gebhart/patrepeval huggingface dataset:
Quantitative Assays for Virus Infectivity (1990)

The infectivity assay is used to titrate virus-containing clarified culture supernatant fluids to determine the 50%-tissue culture infective dose (TCID50) of HIV-1 per ml of original fluid. The ability to measure the amount of infectious virus present in virus-containing fluid is important and useful, particularly for determining the input multiplicity of infection for antiviral experiments [1]. It is a more sensitive and specific assay of virus infectivity than the determination of HIV-1 p24 antigen production or RT activity, as the latter values may also include the measurement of defective virions. This assay can be modified for use with different viral isolates and different cell types.
Diester derivatives as apomorphine prodrugs (1976)

A series of diesters of apomorphine was synthesized to serve as prodrugs. They were converted in vivo to free apomorphine, which could be detected in the brain. Stereotyped gnawing behavior and unilateral rotation similar to that produced by apomorphine were induced by all of the diesters but the time course of action of the latter was prolonged. The duration of action generally increased with the size of the ester substituent and appeared to correlate inversely with the rate of hydrolysis of the esters by liver extracts. It is concluded that the diesters serve as prodrugs of apomorphine and their prolonged duration is partly explained by a decreasing rate of hydrolysis attributable to increased steric hindrance at the acyl carbon atoms.
Structural Basis for HNF-4α Activation by Ligand and Coactivator Binding (2004)

In addition to suggesting that fatty acids are endogenous ligands, our recent crystal structure of HNF-4alpha showed an unusual degree of structural flexibility in the AF-2 domain (helix alpha12). Although every molecule contained a fatty acid within its ligand binding domain, one molecule in each homodimer was in an open inactive conformation with alpha12 fully extended and colinear with alpha10. By contrast, the second molecule in each homodimer was in a closed conformation with alpha12 folded against the body of the domain in what is widely considered to be the active state. This indicates that although ligand binding is necessary, it is not sufficient to induce an activating structural transition in HNF-4alpha as is commonly suggested to occur for nuclear receptors. To further assess potential mechanisms of activation, we have solved a structure of human HNF-4alpha bound to both fatty acid ligand and a coactivator sequence derived from SRC-1. The mode of coactivator binding is similar to that observed for other nuclear receptors, and in this case, all of the molecules adopt the closed active conformation. We conclude that for HNF-4alpha, coactivator rather than ligand binding locks the active conformation.
Analysis of Water Pollution in Gumel Local Government Area, Jigawa State, Nigeria (2014)

Pollution has always been an emotive topic irrespective of whether it occurs in the air, on land or at sea. In the later help of this century much attention has been drawn to water pollution caused by human activities and industrial revolution which experience local levels of high pollution quite unimaginable by present standard. This pollution has passed great risk to the health and immediate surroundings of those involved. It impact is further aggravated by the physical zoning of industrial waste discharge regulation leading to complex problems of water pollution. The conditions characterize the existence of substance in environment in quantities which can be deteriment to the well being of plants and animals
Crystal structure of a soluble fragment of poliovirus 2CATPase (2018)

Poliovirus (PV) 2CATPase is the most studied 2C protein in the Picornaviridae family. It is involved in RNA replication, encapsidation and uncoating and many inhibitors have been found that target PV 2CATPase. Despite numerous investigations to characterize its functions, a high-resolution structure of PV 2C has not yet been determined. We report here the crystal structure of a soluble fragment of PV 2CATPase to 2.55Å, containing an ATPase domain, a zinc finger and a C-terminal helical domain but missing the N-terminal domain. The ATPase domain shares the common structural features with EV71 2C and other Superfamily 3 helicases. The C-terminal cysteine-rich motif folds into a CCCC type zinc finger in which four cysteine ligands and several auxiliary residues assist in zinc binding. By comparing with the known zinc finger fold groups, we found the zinc finger of 2C proteins belong to a new fold group, which we denote the "Enterovirus 2C-like" group. The C-terminus of PV 2CATPase forms an amphipathic helix that occupies a hydrophobic pocket located on an adjacent PV 2CATPase in the crystal lattice. The C-terminus mediated PV 2C-2C interaction promotes self-oligomerization, most likely hexamerization, which is fundamental to the ATPase activity of 2C. The zinc finger is the most structurally diverse feature in 2C proteins. Available structural and virological data suggest that the zinc finger of 2C might confer the specificity of interaction with other proteins. We built a hexameric ring model of PV 2CATPase and visualized the previously identified functional motifs and drug-resistant sites, thus providing a structure framework for antiviral drug development.
Pulmonary Aspergillosis in the Acquired Immunodeficiency Syndrome (1991)

