gebhart/patrepeval huggingface dataset:
Towards On-chip Mid Infrared Photonic Aerosol Spectroscopy (2018)

© 2018 Author(s). We propose an on-chip mid-infrared (MIR) photonic spectroscopy platform for aerosol characterization to obtain highly discriminatory information on the chemistry of aerosol particles. Sensing of aerosols is crucial for various environmental, climatic, warfare threat detection, and pulmonary healthcare applications. Currently, chemical characterization of aerosols is performed using FTIR spectroscopy, yielding chemical fingerprinting because most of the vibrational and rotational transitions of chemical molecules fall in the IR range, and Raman spectroscopy. Both techniques use free space bench-top geometries. Here, we propose miniaturized on-chip MIR photonics-based aerosol spectroscopy consisting of a broadband spiral-waveguide sensor that significantly enhances the particle-light interaction to improve sensitivity. The spiral waveguides are made of a chalcogenide glass material (Ge23Sb7S70) which shows a broad transparency over the IR range (1-10 μm). We demonstrate the sensing of N-methyl aniline-based aerosol particles with the device. We anticipate that the sensor will readily complement existing photonic resonator-based particle sizing and counting techniques to develop a unified framework for on-chip integrated photonic aerosol spectroscopy.
Expression of bile acid synthesis and detoxification enzymes and the alternative bile acid efflux pump MRP4 in patients with primary biliary cirrhosis (2007)

Repression of bile acid synthesis and induction of basolateral bile acid export may represent adaptive mechanisms to limit bile acid burden in chronic cholestasis. As these changes do not sufficiently counteract cholestatic liver damage, future therapeutic strategies should aim at stimulation of bile acid detoxification pathways.
Expression of the Wilms' tumor gene (WT1) in human leukemias. (1992)

Leukemic cells from seventy patients with various types of human leukemias were examined for expression of the WT1 gene, the Wilms' tumor gene located at chromosome 11p13. WT1 was expressed in 7 of 16 cases of acute lymphoblastic leukemia, 15 of 22 with acute myelogenous leukemia and 8 of 10 in blast crisis of chronic myelogenous leukemia. No detectable WT1 RNA was found in chronic leukemias, including chronic lymphocytic leukemia, plasma cell leukemia, hairy cell leukemia and chronic myelogenous leukemia in chronic phase. The expression pattern of WT1 in these human leukemia samples indicates the involvement of this gene in the early stage of hematological cell differentiation.
Distributional part-of-speech tagging (1995)

This paper presents an algorithm for tagging words whose part-of-speech properties are unknown. Unlike previous work, the algorithm categorizes word tokens in context instead of word types. The algorithm is evaluated on the Brown Corpus.
Synthetic peptides: a modern approach to vaccination. (1998)

For induction of humoral or cell-mediated immunity, development of synthetic peptide vaccines present a novel approach and a better alternative to conventional vaccines. Construction of synthetic peptides that mimic antigenic sites is the basis of this approach. In this article various methodologies involved in the peptide synthesis are discussed. This is followed by a discussion on the strategies involved in rendering poor or non-immunogenic peptides immunogenic. These include coupling to large carrier proteins, polymeric presentation and incorporation of an identified Th cell epitope into the peptide.
A Screening Method for Antigen-Specific IgE Using Mast Cells Based on Intracellular Calcium Signaling (2000)

A simple screening method is presented for the measurement of antigen-specific IgEs in sera in which mast cells are used. This method is based on the intracellular calcium signal in mast cells induced by cross-linking the surface high-affinity Fc receptors (FcepsilonRIs) with IgEs and multivalent antigens. When a serum containing various antigen-specific IgEs is added to the mast cell suspension, various antigen-specific IgEs are captured by FcepsilonRIs on the cell surface. However, the required antigen-specific IgE can be specifically detected after the addition of the corresponding antigen. The resulting increase in intracellular calcium concentration ([Ca2+]i), monitored by Ca2+-fluorometry, was found to be an analytical measure for the screening of IgEs. Two kinds of rodent mast cells, cell-lined RBL2H3 cells and primary cultured BMMCs, were used as a representative model system of mast cells. A DNP hapten (DNP35-HSA) and ovalbumin (OVA) were chosen for illustrative antigens, and these antigen-specific IgEs (DNP-specific IgE, OVA-specific IgE) in the corresponding rodent sera were target antibodies. It was found that [Ca2+]i increased linearly with IgE concentrations ranging from 25 to 5000 ng/mL for DNP-specific IgE and from 5 to 50 ng/mL for OVA-specific IgE. For these dynamic ranges, optimum concentrations of antigens were found to be 10 ng/mL and 1 microg/mL for DNP35-HSA and OVA, respectively. It was concluded that by monitoring the increase of [Ca2+]i in mast cells, we could determine the antigen-specific IgEs. The present immunological assay based on the Ca2+ signal transduction in mast cells offers new possibilities for efficient screening of antigen-specific IgEs and the immunogenicity of IgE in sera.
Crystal structure of enoyl–acyl carrier protein reductase (FabK) from Streptococcus pneumoniae reveals the binding mode of an inhibitor (2008)

