gebhart/patrepeval huggingface dataset:
Antibodies Fused to Innate Immune Molecules Reduce Initiation ofCryptosporidium parvumInfection in Mice (2010)

At present no completely effective treatments are available for Cryptosporidium parvum infections in humans and livestock. Based on previous data showing the neutralizing potential of a panel of monoclonal antibodies developed against C. parvum, and based on the fact that innate immune peptides and enzymes have anticryptosporidial activity, we engineered several of these antibodies into antibody-biocide fusion proteins. We hypothesized that the combination of high-affinity antibody targeting with innate immune molecule-mediated killing would result in a highly effective new antiprotozoal agent. To test this hypothesis, we expressed antibody-biocide fusion proteins in a mammalian cell culture system and used the resulting products for in vitro and in vivo efficacy experiments. Antibody-biocide fusion proteins efficiently bound to, and destroyed, C. parvum sporozoites in vitro through a membrane-disruptive mechanism. When antibody-biocide fusion proteins were administered orally to neonatal mice in a prophylactic model of cryptosporidiosis, the induction of infection was reduced by as much as 81% in the mucosal epithelium of the gut, as determined on the basis of histopathological scoring of infectious stages. Several versions of antibody fusion proteins that differed in antigen specificity and in the biocide used had strong inhibitory effects on the initiation of infection. The results lay the groundwork for the development of a new class of antimicrobials effective against Cryptosporidium.
A scalable distributed information management system (2004)

We present a Scalable Distributed Information Management System (SDIMS) that aggregates information about large-scale networked systems and that can serve as a basic building block for a broad range of large-scale distributed applications by providing detailed views of nearby information and summary views of global information. To serve as a basic building block, a SDIMS should have four properties: scalability to many nodes and attributes, flexibility to accommodate a broad range of applications, administrative isolation for security and availability, and robustness to node and network failures. We design, implement and evaluate a SDIMS that (1) leverages Distributed Hash Tables (DHT) to create scalable aggregation trees, (2) provides flexibility through a simple API that lets applications control propagation of reads and writes, (3) provides administrative isolation through simple extensions to current DHT algorithms, and (4) achieves robustness to node and network reconfigurations through lazy reaggregation, on-demand reaggregation, and tunable spatial replication. Through extensive simulations and micro-benchmark experiments, we observe that our system is an order of magnitude more scalable than existing approaches, achieves isolation properties at the cost of modestly increased read latency in comparison to flat DHTs, and gracefully handles failures.
Hypersensitive Radical Probes and the Mechanisms of Cytochrome P450-Catalyzed Hydroxylation Reactions (2000)

The title probes are precursors to kinetically calibrated, aryl-substituted cyclopropylcarbinyl radicals that rearrange with picosecond lifetimes. Applications in studies of cytochrome P450-catalyzed hydroxylation reactions are reviewed. Initially confusing results regarding lifetimes of radicals in the hydroxylation reactions were resolved when second-generation probes that distinguish between radicals and cations were employed. The results indicate that two electrophilic oxidizing species are involved in P450-catalyzed hydroxylations, an iron-oxo species that inserts oxygen and a hydroperoxo-iron species that inserts OH(+). The cationic rearrangement products are ascribed to reactions of the protonated alcohol products formed from the latter.
Lowering the pH Optimum of d-Xylose Isomerase: the Effect of Mutations of the Negatively Charged Residues (1998)

