gebhart/patrepeval huggingface dataset:
Superpolylinkers in Cloning and Expression Vectors (1989)

Versatile DNA polylinkers of more than 300 bp were constructed. They contain the recognition sequences of all restriction enzymes--whether known or still to be discovered--that recognize palindromic hexamers. In addition to these 64 uninterrupted hexameric recognition sites, a number of sites containing interrupted palindromes and nonpalindromic sequences and two recognition sequences with 8 bp are present. Polylinkers (in several variants) were inserted into frequently utilized Escherichia coli cloning vectors such as pBluescript (yielding pSLJ10, pSL250, pSL260, pSL270, and pSL300), pUC18/pUC19 (yielding pSL180 and pSL190, respectively), or pUC118/pUC119 (yielding pSL1180 and pSL1190, respectively). A subtle color discrimination between presence and absence of insert in pSL300 (mid-blue to light-blue or white) was seen in a number of test ligations. The mid-blue color that is generated by pSL300 is presumably due to translational restarts. A different intergenic region for translational restarts was used in plasmids pSL251, pSL261, pSL271, and pSL301. The polylinker was also inserted into expression vector pUC120, yielding pSE1200, and into expression vector pKK233-2, yielding pSE220 and a shortened version thereof, pSE280. Finally, the polylinker was inserted into pTrc99A, resulting in pSE380, which carries a lac repressor gene. This expands the use of the expression system beyond lacIq strains to other bacterial hosts. These versatile vectors have broad applications in genetic engineering.
Electrical characteristics of low atrial septum pacing compared with right atrial appendage pacing (2005)

The electrical characteristics of LAS pacing makes this alternative position in the atrium safe and feasible. Though statistical differences were found in P-wave sensing (LAS higher voltage than in the RAA) and FFRW sensing was higher in the LAS compared with the RAA this did not interfere with the clinical applicability of the LAS as alternative pacing site.
The Ability of Biomarkers to Predict Systemic Progression in Men with High-Risk Prostate Cancer Treated Surgically Is Dependent on ERG Status (2010)

The objective of this study was to assess the relationship of the tumor protein levels of TOP2A and MIB-1 and ERG status with cancer-specific outcomes in men with high-risk prostate cancer treated by radical prostatectomy (RP). A 150-pair case-control study was designed from RP patients who developed systemic progression (SP) within 6 years of RP (cases) and men who were free of disease at least 8 years after RP (controls). The cases and controls were matched on conventional prognostic clinical parameters. TOP2A and MIB-1 levels were assessed by immunohistochemical methods, and ERG status was assessed by quantitative reverse transcription-PCR. The prognostic abilities of TOP2A and MIB-1 were significantly better in ERG(-) patients, and TOP2A was superior to MIB-1. In receiver operating characteristic analysis, the TOP2A and MIB-1 scores exhibited AUCs of 0.81 and 0.78 for ERG(-) patients, versus 0.67 and 0.68 for ERG(+) patients, respectively. Clinical parameters attained an AUC of 0.65 in ERG(-) patients and 0.54 in ERG(+) patients. When both markers were incorporated into a model for ERG(-) patients, the AUC increased to 0.83, with TOP2A showing a stronger association with SP than MIB-1. The time to SP was significantly associated with TOP2A; higher 5-year SP rates were observed in patients with higher TOP2A protein levels. In addition, although patient numbers are small, the response to adjuvant androgen deprivation therapy is associated with ERG status, showing more significant treatment effect in ERG(+) patients.
Photodynamic therapy (PDT) with Hypericum perforatum L extract induced significant in vitro cytotoxicity of human bladder cancer cells (2004)

