gebhart/patrepeval huggingface dataset:
Shear-dependent morphology of von Willebrand factor bound to immobilized collagen (2002)

We have developed an immunogold von Willebrand factor (VWF) detection method that permits almost complete coverage of individual VWF molecules, and by this unequivocal localization and morphologic analysis of collagen-bound VWF by atomic force microscopy (AFM). Perfusion of gel filtration-purified VWF in parallel plate perfusion chambers over glass coverslips coated with calf skin collagen, followed by AFM imaging in air, enabled us to assess possible morphologic differences between VWF bound at low (0.07 N/m(2) = 0.7 dynes/cm(2)) and high (4.55 N/m(2) = 45.5 dynes/cm(2)) shear stresses. No significant differences in VWF morphology were found, the molecules were oriented almost randomly, and there were no clear signs of VWF "uncoiling" either at a high or at a low shear regime. After perfusing 1 microg/mL VWF for 5 minutes, surface coverage at high shear was almost twice the one seen at low shear, and some larger and more irregularly shaped VWF molecules could be seen at high shear. This difference disappeared, however, at 15 minutes of perfusion and was probably caused by diffusion kinetics. Moreover, the presence of 68 x 10(9)/L washed fixed platelets in the perfusate did not have any visible effect on VWF morphology at high versus low shear stress. These findings suggest that shear stress does not influence significantly the overall molecular morphology of VWF during its binding to collagen-coated surface and are consistent with a constitutively expressed affinity of collagen-bound VWF for glycoprotein Ib.
Overexpression of glut1 and glut3 in stage I nonsmall cell lung carcinoma is Associated with poor survival (1997)

In Stage I NSCLC, Glut3 overexpression likely occurs after Glut1 overexpression. The appearance of Glut1 positive clones is associated with aggressive biologic behavior, which is worsened by the emergence of Glut3 positive clones. Glut1 and Glut3 are significant of poor prognosis indicators in cases of NSCLC.
Selection-expression plasmid vectors for use in genetic transformation of higher plants (1985)

Plasmid vectors containing both a selectable marker for plant transformation (kanamycin resistance) and a second, directly adjacent, divergent promoter for the transcription of inserted DNA fragments have been constructed. These vectors make use of a small (479 bp) dual-promoter DNA fragment, originally isolated from the T-DNA of Agrobacterium tumefaciens, fused to the neomycin phosphotransferase gene of Tn5. Several unique restriction enzyme cleavage sites, as well as a polyadenylation signal sequence, have been introduced downstream of the open promoter, allowing simple insertional cloning of DNA fragments to be expressed in plants. To test the vectors, the coding region for the chloramphenicol acetyltransferase gene (CAT) from Tn9 was inserted, and the resulting plasmids introduced into tobacco cells. Transformed calli, selected only for Km resistance, contained, in every case tested, both NPTII and CAT activities.
Nitric Oxide Releases Calcitonin-Gene-Related Peptide from Rat Dura mater Encephali Promoting Increases in Meningeal Blood Flow (2002)

Nitric oxide (NO) and calcitonin-gene-related peptide (CGRP) are implicated in the pathophysiology of vascular headaches. We studied the interaction of these two vasodilatory mediators in an animal model and suggest that NO may increase meningeal blood flow not only by its direct vasodilatory action but also by stimulating CGRP release. First, CGRP release from the rat cranial dura mater was measured in vitro using an enzyme immunoassay. Hemisected skulls with adhering dura mater were filled with synthetic interstitial fluid and stimulated with the NO donor diethylamine-NONOate (10(-5)-10(-3) M) or with NO gas (1,000 ppm), which caused concentration-dependent increases in CGRP release up to 166.8%. Second, meningeal blood flow was recorded in vivo in the exposed dura mater using laser Doppler flowmetry. Topical application of the NO donors NONOate, S-nitroso-N-acetylpenicillamine and N-ethyl-2-(1-ethyl-2-hydroxy-2-nitrosohydrazino)-ethenamine (10(-5)-10(-3) M) caused concentration-dependent increases in blood flow. These increases were significantly reduced by local preliminary application of the CGRP receptor antagonist CGRP(8-37) (10(-4) M). We conclude that NO stimulates the release of CGRP from dural afferents. The blood-flow-increasing effect of NO seems to be partly mediated by CGRP. The interaction of NO and CGRP may be relevant for the development of vascular headaches.
Anisotropic velocity analysis for lithology discrimination (1989)

