gebhart/patrepeval huggingface dataset:
Genetic and molecular characterization of the genes involved in short-chain fatty acid degradation in Escherichia coli: the ato system (1987)

The structural organization and regulation of the genes involved in short-chain fatty acid degradation in Escherichia coli, referred to as the ato system, have been studied by a combination of classic genetic and recombinant DNA techniques. A plasmid containing a 6.2-kilobase region of the E. coli chromosome was able to complement mutations in the ato structural genes, atoA (acetyl-coenzyme A [CoA]:acetoacetyl [AA]-CoA transferase) and atoB (thiolase II), as well as mutations in the ato regulatory locus, atoC. Complementation studies performed with mutants defective in acetyl-CoA:AA-CoA transferase suggest that two loci, atoD and atoA, are required for the expression of functional AA-CoA transferase. The ato gene products were identified by in vitro transcription and translation and maxicell analysis as proteins of 48, 26.5, 26, and 42 kilodaltons for atoC, atoD, atoA, and atoB, respectively. In vitro and insertional mutagenesis of the ato hybrid plasmid indicated that the ato structural genes were arranged as an operon, with the order of transcription atoD-atoA-atoB. Although transcribed in the same direction as the atoDAB operon, the atoC gene appeared to use a promoter which was distinct from that used by the atoDAB operon. A delta atoC plasmid expressed the atoD, atoA, and atoB gene products only in strains containing a functional atoC gene. Although the exact mechanism of control was not evident from these studies, the data suggest that the atoC gene product is an activator which is required for the synthesis or activation of the atoDAB-encoded enzymes.
New Neuronal Growth Factors (1984)

The brain's default mode network consists of discrete, bilateral and symmetrical cortical areas, in the medial and lateral parietal, medial prefrontal, and medial and lateral temporal cortices of the human, nonhuman primate, cat, and rodent brains. Its ...Read More
Synthesis of 3′,5′‐Cyclic Phosphate and Thiophosphate Esters of 2′‐C‐Methyl Ribonucleosides (2012)

Abstract 2′‐ C ‐Methylnucleosides are known to exhibit antiviral activity against Hepatitis C virus. Since the inhibitory activity depends on their intracellular conversion to 5′‐triphosphates, dosing as appropriately protected 5′‐phosphates or 5′‐phosphorothioates appears attractive. For this purpose, four potential pro‐drugs of 2′‐ C ‐methylguanosine, i.e. , 3′,5′‐cyclic phosphorothioate of 2′‐ C ‐methylguanosine and 2′‐ C , O 6 ‐dimethylguanosine, 1 and 2 , respectively, the S ‐[(pivaloyloxy)methyl] ester of 2′‐ C , O 6 ‐dimethylguanosine 3′,5′‐cyclic phosphorothioate and the O ‐methyl ester of 2′‐ C , O 6 ‐dimethylguanosine 3′,5′‐cyclic phosphate, 3 and 4 , respectively, have been prepared.
Synthesen in der Purinreihe, XVI1) Über die Darstellung von 5‐Alkyl‐ bzw. 5‐Arylsulfonylamino‐4‐amino‐uracilen, 4‐Amino‐5alkylamino‐uracilen und 4‐Amino‐5‐[pyridino‐methylenamino]‐uracil‐chloriden (1962)

Abstract Aus 4.5‐Diamino‐uracilen und Alkyl‐bzw. Arylsulfochloriden erhält man in Gegenwart von Pyridin die entsprechenden 4‐Amino‐5‐sulfonylamino‐uracile, die sich mit Dialkylsulfat/Natronlauge zu den 5‐ N ‐Alkyl‐Derivaten umsetzen lassen. Diese werden mit Natrium in flüssigem Ammoniak zu 4‐Amino‐5‐alkylamino‐uracilen gespalten. Aus 4‐Amino‐5‐formylamino‐uracilen entstehen mit Sulfochloriden und Pyridin 4‐Amino‐5[pyridinio‐methylenamino]‐uracil‐chloride.
Inactivation of Viable Ascaris Eggs by Reagents during Enumeration (2001)

