gebhart/patrepeval huggingface dataset:
Regulation of valvular interstitial cell calcification by adhesive peptide sequences (2010)

Knowledge of how valvular interstitial cells (VICs) interact with the extracellular matrix (ECM) would aid in not only better understanding the etiology of valvular disease but also constructing appropriate environments for valve tissue engineering. In this work, the calcification of VICs cultured on ECM coatings (fibronectin, fibrin, collagen, and laminin) or ECM-derived peptide sequences (RGDS, YIGSR, and DGEA) was quantified via several techniques. Neutralizing antibodies to specific adhesion receptors were also applied, followed by quantification of phenotypic markers related to valve calcification. The calcification of VICs varied with the ECM component or peptide that was presented on the culture substrate. VICs calcified the most on RGDS and least on YIGSR and DGEA, while blocking specific receptors revealed that disruption of VIC binding via the alpha(5)beta(1) integrin or the 67-kDa laminin receptor had a dramatic calcification-stimulating effect. Binding via the alpha(2)beta(1) integrin did not alter calcification or VIC phenotype. These findings were translated to 3D peptide-modified scaffold environments that demonstrated varying levels of disease expression by VICs. Thus, specific adhesion receptors play a significant role in mediating the interactions between VICs and ECM that lead to calcification, which provides important information regarding the mechanisms of valvular disease and scaffold design for valve tissue engineering.
Molecular mimicry of integrin ligation: therapeutic potential of arginine-glycine-aspartic acid (RGD) peptides. (1998)

integrins; RGD peptide; renal failure; is a high degree of specificity and selectivity
Comparison of anti-CD3 and anti-CD28-coated beads with soluble anti-CD3 for expanding human T cells: Differing impact on CD8 T cell phenotype and responsiveness to restimulation (2010)

Anti-CD3/CD28 beads are highly effective for expanding CD4 cells, but soluble anti-CD3 has significant potential advantages for expanding CD8 T cells, particularly where preservation of phenotypically "young" CD8 cells would be desirable, or where the T cells of interest have been antigen-stimulated in vitro or in vivo in the recent past.
Quantitative gene expression analysis in microdissected archival tissue by real-time RT-PCR. (2000)

Laser-assisted microdissection is a powerful tool for the analysis of morphologically defined cell populations. We report here that the combination of microdissection and real-time RT-PCR technologies together with an optimized RNA microscale extraction procedure allows the reproducible determination of gene expression levels in archival formalin-fixed, paraffin-embedded tissue samples.
High Level of Androgen Receptor Is Associated With Aggressive Clinicopathologic Features and Decreased Biochemical Recurrence-free Survival in Prostate (2004)

High levels of AR are associated with increased proliferation, markers of aggressive disease and are predictive of decreased biochemical recurrence-free survival independently. This confirms the role of AR in tumor growth and progression in hormonally naive PCa.
p53 involvement in activation of the cytokeratin 8 gene in tumor cell lines. (1996)

We show that the expression of the human cytokeratin 8 (CK8) gene is regulated by wild-type p53. DNA sequence data indicate that the 5' untranslated region of the CK8 gene contains a putative p53-like binding site. In this study we focused on the effect of the p53 protein on the regulation and expression of the CK8 gene. Cotransfection of the H358 p53-negative human lung cancer cell line with a CK8 promoter CAT expression vector and a plasmid expressing the wildtype p53 indicated that p53 induces CK8 expression. A transient assay in which a p53-negative cell line was cotransfected with a CK8 promoter CAT expression vector and a plasmid expressing wildtype or mutant p53 indicated that only wildtype p53 induces the CK8 promoter. Deletion of the putative p53-binding site from the CK8 promoter or introduction of mutations in the p53-binding sequences abolished the wild-type p53-mediated transactivation of CK8. A gel-retardation assay was used to measure DNA binding by the wild-type p53 protein. A 24-bp oligonucleotide corresponding to the putative p53 binding site was used for this assay. The wild-type p53 protein bound weakly to this DNA sequence but much more strongly when three tandem repeat of the binding sequences was used. These studies suggest that the CK8 gene is a downstream target whose expression is regulated by wild-type p53.
Common Sites for Recombination and Cleavage Mediated by Bacteriophage T4 DNA Topoisomerase in vitro (1989)

