gebhart/patrepeval huggingface dataset:
Cloning and molecular characterization of a gene involved in Salmonella adherence and invasion of cultured epithelial cells (1993)

Our laboratories have independently identified a gene in Salmonella choleraesuis and Salmonella typhimurium that is necessary for efficient adherence and entry of these organisms into cultured epithelial cells. Introduction of a mutated gene into several Salmonella strains belonging to different serotypes rendered these organisms deficient for adherence and invasion of cultured cells. This effect was most pronounced in the host-adapted serotypes Salmonella gallinarum, S. choleraesuis, and Salmonella typhi. The nucleotide sequence of this gene, which we have termed invH, encodes a predicted 147-amino-acid polypeptide containing a signal sequence. The InvH predicted polypeptide is highly conserved in S. typhimurium and S. choleraesuis, differing at only three residues. The invH gene was expressed in Escherichia coli using a T7 RNA polymerase expression system and a polypeptide of approximately 16,000 molecular weight was observed, in agreement with the predicted size of its gene product. Upon fractionation, the expressed polypeptide was localized in the bacterial membrane fraction. Southern and colony hybridization analyses indicated that the invH gene is present in all Salmonella strains tested (91 strains belonging to 37 serotypes) with the exception of strains of Salmonella arizonae. No homologous sequences were detected in Yersinia, Shigella, Proteus, and several strains of enteroinvasive and enteropathogenic E. coli. Downstream from the S. choleraesuis (but not S. typhimurium) invH gene, a region with extensive homology to the insertion sequence IS3 was detected.
Spatial Characterization of Water Quality in Seven Eastern Kentucky Reservoirs Using Multivariate Analyses (2001)

Abstract We conducted water quality surveys along seven eastern Kentucky reservoirs three times during the 1994 growing season in order to understand the spatial variability within and between impoundments from a common geological setting. Sixteen parameters were measured at sites along the reservoirs representing each zone (riverine, transition, or lacustrine), and eight of these parameters displayed a statistically significant site/zone effect. Most of these were particle-associated parameters (total Fe, NH4+, total suspended solids, and total phosphorus) that decreased significantly down-reservoir. Water transparency increased significantly down-reservoir, in accordance with this pattern. Temperature and dissolved oxygen also showed a significant spatial effect, as temperature was highest towards the riverine end and dissolved oxygen was highest at the lacustrine end. Six parameters showed significant variability among these reservoirs, including ammonium and chlorophyll a. The remaining four (conductivity, sulfate, alkalinity and pH) displayed similar patterns across reservoirs apparently as a result of local geologic attributes. Another goal of this work was to use a multivariate statistical approach to aid in understanding the relationships between water quality parameters in this region and to group zones within a reservoir according to their similarities in water quality. Principal Components Analysis reduced sixteen parameters to five principal components that accounted for 74 percent of the total variability in water quality. Two of these principal components contained all of the particle-associated and local-geologic parameters, and accounted for 42% of the total variability. Cluster analyses showed that the water quality signatures of two reservoirs were quite different from the rest. Interestingly, these represented the most pristine and most disturbed watersheds of all seven systems. Our findings are relevant to the management of these and other similar reservoir systems.
C1 Coupling via bromine activation and tandem catalytic condensation and neutralization over CaO/zeolite compositesElectronic supplementary information (ESI) available: additional figures. See http://www.rsc.org/suppdata/cc/b3/b314118g/ (2004)

We demonstrate here an alternative scheme for C(1) coupling by way of methane bromination, followed by concurrent bromomethane condensation and quantitative HBr neutralization; regeneration of the metal oxide with O(2) with recovery of Br(2) completes the cycle.
ChemInform Abstract: Interaction Between Functional Groups and Its Consequences in Oxidation of Thioethers (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Integrating functional genomic information into the Saccharomyces Genome Database (2000)

