gebhart/patrepeval huggingface dataset:
Complete nucleotide sequence of alfalfa mosaic virus RNA 4 (1980)

Alfalfa mosaic virus RNA 4, the subgenomic messenger for viral coat protein, was partially digested with RNase T1 or RNase A and the sequence of a number of fragments was deduced by in vitro labeling with polynucleotide kinase and application of RNA sequencing techniques. From overlapping fragments, the complete primary sequence of the 881 nucleotides of RNA 4 was constructed: the coding region of 660 nucleotides (not including the initiation and termination codon) is flanked by a 5' noncoding region of 39 nucleotides and a 3' noncoding region of 182 nucleotides. The RNA sequencing data completely confirm the amino acid sequence of the coat protein as deduced by Van Beynum et al. (Fur.J. Biochem. 72, 63-78, 1977).
Immunoglobulin classes of DNA binding activity in serum and skin in systemic lupus erythematosus. (1977)

36 systemic lupus erythematosus patients with native DNA binding activity (nDNA-BA) in the serum and subepidermal immunoglobulin deposits were studied to determine the relationship of the immunoglobulin (Ig) class distribution of serum nDNA-BA to the clinical characteristics of their disease and to the Ig class present at the dermal-epidermal junction (DEJ). The patients with predominantly (86-98%) IgM nDNA-BA in the serum had less active disease, mild or no renal involvement, and longer survival than those with predominantly (51-95%) IgG nDNA-BA in the serum. Renal biopsies in eight patients with predominantly IgM nDNA-BA in the serum showed relatively benign histologic changes in the kidney. In contrast, renal tissue from 23 patients with predominantly IgG nDNA-BA showed more severe histologic changes. All patients had multiple skin biopsies. Patients with predominantly IgM nDNA-BA consistently had only IgM at the DEJ. Patients with predominantly IgG nDNA-BA had IgG, usually in association with IgM, at the DEJ. The findings demonstrate that a minority of systemic lupus erythematosus patients may exhibit a limited anti-nDNA response characterized by the presence of chiefly IgM nDNA-BA in the serum and that this is reflected by the presence of mild disease and IgM alone at the DEJ. The development of IgG nDNA-BA is associated with more severe and active disease.
TIM-3, a Possible Target for Immunotherapy in Cancer and Chronic Viral Infections. (2014)

Effector T-cell responses are controlled by complex mechanisms involving various soluble factors and co-stimulatory and co-inhibitory molecules. These inhibitory receptors act as immune checkpoints and are extensively investigated as possible therapeutic targets, such as PD-1 and CTLA-4. Recently TIM-3 is also gaining prominence in tumor and chronic viral infection models as a candidate for immunotherapy in conjunction with other inhibitory receptors. This review discusses the recent findings on the expression of TIM-3 and its ligand in tumor and chronic viral infection.
New directions in cryptography (1976)

Two kinds of contemporary developments in cryptography are examined. Widening applications of teleprocessing have given rise to a need for new types of cryptographic systems, which minimize the need for secure key distribution channels and supply the equivalent of a written signature. This paper suggests ways to solve these currently open problems. It also discusses how the theories of communication and computation are beginning to provide the tools to solve cryptographic problems of long standing.
Approaching Exponential Growth with a Self-Replicating Peptide (2002)

Self-replicating peptide systems hold great promise for a wide range of technological applications, as well as to address fundamental questions pertaining to the molecular origins of life. The development of self-replicating compounds capable of high efficiency, however, has remained elusive. Here we disclose a successful strategy whereby modulation of coiled-coil stability results in remarkable catalytic efficiency for self-replication. By shortening the peptide to the minimum length necessary for coiled-coil formation a highly efficient self-replicating system was obtained due to very low background reaction rates, bringing the efficiency close to naturally occurring enzymes.
Effects of beta-mercaptoethanol and hydrogen peroxide on enzymatic conversion of human proinsulin to insulin. (2008)

