gebhart/patrepeval huggingface dataset:
Soluble HER-2/neu neutralizes biologic effects of anti-HER-2/neu antibody on breast cancer cellsin vitro (1997)

Amplification and over-expression of the HER-2/neu proto-oncogene are associated with poor prognosis in women with both node-positive and node-negative breast cancer. Therefore, the encoded surface glycoprotein represents an attractive target for cancer immunotherapies. Furthermore, the extracellular domain of HER-2/neu is released from the cell surface by proteolytic cleavage. In the present experiments, we investigated the potential biologic effects of soluble HER-2/neu with particular emphasis on its interaction with anti-HER-2/neu antibodies. A monoclonal antibody specific for the extracellular domain of HER-2/neu dose dependently inhibited the proliferation of highly HER-2/neu-expressing SK-BR-3 and BT-474 breast cancer cells but had no effect on the proliferation of weakly to moderately HER-2/neu-expressing MCF-7, HBL-100 and ZR-75-1 breast cells. Addition of SK-BR-3 or BT-474 cell supernatants with high concentrations of soluble HER-2/neu led to a neutralization of anti-HER-2/neu antibody-mediated inhibition of proliferation due to a binding of soluble HER-2/neu by the antibody, which could be demonstrated by immunoprecipitation. Furthermore, the ability of anti-HER-2/neu antibodies to mediate antibody-dependent cellular cytotoxicity (ADCC) by lymphokine-activated killer cells was assessed. Cytolysis of SK-BR-3 tumor cells was increased significantly in the presence of anti-HER-2/neu antibodies. Similar to the proliferation inhibition, ADCC was neutralized by addition of soluble HER-2/neu-containing supernatants. Our data suggest that tumors rich in HER-2/neu might thus escape certain steps of immunologic control by neutralizing biologic activities of anti HER-2/neu antibodies due to the presence of soluble HER-2/neu.
Fabrication of Nanometer Scale Patterns within Self-Assembled Monolayers by Nanografting (1999)

A nanofabrication method, nanografting, has been developed to fabricate nanometer scale patterns on surfaces with specified size and geometry. The nanografting process combines the displacement of selected resist molecules by an atomic force microscopy tip and the adsorption of new adsorbate. The present work details the procedure for nanografting and discusses various kinds of patterns produced and the stability of the resulting patterns. Compared with other methods for microfabrication, nanografting allows a more precise control over the size and geometry of patterned features and their locations on surfaces. Nanopatterns comprising various thiol-based components can be produced, where we have demonstrated the fabrication of nanopatterns from thiols with either the same or different chain lengths and terminal groups from the matrix SAM. Furthermore, nanografting allows the fabricated patterns to be altered in situ without the need to change masks or repeat entire fabrication processes. The patterned SAMs produced by nanografting open new opportunities for systematic studies of such size-dependent properties as conductivity, nanotribology, and spatially-confined surface reactions.
A Crucial Role for Exopolysaccharide Modification in Bacterial Biofilm Formation, Immune Evasion, and Virulence (2004)

Biofilms play an important role in many chronic bacterial infections. Production of an extracellular mixture of sugar polymers called exopolysaccharide is characteristic and critical for biofilm formation. However, there is limited information about the mechanisms involved in the biosynthesis and modification of exopolysaccharide components and how these processes influence bacterial pathogenesis. Staphylococcus epidermidis is an important human pathogen that frequently causes persistent infections by biofilm formation on indwelling medical devices. It produces a poly-N-acetylglucosamine molecule that emerges as an exopolysaccharide component of many bacterial pathogens. Using a novel method based on size exclusion chromatography-mass spectrometry, we demonstrate that the surface-attached protein IcaB is responsible for deacetylation of the poly-N-acetylglucosamine molecule. Most likely due to the loss of its cationic character, non-deacetylated poly-acetylglucosamine in an isogenic icaB mutant strain was devoid of the ability to attach to the bacterial cell surface. Importantly, deacetylation of the polymer was essential for key virulence mechanisms of S. epidermidis, namely biofilm formation, colonization, and resistance to neutrophil phagocytosis and human antibacterial peptides. Furthermore, persistence of the icaB mutant strain was significantly impaired in a murine model of device-related infection. This is the first study to describe a mechanism of exopolysaccharide modification that is indispensable for the development of biofilm-associated human disease. Notably, this general virulence mechanism is likely similar for other pathogenic bacteria and constitutes an excellent target for therapeutic maneuvers aimed at combating biofilm-associated infection.
Inhibition of the active lymph pump in rat mesenteric lymphatics by hydrogen peroxide. (1993)

