gebhart/patrepeval huggingface dataset:
Analysis of protein conformational characteristics related to thermostability (1996)

The thermal stability of proteins was studied, 195 single amino acid residue replacements reported elsewhere being analysed for several protein conformational characteristics: type of residue replacement; conservative versus nonconservative substitution; replacement being in a homologous stretch of amino acid residues; change in hydrogen bond, van der Waals and secondary structure propensities; solvent-accessible versus inaccessible replacement; type of secondary structure involved in the substitution; the physico-chemical characteristics to which the thermostability enhancement can be attributed; and the relationship of the replacement site to the folding intermediates of the protein, when known. From the above analyses, some general rules arise which suggest where amino acid substitutions can be made to enhance protein thermostability: substitutions are conservative according to the Dayhoff matrix; mainly occur on conserved stretches of residues; preferentially occur on solvent-accessible residues; maintain or enhance the secondary structure propensity upon substitution; contribute to neutralize the dipole moment of the caps of helices and strands; and tend to increase the number of potential hydrogen bonding or van der Waals contacts or improve hydrophobic packing.
Site specific functionalization of oligonucleotides for attaching two different reporter groups (1990)

The synthesis of an oligonucleotide functionalized to attach two different reporter groups at specific internucleotide linkages is described. To incorporate the amine specific reporter group the internucleotide linkage is modified to phosphoramidate (N-1-aminoalkyl) and for a thiol specific reporter group the internucleotide linkage is modified to a phosphorothioate diester. The synthetic cycle for introducing the modified internucleotide linkages at specific sites can be carried out using an automated DNA synthesizer. Combination of reporter groups have been attached successfully.
Diversified sequences of peptide epitope for same-RNA recognition. (1993)

We replaced an essential RNA-binding, 30-amino acid helix-loop in an Escherichia coli tRNA synthetase with an inactive and simplified "generic" sequence having 23 of the 30 amino acids as alanine and serine. Wild-type residues were restored in random combinations to generate a library with a sequence complexity of about 1.9 x 10(7). Active molecules were obtained by genetic selection at a frequency of approximately 1% and contained variants with as many as 11 alanine/serine replacements and a total of 17 alanine/serine residues. These variants have activities which are thermodynamically competitive with that of the native protein and therefore are functionally and, most likely, conformationally equivalent.
Formation of Sphalerite (ZnS) Deposits in Natural Biofilms of Sulfate-Reducing Bacteria (2000)

Abundant, micrometer-scale, spherical aggregates of 2- to 5-nanometer-diameter sphalerite (ZnS) particles formed within natural biofilms dominated by relatively aerotolerant sulfate-reducing bacteria of the family Desulfobacteriaceae. The biofilm zinc concentration is about 10(6) times that of associated groundwater (0.09 to 1.1 parts per million zinc). Sphalerite also concentrates arsenic (0.01 weight %) and selenium (0.004 weight %). The almost monomineralic product results from buffering of sulfide concentrations at low values by sphalerite precipitation. These results show how microbes control metal concentrations in groundwater- and wetland-based remediation systems and suggest biological routes for formation of some low-temperature ZnS deposits.
Chiral Synthesis via Organoboranes 23. Enantioselective Ring Opening of meso‐Epoxides with B‐Halodiisopinocampheylboranes. The First General Synthesis of Optically Active 1,2‐Halohydrins (1989)

