gebhart/patrepeval huggingface dataset:
Characterization of Growth Factor-binding Structures in Heparin/Heparan Sulfate Using an Octasaccharide Library (2004)

Heparan sulfate (HS) chains interact with various growth and differentiation factors and morphogens, and the most interactions occur on the specific regions of the chains with certain monosaccharide sequences and sulfation patterns. Here we generated a library of octasaccharides by semienzymatic methods by using recombinant HS 2-O-sulfotransferase and HS 6-O-sulfotransferase, and we have made a systematic investigation of the specific binding structures for various heparin-binding growth factors. An octasaccharide (Octa-I, DeltaHexA-GlcNSO(3)-(HexA-GlcNSO(3))(3)) was prepared by partial heparitinase digestion from completely desulfated N-resulfated heparin. 2-O- and 6-O-sulfated Octa-I were prepared by enzymatically transferring one to three 2-O-sulfate groups and one to three 6-O-sulfate groups per molecule, respectively, to Octa-I. Another octasaccharide containing 3 units of HexA(2SO(4))-GlcNSO(3)(6SO(4)) was prepared also from heparin. This octasaccharide library was subjected to affinity chromatography for interactions with fibroblast growth factor (FGF)-2, -4, -7, -8, -10, and -18, hepatocyte growth factor, bone morphogenetic protein 6, and vascular endothelial growth factor, respectively. Based upon differences in the affinity to those octasaccharides, the growth factors could be classified roughly into five groups: group 1 needed 2-O-sulfate but not 6-O-sulfate (FGF-2); group 2 needed 6-O-sulfate but not 2-O-sulfate (FGF-10); group 3 had the affinity to both 2-O-sulfate and 6-O-sulfate but preferred 2-O-sulfate (FGF-18, hepatocyte growth factor); group 4 required both 2-O-sulfate and 6-O-sulfate (FGF-4, FGF-7); and group 5 hardly bound to any octasaccharides (FGF-8, bone morphogenetic protein 6, and vascular endothelial growth factor). The approach using the oligosaccharide library may be useful to define specific structures required for binding to various heparin-binding proteins. Octasaccharides with the high affinity to FGF-2 and FGF-10 had the activity to release them, respectively, from their complexes with HS. Thus, the library may provide new reagents to specifically regulate bindings of the growth factors to HS.
Evaluation of real-time PCR for diagnosis of Bordetella pertussis infection (2006)

The potential pick up of B. holmesii by the IS481 PCR had minimal diagnostic relevance in the Alberta population during the time period of our study. The IS481 PCR assay is now used in our laboratory routinely for front-line screening of samples for B. pertussis with associated enhancement in diagnostic sensitivity compared with DFA and culture. Retrospectively, patients' samples are batched and tested by the IS1001 MB and TPR assays for research purposes and to ensure there is no change in B. holmesii incidence in the population.
Genomic organization of the DGAT2/MOGAT gene family in cattle <i>(Bos taurus)</i> and other mammals (2003)

We report the cloning and initial characterization of the genes encoding DGAT2 (diacylglycerol transferase 2), MOGAT1 and MOGAT2 (monoacylglycerol transferases 1 and 2) in domestic cattle (Bos taurus). The three closely related genes belong to a gene family with at least eight members in mammals and are candidate genes for quantitative traits related to dietary fat uptake, lipid synthesis and storage. MOGAT2 and DGAT2 form a tandem and were mapped to bovine chromosome (BTA) 15q25-->q26 by fluorescence in situ hybridization. MOGAT1 was localized to BTA 2q43-->q44. The three genes were investigated for polymorphisms that might be associated with breeding values for milk fat percentage in the dairy breeds German Holstein, German Simmental and German Brown. All the detected polymorphisms were located outside exons or, with one exception, were silent. In MOGAT1, a missense mutation in exon 4 was found that causes a non-conservative substitution of cysteine170 (uncharged, hydrophobic) by lysine (positively charged, hydrophilic). However, allele frequency estimates from pooled DNA samples revealed no significant association of the observed polymorphisms with breeding values for milk fat percentage. A comparative analysis of chromosomal locations and exon-intron structure of the known members of the DGAT2/MOGAT gene family in humans, rodents and cattle indicates an ancient tandem duplication of the ancestor gene combined with an intron gain (or loss) in one copy. Further members of the family may have arisen by duplications of this gene tandem via two rounds of interchromosomal or genome duplications as well as further local (single) gene duplication and loss events.
Synthesis and Biological Evaluation of Aza-C-disaccharides:  (1→6), (1→4), and (1→1) Linked Sugar Mimics (1997)

