gebhart/patrepeval huggingface dataset:
3-Hydroxypropionyl-Coenzyme A Dehydratase and Acryloyl-Coenzyme A Reductase, Enzymes of the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in the Sulfolobales (2009)

A 3-hydroxypropionate/4-hydroxybutyrate cycle operates in autotrophic CO(2) fixation in various Crenarchaea, as studied in some detail in Metallosphaera sedula. This cycle and the autotrophic 3-hydroxypropionate cycle in Chloroflexus aurantiacus have in common the conversion of acetyl-coenzyme A (CoA) and two bicarbonates via 3-hydroxypropionate to succinyl-CoA. Both cycles require the reductive conversion of 3-hydroxypropionate to propionyl-CoA. In M. sedula the reaction sequence is catalyzed by three enzymes. The first enzyme, 3-hydroxypropionyl-CoA synthetase, catalyzes the CoA- and MgATP-dependent formation of 3-hydroxypropionyl-CoA. The next two enzymes were purified from M. sedula or Sulfolobus tokodaii and studied. 3-Hydroxypropionyl-CoA dehydratase, a member of the enoyl-CoA hydratase family, eliminates water from 3-hydroxypropionyl-CoA to form acryloyl-CoA. Acryloyl-CoA reductase, a member of the zinc-containing alcohol dehydrogenase family, reduces acryloyl-CoA with NADPH to propionyl-CoA. Genes highly similar to the Metallosphaera CoA synthetase, dehydratase, and reductase genes were found in autotrophic members of the Sulfolobales. The encoded enzymes are only distantly related to the respective three enzyme domains of propionyl-CoA synthase from C. aurantiacus, where this trifunctional enzyme catalyzes all three reactions. This indicates that the autotrophic carbon fixation cycles in Chloroflexus and in the Sulfolobales evolved independently and that different genes/enzymes have been recruited in the two lineages that catalyze the same kinds of reactions.
Synthesis and Characterization of Water-Soluble and Photostable L-DOPA Dendrimers (2006)

A small drug molecule, L-DOPA, was converted into well-defined dendritic macromolecules. Their monodisperse nature was shown by NMR, MALDI-TOF-MS, and PAGE. A third-generation L-Dopa dendrimer contained 30 L-Dopa residues, which made up its core, branches, and periphery. Individual L-Dopa moieties in the dendrimer were connected to one another via hydrolyzable diester linkages. These Dopa dendrimers showed a 20-fold increase in aqueous solubility and enhanced photostability in solutions over L-Dopa under identical conditions.
A molecular link between activation and inactivation of sodium channels. (1995)

A pair of tyrosine residues, located on the cytoplasmic linker between the third and fourth domains of human heart sodium channels, plays a critical role in the kinetics and voltage dependence of inactivation. Substitution of these residues by glutamine (Y1494Y1495/QQ), but not phenylalanine, nearly eliminates the voltage dependence of the inactivation time constant measured from the decay of macroscopic current after a depolarization. The voltage dependence of steady state inactivation and recovery from inactivation is also decreased in YY/QQ channels. A characteristic feature of the coupling between activation and inactivation in sodium channels is a delay in development of inactivation after a depolarization. Such a delay is seen in wild-type but is abbreviated in YY/QQ channels at -30 mV. The macroscopic kinetics of activation are faster and less voltage dependent in the mutant at voltages more negative than -20 mV. Deactivation kinetics, by contrast, are not significantly different between mutant and wild-type channels at voltages more negative than -70 mV. Single-channel measurements show that the latencies for a channel to open after a depolarization are shorter and less voltage dependent in YY/QQ than in wild-type channels; however the peak open probability is not significantly affected in YY/QQ channels. These data demonstrate that rate constants involved in both activation and inactivation are altered in YY/QQ channels. These tyrosines are required for a normal coupling between activation voltage sensors and the inactivation gate. This coupling insures that the macroscopic inactivation rate is slow at negative voltages and accelerated at more positive voltages. Disruption of the coupling in YY/QQ alters the microscopic rates of both activation and inactivation.
Controlled Production of Stable Heterologous Proteins in Lactococcus lactis (2002)