Human insulin is a hormone well-known to regulate the blood glucose level. Recombinant preproinsulin, a precursor of authentic insulin, is typically produced in E. coli as an inactive inclusion body, the solubilization of which needs the addition of reducing agents such as beta-mercaptoethanol. To make authentic insulin, recombinant preproinsulin is modified enzymatically by trypsin and carboxypeptidase B. The effects of beta-mercaptoethanol on the formation of human insulin derivatives were investigated in the enzymatic modification by using commercially available human proinsulin as a substrate. Addition of 1 mM beta-mercaptoethanol induced the formation of various insulin derivatives. Among them, the second major one, impurity 3, was found to be identical to the insulin B chain fragment from Phe1 to Glu21. Minimization of the formation of insulin derivatives and concomitant improvement of the production yield of human insulin were achieved by the addition of hydrogen peroxide. Hydrogen peroxide bound with beta-mercaptoethanol and thereby reduced the negative effects of beta-mercaptoethanol considerably. Elimination of the impurity 3 and other derivatives by the addition of over 10 mM hydrogen peroxide in the presence of beta-mercaptoethanol led to a 1.3-fold increase in the recovery efficiency of insulin, compared with those for the case without hydrogen peroxide. The positive effects of hydrogen peroxide were also confirmed with recombinant human preproinsulin expressed in recombinant E. coli as an inclusion body.
DC I-V characteristics of field emitter triodes (1991)

A simple model that is applicable to Spindt-type emitter triodes is presented. Experimentally, it has been observed that the gate current at zero collector voltage follows the same Fowler-Nordheim law as the collector current at high collector voltage, and that for low emission current densities, the sum of gate and collector currents is constant for any collector voltage and is given by the Fowler-Nordheim current I/sub FN/. Based on these observations, a simple model has been developed to calculate the I-V characteristics of a triode. By measuring the Fowler-Nordheim emission, emission area and field enhancement can be obtained assuming a value for the barrier height. Incorporating the gate current, the collector current can be calculated from I/sub c/=I/sub FN/-I/sub g/ as a function of collector voltage. The model's accuracy is best at low current density. At higher emission currents, deviations occur at low collector voltages because the constancy of gate and collector currents is violated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Complex blind source separation for acoustic radiation force impulse imaging in the peripheral vasculature, in vivo (2005)

Complex blind source separation (CBSS) is presented in an application to adaptive clutter filtering for acoustic radiation force impulse (ARFI) imaging in the peripheral vasculature, in vivo. In addition to the conventional challenges of wall filtering for Doppler imaging in peripheral vessels, ARFI imaging introduces the complication of isolating ARFI-induced blood motion from ARFI-induced vessel wall and surrounding elastic tissue motion. Raw RF data was collected using ARFI M-mode imaging sequences from a pulsatile flow vessel phantom, the jugular vein of a male volunteer performing the Valsalva maneuver, and the carotid artery of a female volunteer. The imaginary component of the RF data was computed via the Hilbert transform, and CBSS clutter filtering was performed on the isolated blood signal. Following CBSS filtering, phase-shift estimation reveals radiation force-induced axial blood velocities that peak at 10-25 cm/s. These results demonstrate that CBSS sufficiently rejects elastic tissue and vessel wall signal components to allow for measurement of ARFI-induced axial blood velocities in both phantom and clinical investigation.
DNA-Controlled Partition of Carbon Nanotubes in Polymer Aqueous Two-Phase Systems (2014)

Sorting single-wall carbon nanotubes (SWCNTs) of different chiralities is both scientifically interesting and technologically important. Recent studies have shown that polymer aqueous two-phase extraction is a very effective way to achieve nanotube sorting. However, works published to date have demonstrated only separation of surfactant-dispersed SWCNTs, and the mechanism of chirality-dependent SWCNT partition is not well understood. Here we report a systematic study of spontaneous partition of DNA-wrapped SWCNTs in several polymer aqueous two-phase systems. We show that partition of DNA-SWCNT hybrids in a given polymer two-phase system is strongly sequence-dependent and can be further modulated by salt and polymer additives. With the proper combination of DNA sequence, polymer two-phase system, and partition modulators, as many as 15 single-chirality nanotube species have been effectively purified from a synthetic mixture. As an attempt to provide a unified partition mechanism of SWCNTs dispersed by surfactants and by DNA, we present a qualitative analysis of solvation energy for SWCNT colloids in a polymer-modified aqueous phase. Our observation and analysis highlight the sensitive dependence of the hydration energy on the spatial distribution of hydrophilic functionalities.
Transmission capacity for inhomogeneous overlaid wireless Ad-hoc networks (2013)

