gebhart/patrepeval huggingface dataset:
Molecular Studies on Suspect Very Virulent Infectious Bursal Disease Virus Genomic RNA Samples (2005)

Infectious bursal disease (IBD) associated with high mortality was first observed in Europe in the mid-1980s. The viruses identified in those outbreaks were described as being very virulent infectious bursal disease virus (vvIBDV) strains. These viruses have spread to nearly every continent but have not yet been identified in North America, Australia, and New Zealand. There is a real and immediate concern that the very virulent form of IBDV will continue to spread until it is present on every continent. Genomic RNA samples from IBDV strains suspected of being very virulent were submitted to our laboratory for molecular analysis. Nucleotide sequences of the VP2 gene hypervariable sequence region were determined for 18 of these viruses. A comparison with published vvIBDV sequences indicated that all but one sample (Thai 4) had nucleotide and predicted amino acid sequences consistent with vvIBDV strains. Published sequences and the nucleotide sequences of our 17 putative vvIBDV strains were used to identify unique nucleotides in the VP2 gene. Probe pairs for a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay were designed based on these unique sequences and then used to test the 17 genomic samples that were identified by nucleotide sequencing to be consistent with vvIBDV, plus the one Thai 4 sample that was not consistent with vvIBDV. Using melting temperature (Tm) analysis following real-time RT-PCR, two probe pairs (vv232 and vv256) successfully identified the 17 putative vvIBDV strains and distinguished them from the Thai 4 sample. An additional 26 genomic RNA samples submitted as suspect vvIBDV strains were then tested using the vv232 and vv256 probes. Based on the melting point analysis of these two probes, all 26 samples contained nucleotide sequences consistent with vvIBDV strains. The specificity of the vv232 and vv256 probe pairs was evaluated using 19 non-vvIBDV strains. In every case, the probes distinguished the 19 classic and variant (non-vvIBDV) strains from the putative vvIBDV strains. Diagnostic assays that can reliably identify vvIBDV strains are needed for surveillance programs designed to monitor the spread of these viruses.
Microwave‐Assisted Olefin Metathesis (2007)

Abstract The beneficial effect of microwave irradiation instead of classical thermal conditions in olefin metathesis reactions is illustrated through a series of literature examples of ring‐closing‐metathesis and cross‐metathesis reactions. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)
An Approach to the Functional Analysis of Lecithin-Cholesterol Acyltransferase. Activation by Recombinant Normal and Mutagenized Apolipoprotein AI (1991)

Apolipoprotein AI (apo AI) of human serum high-density lipoprotein functions as an activator of lecithin-cholesterol acyltransferase (LCAT) and therefore plays an important role in reversed cholesterol transport. The mechanism of the acyltransfer, the activating polypeptide domains of apo AI and the active site of LCAT in this transesterification are not yet known. Synthetic peptides of the apo AI sequence have been designed to determine the activating structure, but did not yet lead to conclusive results. This also applies to spontaneous apo AI mutants. We therefore used the method of site-directed mutagenesis of apo AI cDNAs using the overlap extension approach by the polymerase chain reaction. These constructs were cloned into the procaryotic vector pET8c and expressed under the inducible T7 promoter. The engineered apo AI polypeptides were isolated and purified by affinity chromatography and assayed for their activator activity. The essentials of this approach to the structure and function of activators in general have successfully been exemplified for the LCAT activation by engineering apo AI mutant polypeptides a) by the deletion of two adjacent amphipathic helices (amino acid residues 146-186) and b) by introducing a point mutation (Glu111----Gln).
In Vitro Cultivation of Human Tumors: Establishment of Cell Lines Derived From a Series of Solid Tumors2 (1973)