Streptomyces rubiginosus D-xylose isomerase catalyzes the reversible isomerization of D-glucose to D-fructose. The isomerization reaction is maximized in the alkaline region of pH 8.5-8.8. The amino acid residues around two active site histidines (His-54 and His-220) and on the surface of the enzyme were mutated to improve the catalytic efficiency at neutral pH. The mutations have been made by removing the negatively charged residues based upon the sequence comparison of other D-xylose isomerases and the hypothesis proposed by Russell and Fersht (1987). The effects of these substitutions on kinetic parameter, pH dependence, and thermostability were characterized. The kcat values for D56N and E221A mutants on D-glucose are increased by 30-40% over that of the wild-type enzyme at pH 7.3 and the increased activities are maintained between pH 6 and 7.5. However, the surface mutants D65A, D81A, and D163N/E167Q only show 40-60% of the wild-type activity over the entire pH range. The pH activity profiles of the mutants are broader than that of the wild-type enzyme. The optimum pHs and the pKa values for all the mutants are lowered by 0.5-0.8 and 0.1-0.5 units, respectively. The small delta(deltaG) and high Tm values for all the mutants indicate that there is no significant change in the hydrogen bond network in the active site by mutations. These results indicate that D56N and E221A are possible candidates as good catalysts for High-Fructose Corn Syrup (HFCS) production.
Inhibition of microglial inflammation by the MLK inhibitor CEP‐1347 (2005)

CEP-1347 is a potent inhibitor of the mixed lineage kinases (MLKs), a distinct family of mitogen-activated protein kinase kinase kinases (MAPKKK). It blocks the activation of the c-Jun/JNK apoptotic pathway in neurons exposed to various stressors and attenuates neurodegeneration in animal models of Parkinson's disease (PD). Microglial activation may involve kinase pathways controlled by MLKs and might contribute to the pathology of neurodegenerative diseases. Therefore, the possibility that CEP-1347 modulates the microglial inflammatory response [tumour necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6), and monocyte chemotactic protein-1 (MCP-1)] was explored. Indeed, the MLK inhibitor CEP-1347 reduced cytokine production in primary cultures of human and murine microglia, and in monocyte/macrophage-derived cell lines, stimulated with various endotoxins or the plaque forming peptide Abeta1-40. Moreover, CEP-1347 inhibited brain TNF production induced by intracerebroventricular injection of lipopolysaccharide in mice. As expected from a MLK inhibitor, CEP-1347 acted upstream of p38 and c-Jun activation in microglia by dampening the activity of both pathways. These data imply MLKs as important, yet unrecognized, modulators of microglial inflammation, and demonstrate a novel anti-inflammatory potential of CEP-1347.
Pharmacologic modification of acute vascular graft thrombosis. (1982)

A baboon arteriovenous shunt model has been used to study acute vascular graft thrombosis, and to assess the effectiveness of various antithrombotic agents. External velour Dacron (Sauvage) vascular grafts, placed inside Teflon tubing to prevent blood leakage, were interposed between lengths of a Silastic, femoral arteriovenous shunt. After thirty minutes exposure to flowing blood, specimens were removed for evaluation by scanning electron microscopy (SEM). Antithrombotic agents, given singly and in combination, included heparin, the potent platelet inhibitor prostacyclin (PGI2), and the snake venom ancrod (which selectively degrades circulating fibrinogen). Control graft surfaces showed uniform coverage by thrombus with masses of red cells and platelets entrapped in fibrin mesh. Extensive platelet deposition was not prevented by either heparin or PGI2, although heparinized animals showed little fibrin accumulation. Similarly, platelet deposition was extensive in animals receiving ancrod, singly or in combination with PGI2, despite the absence of circulating fibrinogen. Thrombus accumulation was effectively prevented only by heparin in combination with PGI2, demonstrating that in this setting, thrombosis may be initiated by either platelet or coagulation-dependent mechanisms that do not require circulating fibrinogen or its conversion to morphologically detectable amounts of fibrin. These mechanisms remain to be characterized. Two control grafts evaluated at one week showed complete surface coverage by macrophages, and the flow surface appeared nonthrombogenic despite significant underlying thrombus.
Chemokines and chemokine receptors in leukocyte trafficking (2002)

Chemokines regulate inflammation, leukocyte trafficking, and immune cell differentiation. The role of chemokines in homing of naive T lymphocytes to secondary lymphatic organs is probably the best understood of these processes, and information on chemokines in inflammation, asthma, and neurological diseases is rapidly increasing. Over the past 15 years, understanding of the size and functional complexity of the chemokine family of peptide chemoattractants has grown substantially. In this review, we first present information regarding the structure, expression, and signaling properties of chemokines and their receptors. The second part is a systems physiology-based overview of the roles that chemokines play in tissue-specific homing of lymphocyte subsets and in trafficking of inflammatory cells. This review draws on recent experimental findings as well as current models proposed by experts in the chemokine field.
The Effect of Absorbable Stenting on Postoperative Stenosis of the Surgically Enlarged Maxillary Sinus Ostia in a Rabbit Animal Model (1996)

