, the slope of ISR versus glucose became indistinguishable from that of the control subjects without GLP-1. Our results show that GLP-1 increases insulin secretion in patients with type 2 diabetes and control subjects in a dose-dependent manner and that the beta-cell responsiveness to glucose may be increased to normal levels with a low dose of GLP-1 infusion. Nevertheless, the results also indicate that the dose-response relation between beta-cell responsiveness to glucose and GLP-1 is severely impaired in patients with type 2 diabetes.
Structure of complement receptor (CR) 2 and CR2-C3d complexes (2002)

Using X-ray crystallography, we have determined the structure of the first two short consensus repeats (SCRs) of human complement receptor (CR) 2 in complex with C3d. These studies revealed: (i) a primary site of interaction for C3d within SCR2 of CR2, (ii) a hydrophobic patch holding SCR1 to SCR2 in a rigid V-shape, (iii) a dimer formed by interactions between SCR1 of each molecule, (iv) several non-linear sequences on C3d that interact with CR2 and (v) mutations of C3d amino acids within the co-crystal interface that resulted in decreased binding. In addition, a polymorphism that results in decreased C3d binding and introduces a new glycosylation site predicted to disrupt the dimer interface was found in the New Zealand White autoimmune mouse strain. Although the co-crystal complex results are in agreement with a subset of prior studies, our additional findings, which demonstrate an extended SCR1-SCR2 structure in solution and differences in the kinetics of ligand-receptor interactions with longer forms of CR2, have suggested a more complex receptor-ligand interaction. To characterize this interaction further, several approaches directed at the determination of solution phase interactions as well as the analysis of the three-dimensional structure of CR2 alone and key CR2 mutants will be necessary.
Feeder Protection and Monitoring System, Part II: Staged Fault Test Demonstration (1985)

This paper describes the demonstration of three Texas A&M University experimental Feeder Protection and Monitoring Systems during staged fault tests at Houston Lighting and Power and at Public Service Company of New Mexico. The purpose of the experimental devices is to demonstrate improvements in the protection and monitoring capabilities of distribution relays. The Feeder Protection and Monitoring System is a microcomputer-based device installed at a distribution substation which includes arcing fault detection and overcurrent relaying. The arcing fault detector identifies many ground faults which exhibit current too low to be picked up by overcurrent devices. The digital overcurrent relay provides several enhancements over electromechanical relays. The system also demonstrates some of the advantages of computer automation of distribution protective devices by providing remote monitoring, data retrieval and adjustment of settings. These features of the Feeder Protection and Monitoring System were demonstrated during the staged fault tests. The paper includes plotted data and logs of the system performance during the fault tests.
Measurement of the metabolic interconversion of deuterium‐labeled fatty acids by gas chromatography/mass spectrometry (1990)

An analytical method that was developed to analyze deuterium-labeled fatty acids in human blood has been extended to identify labeled fatty acids from C14 to C24 chain length which are formed by metabolic processes such as desaturation, elongation, or shortening of the labeled fatty acids fed. A new computer and a hardware adder have been utilized to assure reliable data acquisition. Relative standard deviations for the analysis of labeled fatty acids were measured at 0.02, 0.03, and 0.04 at the 5%, 1%, and 0.2% levels of the labeled fatty acid methyl esters, respectively. The method makes extensive use of standards and computer processing for accuracy and high productivity. Data from a chylomicron triacylglycerol fraction are included to demonstrate the sensitivity of detection of metabolites formed by desaturation and elongation.
Physical models for coupled electromechanical analysis of silicon nanoelectromechanical systems (2005)

Nanoelectromechanical systems (NEMS) can be designed and characterized by understanding the interaction and coupling between the mechanical, electrical, and the van der Waals energy domains. In this paper, we present physical models and their numerical simulation for coupled electrical and mechanical analysis of silicon NEMS. A nonlinear continuum elastic model is employed for mechanical analysis. The material properties required in the continuum model are extracted from molecular-dynamics simulations. We present three electrostatic models—namely, the classical conductor model, the semiclassical model, and the quantum-mechanical model, for electrostatic analysis of NEMS at various length scales. The electrostatic models also account for the corrections to the energy gap and the effective mass due to the strain in the silicon nanostructure. A continuum layer approach is introduced to compute the van der Waals forces. The coupling between the mechanical, electrical, and the van der Waals energy domains as well as their numerical implementation is described. Numerical results are presented for several silicon NEM switches to understand the static electromechanical pull-in behavior.
The Role of 1 N 6 -Ethenoadenosine Triphosphate and 1 N 6 -Ethenoadenosine Monophosphate in Firefly Luminescence (1973)

1,N(6)-Ethenoadenosine triphosphate (epsilon-ATP) has been found to be inactive as a substrate for firefly luciferase. However, chemically synthesized luciferyl-epsilonAMP is oxidized by luciferase and light is emitted. The color of the light is red in contrast to the normal yellow-green observed with luciferyladenylate. Although epsilonATP will not serve as a substrate in the activation reaction, the reversal of the activation, pyrophosphorolysis of dehydroluciferyladenylate, will occur with the ethenoadenosine analog.
Covalent cross-linking of duplex DNA using 4-thio-2'-deoxyuridine as a readily modifiable platform for introduction of reactive functionality into oligonucleotides (1997)