Journal Article In Vitro Cultivation of Human Tumors: Establishment of Cell Lines Derived From a Series of Solid Tumors Get access Donald J. Giard, Donald J. Giard 3Meloy Laboratories, Inc., 6715 Electronic Drive, Springfield, Va. 22151 Search for other works by this author on: Oxford Academic PubMed Google Scholar Stuart A. Aaronson, Stuart A. Aaronson 4Viral Carcinogenesis Branch, National Cancer Institute, National Institutes of Health, Bethesda, Md. 20014 Search for other works by this author on: Oxford Academic PubMed Google Scholar George J. Todaro, George J. Todaro 5Viral Leukemia and Lymphoma Branch, National Cancer Institute, National Institutes of Health, Bethesda, Md. 20014 Search for other works by this author on: Oxford Academic PubMed Google Scholar Paul Arnstein, Paul Arnstein 6State of California, Department of Public Health, 2151 Berkeley Way, Berkeley, Calif. 94704 Search for other works by this author on: Oxford Academic PubMed Google Scholar John H. Kersey, John H. Kersey 7Department of Pathology and Pediatrics, University of Minnesota Medical School, Minneapolis, Minn. 55455 Search for other works by this author on: Oxford Academic PubMed Google Scholar Harvey Dosik, Harvey Dosik 8Division of Hematology, Jewish Hospital and Medical Center of Brooklyn, 555 Prospect Place, Brooklyn, N.Y. 11238 Search for other works by this author on: Oxford Academic PubMed Google Scholar Wade P. Parks Wade P. Parks 4Viral Carcinogenesis Branch, National Cancer Institute, National Institutes of Health, Bethesda, Md. 20014 Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 51, Issue 5, November 1973, Pages 1417–1423, https://doi.org/10.1093/jnci/51.5.1417 Published: 01 November 1973 Article history Received: 31 January 1973 Accepted: 25 July 1973 Published: 01 November 1973
Therapeutic Monoclonal Antibodies (1990)

A review of therapeutic antibodies which have commercial potential. It discusses PCR cloning of Igs, immortalization by gene transfer, scale up production, infectious diseases, viruses, bacteria, pari
Empirical model functions to calculate hematocrit-dependent optical properties of human blood (2007)

The absorption coefficient, scattering coefficient, and effective scattering phase function of human red blood cells (RBCs) in saline solution were determined for eight different hematocrits (Hcts) between 0.84% and 42.1% in the wavelength range of 250-1100 nm using integrating sphere measurements and inverse Monte Carlo simulation. To allow for biological variability, averaged optical parameters were determined under flow conditions for ten different human blood samples. Based on this standard blood, empirical model functions are presented for the calculation of Hct-dependent optical properties for the RBCs. Changes in the optical properties when saline solution is replaced by blood plasma as the suspension medium were also investigated.
[Relationship between nitric oxide in cervical microenvironment and different HPV types and effect on cervical cancer cells]. (2011)

The presence of HR-HPV is associated with an increased release of NO in the human uterine cervix; NO could inhibit the growth and proliferation and enhance the apoptosis of cervical cancer cells, inhibit the expression of HPV18 E6, E7 mRNA in HeLa cells and activate the expression of p53 protein, the mechanism may be due to higher sensitivity of HeLa cells (cervical adenocarcinoma cell) to SNP. The increasing release of NO may play a role in regulating the elimination of HPV in cervical microenvironment, which is a part of mucous membrane immunity.
Isolation and preservation of peripheral blood mononuclear cells for analysis of islet antigen-reactive T cell responses: position statement of the T-Cell Workshop Committee of the Immunology of Diabetes Society (2010)

Autoimmune T cell responses directed against insulin-producing β cells are central to the pathogenesis of type 1 diabetes (T1D). Detection of such responses is therefore critical to provide novel biomarkers for T1D 'immune staging' and to understand the mechanisms underlying the disease. While different T cell assays are being developed for these purposes, it is important to optimize and standardize methods for processing human blood samples for these assays. To this end, we review data relevant to critical parameters in peripheral blood mononuclear cell (PBMC) isolation, (cryo)preservation, distribution and usage for detecting antigen-specific T cell responses. Based on these data, we propose recommendations on processing blood samples for T cell assays and identify gaps in knowledge that need to be addressed. These recommendations may be relevant not only for the analysis of T cell responses in autoimmune disease, but also in cancer and infectious disease, particularly in the context of clinical trials.
CD40 signaling activates CD11a/CD18 (LFA-1)-mediated adhesion in B cells (1991)