The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the 'locus page' and directs users to the detailed information they seek. SGD is endeavoring to integrate the existing information about yeast genes with the large volume of data generated by functional analyses that are beginning to appear in the literature and on web sites. New features will include searches of systematic analyses and Gene Summary Paragraphs that succinctly review the literature for each gene. In addition to current information, such as gene product and phenotype descriptions, the new locus page will also describe a gene product's cellular process, function and localization using a controlled vocabulary developed in collaboration with two other model organism databases. We describe these developments in SGD through the newly reorganized locus page. The SGD is accessible via the WWW at http://genome-www.stanford.edu/Saccharomyces/
Purification and Properties of 3-Ketosucrose-forming Enzyme from the Cells of Agrobacterium tumefaciens (1967)

Abstract A 3-ketosucrose-forming enzyme was purified from a soluble fraction of a sonic extract prepared from the cells of Agrobacterium tumefaciens grown on a sucrose medium. With the purified enzyme, FAD was shown to be the prosthetic group and it was also proved that the enzyme is a dehydrogenase. d-Glucose and d-glucosides showed the highest affinity for the enzyme and were converted to their corresponding 3-keto sugars. From these findings, in this paper the name of d-glucoside 3-dehydrogenase was proposed as a trivial name for the 3-ketosucrose-forming enzyme. Other characteristic properties of d-glucoside 3-dehydrogenase were as follows: (a) the Km values for sucrose and d-glucose are 3.8 x 10-4 m, and 1.6 x 10-4 m, respectively; (b) the optimum pH is 6.0 to 6.7; (c) the presence of Ca++ ions at 10-3 m inhibits the reaction almost completely; and (d) at acidic pH values, such as 5.2, Atabrine (10-3 m) shows a striking acceleration effect. A close similarity of substrate specificity between the receptor site of the sucrose transport system and that of d-glucoside 3-dehydrogenase in A. tumefaciens was observed. The differences between these functional sites in their relation to sucrose are discussed.
Absence of lipopolysaccharide in the Lyme disease spirochete, Borrelia burgdorferi (1987)

We were unable to demonstrate the presence of the classic enterobacterium-type lipopolysaccharide in the cells of the Lyme disease spirochete, Borrelia burgdorferi B31. This finding was primarily based on chemical analysis and the absence of free lipid A upon mild acid hydrolysis of the appropriate cell extracts. These results do not preclude the possible existence of an unusual lipopolysaccharide-like compound(s) in B. burgdorferi.
The specific binding of retinoic acid to RPE65 and approaches to the treatment of macular degeneration (2004)

RPE65 is essential in the operation of the visual cycle and functions as a chaperone for all-trans-retinyl esters, the substrates for isomerization in the visual cycle. RPE65 stereospecifically binds all-trans-retinyl esters with a K(D) of 47 nM. It is shown here by using a quantitative fluorescence technique, that Accutane (13-cis-retinoic acid), a drug used in the treatment of acne but that causes night blindness, binds to RPE65 with a K(D) of 195 nM. All-trans-retinoic acid binds with a K(D) of 109 nM. The binding of the retinoic acids to RPE65 is competitive with all-trans-retinyl ester binding, and this competition inhibits visual cycle function. A retinoic acid analog that binds weakly to RPE65 is not inhibitory. These data suggest that RPE65 function is rate-limiting in visual cycle function. They also reveal the target through which the retinoic acids induce night blindness. Finally, certain forms of retinal and macular degeneration are caused by the accumulation of vitamin A-based retinotoxic products, called the retinyl pigment epithelium-lipofuscin. These retinotoxic products accumulate during the normal course of rhodopsin bleaching and regeneration after the operation of the visual cycle. Drugs such as Accutane may represent an important approach to reducing the accumulation of the retinotoxic lipofuscin by inhibiting visual cycle function. The identification of RPE65 as the visual cycle target for the retinoic acids makes it feasible to develop useful drugs to treat retinal and macular degeneration while avoiding the substantial side effects of the retinoic acids.
“The” genetic code? (2005)