The lymphatic system plays an important role in the regulation of fluid and macromolecular exchange. It is a key "safety factor" against the formation of gross edema. Spontaneous contractions in collecting lymphatics of the rat intestine are necessary for the normal transportation of lymph. Hydrogen peroxide is one of the compounds released in inflammation. Therefore, the effects of H2O2 on the pumping activity of spontaneously contracting lymphatics were evaluated in the anesthetized rat (n = 16). Diameter oscillations of the mesenteric collecting lymphatics were monitored before and after the application of H2O2 (4 and 37 microM). The activity of the lymph pump was evaluated using: contraction frequency (F), stroke volume (SV), ejection fraction (EF), and lymph pump flow (LPF). These parameters were determined from the lymphatic diameter tracings. The following changes in lymphatic activity were seen after a 20 minute exposure to 37 microM H2O2: 1) F declined 85%, from 11.6 +/- 1.5 to 1.9 +/- 1.9 cpm. 2) SV fell over 93%. 3) EF decreased 93%, from 0.57 +/- .07 to 0.05 +/- .04. 4) LPF fell dramatically (> 95%) from 41.5 +/- 10.5 to 2.6 +/- 2.5 nl/min. In conclusion, H2O2 produced an intense inhibition of the active lymph pump and it is possible that the inhibition of the active pump contributes to the edema which occurs during inflammation.
Hyaluronan synthesis by epiphysial chondrocytes is regulated by growth hormone, insulin-like growth factor-1, parathyroid hormone and transforming growth factor-β1 (1996)

In a previous study, we presented evidence that the synthesis of hyaluronan by hypertrophic chondrocytes is one of the principal factors driving the interstitial expansion of the growth plate (Pavasant et al., J. Cell Sci. 109: 327-334, 1996). To test this possibility further, we used two different approaches to examine the effects of hormones on the production of hyaluronan in the growth plate. In the first approach, we examined the growth plate of the lit/lit mouse that lacks growth hormone and found that its hypertrophic lacunae were smaller and contained less hyaluronan than those of wild type mice. Moreover, the ratios of hyaluronan staining density to total area of the lacunae were similar for the lit/lit and the wt/wt mice, indicating that the amount of hyaluronan is directly related to lacuna size. In the second approach, we examined the effects of hormones on segments of the epiphysial growth plate placed in organ culture. Under normal culture conditions, a band of hyaluronan staining progressed across the length of the growth plate, reflecting the maturation of chondrocytes into the hypertrophic stage. When insulin-like growth factor-1, a factor known to promote chondrocyte maturation, was added to the culture medium, the production of hyaluronan and the enlargement of the lacunae were stimulated. In contrast, when either parathyroid hormone or transforming growth factor-beta 1, both of which inhibit chondrocyte differentiation, was added to the medium of cultured segments, new pericellular hyaluronan was not detected and the lacunae did not enlarge. Taken together, these results indicate that factors that either stimulate or inhibit the maturation of epiphysial chondrocytes have a corresponding effect on the production of hyaluronan. This, in turn, further supports the importance of hyaluronan in the process of lacuna enlargement.
RGB camera-based noncontact imaging of plethysmogram and spontaneous low-frequency oscillation in skin perfusion before and during psychological stress (2019)

We investigated a non-contact imaging method to evaluate plethysmogram and vasomotion with a digital color camera. Monte Carlo simulation for light transport in skin tissue is used to specify a relation among the red-green-blue-values and hemoglobin contents. Applying the FFT band pass filters to each pixel of the sequential images for the total hemoglobin concentration along the time line, two-dimentional plethysmogram and vasomotion can be reconstructed. In vivo experiments with human skin before, during, and after auditory stimulation demonstrated the feasibility of the method to evaluate the activities of autonomic nervous systems.
Antibody-Cytokine Fusion Proteins for the Therapy of Breast Cancer (2000)

