gebhart/patrepeval huggingface dataset:
Morphology-controlled synthesis of silica nanotubes through pH- and sequence-responsive morphological change of bacterial flagellar biotemplates (2012)

Bacterial flagella are naturally-occurring self-assembling protein nanofibers protruding from the bacterial surface to assist the swimming of bacteria. They are rigid and exhibit diverse morphologies depending on the ionic strength, the pH values, temperature, and subunit sequences. Here, the silica nanotubes (SNTs) with controllable morphologies were synthesized using flagella as biological templates in aqueous solution under mild conditions. The morphologies and surface features of flagella-templated SNTs can be simply tuned by adjusting the pH value or surface chemistry of flagella by peptide display. A variety of different morphologies (coiled, straight, and curly with different wavelengths) and surface features (smooth, rough, granular and pear-necklace-like) of SNTs were obtained. When pH varies from acidic to alkaline conditions, in general, SNTs varied from bundled coiled, to characteristic sinusoidal waves, helical, and straight morphology. Under genetic control, flagella displaying negatively-charged peptides exhibited thinner layer of silica condensation but rough surface. However, flagella with positively-charged peptide inserts induced the deposition of thicker silica shell with smooth surface. Incorporation of hydroxyl bearing amino acid residues such as Ser into the peptide displayed on flagella highly enhanced the biotemplated deposition of silica. This work suggests that bacterial flagella are promising biotemplates for developing an environmentally-benign and cost-efficient approach to morphology-controlled synthesis of nanotubes. Moreover, the dependency of the thickness of the silica shell on the peptides displayed on flagella helps us to further understand the mechanism of biomimetic nucleation of silica on biological templates.
Interactions of the chondroitin sulfate proteoglycan phosphacan, the extracellular domain of a receptor-type protein tyrosine phosphatase, with neurons, glia, and neural cell adhesion molecules. (1994)

Phosphacan is a chondroitin sulfate proteoglycan produced by glial cells in the central nervous system, and represents the extracellular domain of a receptor-type protein tyrosine phosphatase (RPTP zeta/beta). We previously demonstrated that soluble phosphacan inhibited the aggregation of microbeads coated with N-CAM or Ng-CAM, and have now found that soluble 125I-phosphacan bound reversibly to these neural cell adhesion molecules, but not to a number of other cell surface and extracellular matrix proteins. The binding was saturable, and Scatchard plots indicated a single high affinity binding site with a Kd of approximately 0.1 nM. Binding was reduced by approximately 15% after chondroitinase treatment, and free chondroitin sulfate was only moderately inhibitory, indicating that the phosphacan core glycoprotein accounts for most of the binding activity. Immunocytochemical studies of embryonic rat spinal phosphacan, Ng-CAM, and N-CAM have overlapping distributions. When dissociated neurons were incubated on dishes coated with combinations of phosphacan and Ng-CAM, neuronal adhesion and neurite growth were inhibited. 125I-phosphacan bound to neurons, and the binding was inhibited by antibodies against Ng-CAM and N-CAM, suggesting that these CAMs are major receptors for phosphacan on neurons. C6 glioma cells, which express phosphacan, adhered to dishes coated with Ng-CAM, and low concentrations of phosphacan inhibited adhesion to Ng-CAM but not to laminin and fibronectin. Our studies suggest that by binding to neural cell adhesion molecules, and possibly also by competing for ligands of the transmembrane phosphatase, phosphacan may play a major role in modulating neuronal and glial adhesion, neurite growth, and signal transduction during the development of the central nervous system.
Modification of glutathione levels in C3H/10T1/2 cells and its relationship to benzo(a)pyrene anti-7,8-dihydrodiol 9,10-epoxide-induced cytotoxicity. (1984)