Pulmonary aspergillosis is a possible late complication of AIDS; if diagnosed early, it may be treated successfully.
Substance P-induced Trafficking of β-Arrestins (1999)

Agonist-induced redistribution of G-protein-coupled receptors (GPCRs) and beta-arrestins determines the subsequent cellular responsiveness to agonists and is important for signal transduction. We examined substance P (SP)-induced trafficking of beta-arrestin1 and the neurokinin-1 receptor (NK1R) in KNRK cells in real time using green fluorescent protein. Green fluorescent protein did not alter function or localization of the NK1R or beta-arrestin1. SP induced (a) striking and rapid (<1 min) translocation of beta-arrestin1 from the cytosol to the plasma membrane, which preceded NK1R endocytosis; (b) redistribution of the NK1R and beta-arrestin1 into the same endosomes containing SP and the transferrin receptor (2-10 min); (c) prolonged colocalization of the NK1R and beta-arrestin1 in endosomes (>60 min); (d) gradual resumption of the steady state distribution of the NK1R at the plasma membrane and beta-arrestin1 in the cytosol (4-6 h). SP stimulated a similar redistribution of immunoreactive beta-arrestin1 and beta-arrestin2. In contrast, SP did not affect Galphaq/11 distribution, which remained at the plasma membrane. Expression of the dominant negative beta-arrestin319-418 inhibited SP-induced endocytosis of the NK1R. Thus, SP induces rapid translocation of beta-arrestins to the plasma membrane, where they participate in NK1R endocytosis. beta-Arrestins colocalize with the NK1R in endosomes until the NK1R recycles and beta-arrestins return to the cytosol.
Synthesis of Biodiesel from Castor Oil and Linseed Oil in Supercritical Fluids (2006)

Biodiesel synthesis (transesterification of triglycerides of higher fatty acid to methyl and ethyl esters) from castor oil and linseed oil using methanol and ethanol was investigated at subcritical and supercritical conditions of methanol and ethanol from 200 to 350 °C at 200 bar. The effect of molar ratio of alcohol to oil, temperature, and time was investigated in supercritical methanol and ethanol. The kinetics of the reaction was first order, and the activation energies were determined from the temperature dependence of the rate coefficients. Biodiesel was also synthesized enzymatically with Novozym 435 in supercritical carbon dioxide (ScCO2). The effect of various parameters such as enzyme loading, alcohol to oil molar ratio, temperature, and time was investigated in these systems. A simplified model, based on the Ping Pong Bi Bi with competitive inhibition mechanism, was proposed to describe the enzymatic transesterification kinetics for castor oil with methanol and ethanol.
Clinical Experience With Intravenous and Oral Formulations of the Novel Histone Deacetylase Inhibitor Suberoylanilide Hydroxamic Acid in Patients With Advanced Hematologic Malignancies (2005)

These results suggest that SAHA has activity in hematologic malignancies including HD and select subtypes of non-Hodgkin's lymphoma.
Collision-induced fragmentation of underivatizedN-linked carbohydrates ionized by electrospray (2000)