The DNA-based code for protein through messenger and transfer RNA is widely regarded as the code of life. But genomes are littered with other kinds of coding elements as well, and all of them probably came after a supercode for the tRNA system itself.
Analysis of five tyiosin biosynthetic genes from the tyllBA region of the Streptomyces fradiae genome (1994)

The tyllBA region of the tylosin biosynthetic gene cluster of Streptomyces fradiae contains at least five open reading frames (ORFs). ORF1 (tylI) encodes a cytochrome P450 and mutations in this gene affect macrolide ring hydroxylation. The product of ORF2 (tylB) belongs to a widespread family of proteins whose functions are speculative, although tylB mutants are defective in the biosynthesis or addition of mycaminose during tylosin production. ORFs 3 and 4 (tylA1 and tylA2) encode delta TDP-glucose synthase and delta TDP-glucose dehydratase, respectively, enzymes responsible for the first two steps common to the biosynthesis of all three deoxyhexose sugars of tylosin via the common intermediate, delta TDP-4-keto, 6-deoxyglucose. ORF5 encodes a thioesterase similar to one encoded in the erythromycin gene cluster of Saccharopolyspora erythraea.
Domain-Independent Task Specification in the TACITUS Natural Language System (1990)

Many seemingly very different application tasks for natural language systems can be viewed as a matter of inferring the instance of a prespecified schema from the information in the text and the knowledge base. We have defined and implemented a schema specification and recognition language for the TACITUS natural language system. This effort entailed adding operators sensitive to resource bounds to the first-order predicate calculus accepted by a theorem-prover. We give examples of the use of this schema language in a diagnostic task, an application involving data base entry from messages, and a script recognition task, and we consider further possible developments.
Survivable network architectures for WDM PON (2005)

We propose and demonstrate a simple self-protecting architecture for WDM PON. The protection time was less than 10 ms, and the power penalty caused by the protection process was negligible.
Primary and Acquired Resistance to Immune Checkpoint Inhibitors in Metastatic Melanoma (2017)

Immune checkpoint inhibitors have revolutionized the treatment of patients with advanced-stage metastatic melanoma, as well as patients with many other solid cancers, yielding long-lasting responses and improved survival. However, a subset of patients who initially respond to immunotherapy, later relapse and develop therapy resistance (termed "acquired resistance"), whereas others do not respond at all (termed "primary resistance"). Primary and acquired resistance are key clinical barriers to further improving outcomes of patients with metastatic melanoma, and the known mechanisms underlying each involves various components of the cancer immune cycle, and interactions between multiple signaling molecules and pathways. Due to this complexity, current knowledge on resistance mechanisms is still incomplete. Overcoming therapy resistance requires a thorough understanding of the mechanisms underlying immune evasion by tumors. In this review, we explore the mechanisms of primary and acquired resistance to immunotherapy in melanoma and detail potential therapeutic strategies to prevent and overcome them. <i>Clin Cancer Res; 24(6); 1260-70. ©2017 AACR</i>.
Surface hydrophobic residues of multiubiquitin chains essential for proteolytic targeting. (1996)

Ubiquitin conjugation is a signal for degradation of eukaryotic proteins by the 26S protease. Conjugation of a homopolymeric multiubiquitin chain to a substrate lysine residue results in 10-fold faster degradation than does conjugation of monoubiquitin, but the molecular basis of enhanced targeting by chains is unknown. We show that ubiquitin residues L8, I44, and V70 are critical for targeting. Mutation of pairs of these residues to alanine had little effect on attachment of ubiquitin to substrates but severely inhibited degradation of the resulting conjugates. The same mutations blocked the binding of chains to a specific subunit (S5a) of the regulatory complex of the 26S protease. The side chains implicated in this binding--L8, I44, and V70--form repeating patches on the chain surface. Thus, hydrophobic interactions between these patches and S5a apparently contribute to enhanced proteolytic targeting by multiubiquitin chains.
Neutralizing antibodies to an immunodominant envelope sequence do not prevent gp120 binding to CD4 (1988)

