gebhart/patrepeval huggingface dataset:
Initiation of chondroitin sulfate biosynthesis: A kinetic analysis of UDP-D-xylose:core protein .beta.-D-xylosyltransferase (1991)

The nature of the primary signals important for the addition of xylose to serines on the core protein of the cartilage chondroitin sulfate proteoglycan has been investigated. The importance of consensus sequence elements (Acidic-Acidic-Xxx-Ser-Gly-Xxx-Gly) in the natural acceptor was shown by the significant decrease in acceptor capability of peptide fragments derived by digestion of deglycosylated core protein with Staphylococcus aureus V8 protease, which cleaves within the consensus sequence, compared to the similar reactivity of trypsin-derived peptide fragments, in which consensus sequences remain intact. A comparison of the acceptor efficiencies (Vmax/Km) of synthetic peptides containing the proposed xylosylation consensus sequence and the natural acceptor (deglycosylated core protein) was then made by use of the in vitro xylosyltransferase assay. The two types of substrates were found to have nearly equivalent acceptor efficiencies and to be competitive inhibitors of each other's acceptor capability, with Km = Kiapparent. These results suggest that the artificial peptides containing the consensus sequence are analogues of individual substitution sites on the core protein and allowed the kinetic mechanism of the xylosyltransferase reaction to be investigated, with one of the artificial peptides as a model substrate. The most probable kinetic mechanism for the xylosyltransferase reaction was found to be an ordered single displacement with UDP-xylose as the leading substrate and the xylosylated peptide as the first product released. This represents the first reported formal kinetic mechanism for this glycosyltransferase and the only one reported for a nucleotide sugar:protein transferase.
Studies on Synthetic Nucleosides. I. Trimethylsilyl Derivatives of Pyrimidines and Purines. (1964)

Pyrimidine and purine bases were readily derived to trimethylsilyl derivatives by treatment with trimethylchlorosilane-triethylamine or hexamethyldisilazane. By the infrared investigation, it was clarified that the obtained derivatives possessed aromatic ring systems and physical properties of the product were reported.
Hexofuranosyladenine nucleosides as substrates and inhibitors of calf intestional adenosine deaminase (1979)

A series of hexofuranosyladenine nucleosides have been tested as substrates and inhibitors of adenosine deaminase from calf intestinal mucosa. The nucleosides differed from each other in configuration at the various carbon atoms of the hexose and had either a methyl group or hydroxymethyl group at the terminal position. It has been confirmed that the best substrates have the beta-D or alpha-L configuration at the anomeric position and an hydroxyl group on the same side of the furanose ring as adenine. However, these properties are not minimal and other nucleosides will act as substrates even if they do not have the preferred configurations or groups available. The effect of having two hydroxyl groups in the same region of the molecule and in the preferred configurations was to greatly reduce Vmax. Most structural changes resulted in changes in Vmax, whereas KM values remained fairly close. Only a change in configuration of the hydroxyl group at C-5' caused a dramatic change in affinity, as reflected in the KM. All nucleosides exhibited competitive inhibitory kinetics. In the latter studies also, a change of configuration at C-5' greatly affected binding.
Collectin-11 detects stress-induced L-fucose pattern to trigger renal epithelial injury (2016)

Physiochemical stress induces tissue injury as a result of the detection of abnormal molecular patterns by sensory molecules of the innate immune system. Here, we have described how the recently discovered C-type lectin collectin-11 (CL-11, also known as CL-K1 and encoded by COLEC11) recognizes an abnormal pattern of L-fucose on postischemic renal tubule cells and activates a destructive inflammatory response. We found that intrarenal expression of CL-11 rapidly increases in the postischemic period and colocalizes with complement deposited along the basolateral surface of the proximal renal tubule in association with L-fucose, the potential binding ligand for CL-11. Mice with either generalized or kidney-specific deficiency of CL-11 were strongly protected against loss of renal function and tubule injury due to reduced complement deposition. Ex vivo renal tubule cells showed a marked capacity for CL-11 binding that was induced by cell stress under hypoxic or hypothermic conditions and prevented by specific removal of L-fucose. Further analysis revealed that cell-bound CL-11 required the lectin complement pathway-associated protease MASP-2 to trigger complement deposition. Given these results, we conclude that lectin complement pathway activation triggered by ligand-CL-11 interaction in postischemic tissue is a potent source of acute kidney injury and is amenable to sugar-specific blockade.
A complete library of point substitution mutations in the glucocorticoid response element of mouse mammary tumor virus. (1986)