The electrospray mass spectra and collision-induced fragmentation of neutral N-linked glycans obtained from glycoproteins were examined with a Q-TOF mass spectrometer. The glycans were ionized most effectively as adducts of alkali metals, with lithium providing the most abundant signal and caesium the least. Singly charged ions generally gave higher ion currents than doubly charged ions. Addition of formic acid could be used to produce [M + H]+ ions, but these ions were always accompanied by abundant cone-voltage fragments. The energy required for collision-induced fragmentation was found to increase in a linear manner as a function of mass with the [M + Na]+ ions requiring about four times as much energy as the [M + H]+ ions for complete fragmentation of the molecular ions. Fragmentation of the [M + H]+ ions gave predominantly B- and Y-type glycosidic fragments whereas the [M + Na]+ and [M + Li]+ ions produced a number of additional fragments including those derived from cross-ring cleavages. Little fragmentation was observed from the [M + K]+ and [M + Rb]+ ions and the only fragment to be observed from the [M + Cs]+ ion was Cs+. The [M + Na]+ and [M + Li]+ ions from all the N-linked glycans gave abundant fragments resulting from loss of the terminal GlcNAc moiety and prominent, though weaker, ions as the result of 0,2A and 2,4A cross-ring cleavages of this residue. Most other ions were the result of successive additional losses of residues from the non-reducing terminus. This pattern was particularly prominent with glycans containing several non-reducing GlcNAc residues where successive losses of 203 u were observed. Many of the ions in the low-mass range were products of several different fragmentation routes but still provided structural information. Possibly of most diagnostic importance was an ion formed by loss of 221 u (GlcNAc molecule) from an ion that had lost the 3-antenna and the chitobiose core. This latter ion, although coincident in mass with some other 'internal' fragments, often provided additional information on the composition of the antennae. Other ions defining antenna composition were weak cross-ring fragments produced from the core branching mannose residue. Glycans containing Gal-GlcNAc residues showed successive losses of this moiety, particularly from the B-type fragments resulting from loss of the reducing-terminal GlcNAc residue. The [M + Na]+ and [M + Li]+ ions from high-mannose and hybrid glycans gave a series of ions of composition (Man)nNa/Li+ where n = 1 to the total number of glycans in the molecule, allowing these sugars to be distinguished from the more highly processed complex glycans. Other ions in the spectra of the high-mannose glycans were diagnostic of chain branching but insufficient information was available to determine their mode of formation.
Increasing Sampling Density Improves Reproducibility of Optical Coherence Tomography Measurements (1999)

Increasing the sampling density of OCT scans provides less variable representation of RNFL thickness. The optimal sampling density to achieve maximal reliability of OCT scans remains to be determined.
cAMP-mediated phosphorylation of the low-Km cAMP phosphodiesterase markedly stimulates its catalytic activity. (1988)

Treatment of intact human platelets with the adenylate cyclase agonist forskolin (100 microM) resulted in an increase in cAMP phosphodiesterase activity in freeze-thaw lysates. When the low-Km (high affinity), cGMP-inhibited cAMP phosphodiesterase was isolated from such lysates by blue dextran-Sepharose chromatography, the specific activity of the enzyme was increased an average of 11-fold over similarly processed control platelets. The increase in the low-Km, cGMP-inhibited cAMP phosphodiesterase activity was inhibited when platelets were incubated with the protein kinase inhibitor H-8 prior to treatment with forskolin, suggesting that the stimulation of cAMP phosphodiesterase activity involved a cAMP-dependent phosphorylation. When intact platelets that had been prelabeled with 32Pi were treated with forskolin and the low-Km, cGMP-inhibited phosphodiesterase was isolated by blue dextran-Sepharose chromatography, a protein of 110,000 kDa was phosphorylated. By using a monospecific antiserum to the purified phosphodiesterase, this protein was shown to be the low-Km, cGMP-inhibited cAMP phosphodiesterase by electrophoretic transfer blot (Western blot) analysis and by immunoprecipitation. The stable prostacyclin analog iloprost also stimulated the low-Km cAMP phosphodiesterase activity about 2-fold and caused phosphorylation of the enzyme. These results suggest that phosphorylation of the low-Km, cGMP-inhibited phosphodiesterase may be an important regulatory mechanism for this enzyme in platelets.
Transthoracic Tissue Doppler Imaging of the Atria: A Novel Method to Determine the Atrial Fibrillation Cycle Length (2006)

(1) Tissue Doppler imaging of the atria during transthoracic echocardiography can be used to reliably determine the AFCL during both acute and persistent or permanent AF. (2) Continuous measurement of AFCL with TDI can be used to monitor the effect of antiarrhythmic drugs on atrial rate during AF. (3) This novel method is attractive because of the ease of acquiring the data and its noninvasive character.
Lanthanide Triflate Catalyzed Imino Diels-Alder Reactions; Convenient Syntheses of Pyridine and Quinoline Derivatives (1995)

Lanthanide triflate catalyzed imino Diels-Alder reactions of imines with dienes or alkenes have been developed. A new group of Lewis acids, lanthanide triflates, are quite effective for the catalytic activation of imines. Unique reactivities of imines which work as both dienophiles and azadienes under certain conditions have been revealed. Three-component coupling reactions between aldehydes, amines, and dienes or alkenes were successfully carried out by using lanthanide triflate as a catalyst to afford pyridine and quinoline derivatives in high yields. The Lewis acid catalysts were stable and kept their activity even in the presence of water and amines. A stepwise reaction mechanism for these reactions is suggested from the experimental results.
Straightforward Access to Hexahydropyrrolo[2,3‐b]indole Core by a Regioselective C3‐Azo Coupling Reaction of Arenediazonium Compounds with Tryptamines (2014)

