gebhart/patrepeval huggingface dataset:
DNA-Linked RNase H For Site-Selective Cleavage Of RNA (1994)

ADNA-linked RNase H (Hybrid Enz-1) (Kanaya et al. (1992) J. Biol. Chem. 267, 8492-8498), in which dGTCATCTCC was attached to E. coli RNase H via a covalent linker of 21 A, was altered to improve the site-specific RNA cleavage by increasing the linker length. The sizes of the linkers on these hybrid enzymes (Hybrid Enz-2, -3, and -4) differed by 3 A, the axial rise of the DNA/RNA hybrid, to give 18-, 24-, and 27-A lengths. The conjugate with a size of A was able to cleave a synthetic 22mer RNA (5'-rAAGAUGUCUACGGAGAUGACCA-3'), containing the complementary 9mer RNA sequence (underlined), at one position, A16-U17. The kinetic parameters of Hybrid Enz-1, -2, -3, and -4 were examined using a 9mer RNA target. The results showed that longer linkers produced higher Km, kcat, and kcat/Km values, and the kcat/Km value of the conjugate with the 27-A linker reached 83% of that of the wild-type RNase H. Hybrid Enz-4 was found to be useful as an RNA restriction endonuclease.
Immunology and efficacy of MF59-adjuvanted vaccines (2018)

Adjuvants are included in vaccine formulations to enhance the immunogenicity and efficacy of vaccines. MF59® is an oil-in-water emulsion adjuvant and licensed for use in pandemic and seasonal influenza vaccines in many countries. MF59 is safe and well tolerated in humans. MF59-adjuvanted vaccination spares vaccine dose and enhances hemagglutination inhibiting antibodies against homologous and heterologous influenza virus strains. The mechanisms of MF59 involve rapid induction of chemokines, inflammatory cytokines, recruiting multiple immune cells, uric acid and benign apoptosis of certain innate immune cells. The adjuvant effects of MF59 on generating vaccine-specific isotype-switched IgG antibodies, effector CD8 T cells, and protective immunity were retained even in a CD4-deficient condition by inducing effective immune-competent microenvironment with various innate and antigen presenting cells in a mouse model. CD4-independent adjuvant effects of MF59 might contribute to improving the vaccine efficacy in children, the elderly, and immunocompromised patients as well as in healthy adults. Further studies will be needed to broaden the use of MF59 in various vaccine antigens and populations as well as lead to better understanding of the action mechanisms of MF59 adjuvant.
Macrophage checkpoint blockade: results from initial clinical trials, binding analyses, and CD47-SIRPα structure–function (2020)

The macrophage checkpoint is an anti-phagocytic interaction between signal regulatory protein alpha (SIRPα) on a macrophage and CD47 on all types of cells - ranging from blood cells to cancer cells. This interaction has emerged over the last decade as a potential co-target in cancer when combined with other anti-cancer agents, with antibodies against CD47 and SIRPα currently in preclinical and clinical development for a variety of hematological and solid malignancies. Monotherapy with CD47 blockade is ineffective in human clinical trials against many tumor types tested to date, except for rare cutaneous and peripheral lymphomas. In contrast, pre-clinical results show efficacy in multiple syngeneic mouse models of cancer, suggesting that many of these tumor models are more immunogenic and likely artificial compared to human tumors. However, combination therapies in humans of anti-CD47 with agents such as the anti-tumor antibody rituximab do show efficacy against liquid tumors (lymphoma) and are promising. Here, we review such trials as well as key interaction and structural features of CD47-SIRPα.
A Proteomic Approach for Quantitation of Phosphorylation Using Stable Isotope Labeling in Cell Culture (2003)

Posttranslational modifications are major mechanisms of regulating protein activity and function in vertebrate cells. It is essential to obtain qualitative information about posttranslational modification patterns of proteins to understand signal transduction mechanisms in greater detail. However, it is equally important to measure the dynamics of posttranslational modifications such as phosphorylation to approach signaling networks from a systems biology perspective. Despite a number of advances, methods to quantitate posttranslational modifications remain difficult to implement due to a number of factors including lack of a generic method, elaborate chemical steps, and requirement for large amounts of sample. We have previously shown that stable isotope-containing amino acids in cell culture (SILAC) can be used to differentially label growing cell populations for quantitation of protein levels. In this report, we extend the use of SILAC as a novel proteomic approach for the relative quantitation of posttranslational modifications such as phosphorylation. We have used SILAC to quantitate the extent of known phosphorylation sites as well as to identify and quantitate novel phosphorylation sites.
Dopant Diffusion in Silicon. III. Acceptors (1971)