Levels of reduced glutathione (GSH) in C3H/10T1/2 cells were selectively altered to determine what quantitative role GSH transferase-catalyzed conjugation plays in regulating the cytotoxic effects of benzo(a)pyrene anti-7,8-dihydrodiol 9,10-epoxide (r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydrobenzo(a)pyrene, anti-diol epoxide). A 65% decrease in 10T1/2 cell GSH content from 0.16 mM (control cell GSH concentration) to 0.06 mM was accompanied by a 46% decrease in the anti-diol epoxide LD80; a 98% increase in GSH content resulted in a 44% increase in anti-diol epoxide LD80. This nonlinear relationship between changes in cellular GSH concentration and anti-diol epoxide LD80 was directly relatable to the nonlinear change in the rate of anti-diol epoxide conjugation which was catalyzed by 10T1/2 cell GSH transferases. Purified 10T1/2 cell cytosol catalyzed the GSH conjugation of anti-diol epoxide to yield a GSH conjugation product with a distinct UV absorbance spectrum; the apparent GSH Km for this cell cytosol-catalyzed reaction was 0.20 mM. Variations in the cellular GSH concentration around the GSH Km resulted in a nonlinear change in the amount of anti-diol epoxide-GSH conjugate formed, and a reciprocal change in the amount of free anti-diol epoxide available for cytotoxic alkylation events. These results clarify in quantitative, biochemical terms how GSH transferase-catalyzed conjugation can regulate the level of an electrophilic carcinogen metabolite in a biological system.
High-resolution calorimetric and optical melting profiles of DNA plasmids: Resolving contributions from intrinsic melting domains and specifically designed inserts (1999)

We demonstrate that differential scanning calorimetry (DSC) can be used to yield high-resolution melting profiles for DNA plasmids that agree in all major features with the corresponding plasmid melting profiles derived using more traditional optical techniques. We further demonstrate that by combining information derived from both calorimetric and optical melting profiles one can glean insights that are unavailable from either melting curve alone. By using both optical and calorimetric observables, we show how one can resolve, identify, and measure the thermodynamic properties of particular sequences/domains of interest within a plasmid. We also show that complementary DSC and optical melting studies on plasmids with and without specifically designed inserts can provide fundamental advantages over the corresponding melting studies on other model system constructs for thermodynamically characterizing nucleic acid sequences/structures.
Emergency Whole-Blood Use in the Field (2013)

Military experience and recent in vitro laboratory data provide a biological rationale for whole-blood use in the treatment of exsanguinating hemorrhage and have renewed interest in the reintroduction of fresh whole blood and cold-stored whole blood to patient care in austere environments. There is scant evidence to support, in a field environment, that a whole blood-based resuscitation strategy is superior to a crystalloid/colloid approach even when augmented by a limited number of red blood cell (RBC) and plasma units. Recent retrospective evidence suggests that, in this setting, resuscitation with a full compliment of RBCs, plasma, and platelets may offer an advantage, especially under conditions where evacuation is delayed. No current evacuation system, military or civilian, is capable of providing RBC, plasma, and platelet units in a prehospital environment, especially in austere settings. As a result, for the vast minority of casualties, in austere settings, with life-threatening hemorrhage, it is appropriate to consider a whole blood-based resuscitation approach to provide a balanced response to altered hemostasis and oxygen debt, with the goal of reducing the risk of death from hemorrhagic shock. To optimize the successful use of fresh whole blood/cold-stored whole blood in combat field environments, proper planning and frequent training to maximize efficiency and safety will be required. Combat medics will need proper protocol-based guidance and education if whole-blood collection and transfusion are to be successfully and safely performed in austere environments. In this article, we present the Norwegian Naval Special Operation Commando unit-specific remote damage control resuscitation protocol, which includes field collection and transfusion of whole blood. This protocol can serve as a template for others to use and adjust for their own military or civilian unit-specific needs and capabilities for care in austere environments.
Immunochemical Approach Using Monoclonal Antibody against &#x394; 9-Tetrahydrocannabinolic Acid (THCA) to Discern Cannabis Plants and to Investigate New Drug Candidates (2011)