A base-mediated regioselective electrophilic addition of arenediazonium salts at the C3-position of tryptamines followed by cyclization provides an efficient entry to C3-nitrogenated hexahydropyrrolo[2,3-<i>b</i>]indoles (HPIs) that can subsequently be transformed into 3-arylhexahydropyrrolo[2,3-<i>b</i>]indoles and other HPI derivatives. The reaction is the first example of a 1,2-diamination that utilizes easily accessible arenediazonium salts as nitrogenous electrophiles.
Production of Protective Human Antipneumococcal Antibodies by Transgenic Mice with Human Immunoglobulin Loci (2000)

Infections with Streptococcus pneumoniae remain a significant cause of morbidity and mortality. To gain insight into structure-function relationships for human antibodies to pneumococcal capsular polysaccharide (PPS), we studied the response of transgenic mice reconstituted with human immunoglobulin loci, XenoMouse, to PPS antigens in a pneumococcal vaccine. Enzyme-linked immunosorbent assays of sera from mice vaccinated with a 23-valent pneumococcal vaccine revealed that they produced serotype-specific human antibodies, with the greatest response being to the PPS of serotype 3 (PPS 3). Molecular sequence analysis of three monoclonal antibodies (MAbs) to PPS 3 generated from lymphoid cells from mice vaccinated with a 23-valent pneumococcal vaccine or a PPS 3-bovine serum albumin conjugate revealed that they all used heavy-chain immunoglobulin genes from the V(H)3 family, two expressed light chain genes from the human Vkappa1 family, and one expressed a mouse lambda light chain. The protective efficacy of the two MAbs was examined in mice. A 10-microgram dose of both, and a 1-microgram dose of one, significantly prolonged survival from a lethal serotype 3 infection in CBA/N mice. Our data show that XenoMouse mice produced protective, serotype-specific human antibodies to PPS 3, and they lend support to the proposal that these animals represent a useful model to study the human antibody response to PPS antigens.
Quantum point contact as a probe of a topological superconductor (2011)

We calculate the conductance of a ballistic point contact to a superconducting wire, produced by the s-wave proximity effect in a semiconductor with spin-orbit coupling in a parallel magnetic field. The conductance G as a function of contact width or Fermi energy shows plateaus at half-integer multiples of 4e^2/h if the superconductor is in a topologically nontrivial phase. In contrast, the plateaus are at the usual integer multiples in the topologically trivial phase. Disorder destroys all plateaus except the first, which remains precisely quantized, consistent with previous results for a tunnel contact. The advantage of a ballistic contact over a tunnel contact as a probe of the topological phase is the strongly reduced sensitivity to finite voltage or temperature.
Antibiotics for preventing recurrent urinary tract infection in non-pregnant women (2004)

Continuous antibiotic prophylaxis for 6-12 months reduced the rate of UTI during prophylaxis when compared to placebo. After prophylaxis two studies showed nodifference between groups. There were more adverse events in the antibiotic group. One RCT compared postcoital versus continuous daily ciprofloxacin and found no significant difference in rates of UTIs, suggesting that postcoital treatment could be offered to woman who have UTI associated with sexual intercourse.
Signal Peptide Subsegments Are Not Always Functionally Interchangeable (1989)

Bacterial signal peptides display little amino acid sequence homology despite their shared role in mediating protein transport. This heterogeneity may exist to permit the establishment of signal peptide conformations that are appropriate for transport of particular proteins. In this paper we explore how signal peptides are composed of structural units that may interact with each other and with the mature protein to effect transport. Using a new application of cassette mutagenesis, we have replaced the hydrophobic core of the Escherichia coli alkaline phosphatase signal peptide with cores from the signals of maltose-binding protein, OmpA, and M13 major coat protein. The core regions from maltose-binding protein and OmpA effectively replaced the alkaline phosphatase core; the resultant hybrid signals performed as well as wild type in periplasmic transport and processing of alkaline phosphatase. However, the core region from M13 major coat protein generated a transport-incompetent hybrid signal peptide. Elimination of a proline-containing portion of the M13 major coat protein core did not improve transport effectiveness. However, restoration of the procoat cleavage region and the negatively charged amino terminus of the mature protein did ameliorate the transport defect. These results suggest that at least in the case of these procoat-derived signal peptide mutants, there is a requirement for complementarity among the hydrophobic core, cleavage region, and part of the mature protein in order for efficient protein transport to occur.
Schizosaccharomyces pombe UDP‐galactose transporter: identification of its functional form through cDNA cloning and expression in mammalian cells (1999)