The use of Lactococcus lactis (the most extensively characterized lactic acid bacterium) as a delivery organism for heterologous proteins is, in some cases, limited by low production levels and poor-quality products due to surface proteolysis. In this study, we combined in one L. lactis strain use of the nisin-inducible promoter P(nisA) and inactivation of the extracellular housekeeping protease HtrA. The ability of the mutant strain, designated htrA-NZ9000, to produce high levels of stable proteins was confirmed by using the staphylococcal nuclease (Nuc) and the following four heterologous proteins fused or not fused to Nuc that were initially unstable in wild-type L. lactis strains: (i) Staphylococcus hyicus lipase, (ii) the bovine rotavirus antigen nonstructural protein 4, (iii) human papillomavirus antigen E7, and (iv) Brucella abortus antigen L7/L12. In all cases, protein degradation was significantly lower in strain htrA-NZ9000, demonstrating the usefulness of this strain for stable heterologous protein production.
Resiquimod as an Immunologic Adjuvant for NY-ESO-1 Protein Vaccination in Patients with High-Risk Melanoma (2015)

The Toll-like receptor (TLR) 7/8 agonist resiquimod has been used as an immune adjuvant in cancer vaccines. We evaluated the safety and immunogenicity of the cancer testis antigen NY-ESO-1 given in combination with Montanide (Seppic) with or without resiquimod in patients with high-risk melanoma. In part I of the study, patients received 100 μg of full-length NY-ESO-1 protein emulsified in 1.25 mL of Montanide (day 1) followed by topical application of 1,000 mg of 0.2% resiquimod gel on days 1 and 3 (cohort 1) versus days 1, 3, and 5 (cohort 2) of a 21-day cycle. In part II, patients were randomized to receive 100-μg NY-ESO-1 protein plus Montanide (day 1) followed by topical application of placebo gel [(arm A; n = 8) or 1,000 mg of 0.2% resiquimod gel (arm B; n = 12)] using the dosing regimen established in part I. The vaccine regimens were generally well tolerated. NY-ESO-1-specific humoral responses were induced or boosted in all patients, many of whom had high titer antibodies. In part II, 16 of 20 patients in both arms had NY-ESO-1-specific CD4⁺ T-cell responses. CD8⁺ T-cell responses were only seen in 3 of 12 patients in arm B. Patients with TLR7 SNP rs179008 had a greater likelihood of developing NY-ESO-1-specific CD8⁺ responses. In conclusion, NY-ESO-1 protein in combination with Montanide with or without topical resiquimod is safe and induces both antibody and CD4⁺ T-cell responses in the majority of patients; the small proportion of CD8⁺ T-cell responses suggests that the addition of topical resiquimod to Montanide is not sufficient to induce consistent NY-ESO-1-specific CD8⁺ T-cell responses.
Drinking and Smoking: a Field Study of their Association (1994)

Abstract Alcohol and tobacco seem to go together: individuals who drink tend to smoke, and vice versa. Users of both substances also seem to use them together; in particular, drinking seems to cue smoking. However, this relationship has not been studied in real-world contexts. We examined the situational association between drinking and smoking using Ecological Momentary Assessments (EMAs). Using a palm-top computer, 57 subjects reported the circumstances surrounding smoking occasions; as a comparison, subjects were assessed at random times when they were not smoking. A total of 4,020 observations were gathered over one week. Drinking was associated with smoking (odds ratio = 2.1). The effect was greater among heavier drinkers. This link persisted even when situational factors, such as time of day and engagement in leisure activity, were controlled, weakening conditioning explanations of the association. The data also did not support pharmacological compensation models: the degree of cognitive impairment when drinking did not predict the likelihood of smoking. The data were also inconsistent with a model based on disinhibition of smoking restraint, in that the relationship was not stronger among more restrained subjects. The data suggested that questionnaire reports of smoking patterns were invalid: the actual, observed link between drinking and smoking was not related to subjects' characterization of this relationship.
Vimentin Dephosphorylation by Protein Phosphatase 2A Is Modulated by the Targeting Subunit B55 (1999)