Enoyl-acyl carrier protein (ACP) reductases are critical for bacterial type II fatty acid biosynthesis and thus are attractive targets for developing novel antibiotics. We determined the crystal structure of enoyl-ACP reductase (FabK) from Streptococcus pneumoniae at 1.7 A resolution. There was one dimer per asymmetric unit. Each subunit formed a triose phosphate isomerase (TIM) barrel structure, and flavin mononucleotide (FMN) was bound as a cofactor in the active site. The overall structure was similar to the enoyl-ACP reductase (ER) of fungal fatty acid synthase and to 2-nitropropane dioxygenase (2-ND) from Pseudomonas aeruginosa, although there were some differences among these structures. We determined the crystal structure of FabK in complex with a phenylimidazole derivative inhibitor to envision the binding site interactions. The crystal structure reveals that the inhibitor binds to a hydrophobic pocket in the active site of FabK, and this is accompanied by induced-fit movements of two loop regions. The thiazole ring and part of the ureido moiety of the inhibitor are involved in a face-to-face pi-pi stacking interaction with the isoalloxazine ring of FMN. The side-chain conformation of the proposed catalytic residue, His144, changes upon complex formation. Lineweaver-Burk plots indicate that the inhibitor binds competitively with respect to NADH, and uncompetitively with respect to crotonoyl coenzyme A. We propose that the primary basis of the inhibitory activity is competition with NADH for binding to FabK, which is the first step of the two-step ping-pong catalytic mechanism.
Genetic polymorphisms of the interleukin-4 receptor alpha gene are associated with an increasing risk and a poor prognosis of sporadic renal cell carcinoma in a Japanese population. (2002)

The present findings show that the preferential Th2-type response to tumors was associated with a poorer prognosis and suggest that polymorphisms of the IL-4Ralpha gene may serve as useful genetic markers for assessing the risk of the development and progression of RCC.
Selective Growth of Crystalline SnO2 on the Polar Surface of ZnO Nanobelts (2006)

A novel nanostructure of a side-to-side SnO2/ZnO/SnO2 triaxial nanobelt has been achieved via a simple oxidation of the separated Zn and Sn powders. Each nanobelt has a broad inner ribbon of ZnO with two symmetric SnO2 sides, and all of the belts are single crystal. This composite structure demonstrates the possibility of selective growth based on the polar surface and also suggests that heterogeneous growth can proceed on both polar surfaces of ZnO ±(0001). The corresponding room-temperature photoluminescence has also been tailored and been discussed in this paper. Our approach presented here would be helpful in designing and preparing many other heterostructures to meet the growing demands of nanoscale science and technology.
Studies of Synthetic Peptides of Human Apolipoprotein A-I Containing Tandem Amphipathic α-Helixes (1998)