The synthesis of (1→6), (1→4), and (1→1) linked aza-C-disaccharides, a novel class of glycomimetic compounds, is described. The polyhydroxylated piperidine ring was synthesized using vinyl bromide 11 as a common intermediate which was synthesized de novo from bromobenzene utilizing the microbial oxidation metabolite bromodiol 10. A Suzuki coupling of 11 with an alkylboron reagent derived from olefinated carbohydrate precursors via hydroboration was used to form the C-glycosidic bond. Ozonolysis and selective reduction of the resultant carbonyl functions served to produce the azasugar ring. Fully deprotected aza-C-disaccharides were obtained upon acidic deprotection. Biological screening of the title compounds against several common glycosidase enzymes as well as in vitro anti-HIV assays are reported.
The biochemical basis for the apparent defect of soluble mutant tissue factor in enhancing the proteolytic activities of factor VIIa. (1994)

Tissue factor (TF), an integral membrane protein, is the cofactor for the serine protease, coagulation factor VIIa (FVIIa). Previous studies of the isolated extracellular domain of TF (sTF) reported a kcat for factor X (FX) activation by the sTF.VIIa complex only 4% that of wild-type TF.VIIa and furthermore, a complete inability of sTF to support FVII autoactivation. We now report that in the presence of poly(L-lysine), sTF promoted both FX activation and FVII autoactivation, the latter with an apparent second-order rate constant higher than reported previously for wild-type TF in phospholipid vesicles. This led us to reexamine the cofactor ability of sTF, using high concentrations of phospholipid to promote nearly quantitative binding of sTF.VII(a) complexes to the phospholipid surface. Rate constants for the activation of FX or FVII by sTF.VIIa were similar to those of wild-type TF.VIIa, indicating that the apparent deficiency of sTF is largely attributable to kinetic consequences of relatively weak affinity of FVIIa (and sTF.VIIa) for phospholipid surfaces in these surface-dependent reactions, compared with TF being embedded in the membrane. This supports the notion that sTF recapitulates the protein-protein interactions of wild-type TF with high, and possibly full, catalytic activity. It also provides a biochemical explanation for the specificity of our recently described, sTF-based clotting assay for plasma FVIIa.
Snap and share your photobooks (2008)

The sharing of photos with others, friends and family, has become even more popular with digital photography and Internet applications such as email or Web albums. At the same time, the physical touch of printed photos is still appreciated and customers use different services to print their photos on post cards, calendars or photobooks, often to give them as a present or to create a physical souvenir. Once printed, however, the sharing of photos with others becomes difficult as there is no link back from the now physical item to its digital counterpart. With Bookmarkr, we developed a system that employs a mobile camera phone to bridge the gap between the printed photo and its digital counterpart. The user takes an image of a photo in a photobook with the mobile phone's camera. The image is transmitted to a photobook server, which employs image analysis techniques to retrieve the corresponding photo. The photo is sent back to the user and establishes the digital-physical match. Bookmarkr allows the user to interact with printed photos in a similar way as interacting with digital photos by using a point-and-shoot metaphor. Our performance evaluation shows that the system is able to return the correct photo in up to 99% of all cases. A conducted user study revealed that the designed interaction is suitable for the participants and their printed photobooks.
Synthesis and pharmacological properties of nebivolol, a new antihypertensive compound. (1991)

The synthesis of alpha,alpha' (iminobis(methylene]-bis-(3,4-dihydro-2H-1benzopyran-2-metha nol) derivatives and the stereochemistry and pharmacological profile of this new class of antihypertensive compounds are described. Finally, the selection and pharmacological profile of the preferred compound of this series, nebivolol and its enantiomers, is discussed.
Influence of lesion size and location on amphetamine-facilitated recovery of beam-walking in rats. (1990)

