gebhart/patrepeval huggingface dataset:
CD4+ T cells induced by virus-like particles expressing a major T cell epitope down-regulate IL-5 production in an ongoing immune response to Der p 1 independently of IFN-γ production (1999)

It has been previously demonstrated that hybrid Ty virus-like particles (VLP) prime effective CD8(+) and CD4(+) T cell responses. In this study, we investigated the effect of treating mice with Ty VLP carrying the immunodominant epitope of Der p 1 after sensitizing them to the group 1 allergen of the house dust mite Dermatophagoides pteronyssinus (Der p 1), under conditions that induce T(h)2 immunity. We show that i.p. treatment with the hybrid VLP abrogated allergen-specific IL-5 production and reduced allergen-specific cell proliferation. This suppression of the response was mediated by CD4(+) T cells and was not accompanied by an increase in IFN-gamma production.
Transmission of Middle East Respiratory Syndrome Coronavirus Infections in Healthcare Settings, Abu Dhabi (2016)

Middle East respiratory syndrome coronavirus (MERS-CoV) infections sharply increased in the Arabian Peninsula during spring 2014. In Abu Dhabi, United Arab Emirates, these infections occurred primarily among healthcare workers and patients. To identify and describe epidemiologic and clinical characteristics of persons with healthcare-associated infection, we reviewed laboratory-confirmed MERS-CoV cases reported to the Health Authority of Abu Dhabi during January 1, 2013-May 9, 2014. Of 65 case-patients identified with MERS-CoV infection, 27 (42%) had healthcare-associated cases. Epidemiologic and genetic sequencing findings suggest that 3 healthcare clusters of MERS-CoV infection occurred, including 1 that resulted in 20 infected persons in 1 hospital. MERS-CoV in healthcare settings spread predominantly before MERS-CoV infection was diagnosed, underscoring the importance of increasing awareness and infection control measures at first points of entry to healthcare facilities.
Optimization of a Tertiary Alcohol Series of Phosphodiesterase-4 (PDE4) Inhibitors:  Structure−Activity Relationship Related to PDE4 Inhibition and Human Ether-a-go-go Related Gene Potassium Channel Binding Affinity (2003)

A SAR study on the tertiary alcohol series of phosphodiesterase-4 (PDE4) inhibitors related to 1 is described. In addition to inhibitory potency against PDE4 and the lipopolysaccharide-induced production of TNFalpha in human whole blood, the binding affinity of these compounds for the human ether-a-go-go related gene (hERG) potassium channel (an in vitro measure for the potential to cause QTc prolongation) was assessed. Four key structural moieties in the molecule were studied, and the impact of the resulting modifications in modulating these activities was evaluated. From these studies, (+)-3d (L-869,298) was identified as an optimized structure with respect to PDE4 inhibitory potency, lack of binding affinity to the hERG potassium channel, and pharmacokinetic behavior. (+)-3d exhibited good in vivo efficacy in several models of pulmonary function with a wide therapeutic index with respect to emesis and prolongation of the QTc interval.
Paris Improves Its Drinking Water Treatment Plants (1992)

ABSTRACT The upgrading of the Ivry‐sur‐Seine water‐treatment plant, which produces potable water for consumption in Paris, is described. This upgrading is based on the slow biological filtration stage. The pretreatment comprises a primary filtration stage through biolite, and a secondary filtration stage through sand, with the possibility of coagulation. The polishing treatment includes ozonation and biological filtration through granular activated carbon. Ozone is produced from pure oxygen, with two ozone generators operating at medium frequency and producing a total of 52 kg/h. A description of pilot tests of the upgraded plant is given, together with the first results.
Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. (1995)