Cell-cell adhesion events play critical roles in the sequential migrations and multiple specific cell-cell interactions which B cells undergo during normal development and function. We have observed that mAb to several B cell-associated molecules, including mAb to CD19, CD37, and CD40, induce homotypic aggregation of freshly isolated human B cells. The aggregation of B cells induced by CD40 mAb was due to activation of a cell-cell adhesion system, and not due to agglutination by mAb, because 1) in addition to being energy dependent and cation dependent, the aggregation was blocked by inhibitors of messenger RNA and protein synthesis; and 2) a mouse B cell line transformed with intact human CD40 aggregated in response to CD40 mAb, whereas a line expressing surface CD40, but lacking the cytoplasmic tail and previously shown incapable of transmitting a signal from the cell surface, did not aggregate. The aggregation, although of slow onset, was persistent and of high avidity. In addition, CD40 mAb induced increased surface expression of intercellular adhesion molecule-1 (CD54), a ligand for CD11a/CD18 (LFA-1), and CD18 mAb blocked aggregation. CD40 mAb also augmented the ability of dense B cells to stimulate the proliferation of allogeneic T cells via a CD18-dependent process. We conclude that signaling through CD40, elicited by cross-linking the CD40 protein on the cell surface, activates the CD18/intercellular adhesion molecule adhesion system; in addition, CD40 cross-linking may activate a second adhesion system since CD40 mAb induced aggregation of the B cell line Ramos, which does not express surface CD18. B cell adhesion may be triggered by signaling through multiple surface proteins, thereby lending specificity of activation to adhesion systems which are broadly expressed.
Human Placenta Feeder Layers Support Undifferentiated Growth of Primate Embryonic Stem Cells (2004)

Various undifferentiated embryonic stem (ES) cells can grow on mouse embryonic fibroblast (MEF) feeders. However, the risk of zoonosis from animal feeders to human ES cells generally excludes the clinical use of these human ES cells. We have found that human placenta is a useful source of feeder cells for the undifferentiated growth of primate ES cells. As on MEF feeders, primate ES cells cultured on human amniotic epithelial (HAE) feeder cells and human chorionic plate (HCP) cells had undifferentiated growth. The cultured primate ES cells expressed Oct-4, alkaline phosphatase, and SSEA-4. The primate ES cells on HAE feeder cells produced typical immature teratomas in vivo after injection into severe combined immunodeficient mice. Human placenta is quite novel and important because it would provide a relatively available source of feeders for the growth of human ES cells for therapeutic purposes that are also free of ethical complications.
Specification of User Interface for Safety-Critical Systems (1995)

Safe operation of a safety-critical computer system depends on appropriate humancomputer interaction, effected through the user interface. Thus, specification of the user interface is a key task in the development of such a system. This thesis presents a comprehensive, structured approach to formally specifying user interfaces for safetycritical systems. Based on a view of an interface as comprising three levels, the approach decomposes the user interface into multiple components: semantic, syntactic, and lexical, respectively addressing application function, dialogue control, and presentation. Each component utilizes a formal notation appropriate to its level, then these component specifications are integrated systematically. This approach promotes a modularization that enables prototyping and change at each level and validation of user input, as well as enabling a correspondence between specification and implementation architectures that facilitates software development and verification of the implementation. Feasibility of this specification method was demonstrated using two case studies involving safety - critica1 systems: phe Magnetic Stereotaxis System (MSS) and the University of Virginia Reactor (UVAR). Note: Abstract extracted from PDF file via OCR
Cyclic Voltammetric Deposition of Hydrous Ruthenium Oxide for Electrochemical Capacitors (1999)

Hydrous ruthenium oxide‐coated titanium electrodes with high pseudocapacitance were prepared by cyclic voltammetry from an aqueous chloride solution in the −200 to 1000 mV range. The growth rate of , represented by (peak current) of the cyclic voltammograms, was constant up to cycle 120, but it decreased slightly between 120 and 240 cycles. Voltammetric responses studied by cyclic voltammetry as well as the charging and discharging behavior examined by chronopotentiometry in demonstrated the suitability of for use in electrochemical capacitors. X‐ray diffraction spectra exhibited an amorphous structure of this hydrous oxide film. The oxide consisted of mixed oxyruthenium species with various oxidation states as demonstrated by X‐ray photoelectron spectroscopy, and the surface showed a porous morphology. © 1999 The Electrochemical Society. All rights reserved.
Comparative Effects of Teriparatide, Denosumab, and Combination Therapy on Peripheral Compartmental Bone Density, Microarchitecture, and Estimated Strength: the DATA-HRpQCT Study (2014)