Stenting did not statistically change the amount of stenosis of the surgically enlarged ostia in a rabbit model, although a trend toward more scarring when compared with the nonstented side was observed.
Matrix Metalloproteinases (1999)

The timely breakdown of extracellular matrix (ECM)1 is essential for embryonic development, morphogenesis, reproduction, and tissue resorption and remodeling. The matrix metalloproteinases (MMPs), also called matrixins, are thought to play a central role in these processes. The expression of most matrixins is transcriptionally regulated by growth factors, hormones, cytokines, and cellular transformation (1, 2). The proteolytic activities of MMPs are precisely controlled during activation from their precursors and inhibition by endogenous inhibitors, α-macroglobulins, and tissue inhibitors of metalloproteinases (TIMPs).
Loops versus Branch Functionality in Model Click Hydrogels (2015)

Through the use of macromolecular design and efficient chemical reactions it is now possible to control the composition of polymer networks and gels with excellent precision. In contrast, topological defects are still impossible to avoid and are generally difficult to quantify. For example, primary loops that form when a bifunctional monomer (A2) reacts twice with the same f functional (f > 2) monomer (Bf) during formation of an end-linked A2 + Bf network represent a pervasive defect that has a detrimental effect on mechanical integrity. Methods for the quantitative analysis of primary loops in such materials have recently emerged; however, these methods have only been applied to the simplest network structure: A2 + B3. Herein, we report strategies for counting primary loops in tetrafunctional (A2 + B4) networks and networks with mixed tri- and tetrafunctional (A2 + B3/B4) junctions. We apply these strategies to the quantitative analysis of primary loops in a series of end-linked poly(ethylene glycol) hydrogels synthesized via copper-catalyzed azide–alkyne cycloaddition “click” chemistry. Our results show that A2 + B4 networks are particularly susceptible to cyclic defects compared to A2 + B3 networks and that higher-order cyclic species must play a significant role in the gel point of the former materials. Our experimental results were compared to rate theory and Monte Carlo simulations. This work reveals new structural insights into a widely studied family of materials and sets the stage for the development of strategies to tune network defects in such gels.
<title>Survey of wavelet-domain watermarking algorithms</title> (2001)

In this paper, we will provide an overview of the wavelet-based watermarking techniques available today. We will see how previously proposed methods such as spread-spectrum watermarking have been applied to the wavelet transform domain in a variety of ways and how new concepts such as the multi-resolution property of the wavelet image decomposition can be exploited. One of the main advantages of watermarking in the wavelet domain is its compatibility with the upcoming image coding standard, JPEG2000. Although many wavelet-domain watermarking techniques have been proposed, only few fit the independent block coding approach of JPEG2000. We will illustrate how different watermarking techniques relate to image compression and examine the robustness of selected watermarking algorithms against image compression.
[Effect of ondansetron in lower extremity bone surgery on morphine and tramadol consumption using patient controlled analgesia]. (2007)

In this study, we aimed to assess the effect of administration of ondansetron on morphine and tramadol consumptions. After approval by the ethics committee, 120 patients with ASA status I or II, who will undergo elective lower extremity surgery, were included in the study. Patients were randomly divided into 4 groups following the anesthesia induction. Group I received tramadol as PCA with an infusion of 0.3 mg/kg following a loading dose of 1.5 mg/kg administered 1 hour before the end of the surgery. Group II received ondansetron 0.1 mg/kg following induction of anesthesia, additionally. Group III received morphine as PCA with an infusion following a loading dose of 0.15 mg/kg administered 30 minutes before the end of surgery. Group IV received ondansetron 0.1 mg/kg following induction of anesthesia, additionally. Pain scores(VAS), nausea, vomitting and sedation scores, analgesic consumptions and adverse effects were recorded at 5th, 15th, 30th, 45th minutes and 4th, 8th, 12th and 24th hours postoperatively. Postoperative VAS, nausea, vomitting and sedation scores were similar among the groups. The analgesic consumption was found significantly higher at 4th, 8th, 12th and 24th hours in group II. No statistically significant difference was found in analgesic consumption between group III and IV at all times. We concluded that, ondansetron, when administered as nausea prophylaxis in patients receiving tramadol and morphine as PCA, did not effect morphine consumption whereas did increased tramadol consumption.
Designing synthetic vaccines for HIV (2015)