4321 Photodynamic therapy (PDT) is a modality for the treatment of cancer involving excitation of photosensitizers with harmless visible light producing reactive oxygen species. The major biological effects of PDT are apoptosis of tumor cells, destruction of the blood supply and activation of the immune system. The objective of this study is to compare in an animal model of metastatic cancer, PDT alone and PDT combined with low-dose cyclophosphamide (CY). Since the tumor we used is highly metastatic it is necessary to generate anti-tumor immunity using PDT to effect total cures and this immunity may be potentiated by cyclophosphamide (CY). In our model we used J774 cells (a Balb/c reticulum cell sarcoma line with the characteristics of macrophages). One million cells were injected subcutaneously in the leg of Balb/c mice. Mice had primary tumors surgically removed at different time points after tumor cell injection, and all mice died of distant metastases even when surgery was as early as 24 hours post-injection. We used the following PDT regimens: benzoporphyrin derivative monoacid ring A (BPD, 2mg/kg injected IV followed after 15 min by 150 J/cm2 of 690-nm light) and Photofrin (PF, 10 mg/kg injected IV followed after 24 hours by 150 J/cm2 635-nm light). CY (50 mg/kg IP was injected 48 hours before light delivery. In addition to following mice for tumor response and survival we studied the induction of tumor specific cytotoxic T-lymphocyte activity through a non-radioactive cytotoxicity assay and quantification of suppressor T cells as one of the possible mechanisms of action for CY. BPD-PDT led to complete regression of the primary tumor in more than half the mice but no permanent cures were obtained. BPD-PDT in combination with CY led to 65% permanent cures but was associated with more treatment related deaths. PF-PDT alone did not lead to regression of primary tumors, while PF-PDT in combination with CY gave mainly regression of primary tumors followed by local recurrence around day 45. Permanent cures were obtained in 18% of mice. CY alone gave no permanent cures. We conclude that BPD-PDT in combination with CY gives best overall results and that this is attributable to immune system activation in addition to PDT-mediated destruction of the tumor.
Conserved Residues Asp16 and Pro24 of TnaC-tRNA Pro Participate in Tryptophan Induction of tna Operon Expression (2008)

In Escherichia coli, interactions between the nascent TnaC-tRNA(Pro) peptidyl-tRNA and the translating ribosome create a tryptophan binding site in the ribosome where bound tryptophan inhibits TnaC-tRNA(Pro) cleavage. This inhibition delays ribosome release, thereby inhibiting Rho factor binding and action, resulting in increased tna operon transcription. Replacing Trp12 of TnaC with any other amino acid residue was previously shown to prevent tryptophan binding and induction of tna operon expression. Genome-wide comparisons of TnaC amino acid sequences identify Asp16 and Pro24, as well as Trp12, as highly conserved TnaC residues. Replacing these residues with other residues was previously shown to influence tryptophan induction of tna operon expression. In this study, in vitro analyses were performed to examine the potential roles of Asp16 and Pro24 in tna operon induction. Replacing Asp16 or Pro24 of TnaC of E. coli with other amino acids established that these residues are essential for free tryptophan binding and inhibition of TnaC-tRNA(Pro) cleavage at the peptidyl transferase center. Asp16 and Pro24 are in fact located in spatial positions corresponding to critical residues of AAP, another ribosome regulatory peptide. Sparsomycin-methylation protection studies further suggested that segments of 23S RNA were arranged differently in ribosomes bearing TnaCs with either the Asp16Ala or the Pro24Ala change. Thus, features of the amino acid sequence of TnaC of the nascent TnaC-tRNA(Pro) peptidyl-tRNA, in addition to the presence of Trp12, are necessary for the nascent peptide to create a tryptophan binding/inhibition site in the translating ribosome.
Purification and Properties of 4-Hydroxy-4-Methyl-2-Oxoglutarate Aldolase from Pseudomonas ochraceae Grown on Phthalate (1990)

4-Hydroxy-4-methyl-2-oxoglutarate aldolase [4-hydroxy-4-methyl-2-oxoglutarate pyruvate-lyase: EC 4.1.3.17] has been purified to homogeneity (about 770-fold purification, yield 11.4%) from Pseudomonas ochraceae grown on phthalate. The enzyme has a molecular weight of 160,000 (gel filtration on Bio-Gel A-1.5m), a subunit molecular weight of 26,000 (SDS-PAGE) and an isoelectric point of 5.0 (isoelectric focusing). The enzyme requires divalent metal ions such as Mg2+, Mn2+, Co2+, Zn2+, and Cd2+ for activity. The enzyme actively cleaves 4-carboxy-4-hydroxy-2-oxoadipate, a physiological substrate of the enzyme, to give pyruvate and oxaloacetate, but shows much lower affinity for 4-hydroxy-4-methyl-2-oxoglutarate. 4-Hydroxy-2-oxoglutarate is cleaved at a low rate to pyruvate and glyoxylate. The l-isomers of the substrates are preferentially cleaved rather than the d-isomers as determined polarimetrically. The enzyme reactions are reversible: the equilibrium constants (pH 8.0, 25 C) for the HMG and HG cleavage reactions are about 0.07 and 0.03 M, respectively, whereas no equilibrium is observed with CHA due to oxaloacetate beta-decarboxylase activity associated with the enzyme. The enzyme activity is hardly affected by thiols and thiol reagents. The non-enzymatic cleavage reaction caused by various metal ions has also been studied to examine the mechanistic similarity to the enzymatic reaction.
Association of thrombospondin of endothelial cells with other matrix proteins and cell attachment sites and migration tracks. (1988)