Abstract B ‐Halodiisopinocampheylboranes, Ipc 2 BX, where X is Cl, Br, or I, cleave cyclohexene oxide at low temperatures to give the 1,2‐halohydrins, in 22, 84, and 91% enantiomeric excess (ee), respectively. 1,2‐Epoxycyclohex‐4‐ene is converted to the bromohydrin and iodohydrin in 84 and 91% ee. cis ‐2,3‐Epoxybutane, cis ‐3,4‐epoxyhexane, and cyclopentene oxide were also studied with all three halides. In general, optical induction increases in the order I &gt; Br &gt; Cl for any given epoxide. Thus cis ‐2,3‐epoxybutane furnishes the corresponding chlorohydrin in 35% ee, the bromohydrin in 69% ee, and the iodohydrin in 78% ee. In certain cases recrystallization provides essentially optically pure material, e.g., (1 R , 2 R )‐2‐bromocyclohexanol, (1 R , 2 R )‐2‐iodocyclohexanol and (1 R , 2 R )‐2‐iodocyclohex‐4‐en‐1‐ol. In all cases examined d Ipc 2 BX (derived from (+)‐α‐pinene) provide (1 R , 2R) halohydrins, in which the enantiotopic S C—O bond is cleaved. Ring cleavage occurs in an anti‐periplanar manner, consistent with an S N 2 type reaction pathway. Modified B ‐chloromonoisopinocampheylboranes, IpcBCl(OR), cleave cyclohexene oxide at a slower rate but furnish the chlorohydrin in up to 35% ee (R = Bnz). This study is not only a novel application of chiral haloboranes, but constitutes the first general synthesis of symmetrical optically active 1,2‐halohydrins.
Lectin-like binding of pertussis toxin to a 165-kilodalton Chinese hamster ovary cell glycoprotein. (1988)

Chinese hamster ovary (CHO) cells cluster in the presence of pertussis toxin, a response that is correlated with the ADP-ribosylation of a Mr = 41,000 membrane protein by the toxin. A ricin-resistant line of CHO cells (CHO-15B) which specifically lacks the terminal NeuAc----Gal beta 4GlcNAc oligosaccharide sequence on glycoproteins did not cluster in response to pertussis toxin. These cells do contain the Mr = 41,000 protein substrate for the enzymatic activity of the toxin which suggests that pertussis toxin, like certain plant lectins, does not bind to or is not internalized by the CHO-15B cells. There was no evidence of pertussis toxin binding to gangliosides or neutral glycolipids isolated from CHO cells but the toxin bound to a Mr = 165,000 component in N-octyglucoside extracts of CHO cells that had been separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electroblotted to nitrocellulose. Plant lectins from Ricinus communis and Erythina cristagalli detected a similar size band in CHO cells and also did not react with CHO-15B cells. Unlike pertussis toxin, these plant lectins recognized two other major bands in CHO cell extracts and reacted best after sialidase treatment of nitrocellulose transfers containing CHO cell extracts. Conversely, sialidase treatment abolished binding a pertussis toxin and wheat germ agglutinin, a plant lectin that reacts with multivalent sialic acid residues on glycoproteins, to the Mr = 165,000 band. Purified B oligomer of pertussis toxin also uniquely detected a Mr = 165,000 component in CHO cell extracts while the A subunit of pertussis toxin was unreactive. These results indicate that pertussis toxin binds to a CHO cell glycoprotein with N-linked oligosaccharides and that sialic acid contributes to the complementary receptor site for the toxin. In addition, they suggest that a glycoprotein may serve as a cell surface receptor for pertussis toxin and that this interaction is mediated by a lectin-like binding site located on the B oligomer.
EWOD Driving of Droplet on NxM Grid using Single-Layer Electrode Patterns (2002)

This paper demonstrates 2-D droplet movement implementing electrowetting-on-dielectric (EWOD) for actuation. Experimentation on different electrode configurations reveals certain requirements and flexibilities for EWOD device design. The current device has a single layer of rectangular electrode rowsone set of rows on top and the other set on bottom plate, orthogonally oriented. The innovation lies in the use of only N+M electrodes to control NxM different positions of a droplet on a 2-D grid without requiring fabrication of multi-layer electrodes.
Motion sensorless control of BLDC PM motor with offline FEM info assisted state observer (2010)

This paper describes a new offline FEM assisted position and speed observer, for brushless dc (BLDC) PM motor drive sensorless control, based on the line-to-line PM flux linkage estimation. The zero-crossing of the line-to-line PM flux linkage occurs right in the middle of two commutation points, which is used as a basis for the position and speed observer. For performance applications, the position between commutation points is obtained by comparing the estimated line-to-line PM flux linkage with the FEM calculated line-to-line PM flux linkage. Even if the proposed observer relies on the fundamental model of the machine, a safe starting strategy under heavy load torque, called I-f control, is used, with seamless transition to the proposed sensorless control. The I-f starting method allows low-speed sensorless control, without knowing the initial position, and without machine parameters identification. Digital simulations and experimental results are shown, demonstrating the reliability of the FEM assisted position and speed observer for BLDC PM motor sensorless control operation.
VEGF 165 mediates formation of complexes containing VEGFR‐2 and neuropilin‐1 that enhance VEGF 165 ‐receptor binding (2002)