The intermediate filament protein vimentin is a major phosphoprotein in mammalian fibroblasts, and reversible phosphorylation plays a key role in its dynamic rearrangement. Selective inhibition of type 2A but not type 1 protein phosphatases led to hyperphosphorylation and concomitant disassembly of vimentin, characterized by a collapse into bundles around the nucleus. We have analyzed the potential role of one of the major protein phosphatase 2A (PP2A) regulatory subunits, B55, in vimentin dephosphorylation. In mammalian fibroblasts, B55 protein was distributed ubiquitously throughout the cytoplasm with a fraction associated to vimentin. Specific depletion of B55 in living cells by antisense B55 RNA was accompanied by disassembly and increased phosphorylation of vimentin, as when type 2A phosphatases were inhibited using okadaic acid. The presence of B55 was a prerequisite for PP2A to efficiently dephosphorylate vimentin in vitro or to induce filament reassembly in situ. Both biochemical fractionation and immunofluorescence analysis of detergent-extracted cells revealed that fractions of PP2Ac, PR65, and B55 were tightly associated with vimentin. Furthermore, vimentin-associated PP2A catalytic subunit was displaced in B55-depleted cells. Taken together these data show that, in mammalian fibroblasts, the intermediate filament protein vimentin is dephosphorylated by PP2A, an event targeted by B55.
Securing Web Servers Using Self Cleansing Intrusion Tolerance (SCIT) (2009)

The number of malware attacks is increasing, Companies have invested millions of dollars in intrusion detection and intrusion prevention (ID/IP) technologies and products, yet many web servers are hacked every year. The current reactive methods of security have proven to be inadequate because the ldquobad guysrdquo are always one step ahead of the Intrusion Detection/Intrusion Prevention community. Our research seeks to prove the feasibility of a completely new and innovative theory of server security called ldquoSelf-Cleansing Intrusion Tolerancerdquo (SCIT). SCIT shifts the focus from detection and prevention to containing losses. SCIT uses virtualization technology in a new and unique way to make it more difficult for attackers to do damage/acquire data by reducing a serverpsilas exposure time from several months to less than a minute. In this way we increase the dependability of the server and provide a new way to balance the trade-off between security and availability. We have applied SCIT to multiple types of servers (DNS, SSO and Web), in this paper we will focus on securing web servers using SCIT. Based on the results of load testing of a web application for various load scenarios under both scit and non-scit environments, we will clearly show that SCIT provides a high degree of security with little degradation in overall response time of the application.
Detergent Effects of Sodium Deoxycholate Are a Major Feature of an Injectable Phosphatidylcholine Formulation Used for Localized Fat Dissolution (2004)

The phosphatidylcholine formula popularly used in subcutaneous injections for fat dissolution works primarily as a detergent causing nonspecific lysis of cell membranes. Our findings suggest that sodium deoxycholate is the major active component responsible for cell lysis. Detergent substances may have a role in eliminating unwanted adipose tissue. It is advised that physicians use caution until adequate safety data are available.
S-Adenosylmethionine-Dependent Reduction of Lysine 2,3-Aminomutase and Observation of the Catalytically Functional Iron−Sulfur Centers by Electron Paramagnetic Resonance (1998)