Abstract : We have proposed to develop novel antibody fusion proteins in which antibodies specific for the breast cancer tumor associated antigen HER2/neu will be genetically fused to the cytokines IL-2, IL-12, and GM-CSF. It is expected that the anti-HER2/neu antibody cytokine fusion protein will localize the cytokine at the tumor and elicit an immune response. During our first year of funding we completed the construction and characterization of an anti-HER2/neu IgG3-(GM-CSF) fusion protein. This novel molecule expressed in myeloma cells was correctly assembled and secreted and showed antibody and cytokine related activities. In addition, anti-HER2/neu IgG3-(GM-CSF) was able to target the HER2/neu expressing murine tumor CT26-HER2/neu and enhance the immune response against the targeted antigen, HER2/neu, suggesting its potential use in the treatment of HER2/neu expressing tumors. We also expanded our repertoire of human HER2/neu expressing murine cell lines by transducing the murine B cell lymphoma 38C13 with the cDNA encoding human HER2/neu. We studied the in vivo properties of this new tumor model (38C13-HER2/neu) and found that this model provides a useful tool for the evaluation of different therapeutic approaches designed to stimulate the tumor specific immune response.
Purification and analysis of RNA from paraffin-embedded tissues. (1988)

We have developed methods for the purification and analysis of RNA from formalin-fixed and paraffin-embedded tissue. The methods allow retrospective analysis of gene expression or viral infection. RNA extraction uses prolonged solubilization of tissue with detergent and protease in the presence of high concentrations of a ribonuclease inhibitor. The purified RNA is moderately degraded but its hybridization behavior is essentially unaffected. We were able to quantify specific mRNAs by dot-blot hybridization.
Sensory-motor problems in Autism (2013)

Despite being largely characterized as a social and cognitive disorder, strong evidence indicates the presence of significant sensory-motor problems in Autism Spectrum Disorder (ASD). This paper outlines our progression from initial, broad assessment using the Movement Assessment Battery for Children (M-ABC2) to subsequent targeted kinematic assessment. In particular, pronounced ASD impairment seen in the broad categories of manual dexterity and ball skills was found to be routed in specific difficulties on isolated tasks, which were translated into focused experimental assessment. Kinematic results from both subsequent studies highlight impaired use of perception-action coupling to guide, adapt and tailor movement to task demands, resulting in inflexible and rigid motor profiles. In particular difficulties with the use of temporal adaption are shown, with "hyperdexterity" witnessed in ballistic movement profiles, often at the cost of spatial accuracy and task performance. By linearly progressing from the use of a standardized assessment tool to targeted kinematic assessment, clear and defined links are drawn between measureable difficulties and underlying sensory-motor assessment. Results are specifically viewed in-light of perception-action coupling and its role in early infant development suggesting that rather than being "secondary" level impairment, sensory-motor problems may be fundamental in the progression of ASD. This logical and systematic process thus allows a further understanding into the potential root of observable motor problems in ASD; a vital step if underlying motor problems are to be considered a fundamental aspect of autism and allow a route of non-invasive preliminary diagnosis.
Domain Structure Characterization of the Multifunctional α-Aminoadipate Reductase from Penicillium chrysogenum by Limited Proteolysis (2003)

The alpha-aminoadipate reductase (alpha-AAR) of Penicillium chrysogenum, an enzyme that activates the alpha-aminoadipic acid by forming an alpha-aminoadipyl adenylate and reduces the activated intermediate to alpha-aminoadipic semialdehyde, was purified to homogeneity by immunoaffinity techniques, and the kinetics for alpha-aminoadipic acid, ATP, and NADPH were determined. Sequencing of the N-terminal end confirmed the 10 first amino acids deduced from the nucleotide sequence. Its domain structure has been investigated using limited proteolysis and active site labeling. Trypsin and elastase were used to cleave the multienzyme, and the location of fragments within the primary structure was established by N-terminal sequence analysis. Initial proteolysis generated two fragments: an N-terminal fragment housing the adenylation and the peptidyl carrier protein (PCP) domains (116 kDa) and a second fragment containing most of the reductive domain (28 kDa). Under harsher conditions the adenylation domain (about 64 kDa) and the PCP domain (30 kDa) become separated. Time-dependent acylation of alpha-AAR and of fragments containing the adenylation domain with tritiated alpha-aminoadipate occurred in vitro in the absence of NADPH. Addition of NADPH to the labeled alpha-AAR released most of the radioactive substrate. A fragment containing the adenylation domain was labeled even in absence of the PCP box. The labeling of this fragment (lacking PCP) was always weaker than that observed in the di-domain (adenylating and PCP) fragment suggesting that the PCP domain plays a role in the stability of the acyl intermediate. Low intensity direct acylation of the PCP box has also been observed. A domain structure of this multienzyme is proposed.
Independent Modes of Natural Killing Distinguished in Mice Lacking Lag3 (1996)