The glucocorticoid response element (GRE) of mouse mammary tumor virus (MMTV) was chemically synthesized as two complementary DNA strands bearing cohesive termini. During automated synthesis, random mutations were introduced into the DNA by "doping" each of the four nucleoside phosphoramidites (A, G, C, and T) with a low level of the other three. These preparations were annealed and cloned into an M13 phage vector to produce a library of GRE mutants. Mutations within the synthesized region were identified by sequencing phage isolates at random. All of the chemically distinct classes of transition and transversion mutations have been observed. Statistical considerations indicate that the library contains all of the possible 90 point substitution mutations within a 30-nucleotide mutagenic target. So far 88 of these substitutions have been isolated, 74 as single mutants. At least two of the three possible single mutants at each of the 30 positions have been identified.
Advanced glycation end products cause epithelial-myofibroblast transdifferentiation via the receptor for advanced glycation end products (RAGE) (2001)

Tubulointerstitial disease, a prominent phenomenon in diabetic nephropathy, correlates with decline in renal function. The underlying pathogenic link between chronic hyperglycemia and the development of tubulointerstitial injury has not been fully elucidated, but myofibroblast formation represents a key step in the development of tubulointerstitial fibrosis. RAGE, the receptor for advanced glycation end products (AGEs), induces the expression of TGF-beta and other cytokines that are proposed to mediate the transdifferentiation of epithelial cells to form myofibroblasts. Here we report specific binding of (125)I-AGE-BSA to cell membranes prepared from a rat proximal tubule cell line and show that the binding site was RAGE. AGE exposure induced dose-dependent epithelial-myofibroblast transdifferentiation determined by morphological changes, de novo alpha smooth-muscle actin expression, and loss of epithelial E-cadherin staining. These effects could be blocked with neutralizing Ab's to RAGE or to TGF-beta. Transdifferentiation was also apparent in the proximal tubules of diabetic rats and in a renal biopsy from a patient with type 1 diabetes. The AGE cross-link breaker, phenyl-4,5-dimethylthiazolium bromide (ALT 711) reduced transdifferentiation in diabetic rats in association with reduced tubular AGE and TGF-beta expression. This study provides a novel mechanism to explain the development of tubulointerstitial disease in diabetic nephropathy and provides a new treatment target.
Hepatit B ve Hepatit C (1997)

Hepatitis B and Hepatitis CHepatitis B (HBV) and hepatitis C virus (HCV) are two important agents which causing hepatitis transmitted by parenteral route. These viruses are responsible for life treating health problem and remarkable economical loss. Yearly more than million cases of hepatit B and hepatit C are reported all over the world. Chronicty, cirrhosis and hepatocelluler carcinoma are major complications of these diseases. In this article; epidemiolgical features, clinical patterns, therapy and immunization of hepatit B and hepatit C were reviewed.Hepatit B ve C virusu parenteral yolla bulaşan iki önemli hepatit etkenidir. Bu virusların neden olduğu hepatit ciddi sağlık sorunlarına ve önemli ekonomik kayıplara yol açmaktadır. Her yıl milyonlarca insan bu hastalıklara yakalanmaktadır. Kronikleşme, siroz ve hepatosellüler karsinoma önemli komplikasyonlarıdır. Bu derlemede hepatit B ve C&amp;#039;nin epidemiyolojik özellikleri, klinik formları, risk grupları, tedavi ve korunma yöntemleri gözden geçirilmiştir.
Carboxy-Substituted Cinnamides:  A Novel Series of Potent, Orally Active LTB4 Receptor Antagonists (1998)