A monoclonal antibody (MAb-4A4) against Δ9- tetrahydrocannabinolic acid (THCA) showing extensive cross-reactivity against various cannabinoids was prepared. Using this antibody, a competitive enzyme-linked immunoassay (ELISA) was developed to detect Δ9-THCA in the range of 1 to 100 mg/ml. Various cannabinoids including Δ9-THC (Δ9-tetrahydrocannabinolic acid), Δ8-THCA (Δ8-tetrahydrocannabinolic acid), Δ8-THC (Δ8-tetrahydrocannabinol), CBD (cannabidiol), and CBN (cannabinol) were recognized by MAb-4A4, and their cross-reactivities were 55-1600% compared with Δ9-THCA (100%). This novel characteristic of this MAb enabled detection of marijuana residues in biological samples by detection of residual cannabinoids. The ELISA using MAb-4A4 was found to be applicable even for withered samples which contained only trace amounts of Δ9-THCA and Δ9-THC. In addition, this method using MAb-4A4 could be useful in forensic analysis since the MAb-4A4 also shows cross-reactivities against cannabinoid metabolites in body fluids. As well as forensic applications using this MAb, an investigation of new drug candidates focusing on cannabinoid metabolites arising from biotransformation in plant tissue was performed using immunochemical screening. The resulting new drug candidates were cannabinoid glycosides biotransformed by Pinellia ternata whose bioactivity is as yet unidentified. Our results indicate the utility of the application of ELISA using MAb-4A4 for further experiments involving marijuana and cannabinoids not only in the forensic field but also in the context of drug discovery.
Hippocampal Synaptic Plasticity in Mice Overexpressing an Embryonic Subunit of the NMDA Receptor (1998)

The effects of changing NMDA receptor subunit composition on synaptic plasticity in the hippocampus were analyzed by creating transgenic mice overexpressing NR2D, a predominantly embryonic NMDA receptor subunit. NMDA-evoked currents in the transgenic mice had smaller amplitudes and slower kinetics. The transgenics also displayed age-dependent deficits in synaptic plasticity in area CA1 of the hippocampus. Long-term depression was selectively impaired in juvenile mice when NR2D overexpression was moderate. In mature mice, overexpression of NR2D was associated with a reduction of both NR2B and Ca2+-independent activity of Ca2+- and calmodulin-dependent protein kinase II. These biochemical changes were correlated with a marked impairment of NMDA-dependent long-term potentiation, but spatial behavior was normal in these mice. These results show that the developmental regulation of NMDA receptor subunit composition alters the frequency at which modification of synaptic responses occur after afferent stimulation.
Uniform fiber Bragg grating first- and second-order diffraction wavelength experimental characterization for strain-temperature discrimination (2001)

A full experimental characterization of the first- and second-order diffraction wavelengths of fiber Bragg gratings (FBGs) fabricated in a single optimized UV-writing process is presented in this letter. These devices are useful for the simultaneous measurement of strain and temperature.
Evaluation of glycolamide esters and various other esters of aspirin as true aspirin prodrugs (1989)