Various reagents commonly used to enumerate viable helminth eggs from wastewater and sludge were evaluated for their potential to inactivate Ascaris eggs under typical laboratory conditions. Two methods were used to enumerate indigenous Ascaris eggs from sludge samples. All steps in the methods were the same except that in method I a phase extraction step with acid-alcohol (35% ethanol in 0.1 N H(2)SO(4)) and diethyl ether was used whereas in method II the extraction step was avoided by pouring the sample through a 38-microm-mesh stainless steel sieve that retained the eggs. The concentration of eggs and their viability were lower in the samples processed by method I than in the samples processed by method II by an average of 48 and 70%, respectively. A second set of experiments was performed using pure solutions of Ascaris suum eggs to elucidate the effect of the individual reagents and relevant combination of reagents on the eggs. The percentages of viable eggs in samples treated with acid-alcohol alone and in combination with diethyl ether or ethyl acetate were 52, 27, and 4%, respectively, whereas in the rest of the samples the viability was about 80%. Neither the acid nor the diethyl ether alone caused any decrease in egg viability. Thus, the observed inactivation was attributed primarily to the 35% ethanol content of the acid-alcohol solution. Inactivation of the eggs was prevented by limiting the direct exposure to the extraction reagents to 30 min and diluting the residual concentration of acid-alcohol in the sample by a factor of 100 before incubation. Also, the viability of the eggs was maintained if the acid-alcohol solution was replaced with an acetoacetic buffer. None of the reagents used for the flotation step of the sample cleaning procedure (ZnSO(4), MgSO(4), and NaCl) or during incubation (0.1 N H(2)SO(4) and 0.5% formalin) inactivated the Ascaris eggs under the conditions studied.
DNA polymers of protein binding sequences generated by PCR (1990)

Journal Article DNA polymers of protein binding sequences generated by PCR Get access William A. Rudert, William A. Rudert Department of Pediatrics, University of PittsburghPittsburgh, PA 15213–2583, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Massimo Trucco Massimo Trucco * Department of Pediatrics, University of PittsburghPittsburgh, PA 15213–2583, USA * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 21, 21 November 1990, Page 6460, https://doi.org/10.1093/nar/18.21.6460 Published: 21 November 1990 Article history Received: 19 September 1990 Published: 21 November 1990
Structures on T cells and macrophages involved in interleukin 1 (Il-1) secretion by macrophages upon contact with syngeneic thymocytes. (1989)

We demonstrate, using a new rosette method of determination of interleukin 1 activity that macrophages secrete Il-1 upon contact with syngeneic thymocytes or with thymocytes homologous in the Ia region of MHC complex. The phenomenon takes place in the absence of foreign antigen. Blocking of class II MHC antigens on macrophages with monoclonal antibodies against structures of the T-cell receptor complex (alpha/beta T-cell receptor-TCR, CD3 and L3T4) inhibits production of Il-1 to the background level. We conclude that secretion of Il-1 from macrophages, upon contact with syngeneic thymocytes, is triggered by a T-cell signal following interaction: TCR-Ia molecules.
Membrane‐type 6 matrix metalloproteinase (MT6‐MMP, MMP‐25) is the second glycosyl‐phosphatidyl inositol (GPI)‐anchored MMP (2000)

A recently identified membrane-type 6 matrix metalloproteinase (MT6-MMP) has a hydrophobic stretch of 24 amino acids at the C-terminus. This hydrophobicity pattern is similar to glycosyl-phosphatidyl inositol (GPI)-anchored MMP, MT4-MMP, and other GPI-anchored proteins. Thus, we tested the possibility that MT6-MMP was also a GPI-anchored proteinase. Our results showed that MT6-MMP as well as MT4-MMP were labeled with [3H]ethanolamine indicating the presence of a GPI unit with incorporated label. In addition, phosphatidyl inositol-specific phospholipase C treatment released MT6-MMP from the surface of transfected cells. These results strongly indicate that MT6-MMP is a GPI-anchored protein. Since two members of MT-MMPs are now assigned as GPI-anchored proteinase, MT-MMPs can be subgrouped into GPI type and transmembrane type.
Disruption of TLR3 Signaling Due to Cleavage of TRIF by the Hepatitis A Virus Protease-Polymerase Processing Intermediate, 3CD (2020)