Fluorescent dye-labeled DNA primers have been developed that exploit fluorescence energy transfer (ET) to optimize the absorption and emission properties of the label. These primers carry a fluorescein derivative at the 5' end as a common donor and other fluorescein and rhodamine derivatives attached to a modified thymidine residue within the primer sequence as acceptors. Adjustment of the donor-acceptor spacing through the placement of the modified thymidine in the primer sequence allowed generation of four primers, all having strong absorption at a common excitation wavelength (488 nm) and fluorescence emission maxima of 525, 555, 580, and 605 nm. The ET efficiency of these primers ranges from 65% to 97%, and they exhibit similar electrophoretic mobilities by gel electrophoresis. With argon-ion laser excitation, the fluorescence of the ET primers and of the DNA sequencing fragments generated with ET primers is 2- to 6-fold greater than that of the corresponding primers or fragments labeled with single dyes. The higher fluorescence intensity of the ET primers allows DNA sequencing with one-fourth of the DNA template typically required when using T7 DNA polymerase. With single-stranded M13mp18 DNA as the template, a typical sequencing reaction with ET primers on a commercial sequencer provided DNA sequences with 99.8% accuracy in the first 500 bases. ET primers should be generally useful in the development of other multiplex DNA sequencing and analysis methods.
Antisense Oligonucleotides Demonstrate a Dominant Role of c-Ki-RAS Proteins in Regulating the Proliferation of Diploid Human Fibroblasts (1996)

Although members of the RAS protein family (Ha-, Ki-, and N-RAS) are known to play a key role in normal cell proliferation and to be frequently mutated in naturally occurring tumors, it remains unclear which of these proteins functions to regulate growth in normal cells. Gene-specific oligonucleotides (oligos) against c-Ki-RAS (ISIS 6957), c-Ha-RAS (ISIS 2503), and oncogenic Ha-RAS (ISIS 2570) were used to analyze the requirement for individual RAS proteins in the proliferation of diploid human lung fibroblasts (MRC-5), and human bladder carcinoma cell lines with (T24) or without (J-82) a RAS mutation. The oncogenic Ha-RAS oligo substantially inhibited T24 cell proliferation, whereas the c-Ki-RAS and control (ISIS 1966) oligos had little effect. Interestingly, in MRC-5 cells the c-Ki-RAS but not c-Ha-RAS oligo was effective in inhibiting cell proliferation. No inhibition was seen in the J-82 cells with either oligo. In Western analysis, p21 RAS protein was decreased following treatment with the oncogenic Ha-RAS oligo in T24 cells or the c-Ki-RAS oligo in MRC-5 cells, whereas no reductions were observed in J-82 cells with either oligo. The specificity of these oligos was demonstrated in Northern analyses in which both Ha-RAS and Ki-RAS oligo treatment resulted in reduced levels of their respective mRNAs in all three cell lines, whereas the mutant Ha-RAS mRNA in T24 cells was most effectively reduced with the oncogenic Ha-RAS oligo. These results demonstrate that oncogenic Ha-RAS plays an important role in the proliferation of T24 cells, whereas c-Ki-RAS contributes predominantly to the proliferation of normal MRC-5 cells.
The Syk family of protein tyrosine kinases in T‐cell activation and development (1998)

The processes of T-cell development and activation employ similar immature and mature receptors as well as similar signal transduction pathways to achieve different outcomes. Many signaling molecules are shared between the receptor signaling pathways, including two families of cytoplasmic protein tyrosine kinases, the Src family and the Syk family. The two Syk family members expressed in T cells, Syk and ZAP-70, are structurally similar but are expressed at different times during thymic development and during T-cell activation. These two kinases, although they share many physical features, differ in terms of biochemical activity and regulation. We discuss the overlapping and distinct characteristics of Syk and ZAP-70 in T-cell signaling and the potential biological importance of their differences.
The Disposition and Metabolism of 3',4',7-Tri-O-(β-hydroxyethyl) rutoside and 7-Mono-O-(β-hydroxyethyl)rutoside in the Mouse (1977)

1. Following intravenous administration of 3',4',7-tri-O-(β-hydroxy[14C2]ethyl)rutoside or 7-mono-O-(β-hydroxy[14C2]ethyl)rutoside to male mice, 68% of the dose of each is excreted in faeces as the corresponding hydroxyethyl-quercetin within 72 h of dosage. Mean urinary excretions of mono- and tri-hydroxyethylrutosides in 72 h were 27 and 21% respectively. Unchanged rutosides and their glucuronides were detected in urine.2. In biliary-cannulated animals, the mean biliary excretion of both tri- and mono-hydroxyethylrutosides was 71%, in 24 h of dosage. In both cases most 14C was excreted in 3 h, as unchanged rutosides and glucuronide conjugates.3. Fall of blood 14C concn. was rapid for both compounds. Neither compound was detected in brain but there was short-term accumulation in liver and kidney, and 2-3 h after dosage, most 14C for both compounds was associated with the gastro-intestinal contents.4. Animals killed 72 h after dosage of either compound contained <7% of dose, mostly in the color and caecal contents.5. Foetuses removed 3 h after dosage of either compound to the dams did not contain 14C; foetuses removed 5 min after dosage contained low levels of 14C, substantially below the maternal blood level and equiv. to <0·1% of dose in each case. No 14C was detected in amniotic fluid.
Optoelectronic Chip for the Implementation of Back Error Propagation (2005)