Combined teriparatide and denosumab increases spine and hip bone mineral density more than either drug alone. The effect of this combination on skeletal microstructure and microarchitecture, however, is unknown. Because skeletal microstructure and microarchitecture are important components of skeletal integrity, we performed high-resolution peripheral quantitative computed tomography (HR-pQCT) assessments at the distal tibia and radius in postmenopausal osteoporotic women randomized to receive teriparatide 20 µg daily (n = 31), denosumab 60 mg every 6 months (n = 33), or both (n = 30) for 12 months. In the teriparatide group, total volumetric bone mineral density (vBMD) did not change at either anatomic site but increased in both other groups at both sites. The increase in vBMD at the tibia was greater in the combination group (3.1 ± 2.2%) than both the denosumab (2.2 ± 1.9%) and teriparatide groups (-0.3 ± 1.9%) (p < 0.02 for both comparisons). Cortical vBMD decreased by 1.6 ± 1.9% at the tibia and by 0.9 ± 2.8% at the radius in the teriparatide group, whereas it increased in both other groups at both sites. Tibia cortical vBMD increased more in the combination group (1.5 ± 1.5%) than both monotherapy groups (p < 0.04 for both comparisons). Cortical thickness did not change in the teriparatide group but increased in both other groups. The increase in cortical thickness at the tibia was greater in the combination group (5.4 ± 3.9%) than both monotherapy groups (p < 0.01 for both comparisons). In the teriparatide group, radial cortical porosity increased by 20.9 ± 37.6% and by 5.6 ± 9.9% at the tibia but did not change in the other two groups. Bone stiffness and failure load, as estimated by finite element analysis, did not change in the teriparatide group but increased in the other two groups at both sites. Together, these findings suggest that the use of denosumab and teriparatide in combination improves HR-pQCT measures of bone quality more than either drug alone and may be of significant clinical benefit in the treatment of postmenopausal osteoporosis.
Thresholds for biological effects of time-varying magnetic fields (1984)

Investigations of the biological effects of time-varying magnetic fields in the extremely low frequency range have been carried out with particular reference to NMR imaging. One effect encountered is the stimulation of nerves and muscles by induced eddy currents. The nature of this effect has been studied in rats exposed to whole body homogeneous fields and in the human forearm with local exposures. Electromyography was used to provide quantitative measurements of thresholds and responses for human exposures. The field exposures required to produce a detectable response are dependent upon the pulse period, pulse waveform and the current path in tissue. For the rat experiments the lowest threshold occurred for a damped sinusoidal pulse of period 0.33 ms with a maximum rate of change of field of 2400 T s-1. The lowest threshold for sensation in the human experiments was 2100 T s-1 for a similar type of field. Simple theory for conduction is considered and current densities induced are estimated as 5 A m-2.
Listeria monocytogenes Delivery of HPV-16 Major Capsid Protein L1 Induces Systemic and Mucosal Cell-Mediated CD4 + and CD8 + T-Cell Responses After Oral Immunization (2009)

Neutralizing antibodies are thought to be required at mucosal surfaces to prevent human papillomavirus (HPV) transmission. However, the potential for cell-mediated immunity in mediating protection against HPV infection has not been well explored. We generated recombinant Listeria monocytogenes (Lm) constructs that secrete listeriolysin O (LLO) fused with overlapping N-terminal (LLO-L1(1-258)) or C-terminal (LLO-L1(238-474)) fragments of HPV type 16 major capsid protein L1 (HPV-16-L1). Oral immunization of mice with either construct induced IFN-gamma-producing CD8+ and CD4+ T cells in the spleen and in the Peyer's patches with the C-terminal construct. Oral immunization with both constructs resulted in diminished viral titers in the cervix and uterus of mice after intravaginal challenge with vaccinia virus expressing HPV-16-L1.
The 1994 HTK large vocabulary speech recognition system (2002)

