gebhart/patrepeval huggingface dataset:
Novel Fluorogenic Substrates for Assaying Retroviral Proteases by Resonance Energy Transfer (1990)

The 11-kD protease (PR) encoded by the human immunodeficiency virus 1 (HIV-1) is essential for the correct processing of viral polyproteins and the maturation of infectious virus, and is therefore a target for the design of selective acquired immunodeficiency syndrome (AIDS) therapeutics. To facilitate the identification of novel inhibitors of HIV-1 PR, as well as to permit detailed studies on the enzymology and inhibition of this enzyme, a continuous assay for its activity was developed that was based on intramolecular fluorescence resonance energy transfer (RET). The assay used the quenched fluorogenic substrate 4-(4-dimethylaminophenylazo)benzoic acid (DABCYL)--Ser Gln Asn Tyr Pro Ile Val Gln--5-[(2-aminoethyl)amino]naphthalene-1 sulfonic acid (EDANS), whose peptide sequence is derived from a natural processing site for HIV-1 PR. Incubation of recombinant HIV-1 PR with the fluorogenic substrate resulted in specific cleavage at the Tyr-Pro bond and a time-dependent increase in fluorescence intensity that was linearly related to the extent of substrate hydrolysis. An internally quenched fluorogenic substrate was also designed that was selectively cleaved by the related PR from avian myeloblastosis virus (AMV). The fluorescence quantum yields of the HIV-1 PR and AMV PR substrates in the RET assay increased by 40.0- and 34.4-fold, respectively, per mole of substrate cleaved. Because of its simplicity, rapidity, and precision in the determination of reaction rates required for kinetic analysis, this method offers many advantages over the commonly used high-performance liquid chromatography- or electrophoresis-based assays for peptide substrate hydrolysis by retroviral PRs.
Ligand-induced internalization selects use of common receptor neuropilin-1 by VEGF165 and semaphorin3A (2006)

Neuropilin-1 (Npn-1) is a receptor shared by class 3 semaphorins and heparin-binding forms of vascular endothelial growth factor (VEGF), protein families that regulate endothelial and neuronal-cell function. Ligand interaction with Npn-1 dictates the choice of signal transducer; plexins transduce semaphorin signals, and VEGF receptors transduce VEGF signals. It is not clear how class 3 semaphorins affect endothelial-cell function and how the shared receptor Npn-1 selects its ligand. We report that semaphorin3A (Sema3A) inhibits endothelial-cell lamellipodia formation, adhesion, survival, proliferation, and cord formation. VEGF(165), but not VEGF(121), could block all these effects of Sema3A. VEGF(165) competed with Sema3A for binding to endothelial cells, effectively reduced cell-surface Npn-1, and promoted its internalization. Use of soluble forms of Npn-1 or VEGF receptor-1 to block VEGF(165) binding to Npn-1 or to VEGF receptors provided evidence that surface Npn-1 and VEGF receptors are required for VEGF(165)-induced Npn-1 internalization. Sema3A also reduced cell-surface Npn-1 in endothelial cells and promoted its internalization, but required a higher concentration than VEGF(165). These results demonstrate that preferential receptor binding and internalization by a ligand are mechanisms by which the common receptor Npn-1 can play an essential role in prioritizing conflicting signals.
Stimulation of Integrin-mediated Cell Contractility by Fibronectin Polymerization (2000)

Ligation of integrins with extracellular matrix molecules induces the clustering of actin and actin-binding proteins to focal adhesions, which serves to mechanically couple the matrix with the cytoskeleton. During wound healing and development, matrix deposition and remodeling may impart additional tensile forces that modulate integrin-mediated cell functions, including cell migration and proliferation. We have utilized the ability of cells to contract floating collagen gels to determine the effect of fibronectin polymerization on mechanical tension generation by cells. Our data indicate that fibronectin polymerization promotes cell spreading in collagen gels and stimulates cell contractility by a Rho-dependent mechanism. Fibronectin-stimulated contractility was dependent on integrin ligation; however, integrin ligation by fibronectin fragments was not sufficient to induce either tension generation or cell spreading. Furthermore, treatment of cells with polyvalent RGD peptides or pre-polymerized fibronectin did not stimulate cell contractility. Fibronectin-induced contractility was blocked by agents that inhibit fibronectin polymerization, suggesting that the process of fibronectin polymerization is critical in triggering cytoskeletal tension generation. These data indicate that Rho-mediated cell contractility is regulated by the process of fibronectin polymerization and suggest a novel mechanism by which extracellular matrix fibronectin regulates cytoskeletal organization and cell function.
Nosography and immunopathogenesis of viral hepatitis. (1992)