In mature human apolipoprotein A-I (apo A-I), the amino acid residues 1-43 are encoded by exon 3, whereas residues 44-243 are encoded by exon 4 of the apo A-I gene. The region encoded by exon 4 of the apo A-I gene contains 10 tandem amphipathic alpha-helixes; their location and the class to which they belong are as follows: helix 1 (44-65, class A1), helix 2 (66-87, class A1), helix 3 (88-98, class Y), helix 4 (99-120, class Y), helix 5 (121-142, class A1), helix 6 (143-164, class A1), helix 7 (165-186, class A1), helix 8 (187-208, class A1), helix 9 (209-219, class Y), and helix 10 (220-241, class Y). To examine the effects of multiple tandem amphipathic helixes compared to individual helixes of apo A-I on lipid association, we have studied lipid-associating properties of the following peptides: Ac-44-87-NH2 (peptide 1-2), Ac-66-98-NH2 (peptide 2-3), Ac-66-120-NH2 (peptide 2-3-4), Ac-88-120-NH2 (peptide 3-4), Ac-99-142-NH2 (peptide 4-5), Ac-121-164-NH2 (peptide 5-6), Ac-143-186-NH2 (peptide 6-7), Ac-165-208-NH2 (peptide 7-8), Ac-187-219-NH2 (peptide 8-9), and Ac-209-241-NH2 (peptide 9-10). To study lipid-associating properties of the region encoded by exon 3 of the apo A-I gene, 1-33-NH2 (peptide G) has also been studied. The results of the present study indicate that, among the peptides studied, peptides 1-2 and 9-10 possess significantly higher lipid affinity than the other peptides, with peptide 9-10 having higher lipid affinity than peptide 1-2, as evidenced by (i) higher helical content in the presence of 1, 2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), (ii) faster rate of association with DMPC multilamellar vesicles (MLV), (iii) greater reduction in the enthalpy of gel to liquid-crystalline phase transition of DMPC MLV, (iv) higher exclusion pressure from an egg yolk phosphatidylcholine monolayer, and (v) higher partitioning into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine MLV. A comparison of the free energies of lipid association (DeltaG) of the peptides studied here with those studied previously by us [Palgunachari, M. N. , et al. (1996) Arterioscler. Thromb. Vasc. Biol. 16, 328-338] indicates that, except for the peptides 4-5 and 5-6, other peptides possess higher lipid affinities compared to constituent helixes. However, the lipid affinities of the peptides studied here are neither higher than nor equal to the sum of the lipid affinities of the constituent helixes. This indicates the absence of cooperativity among the adjacent amphipathic helical domains of apo A-I for lipid association. As indicated by DeltaG, the lipid affinity of peptide 4-5 is higher than peptide 5 but lower than peptide 4; the lipid affinity of peptide 5-6 is lower than both peptides 5 and 6. Implications of these results for the structure and function of apo A-I are discussed.
Suppression of retroviral MA deletions by the amino-terminal membrane-binding domain of p60src (1991)

The molecular mechanism by which retroviral Gag proteins are directed to the plasma membrane for the formation of particles (budding) is unknown, but it is widely believed that the MA domain, located at the amino terminus, plays a critical role. Consistent with this idea, we found that small deletions in this segment of the Rous sarcoma virus Gag protein completely blocked particle formation. The mutant proteins appear to have suffered only localized structural damage since they could be rescued (i.e., packaged into particles) when coexpressed with Gag proteins that are competent for particle formation. To our surprise, the effects of the MA deletions could be completely suppressed by fusing as few as seven residues of the myristylated amino terminus of the oncoprotein p60src to the beginning of the mutant Gag proteins. Particles produced by the chimeras were of the same density as the wild type. Two myristylated peptides having sequences distinct from that of p60src were entirely unable to suppress MA deletions, indicating that myristate alone is not a sufficient membrane targeting signal. We hypothesize that the amino terminus of p60src suppresses the effects of MA deletions by diverting the Rous sarcoma virus Gag protein from its normal site of assembly to the Src receptor for particle formation.
Antiproliferative effect of fermented milk on the growth of a human breast cancer cell line (1997)

In vivo and in vitro studies have shown an antitumor activity of Lactobacilli in colon cancer, and some epidemiologic studies have indicated a reduced risk of breast cancer in women who consume fermented milk products. We studied the direct effect of milk fermented by five bacteria strains (Bifidobacterium infantis, Bifidobacterium bifidum, Bifidobacterium animalis, Lactobacillus acidophilus, and Lactobacillus paracasei) on the growth of the MCF7 breast cancer cell line. Our results showed a growth inhibition induced by all fermented milks, even though B. infantis and L. acidophilus were the most effective (85% inhibition after 9 days). The antiproliferative effect was not related to the presence of bacteria in fermented milk, and neither whole milk (crude or ultrahigh temperature sterlizied) nor its main fractions (lactalbumin or beta-lactoglobulin fraction) affected cell growth. Our findings suggest the presence of an ex novo soluble compound produced by lactic acid bacteria during milk fermentation or the microbial transformation of some milk components in a biologically active form. Although the mechanism of the antitumor activity is not clear, the present study suggests the potentiality offered by fermented milk as producers of compounds with antiproliferative activity useful in the prevention and therapy of solid tumors like breast cancer.
The Girls' Story: Adolescent Novels Set in the Middle Ages (2001)