We have previously shown that purified T4 DNA topoisomerase promotes illegitimate recombination between two lambda DNA molecules, or between lambda and plasmid DNA in vitro (Ikeda, H. (1986) Proc. Natl. Acad. Sci. U. S. A. 83, 922-926). Since the recombinant DNA contains a duplication or deletion, it is inferred that the cross-overs take place between nonhomologous sequences of lambda DNA. In this paper, we have examined the sequences of the recombination junctions produced by the recombination between two lambda DNA molecules mediated by T4 DNA topoisomerase. We have shown that there is either no homology or there are 1-5-base pair homologies between the parental DNAs in seven combinations of lambda recombination sites, indicating that homology is not essential for the recombination. Next, we have shown an association of the recombination sites with the topoisomerase cleavage sites, indicating that a capacity of the topoisomerase to make a transient double-stranded break in DNA plays a role in the illegitimate recombination. A consensus sequence for T4 topoisomerase cleavage sites, RNAY decreases NNNNRTNY, was deduced. The cleavage experiment showed that T4 topoisomerase-mediated cleavage takes place in a 4-base pair staggered fashion and produces 5'-protruding ends.
Use of the CO2 laser in soft tissue and periodontal surgery. (1994)

The use of laser energy is by now established in some areas of the medical and dental professions. This article reviews the history of the carbon dioxide laser and discusses the advantages, indications, and contraindications of laser in soft tissue and periodontal surgery. Four clinical cases are presented to illustrate laser techniques in excisional biopsy, gingivectomy, coagulation of graft donor site, and a frenectomy procedure. The learning objective of this article is to familiarize the reader with this relatively new addition to oral surgical procedures.
The Lectin-Like Domain of Complement Receptor 3 Protects Endothelial Barrier Function from Activated Neutrophils (2004)

The adhesion of neutrophils to endothelial cells is a central event leading to diapedesis and involves the binding of the I-domain of beta(2) integrins (CD11/CD18) to endothelial ICAMs. In addition to the I-domain, the beta(2) integrin complement receptor 3 (CR3) (CD11b/CD18) contains a lectin-like domain (LLD) that can alter leukocyte functions such as chemotaxis and cytotoxicity. The present study demonstrates that, in contrast to the CR3 I-domain, Ab blockade of the CR3 LLD has no role in mediating neutrophil-induced loss of endothelial barrier function. However, activation of CR3 with the LLD agonist beta-glucan protects the barrier function of endothelial cells in the presence of activated neutrophils and reduces transendothelial migration without affecting adhesion of the neutrophils to the endothelium. The LLD site-specific mAb VIM12 obviates beta-glucan protection while activation of the LLD by VIM12 cross-linking mimics the beta-glucan response by both preserving endothelial barrier function and reducing neutrophil transendothelial migration. beta-glucan has no direct effect on endothelial cell function in the absence of activated neutrophils. These findings demonstrate that signaling through the CR3 LLD prevents neutrophil-induced loss of endothelial barrier function and reduces diapedesis. This suggests that the LLD may be a suitable target for oligosaccharide-based anti-inflammatory therapeutics.
Phase I Single-Dose Study of Intracavitary-Administered Iodine-131-TM-601 in Adults With Recurrent High-Grade Glioma (2006)

A single dose of 10 mCi 131I-TM-601 was well tolerated for 0.25 to 1.0 mg TM-601 and may have an antitumoral effect. Dosimetry and biodistribution from this first trial suggest that phase II studies of 131I-TM-601 are indicated.
Efficient Transfer of a Tumor Antigen-Reactive TCR to Human Peripheral Blood Lymphocytes Confers Anti-Tumor Reactivity (1999)