Five viruses are responsible for the vast majority of cases of viral related hepatitis. They have been named hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), hepatitis E virus (HEV). The more recent literature concerning the viral structure, the epidemiology, the serological identification, the clinical course and the prevention of each type of hepatitis is reviewed. HBV is not directly cytopathic. Hepatitis is a consequence of the destruction of the virus-infected cells. The efficient elimination of the virus relies on the viral antigenic determinants (HBs, pre-S1, pre-S2, HBc, HBe) and on the immune system of the host. The viral persistence may be caused by defect of the host immunity (interferon production, T and B lymphocyte function) or by factors related to the virus such as a genome mutation (lack of HBe formation). Some evidence suggesting an immunopathogenetic mechanism also for HCV, HDV and HAV is reported.
Purification and characterization of multiple components of human lymphoblastoid interferon-alpha. (1992)

Twenty-two components of human interferon-alpha (IFN-alpha) derived from Sendai virus-induced Namalwa cells were purified by sequential immunoadsorbent affinity chromatography using four monoclonal antibody affinity columns followed by ultrafiltration and reversed-phase high-performance liquid chromatography. The specific activity ranged from 0.2 to 2.6 x 10(8) IU/mg protein on Madin-Darby bovine kidney cells, 0.3 to 4.6 x 10(8) IU/mg protein on human WISH cells, and 10(4) to 7 x 10(5) units/mg protein on mouse L929 cells. The apparent molecular weights of the components ranged from 17,500 to 23,300 using nonreducing sodium dodecyl polyacrylamide-gel electrophoresis and 17,500 to 27,600 using reducing sodium dodecyl polyacrylamide-gel electrophoresis. The amino-terminal amino acid sequences were similar among the components as well as to those reported for the cloned human IFN-alpha genes (Pestka, S. (1986) Methods Enzymol. 119, 3-14). However, four components, f, i, l, and m, have amino-terminal amino acid sequences which appear to be unique when compared to those predicted from the cDNA clones. One component, pre-a, has a potential N-linked glycosylation site on the Asn of residues 2 through 4, Asn-Leu-Ser.
A single serine residue confers tetrodotoxin insensitivity on the rat sensory‐neuron‐specific sodium channel SNS (1997)

Sensory neurons express a sodium channel (SNS) that is highly resistant to block by tetrodotoxin (IC50 = 60 microM). SNS is 65% homologous to the cardiac sodium channel, in which a single hydrophilic residue in the SS2 segment is critical for tetrodotoxin resistance. By site-directed mutagenesis, we have substituted phenylalanine for serine at the equivalent position in SNS: this mutated (S356F) SNS channel is functionally similar to wild-type SNS when expressed in Xenopus oocytes, but is potently blocked by tetrodotoxin and saxitoxin with IC50s of 2.8 nM and 8.2 nM, respectively. These data provide clues to the rational design of selective blockers of SNS with potential as analgesic drugs.
Expression and Y435-phosphorylation of Abelson interactor 1 (Abi1) promotes tumour cell adhesion, extracellular matrix degradation and invasion by colorectal carcinoma cells (2014)

Our data indicate that phosphorylated Abi1 contributes to the invasive properties of colorectal cancer.
Chemical Constituents and Their Bioactivities of “Tongling White Ginger” (Zingiber officinale) (2011)