Toll-like receptor 3 (TLR3) and cytosolic RIG-I-like helicases (RIG-I and MDA5) sense viral RNAs and activate innate immune signaling pathways that induce expression of interferon (IFN) through specific adaptor proteins, TIR domain-containing adaptor inducing interferon-β (TRIF), and mitochondrial antiviral signaling protein (MAVS), respectively. Previously, we demonstrated that hepatitis A virus (HAV), a unique hepatotropic human picornavirus, disrupts RIG-I/MDA5 signaling by targeting MAVS for cleavage by 3ABC, a precursor of the sole HAV protease, 3Cpro, that is derived by auto-processing of the P3 (3ABCD) segment of the viral polyprotein. Here, we show that HAV also disrupts TLR3 signaling, inhibiting poly(I:C)-stimulated dimerization of IFN regulatory factor 3 (IRF-3), IRF-3 translocation to the nucleus, and IFN-β promoter activation, by targeting TRIF for degradation by a distinct 3ABCD processing intermediate, the 3CD protease-polymerase precursor. TRIF is proteolytically cleaved by 3CD, but not by the mature 3Cpro protease or the 3ABC precursor that degrades MAVS. 3CD-mediated degradation of TRIF depends on both the cysteine protease activity of 3Cpro and downstream 3Dpol sequence, but not 3Dpol polymerase activity. Cleavage occurs at two non-canonical 3Cpro recognition sequences in TRIF, and involves a hierarchical process in which primary cleavage at Gln-554 is a prerequisite for scission at Gln-190. The results of mutational studies indicate that 3Dpol sequence modulates the substrate specificity of the upstream 3Cpro protease when fused to it in cis in 3CD, allowing 3CD to target cleavage sites not normally recognized by 3Cpro. HAV thus disrupts both RIG-I/MDA5 and TLR3 signaling pathways through cleavage of essential adaptor proteins by two distinct protease precursors derived from the common 3ABCD polyprotein processing intermediate.
Comparative Genomics of Herpesviridae Family to Look for Potential Signatures of Human Infecting Strains (2016)

Herpesviridae family is one of the significant viral families which comprises major pathogens of a wide range of hosts. This family includes at least eight species of viruses which are known to infect humans. This family has evolved 180-220 million years ago and the present study highlights that it is still evolving and more genes can be added to the repertoire of this family. In addition, its core-genome includes important viral proteins including glycoprotein B and helicase. Most of the infections caused by human herpesviruses have no definitive cure; thus, search for new therapeutic strategies is necessary. The present study finds core-genome of human herpesviruses that differs from that of Herpesviridae family and nonhuman herpes strains of this family and might be a putative target for vaccine development. The phylogenetic reconstruction based upon the protein sequences of core gene set of Herpesviridae family reveals the sharp splits of its different subfamilies and supports the hypothesis of coevolution of viruses with their hosts. In addition, data mining for cis-elements in the genomes of human herpesviruses results in the prediction of numerous regulatory elements which can be used for regulating the expression of viral based vectors implicated in gene therapies.
Design, Synthesis and Biological Evaluation of Noncovalent Inhibitors of Human CD38 NADase (2012)

Shoot the messenger! CD38 is a multifunctional enzyme responsible for the generation of calcium ion messengers. A structural optimization was carried out to develop noncovalent CD38 inhibitors based on hit compound S125 (top) (IC50=86 μM). The best compound inhibited CD38 NADase with an IC50 value of 4.7 μM (bottom). Molecular modeling was used to predict potentially important interactions between the inhibitor and enzyme.
Coexistence of perinatal and adult forms of a glial progenitor cell during development of the rat optic nerve (1990)

We have studied the developmental appearance of the O-2A(adult) progenitor cell, a specific type of oligodendrocyte-type-2 astrocyte (O-2A) progenitor cell that we have identified previously in cultures prepared from the optic nerves of adult rats. O-2A(adult) progenitors differ from their counterparts in perinatal animals (O-2A perinatal progenitor cells) in antigenic phenotype, morphology, cell cycle time, rate of migration, time course of differentiation into oligodendrocytes or type-2 astrocytes and sensitivity to the lytic effects of complement in vitro. In the present study, we have found that O-2A(adult) progenitor-like cells first appear in the developing optic nerve approximately 7 days after birth and that by 1 month after birth these cells appear to be the dominant progenitor population in the nerve. However, the perinatal-to-adult transition in progenitor populations is a gradual one and O-2A(adult) and O-2A perinatal progenitors coexist in the optic nerve for 3 weeks or more. In addition, cells derived from optic nerves of P21 rats express characteristic features of O-2adult and O-2A perinatal progenitors for extended periods of growth in the same tissue culture dish. Our results thus indicate that the properties that distinguish these two types of O-2A progenitors from each other are expressed in apparently identical environments. Thus, these cells must either respond to different signals present in the environment, or must respond with markedly different behaviours to the binding of identical signalling molecules.
Purification and characterization of a tumor-associated trypsin inhibitor from the urine of a patient with ovarian cancer. (1982)

