gebhart/patrepeval huggingface dataset:
Arteriogenesis and angiogenesis in rat ischemic hindlimb: role of nitric oxide (2001)

Nitric oxide (NO) has been implicated in both collateral expansion (arteriogenesis) and capillary growth (angiogenesis). Exercise training increases collateral-dependent blood flow to tissues at risk of ischemia and enhances capillarity in active skeletal muscle. Exercise also acutely elevates NO. Thus we assessed the role of NO in training-induced arteriogenesis and angiogenesis. These studies utilized a rat model of peripheral vascular disease (bilateral femoral artery ligation). Untreated rats (control) and rats treated with the NO synthase inhibitor N(omega)-nitro-L-arginine methyl ester (L-NAME; 65-70 mg x kg(-1) x day(-1), via drinking water) were divided into sedentary or exercise-trained subgroups. After approximately 3 wk, L-NAME treatment had elevated preexercise mean arterial pressure approximately 39-58%, confirming NO synthesis inhibition. The training program (treadmill exercise twice per day, 20-25 m/min, 15% grade, approximately 18 days) increased collateral-dependent blood flow to the distal hindlimb, with the greatest increase (approximately 59%) in the calf (P < 0.001). This increase was inhibited by L-NAME. In contrast, the training-induced increase in muscle capillarity was not blocked by L-NAME. Thus arteriogenesis and angiogenesis appear to differ in their requirement for NO.
RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans (1998)

Introduction of exogenous double-stranded RNA (dsRNA) into Caenorhabditis elegans has been shown to specifically and potently disrupt the activity of genes containing homologous sequences. In this study we present evidence that the primary interference effects of dsRNA are post-transcriptional. First, we examined the primary DNA sequence after dsRNA-mediated interference and found no evidence for alterations. Second, we found that dsRNA-mediated interference with the upstream gene in a polar operon had no effect on the activity of the downstream gene; this finding argues against an effect on initiation or elongation of transcription. Third, we observed by in situ hybridization that dsRNA-mediated interference produced a substantial, although not complete, reduction in accumulation of nascent transcripts in the nucleus, while cytoplasmic accumulation of transcripts was virtually eliminated. These results indicate that the endogenous mRNA is the target for interference and suggest a mechanism that degrades the targeted RNA before translation can occur. This mechanism is not dependent on the SMG system, an mRNA surveillance system in C. elegans responsible for targeting and destroying aberrant messages. We suggest a model of how dsRNA might function in a catalytic mechanism to target homologous mRNAs for degradation.
Effect of prostaglandin E2 on recombinant human bone morphogenetic protein‐2‐stimulated osteoblastic differentiation in human periodontal ligament cells (1999)

Recombinant human (rh) bone morphogenetic protein-2 (BMP-2) stimulates osteoblastic differentiation in cells isolated from human periodontal ligament (HPLC), and this action of rhBMP-2 may be modulated by prostaglandins (PGs), which are local regulatory factors in the bone metabolism. In the present study, we investigated the effect of prostaglandin E2 (PGE2) on rhBMP-2-stimulated osteoblastic differentiation in cultured HPLC. rhBMP-2 (500 ng/ml)-stimulated alkaline phosphatase (ALPase) activity was enhanced by simultaneous treatment with low concentrations (10(-10)-10(-8) M) of PGE2, whereas a high concentration (10(-6) M) of PGE2 suppressed it. rhBMP-2 did not induce cyclo-oxygenase-2 (COX-2) mRNA expression or subsequent PGE2 production, whereas it remarkably suppressed rhIL-1 beta-induced COX-2 mRNA expression and PGE2 production. The rhBMP-2 action on osteoblastic differentiation in HPLC was also enhanced by co-treatment with 0.25 to 25 ng/ml of rh interleukin-1 beta (IL-1 beta). The ALPase activity stimulated by simultaneous treatment with rhBMP-2 and rhIL-1 beta was partially inhibited by addition of 10(-6) M of indomethacin, which completely inhibited rhIL-1 beta-induced PGE2 production. These results reveal that PGE2 at different concentrations exerts a biphasic effect on BMP-2-stimulated osteoblastic differentiation in HPLC, BMP-2 inhibits IL-1 beta-induced PGE2 production through suppressing COX-2 expression, and the BMP-2-stimulated osteoblastic differentiation may be enhanced by the endogenous PGE2 induced by BMP-2 and IL-1 beta. These suggest that BMP-2 action on osteoblastic differentiation in HPLC may be modulated by PGE2 in autocrine and paracrine fashions.
Low-contact-angle polydimethyl siloxane (PDMS) membranes for fabricating micro-bioarrays (2003)