Abstract A new velocity analysis technique is presented for analyzing moveout of signals on multichannel surface seismic or VSP data. An approximate, skewed hyperbolic moveout formula is derived for horizontally layered, transversely isotropic media. This formula involves three measurement parameters: the average vertical velocity and horizontal and skew moveout velocities. By extending Dix-type hyperbolic moveout analysis, we obtain improved coherence over large source-geophone offsets for more accurate moveout correction. Compared with the stacking velocity obtained by simple hyperbolic analysis methods, the three velocity parameters estimated by this technique contain more physically meaningful geologic informa-tion regarding the anisotropy and/or velocity heterogeneity of the subsurface.Synthetic P-wave model experiments demonstrate that the skewed hyperbolic moveout formula yields an excellent fit to time-distance curves over a wide range of ray angles. Consequently, the measurement parameters are shown to reflect adequately the characteristics of velocity dependence on ray angle, i.e., velocity anisotropy. The technique is then applied to two field offset VSP data sets to measure and analyze the velocity parameters. The results show that the apparent anisotropy, defined as the ratio between the horizontal moveout velocity and average vertical velocity, correlates reasonably well with lithology. Highly anisotropic shale and chalk exhibit higher horizontal-to-vertical velocity ratios and sandstones show lower ratios.
The type IV secretion system affects the expression of Omp25/Omp31 and the outer membrane properties ofBrucella melitensis (2009)

The type IV secretion system (T4SS) contributes to Brucella intracellular survival through its effector proteins. Comparative proteomic analysis showed that intracellular survival proteins are expressed differentially in a virB mutant. Interestingly, several outer membrane proteins (OMPs) are also differentially expressed, implying that T4SS might affect the OM properties of Brucella. To further evaluate the impact of T4SS on OM, in the present study, the OM proteomes were isolated and compared. Many more products of OMPs, particularly different products of the Omp25/Omp31 family, were found to be altered in the virB mutant. The transcription profiles of Omp25/Omp31 were different from those of their protein products, implying their regulation by virB at both transcriptional and post-transcriptional levels. The virB mutant aggregates at a high cell density and produces exopolysaccharide, a phenotype resembling that of the vjbR mutant. The virB mutant showed increased sensitivity to polymyxin B and decreased survival under oxidative, high-salt and high-osmolarity stresses, indicating drastic membrane alterations. These results indicated that in addition to being an effector protein secretion system, T4SS affects OM properties that might be important for the adaptation of Brucella to both in vitro and in vivo hostile environments.
SNP rs2057482 in HIF1A gene predicts clinical outcome of aggressive hepatocellular carcinoma patients after surgery (2015)

Hypoxia-inducible factor 1α (HIF-1α) plays an important role in tumor growth and metastasis. Genetic variations of HIF1A gene have been shown to influence the developing risk and prognosis in many types of human malignancies. However, their association with clinical outcomes of hepatocellular carcinoma (HCC) patients remains unclear. To investigate the predictive role of single nucleotide polymorphisms (SNPs) in HIF1A gene in HCC patients' outcomes, we genotyped three functional SNPs (rs2057482, rs1957757 and rs2301113) in HIF1A gene and assessed their associations with clinicopathological parameters and prognosis of 492 surgical HCC patients. The patients with variant alleles (CT+TT) of SNP rs2057482 had a significantly lower recurrence risk when compared with patients with the CC genotype. In stratified analysis, the protective effect of rs2057482 CT+TT genotype was more evident in patients with adverse strata, compared with patients with favorable strata. Additionally, strong joint predictive effect between rs2057482 genotypes and AFP level, stage or differentiation were observed. Functional assay also indicated the significant effect of rs2057482 on gene expression. In conclusion, SNP rs2057482 in HIF1A gene is significantly associated with clinical outcomes of Chinese HCC patients after surgery, especially in those with aggressive status, which warrants further validation in other patient populations.
Policy optimization of dialogue management in spoken dialogue system for out-of-domain utterances (2016)

