gebhart/patrepeval huggingface dataset:
West Nile Virus Recombinant DNA Vaccine Protects Mouse and Horse from Virus Challenge and Expresses In Vitro a Noninfectious Recombinant Antigen That Can Be Used in Enzyme-Linked Immunosorbent Assays (2001)

Introduction of West Nile (WN) virus into the United States in 1999 created major human and animal health concerns. Currently, no human or veterinary vaccine is available to prevent WN viral infection, and mosquito control is the only practical strategy to combat the spread of disease. Starting with a previously designed eukaryotic expression vector, we constructed a recombinant plasmid (pCBWN) that expressed the WN virus prM and E proteins. A single intramuscular injection of pCBWN DNA induced protective immunity, preventing WN virus infection in mice and horses. Recombinant plasmid-transformed COS-1 cells expressed and secreted high levels of WN virus prM and E proteins into the culture medium. The medium was treated with polyethylene glycol to concentrate proteins. The resultant, containing high-titered recombinant WN virus antigen, proved to be an excellent alternative to the more traditional suckling-mouse brain WN virus antigen used in the immunoglobulin M (IgM) antibody-capture and indirect IgG enzyme-linked immunosorbent assays. This recombinant antigen has great potential to become the antigen of choice and will facilitate the standardization of reagents and implementation of WN virus surveillance in the United States and elsewhere.
Procaryotic expression of phosphorylated tegument protein pp65 of human cytomegalovirus and application of recombinant peptides for immunoblot analyses (1990)

The tegument of human cytomegalovirus (HCMV) contains a phosphorylated protein of 65 kilodaltons, termed pp65, which was reported to carry significant epitopes for the stimulation of the humoral immune response during natural infection. A monoclonal antibody directed against this protein was used to screen a lambda gt11 cDNA library for recombinant polypeptides. Two DNA fragments from purified lambda clones and one fragment from genomic DNA were used for cloning in a bacterial high-level expression vector. The resulting fusion proteins were tested for their reactivity with a panel of monoclonal antibodies directed against pp65 and with polyspecific anti-HCMV rabbit antisera. The binding site for all the monoclonal antibodies tested was found to be contained in one of the recombinant proteins with a viral portion of 26 amino acids. Immunoblot analyses with HCMV-positive human sera revealed that pp65 alone is not a reliable antigen for serodiagnosis but may be very useful in combination with other HCMV proteins.
Fabrication of Monodisperse Gel Shells and Functional Microgels in Microfluidic Devices (2007)

Microgel structures such as spherical microgel shells (picture on the upper left) and spherical microgel particles that incorporate quantum dots, magnetic nanoparticles, and polymer microparticles (other images) have been prepared by a capillary microfluidic technique. Because these particles change their volume with changes in temperature, they may find application in, for example, drug delivery. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604206_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Recombinant Pfs25 protein of Plasmodium falciparum elicits malaria transmission-blocking immunity in experimental animals. (1991)

Pfs25 is a sexual stage antigen of Plasmodium falciparum that is expressed on the surface of zygote and ookinete forms of the parasite. Monoclonal antibodies directed against native Pfs25 can block completely the development of P. falciparum oocysts in the midgut of the mosquito vector. Thus, this 25-kD protein is a potential vaccine candidate for eliciting transmission-blocking immunity in inhabitants of malaria endemic regions. We have synthesized, by secretion from yeast, a polypeptide analogue of Pfs25 that reacts with conformation-dependent monoclonal antibodies, and elicits transmission-blocking antibodies when used to immunize mice and monkeys in conjunction with a muramyl tripeptide adjuvant. Our results suggest the further evaluation of recombinant DNA-derived Pfs25 in transmission-blocking vaccination studies in humans.
TU‐B‐BRB‐02: Monte Carlo — II: Application of Monte Carlo to Clinical IMRT Treatment Planning (2007)