Lysine 2,3-aminomutase catalyzes the interconversion of l-alpha-lysine and l-beta-lysine. The enzyme contains an iron-sulfur cluster with unusual properties, and it requires pyridoxal-5'-phosphate (PLP) and S-adenosylmethionine (AdoMet) for activity. The reaction proceeds by a substrate radical rearrangement mechanism, in which the external aldimine formed between PLP and lysine is initially converted into a lysyl-radical intermediate by hydrogen abstraction from C3. The present research concerns the mechanism by which a hydrogen-abstracting species is generated at the active site of lysine 2,3-aminomutase. Earlier tritium tracer experiments have implicated the 5'-deoxyadenosyl moiety of AdoMet in this process. AdoMet is here shown to interact with the iron-sulfur cluster at the active site of Clostridial lysine 2,3-aminomutase. Reduction of the iron-sulfur cluster from its EPR-silent form [4Fe-4S]2+ to the fully reduced form [4Fe-4S]1+ requires the presence of either AdoMet or S-adenosylhomocysteine (SAH) and a strong reducing agent such as dithionite or deazariboflavin and light. The reduced forms are provisionally designated E-[4Fe-4S]1+/AdoMet and E-[4Fe-4S]1+/SAH, and they display similar low-temperature EPR spectra centered at gav = 1.91. The reduced form E-[4Fe-4S]1+/AdoMet is fully active in the absence of any added reducing agent, whereas the form E-[4Fe-4S]1+/SAH is not active. It is postulated that the active form E-[4Fe-4S]1+/AdoMet is in equilibrium with a low concentration of a radical-initiating form that contains the 5'-deoxyadenosyl radical. Initiation of the radical rearrangement mechanism is postulated to take place by action of the 5'-deoxyadenosyl radical in abstracting a hydrogen atom from carbon-3 of lysine, which is bound as its external aldiminine with PLP. This process accounts for the results of tritium tracer experiments, it explains the radical rearrangement mechanism, and it rationalizes the roles of AdoMet and the [4Fe-4S] cluster in the reaction.
Differentiation-independent Constitutive Expression of the Human Papillomavirus Type 16 E6 and E7 Oncogenes in the CaSki Cervical Tumour Cell Line (1994)

CaSki cells are a human papillomavirus type 16 (HPV-16)-positive cell line that serves as a model for the study of advanced cervical carcinoma. Calcium is an important regulator of normal ectocervical epithelial cell differentiation. HPV E6 and E7 gene products are thought to be important in the process of cervical cell immortalization and hence important in the development of cervical cancer. In the present study we examine the relationship between CaSki cell differentiation and expression of the papillomavirus oncogenes. Shifting CaSki cells from medium containing low (0.06 mM) to high (1.4 mM) calcium results in an increase in cell-cell contact and increased differentiation as measured by an increase in the level of mRNA encoding cytokeratin K13, involucrin and type 1 transglutaminase, which are markers of differentiation in the cervical epithelium. In contrast, E6/E7 transcripts are produced in a differentiation-independent constitutive manner. These results and those from our previous experiments with HPV-16-immortalized but non-tumorigenic cell lines suggest that the constitutive, differentiation-independent expression of E6/E7 levels is a property of both tumorigenic and non-tumorigenic HPV-16-positive cancer cells.
Snakin-2, an Antimicrobial Peptide from Potato Whose Gene Is Locally Induced by Wounding and Responds to Pathogen Infection (2002)

The peptide snakin-2 (StSN2) has been isolated from potato (Solanum tuberosum cv Jaerla) tubers and found to be active (EC(50) = 1-20 microM) against fungal and bacterial plant pathogens. It causes a rapid aggregation of both Gram-positive and Gram-negative bacteria. The corresponding StSN2 cDNA encodes a signal sequence followed by a 15-residue acidic sequence that precedes the mature StSN2 peptide, which is basic (isoelectric point = 9.16) and 66 amino acid residues long (molecular weight of 7,025). The StSN2 gene is developmentally expressed in tubers, stems, flowers, shoot apex, and leaves, but not in roots, or stolons, and is locally up-regulated by wounding and by abscisic acid treatment. Expression of this gene is also up-regulated after infection of potato tubers with the compatible fungus Botritys cinerea and down-regulated by the virulent bacteria Ralstonia solanacearum and Erwinia chrysanthemi. These observations are congruent with the hypothesis that the StSN2 is a component of both constitutive and inducible defense barriers.
Cryosurgery for Prostate Cancer (2008)