The Schizosaccharomyces pombe UDP-galactose transporter cDNA (SpUGT cDNA), encoding the product of the gms1+ gene which consists of two exon sequences separated by a 173-bp intron, was cloned by RT-PCR. Its product, a hydrophobic protein of 353 amino acid residues resembling its human counterpart, was expressed in the Golgi membranes of UDP-galactose transporter-deficient Lec8 cells, and complemented the genetic defect of the mutant cells. This indicated that SpUGT cDNA encodes the functional S. pombe UDP-galactose transporter. The product of an ORF found in the second exon, which was previously assumed to be the S. pombe UDP-galactose transporter, thus represents an inactive, truncated form of the SpUGT protein.
Molecular cloning of a novel rat G‐protein‐coupled receptor gene expressed prominently in lung, adrenal, and liver (1993)

A gene and cDNA (named G10d) encoding a novel member of the G-protein-coupled receptor (GCR) superfamily has been isolated from a rat genomic library and a rat liver cDNA library by tandom polymerase chain reaction (PCR) amplification and hybridization screening. Comparison of the sequence of the encoded protein to other members of the rhodopsin family of the GCR superfamily suggests that this new member is a peptide receptor. The G10d gene is present as a single copy in the rat genome and its translational open reading frame is intronless. Northern analysis demonstrates a wide and uneven distribution of G10d mRNA in the adult rat, with the highest mRNA abundance in lung, liver and adrenal gland extracts.
Protein kinase C regulates the stimulated accumulation of 3-phosphorylated phosphoinositides in platelets (1991)

We have shown that platelets stimulated with thrombin or guanosine 5'-[gamma-thio]triphosphate (GTP[S]), both of which activate phospholipase C and protein kinase C (PKC), show enhancement of 3-phosphorylated phosphoinositide accumulation (3-PPI). We now report the following. (1) Inhibition of thrombin- or GTP[S]-stimulated PKC by pseudo-substrate peptide (RFARK) added to permeabilized platelets markedly inhibits 3-PPI, whereas the serine/threonine phosphatase inhibitor, okadaic acid, promotes 3-PPI. PKC activity, insufficient in itself for fully activating 3-PPI, appears crucial to receptor and post-receptor stimulation of 3-PPI, even when tyrosine phosphorylation is unimpaired. (2) Alteration of Gi by ADP-ribosylation only slightly affects the stimulation of 3-PPI by thrombin, and activation of the G-protein Gi by adrenaline has no effect on 3-PPI. (3) Inhibition of PKC blocks activated secretion of platelet-derived growth factor (PDGF). However, PDGF cannot promote platelet 3-PPI, and thus cannot account for the inhibitory effects of RFARK on 3-PPI.
Spatial Distribution of Cobalt Nanoclusters in Block Copolymers (2002)

This paper describes the selective phase separation of cobalt metal nanoclusters within a PS25300-b-PMMA25900 block copolymer. This selective phase separation was achieved due to the different reactivities of the functional groups in the blocks toward the metal fragments. Transmission electron micrographs showed that the cobalt clusters aggregated primarily in the poly(methyl methacrylate) block, while no cobalt nanoclusters were observed in the polystyrene block, thus creating a patterned distribution that coincided with the morphology of the block copolymer. Fourier transform infrared studies demonstrated the development of a reactive adsorption process between cobalt nanoclusters and the poly(methyl methacrylate) block, as evidenced by the appearance of new absorption bands corresponding to the formation of Co(CO)4- and COO- and the shift of C−C−O and C−O combination bands.
Smoking and vertical bone defects in a Saudi Arabian population. (2005)

The present observations suggest that prevalence and severity of vertical periodontal bone defects are increased in tobacco smokers. The association of vertical bone loss with water pipe smoking is comparable to the association with cigarette smoking.