The tumor-associated-Ag MART-1 is expressed by most human melanomas. The genes encoding an alphabeta TCR from a MART-1-specific, HLA-A2-restricted, human T cell clone have been efficiently transferred and expressed in human PBL. These retrovirally transduced PBL cultures were MART-1 peptide reactive, and most cultures recognized HLA-A2+ melanoma lines. Limiting dilution clones were generated from three bulk transduced PBL cultures to investigate the function of individual clones within the transduced cultures. Twenty-nine of 29 CD8+ clones specifically secreted IFN-gamma in response to T2 cells pulsed with MART-1(27-35) peptide, and 23 of 29 specifically secreted IFN-gamma in response to HLA-A2+ melanoma lines. Additionally, 23 of 29 CD8+ clones lysed T2 cells pulsed with the MART-1(27-35) peptide and 15 of 29 lysed the HLA-A2+ melanoma line 888. CD4+ clones specifically secreted IFN-gamma in response to T2 cells pulsed with the MART-1(27-35) peptide. TCR gene transfer to patient PBL can produce CTL with anti-tumor reactivity in vitro and could potentially offer a treatment for patients with metastatic melanoma. This approach could also be applied to the treatment of other tumors and viral infections. Additionally, TCR gene transfer offers unique opportunities to study the fate of adoptively transferred T cells in vivo.
Particle Size Distribution of Mainstream and Exhaled Cigarette Smoke and Predictive Deposition in Human Respiratory Tract (2013)

The particle size distribution of cigarette smoke is an important factor in predicting the deposition fraction of the inhaled particles in various regions of the respiratory tract. Mainstream cigarette smoke is a direct concern for smokers, while the exhaled and side stream smoke contribute to passive (second hand) smoking. The particle size distribution of tobacco smoke for mainstream and exhaled smoke has been studied in this work. This study investigates how smoking behavior, including puff volume and number of puffs, affect the particle size distribution of mainstream cigarette smoke. Scanning Mobility Particle Sizer (SMPS) was used to measure the particle size distribution of mainstream and exhaled cigarette smoke. The values of count median diameter (CMD) mobility size for the first four consecutive puffs were found to be 193 nm, 198 nm, 194 nm and 186 nm. As the volume of a puff increases from 35 mL to 85 mL, the CMD shifted slightly towards the higher particle size ranges, because of increased probability of coagulation and other combination processes. For the exhaled cigarette smoke, the growth factor was found to be 1.5 ± 0.3 with respect to mainstream cigarette smoke. The experimental results of particle size distributions were used in a Multiple Path Particle Dosimetry (MPPD) model to predict deposition patterns in the human respiratory tract. The MPPD model results show the deposition fractions for mainstream cigarette smoke were 0.163, 0.152 and 0.298 for the head, trachea and bronchi (TB) and pulmonary region, and those for exhaled cigarette smoke were 0.273, 0.064 and 0.134 respectively. The total calculated deposition fraction for mainstream and exhaled cigarette smoke was found to be 0.613 and 0.471, respectively.
[(Pro) renin receptor in the pathogenesis of proliferative diabetic retinopathy]. (2014)

The renin-angiotensin system (RAS), originally regarded as an important controller of systemic blood pressure (circulatory RAS), plays a pivotal role in pathological vascular conditions including inflammation and angiogenesis (tissue RAS). (Pro) renin receptor [(P) RR] is known to bind with prorenin causing the dual activation of tissue renin-angiotensin system (RAS) together with RAS-independent intracellular signaling pathways and contributes to the molecular pathogenesis of end-organ damage. In this review, we investigated localization and expression of (P)RR in fibrovascular tissues and vitreous fluids from patients with proliferative diabetic retinopathy and evaluated the molecular mechanisms in vitro in order to confirm the conclusions regarding (P) RR from animal studies. (P)RR immunoreactivity was detected in vascular endothelial cells, co-localized with prorenin, phosphorylated extracellular signal-regulated kinase and vascular endothelial growth factor (VEGF). Protein levels of soluble (P) RR in the vitreous fluids were higher in proliferative diabetic retinopathy (PDR) eyes than in non-diabetic control eyes, and were significantly correlated with vitreous VEGF levels and the vascular density of fibrovascular tissues. We herein report the first evidence that shows the close association of (P) RR with angiogenic activity in human PDR. The present data suggest the validity of (P) RR as a molecular target for the treatment of PDR.
A Continuous-Flow Polymerase Chain Reaction Microchip With Regional Velocity Control (2006)