Aluminum, gallium, indium, and thallium acceptors have been diffused into (111) silicon from doped epitaxially deposited source layers in a flowing hydrogen atmosphere. As in the case of P, As, Sb, and Bi donors reported earlier, all these acceptors show significantly lower mobilities when freed from surface effects. The temperature dependence of the intrinsic diffusion coefficients, obtained above 1120 \ifmmode^\circ\else\textdegree\fi{}C, are characterized by the following preexponential and activation-energy parameters: 1.385, 0.374, 0.785, (1.37) ${\mathrm{cm}}^{2}$/sec, and 3.41, 3.39, 3.63, (3.70) eV/atom for Al, Ga, In, Tl, respectively. An analysis of these diffusion characteristics indicate a similar point-defect mechanism for both group-III and group-V dopants in silicon.
Biological effects of anti-peptide antibodies against the her-2/neu receptor tyrosine kinase : implications for therapy of human breast cancer / (1997)

Cancer is the second leading cause o f death in the United States and o f breast cancers, about one quarter over express the erbB-2 oncogene.This gene encodes a 185kD growth factor receptor, HER-2/neu and its overexpression correlates with a poor prognosis.Thus, the ability to control the expression o f this protein could favorably reduce the number of cancer related deaths.HER-2 is composed o f four domains; an extracellular cysteine rich domain, a transmembrane sequence, tyrosine kinase domain and the C-terminal tyrosine autophosphorylation sites.The extracellular accessibility o f HER-2 makes it an ideal candidate for immimotherapy.The abihty o f tumor inhibitory antibodies to recognize linear epitopes o f the receptor prompted us to test the efficacy o f peptide antibodies raised to p 185.Previous work in oim lab has demonstrated the ability o f high titered antibodies fi-om an outbred population to recognize native protein.No ligand has yet been found for HER-2.Studies have shown that its action is mediated by heterodimerization with the other three members o f the epidermal growth factor receptor family: EGFR, HER-3 and HER-4, recruiting diverse molecules to the membrane and increasing the niunber o f signaling pathways accessible to the receptor complex.Dimerization engages HER-2's tyrosine kinase (TK) activity signaling a cascade o f intracellular events which result in aberrant growth.Monoclonal antibodies can modulate this TK activity by causing receptor internalization, tumor retardation and differentiation to ii the mature state.Our studies involve generating antibodies to conformational epitopes o f Her-2/neu by peptide immunization in an attempt to generate antibodies o f defined specificity.Peptide candidate antigens firom HER-2/neu were studied by computer-aided analysis.B cell epitopes were synthesized coUinearly with a T cell epitope, MVP 288-302, capable o f binding to a broad range o f MHC haplotypes.We have raised a panel o f peptide antibodies capable o f affecting the biology o f HER-2: DW IM V F (376-395), MVFDW4 (628-647), DW5MVF (115-136), DW6MVF (410-429).The MVF sequences were engineered into chimeric constructs with HER-2 B cell epitopes and elicited high titered antibodies.These antibodies are able to specifically recognize HER-2 and selectively inhibit tumor cell proliferation in vitro.The anti-peptide antibodies also retarded tumor growth in a nude mouse model.These findings suggest that antibodies raised to a peptide vaccine in humans may offer an effective, selective and less toxic system o f HER-2 positive tumor management than currently available methods.Synthetic vaccines would also avoid the dangers involved in using attenuated strains o f viruses or infectious biological material as carriers and provide a cost-effective method o f treatment.Further studies to induce a CTL response will explore the efScacy o f CTL involvement in this form o f therapy.Ill Dedicated to my family.IV
Differential suppression of allergen‐induced airway inflammation in murine model of asthma by lactic acid bacteria (2008)