This paper addresses the policy optimization of a dialogue management scheme based on partially observable Markov decision processes (POMDP), which is designed for out-of-domain (OOD) utterances processing in spoken dialogue system. First, POMDP-Based DM Modeling for OOD Utterances is proposed, together with detail of some principal elements. Then, joint state transition exploration and dialogue policy optimization are performed in batch. Value iteration method of reinforcement learning framework is employed to optimize the dialogue policy. Our approach is tested through interaction with user in a Chinese restricted domain dialogue system supporting to act as a mobile phone recommendation assistant. Evaluation results show that a usable policy can be learnt in just a few hundred dialogues, and the optimized policy can obtain a convergence of good dialogue reward.
Prevention of Canine Coronary Artery Thrombosis with Echistatin, a Potent Inhibitor of Platelet Aggregation from the Venom of the Viper, Echis carmatus (1990)

A model of acute, platelet-dependent canine coronary artery thrombosis was utilized to assess the antithrombotic effect of a synthetic, RGD-containing 49-residue protein termed echistatin. This protein is derived from the venom of the viper, Echis carinatus. In vitro, echistatin inhibited ADP (10 microM)-induced platelet aggregation with IC50 values in human and canine platelet-rich plasma of 101 +/- 4 and 127 +/- 32 nM, respectively. In vivo, in the dog, infusion of echistatin for 30 min at 20 micrograms kg-1 min-1 or 2.6 nM kg-1 min-1 resulted in total abolition of acute platelet-dependent coronary thrombus formation in all dogs tested (n = 5). Infusion of a lower dose (10 micrograms kg-1 min-1) was not effective in prevention of thrombus formation. Blood samples were taken before and after infusion of echistatin in order to determine ex vivo platelet aggregatory responses. Echistatin (20 micrograms kg-1 min-1, i.v.) attenuated ex vivo platelet aggregation elicited by ADP, U-46619 and collagen and increased bleeding time by 2.9 +/- 0.5-fold over control. Thus, in the dog, echistatin is an effective antithrombotic agent inhibiting both platelet aggregation in vivo in the coronary artery as well as ex vivo with a concomitant increase in bleeding time. Furthermore, the effects of echistatin on platelet aggregation and bleeding time are reversible with restoration to control levels occurring 30-60 min after termination of the infusion.
Targeting Insulin-Like Growth Factor Binding Protein-3 Signaling in Triple-Negative Breast Cancer (2015)

Insulin-like growth factor binding protein-3 (IGFBP-3) is a key regulatory molecule of the IGF axis and can function in a tissue-specific way as both a tumor suppressor and promoter. Triple-negative breast cancer (TNBC) has high tumor expression of IGFBP-3 associated with markers of poor prognosis and, although accounting for 15-20% of all breast cancers, is responsible for disproportionate rates of morbidity and mortality. Because they lack estrogen and progesterone receptors and overexpression of HER2, TNBC are resistant to treatments that target these molecules, making the development of new therapies an important goal. In addition to frequent high expression of IGFBP-3, these tumors also express EGFR highly, but targeting EGFR signaling alone in TNBC has been of little success. Identification of a functional growth-stimulatory interaction between EGFR and IGFBP-3 signaling prompted investigation into cotargeting these pathways as a novel therapy for TNBC. This involves inhibition of both EGFR kinase activity and a mediator of IGFBP-3's stimulatory bioactivity, sphingosine kinase-1 (SphK1), and has shown promise in a preclinical setting. Functional interaction between EGFR and IGFBP-3 may also promote chemoresistance in TNBC, and delineating the mechanisms involved may identify additional targets for development of therapies in cancers that express both IGFBP-3 and EGFR.
Multi-Purpose Utility of Circulating Plasma DNA Testing in Patients with Advanced Cancers (2012)