Animals immunized with the human immunodeficiency virus type 1 gp160 glycoprotein or certain recombinant envelope components develop potent virus-neutralizing activity. This activity is principally due to antibodies directed toward a hypervariable region of gp120 between cysteine residues 302 and 337 and is virus isolate specific. These antisera, as well as two neutralizing monoclonal antibodies directed against the same hypervariable sequence, do not appreciably block gp120 from binding CD4. In contrast, serum samples from infected humans possess high titers of antibodies that block gp120-CD4 binding; these titers approximately correlate with the serum neutralization titers. Our results suggest that there are at least two targets on the envelope glycoprotein for virus neutralization. The target responsible for the broader neutralizing activity of human serum may be a conserved region of gp120 involved in CD4 binding. The antibodies directed at the hypervariable region of the envelope inhibit a different step in virus infection which is subsequent to receptor binding. The extent to which these two different epitopes of gp120 may be involved in protection against human immunodeficiency virus infection is discussed.
Lumbar Discectomy—Percentage of Disc Removal and Detection of Anterior Annulus Perforation (1981)

A prospective study was carried out to estimate the percentage of disc removal at the time of lumbar laminectomy and discectomy. Intraoperative discograms were obtained which afforded a method of calculating the percentage of disc removal. The technique permits localization of the level of discectomy and provides a means of detecting anterior annulus perforation intraoperatively, which we hope will reduce the morbidity of anterior annulus perforation. A comparison between the efficacy of disc removal (microdiscectomy vs. laminectomy) is also presented.
Structural characterization and independent folding of a chimeric glycoprotein comprising granulocyte-macrophage colony stimulating factor and erythropoietin sequences (1998)

MEN 11300 is a hybrid glycoprotein of 297 amino acids obtained by fusion of the cDNA encoding GM-CSF with the cDNA encoding EPO followed by transfection of the hybrid gene into CHO cells. The oligonucleotide construct incorporated a spacing sequence between the two individual cDNAs which encodes eight amino acids constituting a linker peptide intended to separate the GM-CSF and EPO moieties. The recombinant MEN 11300 protein was submitted to a detailed structural characterization including the verification of the entire amino acid sequence, the assignment of the disulfide bridges pattern, the identification of the glycosylation sites and the definition of the glycosidic moiety, including site-specificity. Partial processing of the C-terminal Arg residue and the occurrence of N-glycosylation sites at Asn27, Asn155, Asn169, Asn214 were established. Moreover, O-glycosylation at Ser257 and at the N-terminal region was also detected. A large heterogeneity was observed in the N-glycans due to the presence of differently sialylated and fucosylated branched complex type oligosaccharides whereas O-linked glycans were constituted by GalGalNAc chains with a different number of sialic acids. The disulfide bridges pattern was established by direct FABMS analysis of the proteolytic digests or by ESMS analysis of HPLC purified fractions. Pairing of the eight cysteine residues resulted in Cys54-Cys96, Cys88-Cys121, Cys138-Cys292, and Cys160-Cys164. This S-S bridges pattern is identical to that occurring in the individual natural GM-CSF and EPO, thus showing that the two protein moieties in MEN 11300 can independently acquire their native three-dimensional structure.
Today’s Treatment of Airway Obstruction... and Tomorrow’s? (1989)

Airflow limitation results from loss of elastic recoil (as in emphysema), or narrowing of large and small airways from smooth muscle contraction, mucosal swelling and/or oedema, mucous plugging (as in asthma), and loss of small airways (as in COPD). Bronchodilator regimes in asthma include inhaled beta 2-agonists, but these do not reduce bronchial hyper-reactivity but act quickly and synergise with oral slow-release theophyllines (serum level 10-20 micrograms/ml), without potentiating tremor which occurs with oral beta 2-agonists. Airway inflammation as the mechanism of asthma, although fashionable, remains unproven, and clearly requires to be specified for asthma. Inhaled steroids slowly improve FEV1 in asthma and in 10-20% of COPD, and reduce hyper-reactivity. Nedocromil has yet to reveal similar potency. Clinical trial of effective anti-PAF drugs or anti-leukotriene agents are awaited, but understanding the specific asthmatic inflammation is still needed for rational therapy. In COPD combining inhaled beta 2-agonists with ipratropium--both given by a reservoir device--can be effective, along with oral slow-release theophylline and possibly inhaled steroids. New inhalation devices (i.e. modified dry powder inhalers) will be needed as the freon propellents in MDI may soon cease manufacture due to potential environmental hazards.
Physical characteristics and properties of estradiol softgel vaginal inserts (2019)