Probiotics are demonstrated to be effective in reducing allergic symptoms. However, there are few reports to investigate therapeutic effects of lactobacillus on allergen‐induced airway inflammation. In this study, we examined whether lactic acid bacteria had therapeutic effects on lung airway inflammation. Three different strains of lactobacillus isolated from Korean traditional food Kimchi ( L. plantarum , L. sakei subsp. sakei and L. curvatus ) were chosen and evaluated in murine asthma model using ovalumin (OVA) as a model allergen. Airway hyperresponsiveness was suppressed in all lactobacillus‐administered mice, with the highest inhibition in the L. plantarum ‐administered group. The mRNA expression levels of genes related to mucus production were down‐regulated in lung homogenates of the lactobacillus‐administered mice. In addition, the levels of IL‐4 production in lymph node cells and IgE in sera were significantly lower in the lactobacillus‐administered mice than in untreated mice. Importantly, production levels of IL‐4 and IL‐13 were lower in bone marrow‐derived dendritic cells than those administered with other two strains, whereas the expression of IFN‐γ and IL‐12 were similarly up‐regulated in all lactobacillus‐treated groups. These results indicate that lactic acid bacteria may differentially suppress allergen‐induced airway inflammation through up‐regulation of Th1 cytokines and downregulation of Th2 cytokines in dendritic cells in vivo , and suggest that L. plantarum isolated from Kimchi is an effective probiotic for inhibiting allergic airway diseases.
Down-Regulation of Vascular Endothelial Cell Growth Factor-C Expression Using Small Interfering RNA Vectors in Mammary Tumors Inhibits Tumor Lymphangiogenesis and Spontaneous Metastasis and Enhances Survival (2005)

Tumor production of vascular endothelial cell growth factor (VEGF)-C is associated with tumor lymphangiogenesis and lymph node metastasis. In this study, we examined the effects of small interfering RNA (siRNA)-mediated inhibition of VEGF-C on murine mammary tumor growth, metastasis, and survival. The mRNA and protein expression of VEGF-C in murine mammary tumor cells stably transfected with a VEGF-C siRNA vector were significantly lower compared with VEGF-C-control vector-transfected cells. Cl66-siVEGFC tumors had lower levels of lymphangiogenesis and lymph node and spontaneous lung metastasis than Cl66-control tumors. However, we did not observe significant differences in primary tumor growth and experimental lung metastasis between mice injected with Cl66-siVEGFC and Cl66-control cells. In addition, mice bearing Cl66-siVEGFC tumors lived significantly longer than mice bearing Cl66-control tumors. Furthermore, our data suggest that inhibition of VEGF-C modulates immune cell infiltration and their function, which might be critical in tumor immunity. In summary, our data show that inhibition of VEGF-C expression using siRNA-mediated gene silencing vectors reduces lymphangiogenesis and lymph node and spontaneous lung metastasis, and enhances survival.
Document image defect models and their uses (2002)

The accuracy of today's document recognition algorithms falls abruptly when image quality degrades even slightly. In an effort to surmount this barrier, researchers have in recent years intensified their study of explicit, quantitative, parameterized models of the image defects that occur during printing and scanning. The author reviews the recent literature and discusses the form these models might take. A preview of a large public-domain database of character images, labeled with ground-truth including all defect model parameters, is given. The use of massive pseudo-randomly generated training sets for the construction of high-performance decision trees for preclassification is described. In a more theoretical vein, the author reports preliminary results in the estimation of the intrinsic error of precisely-specified text recognition problems. Finally, the author calls attention to some open problems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization and Optimization of Field of View in a Holographic Waveguide Display (2017)

The paper presents the characterization of the field of view (FOV) in a holographic waveguide display (HWD) with a broadband spectrum image source. The influences of parameters such as grating slanted angle of volume holographic grating (VHG), grating period, and effective refractive index are systematically analyzed. We optimized the parameters and calculated the maximum FOV of monochromatic and chromatic HWD. A multilayered VHGs structure is proposed to enlarge the FOV effectively without additional cost and optical design. We also build a rigorous simulation model to verify the feasibility of the multilayered structure. The theoretical maximum FOV of monochromatic and chromatic HWD are presented after optimization.
The plasma pharmacokinetics and cerebral spinal fluid penetration of intravenous topiramate in newborn pigs (2004)

Topiramate administered intravenously was well tolerated. Slow clearance of the drug allowed for maintenance of potential neuroprotective concentrations following a single dose of drug for 24 h. High drug penetration into the CSF is an ideal pharmacologic characteristic of any potential neuroprotective agent. The pharmacokinetic profile of intravenously administered topiramate, including its penetration into the CSF, appears to achieve this goal.
Investigation by 13C-NMR and tricarboxylic acid (TCA) deletion mutant analysis of pathways for succinate formation in Saccharomyces cerevisiae during anaerobic fermentation (2003)