We present a CMOS silicon chip that optically implements the back error propagation (BEP) algorithm [1] of a two layer neural network. The chip has eight units (or neurons) on a area of approximately 2x2 mm. Each unit consists of a phototransistor as the detector, a modulator pad for light modulation, sample-and-hold circuits, and additional circuits necessary to perform the BEP algorithm.
Removal of CO2Greenhouse Gas by Ammonia Scrubbing (1997)

This paper provides preliminary results on the novel study of ammonia scrubbing for the removal of carbon dioxide from flue gas. Experimental results indicated the potential of CO2 reduction by NH3 scrubbing is very promising. The overall CO2 removal efficiencies could be above 95% under proper operation conditions. The absorption capacity of NH3 was around 0.9 kg of CO2/kg of NH3 reagent being used. This should be higher than that by a MEA solution. The reaction products were analyzed and determined by X-ray diffraction analysis, SEM picture, and pH measurements. All the measurements indicated that an ammonium bicarbonate solution and its crystalline solids are the major products of reaction.
Generation of polyketide libraries via combinatorial biosynthesis (1996)

Polyketides are a family of structurally complex natural products that include a number of important pharmaceuticals. Motivated by the value of these natural products, there has been much research focused on developing guidelines for engineering polyketide synthases (PKSs) to generate novel polyketides. Recent studies have provided interesting insights into the enzymatic specificity of the polyketide synthesis pathway, and have demonstrated that various PKSs can be genetically manipulated to synthesize 'unnatural' polyketide natural products. In this article, we discuss the synthesis of polyketides and polyketide libraries by combinatorial biosynthesis.
Drug delivery systems based on sugar-macromolecule conjugates. (2002)

The specificity of carbohydrate-protein interactions can greatly outstrip that of many other ligand-binding systems; such is the enormous density of information that sugars can convey. In addition, macromolecules allow for the fine-tuning of active drug delivery through their great ability to undergo site-specific modification and their inherent physicochemical properties. Once combined, these two factors suggest that sugar-macromolecule conjugates, targeted using endogenous carbohydrate binding proteins, are a promising route to the 'magic bullet'.
Minimal information disclosure with efficiently verifiable credentials (2008)

Public-key based certificates provide a standard way to prove one's identity, as attested by some certificate authority (CA). However, plain certificates provide a binary identification: either the whole identity of the subject is known, or nothing is known. We propose using a Merkle hash tree structure, whereby it is possible for a single certificate to contain many separate claims or attributes, each of which may be proved independently, without revealing the others. Additionally, we demonstrate how trees from multiple sources can be combined together by modifying the tree structure. This allows claims by different authorities, such as an employer or professional organization, to be combined under a single certificate, without the CA needing to know (or to verify) all of the claims. In addition to describing the hash tree structure and protocols for constructing and verifying our proposed credential, we formally prove that it provides unforgeability and privacy and we present performance results demonstrating its efficiency. As services move from user names and passwords to attribute-based identity verification, efficiency and scalability of claims verification will become a major issue. We have implemented a prototype client-server system, deployed the prototype in Emulab, and evaluated the server-side throughput for attribute-based identity verification. The results show that our approach can perform about 200 identity verifications per second, while the best competing approach can perform only about 2--5 verifications per second. Our approach is, therefore, better suited to today's high-volume Web-based services that demand the highest possible throughput.
Modeling and predicting user behavior in sponsored search (2009)