The presented data support rapid dissolution of the softgel capsule and similar E2 pharmacokinetic parameters regardless of body position after dosing.
Modulation of the Escherichia coliσE (RpoE) heat‐shock transcription‐factor activity by the RseA, RseB and RseC proteins (1997)

The sigma(E) (RpoE) transcription factor of Escherichia coli regulates the expression of genes whose products are devoted to extracytoplasmic activities. The sigma(E) regulon is induced upon misfolding of proteins in the periplasm or the outer membrane. Similar to other alternative sigma factors, the activity of sigma(E) is tightly regulated in E. coli. We have previously shown that sigma(E) is positively autoregulated at the transcriptional level. DNA sequencing, coupled with transcriptional analyses, have shown that sigma(E) is encoded by the first gene of a four-gene operon. The second gene of this operon, rseA, encodes an anti-sigma(E) activity. This was demonstrated at both the genetic and biochemical levels. For example, mutations in rseA constitutively increase sigma(E) activity. Consistent with this, overproduction of RseA leads to an inhibitory effect on sigma(E) activity. Topological analysis of RseA suggests the existence of one transmembrane domain, with the N-terminal part localized in the cytoplasm. Overproduction of this N-terminal domain alone was shown to inhibit sigma(E) activity. These observations were confirmed in vitro, because either purified RseA or only its purified N-terminal domain inhibited transcription from Esigma(E)-dependent promoters. Furthermore, RseA and sigma(E) co-purify, and can be co-immunoprecipitated, and chemically cross-linked. The sigma(E) activity is further modulated by the products of the remaining genes in this operon, rseB and rseC. RseB is a periplasmic protein, which negatively regulates sigma(E) activity and specifically interacts with the C-terminal periplasmic domain of RseA. In contrast, RseC is an inner membrane protein that positively modulates sigma(E) activity. Most of these protein-protein interactions were verified in vivo using the yeast two-hybrid system.
Proposals and rationale for revision of the World Health Organization diagnostic criteria for polycythemia vera, essential thrombocythemia, and primary myelofibrosis: recommendations from an ad hoc international expert panel (2007)

The Janus kinase 2 mutation, JAK2617V>F, is myeloid neoplasm-specific; its presence excludes secondary polycythemia, thrombocytosis, or bone marrow fibrosis from other causes. Furthermore, JAK2617V>F or a JAK2 exon 12 mutation is present in virtually all patients with polycythemia vera (PV), whereas JAK2617V>F also occurs in approximately half of patients with essential thrombocythemia (ET) or primary myelofibrosis (PMF). Therefore, JAK2 mutation screening holds the promise of a decisive diagnostic test in PV while being complementary to histology for the diagnosis of ET and PMF; the combination of molecular testing and histologic review should also facilitate diagnosis of ET associated with borderline thrombocytosis. Accordingly, revision of the current World Health Organization (WHO) diagnostic criteria for PV, ET, and PMF is warranted; JAK2 mutation analysis should be listed as a major criterion for PV diagnosis, and the platelet count threshold for ET diagnosis can be lowered from 600 to 450 x 10(9)/L. The current document was prepared by an international expert panel of pathologists and clinical investigators in myeloproliferative disorders; it was subsequently presented to members of the Clinical Advisory Committee for the revision of the WHO Classification of Myeloid Neoplasms, who endorsed the document and recommended its adoption by the WHO.