Gingerols and their corresponding dehydration products shogaols were considered as the active principles of ginger, the rhizome of the plant Zingiber officinale, for its antioxidant, anti-inflammatory, and antitumor activities. Ginger (Z. officinale) has been cultivated for thousands of years as a spice and for medicinal purposes in China. Tongling (Anhui province, China) has traditionally been regarded as an ideal cultivation place. "Tongling White Ginger" enjoys a reputation for being one of the top gingers in China for its thin white peel, tender flesh, rich juice, and flavor. In this study, we have isolated and identified two novel gingerdione dimers, bisgingerdiones A (1) and B (2); two new gingerol derivatives, (5R)-5-acetoxy-1,7-bis(4-hydroxy-3-methoxyphenyl)heptan-3-one (3) and methyl (Z)-neral acetal-[6]-gingerdiol (4); and 38 known compounds (5-42) from rhizomes of Zingiber officinale collected from Tongling, China. Their structures were elucidated by means of spectroscopic methods. Compounds 1-4 showed weak cytotoxic and anti-HIV-1 activities. Compounds 6, 8, and 26 showed inhibitory activities against human and mouse 11β-HSD1 (11β-hydroxysteroid dehydrogenases) with IC(50) values between 1.09 and 1.30 μM.
Intelligent microrobot DDS (drug delivery system) measured and controlled by ultrasonics (2002)

Proposes a new concept of a micro-robot drug delivery system (DDS) in which drug-carriers of air-filled microcapsules are measured with echography and are controlled with resonant ultrasound. The authors have confirmed physical possibility of resonance design of drug-carriers depending on shell structure of microcapsule. Furthermore, as a measurement system for microrobot DDS, they have developed novel echographic imaging system. Path lines of microcapsules in the blood flow were clearly visualized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Scarcity of ars sequences isolated in a morphogenesis mutant of the yeast Yarrowia lipolytica (1991)

Previous attempts is isolate autonomously replicating sequences (ars) from the dimorphic yeast Yarrowia lipolytica have been unsuccessful. We isolated a Fil- mutant unable to produce hyphae and growing only in a yeast form to facilitate ars isolation. This mutant was transformed with a Y. lipolytica DNA bank and several unstable clones were obtained. Extrachromosomal plasmids were evidenced in yeast, recovered in Escherichia coli and characterized by restriction mapping. They were able to retransform Fil- and Fil+ yeast strains at high frequency and transformants displayed a slightly unstable phenotype. The detailed analysis of the plasmids showed that only two different ars sequences had been isolated, each of them corresponding to a unique sequence in the Y. lipolytica genome. We concluded that functional ars sequences that can be cloned on plasmids are rare in this yeast.
Mechanical Treatment of Plantar Fasciitis (2001)

A randomized, prospective study was conducted to compare the effectiveness of three individual mechanical modalities in the treatment of plantar fasciitis. Two hundred fifty-five subjects were randomly assigned to one of three treatment groups: custom-made orthoses, over-the-counter arch supports, or tension night splints. Subjects were treated for 3 months, with follow-up visits at 2, 6, and 12 weeks. No statistically significant difference was noted among treatment groups with respect to final outcomes based on first-step pain or pain felt during the day. However, there was a statistically significant difference among the three groups with respect to early patient withdrawal from the study due to continued severe pain, noncompliance, or inability to tolerate the device. Patient compliance was greatest with the use of custom-made orthoses.
BindingDB Entry 5199: Molecular and ligand-binding characterization of the sigma-receptor in the Jurkat human T lymphocyte cell line. (2012)

The sigma binding site present in the Jurkat human T lymphocyte cell line was investigated. Jurkat cell membranes were found to have a single saturable binding site for [3H]haloperidol, a sigma ligand (dissociation constant, 3.9 +/- 0.3 nM). The binding of [3H]haloperidol was inhibited by several sigma ligands. Northern analysis and reverse transcription-polymerase chain reaction provided evidence for the expression of the recently cloned type 1 sigma-receptor (sigma-R1) in Jurkat cells. The sigma-R1 cDNA cloned from these cells was functional in heterologous expression systems. When expressed in mammalian cells, the cDNA-induced binding was saturable with dissociation constants of 1.9 +/- 0.3 nM for [3H]haloperidol and 12 +/- 2 nM for (+)-pentazocine. The binding of [3H]progesterone, a putative endogenous ligand to sigma-R1, to the Jurkat cell sigma-receptor could be directly demonstrated by using heterologously expressed sigma-R1 cDNA. The binding of [3H]progesterone was saturable, with a dissociation constant of 88 +/- 7 nM. Progesterone and haloperidol interacted with the receptor competitively. Reverse transcription-polymerase chain reaction also produced evidence for the existence of an alternatively spliced sigma-R1 variant in Jurkat cells. This splice variant was found to be nonfunctional in ligand binding assays. This constitutes the first report on the molecular characterization of the sigma-receptor in immune cells.
Review of Atrophic Gastritis and Intestinal Metaplasia as a Premalignant Lesion of Gastric Cancer (2015)