The LAG3 protein has several features in common with CD4, suggesting that it may be important in controlling T cell reactivity. However, mice with a Lag3 null mutation have now been shown to exhibit a defect in the natural killer cell, rather than the T cell, compartment. Killing of certain tumor targets by natural killer cells from these mice was inhibited or even abolished, whereas lysis of cells displaying major histocompatibility complex class I disparities remained intact. It appears that LAG3 is a receptor or coreceptor that defines different modes of natural killing.
Molecular Cloning and Characterization of STAMP1, a Highly Prostate-specific Six Transmembrane Protein that Is Overexpressed in Prostate Cancer (2002)

We have identified a novel gene, six transmembrane protein of prostate 1 (STAMP1), which is largely specific to prostate for expression and is predicted to code for a 490-amino acid six transmembrane protein. Using a form of STAMP1 labeled with green fluorescent protein in quantitative time-lapse and immunofluorescence confocal microscopy, we show that STAMP1 is localized to the Golgi complex, predominantly to the trans-Golgi network, and to the plasma membrane. STAMP1 also localizes to vesicular tubular structures in the cytosol and colocalizes with the early endosome antigen 1 (EEA1), suggesting that it may be involved in the secretory/endocytic pathways. STAMP1 is highly expressed in the androgen-sensitive, androgen receptor-positive prostate cancer cell line LNCaP, but not in androgen receptor-negative prostate cancer cell lines PC-3 and DU145. Furthermore, STAMP1 expression is significantly lower in the androgen-dependent human prostate xenograft CWR22 compared with the relapsed derivative CWR22R, suggesting that its expression may be deregulated during prostate cancer progression. Consistent with this notion, in situ analysis of human prostate cancer specimens indicated that STAMP1 is expressed exclusively in the epithelial cells of the prostate and its expression is significantly increased in prostate tumors compared with normal glands. Taken together, these data suggest that STAMP1 may have an important role in the normal prostate cell as well as in prostate cancer progression.
Real-time speaker identification and verification (2005)

In speaker identification, most of the computation originates from the distance or likelihood computations between the feature vectors of the unknown speaker and the models in the database. The identification time depends on the number of feature vectors, their dimensionality, the complexity of the speaker models and the number of speakers. In this paper, we concentrate on optimizing vector quantization (VQ) based speaker identification. We reduce the number of test vectors by pre-quantizing the test sequence prior to matching, and the number of speakers by pruning out unlikely speakers during the identification process. The best variants are then generalized to Gaussian mixture model (GMM) based modeling. We apply the algorithms also to efficient cohort set search for score normalization in speaker verification. We obtain a speed-up factor of 16:1 in the case of VQ-based modeling with minor degradation in the identification accuracy, and 34:1 in the case of GMM-based modeling. An equal error rate of 7% can be reached in 0.84 s on average when the length of test utterance is 30.4 s.
Cu depletion at the CuInSe2 surface (2003)

The chemical composition of the (112)B surface of epitaxial CuInSe2 thin films is investigated by angle resolved x-ray photoelectron spectroscopy. Results show that a severe Cu depletion exists in the top 1–2 atomic layers. No bulk second phase is found at the surface. The source of this depletion and its relation to the Cd doping at the CdS/CuInSe2 interface are discussed.
Compatibility of dual metal gate electrodes with high-k dielectrics for CMOS (2004)

Dual metal electrodes such as Ru, Ru-Ta alloy, TaN and TaSiN were investigated on low EOT single layer HfO/sub 2/ and stacked HfO/sub 2//SiO/sub 2/ gate dielectrics. It was found that the work function values of metal gates on HfO/sub 2/ and on SiO/sub 2/ are similar. Thermal anneal studies of selected metals on the above dielectrics were also performed to evaluate the change in EOT and V/sub FB/ values.
Oestrogen receptors in benign epithelial lesions and intraduct carcinomas of the breast: an immunohistological study (1989)