Co-expression of NRP1 and (VEGFR-2) KDR on the surface of endothelial cells (EC) enhances VEGF165 binding to KDR and EC chemotaxis in response to VEGF165. Overexpression of NRP1 by prostate tumor cells in vivo results in increased tumor angiogenesis and growth. We investigated the molecular mechanisms underlying NRP1-mediated angiogenesis by analyzing the association of NRP1 and KDR. An intracellular complex containing NRP1 and KDR was immunoprecipitated from EC by anti-NRP1 antibodies only in the presence of VEGF165. In contrast, VEGF121, which does not bind to NRP1, did not support complex formation. Complexes containing VEGF165, NRP1, and KDR were also formed in an intercellular fashion by co-culture of EC expressing KDR only, with cells expressing NRP1 only, for example, breast carcinoma cells. VEGF165 also mediated the binding of a soluble NRP1 dimer to cells expressing KDR only, confirming the formation of such complexes. Furthermore, the formation of complexes containing KDR and NRP1 markedly increased 125I-VEGF165 binding to KDR. Our results suggest that formation of a ternary complex of VEGF165, KDR, and NRP1 potentiates VEGF165 binding to KDR. These complexes are formed on the surface of EC and in a juxtacrine manner via association of tumor cell NRP1 and EC KDR.
Force generation simplified. Insights from laser temperature-jump experiments on contracting muscle fibers. (1998)

Raising the temperature of a maximally Ca(2+)-activated muscle fiber causes a sigmoidal increase in tension. The kinetics that govern this process can be explored by step-heating the fiber a few degrees with a laser temperature-jump. A biexponential increase in tension results; a third exponential phase that opposes this biphasic rise in tension is only observed when phosphate, a reaction product normally at low concentration, is added to the fiber. This chapter explains how the temperature dependencies of isometric tension and the temperature jump kinetics interrelate, and how these insights have modified and simplified our understanding of current mechanisms of force generation. The fast kinetic phase of the tension rise appears associated with single-step force generation or a power stroke, a process largely isolated from adjacent steps in the crossbridge cycle. The amplitude of the slow phase of the tension rise exhibits a remarkable approximately 1:1 ratio to the amplitude of the fast, tension generating phase above 10 degrees C. The similarity of these two amplitudes, that combine to give the complete rise in isometric tension with temperature, appear to fit a model in which one of a pair of myosin heads generates force while the second head is poised to function after the power stroke of the first has occurred. The phase with the negative amplitude seen with added phosphate points to a mechanism in which phosphate release is indirectly linked to the tension generation by forward flow through the crossbridge cycle to tension generation.
Statistics for experimenters. An introduction to design, data analysis, and model building. (1978)

Science and Statistics. COMPARING TWO TREATMENTS. Use of External Reference Distribution to Compare Two Means. Random Sampling and the Declaration of Independence. Randomization and Blocking with Paired Comparisons. Significance Tests and Confidence Intervals for Means, Variances, Proportions and Frequences. COMPARING MORE THAN TWO TREATMENTS. Experiments to Compare k Treatment Means. Randomized Block and Two--Way Factorial Designs. Designs with More Than One Blocking Variable. MEASURING THE EFFECTS OF VARIABLES. Empirical Modeling. Factorial Designs at Two Levels. More Applications of Factorial Designs. Fractional Factorial Designs at Two Levels. More Applications of Fractional Factorial Designs. BUILDING MODELS AND USING THEM. Simple Modeling with Least Squares (Regression Analysis). Response Surface Methods. Mechanistic Model Building. Study of Variation. Modeling Dependence: Times Series. Appendix Tables. Index.
The use of a monoclonal anti-idiotype antibody to study the biology of a human B cell lymphoma. (1981)