Atrophic gastritis (AG) and intestinal metaplasia (IM) are the main precursor lesions of gastric cancer as the incidence of gastric cancer increases in the gastric mucosa involved with AG and IM. The prevalence of AG and IM vary depending on countries, even it represents diverse results in the same nation. Usually AG is antecedent of IM but the etiologies of AG and IM are not always the same. The sensitivity and specificity of diagnostic methods to detect AG and IM are different. Furthermore, the management strategy of AG and IM has not been established, yet. Helicobacter pylori infection has been proved as the most important cause of AG and IM. Thus the eradication of H. pylori is very important to prevent the progression to gastric cancer which is still placed in the high rank in morbidity and mortality among cancers. However, the reversibility of AG and IM by eradication of H. pylori which was assumed to be certain by meta-analysis is; however, controversial now. Therefore, the understanding and early diagnosis of AG and IM are very important, especially, in high incidence area of gastric cancer such as Republic of Korea.
VoxCeleb2: Deep Speaker Recognition (2018)

The objective of this paper is speaker recognition under noisy and unconstrained conditions. We make two key contributions. First, we introduce a very large-scale audio-visual speaker recognition dataset collected from open-source media. Using a fully automated pipeline, we curate VoxCeleb2 which contains over a million utterances from over 6,000 speakers. This is several times larger than any publicly available speaker recognition dataset. Second, we develop and compare Convolutional Neural Network (CNN) models and training strategies that can effectively recognise identities from voice under various conditions. The models trained on the VoxCeleb2 dataset surpass the performance of previous works on a benchmark dataset by a significant margin.
Improved Measurements in Conductivity for Highly Disorganized Resistive Materials (2014)

Determining the electrical properties of highly insulating materials can be a challenging task. These materials are designed to greatly resist the flow of electrical current. This makes them useful for various applications including terrestrial transmission lines, spacecraft charging, and capacitor-driven charge storage devices. Every year over 370 billion kWhr are lost during transportation along power lines in the US. That is roughly $36B which is thrown away each year due to inefficiency in our power transmission network (1). Due to the fact that satellites are isolated from ground, charging caused by the plasma environment found at typical orbital radii (2) is of concern to the designers of modern spacecraft (3). In an effort to measure extremely low currents and low conductivity, the Utah State University Materials Physics Group has designed a Constant Voltage Chamber (CVC) capable of measuring conductivity with a low degree of uncertainty. Over the last nine years, many changes have been made to improve the accuracy and precision of measurements made with the CVC, now allowing currents as low as hundreds of atto-amps to be measured (3, 4, 5,6). Through the use of a variety of data analysis programs, numerous studies of the conductivity, current, and temperature have been done with detailed error analysis. Statistical analysis has been performed for the data collected and the instrumentation error for the system has been determined (7). These data have allowed for analysis of the different aspects of current, and allowed for better measurements to be made. Using these measurements we have been able to create a model for the rate of change for the different aspects of current involved with a highly resistive material.
Differential Effect of Site-directed Mutations in pelC on Pectate Lyase Activity, Plant Tissue Maceration, and Elicitor Activity (1996)

Oligonucleotide site-directed mutations were introduced into the pelC gene of Erwinia chrysanthemi EC16 that directed single or double amino acid changes affecting disulfide linkages, calcium binding, catalysis, and protein folding. Subsequent characterization of the purified PelC mutant proteins demonstrated that pectinolytic function involves amino acids located near the calcium binding site rather than those surrounding an invariant vWiDH sequence. Wild-type PelC and the tested mutant proteins generally macerated plant tissue in proportion to their specific pectinolytic activity in vitro. However, some mutants gave higher maceration activity in plant tissue and elicited greater production of the phytoalexin, glyceollin, in soybean cotyledons than predicted by their in vitro pectinolytic activity. Most notable in this regard were three different mutations at lysine 172 with greatly reduced pectinolytic activity but as much elicitor activity as the wild-type protein. PelE macerated plant tissue 10 times more efficiently than PelC, as observed previously, but surprisingly showed equal activity in the elicitor assay. The results indicate that factors other than pectinolytic activity per se are involved in plant tissue maceration and elicitor activity.
Manual deskterity (2010)