Different biochemical and cytochemical techniques were applied to characterize the sites of localization of thrombospondin in cultured endothelial cells. The results obtained by [35S]methionine labeling, immunoblotting, immunoprecipitation, fluorescence microscopy, ultracytochemistry, immunogold labeling, and silver enhancement experiments revealed that thrombospondin secreted by endothelial cells is structurally organized together with proteoheparan sulfate in spherical granules at the cell surface. These granules are about 100 to 300 nm in size. Heparin or enzymatic degradation with heparitinase, but not with ABC lyase, release thrombospondin from the cell surface. Fibronectin is expressed in the extracellular matrix of endothelial cells in a fibrillar organization, clearly distinct from the punctate pattern of thrombospondin on the cell surface. Furthermore, secreted thrombospondin is highly enriched together with fibronectin and proteoheparan sulfate in cell attachment sites and in cell migration tracks. In cell migration tracks proteoheparan sulfate more clearly resembles the fibrillar distribution pattern of fibronectin, whereas thrombospondin reveals a rather monodisperse pattern. The obtained data suggest preferential sites of interaction between thrombospondin and heparan sulfate proteoglycans on the cell surface and a participation of thrombospondin in cell adhesion and cell migration.
Cyclodextrin Derivatives in Pharmaceutics (1995)

The current cyclodextrin (CD) literature is reviewed concerning synthesis, characterization, and pharmaceutical relevant applications of CD derivatives. Although natural CDs have been used extensively to improve pharmaceutical properties, the effects of chemically modified CDs on the solubility, dissolution rate, and stability of drugs are overproportional. Concerning the parenteral application, the major interest is focussed on highly water-soluble, randomly substituted hydroxyalkyl derivatives of beta- and gamma-CD such as 2-hydroxypropyl-beta-cyclodextrin (2-HP-beta-CD). Although the heptakis-(2,6-di-O-methyl)-beta-cyclodextrin is applied in the pharmaceutical field, 2-HP-beta-CD is predestined as a parenteral drug carrier owing to its weak hemolytic activity and intrinsically amorphous character. A minimal average degree of substitution is especially preferred when 2-HP-beta-CD is used as solubilizer of pharmaceuticals for the use in parenteral applications. The influence of the type, degree, and pattern of substitution of the CDs, as well as substituent effects of the guest molecule is elucidated.
Crack-free 2D-inverse opal anatase TiO2 films on rigid and flexible transparent conducting substrates: low temperature large area fabrication and electrochromic properties (2014)

A ‘dynamic-hard-template’ strategy is developed for large-area crack-free synthesis of 2D anatase TiO<sub>2</sub> inverse opal film on rigid and flexible ITO substrates by using PS templates.
Immunocytochemical Detection ofEhrlichia PlatysAntigens in Canine Blood Platelets (1991)

An avidin-biotin immunoperoxidase complex (ABC) immunocytochemical (ICC) stain procedure was optimized for detection of Ehrlichia platys antigens. Positive immunoreactivity was detected with dilutions of canine immune serum on acetone-fixed smears of platelet-rich plasma from E. platys-infected dogs. No E. platys antigens were detected when this ICC stain was applied to frozen or paraffin-embedded formalin- or acetone-fixed tissue sections from dogs with acute E. platys infection. Acetone fixation and freezing preserved ICC staining of ehrlichial antigens in infected blood platelets, whereas formalin treatment of similarly preserved E. platys -infected platelets nullified positive immunoreactivity. Significant E. platys infection of cells and tissues other than platelets may not occur.
Saliva of the Lyme disease vector, Ixodes dammini, blocks cell activation by a nonprostaglandin E2-dependent mechanism. (1994)