A series of glycolamide, glycolate, (acyloxy)methyl, alkyl, and aryl esters of acetylsalicylic acid (aspirin) were synthesized and evaluated as potential prodrug forms of aspirin. N,N-Disubstituted glycolamide esters were found to be rapidly hydrolyzed in human plasma, resulting in the formation of aspirin as well as the corresponding salicylate esters. These in turn hydrolyzed rapidly to salicylic acid. The largest amount of aspirin formed from the esters were 50 and 55% in case of the N,N-dimethyl- and N,N-diethylglycolamide esters, respectively. Similar results were obtained in blood with the N,N-dimethyl- and N,N-diethylglycolamide esters. Unsubstituted and monosubstituted glycolamide esters as well as most other esters previously suggested to be aspirin prodrugs were shown to hydrolyze exclusively to the corresponding salicylic acid esters. Lipophilicity parameters and water solubilities of the esters were determined, and structural factors favoring ester prodrug hydrolysis at the expense of deacetylation to yield salicylate ester are discussed. The properties of some N,N-disubstituted glycolamide esters of aspirin are highlighted with respect to their use as potential aspirin prodrugs.
Can Continuous Glucose Monitoring Be Used for the Treatment of Diabetes (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCan Continuous Glucose Monitoring Be Used for the Treatment of DiabetesGérard Reach and George S. WilsonCite this: Anal. Chem. 1992, 64, 6, 381A–386APublication Date (Print):March 15, 1992Publication History Published online31 May 2012Published inissue 15 March 1992https://pubs.acs.org/doi/10.1021/ac00030a718https://doi.org/10.1021/ac00030a718research-articleACS PublicationsRequest reuse permissionsArticle Views757Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A data-driven finite state machine model for analyzing security vulnerabilities (2004)

This paper combines an analysis of data on security vulnerabilities (published in Bugtraq database) and a focused source-code examination to develop a finite state machine (FSM) model to depict and reason about security vulnerabilities. An in-depth analysis of the vulnerability reports and the corresponding source code of the applications leads to three observations: (i) exploits must pass through multiple elementary activities, (ii) multiple vulnerable operations on several objects are involved in exploiting a vulnerability, and (iii) the vulnerability data and corresponding code inspections allow us to derive a predicate for each elementary activity. Each predicate is represented as a primitive FSM (pFSM). Multiple pFSMs are then combined to create an FSM model of vulnerable operations and possible exploits. The proposed FSM methodology is exemplified by analyzing several types of vulnerabilities reported in the data: stack buffer overflow, integer overflow, heap overflow, input validation vulnerabilities, and format string vulnerabilities. For the studied vulnerabilities, we identify three types of pFSMs, which can be used to analyze operations involved in exploiting vulnerabilities and to identify the security checks to be performed at the elementary activity level. A demonstration of the practical usefulness of the FSM modeling approach was the discovery of a new heap overflow vulnerability now published in Bugtraq.
Applying an information gathering architecture to Netfind: a white pages tool for a changing and growing Internet (1994)

The Internet is quickly becoming an indispensable means of communication and collaboration, based on applications such as electronic mail, remote information retrieval, and multimedia conferencing. A fundamental problem for such applications is supporting resource discovery in a fashion that keeps pace with the Internet's exponential growth in size and diversity. Netfind is a scalable tool that locates current electronic mail addresses and other information about Internet users. Since the time we first deployed Netfind in 1990, it has evolved considerably, making use of more types of information sources. As well as more sophisticated mechanisms to gather and cross-correlate information. In this paper, we describe these techniques, and present a general framework for gathering and harnessing widely distributed information in a diverse and growing Internet environment. At present, Netfind gathers information from 17 different types of sources, providing a particularly thorough demonstration of an information gathering architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Life before the chips: simulating digital video interactive technology (1989)

Advances in computers, such as DVI technology, are driven by new hardware functionality—more magic in the silicon. But before the chips came the ideas, and years of visual and interactive technical simulations to evaluate product designs and build the support necessary to develop them.
The Bacillus subtilis clpC operon encodes DNA repair and competence proteins (1997)

ClpC of Bacillus subtilis, controlling competence gene expression and survival under stress conditions, is encoded by the fourth gene of a six-gene operon. The product of orf1 contains a potential helix-turn-helix motif, but shows no significant similarities with known protein sequences. The second and third genes encode proteins with similarities to zinc-finger proteins (orf2) and arginine kinases (orf3), respectively. The product of orf5 contains a zinc-finger motif and an ATP-binding domain, and is highly similar to the product of the Escherichia coli sms gene. A strain bearing a disruption of orf5 showed increased sensitivity to the alkylating agent methyl methanesulfonate. Furthermore, this mutant strain displayed decreased capacity for genetic recombination as measured by transformation experiments. The last open reading frame, orf6, encodes a protein with limited similarity in its C-terminal part to the B. subtilis comEA gene product and to the UvrC DNA repair excinuclease. Inactivation of orf5 resulted in strongly diminished transformation with all types of DNA. Mutations affecting either orf5 or orf6 resulted in strains with decreased resistance to UV-irradiation in the stationary phase, indicating that these proteins play a role in the development of a non-specific stationary-phase resistance to UV-irradiation. Moreover, these results suggest an involvement of both proteins in transformation and presumably in DNA repair.
Design and implementation of a new autonomous sensor fish to support advanced hydropower development (2014)