The goal of this course is to familiarize participants with the clinical use of Monte Carlo (MC) dose calculation algorithms in IMRT photon‐beam treatment planning. Particular focus will be applied to the actual and potential clinical impact of MC dose calculation algorithms on patient treatments. Following a brief description of the integration of MC algorithms with commercial planning systems, MC dose re‐calculation results will be compared with plans computed using the conventional commercial treatment planning system algorithms. Specific patient examples where MC computed doses differ significantly from those computed with standard treatment planning system algorithms will be presented, with the causes of the dose discrepancies identified. With this background, the roles that MC has played in actual clinical practice will be described: as a QA tool to validate treatment planning system algorithms, as a QA tool to validate individual IMRT plans, and as a treatment planning tool to improve conformity between optimized and delivered IMRT plans. Strategies to minimize MC dose calculation time during IMRT optimization will be described. Educational Objectives: 1. To instruct clinical physicists regarding roles of Monte Carlo dose calculations for clinical IMRT patient treatment planning. 2. To describe the role of Monte Carlo in IMRT treatment planning system and patient specific quality assurance. 3. To describe clinical cases where Monte Carlo dose calculation either resulted —or would have resulted— in a change in the clinical treatment. 4. To describe the applications of and impact of Monte Carlo dose calculations for IMRT optimization. 5. This work was sponsored in part by Philips Medical Systems and Varian Medical Systems.
Content-enriched classifier for web video classification (2010)

With the explosive growth of online videos, automatic real-time categorization of Web videos plays a key role for organizing, browsing and retrieving the huge amount of videos on the Web. Previous work shows that, in addition to text features, content features of videos are also useful for Web video classification. Unfortunately, extracting content features is computationally prohibitive for real-time video classification. In this paper we propose a novel video classification framework that is able to exploit both content and text features for video classification while avoiding the expensive computation of extracting content features at classification time. The main idea of our approach is to utilize the content features extracted from training data to enrich the text based semantic kernels, yielding content-enriched semantic kernels. The content-enriched semantic kernels enable to utilize both content and text features for classifying new videos without extracting their content features. The experimental results show that our approach significantly outperforms the state-of-the-art video classification methods.
Abdominal muscle fatigue following exercise in chronic obstructive pulmonary disease (2010)

In patients with COPD, abdominal muscle but not diaphragm fatigue develops following symptom limited incremental cycle ergometry. Further work is needed to establish whether abdominal muscle fatigue is relevant to exercise limitation in COPD, perhaps indirectly through an effect on quadriceps fatigability.
Molecular cloning of MINK, a novel member of mammalian GCK family kinases, which is up‐regulated during postnatal mouse cerebral development (2000)

A new germinal center kinase (GCK) family kinase, Misshapen/NIKs-related kinase (MINK), has been cloned and its expression has been characterized in several tissues and various developmental stages of the mouse brain. MINK encodes a 1300 amino acid polypeptide, consisting of an N-terminal kinase domain, a proline-rich intermediate region, and a C-terminal GCK homology region. The expression of MINK is up-regulated during the postnatal development of the mouse brain. MINK activates the cJun N-terminal kinase and the p38 pathways.
Sequencing the erb A Gene of Avian Erythroblastosis Virus Reveals a New Type of Oncogene (1984)

Avian erythroblastosis virus (AEV) contains two distinct oncogenes, erbA and erbB . The erbB oncogene, which is homologous to a portion of the epidermal growth factor receptor, is related to the src family of oncogenes and efficiently transforms erythroblasts, whereas erbA potentiates the effects of erbB by blocking the differentiation of erythroblasts at an immature stage. This "potentiator" was sequenced; the amino acid sequence deduced from it was clearly different from the sequences of other known oncogene products and was related to carbonic anhydrases. These enzymes participate in the transport of carbon dioxide by erythrocytes, the precursors of which are main targets of avian erythroblastosis virus. A src-related oncogene such as erbB in synergy with an activated specific cell-derived gene such as erbA can profoundly affect early erythroid differentiation.
From well-defined Pt(ii) surface species to the controlled growth of silica supported Pt nanoparticles (2012)