Amphetamine treatment facilitates recovery of beam-walking in rats with unilateral sensorimotor cortex lesions. Lesion extent was studied in amphetamine- and saline-treated rats selected for rapid and slow recoveries. Lesion volume, lesion depth, and the amount of medial cortex damage were not different among the 4 groups of rats. When the data were analyzed without regard to drug treatment, both lesion depth in rostral forebrain and maximum amount of medial cortex damage negatively correlated with recovery rate. Thus, lesion extent influences the rate of recovery of beam-walking in rats but does not explain the lack of effectiveness of amphetamine in selected animals.
Enhancing the specificity of polymerase chain reaction by graphene oxide through surface modification: zwitterionic polymer is superior to other polymers with different charges (2016)

Graphene oxides (GOs) with different surface characteristics, such as size, reduction degree and charge, are prepared, and their effects on the specificity of polymerase chain reaction (PCR) are investigated. In this study, we demonstrate that GO with a large size and high reduction degree is superior to small and nonreduced GO in enhancing the specificity of PCR. Negatively charged polyacrylic acid (PAA), positively charged polyacrylamide (PAM), neutral polyethylene glycol (PEG) and zwitterionic polymer poly(sulfobetaine) (pSB) are used to modify GO. The PCR specificity-enhancing ability increases in the following order: GO-PAA < GO-PAM < GO-PEG < GO-pSB. Thus, zwitterionic polymer-modified GO is superior to other GO derivatives with different charges in enhancing the specificity of PCR. GO derivatives are also successfully used to enhance the specificity of PCR for the amplification of human mitochondrial DNA using blood genomic DNA as template. Molecular dynamics simulations and molecular docking are performed to elucidate the interaction between the polymers and <i>Pfu</i> DNA polymerase. Our data demonstrate that the size, reduction degree and surface charge of GO affect the specificity of PCR. Based on our results, zwitterionic polymer-modified GO may be used as an efficient additive for enhancing the specificity of PCR.
Web Project Management: Delivering Successful Commercial Web Sites (2000)

Preface. The World of the Web Project Manager: Setting the Scene. Method: A Web Project Method The Project Road Map Work Stage 1: Project Clarification Work Stage 2: Solution Definition Work Stage 3: Project Specification Work Stage 4: Content Work Stage 5: Design and Construction Work Stage 6: Testing, Launch, and Handover Work Stage 7: Maintenance Work Stage 8: Review and Evaluation. Case Study: Reality Bytes. Appendix A Resources. Appendix B Recommended Reading. Index.
Ischaemia and reperfusion effects on skeletal muscle tissue: morphological and histochemical studies (2007)

This was a study on the oxidative stress due to ischaemia (I) and reperfusion (R) in skeletal muscle tissue. Using a tourniquet, groups of rats were submitted to ischaemia for 4 h, followed by different reperfusion periods. The animals were divided in four groups: control; 4 h of ischaemia (IR); 4 h of ischaemia plus 1 h reperfusion (IR-1 h); 4 h of ischaemia plus 24 h reperfusion (IR-24 h); and 4 h of ischaemia plus 72 h reperfusion (IR-72 h). At the end of the procedures, samples of soleus muscle were collected and frozen in n-hexane at -70 degrees C. Cryostat sections were submitted to haematoxylin-eosin, succinate dehydrogenase (SDH) and nicotinamide adenine dinucleotide-tetrazolium reductase (NADH-TR) stains. An additional muscle sample was processed for electron microscopy. No alterations were found in control animals. IR group showed fibres had normal aspect besides some round, acidophilic and hypertrophic fibres. There were several fibres with angular outlines and smaller diameters in this group compared with control group. NADH-TR/SDH reaction was moderately intense in most fibres. In some fibres, cytoplasm showed areas without activity and other fibres had very intense reactivity. IR-1 h group showed oedema hypercontracted fibres with disorganized myofibrils, mitochondria with focal lesions and dilated sarcoplasmic reticulum. NADH-TR/SDH reaction was moderate to weak. IR-24 h showed intense inflammatory infiltrate in the endomysium and perimysium. NADH-TR/SDH reaction was similar to IR-1 h. IR-72 h showed necrotic fibres, areas with inflammatory infiltrate, reduced muscle fibres at different stages of necrosis and phagocytosis, and many small round and basophilic fibres characterizing a regeneration process. NADH-TR/SDH reaction was weak to negative. Our results suggest that ischaemia and the subsequent 1-, 24- and 72-h reperfusions induced progressive histological damage. Although progressive, it may be reversible because there were ultrastructural signs of recovery after 72-h reperfusion. This recovery could in part be due to the low oxidative stress identified by the morphological and histochemical analysis.
The alanine racemase gene is essential for growth of Lactobacillus plantarum (1997)