Immunoglobulin was obtained from the tumor cells of a patient with nodular lymphoma by hybridization to mouse myeloma cells. The human immunoglobulin secreted by these hybridoma cells was used as an immunogen to make murine monoclonal antibodies. Antibodies specific for idiotype, mu heavy chain and lambda light chain, were produced. One anti-idiotype antibody was used to document that idiotype-positive cells and low levels of 19S IgM idiotype were present in the patient's blood. The levels of each were found to correlate with the patient's disease activity. The monoclonal anti-idiotype was effective in eliminating idiotype-positive cells in vitro by solid phase absorption or by complement-mediated cytotoxicity. The anti-idiotype was also used to analyze the host's immunologic response to his own tumor idiotype. There was neither a detectable anti-idiotype antibody response produced in vivo nor a detectable population of T cells that expressed idiotype of could bind idiotype.
Silicone‐specific imaging using an inversion‐recovery‐prepared fast three‐point Dixon technique (2004)

The feasibility and potential application of the new technique were demonstrated via imaging a phantom and a silicone breast prosthesis in vivo, and it may be used for more consistent imaging of the silicone implants without compromising the image quality or overall scan time.
Attachment of fibronectin to poly(vinyl alcohol) hydrogels promotes NIH3T3 cell adhesion, proliferation, and migration (2001)

Hydrogels have been used in biology and medicine for many years, and they possess many properties that make them advantageous for tissue engineering applications. Their high water content and tissue-like elasticity are similar to the native extracellular matrix of many tissues. In this work, we investigated the potential of a modified poly(vinyl alcohol) (PVA) hydrogel as a biomaterial for tissue engineering applications. First, the ability of NIH3T3 fibroblast cells to attach to PVA hydrogels was evaluated. Because of PVA's extremely hydrophilic nature, important cell adhesion proteins do not adsorb to PVA hydrogels, and consequently, cells are unable to adhere to the hydrogel. By covalently attaching the important cell adhesion protein fibronectin onto the PVA hydrogel surface, the rate of fibroblast attachment and proliferation was dramatically improved, and promoted two-dimensional cell migration. These studies illustrate that a fibronectin-modified PVA hydrogel is a potential biomaterial for tissue engineering applications.
Turbulent characteristics of flow field over a three-dimensional steep hill (1997)

The turbulence flow over a circular hill, having a cosine-squared cross-section and a maximum slope of about 32°, was investigated using split-fiber probes designed for measuring flows with a high turbulence and separation. Profiles of the means and variances for the three velocity components are presented and compared with those in the undisturbed (no- hill) boundary layer. The turbulent boundary layer separated behind the crest and reattached just at the lee foot of hill. The pronounced speed- up of flow occurs not only at the hilltop but also at the midway slope on its side. The maximum perturbations in the longitudinal and vertical velocity variances were observed at the height of hill (z/h=1), corresponding to the separated recirculating flow on the lee slope of the hill, while the maximum in the lateral velocity variance appeared at the height of z/h=0.125 beyond the hill, corresponding to the low-frequency motion in the wall layer.
A medium‐term rat liver bioassay for rapid in vivo detection of carcinogenic potential of chemicals (2003)

A reliable medium-term bioassay system for rapid detection of carcinogenic potential of chemicals in the human environment has been developed. The 8-week-protocol consists of 2 stages; male F344 rats are given a single intraperitoneal injection of diethylnitrosamine (200 mg/kg) for initiation of liver carcinogenesis, followed by a 6-week test chemical treatment starting 2 weeks thereafter. Test chemicals are usually given in the diet or the drinking water and in the 2nd week of test chemical treatment, all rats are subjected to two-thirds partial hepatectomy in order to induce regenerative cell replication. The end-point marker is the glutathione S-transferase placental form (GST-P)-positive hepatic focus, the numbers and sizes of which are analyzed using an image-analyzer and expressed as values per unit liver section (1 cm2). When the yield of GST-P-positive foci is significantly enhanced (P<0.05) over the control value, a chemical is judged to possess carcinogenic or promotion potential for the liver. Among 313 chemicals already tested in this system in our laboratory, 30/31 (97%) mutagenic hepatocarcinogens and 29/33 (88%) non-mutagenic hepatocarcinogens gave positive results. Ten out of 43 (23%) agents known to be carcinogenic in organs other than the liver were also positive. It is particularly important that only one of 48 non-carcinogens gave a very weak positive result, so that the system has a very low false-positivity rate. It is now well documented that the assay system is highly effective for detecting hepatocarcinogens, bridging the gap between traditional long-term carcinogenicity tests and short-term screening assays. At the Fourth International Conference on Harmonization, our medium-term liver bioassay based on an initiation and promotion protocol was recommended in the guidelines as an acceptable alternative to the long-term rodent carcinogenicity test.
Lactate shuttles in Nature (2002)