Tick-borne pathogens would appear to be vulnerable to vertebrate host immune responses during the protracted duration of feeding required by their vectors. However, tick salivary components deposited during feeding may inhibit hemostasis and induce immunosuppression. The mode of action and the nature of immunosuppressive salivary components remains poorly described. We determined that saliva from the main vector of the agent of Lyme disease, Ixodes dammini, profoundly inhibited splenic T cell proliferation in response to stimulation with concanavalin A or phytohemagglutin, in a dose-dependent manner. In addition, interleukin 2 secretion by the T cells was markedly diminished by saliva. Tick saliva also profoundly suppressed nitric oxide production by macrophages stimulated with lipopolysaccharide. Finally, we analyzed the molecular basis for the immunosuppressive effects of saliva and discovered that the molecule in saliva responsible for our observations was not PGE2, as hypothesized by others, but rather, was a protein of 5,000 mol wt or higher.
MPEG Surround: The Forthcoming ISO Standard for Spatial Audio Coding (2006)

S.213-230
Can we Target the Chemokine Network for Cancer Therapeutics? (2006)

The paradigm of cancer development and metastasis has been redefined to encompass a more comprehensive interaction between the tumor and microenvironment within which the tumor cells reside. Despite the realization that this more comprehensive relationship has changed the current paradigm of cancer research, the struggle continues to more completely understand the pathogenesis of the disease and the ability to appropriately identify and design novel targets for therapy. Chemokines and chemokine receptors are being investigated for their role in tumor development and metastasis and may prove to be useful therapeutic targets. The chemokine family is a complex network of molecules that are ubiquitously expressed and perform a variety of functions most notably regulating the immune system. Here we review the importance of chemokines in the tumor-stromal interaction and discuss current concepts for targeting the chemokine network.
Parallel Fabrication of Sub-50-nm Uniformly Sized Nanoparticles by Deposition through a Patterned Silicon Nitride Nanostencil (2005)

Using low-pressure chemical vapor deposition of silicon dioxide, we have reduced the size of 56-nm features in a silicon nitride membrane, called a stencil, down to 36 nm. Sub-50-nm uniformly sized nanoparticles are fabricated by electron-beam deposition of Pt through the stencil mask. A self-assembled monolayer (SAM) of tridecafluoro-1,1,2,2-tetrahydrooctyl-1-trichlorosilane was used to reduce Pt clogging of the nanosize holes during deposition as well as to protect the stencil during the postdeposition Pt removal. X-ray photoelectron spectroscopy shows that the SAM protects the stencil efficiently during this postdeposition removal of Pt.
Implications of hypoxia on mucosal barrier function. (2003)

Epithelial cells which line mucosal surfaces (e.g. lung, intestine) critically function as a semi-permeable barrier to the outside world. Mucosal organs are highly vascular with extensive metabolic demands, and for this reason, are particularly susceptible to diminished blood flow and resultant tissue hypoxia. Recent work from a number of groups have defined the critical molecular and cellular determinants of barrier function in hypoxic/ischemic tissues. Here, we will briefly highlight some of these studies from both a basic and clinical viewpoint and provide a perspective on future work related to tigh tjunction function in mucosal hypoxia.
Translocation of a hybrid YopE‐adenylate cyclase from Yersinia enterocolitica into HeLa cells (1994)

Pathogenic bacteria of the genus Yersinia release in vitro a set of antihost proteins called Yops. Upon infection of cultured epithelial cells, extracellular Yersinia pseudotuberculosis transfers YopE across the host cell plasma membrane. To facilitate the study of this translocation process, we constructed a recombinant Yersinia enterocolitica strain producing YopE fused to a reporter enzyme. As a reporter, we selected the calmodulin-dependent adenylate cyclase of Bordetella pertussis and we monitored the accumulation of cyclic AMP (cAMP). Since bacteria do not produce calmodulin, cyclase activity marks the presence of hybrid enzyme in the cytoplasmic compartment of the eukaryotic cell. Infection of a monolayer of HeLa cells by the recombinant Y. enterocolitica strain led to a significant increase of cAMP. This phenomenon was dependent not only on the integrity of the Yop secretion pathway but also on the presence of YopB and/or YopD. It also required the presence of the adhesin YadA at the bacterial surface. In contrast, the phenomenon was not affected by cytochalasin D, indicating that internalization of the bacteria themselves was not required for the translocation process. Our results demonstrate that Y. enterocolitica is able to transfer hybrid proteins into eukaryotic cells. This system can be used not only to study the mechanism of YopE translocation but also the fate of the other Yops or even of proteins secreted by other bacterial pathogens.
Role of conserved glycosylation sites in maturation and transport of influenza A virus hemagglutinin (1993)