This paper presents a continuous-flow polymerase chain reaction (PCR) microchip with a serpentine microchannel of varying width for "regional velocity control." Varying the channel width by incorporating expanding and contracting conduits made it possible to control DNA sample velocities for the optimization of the exposure times of the sample to each temperature phase while minimizing the transitional periods during temperature transitions. A finite element analysis (FEA) and semi-analytical heat transfer model was used to determine the distances between the three heating assemblies that are responsible for creating the denaturation (96 degrees C), hybridization (60 degrees C), and extension (72 degrees C) temperature zones within the microchip. Predictions from the thermal FEA and semi-analytical model were compared with temperature measurements obtained from an infrared (IR) camera. Flow-field FEAs were also performed to predict the velocity distributions in the regions of the expanding and contracting conduits to study the effects of the microchannel geometry on flow recirculation and bubble nucleation. The flow fields were empirically studied using micro particle image velocimetry (mu-PIV) to validate the flow-field FEA's and to determine experimental velocities in each of the regions of different width. Successful amplification of a 90 base pair (bp) bacillus anthracis DNA fragment was achieved.
Antigen-Specific Inhibition of Experimental Autoimmune Uveoretinitis by Bone Marrow-Derived Immature Dendritic Cells (2003)

The data suggest that induction of tolerance to an autoantigen by peptide-loaded DCs requires presentation of antigen by iDCs and involves the generation of a high-level IL-10 and IL-5 immune response in DLN cells.
Colour-Consistent Structure-from-Motion Models using Underwater Imagery (2012)

This paper presents an automated approach to correcting for colour inconsistency in underwater images collected from multiple perspectives during the construction of 3D structure-from-motion models. When capturing images underwater, the water column imposes several effects on images that are negligible in air such as colour-dependant attenuation and lighting patterns. These effects cause problems for human interpretation of images and also confound computer-based techniques for clustering and classification. Our approach exploits the 3D structure of the scene generated using structure-from-motion and photogrammetry techniques accounting for distance-based attenuation, vignetting and lighting pattern, and improves the consistency of photo-textured 3D models. Results are presented using imagery collected in two different underwater environments using an Autonomous Underwater Vehicle (AUV).
A single chip sensor and image processor for fingerprint verification (2002)

The authors describe a real-time image processing system, including an image sensing array, which is implemented as a single VLSI device. An architectural overview and system performance figures demonstrate that, through efficient integration of the sensing, processing, and memory elements of the image-processing system, increased performance and greatly reduced manufacturing costs can be achieved for a specific application (in this case, fingerprint verification). The device, designed and fabricated using a standard 1.2- mu m ASIC (application-specific integrated circuit) CMOS process and 18-MHz operation, includes a 258*258 image sensor array, real-time image normalization and image matching circuitry, 8 kb of fast access memory, and 16 kb of ROM.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Primordial germ cell migration (2004)

Mutational and antisense screens in Drosophila and zebrafish, and transcriptional profiling and time-lapse analysis in the mouse, have contributed greatly to our understanding of PGC development. In all three systems, the behavior of PGCs is controlled by growth factors which signal through G-protein coupled receptors and/or tyrosine kinase receptors. Additionally, regulated cell-cell and cell-substrate adhesion is important for PGC motility. Finally, localized growth factors may control PGC survival and consequently PGC position. Chemotaxis, regulated adhesion and cell survival are important for multiple migration processes which occur during development and disease. PGC migration shares these features.
Rabies Virus Glycoprotein (RVG) Is a Trimeric Ligand for the N-terminal Cysteine-rich Domain of the Mammalian p75 Neurotrophin Receptor (2002)

Rabies virus glycoprotein (RVG) is a trimeric and surface-exposed viral coat protein that has been shown to interact with the murine p75 neurotrophin receptor. We have investigated binding of RVG to p75 and describe several features that distinguish the p75-RVG interaction from conventional neurotrophin binding to p75. RVG binds mammalian but not avian p75 and does not bind to any of the Trk neurotrophin receptors. The mammalian p75 specificity of RVG binding may partly explain the phyletic specificity of rabies infection. Radioiodinated nerve growth factor (NGF) and RVG both bind to rat p75 but do not compete with each other's binding site. Although neurotrophins bind to the second and third cysteine-rich domains (CRD) of p75, RVG specifically interacts with high affinity (K(d) 30-35 pm) with the first CRD (CRD1). Substitution of Gln(33) in p75-CRD1 by Glu completely abolishes RVG binding. Our data therefore firmly establish RVG as a trimeric high affinity ligand for a non-neurotrophin binding site on p75. Interestingly, the CRD1 in another TNF/NGF family receptor was recently shown to be involved in the binding of the herpes virus glycoprotein gD, suggesting that the CRD1 of TNF/NGF family members may be a widely used binding domain for viral glycoproteins.
Preventing denial of service attacks on quality of service (2002)