Scholarly Communication is located on the fourth floor of Carol M. Newman Library at Virginia Tech. Scholarly Communication is a dynamic landscape, and we are continually evolving. Many scholarly communications activities have spun-off into their own departments, such as VT Publishing and Digital Imaging and Preservation Services, and Digital Library Development. Our focus is on supporting the creation and dissemination of scholarship.
8-bromo-cyclicAMP stimulates glucose transporter-1 expression in a human choriocarcinoma cell line (2000)

Facilitative glucose transporter-1 (GLUT1) is abundant in trophoblast cells and is responsible for glucose transport in the placenta. However, the change in GLUT expression in human placenta upon trophoblast differentiation remains to be clarified. Therefore, we first examined the localization of GLUT1 and GLUT3 using human first-trimester chorionic villi. We found that GLUT1 and GLUT3 were mainly localized to syncytiotrophoblast and cytotrophoblast cells respectively. We analyzed whether placental GLUT1 and GLUT3 expression changes during differentiation using a human choriocarcinoma (BeWo) cell line which is known to show functional and morphological differentiation in response to cAMP in culture. Treatment of BeWo cells with 8-bromo-cyclicAMP (8-bromo-cAMP) increased the level of hCG secretion and induced cell fusion leading to the formation of large syncytia. Treatment of BeWo cells with 8-bromo-cAMP also resulted in a significant increase in glucose uptake on days 2-3 of culture. The stimulating effect of 8-bromo-cAMP on glucose uptake was concentration dependent. Northern and immunoblot analyses revealed that the levels of mRNA and protein of GLUT1, but not of GLUT3, were significantly increased by 8-bromo-cAMP. These findings suggest that 8-bromo-cAMP stimulates GLUT1 expression with differentiation in BeWo cells.
Inhibition of Tumor Necrosis Factor-induced Cell Death in MCF7 by a Novel Inhibitor of Neutral Sphingomyelinase (2002)

A high throughput screen for neutral, magnesium-dependent sphingomyelinase (SMase) was performed. One inhibitor discovered in the screen, GW4869, functioned as a noncompetitive inhibitor of the enzyme in vitro with an IC(50) of 1 microm. It did not inhibit acid SMase at up to at least 150 microm. The compound was then evaluated for its ability to inhibit tumor necrosis factor (TNF)-induced activation of neutral SMase (N-SMase) in MCF7 cells. GW4869 (10 microm) partially inhibited TNF-induced sphingomyelin (SM) hydrolysis, and 20 microm of the compound was protected completely from the loss of SM. The addition of 10-20 microm GW4869 completely inhibited the initial accumulation of ceramide, whereas this effect was partially lost at later time points (24 h). These data therefore support the inhibitory action of GW4869 on N-SMase not only in vitro but also in a cellular model. The addition of GW4869 at both 10 and 20 microm did not modify cellular glutathione levels in response to TNF, suggesting that the action of GW4869 occurred downstream of the drop in glutathione, which was shown previously to occur upstream of the activation of N-SMase. Further, whereas TNF treatment also caused a 75% increase of de novo synthesized ceramide after 20 h of incubation, GW4869, at either 10 or 20 microm, had no effect on this pathway of ceramide generation. In addition, GW4869 did not significantly impair TNF-induced NF-kappaB translocation to nuclei. Therefore, GW4869 does not interfere with other key TNF-mediated signaling effects. GW4869 was able, in a dose-dependent manner, to significantly protect from cell death as measured by nuclear condensation, caspase activation, PARP degradation, and trypan blue uptake. These protective effects were accompanied by significant inhibition of cytochrome c release from mitochondria and caspase 9 activation, therefore localizing N-SMase activation upstream of mitochondrial dysfunction. In conclusion, our results indicate that N-SMase activation is a necessary step for the full development of the cytotoxic program induced by TNF.
Report of the First International Workshop on Equine Leucocyte Antigens, Cambridge, UK, July 1991 (1994)