The role of three N-linked glycans which are conserved among various hemagglutinin (HA) subtypes of influenza A viruses was investigated by eliminating the conserved glycosylation (cg) sites at asparagine residues 12 (cg1), 28 (cg2), and 478 (cg3) by site-directed mutagenesis. An additional mutant was constructed by eliminating the cg3 site and introducing a novel site 4 amino acids away, at position 482. Expression of the altered HA proteins in eukaryotic cells by a panel of recombinant vaccinia viruses revealed that rates and efficiency of intracellular transport of HA are dependent upon both the number of conserved N-linked oligosaccharides and their respective positions on the polypeptide backbone. Glycosylation at two of the three sites was sufficient for maintenance of transport of the HA protein. Conserved glycosylation at either the cg1 or cg2 site alone also promoted efficient transport of HA. However, the rates of transport of these mutants were significantly reduced compared with the wild-type protein or single-site mutants of HA. The transport of HA proteins lacking all three conserved sites or both amino-terminally located sites was temperature sensitive, implying that a polypeptide folding step had been affected. Analysis of trimer assembly by these mutants indicated that the presence of a single oligosaccharide in the stem domain of the HA molecule plays an important role in preventing aggregation of molecules in the endoplasmic reticulum, possibly by maintaining the hydrophilic properties of this domain. The conformational change observed after loss of all three conserved oligosaccharides also resulted in exposure of a normally mannose-rich oligosaccharide at the tip of the large stem helix that allowed its conversion to a complex type of structure. Evidence was also obtained suggesting that carbohydrate-carbohydrate interactions between neighboring oligosaccharides at positions 12 and 28 influence the accessibility of the cg2 oligosaccharide for processing enzymes. We also showed that terminal glycosylation of the cg3 oligosaccharide is site specific, since shifting of this site 4 amino acids away, to position 482, yielded an oligosaccharide that was arrested in the mannose-rich form. In conclusion, carbohydrates at conserved positions not only act synergistically by promoting and stabilizing a conformation compatible with transport, they also enhance trimerization and/or folding rates of the HA protein.
Immunodetection of the Ligand-Activated Receptor for Epidermal Growth Factor (1991)

Many receptors for cellular growth factors are known to be protein tyrosine kinases which become activated upon ligand binding at their extracellular domain. We describe here a method to detect the activation state of Epidermal Growth Factor receptor (EGFr) with a monoclonal antibody (mAb74). This antibody was found to preferentially recognize the ligand-activated EGFr as detected by immunoprecipitation, Western blotting and immunocytochemical techniques. mAb74 did not recognize other tyrosine-phosphorylated proteins and was not inhibited by phosphotyrosine, suggesting that it is recognizing an epitope specific for the ligand-activated EGF receptor. The reactivity of mAb74 towards EGFr was closely correlated with the EGF-dependent tyrosine phosphorylation of endogenous substrates. This antibody allows one to detect the activated EGF receptor in vitro or in vivo even in a complex mixture of other tyrosine kinases and substrates.
Hepatoprotection by L-Ornithine L-Aspartate in Non-Alcoholic Fatty Liver Disease (2018)

L-ornithine L-aspartate (LOLA) has hepatoprotective properties in patients with fatty liver of diverse etiology and results of a multicenter randomized clinical trial reveal that 12 weeks treatment with oral LOLA (6-9 g/d) results in a dose-related reduction in activities of liver enzymes and triglycerides together with significant improvements of liver/spleen CT ratios. A preliminary report described improvements of hepatic microcirculation in patients with non-alcoholic steatohepatitis (NASH) following treatment with LOLA. Mechanisms responsible for the beneficial effects of LOLA in NAFLD/NASH involve, in addition to its established ammonia-lowering effect, metabolic transformations of the LOLA-constituent amino acids L-ornithine and L-aspartate into L-glutamine, L-arginine, and glutathione. These metabolites have well-established actions implicated in the prevention of lipid peroxidation, improvement of hepatic microcirculation in addition to anti-inflammatory, and anti-oxidant properties. Key Messages: (1) LOLA is effective for the treatment of key indices in NAFLD/NASH. (2) Mechanisms other than LOLA's ammonia-lowering action have been postulated. (3) Further assessments in the clinical setting are now required.