Immunochemical studies on urine from a patient with ovarian cancer revealed the presence of a tumor-associated peptide. This peptide occurred in elevated concentrations in the urine of some patients with gynecologic cancer, in early amniotic fluid, and in some cancer tumor extracts from these patients as described previously (Stenman, U.-H., Huhtala, M.-L., Koistinen, R., and Seppälä, M. (1982) Int. J. Cancer 30, 53-47). The peptide has now been purified from the urine of a patient with ovarian cancer by gel chromatography, ion exchange chromatography, and reverse phase liquid chromatography. The amino acid composition of the peptide is: Lys (4), Arg (3), Asx (8), Thr (4), Ser (3), Glx (6), Pro (3), Gly (5), Ala (1), Val (2), Ile (3), Leu (4), Tyr (3), Phe (1), and Cys (6). These 56 amino acids correspond to Mr = 62000 for the peptide, a value that is in agreement with the molecular weight established by gel chromatography. The molecule contains no carbohydrate. It is microheterogeneous in charge, the isoelectric point of the main component being 5.8. The purity of the peptide was confirmed by determination of the NH2-terminal amino acid sequence. The 21 residues determined were found to be identical with the corresponding ones of human pancreatic trypsin inhibitor. The purified peptide also inhibited bovine trypsin effectively.
Interaction of rabbit lipoproteins and red blood cells with liposomes of egg yolk phospholipids (1988)

After intravenous injection of liposomes prepared from egg yolk phospholipids into rabbits, the phospholipids were readily assimilated by the lipoproteins, and there were increases in the circulating levels of cholesterol and phospholipids. The increases in cholesterol level were mainly due to increases of free cholesterol. Gradient ultracentrifugation showed that the lipoproteins decreased in density, and gel filtration chromatography showed that they increased in particle size. Upon electrophoresis, they exhibited slower mobility. Liposomes recovered from rabbits 3 hr after the injection contained free cholesterol, apolipoproteins A-I, E and traces of C. The apolipoprotein may target the liposomes for uptake by hepatocytes. Incubation of the liposomes with rabbit red blood cell membranes in vitro caused a decrease in cholesterol content of the membranes. However, the cholesterol/phosphate ratio in red blood cells isolated from the rabbits after the injection of liposomes did not change significantly, suggesting rapid replenishment of red blood cell cholesterol in vivo, possibly by equilibration with lipoprotein cholesterol or tissue cholesterol. These results suggest that the injection of phospholipid liposomes may have an antiatherogenic effect by the removal of tissue cholesterol and enhancing hepatic disposal of cholesterol through the reverse cholesterol transport mechanism.
AUTOMATIC GEO-REGISTRATION FOR PORT SURVEILLANCE (2010)

This paper proposes a new solution to geo-register the nearly feature-less maritime video feeds. We detect the horizon using sizable or uniformly moving vessels, and estimate the vertical apex using water reflections of the street lamps. The computed horizon and apex provide a metric rectification that removes the affine distortions and reduces the searching space for geo-registration. Geo-registration is obtained by searching the best orientation where the estimated water masks on satellite images and camera views are matched. The proposed solution has the following contributions: first, water and coastlines are used as features for registration between horizontally looking maritime views and satellite images. Second, water reflections are proposed to estimate the vertical vanishing point. Third, we give algorithms for the detection of water areas in both satellite images and camera views. Experimental results and applications on cross camera tracking are demonstrated. We also discuss several observations, as well as limitations of the proposed approach.
Antigen-dependent CD28 Signaling Selectively Enhances Survival and Proliferation in Genetically Modified Activated Human Primary T Lymphocytes (1998)

Most tumor cells function poorly as antigen-presenting cells in part because they do not express costimulatory molecules. To provide costimulation to T lymphocytes that recognize tumor cells, we constructed a CD28-like receptor specific for GD2, a ganglioside overexpressed on the surface of neuroblastoma, small-cell lung carcinoma, melanoma, and other human tumors. Recognition of GD2 was provided by a single-chain antibody derived from the GD2-specific monoclonal antibody 3G6. We demonstrate that the chimeric receptor 3G6-CD28 provides CD28 signaling upon specific recognition of the GD2 antigen on tumor cells. Human primary T lymphocytes retrovirally transduced with 3G6-CD28 secrete interleukin 2, survive proapoptotic culture conditions, and selectively undergo clonal expansion in the presence of an antiidiotypic antibody specific for 3G6-CD28. Polyclonal CD8(+) lymphocytes expressing 3G6-CD28 are selectively expanded when cultured with cells expressing allogeneic major histocompatibility complex class I together with GD2. Primary T cells given such an antigen-dependent survival advantage should be very useful to augment immune responses against tumor cells.
Expression of a human gene for polyamine transport in Chinese-hamster ovary cells (1989)