在覆盖无线特定的网络的分析，内在的节点分布通常被假定是二独立同类的泊松点进程。在这份报纸，由使用随机的几何学工具，一个新不同类的覆盖无线特定的网络模型被学习，停止概率被分析。由假定那主要( PR )网络节点作为一个泊松点过程( PPP )被散布并且第二等( SR )网络节点作为 Matern 簇被散布过程，一上面并且一为主要网络和第二等的网络的传播能力的更低的界限被介绍。模拟结果证明 PR 和 SR 网络的传播能力将两个都由于 SR 网络的不同类有小增长。
In vivo modulation of extracellular hippocampal glutamate and GABA levels and limbic seizures by group I and II metabotropic glutamate receptor ligands (2004)

The effects of several metabotropic receptor (mGluR) ligands on baseline hippocampal glutamate and GABA overflow in conscious rats and the modulation of limbic seizure activity by these ligands were investigated. Intrahippocampal mGluR group I agonist perfusion via a microdialysis probe [1 mm (R,S)-3,5-dihydroxyphenylglycine] induced seizures and concomitant augmentations in amino acid dialysate levels. The mGlu1a receptor antagonist LY367385 (1 mm) decreased baseline glutamate but not GABA concentrations, suggesting that mGlu1a receptors, which regulate hippocampal glutamate levels, are tonically activated by endogenous glutamate. This decrease in glutamate may contribute to the reported LY367385-mediated anticonvulsant effect. The mGlu5 receptor antagonist 2-methyl-6-(phenylethynyl)-pyridine (50 mg/kg) also clearly abolished pilocarpine-induced seizures. Agonist-mediated actions at mGlu2/3 receptors by LY379268 (100 microm, 10 mg/kg intraperitoneally) decreased basal hippocampal GABA but not glutamate levels. This may partly explain the increased excitation following systemic LY379268 administration and the lack of complete anticonvulsant protection within our epilepsy model with the mGlu2/3 receptor agonist. Group II selective mGluR receptor blockade with LY341495 (1-10 microm) did not alter the rats' behaviour or hippocampal amino acid levels. These data provide a neurochemical basis for the full anticonvulsant effects of mGlu1a and mGlu5 antagonists and the partial effects observed with mGlu2/3 agonists in vivo.
Characterization of lymphotoxin-alpha beta complexes on the surface of mouse lymphocytes (1997)

The lymphotoxin-alpha beta complex (LT alpha beta) is found on the surface of activated lymphocytes and binds to a specific receptor called the LT beta receptor (LT beta R). In the mouse, signaling through this pathway is important for lymph node development and splenic organization, yet the biochemical properties of murine LT alpha and LT beta are essentially unknown. Here we have used soluble receptor-Ig forms of LT beta R and TNF-R55 and mAbs specific for murine LT alpha, LT beta, and LT beta R to characterize the appearance of surface LT alpha beta complexes and LT beta R on several common murine cell lines. Cells that bound LT beta R also bound anti-LT alpha and anti-LT beta mAbs in a FACS analysis. The ability of these reagents to discriminate between surface TNF and LT was verified by analysis of surface TNF-positive, LPS-activated murine RAW 264.7 monocytic cells. Primary mouse leukocytes from spleen, thymus, lymph node, and peritoneum were activated in vitro, and CD4+ and CD8+ T cells as well as B cells expressed surface LT ligand but not the LT beta R. Conversely, elicited peritoneal monocytes/macrophages were surface LT negative yet LT beta R positive. This study shows that on mononuclear cells, surface LT complexes and receptor are expressed similarly in mice and man, and the tools described herein form the foundation for study of the functional roles of the LT system in the mouse.
Intelligent user interface for expert systems applied to power plant maintenance and troubleshooting (1988)

A research and development project is under way to specify, design, construct, and evaluate a user interface system to meet the requirements of a knowledge-based system for gas turbine electronics equipment maintenance and troubleshooting. The user interface is a portable device with text display, video and overlay graphics display, voice recognition and speech production, special-function keypad, and printer. A modular software structure based on a serial communications protocol between the user interface device and expert system host computer provides flexibility, expandability, and a simple, effective user-interface dialog.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Discovery of sarolaner: A novel, orally administered, broad-spectrum, isoxazoline ectoparasiticide for dogs (2016)