NMR isotopic filiation of 13 C-labelled aspartate and glutamate was used to explore the tricarboxylic acid (TCA) pathway in Saccharomyces cerevisiae during anaerobic glucose fermentation. The assimilation of [3- 13 C]aspartate led to the formation of [2,3- 13 C]malate and [2,3- 13 C]succinate, with equal levels of 13 C incorporation, whereas site-specific enrichment on C-2 and C-3 of succinate was detected only with [3- 13 C]glutamate. The non-random distribution of 13 C labelling in malate and succinate demonstrates that the TCA pathway operates during yeast fermentation as both an oxidative and a reductive branch. The observed 13 C distribution suggests that the succinate dehydrogenase (SDH) complex is not active during glucose fermentation. This hypothesis was tested by deleting the SDH1 gene encoding the flavoprotein subunit of the SDH complex. The growth, fermentation rate and metabolite profile of the sdh1 mutant were similar to those of the parental strain, demonstrating that SDH was indeed not active. Filiation experiments indicated the reductive branch of the TCA pathway was the main pathway for succinate production if aspartate was used as the nitrogen source, and that a surplus of succinate was produced by oxidative decarboxylation of 2-oxoglutarate if glutamate was the sole nitrogen source. Consistent with this finding, a kgd1 mutant displayed lower levels of succinate production on glutamate than on other nitrogen sources, and higher levels of oxoglutarate dehydrogenase activity were observed on glutamate. Thus, the reductive branch generating succinate via fumarate reductase operates independently of the nitrogen source. This pathway is the main source of succinate during fermentation, unless glutamate is the sole nitrogen source, in which case the oxidative decarboxylation of 2-oxoglutarate generates additional succinate.
Advanced biochemical engineering (1987)

An Overview of Biochemical Engineering Microbial Cells and Enzymes Analysis of Biological Reactors Biomass Refining Applied Genetics for Biochemical Engineering: Recombinant DNA Molecular Enzyme Engineering Applied Genetics and Molecular Biology of Industrial Microorganisms Challenges and Opportunities in Product Recovery Separation by Sorption Membrane Separation Technology: An Overview Index.
Triisopropyltriazacyclononane Copper(II):  An Efficient Phosphodiester Hydrolysis Catalyst and DNA Cleavage Agent (2002)

A 6000-fold rate enhancement has been observed for the hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) in the presence of 0.2 mM Cu(i-Pr(3)[9]aneN(3))(2+) at pH 9.2 and 50 degrees C. In a direct comparison, the rate of hydrolysis of BNPP is accelerated at least 60-fold over the previously reported catalyst Cu([9]aneN(3))(2+). As observed for Cu([9]aneN(3))(2+), hydrolysis is selective for diesters over monoesters. Hydrolysis of BNPP by Cu(i-Pr(3)[9]aneN(3))(2+) is catalytic, exhibiting both rate enhancement and turnover. The reaction is inhibited by both p-nitrophenyl phosphate and inorganic phosphate. The reaction is first-order in substrate and half-order in metal complex, with a k(1.5) of 0.060 +/- 0.004 M(-1/2) s(-1) at 50 degrees C. The temperature dependence of the rate constant results in a calculated activation enthalpy (Delta H(++) of 51 +/- 2 kJ mol(-1) and activation entropy (Delta S(++)) of -110 +/- 6 J mol(-1) K(-1). The kinetic pK(a) of 7.8 +/- 0.2 is close to the thermodynamic pK(a) of 7.9 +/- 0.2, consistent with deprotonation of a coordinated water molecule in the active form of the catalyst. The active catalyst [Cu(i-Pr(3)[9]aneN(3))(OH)(OH(2))](+) is in equilibrium with an inactive dimer, and the formation constant for this dimer is between 216 and 1394 M(-1) at pH 9.2 and 50 degrees C. Temperature dependence of the dimer formation constant K(f) indicates an endothermic enthalpy of formation for the dimer of 27 +/- 3 kJ mol(-1). The time course of anaerobic DNA cleavage by Cu(i-Pr(3)[9]aneN(3))(2+) is presented over a wide range of concentrations at pH 7.8 at 50 degrees C. The concentration dependence of DNA cleavage by Cu([9]aneN(3))(2+) and Cu(i-Pr(3)[9]aneN(3))(2+) reveals a maximum cleavage efficiency at sub-micromolar concentrations of cleavage agent. DNA cleavage by Cu(i-Pr(3)[9]aneN(3))(2+) is twice as efficient at pH 7.8 as at pH 7.2.
Ethanol production from paper sludge by simultaneous saccharification and co‐fermentation using recombinant xylose‐fermenting microorganisms (2010)