Implicit user feedback, including click-through and subsequent browsing behavior, is crucial for evaluating and improving the quality of results returned by search engines. Several recent studies [1, 2, 3, 13, 25] have used post-result browsing behavior including the sites visited, the number of clicks, and the dwell time on site in order to improve the ranking of search results. In this paper, we first study user behavior on sponsored search results (i.e., the advertisements displayed by search engines next to the organic results), and compare this behavior to that of organic results. Second, to exploit post-result user behavior for better ranking of sponsored results, we focus on identifying patterns in user behavior and predict expected on-site actions in future instances. In particular, we show how post-result behavior depends on various properties of the queries, advertisement, sites, and users, and build a classifier using properties such as these to predict certain aspects of the user behavior. Additionally, we develop a generative model to mimic trends in observed user activity using a mixture of pareto distributions. We conduct experiments based on billions of real navigation trails collected by a major search engine's browser toolbar.
Extraction of DNA from Orange Juice, and Detection of Bacterium Candidatus Liberibacter asiaticus by Real-Time PCR (2013)

Orange juice processed from Huanglongbing (HLB) affected fruit is often associated with bitter taste and/or off-flavor. HLB disease in Florida is associated with Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacterium. The current standard to confirm CLas for citrus trees is to take samples from midribs of leaves, which are rich in phloem tissues, and use a quantitative real-time polymerase chain reaction (qPCR) test to detect the 16S rDNA gene of CLas. It is extremely difficult to detect CLas in orange juice because of the low CLas population, high sugar and pectin concentration, low pH, and possible existence of an inhibitor to DNA amplification. The objective of this research was to improve extraction of DNA from orange juice and detection of CLas by qPCR. Homogenization using a sonicator increased DNA yield by 86% in comparison to mortar and pestle extraction. It is difficult to separate DNA from pectin; however, DNA was successfully extracted by treating the juice with pectinase. Application of an elution column successfully removed the unidentified inhibitor to DNA amplification. This work provided a protocol to extract DNA from whole orange juice and detect CLas in HLB-affected fruit.
Laminin-10/11 and Fibronectin Differentially Prevent Apoptosis Induced by Serum Removal via Phosphatidylinositol 3-Kinase/Akt- and MEK1/ERK-dependent Pathways (2002)

Cell adhesion to the extracellular matrix inhibits apoptosis, but the molecular mechanisms underlying the signals transduced by different matrix components are not well understood. Here, we examined integrin-mediated antiapoptotic signals from laminin-10/11 in comparison with those from fibronectin, the best characterized extracellular adhesive ligand. We found that the activation of protein kinase B/Akt in cells adhering to laminin-10/11 can rescue cell apoptosis induced by serum removal. Consistent with this, wortmannin, a specific inhibitor of phosphatidylinositol 3-kinase, or ectopic expression of a dominant-negative mutant of Akt selectively accelerated cell death upon serum removal. In contrast to laminin-10/11, fibronectin rescued cells from serum depletion-induced apoptosis mainly through the extracellular signal-regulated kinase pathway. Cell survival on fibronectin but not laminin was significantly reduced by treatment with PD98059, a specific inhibitor of mitogen- or extracellular signal-regulated kinase kinase-1 (MEK1) and by expression of a dominant-negative mutant of MEK1. Laminin-10/11 was more potent than fibronectin in preventing apoptosis induced by serum depletion. These results, taken together, demonstrate laminin-10/11 potency as a survival factor and demonstrate that different extracellular matrix components can transduce distinct survival signals through preferential activation of subsets of multiple integrin-mediated signaling pathways.
A completely biological tissue‐engineered human blood vessel (1998)

Mechanically challenged tissue‐engineered organs, such as blood vessels, traditionally relied on synthetic or modified biological materials for structural support. In this report, we present a novel approach to tissue‐engineered blood vessel (TEBV) production that is based exclusively on the use of cultured human cells, i.e., without any synthetic or exogenous biomaterials. Human vascular smooth muscle cells (SMC) cultured with ascorbic acid produced a cohesive cellular sheet. This sheet was placed around a tubular support to produce the media of the vessel. A similar sheet of human fibroblasts was wrapped around the media to provide the adventitia. After maturation, the tubular support was removed and endothelial cells were seeded in the lumen. This TEBV featured a well‐defined, three‐layered organization and numerous extracellular matrix proteins, including elastin. In this environment, SMC reexpressed desmin, a differentiation marker known to be lost under standard culture conditions. The endothelium expressed von Willebrand factor, incorporated acetylated LDL, produced PGI2, and strongly inhibited platelet adhesion in vitro. The complete vessel had a burst strength over 2000 mmHg. This is the first completely biological TEBV to display a burst strength comparable to that of human vessels. Short‐term grafting experiment in a canine model demonstrated good handling and suturability characteristics. Taken together, these results suggest that this novel technique can produce completely biological vessels fulfilling the fundamental requirements for grafting: high burst strength, positive surgical handling, and a functional endothelium.—L'Heureux, N., Paquet, S., Labbe, R., Germain, L., Auger, F. A. A completely biological tissue‐engineered human blood vessel. FASEB J. 12, 47–56 (1998)
Differences in the protein composition of bovine retinal rod outer segment disk and plasma membranes isolated by a ricin-gold-dextran density perturbation method. (1987)