A series of carboxy-substituted cinnamides were investigated as antagonists of the human cell surface leukotriene B4 (LTB4) receptor. Binding was determined through measurement of [3H]LTB4 displacement from human neutrophils. Receptor antagonism was confirmed through a functional assay, which measures inhibition of Ca2+ release in human neutrophils. Potent antagonists were discovered through optimization of a random screening hit, a p-(alpha-methylbenzyloxy)cinnamide, having low-micromolar activity. Substantial improvement of in vitro potency was realized by the attachment of a carboxylic acid moiety to the cinnamide phenyl ring through a flexible tether, leading to identification of compounds with low-nanomolar potency. Modification of the benzyloxy substituent, either through ortho-substitution on the benzyloxy phenyl group or through replacement of the ether oxygen with a methylene or sulfur atom, produced achiral antagonists of equal or greater potency. The most potent compounds in vitro were assayed for oral activity using the arachidonic acid-induced mouse ear edema model of inflammation. Several compounds in this series were found to significantly inhibit edema formation and myeloperoxidase activity in this model up to 17 h after oral administration. Representatives of this series have been shown to be potent and long-acting orally active inhibitors of the LTB4 receptor.
Molecular characterization of the capsule locus from non‐typeable Staphylococcus aureus (2005)

Most Staphylococcus aureus express a serotype 5 or 8 capsular polysaccharide (CP). However, 20-25% of human isolates and up to 86% of bovine strains of S. aureus are non-typeable (NT), i.e. non-reactive with antibodies to CP types 1, 2, 5 or 8. A vaccine that targets the S. aureus CP would not protect against NT strains. The aim of this study was to characterize NT S. aureus isolates at the molecular level to explain their lack of type 5 or 8 capsule production. The cap5(8) locus was present in all 22 NT clinical isolates from humans, eight of 21 bovine isolates, and in all eight sequenced strains. NT strains positive for the cap5(8) transcript had mutations within essential capsule genes and could be complemented in trans. S. aureus strains with reduced cap5(8) transcript had mutations within the cap5A promoter, decreased RNAIII levels, or a truncated arlR gene product. More than one mutation was identified in several isolates. The cap5(8) locus was replaced by IS257 in 13 of 21 NT bovine isolates of S. aureus. Lack of capsule expression in NT S. aureus can be explained by multiple mechanisms, and the data argue against the existence of capsule serotypes other than 1, 2, 5 and 8.
A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer (2017)

Genomic rearrangements that give rise to oncogenic gene fusions can offer actionable targets for cancer therapy. Here we present a systematic analysis of oncogenic gene fusions among a clinically well-characterized, prospectively collected set of 278 primary colon cancers spanning diverse tumor stages and clinical outcomes. Gene fusions and somatic genetic variations were identified in fresh frozen clinical specimens by Illumina RNA-sequencing, the STAR fusion gene detection pipeline, and GATK RNA-seq variant calling. We considered gene fusions to be pathogenically relevant when recurrent, producing divergent gene expression (outlier analysis), or as functionally important (e.g., kinase fusions). Overall, 2.5% of all specimens were defined as harboring a relevant gene fusion (kinase fusions 1.8%). Novel configurations of <i>BRAF, NTRK3</i>, and <i>RET</i> gene fusions resulting from chromosomal translocations were identified. An R-spondin fusion was found in only one tumor (0.35%), much less than an earlier reported frequency of 10% in colorectal cancers. We also found a novel fusion involving USP9X-ERAS formed by chromothripsis and leading to high expression of ERAS, a constitutively active RAS protein normally expressed only in embryonic stem cells. This USP9X-ERAS fusion appeared highly oncogenic on the basis of its ability to activate AKT signaling. Oncogenic fusions were identified only in lymph node-negative tumors that lacked BRAF or KRAS mutations. In summary, we identified several novel oncogenic gene fusions in colorectal cancer that may drive malignant development and offer new targets for personalized therapy. <i>Cancer Res; 77(14); 3814-22. ©2017 AACR</i>.
A real-time Java server for Real-Time Mach (2002)

The authors have developed a real-time Java server on the Real-Time Mach microkernel which is suitable for embedded systems and distributed real-time systems. By implementing it as a user-level server on Real-Time Mach, applications such as WWW browsers and embedded applications can both execute Java byte codes. They describe the real-time issues in Java and the architecture of the Java server. The real-time extension of the Java server and Java threads using kernel-level and user-level real-time threads was also evaluated.
An experimental multimedia mail system (1988)