Silica-supported Pt nanoparticles were prepared from well-defined surface platinum(II) surface species, obtained by grafting of well-defined Pt(II) molecular precursors with specific ligands (Cl, Me, N(SiMe(3))(2), OSi(OtBu)(3)) onto silica partially dehydroxylated at 200 and 700 °C yielding well-defined platinum(II) surface species. This approach allowed for testing the effect of Pt density and ligands on nanoparticle size. Higher grafting densities are achieved on silica partially dehydroxylated at 200 °C due to its initially higher surface silanol density. Surface species have been synthesized from symmetrical and dissymmetrical complexes, namely (COD)Pt(Me)(2), (COD)Pt(OSi(OtBu)(3))(2), (COD)Pt(Me)(OSi(OtBu)(3)), (COD)Pt(Me)(N(SiMe(3))(2)), (COD)Pt(Cl)(N(SiMe(3))(2)) and (COD)Pt(N(SiMe(3))(2))(OSi(OtBu)(3)) yielding mono-grafted complexes of general formula (COD)Pt(R)(OSi≡) according to elemental analyses, diffuse reflectance infrared fourier transform (DRIFT) and carbon-13 solid-state nuclear magnetic resonance (NMR) spectroscopies. While the dimethyl-complex shows low reactivity towards grafting, bis-siloxy and dissymmetric complexes demonstrate better reactivity yielding platinum loadings up to 7.4 wt%. Upon grafting amido complexes, the surface passivation yielding Me(3)SiOSi≡ surface species is demonstrated. Nanoparticles have been synthesized from these well-defined surface species by reduction under H(2) at 300 °C, under static or flow conditions. This process yields nanoparticles with sizes ranging from 2 to 3.3 nm and narrow size dispersion from 0.5 to 1.2 nm. Interestingly, the chloride complex yields large nanoparticles from 5 to 40 nm demonstrating the strong influence of chloride over the nanoparticles growth.
Marker-Assisted Introgression in Backcross Breeding Programs (1996)

The efficiency of marker-assisted introgression in backcross populations derived from inbred lines was investigated by simulation. Background genotypes were simulated assuming that a genetic model of many genes of small effects in coupling phase explains the observed breed difference and variance in backcross populations. Markers were efficient in introgression backcross programs for simultaneously introgressing an allele and selecting for the desired genomic background. Using a marker spacing of 10-20 cM gave an advantage of one to two backcross generations selection relative to random or phenotypic selection. When the position of the gene to be introgressed is uncertain, for example because its position was estimated from a trait gene mapping experiment, a chromosome segment should be introgressed that is likely to include the allele of interest. Even for relatively precisely mapped quantitative trait loci, flanking markers or marker haplotypes should cover approximately 10-20 cM around the estimated position of the gene, to ensure that the allele frequency does not decline in later backcross generations.
Electrospinning of ultrahigh‐molecular‐weight polyethylene nanofibers (2007)

Abstract The electrospinning method has been employed to fabricate ultrafine nanofibers of ultrahigh‐molecular‐weight polyethylene for the first time with a mixture of solvents of different dielectric constants and conductivities. The possibility of producing highly oriented nanofibers from ultrahigh‐molecular‐weight polymers suggests new ways of fabricating ultrastrong, porous, and single‐component nanocomposite fibers with improved properties. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 766–773, 2007
Pronunciation learning for named-entities through crowd-sourcing (2014)

Obtaining good pronunciations for named-entities poses a challenge for automated speech recognition because namedentities are diverse in nature and origin, and new entities come up every day. In this paper, we investigate the feasibility of learning named-entity pronunciations using crowd-sourcing. By collecting audio samples from non-linguistic-expert speakers with Mechanical Turk and learning from them, we can quickly derive pronunciations that are more accurate in speech recognition tests than manual pronunciations generated by linguistic experts. Compared to traditional approaches of generating pronunciations, this new approach proves to be cheap, fast, and quite accurate.
Transport of hydrophobized fragments of antibodies through the blood-brain barrier (1995)

Hydrophobized and non-hydrophobized Fab fragments of human antibodies against gliofibrillar acid protein (GFAP) and brain specific alpha 2-glycoprotein (alpha 2GP) were used to study their penetration through the blood-brain barrier (BBB). These Fab fragments were modified by stearoyl chloride in reversed micelles of aerosol OT in octane (one or two fatty acid residues attached to protein molecule). Modified and non-modified 125I-labelled Fab fragments were intracardially administered to rats. The amount of label accumulated in brain was 55% higher than the total amount in all other organs. In contrast, non-hydrophobized Fab fragments did not penetrate through the BBB. We assume that the artificial hydrophobization of Fab fragments can increase their capability to penetrate through the cell membranes and, in particular, the BBB.
Antibiotics enhance binding by human lipid A-reactive monoclonal antibody HA-1A to smooth gram-negative bacteria (1993)