Despite three decades of intensive research efforts, the development of an effective prophylactic vaccine against HIV remains an unrealized goal in the global campaign to contain the HIV/AIDS pandemic. Recent characterization of novel epitopes for inducing broadly neutralizing antibodies has fueled research in the design and synthesis of new, well-defined antigenic constructs for the development of HIV envelope-directed vaccines. The present review will cover previous and recent efforts toward the design of synthetic vaccines based on the HIV viral envelope glycoproteins, with special emphasis on examples from our own laboratories. The biological evaluation of some of the most representative vaccine candidates, in terms of their antigenicity and immunogenicity, will also be discussed to illustrate the current state-of-the-art toward the development of fully synthetic HIV vaccines.
Characteristics of epithelial cella cultured from feline lung. (1976)

Cell cultures were initiated by trypsinization of lung tissues obtained from 55-day-old fetuses of Felis catus. After a period of cultivation, the cells were cloned and several clones with an epithelial morphology were established. On electron microscopy, at least four of the clones contained intracytoplasmic lamellar inclusion bodies typical in appearance to those observed in type II alveolar cell in situ. These clones should be invaluable for the study of the biosynthesis of long surfactant.
Natural killer (NK) cells are present in mice with severe combined immunodeficiency (scid). (1985)

Spleen cells from C.B- 17 scid mice with severe combined immunodeficiency disease exhibit natural killer cell (NK) activity against YAC lymphoma targets in a standard 4-hr 51Cr release assay. The cytolytic activity is demonstrable only at high effector to target ratios but can be augmented at least sevenfold by the interferon inducer poly I:C. The pattern of target lysis is specific, because splenocytes from poly I:C-primed C.B-17 scid mice lyse NK-sensitive YAC cells and not the insensitive P815 mastocytoma. The presence of several NK-associated antigens on C.B-17 scid splenocytes was tested by pretreating cells with the appropriate antiserum plus complement before testing for NK activity. The results indicate that a proportion of NK effectors in C.B-17 scid mice bear surface NK 2.1 and Asialo GM1 but are negative for Thy-1.
Low Concentrations of Acid-Soluble Thiol (Cysteine) in the Blood Plasma of HIV-1-Infected Patients (1989)

Blood plasma samples from HIV-1-infected persons contain elevated glutamate concentrations up to 6-fold the normal level and relatively low concentrations of acid-soluble thiol (i.e. decreased cysteine concentrations). The intracellular glutathione concentration in peripheral blood-mononuclear cells (PBMC) and monocytes from HIV antibody-positive persons are also significantly decreased. Therapy with azidothymidine (AZT) causes a substantial recovery of the plasma thiol levels; but glutamate levels remain significantly elevated and intracellular glutathione levels remain low. Cell culture experiments with approximately physiological amino-acid concentrations revealed that variations of the extracellular cysteine concentration have a strong influence on the intracellular glutathione level and the rate of DNA synthesis [( 3H]thymidine incorporation) in T cell clones and human and murine lymphocyte preparations even in the presence of several-fold higher cystine and methionine concentrations. Cysteine cannot be replaced by a corresponding increase of the extracellular cystine or methionine concentration. These experiments suggest strongly that the low cysteine concentration in the plasma of HIV-infected persons may play a role in the pathogenetic mechanism of the acquired immunodeficiency syndrome.
In vivo Color-Coded Imaging of the Interaction of Colon Cancer Cells and Splenocytes in the Formation of Liver Metastases (2006)