No AccessJournal of UrologyEditorial1 Nov 2008Cryosurgery for Prostate Canceris companion ofBest Practice Statement on Cryosurgery for the Treatment of Localized Prostate Cancer Gunnar Aus Gunnar AusGunnar Aus More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2008.08.085AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Cryosurgery for Prostate Cancer." The Journal of Urology, 180(5), pp. 1882–1883 References 1 : Treatment of organ confined prostate cancer with third generation cryosurgery: preliminary multicenter experience. J Urol2003; 170: 1126. Link, Google Scholar 2 : Active rectal wall protection using direct transperineal cryo-needles for histologically proven prostate adenocarcinomas. Eur Urol2003; 44: 315. Google Scholar 3 : Current status of HIFU and cryotherapy in prostate cancer–a review. Eur Urol2006; 50: 927. Google Scholar 4 : A randomized trial comparing radical prostatectomy with watchful waiting in early prostate cancer. N Engl J Med2002; 347: 781. Google Scholar 5 : Targeted cryoablation of the prostate: 7-year outcomes in the primary treatment of prostate cancer. Urology2002; 60: 3. Google Scholar 6 : A critical analysis of the interpretation of biochemical failure in surgically treated patients using the American Society for Therapeutic Radiation and Oncology criteria. J Urol2002; 168: 1419. Link, Google Scholar 7 : Five-year retrospective, multi-institutional pooled analysis of cancer-related outcomes after cryosurgical ablation of the prostate. Urology2001; 57: 518. Google Scholar 8 : Short-term cancer control after primary cryosurgical ablation for clinically localized prostate cancer using third-generation cryotechnology. Urology2007; 70: 117. Google Scholar 9 : Cryotherapy for localised prostate cancer. Cochrane Database Syst Rev2007; 3. CD005010.. Google Scholar Department of Urology, Sahlgrens University Hospital, Göteborg, Sweden© 2008 by American Urological AssociationFiguresReferencesRelatedDetailsRelated articlesJournal of Urology25 Sep 2008Best Practice Statement on Cryosurgery for the Treatment of Localized Prostate Cancer Volume 180Issue 5November 2008Page: 1882-1883 Advertisement Copyright & Permissions© 2008 by American Urological AssociationMetricsAuthor Information Gunnar Aus More articles by this author Expand All Advertisement PDF downloadLoading ...
[The properties of plasminogen activator from human blood plasma taken at sudden death]. (1983)

Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.
Immunological characterization of the lipooligosaccharide B band of Bordetella pertussis (1992)

Two structurally and immunologically different components of Bordetella pertussis endotoxin can be visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and silver staining: a major A band and a faster-migrating minor B band. Certain mutant strains of B. pertussis express only the B band, while the wild-type strains produce both lipooligosaccharides (LOS). Two monoclonal antibodies (MAbs) directed against the minor LOS B band were generated, allowing the study of this surface molecule on different strains of Bordetella. These two MAbs, designated BL-8 and BL-9, reacted strongly with phenol-water-purified LOS obtained from a B. pertussis LOS B mutant strain. Sodium periodate treatment of the purified LOS prevented binding of the MAbs, indicating the carbohydrate nature of the epitope(s). Western immunoblotting experiments revealed that the epitope(s) recognized by these MAbs is conserved on all B. pertussis and Bordetella bronchiseptica Vir- (avirulent) variant strains tested but is not present on Bordetella parapertussis and B. bronchiseptica Vir+ (virulent) wild-type strains. Further studies showed that although present in the lipopolysaccharide B band expressed by Vir- strains, the epitope(s) recognized by the MAbs is not accessible on the surface of intact B. bronchiseptica cells. For B. pertussis, the density and accessibility of this epitope(s) are dependent on the virulence-associated or LOS phenotype expressed by the strain. Our data demonstrate that the expression and accessibility of the epitope(s) are significantly greater on the LOS B variant strains and LOS AB Vir- strains compared with fresh B. pertussis clinical isolates. For these latter strains, which are Vir+, this epitope(s) was barely detectable on the surface of intact bacteria, despite Western blot analyses that revealed specific reactions between the MAbs and the LOS B band. The two LOS B-specific MAbs had no bacteriolytic activity against a LOS AB wild-type strain, while the control MAb BL-2, which is specific for the B. pertussis LOS A band, significantly reduced the number of living bacteria in the same assay. Moderate lytic activity against a mutant strain expressing only the LOS B band was observed for MAb BL-8 but not for MAb BL-9 or BL-2. These data demonstrate that the type, amount, and surface exposure of the LOS are related to the phenotype expressed by a specific B. pertussis strain. In addition, the LOS B MAbs also reveal the antigenic conservation of carbohydrate epitopes among B. pertussis and B. bronchiseptica strains.