The effect of antibiotic exposure of phenotypically smooth gram-negative bacteria on binding by the human lipid A-reactive monoclonal antibody HA-1A (trademark of Centocor, Inc.) was examined by liquid-phase immunoassay and by dual-parameter flow cytometry (fluorescence-activated cell sorter [FACS]) analysis. HA-1A exhibited dose-dependent binding to untreated rough gram-negative bacteria such as the Escherichia coli D21F2 Re chemotype strain but little binding to untreated smooth strains such as E. coli O111:B4, or to gram-positive bacteria. However, overnight incubation of E. coli O111:B4 with inhibitory concentrations of ceftazidime produced dose-dependent enhancement of HA-1A binding. Similar augmentation of HA-1A binding was observed when other smooth strains were exposed to cell wall-active agents. Dual-parameter FACS analysis of E. coli O111:B4 exposed overnight to two times the MIC of ceftazidime revealed a decrease in forward light scatter, indicating a reduction in average cell size or bacterial fragmentation, accompanied by a striking increase in lipid A-inhibitable HA-1A binding. Moreover, ceftriaxone, but not gentamicin, produced a marked increase in propidium iodide uptake, indicating an increase in bacterial cell permeability, and a corresponding enhancement of HA-1A binding. Antibiotic-induced enhancement of HA-1A binding to smooth strains of gram-negative bacteria thus appears related to specific alterations in bacterial cell morphology resulting in exposure of the epitope recognized by HA-1A.
New agents forClostridium difficile-associated disease (2008)

The new antibiotics in development and preclinical development reflect next-generation versions of older drugs or two new mechanism-of-action class drugs (OPT-80, REP3123). Based on the current preclinical and clinical data, the next-generation drugs impart only a subtle difference from the intrinsic weaknesses of their genre. In contrast, OPT-80 and REP3123 seem to be differentiated.
Connective tissue growth factor mediates transforming growth factor β‐induced collagen synthesis: down‐regulation by cAMP (1999)

Connective tissue growth factor (CTGF) is a cysteine-rich peptide synthesized and secreted by fibroblastic cells after activation with transforming growth factor beta (TGF-beta) that acts as a downstream mediator of TGF-beta-induced fibroblast proliferation. We performed in vitro and in vivo studies to determine whether CTGF is also essential for TGF-beta-induced fibroblast collagen synthesis. In vitro studies with normal rat kidney (NRK) fibroblasts demonstrated CTGF potently induces collagen synthesis and transfection with an antisense CTGF gene blocked TGF-beta stimulated collagen synthesis. Moreover, TGF-beta-induced collagen synthesis in both NRK and human foreskin fibroblasts was effectively blocked with specific anti-CTGF antibodies and by suppressing TGF-beta-induced CTGF gene expression by elevating intracellular cAMP levels with either membrane-permeable 8-Br-cAMP or an adenylyl cyclase activator, cholera toxin (CTX). cAMP also inhibited collagen synthesis induced by CTGF itself, in contrast to its previously reported lack of effect on CTGF-induced DNA synthesis. In animal assays, CTX injected intradermally in transgenic mice suppressed TGF-beta activation of a human CTGF promoter/lacZ reporter transgene. Both 8-Br-cAMP and CTX blocked TGF-beta-induced collagen deposition in a wound chamber model of fibrosis in rats. CTX also reduced dermal granulation tissue fibroblast population increases induced by TGF-beta in neonatal mice, but not increases induced by CTGF or TGF-beta combined with CTGF. Our data indicate that CTGF mediates TGF-beta-induced fibroblast collagen synthesis and that in vivo blockade of CTGF synthesis or action reduces TGF-beta-induced granulation tissue formation by inhibiting both collagen synthesis and fibroblast accumulation.
Construction, expression, and characterization of a novel fully activated recombinant single‐chain hepatitis C virus protease (1998)