The role of host cells in tumor progression and metastasis is critical. Intrasplenic injection of tumor cells has long been known as an effective method of developing liver metastases in nude mice, whereas portal vein (PV) injection of tumor cells can result in rapid death of the tumor cells. Host cells were thought to play a role in these phenomena. We report here that after splenic injection of tumor cells, splenocytes cotraffic with the tumor cells to the liver and facilitate metastatic colony formation. Human colon cancer cells that express green fluorescent protein (GFP) linked to histone H2B in the nucleus and red fluorescent protein (RFP) in the cytoplasm (HCT-116-GFP-RFP) were injected in either the PV or spleen of nude mice and imaged at the subcellular level in vivo. Extensive clasmocytosis (destruction of the cytoplasm) of the cancer cells occurred within 6 hours after PV injection and essentially all the cancer cells died. In contrast, splenic injection of these tumor cells resulted in the aggressive formation of liver and distant metastasis. GFP spleen cells were found in the liver metastases that resulted from intrasplenic injection of the tumor cells in transgenic nude mice ubiquitously expressing GFP. When GFP spleen cells and the RFP cancer cells were coinjected in the PV, liver metastasis resulted that contained GFP spleen cells. These results suggest a novel tumor-host interaction that enables efficient formation of liver metastasis via intrasplenic injection.
Biosynthesis of polylactic acid and its copolymers using evolved propionate CoA transferase and PHA synthase (2009)

For the synthesis of polylactic acid (PLA) and its copolymers by one-step fermentation process, heterologous pathways involving Clostridium propionicum propionate CoA transferase (Pct(Cp)) and Pseudomonas sp. MBEL 6-19 polyhydroxyalkanoate (PHA) synthase 1 (PhaC1(Ps6-19)) were introduced into Escherichia coli for the generation of lactyl-CoA endogenously and incorporation of lactyl-CoA into the polymer, respectively. Since the wild-type PhaC1(Ps6-19) did not efficiently accept lactyl-CoA as a substrate, site directed mutagenesis as well as saturation mutagenesis were performed to improve the enzyme. The wild-type Pct(Cp) was not able to efficiently convert lactate to lactyl-CoA and was found to exert inhibitory effect on cell growth, random mutagenesis by error-prone PCR was carried out. By employing engineered PhaC1(Ps6-19) and Pct(Cp), poly(3-hydroxybutyrate-co-lactate), P(3HB-co-LA), containing 20-49 mol% lactate could be produced up to 62 wt% from glucose and 3HB. By controlling the 3HB concentration in the medium, PLA homopolymer and P(3HB-co-LA) containing lactate as a major monomer unit could be synthesized. Also, P(3HB-co-LA) copolymers containing various lactate fractions could be produced from glucose alone by introducing the Cupriavidus necator beta-ketothiolase and acetoacetyl-CoA reductase genes. Fed-batch cultures were performed to produce P(3HB-co-LA) copolymers having 9-64 mol% of lactate, and their molecular weights, thermal properties, and melt flow properties were determined.
Reactions of Nitroparaffins. I. Synthesis and Reduction of Some γ-Nitroketones (1947)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of Nitroparaffins. I. Synthesis and Reduction of Some γ-NitroketonesMilton C. KloetzelCite this: J. Am. Chem. Soc. 1947, 69, 10, 2271–2275Publication Date (Print):October 1, 1947Publication History Published online1 May 2002Published inissue 1 October 1947https://pubs.acs.org/doi/10.1021/ja01202a010https://doi.org/10.1021/ja01202a010research-articleACS PublicationsRequest reuse permissionsArticle Views250Altmetric-Citations34LEARN 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
MicroRNAs MiR-17, MiR-20a, and MiR-106b Act in Concert to Modulate E2F Activity on Cell Cycle Arrest during Neuronal Lineage Differentiation of USSC (2011)

Mir-17, -20a, and -106b downregulate a common set of pro- and anti-proliferative target genes to impact cell cycle progression of USSC and increase intracellular activity of E2F transcription factors to govern G(1)/S transition.