The novel isoxazoline ectoparasiticide, sarolaner, was identified during a lead optimization program for an orally-active compound with efficacy against fleas and ticks on dogs. The aim of the discovery program was to identify a novel isoxazoline specifically for use in companion animals, beginning with de novo synthesis in the Zoetis research laboratories. The sarolaner molecule has unique structural features important for its potency and pharmacokinetic (PK) properties, including spiroazetidine and sulfone moieties. The flea and tick activity resides in the chirally pure S-enantiomer, which was purified to alleviate potential off-target effects from the inactive enantiomer. The mechanism of action was established in electrophysiology assays using CHO-K1 cell lines stably expressing cat flea (Ctenocephalides felis) RDL (resistance-to-dieldrin) genes for assessment of GABA-gated chloride channel (GABACls) pharmacology. As expected, sarolaner inhibited GABA-elicited currents at both susceptible (CfRDL-A285) and resistant (CfRDL-S285) flea GABACls with similar potency. Initial whole organism screening was conducted in vitro using a blood feeding assay against C. felis. Compounds which demonstrated robust activity in the flea feed assay were subsequently tested in an in vitro ingestion assay against the soft tick, Ornithodoros turicata. Efficacious compounds which were confirmed safe in rodents at doses up to 30mg/kg were progressed to safety, PK and efficacy studies in dogs. In vitro sarolaner demonstrated an LC80 of 0.3μg/mL against C. felis and an LC100 of 0.003μg/mL against O. turicata. In a head-to-head comparative in vitro assay with both afoxolaner and fluralaner, sarolaner demonstrated superior flea and tick potency. In exploratory safety studies in dogs, sarolaner demonstrated safety in dogs≥8 weeks of age upon repeated monthly dosing at up to 20mg/kg. Sarolaner was rapidly and well absorbed following oral dosing. Time to maximum plasma concentration occurred within the first day post-dose. Bioavailability for sarolaner was calculated at >85% and the compound was highly protein bound (>99.9%). The half-life for sarolaner was calculated at 11-12 days. Sarolaner plasma concentrations indicated dose proportionality over the range 1.25-5mg/kg, and these same doses provided robust efficacy (>99%) for ≥35days against both fleas (C. felis) and multiple species of ticks (Rhipicephalus sanguineus, Ixodes ricinus and Dermacentor reticulatus) after oral administration to dogs. As a result of these exploratory investigations, sarolaner was progressed for development as an oral monthly dose for treatment and control of fleas and ticks on dogs.
Engraftment of human iPS cells and allogeneic porcine cells into pigs with inactivated RAG2 and accompanying severe combined immunodeficiency (2014)

Pigs with severe combined immunodeficiency (SCID) may provide useful models for regenerative medicine, xenotransplantation, and tumor development and will aid in developing therapies for human SCID patients. Using a reporter-guided transcription activator-like effector nuclease (TALEN) system, we generated targeted modifications of recombination activating gene (RAG) 2 in somatic cells at high efficiency, including some that affected both alleles. Somatic-cell nuclear transfer performed with the mutated cells produced pigs with RAG2 mutations without integrated exogenous DNA. Biallelically modified pigs either lacked a thymus or had one that was underdeveloped. Their splenic white pulp lacked B and T cells. Under a conventional housing environment, the biallelic RAG2 mutants manifested a "failure to thrive" phenotype, with signs of inflammation and apoptosis in the spleen compared with age-matched wild-type animals by the time they were 4 wk of age. Pigs raised in a clean environment were healthier and, following injection of human induced pluripotent stem cells (iPSCs), quickly developed mature teratomas representing all three germ layers. The pigs also tolerated grafts of allogeneic porcine trophoblast stem cells. These SCID pigs should have a variety of uses in transplantation biology.
CXCL12-induced chemotaxis is impaired in T cells from patients with ZAP-70-negative chronic lymphocytic leukemia (2010)

Impaired migration towards CXCL12 may reduce the access of T cells from ZAP-70-negative patients to lymphoid organs, creating a less favorable microenvironment for leukemic cell survival and proliferation.
Integrin αvβ5-Mediated TGF-β Activation by Airway Smooth Muscle Cells in Asthma (2011)