Manual Deskterity is a prototype digital drafting table that supports both pen and touch input. We explore a division of labor between pen and touch that flows from natural human skill and differentiation of roles of the hands. We also explore the simultaneous use of pen and touch to support novel compound gestures.
THE EVOLUTION OF POSTZYGOTIC ISOLATION: ACCUMULATING DOBZHANSKY-MULLER INCOMPATIBILITIES (2001)

Hybrid sterility and inviability often result from the accumulation of substitutions that, while functional on their normal genetic backgrounds, cause a loss of fitness when brought together in hybrids. Previous theory has shown that such Dobzhansky-Muller incompatibilities should accumulate at least as fast as the square of the number of substitutions separating two species, the so-called snowball effect. Here we explicitly describe the stochastic accumulation of these incompatibilities as a function of time. The accumulation of these incompatibilities involves three levels of stochasticity: (1) the number of substitutions separating two allopatric lineages at a given time; (2) the number of incompatibilities resulting from these substitutions; and (3) the fitness effects of individual incompatibilities. Previous analyses ignored the stochasticity of molecular evolution (level 1) as well as that due to the variable effects of incompatibilities (level 3). Here we approximate the full stochastic process characterizing the accumulation of hybrid incompatibilities between pairs of loci. We derive the distribution of the number of incompatibilities as a function of divergence time between allopatric taxa as well as the distribution of waiting times to speciation by postzygotic isolation. We provide simple approximations for the mean and variance of these waiting times. These results let us estimate. albeit crudely, the probability, p, that two diverged sites from different species will contribute to hybrid sterility or inviability. Our analyses of data from Drosophila and Bombina suggest that p is generally very small, on the order of 10(-6) or less.
A phase 1 trial of the anti-KIR antibody IPH2101 in patients with relapsed/refractory multiple myeloma (2012)

Natural killer (NK) cells elicit cytotoxicity against multiple myeloma (MM); however, MM cells express HLA class I molecules as ligands to NK cell inhibitory killer immunoglobulin-like receptors (KIRs) as a means of immunoevasion. KIR-ligand mismatch may improve outcomes in allogeneic transplantation for MM. Extrapolating on this concept, we conducted a phase 1 trial of IPH2101, an anti-KIR antibody, in patients with relapsed/refractory MM. IPH2101 was administered intravenously every 28 days in 7 dose-escalated cohorts (0.0003-3 mg/kg) for up to 4 cycles. Pharmacokinetic, pharmacodynamic, and correlative immunologic studies were completed. A total of 32 patients were enrolled. The biologic endpoint of full KIR2D occupancy across the dosing cycle was achieved without dose-limiting toxicity or maximally tolerated dose. One severe adverse event was noted. Pharmacokinetic and pharmacodynamic findings approximated preclinical predictions, and IPH2101 enhanced ex vivo patient-derived NK cell cytotoxicity against MM. No objective responses were seen. No evidence of autoimmunity was observed. These findings suggest that IPH2101 is safe and tolerable at doses that achieve full inhibitory KIR saturation, and this approach warrants further development in MM. This trial was registered at www.clinicaltrials.gov as #NCT00552396.
High affinity type I interleukin 1 receptor antagonists discovered by screening recombinant peptide libraries. (1996)

Two families of peptides that specifically bind the extracellular domain of the human type I interleukin I (IL-1) receptor were identified from recombinant peptide display libraries. Peptides from one of these families blocked binding of IL-lalpha to the type I IL-1 receptor with IC50 values of 45-140 microM. Affinity-selective screening of variants of these peptides produced ligands of much higher affinity (IC50 approximately 2 nM). These peptides block IL-1-driven responses in human and monkey cells; they do not bind the human type II IL-1 receptor or the murine type I IL-1 receptor. This is the first example (that we know of) of a high affinity peptide that binds to a cytokine receptor and acts as a cytokine antagonist.