A computer-based experimental multimedia mail system that allows the user to read, create, edit, send, and receive messages containing text, images, and voice is discussed.
Functional Characterization of the Human Immunodeficiency Virus Type 1 Genome by Genetic Footprinting (2000)

We present a detailed and quantitative analysis of the functional characteristics of the 1,000-nucleotide segment at the 5' end of the human immunodeficiency virus type 1 (HIV-1) RNA genome. This segment of the viral genome contains several important cis-acting sequences, including the TAR, polyadenylation, viral att site, minus-strand primer-binding site, and 5' splice donor sequences, as well as coding sequences for the matrix protein and the N-terminal half of the capsid protein. The genetic footprinting technique was used to determine quantitatively the abilities of 134 independent insertion mutations to (i) make stable viral RNA, (ii) assemble and release viral RNA-containing viral particles, and (iii) enter host cells, complete reverse transcription, enter the nuclei of host cells, and generate proviruses in the host genome by integration. All of the mutants were constructed and analyzed en masse, greatly decreasing the labor typically involved in mutagenesis studies. The results confirmed the presence of several previously known functional features in this region of the HIV genome and provided evidence for several novel features, including newly identified cis-acting sequences that appeared to contribute to (i) the formation of stable viral transcripts, (ii) viral RNA packaging, and (iii) an early step in viral replication. The results also pointed to an unanticipated trans-acting role for the N-terminal portion of matrix in the formation of stable viral RNA transcripts. Finally, in contrast to previous reports, the results of this study suggested that detrimental mutations in the matrix and capsid proteins principally interfered with viral assembly.
Beyond Bags of Features: Spatial Pyramid Matching for Recognizing Natural Scene Categories (2006)

This paper presents a method for recognizing scene categories based on approximate global geometric correspondence. This technique works by partitioning the image into increasingly fine sub-regions and computing histograms of local features found inside each sub-region. The resulting "spatial pyramid" is a simple and computationally efficient extension of an orderless bag-of-features image representation, and it shows significantly improved performance on challenging scene categorization tasks. Specifically, our proposed method exceeds the state of the art on the Caltech-101 database and achieves high accuracy on a large database of fifteen natural scene categories. The spatial pyramid framework also offers insights into the success of several recently proposed image descriptions, including Torralba’s "gist" and Lowe’s SIFT descriptors.
Expression and function of the ST2 gene in a murine model of allergic airway inflammation (2002)

These results suggest that increases in endogenous mST2 protein after allergen exposure may modulate Th2-mediated airway inflammation, and that in vivo gene transfer of mST2 can be applicable to use in a novel immunotherapy for allergic diseases.
The human beta-globin locus activation region alters the developmental fate of a human fetal globin gene in transgenic mice. (1989)

We linked a 3.3-kilobase fragment containing the entire A gamma-globin gene together with 1.3 kilobases of 5' flanking and 0.37 kilobase of 3' flanking DNA to a 2.5-kilobase fragment containing four of the developmentally stable hypersensitive sites normally located in the 5' region of the human beta-globin locus. This construct was injected into fertilized mouse eggs, and its expression was analyzed in the primitive and definitive erythroid cells, as well as the brain of 14-day embryos. All six transgenic individuals that contained intact copies of the construct expressed the transgene in an erythroid-specific fashion. Expression was observed in both primitive and definitive erythroid cells. This is in marked contrast to previous transgenic mice experiments using the same A gamma-globin gene fragment in isolation, where expression was restricted to primitive erythroid cells. Our results show that the region containing the developmentally stable globin locus hypersensitive sites changes the developmental stage specificity of a human fetal globin gene in transgenic mice. These observations imply that sequences additional to those used here are involved in the developmental control of fetal globin gene expression in vivo. The ability to express fetal globin in adult erythroid cells allows one to consider using fetal globin genes for gene therapy of sickle cell disease.
HIV-1 Fitness Cost Associated with Escape from the VRC01 Class of CD4 Binding Site Neutralizing Antibodies (2015)