In efforts to design improved biological microarrays, we use a polydimethyl siloxane (PDMS) membrane as a template that allows biological solutions of interest to interact with the surface only at discrete locations (the array sites). In current techniques, in which solutions are "spotted" on an unpatterned surface, cross-contamination and limited feature size (>50/spl mu/m) cause limitations in the information density available on the microarray. Because of these issues and the need for mechanical loading in non-DNA applications (enzymes, other proteins, cells, polysaccharides, catalysts), in which other methods are not appropriate, microarrays with superior information density on a variety of substrates are desirable. PDMS membranes provide the means for doing so. The membrane can be applied to any surface without a chemical patterning methodology. When a surface with a patterned membrane affixed to it is exposed to an aqueous solution, the biological species in the solution attach only to the specific regions of the surface defined by the holes in the membrane. However, the high hydrophobicity of PDMS membranes becomes an obstacle when loading aqueous solutions into very small openings. The fluid is rejected even though the array elements are hydrophilic. Exposure of the PDMS membrane to an oxygen plasma, a common practice, provides only a temporary reduction in contact angle. To produce a permanent change, we have used a novel RF-plasma process, in which O/sub 2/-plasma-treated PDMS surfaces are exposed to a second plasma, which generates functionalities on the PDMS surfaces that are converted in the presence of moisture into low-mobility, large, -Si(OH)/sub x/ groups. This process stabilizes the PDMS surface and produces a permanent reduction in contact angle. Tuneability in the con tact angle is possible by varying the process. We present XPS, FTIR, contact angle, and surface roughness measurements to support these conclusions. The process we describe for permanent modification of the wettability of PDMS can easily be extended to other applications of PDMS and to other polymeric substrates.
Tissue mimicking materials for ultrasound phantoms (1978)

Up until now, no material has been found whose attenuation and speed of sound properties not only mimic those of human soft tissue, but are controllable in magnitude. We have discovered such a material in the form of water-based pharmaceutical gels containing uniform distributions of graphite powder and known concentrations of alcohol. The magnitude of the attenuation coefficient can be controlled easily between 0.2 and 1.5 dB/cm at 1 MHz, by varying the concentration of graphite. These attenuation coefficients are nearly proportional to the frequency. The speed of sound varies between 1520 and 1650 m/s at room temperature, depending primarily upon the concentration of alcohol. Bacterial invasion has been prevented by sterilization procedures and the introduction of appropriate preservatives. The ultrasonic properties exhibit temporal stability and change little over the range of room temperatures.
Surface Plasmon Amplification by Stimulated Emission of Radiation: Quantum Generation of Coherent Surface Plasmons in Nanosystems (2003)

We make a step towards quantum nanoplasmonics: surface plasmon fields of a nanosystem are quantized and their stimulated emission is considered. We introduce a quantum generator for surface plasmon quanta and consider the phenomenon of surface plasmon amplification by stimulated emission of radiation (spaser). Spaser generates temporally coherent high-intensity fields of selected surface plasmon modes that can be strongly localized on the nanoscale, including dark modes that do not couple to far-zone electromagnetic fields. Applications and related phenomena are discussed.
Structure of the VHL-ElonginC-ElonginB Complex: Implications for VHL Tumor Suppressor Function (1999)

Mutation of the VHL tumor suppressor is associated with the inherited von Hippel-Lindau (VHL) cancer syndrome and the majority of kidney cancers. VHL binds the ElonginC-ElonginB complex and regulates levels of hypoxia-inducible proteins. The structure of the ternary complex at 2.7 angstrom resolution shows two interfaces, one between VHL and ElonginC and another between ElonginC and ElonginB. Tumorigenic mutations frequently occur in a 35-residue domain of VHL responsible for ElonginC binding. A mutational patch on a separate domain of VHL indicates a second macromolecular binding site. The structure extends the similarities to the SCF (Skp1-Cul1-F-box protein) complex that targets proteins for degradation, supporting the hypothesis that VHL may function in an analogous pathway.
Ophthalmology. (1999)