The First International Workshop on Equine Leucocyte Antigens was organized and convened for the purposes of identifying immunologically relevant cell surface molecules of equine leucocytes and establishing a system of nomenclature for those molecules. Participating members of the workshop represented the majority of laboratories world-wide engaged in the tasks of production and characterization of equine leucocyte and lymphocyte markers using monoclonal antibodies. The workshop confirmed the identification of several equine CD molecules described previously by individual laboratories, and in addition recognized antibodies identifying new CD molecules. The workshop also succeeded in fostering co-operation between laboratories around the world which study equine immunobiology. Equine CD molecules identified by the current battery of monoclonal antibodies include EqCD2, EqCD4, EqCD5, EqCD8, EqCD11a/18, EqCD13 and EqCD44. Other antibodies are markers for MHC class I and class II molecules, for B cells, granulocytes, macrophages, T cell subsets distinct from those defined by CD4 and CD8, and other sub-populations of horse leucocytes that do not have obvious counterparts in humans, rodents, or other species. Despite the progress made in the first workshop, there are still substantial gaps in the armory of reagents available to study equine leucocyte biology, and further definition of the structure, function, and genetics of the antigens identified by the workshop clusters (WC1, WC2 etc.) and other molecules of immunological importance will be a goal of future workshops. The study of equine immunobiology and resistance to disease also urgently requires the development of tools to study equine immunoglobulins and cytokines, and these needs will provide ample scope for future studies.
Identification of the chloride-binding site in the human red and green color vision pigments (1993)

Chloride ions are known to bind and alter the absorption spectra of some but not all visual pigments. In this report, the human red and green color vision pigments are shown to bind Cl- and to undergo a large red shift in their absorption maxima. Mutation of 18 different positively charged amino acids in these pigments identified two residues, His197 and Lys200, in the Cl(-)-binding site. His197 and Lys200 are strictly conserved in all long-wavelength cone pigments but are absent in all rhodopsins and short-wavelength cone pigments. This fact suggests that the evolutionary branch of the long-wavelength pigments was established when an ancestral pigment acquired the ability to bind Cl- and, as a result, shift the absorption maximum to longer wavelengths.
Negative Pressure Wound Therapy (1998)

Negative Pressure Wound Therapy, also known as Vacuum Assisted Closure (V.A.C.), is a new treatment in which controlled negative pressure is used to provide evacuation of wound fluid, stimulation of granulation tissue, and a decrease in bacterial colonization. A brief discussion of the physiology of wound healing is accompanied by an explanation of vacuum assisted wound closure. Indications and contraindications for V.A.C. are discussed. The authors present several case studies of patients with nonhealing wounds who benefitted from V.A.C.
Cloning and sequence analysis of the human major histocompatibility complex gene DC-3 beta. (1984)

The DC antigen is one of the class II major histocompatibility antigens involved in the regulation of the immune response. This molecule is a heterodimer composed of an alpha and a beta chain. Southern blot analysis of several homozygous cell lines shows that there are two DC beta genes. The DC-3 beta gene, corresponding to a polymorphic restriction fragment, was cloned and sequenced and found to exist in five exons spanning 8 kilobase pairs of DNA. These exons correspond to the functional domains of the DC beta protein. Comparison of the beta 1 domains of known DC beta chains shows that the polymorphism is clustered in four regions. A similar comparison of the mouse A beta sequences shows only two prominent diversity regions. The DC beta chain sequences are eight amino acids shorter than the A beta chain sequences due to the elimination of a small exon by an aberrant splice acceptor.
Chemical, Microbiological and Sensory Properties of Plain Nonfat Yogurt (1993)

ABSTRACT Chemical and microbiological properties of plain nonfat yogurt were determined after 2, 6 and 12 days refrigerated storage. Sensory properties were determined after 6 days storage. Viable culture bacteria concentrations ranged from 140 to 8,000 × 10 6 /g and ratios of lactobacillus to streptococcus ranged from 0.18 to 15.4. Chemical criteria used to characterize products included: pH, titratable acidity, lactic and four other organic acids and lactose by HPLC, and 23 major volatile organic compounds by dynamic headspace analysis. Lactic acid concentrations ranged from 7.5 to 9.9 mg/g. Major flavor volatiles in all yogurts included: acetaldehyde, heptane, acetone, diacetyl, and benzothiazole. Untrained sensory panels showed differences for flavor, aroma and acceptability.
In-memory databases: an industry perspective (2003)

Main memory databases store all or part of the data in memory and subsequently reduce or eliminate disk access. This paper presents an architectural study of memory databases with respect to cost/performance trade-offs and applicability issues. Potential performance advantages depend primarily on whether the system is used as an online transaction processing or a decision support system. A major constraint to the storing of data in main memory is the vulnerability of its content to software errors. This fact may force a two level architecture even if main memories cost is considerably reduced.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>