The Lactobacillus plantarum alr gene encoding alanine racemase was cloned by complementation of an Escherichia coli Alr- DadX- double mutant strain. Knockout of the alr gene abolished all measurable alanine racemase activity, and the mutant was shown to be strictly dependent on D-alanine for growth.
PET amyloid ligand [ 11 C]PIB uptake is increased in mild cognitive impairment (2007)

At group level the elevated N-methyl-[(11)C]2-(4'-methylaminophenyl)-6-hydroxybenzothiazole ([(11)C]PIB) uptake in patients with mild cognitive impairment (MCI) resembled that seen in Alzheimer disease (AD). At the individual level, about half of the MCI patients had [(11)C]PIB uptake in the AD range, suggestive of early AD process.
Differential Intensity Sensitivity of the Ear for Pure Tones (1928)

The ratio of the minimum perceptible increment in sound intensity to the total intensity, $\frac{\ensuremath{\Delta}E}{E}$, which is called the differential sensitivity of the ear, was measured as a function of frequency and intensity. Measurements were made over practically the entire range of frequencies and intensities for which the ear is capable of sensation. The method used was that of beating tones, this method giving the simplest transition from one intensity to another. The source of sound was a special moving coil telephone receiver having very little distortion, actuated by alternating currents from vacuum tube oscillators. Observations were made on twelve male observers. Average curves show that at any frequency, $\frac{\ensuremath{\Delta}E}{E}$ is practically constant for intensitites greater than ${10}^{6}$ times the threshold intensity; near the auditory threshold $\frac{\ensuremath{\Delta}E}{E}$ increases. Weber's law holds above this intensity, the value of $\frac{\ensuremath{\Delta}E}{E}=\mathrm{constant}$ lying between 0.05 and 0.15 depending on the frequency. As a function of frequency $\frac{\ensuremath{\Delta}E}{E}$ is a minimum at about 2500 c.p.s., the minimum being more sharply defined at low sound intensities than it is at high. This frequency corresponds to the region of greatest absolute sensitivity of the ear. Analytical expressions are given [Eqs. (2), (3), (4) and (5)] which represent $\frac{\ensuremath{\Delta}E}{E}$, within the error of observation, as a function of frequency and intensity. Using these equations it is calculated that at about 1300 c.p.s. the ear can distinguish 370 separate tones between the threshold of audition and the threshold of feeling.
Carbodiimide EDC Induces Cross-Links That Stabilize RNase A C-Dimer against Dissociation: EDC Adducts Can Affect Protein Net Charge, Conformation, and Activity (2009)