Philadelphia: Mosby, 1998, 1,616 pp. 1The Greater Baltimore Medical Center and The Johns Hopkins University Baltimore, Maryland
Antibody-radionuclide conjugates as part of a myeloablative preparative regimen for marrow transplantation (1989)

The behaviors of an anti-Ia antibody (7.2) and an antibody directed at a lymphocyte adhesion molecule (S.5) radiolabeled with 131I were studied in normal dogs. Antibody 7.2 localized to spleen and, to a lesser extent, to marrow and lymph nodes. Antibody S.5 rapidly localized to marrow and spleen, achieving tissue/blood ratios greater than 6:1 within three hours of injection that were maintained for at least 48 hours. Prior treatment with cyclophosphamide (CY) markedly altered the distribution of S.5 but had much less effect on the distribution of 7.2 and almost no effect on the distribution of a control antibody. When animals were treated with increasing doses of 131I labeled to S.5, lethal myelosuppression occurred when a dose of 6 mCi/kg was reached. At this dose, the otherwise lethal effects of 131I could be reversed with autologous marrow transplant support.
Time-Delayed Bottleneck Highway Networks Using a DFT Feature for Keyword Spotting (2018)

This paper presents a novel deep neural network (DNN) architecture with highway blocks (HWs) using a complex discrete Fourier transform (DFT) feature for keyword spotting. In our previous work, we showed that the feed-forward DNN with a time-delayed bottleneck layer (TDB-DNN) directly trained from the audio input outperformed the model with the log-mel filter bank energy feature (LFBE), given a large amount of training data [1]. However, the deeper structure of such an audio input DNN makes an optimization problem more difficult, which could easily fall in one of the local minimum solutions. In order to alleviate the problem, we propose a new HW network with a time-delayed bottleneck layer (TDB-HW). Our TDB-HW networks can learn a bottleneck feature representation through optimization based on the cross-entropy criterion without stage-wise training proposed in [1]. Moreover, we use the complex DFT feature as a method of pre-processing. Our experimental results on the real data show that the TDB-HW network with the complex DFT feature provides significantly lower miss rates for a range of false alarm rates over the LFBE DNN, yielding approximately 20 % relative improvement in the area under the curve (AUC) of the detection error tradeoff (DET) curves for keyword spotting. Furthermore, we investigate the effects of different pre-processing methods for the deep highway network.
A PHASE IA DOSE-ESCALATION STUDY OF THE ANTI-FACTOR D MONOCLONAL ANTIBODY FRAGMENT FCFD4514S IN PATIENTS WITH GEOGRAPHIC ATROPHY (2013)

Single-dose intravitreal FCFD4514S administrations were safe and well tolerated and not associated with any study drug-related ocular or systemic adverse events. These data support a multidose safety and tolerability assessment of FCFD4514S in geographic atrophy.
Synergistic Interactions between Transcription Factors Control Expression of the Apolipoprotein AI Gene in Liver Cells (1991)

The gene coding for apolipoprotein AI (apoAI), a plasma protein involved in the transport of cholesterol and other lipids in the plasma, is expressed predominantly in liver and intestine. Previous work in our laboratory has shown that different cis-acting elements in the 5'-flanking region of the human apoAI gene control its expression in human hepatoma (HepG2) and colon carcinoma (Caco-2) cells. Hepatocyte-specific expression is mediated by elements within the -256 to -41 DNA region relative to the apoAI gene transcription start site (+1). In this study it was found that the -222 to -110 apoAI gene region is necessary and sufficient for expression in HepG2 cells. It was also found that this DNA region functions as a powerful hepatocyte-specific transcriptional enhancer. Gel retardation and DNase I protection experiments showed that HepG2 cells contain proteins that bind to specific sites, sites A (-214 to -192), B (-169 to -146), and C (-134 to -119), within this enhancer. Site-directed mutagenesis that prevents binding of these proteins to individual or different combinations of these sites followed by functional analysis of these mutants in HepG2 cells revealed that protein binding to any one of these sites in the absence of binding to the others was not sufficient for expression. Binding to any two of these sites in any combination was sufficient for only low levels of expression. Binding to all three sites was essential for maximal expression. These results indicate that the transcriptional activity of the apoAI gene in liver cells is dependent on synergistic interactions between transcription factors bound to its enhancer.
A cautionary note on the use of the TUNEL stain to determine apoptosis (1995)