A molecular-genetic approach towards isolating mammalian polyamine-transport genes and their encoded proteins was devised involving the production of Chinese-hamster ovary (CHO) cells expressing a human polyamine-transport protein. CHO cells and a polyamine-transport-deficient CHO mutant cell line (CHOMG) were equally sensitive to the antiproliferative effects of alpha-difluoromethylornithine (DFMO), which blocked endogenous polyamine synthesis. Exposure to exogenous polyamines increased intracellular polyamine levels and reversed this DFMO-induced cytostasis in the CHO cells, but not in the CHOMG cells. CHOMG cells were therefore transfected with human DNA (isolated from HT-29 colon carcinoma cells) and cells expressing the human polyamine-transport system were identified by the ability of these cells to grow in a medium containing DFMO and polyamines. A number of different positive clones were identified and shown to have the capacity for polyamine uptake and an increased sensitivity to the toxic effects of the polyamine analogue methylglyoxal bis(guanylhydrazone). Differences in these properties between the clones are consistent with a multiplicity of polyamine-transport systems. Some clones also showed a change in growth characteristics, which may indicate a relationship between genes involved in the polyamine-transport system and in cell proliferation.
Affinity labeling of cAMP-dependent protein kinase with p-fluorosulfonylbenzoyl adenosine. Covalent modification of lysine 71. (1981)

p-Fluorosulfonylbenzoyl 5'-adenosine (FSO2BzAdo) was shown previously to be an irreversible inhibitor of the catalytic subunit of cAMP-dependent protein kinase II from porcine skeletal muscle (Zoller, M. J., and Taylor, S. S. (1979) J. Biol. Chem. 254, 8363-8368). The catalytic subunit of porcine heart cAMP-dependent protein kinase was also inhibited following incubation with FSO2[14C]BzAdo, and inhibition was shown to result from the stoichiometric, covalent modification of a single lysine residue. The amino acid sequence in an extended region around the carboxybenzenesulfonyl lysine (CBS-lysine) was elucidated by characterizing both tryptic and cyanogen bromide peptides containing the 14C-modified residue. The sequence in this region was Leu-Val-Lys-His-Lys-Glu-Thr-Gly-Asn-His-Phe-Ala-Met-Lys(CBS)-Ile-Leu-Asp-Lys-Glu-Lys-Val-Val-Lys-Leu-Lys-Gln-Ile. The covalently modified residue corresponded to lysine 71 in the overall polypeptide chain. Homologies to bovine heart catalytic subunit and to a site modified by FSO2BzAdo in phosphofructokinase are considered.
Highly Sensitive Multiplex Assay for Detection of Human Immunodeficiency Virus Type 1 and Hepatitis C Virus RNA (2002)

Various nucleic acid assays have been developed and implemented for diagnostics and therapeutic monitoring of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infections. The high-throughput, semiautomated assays described here were developed to provide a method suitable for screening plasma specimens for the presence of HIV-1 and HCV RNAs. Three assays were developed: a multiplex HIV-1/HCV assay for simultaneous detection of HIV-1 and HCV, and discriminatory assays for specific detection of HIV-1 and HCV. The assay systems utilize three proprietary technologies: (i) target capture-based sample preparation, (ii) transcription-mediated amplification (TMA), and (iii) hybridization protection assay (HPA). An internal control is incorporated into each reaction to control for every step of the assay and identify random false-negative reactions. The assays demonstrated a sensitivity of at least 100 copies/ml for each target, and they detected with similar sensitivity all major variants of HCV and HIV-1, including HIV-1 group O strains. Assay sensitivity for one virus was not affected by the presence of the other. The specificity of these TMA-driven assays was >or=99.5% in both normal donor specimens and plasma containing potentially interfering substances or other blood-borne pathogens. Statistical receiver operating characteristic plots of 1 - specificity versus sensitivity data determined very wide analyte cutoff values for each assay at the point at which the assay specificity and sensitivity were both >or=99.5%. The sensitivity, specificity, and throughput capability predict that these assays will be valuable for large-volume plasma screening, either in a blood bank setting or in other diagnostic applications.