We examined 198 breast lesions, representing commonly encountered benign epithelial proliferative disorders, lobular carcinoma in situ and intraduct carcinoma, immunohistologically for oestrogen receptors (ER). A mixture of three ER monoclonal antibodies--H222, D75 and D547--was used on sections of routinely processed and paraffin-embedded tissue blocks. Over 65% of the benign and malignant lesions showed some evidence of ER expression and significant staining was recorded by two observers in 28-31% of fibroadenomas, 18-28% of ductal epithelial hyperplasias, 30-40% of sclerosing adenosis cases, 38-45% of papillomas, 60% of in situ lobular carcinomas and 42-45% of intraduct carcinomas. Apocrine metaplastic cells and myoepithelial cells showed absent or only weak staining. Amongst intraduct carcinomas, less than 20% of comedo carcinomas and over 50% of cribriform, papillary and solid variants showed significant ER staining.
A compact and low loss Y-junction for submicron silicon waveguide (2013)

We designed a compact, low-loss and wavelength insensitive Y-junction for submicron silicon waveguide using finite difference time-domain (FDTD) simulation and particle swarm optimization (PSO), and fabricated the device in a 248 nm complementary metal-oxide-semiconductor (CMOS) compatible process. Measured average insertion loss is 0.28 ± 0.02 dB, uniform across an 8-inch wafer. The device footprint is less than 1.2 μm x 2 μm, an order of magnitude smaller than typical multimode interferometers (MMIs) and directional couplers.
GEOLOGIC AND HYDROCARBON EVOLUTION OF BARBADOS (1991)

Barbados island has risen above sea‐level in the last one million years as a pinnacle on the structural high of the extensive Barbados accretionary prism. The island provides by outcrop and many wells a glimpse of the structural history of the oldest and thickest realm of the prism, and a model for evolution of oil and gas in an accretionary terrane rich in quartz sanaktones and muddy temgenous and hemipelagic rocks that are moderately rich in organic substances. The island contains four major tectonostratigraphic units: basal complex of Eocene accretionary origin: prism cover: the Oceanic allochthon, of marly forearc basin strata, that was thrust over the basal complex and prism cover: and mud‐matrix mélange diapirs. Oil and gas are sourced chiefly from the basal complex at depths below 7 km, the minimum maturation depth. Oil reservoirs are in sandstones of the basal complex in fault‐fold structures. Seals are provided by mudstones of the basal complex and, more regionally, by thick, impermeable successions of prism cover and the Oceanic allochthon. Current oil reservoirs probably evolved mainly in Late Neogene time during a late stage of deformations. Oil reservoirs are best known in southern Barbados, in the Woodboume Trough, where sealing conditions were optimized. Barbados' marine territory also includes an extensive fold‐thrust belt for some 50 km west of the island. This belt includes rocks of both the Barbados accretionary prism and strata of the Tobago Trough forearc basin. The thrusting is due to the westward wedging of the prism into the forearc basin between roof and floor detachments.
Cesarean Section Is Associated with Increased Peripheral and Central Adiposity in Young Adulthood: Cohort Study (2013)

Subjects born by CS had a higher risk for increased peripheral and central adiposity during young adult age compared to those born by vaginal delivery. The association of CS with adiposity was consistently observed for all indicators and was robust after adjustment for a variety of early life confounders.
Thermal Stability of Low-Temperature GaN and AlN Buffer Layers During Metalorganic Vapor Phase Epitaxy Monitored by In Situ Shallow-Angle Reflectance Using Ultraviolet Light (1998)

The thermal stability of low-temperature (LT) GaN and AlN buffer layers during the annealing process in metalorganic vapor phase epitaxy (MOVPE) was monitored in situ by shallow-angle reflectance using p -polarized ultra-violet light (325 nm). A LT-GaN or LT-AlN buffer layer was grown on c -plane sapphire substrates at 600 and 700°C, respectively, by low pressure (76 Torr) MOVPE. These LT-buffer layers were annealed in H 2 or N 2 carrier gases and their thermal stability was examined. During annealing at 1020°C under NH 3 supply with H 2 carrier gas, the reflectivity dipped, indicating the desorption of the LT-GaN. In contrast, the reflectivity remained constant during annealing in N 2 carrier gas, indicating the LT-GaN layer was stable in N 2 . The LT-AlN buffer layer was stable even in H 2 carrier gas. These results indicate that N 2 carrier gas stabilizes the LT-GaN buffer layer during annealing over 1000°C.