Once thought to be the consequence of oxygen lack in contracting skeletal muscle, the glycolytic product lactate is formed and utilized continuously under fully aerobic conditions. "Cell-cell" and "intracellular lactate shuttle" concepts describe the roles of lactate in the delivery of oxidative and gluconeogenic substrates, as well as in cell signalling. Examples of cell-cell shuttles include lactate exchanges between white-glycolytic and red-oxidative fibres within a working muscle bed, between working skeletal muscle and heart, and between tissues of net lactate release and gluconeogenesis. Lactate exchange between astrocytes and neurons that is linked to glutamatergic signalling in the brain is an example of a lactate shuttle supporting cell-cell signalling. Lactate uptake by mitochondria and pyruvate-lactate exchange in peroxisomes are examples of intracellular lactate shuttles. Lactate exchange between sites of production and removal is facilitated by monocarboxylate transport proteins, of which there are several isoforms, and, probably, also by scaffolding proteins. The mitochondrial lactate-pyruvate transporter appears to work in conjunction with mitochondrial lactate dehydrogenase, which permits lactate to be oxidized within actively respiring cells. Hence mitochondria function to establish the concentration and proton gradients necessary for cells with high mitochondrial densities (e.g. cardiocytes) to take up and oxidize lactate. Arteriovenous difference measurements on working cardiac and skeletal muscle beds as well as NMR spectral analyses of these tissues show that lactate is formed and oxidized within the cells of formation in vivo. Glycolysis and lactate oxidation within cells permits high flux rates and the maintenance of redox balance in the cytosol and mitochondria. Other examples of intracellular lactate shuttles include lactate uptake and oxidation in sperm mitochondria and the facilitation of beta-oxidation in peroxisomes by pyruvate-lactate exchange. An ancient origin to the utility of lactate shuttling is implied by the observation that mitochondria of Saccharomyces cerevisiae contain flavocytochrome b(2), a lactate-cytochrome c oxidoreductase that couples lactate dehydrogenation to the reduction of cytochrome c. The presence of cell-cell and intracellular lactate shuttles gives rise to the notion that glycolytic and oxidative pathways can be viewed as linked, as opposed to alternative, processes, because lactate, the product of one pathway, is the substrate for the other.
S‐100 protein: Is it useful as a tumour marker in diagnostic immunocytochemistry? (1989)

A heterogeneous group of 159 tumours was studied for the presence of S-100 protein by the immunoperoxidase technique in order to determine whether this marker may be of value in facilitating immunocytochemical diagnosis. Among cases of melanocytic and pigmented lesions, S-100 was widely distributed and demonstrated the strongest degrees of reactivity. S-100 protein was identified in virtually all nerve sheath tumours such as schwannomas, neurofibromas, myxoid sheath nerve tumour and also in some tumours of controversial histogenesis such as granular cell tumours. The great majority of carcinomas did not express S-100, with only two cases of breast carcinoma displaying focal S-100 staining. In a miscellaneous group of tumours S-100 was demonstrated in chordomas, myoepitheliomas and Wilms' tumour with Schwann cell differentiation. Despite its presence in a wide array of cell types, S-100 protein continues to be an extremely useful marker especially for soft tissue and peripheral nervous system tumours.
Enzyme assays : a practical approach (2002)

1. Principles of enzyme assay and kinetic studies 2. Photometric assays 3. Radiometric assays 4. High performance liquid chromatography assays 5. Electrochemical assays: the oxygen electrode 6. Electrochemical assays: the nitric oxide electrode 7. Electrochemical assays: the pH-stat 8. Enzyme assays after gel electrophoresis 9. Techniques for enzyme extraction 10. Determination of active site concentration 11. High throughput screening - considerations for enzyme assays 12. Statistical analysis of enzyme kinetic data