Efficient proteolytic processing of essential junctions of the hepatitis C virus (HCV) polyprotein requires a heterodimeric complex of the NS3 bifunctional protease/helicase and the NS4A accessory protein. A single-chain recombinant form of the protease has been constructed in which NS4A residues 21-32 (GSVVIVGRIILS) were fused in frame to the amino terminus of the NS3 protease domain (residues 3-181) through a tetrapeptide linker. The single-chain recombinant protease has been overexpressed as a soluble protein in E. coli and purified to homogeneity by a combination of metal chelate and size-exclusion chromatography. The single-chain recombinant protease domain shows full proteolytic activity cleaving the NS5A-5B synthetic peptide substrate, DTEDVVCCSMSYTWTGK with a Km and k(cat) of 20.0 +/- 2.0 microM and 9.6 +/- 2.0 min(-1), respectively; parameters identical to those of the authentic NS3(1-631)/NS4A(1-54) protein complex generated in eukaryotic cells (Sali DL et al., 1998, Biochemistry 37:3392-3401).
Exchange Reactions Catalyzed by Methioninase from Pseudomonas putida (1976)

Gel-electrophoretically homogeneous methioninase [L-methionine methanethiol-lyase (deaminating), EC 4.4.1.11] of Pseudomonas putida, which catalyzes alpha, beta- and alpha, gamma-eliminations from S-substituted amino acids, could also catalyze a variety of beta- and gamma-exchange reactions, according to the following equations: RSCH2CH(NH2)COOH+R'SH in equilibrium R'SCH2CH(NH2)COOH+RSH (beta-exchange) and RSCH2CH2CH(NH2)COOH+R'SH in equilibrium R'SCH2CH2CH(NH2)COOH+RSH (gamma-exchange), where R'SH represents an exogeneously added alkanethiol or a substituted thiol. Related amino acids not available for elimination reactions appeared to be inert as substrates for exchange. The maximum activity for the exchange reactions was observed at pH 8.5 in potassium pyrophosphate buffer. The activity increased linearly with the increase in protein concentration from zero to 3.0 mug per ml, and with incubation time up to at least 15 min at 30 degrees. Some of the exchange reaction products were purified by a combination of paper and ion exchange chromatographies, and charcoal treatment: their structures were confirmed by physicochemical methods including elemental analysis and proton magnetic resonance, infrared, and mass spectrometries.
Precise genome-wide base editing by the CRISPR Nickase system in yeast (2017)

The CRISPR/Cas9 system has been applied to efficient genome editing in many eukaryotic cells. However, the bases that can be edited by this system have been limited to those within the protospacer adjacent motif (PAM) and guide RNA-targeting sequences. In this study, we developed a genome-wide base editing technology, "CRISPR Nickase system" that utilizes a single Cas9 nickase. This system was free from the limitation of editable bases that was observed in the CRISPR/Cas9 system, and was able to precisely edit bases up to 53 bp from the nicking site. In addition, this system showed no off-target editing, in contrast to the CRISPR/Cas9 system. Coupling the CRISPR Nickase system with yeast gap repair cloning enabled the construction of yeast mutants within only five days. The CRISPR Nickase system provides a versatile and powerful technology for rapid, site-specific, and precise base editing in yeast.
Federated, secure trust networks for distributed healthcare it services (2004)

Recent US regulations mandate the privacy and security of healthcare data at a level never previously contemplated. Our research group is developing a prototype healthcare IT system and medical data portal based upon a Web services approach. An authentication Web service manages trust levels, issues authorization tickets, and uses biometric devices to establish identity; an authorization Web service determines what data may be accessed, in what way, and by whom. Hospital administrators set access privileges for recursively-defined groups, subgroups, and individuals. All patient records and medical images are protected using AES encryption with 256-bit keys. Offnetwork entities such as pharmacies, insurance companies, and other medical service providers participate through a federated trust-sharing arrangement. Electronic prescriptions are transmitted securely to participating pharmacies and pick-up notifications are provided to the patient using the preferred notification method (email, alerts to a PDA, automated telephone call) stored in the patient's profile.