Capabilities are being added to IP networks to support quality of service (QoS) guarantees. These guarantees are needed for many applications, such as voice and video transmission, real-time control, etc. Little attention has been paid to making these capabilities secure; in their present form, they are vulnerable to attack. The ARQoS project is examining these vulnerabilities, and ways to prevent denial-of-service attacks on QoS capabilities. In this paper, we describe two important parts of the project. The first part is the application of a pricing paradigm to resource allocation. User acquisition of network resources must be authorized, and the relative amount of resources that can be requested is carefully controlled. We present a distributed method of pricing which is highly flexible and responsive to changing conditions. Experimental results illustrate its effectiveness. The second part is the detection of TCP dropping attacks by compromised routers. The detection occurs at the end system and does not require any cooperation from the network. We have enhanced a method of statistically analyzing traffic patterns to detect dropping attacks. The method has been implemented and tested over the Internet, and results are presented.
A FACILE APPROACH TO N-HETEROCYCLES. THE REACTIONS OF YLIDE PHOSPHORANES WITH HYDRAZONES (2001)

The reactions of isatin--phenylhydrazone 1 and benzil monophenvlhydrazone 2 with some ester-3a,b and keto ylides 3c were studied in details, under different experimental conditions with the aim of evaluating the synthetic potential of this approach for the synthesis of N-heterocvclic systems. Structures of the new compounds were established on the basis of elemental and spectroscopic analyses.
An Immunoglobulin G1 Monoclonal Antibody Highly Specific to the Wall of Cryptosporidium Oocysts (2000)

The detection of Cryptosporidium oocysts in drinking water is critically dependent on the quality of immunofluorescent reagents. Experiments were performed to develop a method for producing highly specific antibodies to Cryptosporidium oocysts that can be used for water testing. BALB/c mice were immunized with six different antigen preparations and monitored for immunoglobulin G (IgG) and IgM responses to the surface of Cryptosporidium oocysts. One group of mice received purified oocyst walls, a second group received a soluble protein preparation extracted from the outside of the oocyst wall, and the third group received whole inactivated oocysts. Three additional groups were immunized with sequentially prepared oocyst extracts to provide for a comparison of the immune response. Mice injected with the soluble protein extract demonstrated an IgG response to oocysts surface that was not seen in the whole-oocyst group. Mice injected with whole oocysts showed an IgM response only, while mice injected with purified oocyst walls showed little increase in IgM or IgG levels. Of the additional reported preparations only one, BME (2-mercaptoethanol treated), produced a weak IgM response to the oocyst wall. A mouse from the soluble oocyst extract group yielding a high IgG response was utilized to produce a highly specific IgG(1) monoclonal antibody (Cry104) specific to the oocyst surface. Comparative flow cytometric analysis indicated that Cry104 has a higher avidity and specificity to oocysts in water concentrates than other commercially available antibodies.
Acute Lymphoblastic Leukemia (2004)

This comprehensive survey emphasizes how recent advances in the knowledge of molecular mechanisms involved in acute lymphoblastic leukemia have influenced diagnosis, prognosis, and treatment.
Temporary suppression of visual processing in an RSVP task: An attentional blink? (1992)

Through rapid serial visual presentation (RSVP), we asked Ss to identify a partially specified letter (target) and then to detect the presence or absence of a fully specified letter (probe). Whereas targets are accurately identified, probes are poorly detected when they are presented during a 270-ms interval beginning 180 ms after the target. Probes presented immediately after the target or later in the RSVP stream are accurately detected. This temporary reduction in probe detection was not found in conditions in which a brief blank interval followed the target or Ss were not required to identify the target. The data suggest that the presentation of stimuli after the target but before target-identification processes are complete produces interference at a letter-recognition stage. This interference may cause the temporary suppression of visual attention mechanisms observed in the present study.