Detection of DNA fragments in situ using the terminal deoxyribonucleotidyl transferse (TdT)-mediated biotin-16-dUTP nick-end labelling (TUNEL assay) is now commonly used to investigate apoptosis. Previous reports suggested that physiologically appropriate death is due to apoptosis and that pathological mechanisms involve necrosis. Strong evidence of apoptosis, following ischaemia and epilepsy, has been recently provided by combining genomic DNA gel electrophoresis, light and electron microscopy and in situ, DNA-break labelling. However, only an observation in light microscopy with high magnification permits the detection of chromatin condensation and apoptotic bodies. We report that a positive TUNEL assay reaction should not be considered as a specific marker of apoptosis but can also indicate necrotic cell death.
Phase II Enzymes Induction Blocks the Enhanced IgE Production in B Cells by Diesel Exhaust Particles (2006)

Oxidant pollutants such as diesel exhaust particles (DEPs) can initiate and exacerbate airway allergic responses through enhanced IgE production. These effects are especially pronounced in individuals in whom phase II antioxidant enzyme responses are impaired. We confirmed that DEPs and DEP extracts (DEPX) can act directly on B lymphocytes and showed that DEPX could enhance IgH epsilon germline transcription in a B cell line and in PBMCs. We therefore studied the regulation in B cells of NAD(P)H: quinone oxidoreductase (NQO1) as a typical model phase II enzyme and its role in modulating DEPX-enhanced IgE responses. DEPX increased NQO1 mRNA expression in a dose-dependent manner. NQO1 protein induction by DEPX was confirmed by Western blot. DEPs induced activity of the antioxidant response element located in the NQO1 gene promoter. Induction of both NQO1 mRNA and protein expression could be blocked by coculture with an antioxidant and partly repressed by inhibitors of PI3K and p38 MAPK, but not by inhibitors of MAPK/ERK kinase (MEK/ERK) or protein kinase C. The ability of DEPX to enhance IgE production was blocked by the induction of phase II enzymes, including NQO1 in B cells by the chemical sulforaphane. These findings suggest that a natural protective mechanism in B cells from oxidant pollutants such as diesel particles is the expression of phase II enzymes through induction of antioxidant response elements and support the approach of overexpression of these enzymes as a potential future chemopreventative strategy.
Analysis of terpenes and turpentines using gas chromatography with vacuum ultraviolet detection (2016)

The separation and identification of natural mixtures of terpenes is challenging and laborious. A gas chromatographic method based on vacuum ultraviolet spectroscopic detection, which is characterized by full-scan absorption in the range of 125-240 nm, was developed and applied to analyze terpenes. In this study, the vacuum ultraviolet absorption spectra of 41 different standard terpenes were investigated and compared. The spectra were found to be highly featured and easily differentiated. Several commercial turpentine samples were analyzed and the vacuum ultraviolet detector demonstrated good specificity for qualitative identification of constituent terpenes. A total of 31 terpenes were detected in the four turpentine samples. α-Pinene was the predominant terpene ranging from 744.2 ± 9.7 to 917 ± 21 mg/mL. The other major constituents in the turpentines included β-pinene, δ-3-carene, camphene, and p-isopropyltoluene. Deconvolution of co-eluting signals of terpenes was achieved utilizing the data analysis software. The technique has been demonstrated to be a powerful tool for reliable and accurate qualitative and quantitative analysis of terpenes from complex natural mixtures.
Chemokines in ischemia and reperfusion (2007)

Chemokine signaling plays an important role in the postischemic inflammatory response. Overlapping pathways involving reactive oxygen intermediates, Toll-like receptor (TLR) activation, the complement cascade and the nuclear factor (NF)-kappaB system induce both CXC and CC chemokines in ischemic tissues. Reperfusion accentuates chemokine expression promoting an intense inflammatory reaction. ELR-containing CXC chemokines regulate neutrophil infiltration in the ischemic area, whereas CXCR3 ligands may mediate recruitment of Th1 cells. CC chemokines, on the other hand, induce mononuclear cell infiltration and macrophage activation. Evidence suggests that chemokine signaling mediates actions beyond leukocyte chemotaxis and activation, regulating angiogenesis and fibrous tissue deposition. Effective repair of ischemic tissue is dependent on a well-orchestrated cellular response and on timely induction and suppression of chemokines in a locally restricted manner. This manuscript reviews the evidence suggesting a role for chemokine-mediated effects in ischemia/reperfusion and discusses the potential significance of these interactions in injury and repair of ischemic tissues.
Wavelet Analysis of Vibration: Part 1—Theory (1994)