The plasma membrane and disk membranes of bovine retinal rod outer segments (ROS) have been purified by a novel density-gradient perturbation method for analysis of their protein compositions. Purified ROS were treated with neuraminidase to expose galactose residues on plasma membrane-specific glycoproteins and labeled with ricin-gold-dextran particles. After the ROS were lysed in hypotonic buffer, the plasma membrane was dissociated from the disks by either mild trypsin digestion or prolonged exposure to low ionic strength buffer. The dense ricin-gold-dextran-labeled plasma membrane was separated from disks by sucrose gradient centrifugation. Electron microscopy was used to follow this fractionation procedure. The dense red pellet primarily consisted of inverted plasma membrane vesicles containing gold particles; the membrane fraction of density 1.13 g/cc consisted of unlabeled intact disks and vesicles. Ricin-binding studies indicated that the plasma membrane from trypsin-treated ROS was purified between 10-15-fold. The protein composition of plasma membranes and disks was significantly different as analyzed by SDS gels and Western blots labeled with lectins and monoclonal antibodies. ROS plasma membrane exhibited three major proteins of 36 (rhodopsin), 38, and 52 kD, three ricin-binding glycoproteins of 230, 160, and 110 kD, and numerous minor proteins in the range of 14-270 kD. In disk membranes rhodopsin appeared as the only major protein. A 220-kD concanavalin A-binding glycoprotein and peripherin, a rim-specific protein, were also present along with minor proteins of 43 and 57-63 kD. Radioimmune assays indicated that the ROS plasma membrane contained about half as much rhodopsin as disk membranes.
Determination of Maturity and Degree Day Indices and their Success in Predicting Peanut Maturity1 (2006)

Abstract The ability to accurately assess and predict peanut maturity is a strong determinant of the economic return to the producer as it governs crop quality, flavor, and yield. However, the currently available methods used to predict peanut maturity are based on hull color determination and are somewhat labor-intensive and subject to the observer's ability to finely discriminate color classes. The objectives in this study were: 1) create an index of maturity based on the distribution of peanut pods within the accepted maturity profile board classes that give the best quantifiable correlation with peanut yield, grade, and net value; and 2) test degree day models to determine their efficacy in predicting the optimum maturity index. Peanuts were harvested on 7 and 6 sequential dates in 2003 and 2004, respectively, at two sites in southwest Georgia, USA. Several maturity indices were calculated at each harvest based on the percentage of pods in each color class of the maturity profile board. For both sites...
Assay, Isolation and Characterization of Circulating Immune Complexes from Serum of Gastrointestinal Cancer, Stage III and IV Melanoma and Chronic Inflammatory Bowel Disease Patients (1993)

Circulating immune complexes (CIC) have been detected in several autoimmune diseases, and studies have also suggested that CIC provide a useful tool as tumor markers. In order to identify differences or similarities in antigenic composition, CIC from 23 patients with gastrointestinal (GI) tumors, from 20 patients with stage III and IV melanoma and from 6 patients with inflammatory bowel disease (IBD) were studied. Serum from all GI, melanoma and IBD patients showed higher levels of CIC than controls. SDS/PAGE electrophoresis under reducing conditions revealed some differences between cancer and IBD patients as far as the CIC protein composition was concerned. In melanoma patients, two fast-migrating bands, in the regions of 71-74 and 30-49 kD, were found, consistent with previously isolated and characterized antigens described in the literature.