Acceleration in development of additional conventional hydropower requires tools and methods to perform laboratory and in-field validation of turbine performance and fish passage claims. The new-generation Sensor Fish has been developed with more capabilities to accommodate a wider range of users over a broader range of turbine designs and operating environments. It provides in situ measurements of three-dimensional (3D) linear accelerations, 3D rotational velocities, 3D orientation, pressure, and temperature at a sampling frequency of 2048 Hz. It also has an automatic floatation system and built-in radio-frequency transmitter for recovery. The relative errors of the pressure, acceleration, and rotational velocity were within ±2%, ±5%, and ±5%, respectively. The accuracy of orientation was within ±4° and accuracy of temperature was ±2 °C. The new-generation Sensor Fish is becoming a major technology and being deployed for evaluating the conditions for fish passage of turbines or other hydraulic structures in both the United States and several other countries.
Studies on Rubia akane(RA) derivatives. Part 8. Design, syntheses and antitumour activity of cyclic hexapeptide RA analogues possessing an alkyl substituent on the Tyr-3 aromatic ring (1996)

The effective conversion of RA-VII 1 into the naturally less-accessible RA-II 4 has been devised through boron tribromide bis-O-demethylation and successive selective partial O-methylation using diazo(trimethylsilyl)methane. The O-triflate 11 prepared from RA-II 4 was subjected to cross-coupling reaction with alkylstannanes to produce analogues 12, 13 and 15, while compounds 13 and 15 were later converted into analogues 14 and 16, respectively. Analogues 12–16 showed antitumour activity against P-388 leukaemia both in vitro and in vivo.
IL-13 induces proliferation and differentiation of human B cells activated by the CD40 ligand (1993)

We cloned the human CD40 ligand (hCD40L) from a cDNA library constructed from an activated CD8+T cell clone. Two cDNAs representing a 2.1 and a 1.4 kb clone were detected. Both cDNA clones had identical open reading frames of 261 amino acids and differed only in the length of their 3' untranslated ends, and probably represent the 2.1 and 1.4 kb mRNA species detected by Northern analysis in an activated CD4+ T cell clone. hCD40L transcripts could also be detected in CD4+ and CD8+ TCR alpha beta T cells, TCR gamma delta T cells, natural killer cells, monocytes, small intestine, and fetal thymocytes, but not in purified B cells, fetal liver, fetal bone marrow, brain, kidney, or heart. COS-7 cells transfected with hCD40L (COS-7/hCD40L) induced human B cell activation as judged by the induction of homotypic aggregates of Epstein-Barr virus transformed and normal B cells. In addition, COS-7/hCD40L induced B cell proliferation, which was further enhanced by IL-4, or IL-13. IL-13, like IL-4, synergized with the mouse and hCD40L to induce IgM, total IgG, IgG4, and IgE, but not IgA, production by highly purified B cells. Anti-IL-4 antibodies inhibited IL-4 and COS-7/hCD40L induced Ig production by B cells, but had no effect on IL-13 and COS-7/hCD40L induced B cell differentiation, indicating that IL-13 and hCD40L induced Ig production, including isotype switching to IgE, independently of IL-4. hCD40L induced B cell differentiation was blocked by soluble CD40, confirming the requirement for specific engagement of CD40L.(ABSTRACT TRUNCATED AT 250 WORDS)