Tumor genomic instability and selective treatment pressures result in clonal disease evolution; molecular stratification for molecularly targeted drug administration requires repeated access to tumor DNA. We hypothesized that circulating plasma DNA (cpDNA) in advanced cancer patients is largely derived from tumor, has prognostic utility, and can be utilized for multiplex tumor mutation sequencing when repeat biopsy is not feasible. We utilized the Sequenom MassArray System and OncoCarta panel for somatic mutation profiling. Matched samples, acquired from the same patient but at different time points were evaluated; these comprised formalin-fixed paraffin-embedded (FFPE) archival tumor tissue (primary and/or metastatic) and cpDNA. The feasibility, sensitivity, and specificity of this high-throughput, multiplex mutation detection approach was tested utilizing specimens acquired from 105 patients with solid tumors referred for participation in Phase I trials of molecularly targeted drugs. The median cpDNA concentration was 17 ng/ml (range: 0.5-1600); this was 3-fold higher than in healthy volunteers. Moreover, higher cpDNA concentrations associated with worse overall survival; there was an overall survival (OS) hazard ratio of 2.4 (95% CI 1.4, 4.2) for each 10-fold increase in cpDNA concentration and in multivariate analyses, cpDNA concentration, albumin, and performance status remained independent predictors of OS. These data suggest that plasma DNA in these cancer patients is largely derived from tumor. We also observed high detection concordance for critical 'hot-spot' mutations (KRAS, BRAF, PIK3CA) in matched cpDNA and archival tumor tissue, and important differences between archival tumor and cpDNA. This multiplex sequencing assay can be utilized to detect somatic mutations from plasma in advanced cancer patients, when safe repeat tumor biopsy is not feasible and genomic analysis of archival tumor is deemed insufficient. Overall, circulating nucleic acid biomarker studies have clinically important multi-purpose utility in advanced cancer patients and further studies to pursue their incorporation into the standard of care are warranted.
Phase-modulated Mueller ellipsometry characterization of scattering by latex sphere suspensions (2000)

Phase-modulated Mueller ellipsometry (PMME) is used to probe scattering by suspensions of polystyrene latex spheres, with particle diameters ranging from 400 nm to 3 microm. PMME allows simultaneous measurement of the 16 coefficients of the Mueller matrix. Furthermore PMME measurements can easily be carried out owing to a calibration procedure implemented in a scattering configuration. The measurements performed on low concentrations show good agreement with Mie theory. Moreover size distribution could be obtained with a least-squares method based on a genetic fit algorithm. Experimental evidence of multiple scattering on PMME measurements is also presented.
Foxj1 regulates basal body anchoring to the cytoskeleton of ciliated pulmonary epithelial cells (2004)

The forkhead box transcription factor Foxj1 is required for cilia formation and left-right axis determination. To define the role of Foxj1 in ciliogenesis, microarray analysis was performed to identify differentially expressed genes in the pulmonary epithelium of foxj1(+/+) and foxj1(-/-) mice. In the absence of Foxj1, the expression of calpastatin, an inhibitor of the protease calpain, decreased. RNase protection confirmed the decrease in calpastatin expression and decreased calpastatin was detected in the proximal pulmonary epithelium of foxj1(-/-) mice by immunohistochemistry. No change was detected in the expression of calpain 2 in the pulmonary epithelium by western blot or immunohistochemistry. By western blot and immunofluorescence, ezrin, a substrate for calpain, was also found to decrease in the pulmonary epithelium of foxj1(-/-) mice. No change in ezrin gene expression was found by RT-PCR. A decrease in ezrin binding phosphoprotein-50 (EBP-50) was also detected by immunofluorescence in the foxj1(-/-) mouse pulmonary epithelium. Immunoelectron microscopy demonstrated ezrin associated with the basal bodies of cilia in the pulmonary epithelium. Treatment of tracheal explants from foxj1(-/-) mice with a calpain inhibitor resulted in a partial reappearance of cilia observed in these mice. Additionally, following treatment of foxj1(-/-) tracheal explants with calpain inhibitor, basal bodies were observed in an apical location along with relocalization of ezrin and EBP-50. Regulation of calpain activity by calpastatin thus provides a mechanism for regulating the anchoring of basal bodies to the apical cytoskeleton in ciliated cells. In the absence of Foxj1, decreased calpastatin expression with decreased ezrin and EBP-50 results in an inability of basal bodies to anchor to the apical cytoskeleton and subsequent failure of axonemal formation.
Retinoic acid and neurotrophins collaborate to regulate neurogenesis in adult‐derived neural stem cell cultures (1999)