Some antibodies that arise during natural HIV-1 infection bind to conserved regions on the virus envelope glycoprotein and potently neutralize the majority of diverse HIV-1 strains. The VRC01 class of antibodies blocks the conserved CD4 receptor binding site interaction that is necessary for viral entry, raising the possibility that viral escape from antibody neutralization might exert detrimental effects on viral function. Here, we show that escape from VRC01 class antibodies can be associated with impaired viral entry and replication; however, during the course of natural infection, compensatory mutations restore the ability of the virus to replicate normally.
Helicobacter hepaticusTriggers Colitis in Specific-Pathogen-Free Interleukin-10 (IL-10)-Deficient Mice through an IL-12- and Gamma Interferon-Dependent Mechanism (1998)

Mice rendered deficient in interleukin-10 (IL-10) by gene targeting (IL-10(-/-) mice) develop chronic enterocolitis resembling human inflammatory bowel disease (IBD) when maintained in conventional animal facilities. However, they display a minimal and delayed intestinal inflammatory response when reared under specific-pathogen-free (SPF) conditions, suggesting the involvement of a microbial component in pathogenesis. We show here that experimental infection with a single bacterial agent, Helicobacter hepaticus, induces chronic colitis in SPF-reared IL-10(-/-) mice and that the disease is accompanied by a type 1 cytokine response (gamma interferon [IFN-gamma], tumor necrosis factor alpha, and nitric oxide) detected by restimulation of spleen and mesenteric lymph node cells with a soluble H. hepaticus antigen (Ag) preparation. In contrast, wild-type (WT) animals infected with the same bacteria did not develop disease and produced IL-10 as the dominant cytokine in response to Helicobacter Ag. Strong H. hepaticus-reactive antibody responses as measured by Ag-specific total immunoglobulin G (IgG), IgG1, IgG2a, IgG2b, IgG3, and IgA were observed in both WT and IL-10(-/-) mice. In vivo neutralization of IFN-gamma or IL-12 resulted in a significant reduction of intestinal inflammation in H. hepaticus-infected IL-10(-/-) mice, suggesting an important role for these cytokines in the development of colitis in the model. Taken together, these microbial reconstitution experiments formally establish that a defined bacterial agent can serve as the immunological target in the development of large bowel inflammation in IL-10(-/-) mice and argue that in nonimmunocompromised hosts IL-10 stimulated in response to intestinal flora is important in preventing IBD.
Biochemical characterization of proteins that co-purify with class II antigens of the murine MHC. (1988)

Careful analysis of affinity-purified class II molecules (Ia Ag) from the murine MHC revealed the existence of a set of associated molecules that consistently co-purified with the Ia Ag. SDS-PAGE revealed that molecules of Mr of 41 to 43 kDa and 56 to 58 kDa were associated with the affinity-purified I-Ak Ag from the AKR B cell lymphoma AKTB-1b. Two-dimensional electrophoresis (IEF vs SDS-PAGE) allowed further characterization of four molecules in the 41- to 43-kDa range and two in the 56- to 58-kDa range. All co-purifying proteins had isoelectric points between 5.2 and 6.2. The specificity of the association of the co-purifying molecules with the I-Ak Ag was established by using two criteria. First, with the exception of actin, proteins co-purifying with the I-Ak molecule were not found in samples of affinity-purified class I (H-2Kk) Ag or membrane Ig from the AKTB-1b lymphoma. Second, the use of the amino group-reactive homobifunctional cross-linker 3,3'-dithiobisproprionimidate with crude membranes from AKTB-1b increased the relative amount of materials co-purifying with I-Ak. The use of the membrane-impermeant cross-linker 3,3'-dithiobis(sulfosuccinimidyl) proprionate provided evidence that the interaction between I-Ak and one or more of the co-purifying components occurs on the cytoplasmic face of the membrane. Two of the co-purifying molecules have been identified. The major material in the 41- to 43-kDa range was partially sequenced, leading to its identification as cytoplasmic actin. One of the components in the 56- to 58-kDa range was tentatively identified as one of the isozymes (RII) of the regulatory subunit of the cAMP-dependent protein kinase, based on the use of the photoaffinity label 8-azido-cAMP.