Full details of the template-directed covalent cross-linking of duplex oligodeoxynucleotides are presented. 4-Thio-2'-deoxyuridine was incorporated synthetically into a 17mer oligodeoxynucleotide, and the thiocarbonyl group of the modified base was alkylated with a variety of alpha-bromoacetyl-derivatized diamines. Covalent cross-linking was initiated by annealing the electrophilic probe oligomers with their complementary sequences, where a dG base was targeted at the position complementary to the modified 4-thio-2'-deoxyuridine. The sequence selectivity of cross-link formation as a function of tether topology and rigidity was examined, and the thermal stability of the modified duplexes was measured by UV melting experiments.
An Optimized RAD51 Inhibitor That Disrupts Homologous Recombination without Requiring Michael Acceptor Reactivity (2012)

Homologous recombination (HR) is an essential process in cells that provides repair of DNA double-strand breaks and lesions that block DNA replication. RAD51 is an evolutionarily conserved protein that is central to HR. Overexpression of RAD51 protein is common in cancer cells and represents a potential therapeutic target in oncology. We previously described a chemical inhibitor of RAD51, called RI-1 (referred to as compound 1 in this report). The chloromaleimide group of this compound is thought to act as a Michael acceptor and react with the thiol group on C319 of RAD51, using a conjugate addition-elimination mechanism. In order to reduce the likelihood of off-target effects and to improve compound stability in biological systems, we developed an analogue of compound 1 that lacks maleimide-based reactivity but retains RAD51 inhibitory activity. This compound, 1-(3,4-dichlorophenyl)-3-(4-methoxyphenyl)-4-morpholino-1H-pyrrole-2,5-dione, named RI-2 (referred to as compound 7a in this report), appears to bind reversibly to the same site on the RAD51 protein as does compound 1. Like compound 1, compound 7a specifically inhibits HR repair in human cells.
An influential principal point on camera parameters (2008)

This paper proposes a method of camera calibration and the influence of principal point on camera parameters. The camera parameters are represented in terms of a set of intermediate parameters. The intermediate parameters and lens distortion coefficients are iteratively computed. The image coordinates are rectified on each cycle of iteration. Once the iteration is terminated, the initial parameters are computed from the obtained intermediate parameters. Then, the camera parameters and distortion coefficients are iteratively computed from the obtained initial parameters and the image coordinates are rectified too. In the experimental results, the proposed method is tested by change principal point to observe the influential principal point on camera parameters and compared the results with the conventional method.
Minireview: Ghrelin and the Regulation of Energy Balance—A Hypothalamic Perspective (2001)

The recently discovered hormone, ghrelin, has been recognized as an important regulator of GH secretion and energy homeostasis. Orexigenic and adipogenic ghrelin is produced by the stomach, intestine, placenta, pituitary, and possibly in the hypothalamus. The concentration of circulating ghrelin, principally derived from the stomach, is influenced by acute and chronic changes in nutritional state. To date, most studies focused on the role of ghrelin in GH secretion or its function in complementing leptin action to prevent energy deficits. The potential significance of ghrelin in the etiology of obesity and cachexia as well as in the regulation of growth processes is the subject of ongoing discussions. A large quantity of information based on clinical trials and experimental studies with ghrelin and previously available synthetic ghrelin receptor agonists (GH secretagogues) must now be integrated with a rapidly increasing amount of data on the central regulation of metabolism and appetite. In this overview, we summarize recent findings and strategies on the integration of ghrelin into neuroendocrine networks that regulate energy homeostasis.
Effects of the human immunodeficiency virus type 1 Tat protein on the expression of inflammatory cytokines (1992)

Increased levels of inflammatory cytokines, including tumor necrosis factor (TNF), interleukin-1 (IL-1), and IL-6, have been detected in specimens from human immunodeficiency virus type 1 (HIV-1)-infected individuals. Here we demonstrate that HIV-1 activates the expression of TNF but not of IL-1 and IL-6 in acutely and chronically infected T cells. The increase in TNF gene expression is due to activation of the TNF promoter by the viral gene product Tat. Transactivation of TNF gene expression requires the product of the first exon of the tat gene and is cell type independent. T cells chronically infected with pol-defective HIV-1 provirus constitutively express both Tat and TNF at levels significantly higher (fivefold) than those seen in control cells, and treatment with phorbol myristate acetate greatly enhances Tat expression and TNF production. As TNF can increase the production of IL-1 and IL-6 and these inflammatory cytokines all enhance HIV-1 gene expression and affect the immune, vascular, and central nervous systems, the activation of TNF by Tat may be part of a complex pathway in which HIV-1 uses viral products and host factors to increase its own expression and infectivity and to induce disease.