Severe asthma is associated with airway remodeling, characterized by structural changes including increased smooth muscle mass and matrix deposition in the airway, leading to deteriorating lung function. TGF-β is a pleiotropic cytokine leading to increased synthesis of matrix molecules by human airway smooth muscle (HASM) cells and is implicated in asthmatic airway remodeling. TGF-β is synthesized as a latent complex, sequestered in the extracellular matrix, and requires activation for functionality. Activation of latent TGF-β is the rate-limiting step in its bioavailability. This study investigated the effect of the contraction agonists LPA and methacholine on TGF-β activation by HASM cells and its role in the development of asthmatic airway remodeling. The data presented show that LPA and methacholine induced TGF-β activation by HASM cells via the integrin αvβ5. Our findings highlight the importance of the β5 cytoplasmic domain because a polymorphism in the β5 subunit rendered the integrin unable to activate TGF-β. To our knowledge, this is the first description of a biologically relevant integrin that is unable to activate TGF-β. These data demonstrate that murine airway smooth muscle cells express αvβ5 integrins and activate TGF-β. Finally, these data show that inhibition, or genetic loss, of αvβ5 reduces allergen-induced increases in airway smooth muscle thickness in two models of asthma. These data highlight a mechanism of TGF-β activation in asthma and support the hypothesis that bronchoconstriction promotes airway remodeling via integrin mediated TGF-β activation.
Distinct metal-binding configurations in metallothionein. (1985)

In a study of the binding stoichiometry of various metals to rat liver metallothionein, the protein appears to coordinate metals in 2 distinct configurations. Ions of at least 18 different metals were shown to associate with the protein suggesting that there is little specificity in binding. Most metals exhibited saturation binding at 7 mol eq forming M7-metallothionein. These included Bi(III), Cd(II), Co(II), Hg(II), In(III), Ni(II), Pb(II), Sb(III), and Zn(II). Others metals including Os(III), Pd(II), Pt(IV), Re(V), Rh(III), and Tl(III) give a positive indication of binding, but stoichiometries were unclear. Ag(I) and Cu(I) bound in clusters as M12-metallothionein. This binding stoichiometry was determined in 3 ways: (a) by determining the equivalence point in Cu- and Ag-titrated samples where resistance to proteolysis is maximal; (b) by determining the point where Zn ions are completely displaced from Zn7-metallothionein; and (c) by direct binding studies. Ag-reconstituted protein, recovered from gel filtration, had an average Ag content of 11.5 g atoms/mol of protein. A similar stoichiometry for the Cu-protein resulted from displacement of Zn from Zn7-metallothionein by Cu(I). The M12-protein was converted to the M7-protein by displacement of Ag(I) or Cu(I) with 7 mol eq of Hg(II). Whereas the distribution of metals in the 2 domains of M7-metallothionein is M4 alpha and M3 beta, the arrangement in the M12-molecule is probably M6 alpha and M6 beta. We propose that metallothionein ligates Ag(I) and Cu(I) in a trigonal geometry by bridging thiolates. This is in contradistinction to a tetrahedral binding geometry in the M7-protein. Distinct binding configurations may result in different tertiary structures for M7- and M12-proteins which may relate to metabolic specificity of Zn-metallothionein and Cu-metallothionein, respectively.
Vaccine-Elicited V3 Loop-Specific Antibodies in Rhesus Monkeys and Control of a Simian-Human Immunodeficiency Virus Expressing a Primary Patient Human Immunodeficiency Virus Type 1 Isolate Envelope (2001)

Vaccine-elicited antibodies specific for the third hypervariable domain of the surface gp120 of human immunodeficiency virus type 1 (HIV-1) (V3 loop) were assessed for their contribution to protection against infection in the simian-human immunodeficiency virus (SHIV)/rhesus monkey model. Peptide vaccine-elicited anti-V3 loop antibody responses were examined for their ability to contain replication of SHIV-89.6, a nonpathogenic SHIV expressing a primary patient isolate HIV-1 envelope, as well as SHIV-89.6P, a pathogenic variant of that virus. Low-titer neutralizing antibodies to SHIV-89.6 that provided partial protection against viremia following SHIV-89.6 infection were generated. A similarly low-titer neutralizing antibody response to SHIV-89.6P that did not contain viremia after infection with SHIV-89.6P was generated, but a trend toward protection against CD4+ T-lymphocyte loss was seen in these infected monkeys. These observations suggest that the V3 loop on some primary patient HIV-1 isolates may be a partially effective target for neutralizing antibodies induced by peptide immunogens.