The adult rat hippocampus contains fibroblast growth factor 2–responsive stem cells that are self-renewing and have the ability to generate both neurons and glia in vitro, but little is known about the molecular events that regulate stem cell differentiation. Hippocampus-derived stem cell clones were used to examine the effects of retinoic acid (RA) on neuronal differentiation. Exposure to RA caused an immediate up-regulation of NeuroD, increased p21 expression, and concurrent exit from cell cycle. These changes were accompanied by a threefold increase in the number of cells differentiating into immature neurons. An accompanying effect of RA was to sustain or up-regulate trkA, trkB, trkC, and p75NGFR expression. Without RA treatment, cells were minimally responsive to neurotrophins (NTs), whereas the sequential application of RA followed by brain-derived neurotrophic factor or NT-3 led to a significant increase in neurons displaying mature γ-a-minobutyric acid, acetylcholinesterase, tyrosine hydroxylase, or calbindin phenotypes. Although NTs promoted maturation, they had little effect on the total number of neurons generated, suggesting that RA and neurotrophins acted at distinct stages in neurogenesis. RA first promoted the acquisition of a neuronal fate, and NTs subsequently enhanced maturation by way of RA-dependent expression of the Trk receptors. In combination, these sequential effects were sufficient to stimulate stem cell–derived progenitors to differentiate into neurons displaying a variety of transmitter phenotypes. © 1999 John Wiley & Sons, Inc. J Neurobiol 38: 65–81, 1999
Response of Gut Microbiota to Fasting and Hibernation in Syrian Hamsters (2009)

Although hibernating mammals wake occasionally to eat during torpor, this period represents a state of fasting. Fasting is known to alter the gut microbiota in nonhibernating mammals; therefore, hibernation may also affect the gut microbiota. However, there are few reports of gut microbiota in hibernating mammals. The present study aimed to compare the gut microbiota in hibernating torpid Syrian hamsters with that in active counterparts by using culture-independent analyses. Hamsters were allocated to either torpid, fed active, or fasted active groups. Hibernation was successfully induced by maintaining darkness at 4 degrees C. Flow cytometry analysis of cecal bacteria showed that 96-h fasting reduced the total gut bacteria. This period of fasting also reduced the concentrations of short chain fatty acids in the cecal contents. In contrast, total bacterial numbers and concentrations of short chain fatty acids were unaffected by hibernation. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments indicated that fasting and hibernation modulated the cecal microbiota. Analysis of 16S rRNA clone library and species-specific real-time quantitative PCR showed that the class Clostridia predominated in both active and torpid hamsters and that populations of Akkermansia muciniphila, a mucin degrader, were increased by fasting but not by hibernation. From these results, we conclude that the gut microbiota responds differently to fasting and hibernation in Syrian hamsters.
Expression of STATs and their inhibitors SOCS and PIAS in brain tumors. In vitro and in vivo study. (2008)

Proteins of STAT family belongs to the transcription factors. Through their binding to the DNA specific sites and consequent regulation of transcription of various genes, these signaling proteins play an important role in many cell functions. Recent studies demonstrated persistent activation of STATs and loss of their natural inhibitors SOCS and PIAS in various human cancers. There is also evidence that experimental pharmacologic or genetic modulation of their function mignt by a new approach in anticancer treatment. The aim of this study was in vitro assesment and analysis of expression of STATs, SOCS and PIAS in glioblastoma cell lines undergoing treatment by PPARgamma agonists/antagonists because PPARgamma and STATs are tightly regulated by an overlapping set of nuclear regulatory proteins. We further analysed immunohistochemical expression of these proteins in vivo, with its correlation to grading in various brain tumors. The results of in vitro study showed decreased expression of phosphorylated form of STAT3 and increase of its inhibitors SOCS3 and PIAS3 in glioblastoma cell lines after treatment with IC50 of PPARgamma agonist ciglitazone. In vivo study failed to reveal changes in STAT3 and SOCS3 expression in either low and high grade astrocytomas, however we detect lower expression of STAT2 in low grade astrocytomas when comparing with high grade astrocytomas and lower expression of STAT3 in ependymomas when comparing with anaplastic ones. The results showed existing relationship between STAT and PPARgamma signaling in glial tumors and further suppport expected important role of STATs in regulation of growth and differentiation in these tumors.