This paper describes recent work on the HTK large vocabulary speech recognition system. The system uses tied-state cross-word context-dependent mixture Gaussian HMMs and a dynamic network decoder that can operate in a single pass. In the last year the decoder has been extended to produce word lattices to allow flexible and efficient system development, as well as multi-pass operation for use with computationally expensive acoustic and/or language models. The system vocabulary can now be up to 65 k words, the final acoustic models have been extended to be sensitive to more acoustic context (quinphones), a 4-gram language model has been used and unsupervised incremental speaker adaptation incorporated. The resulting system gave the lowest error rates on both the H1-P0 and H1-C1 hub tasks in the November 1994 ARPA CSR evaluation.
Evidence for cooperativity between E2 binding sites in E2 trans-regulation of bovine papillomavirus type 1 (1988)

The long control region of bovine papillomavirus type 1 (BPV-1) can function in an orientation- and position-independent manner as an E2-dependent enhancer. Dissection of the long control region has revealed two E2-responsive elements, E2RE1 and E2RE2, which map, respectively, between nucleotides 7611 and 7806 and between nucleotides 7200 and 7386 of the BPV-1 genome. In this study, we have carried out a detailed analysis of E2RE1, which has previously been shown to be involved in the regulation of the BPV-1 promoters P89 and P7940. One characteristic of E2RE1 is the presence of a pair of ACCN6GGT motifs (E2 binding sites) at each end of the element. To determine the contribution of these sites, as well as other sequences within E2RE1, to enhancer function, specific mutations and deletions were generated by oligonucleotide reconstruction. The functional analysis of these mutations confirmed that a pair of E2 binding sites was essential for E2-dependent enhancer activity but also indicated that cooperativity between the motifs at each end of E2RE1 creates a highly responsive element. Isolated ACCN6GGT motif pairs could also act as E2-dependent enhancers but at a significantly reduced level in comparison to the intact element. The sequences between the E2 binding sites in E2RE1 were not required for enhancer function and could actually block the enhancer activity of an isolated pair of E2 binding sites when positioned between the binding sites and the enhancer-deleted simian virus 40 early promoter.
Conversion of the omega subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target (1998)

Evidence obtained in both eukaryotes and prokaryotes indicates that arbitrary contacts between DNA-bound proteins and components of the transcriptional machinery can activate transcription. Here we demonstrate that the Escherichia coli omega protein, which copurifies with RNA polymerase, can function as a transcriptional activator when linked covalently to a DNA-binding protein. We show further that omega can function as an activation target when this covalent linkage is replaced by a pair of interacting polypeptides fused to the DNA-binding protein and to omega, respectively. Our findings imply that the omega protein is associated with RNA polymerase holoenzyme in vivo, and provide support for the hypothesis that contact between a DNA-bound protein and any component of E. coli RNA polymerase can activate transcription.
Signals From the Embryonic Mouse Pancreas Induce Differentiation of Human Embryonic Stem Cells Into Insulin-Producing β-Cell–Like Cells (2005)

The recent success in restoring normoglycemia in type 1 diabetes by islet cell transplantation indicates that cell replacement therapy of this severe disease is achievable. However, the severe lack of donor islets has increased the demand for alternative sources of beta-cells, such as adult and embryonic stem cells. Here, we investigate the potential of human embryonic stem cells (hESCs) to differentiate into beta-cells. Spontaneous differentiation of hESCs under two-dimensional growth conditions resulted in differentiation of Pdx1(+)/Foxa2(+) pancreatic progenitors and Pdx1(+)/Isl1(+) endocrine progenitors but no insulin-producing cells. However, cotransplantation of differentiated hESCs with the dorsal pancreas, but not with the liver or telencephalon, from mouse embryos resulted in differentiation of beta-cell-like cell clusters. Comparative analysis of the basic characteristics of hESC-derived insulin(+) cell clusters with human adult islets demonstrated that the insulin(+) cells share important features with normal beta-cells, such as synthesis (proinsulin) and processing (C-peptide) of insulin and nuclear localization of key beta-cell transcription factors, including Foxa2, Pdx1, and Isl1.