Wavelets provide a new tool for the analysis of vibration records. They allow the changing spectral composition of a nonstationary signal to be measured and presented in the form of a time-frequency map. The purpose of this paper, which is Part 1 of a pair, is to introduce and review the theory of orthogonal wavelets and their application to signal analysis. It includes the theory of dilation wavelets, which have been developed over a period of about ten years, and of harmonic wavelets which have been proposed recently by the author. Part II is about presenting the results on wavelet maps and gives a selection of examples. The papers will interest those who work in the field of vibration measurement and analysis and who are in positions where it is necessary to understand and interpret vibration data.
ON NONLINEAR GALERKIN APPROXIMATION (1997)

Nonlinear Galerkin methods are numerical schemes adapted well to the long time integration of evolution partial differential equations. The aim of this paper is to discuss such schemes for reaction diffusion equations. The convergence results are proved.
Dimerization of Receptor Protein-Tyrosine Phosphatase alpha in living cells (2001)

We demonstrate here that RPTPalpha dimerized constitutively in living cells, which may be mediated by the transmembrane domain, providing strong support for the model that dimerization is involved in regulation of RPTPs.
Inflammation: imaging with methoxy poly(ethylene glycol)-poly-L-lysine-DTPA, a long-circulating graft copolymer. (1995)

Nontargeted, long-circulating, copolymers can efficiently accumulate in sites of inflammation and thus represent an alternative to inflammation-specific agents.
Islet filtration: a simple and rapid new purification procedure that avoids ficoll and improves islet mass and function. (2002)

Islet isolation is a time-consuming process. Islet yields vary, and previous in vitro studies suggest that Ficoll may be an islet toxin. Here, we describe an alternative, Ficoll-free method to purify murine islets by filtration through a cell strainer. Collagenase digestion of pancreata was carried out using standard procedures. The pancreatic digest was divided into aliquots and purified either by Ficoll or by filtration. Following filtration, islets were intact and separated from nondigested tissue. Purity was similar to that achieved using Ficoll. However, purification by filtration was faster, increased islet yield, and resulted in higher insulin secretion in vitro. Moreover, when syngeneic diabetic hosts were transplanted with a marginal islet mass, islets purified by filtration restored normoglycemia significantly faster than those isolated by Ficoll. This suggests that Ficoll exposure negatively impacts islet function. In conclusion, islet filtration is a simple and rapid procedure for purification of islets that demonstrate improved functional mass.
Identifying Superficial, Muscle-Invasive, and Metastasizing Transitional Cell Carcinoma of the Bladder (2004)

Gene expression profiling of human bladder cancers provides insight into the biology of bladder cancer progression and identifies patients with distinct clinical phenotypes.
X-ray photoelectron spectroscopy of clean and gas-doped films of phthalocyanines (1991)

Films of a range of phthalocyanines which had been deposited by vacuum sublimation were analysed using X-ray photoelectron spectroscopy (XPS). Spectra of the major peaks were recorded before exposure to NOX (NO2+N2O4), after exposure to 9 vpm NOX in air, after exposure to undiluted NOX and finally after heating the exposed film to 150 degrees C. The phthalocyanines studied were: metal-free (H2Pc), magnesium (MgPc), vanadyl (VOPc), manganese (MnPc), iron (FePc), cobalt (CoPc), nickel (NiPc) and copper (CuPc). The presence of NOX (which would have given rise to new N 1s and O 1s peaks in the XPS spectra) was not detected in any of the films following the exposure to 9 vpm, although slight shifts in the positions of some peaks were observed. All XPS spectra exhibited changes following the exposure of the films to undiluted NOX. H2Pc clearly suffered severe chemical attack. The effect on the metal phthalocyanines was not so severe, but was different for each metal complex. None of the spectra was restored to the pre-NOX form by heating to 150 degrees C after exposure to the undiluted NOX. In order to explain the changes in the C 1s XPS spectra which were observed during these experiments, it was found necessary to modify a previous interpretation of the C 1s spectrum.