Simultaneous saccharification and co-fermentation (SSCF) of waste paper sludge to ethanol was investigated using two recombinant xylose-fermenting microbes: Zymomonas mobilis 8b and Saccharomyces cerevisiae RWB222. S. cerevisiae RWB222 produced over 40 g/L ethanol with a yield of 0.39 g ethanol/g carbohydrate on paper sludge at 37 degrees C, while similar titers and yields were achieved by Z. mobilis 8b at 30 degrees C. Both S. cerevisiae RWB222 and Z. mobilis 8b exhibited decreasing cell viability at 37 degrees C when producing over 40 g/L ethanol. A high ethanol concentration can account for S. cerevisiae RWB222 viability loss, but ethanol concentration was not the only factor influencing Z. mobilis 8b viability loss at 37 degrees C. Over 3 g/L residual glucose was observed at the end of paper sludge SSCF by Z. mobilis 8b, and a statistical analysis revealed that a high calcium concentration originating from paper sludge, a high ethanol concentration, and a high temperature were the key interactive factors resulting in glucose accumulation. The highest ethanol yields were achieved by SSCF of paper sludge with S. cerevisiae RWB222 at 37 degrees C and Z. mobilis 8b at 30 degrees C. With good sugar consumption at 37 degrees C, S. cerevisiae RWB222 was able to gain an improvement in the polysaccharide to sugar yield compared to that at 30 degrees C, whereas Z. mobilis 8b at 30 degrees C had a lower polysaccharide to sugar yield, but a higher sugar to ethanol yield than S. cerevisiae. Both organisms under optimal conditions achieved a 19% higher overall conversion of paper sludge to ethanol than the non-xylose utilizing S. cerevisiae D5A at its optimal process temperature of 37 degrees C.
Somatosensory Evoked Potential Monitoring Used to Compare the Effect of Three Asymmetric Sternal Retractors on Brachial Plexus Function (1999)

We used somatosensory evoked potentials to assess the effect of several different asymmetric sternal retractors on brachial plexus dysfunction and to determine which produced the least evidence of nerve damage during surgical exposure of the internal mammary artery.
Dipeptidyl peptidase IV (CD 26) gene expression in enterocyte-like colon cancer cell lines HT-29 and Caco-2. Cloning of the complete human coding sequence and changes of dipeptidyl peptidase IV mRNA levels during cell differentiation. (1992)

A cDNA (DPCR1) specific for human intestinal dipeptidyl peptidase IV (DPP IV) has been isolated. This 1.7-kilobase cDNA, together with a previously published partial sequence, covers the entire open reading frame of human DPP IV plus 67 base pairs of the 3'-untranslated end. Human DPP IV is a 766-amino acid polypeptide with a high degree of homology with the rat liver protein. The characterization of this molecular probe allowed us to definitively confirm the identity of DPP IV with CD 26, a mouse thymocyte activation antigen, a conclusion strengthened by the fact that we observed identical patterns on Southern blot of human genomic DNA hybridized either with human DPP IV or mouse CD 26 cDNA probe. Using this new tool, we have investigated the expression of DPP IV during the onset of enterocytic differentiation of two cultured human colon cancer cell lines, HT-29 and Caco-2. Whatever the cell line and the culture conditions, DPP IV expression strictly correlates with the presence of a differentiated phenotype, as shown by enzyme activity and the steady state amount of the protein measured by indirect immunofluorescence and Western blot. Accordingly, DPP IV biosynthesis exclusively increases in cells that display an enterocytic differentiation. Neither the glycosylation nor the stability of the protein appear to be dependent on the state of enterocytic differentiation. The DPP IV mRNA level remains very low in undifferentiated cell populations and specifically increases in cells that undergo an enterocytic differentiation. These results strongly suggest that DPP IV gene expression is controlled at the transcriptional or posttranscriptional level during intestinal differentiation.