RNase A self-associates under certain conditions to form a series of domain-swapped oligomers. These oligomers show high catalytic activity against double-stranded RNA and striking antitumor actions that are lacking in the monomer. However, the dissociation of these metastable oligomers limits their therapeutic potential. Here, a widely used conjugating agent, 1-ethyl-3-(3-dimethylaminoisopropyl) carbodiimide (EDC), has been used to induce the formation of amide bonds between carboxylate and amine groups of different subunits of the RNase A C-dimer. A cross-linked C-dimer which does not dissociate was isolated and was found have augmented enzymatic activity toward double-stranded RNA relative to the unmodified C-dimer. Characterization using chromatography, electrophoresis, mass spectrometry, and NMR spectroscopy revealed that the EDC-treated C-dimer retains its structure and contains one to three novel amide bonds. Moreover, both the EDC-treated C-dimer and EDC-treated RNase A monomer were found to carry an increased number of positive charges (about 6 ± 2 charges per subunit). These additional positive charges are presumably due to adduct formation with EDC, which neutralizes a negatively charged carboxylate group and couples it to a positively charged tertiary amine. The increased net positive charge endowed by EDC adducts likely contributes to the heightened cleavage of double-stranded RNA of the EDC-treated monomer and EDC-treated C-dimer. Further evidence for EDC adduct formation is provided by the reaction of EDC with a dipeptide Ac-Asp-Ala-NH(2) monitored by NMR spectroscopy and mass spectrometry. To determine if EDC adduct formation with proteins is common and how this affects protein net charge, conformation, and activity, four well-characterized proteins, ribonuclease Sa, hen lysozyme, carbonic anhydrase, and hemoglobin, were incubated with EDC and the products were characterized. EDC formed adducts with all these proteins, as judged by mass spectrometry and electrophoresis. Moreover, all suffered conformational changes ranging from slight structural modifications in the case of lysozyme, to denaturation for hemoglobin as measured by NMR spectroscopy and enzyme assays. We conclude that EDC adduct formation with proteins can affect their net charge, conformation, and enzymatic activity.
Abnormality in calcium release from skeletal sarcoplasmic reticulum of pigs susceptible to malignant hyperthermia. (1983)

A B S T R A C T Two fractions of sarcoplasmic reticu- lum, one light (LSR) and one heavy (HSR), were iso- lated from gracilis muscle of control and malignant hyperthermia (MH)-susceptible pigs. Part of the gra- cilis muscle biopsy was used to compare the contrac- ture sensitivity of the muscle to the calcium-releasing effects of caffeine on isolated SR membranes. Gracilis muscle of MH pigs was more sensitive to the contrac- ture-producing effects of caffeine than control pig muscle. The caffeine dose-cumulative contracture re- sponse curve for MH muscle was shifted left of that for controls.
Instability Studies of Porcine Somatotropin in Aqueous Solutions and the Possible Reagents for Its Stabilization (2000)

The instability of porcine somatotropin (pST) in various solutions and possible stabilization of the hormone by sugars and mild detergents were studied. Aggregation and decomposition of the hormone molecules in various pH solutions and under presence of sugar or detergent were monitored by gel permeation chromatography (GPC) or ultraviolet spectroscopy (UV). The pST is a very unstable hormone in an aqueous environment. It was found in this project that the peptide hormone underwent aggregation or decomposition quickly in acidic and alkaline solutions but slowly in neutral pH solutions. High losses of pST monomers were seen in concentrated solutions of the hormone. On the other hand, pST monomers were stabilized to a certain degree in glucose solutions and at a low concentration of urea. These results should facilitate the development of efficient controlled-release systems which are essential for commercializing porcine somatotropin.
The general concept of molecular chaperones (1993)

This introductory article proposes a conceptual framework in which to consider the information that is emerging about the proteins called molecular chaperones, and suggests some definitions that may be useful in this new field of biochemistry. Molecular chaperones are currently defined in functional terms as a class of unrelated families of protein that assist the correct non-covalent assembly of other polypeptide-containing structures in vivo, but which are not components of these assembled structures when they are performing their normal biological functions. The term assembly in this definition embraces not only the folding of newly synthesized polypeptides and any association into oligomers that may occur, but also includes any changes in the degree of either folding or association that may take place when proteins carry out their functions, are transported across membranes, or are repaired or destroyed after stresses such as heat shock. Known molecular chaperones do not convey steric information essential for correct assembly, but appear to act by binding to interactive protein surfaces that are transiently exposed during various cellular processes; this binding inhibits incorrect interactions that may otherwise produce non-functional structures. Thus the concept of molecular chaperones does not contradict the principle of protein self-assembly, but qualifies it by suggesting that in vivo self-assembly requires assistance by other protein molecules.
Isotope effect in the photodissociation of HDO at 157.5 nm (1989)

Experimental values for the absorption coefficient and the branching ratio of HDO at 157.5 nm are reported. The experimental evidence strongly supports the analysis of Zhang et al. (ref.10).(AIP)