gebhart/patrepeval huggingface dataset:
Phenotypes of apolipoprotein B and apolipoprotein E after liver transplantation. (1991)

Apolipoprotein (apo) E and the two B apolipoproteins, apoB48 and apoB100, are important proteins in human lipoprotein metabolism. Commonly occurring polymorphisms in the genes for apoE and apoB result in amino acid substitutions that produce readily detectable phenotypic differences in these proteins. We studied changes in apoE and apoB phenotypes before and after liver transplantation to gain new insights into apolipoprotein physiology. In all 29 patients that we studied, the postoperative serum apoE phenotype of the recipient, as assessed by isoelectric focusing, converted virtually completely to that of the donor, providing evidence that greater than 90% of the apoE in the plasma is synthesized by the liver. In contrast, the cerebrospinal fluid apoE phenotype did not change to the donor's phenotype after liver transplantation, indicating that most of the apoE in CSF cannot be derived from the plasma pool and therefore must be synthesized locally. The apoB100 phenotype (assessed with immunoassays using monoclonal antibody MB19, an antibody that detects a two-allele polymorphism in apoB) invariably converted to the phenotype of the donor. In four normolipidemic patients, we determined the MB19 phenotype of both the apoB100 and apoB48 in the "chylomicron fraction" isolated from plasma 3 h after a fat-rich meal. Interestingly, the apoB100 in the chylomicron fraction invariably had the phenotype of the donor, indicating that the vast majority of the large, triglyceride-rich apoB100-containing lipoproteins that appear in the plasma after a fat-rich meal are actually VLDL of hepatic origin. The MB19 phenotype of the apoB48 in the plasma chylomicron fraction did not change after liver transplantation, indicating that almost all of the apoB48 in plasma chylomicrons is derived from the intestine. These results were consistent with our immunocytochemical studies on intestinal biopsy specimens of organ donors; using apoB-specific monoclonal antibodies, we found evidence for apoB48, but not apoB100, in donor intestinal biopsy specimens.
Photo-induced inactivation of viruses: adsorption of methylene blue, thionine, and thiopyronine on Qbeta bacteriophage. (1996)

The adsorption of cationic organic dyes (methylene blue, thionine, and thiopyronine) on Qbeta bacteriophage was studied by UV-visible and fluorescence spectroscopy. The dyes have shown a strong affinity to the virus and some have been used as sensitizers for photo-induced inactivation of virus. In the methylene blue concentration range of 0.1-5 microM and at high ratios of dye to virus (greater than 1000 dye molecules per virion), the dyes bind as aggregates on the virus. Aggregation lowers the efficiency of photoinactivation because of self-quenching of the dye. At lower ratios of dye to virus (lower than 500 dye molecules per virion), the dye binds to the virus as a monomer. Fluorescence polarization and time-resolved studies of the fluorescence support the conclusions based on fluorescence quenching. Increasing the ionic strength (adding NaCl) dissociates bound dye aggregates on the virus and releases monomeric dye into the bulk solution.
Small-bore hollow waveguides for delivery of 3-μm laser radiation (1996)

Flexible hollow glass waveguides with bore diameters as small as 250 µm have been developed for 3-µm laser delivery. All the guides exhibit straight losses between 0.10 and 1.73 dB/m, and the loss increases to between 2.4 and 5.1 dB/m upon bending 1 m of the guides into 15-cm-diameter coils. This behavior is shown to depend strongly on the launch conditions and mode quality of the input beam. The waveguides are capable of efficiently delivering up to 8 W of Er:YAG laser power with proper input coupling, and they are suitable for use in both medical and industrial applications.
Mechanism of adenylate kinase. Demonstration of a functional relationship between aspartate 93 and magnesium by site-directed mutagenesis and proton, phosphorus-31, and magnesium-25 NMR (1991)

Earlier magnetic resonance studies suggested no direct interaction between Mg2+ ions and adenylate kinase (AK) in the AK.MgATP (adenosine 5'-triphosphate) complex. However, recent NMR studies concluded that the carboxylate of aspartate 119 accepts a hydrogen bond from a water ligand of the bound Mg2+ ion in the muscle AK.MgATP complex [Fry, D.C., Kuby, S.A., & Mildvan, A.S. (1985) Biochemistry 24, 4680-4694]. On the other hand, in the 2.6-A crystal structure of the yeast AK.MgAP5A [P1,P5-bis(5'-adenosyl)pentaphosphate] complex, the Mg2+ ion is in proximity to aspartate 93 [Egner, U., Tomasselli, A.G., & Schulz, G.E. (1987) J. Mol. Biol. 195, 649-658]. Substitution of Asp-93 with alanine resulted in no change in dissociation constants, 4-fold increases in Km, and a 650-fold decrease in kcat. Notable changes have been observed in the chemical shifts of the aromatic protons of histidine 36 and a few other aromatic residues. However, the results of detailed analyses of the free enzymes and the AK.MgAP5A complexes by one- and two-dimensional NMR suggested that the changes are due to localized perturbations. Thus it is concluded that Asp-93 stabilizes the transition state by ca. 3.9 kcal/mol. The next question is how. Since proton NMR results indicated that binding of Mg2+ to the AK.AP5A complex induces some changes in the proton NMR signals of WT but not those of D93A, the functional role of Asp-93 should be in binding to Mg2+.(ABSTRACT TRUNCATED AT 250 WORDS)
Collaborative interface agents (1994)

Interface agents are semi-intelligent systems which assist users with daily computer-based tasks. Recently, various researchers have proposed a learning approach towards building such agents and some working prototypes have been demonstrated. Such agents learn by `watching over the shoulder&amp;apos; of the user and detecting patterns and regularities in the user&amp;apos;s behavior. Despite the successes booked, a major problem with the learning approach is that the agent has to learn from scratch and thus takes some time becoming useful. Secondly, the agent&amp;apos;s competence is necessarily limited to actions it has seen the user perform. Collaboration between agents assisting different users can alleviate both of these problems. We present a framework for multiagent collaboration and discuss results of a working prototype, based on learning agents for electronic mail. Introduction Learning interface agents are computer programs that employ machine learning techniques in order to provide assistance to a u...
Doping effects on the Raman spectra of silicon nanowires (2006)

Un-doped, $N$-type, and $P$-type doped silicon nanowires (SiNWs) were grown at $460\phantom{\rule{0.2em}{0ex}}\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$ and $25\phantom{\rule{0.3em}{0ex}}\text{Torr}$ via the vapor-liquid-solid (VLS) mechanism. The intensity ratio of anti-Stokes/Stokes $({I}_{\mathrm{AS}}∕{I}_{\mathrm{S}})$ peaks is used as an index of the sample temperature. Different SiNWs exhibit different Raman frequency shifts because their compressive stresses due to heating differ. The slopes of the ${I}_{\mathrm{AS}}∕{I}_{\mathrm{S}}$ peak ratio versus the Raman frequency for boron-doped, un-doped, phosphorous-doped SiNWs, and bulk Si are $\ensuremath{-}0.078$, $\ensuremath{-}0.036$, $\ensuremath{-}0.035$ and $\ensuremath{-}0.02\phantom{\rule{0.3em}{0ex}}\text{per}\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$, respectively. The different slopes reveal the different heating-induced compressive stresses in the SiNWs with different dopants and bulk Si.
A review of the influence the anxiety exerts on human life. (2018)

Our intention has been to review the literature addressing the anxiety phenomenon from as many points of view as possible. By searching in PubMed and Web of Science and by using multiple filters, we have included, of the over 1800 results, 93 studies with the aim of covering more aspects of life anxiety exerts its influence upon. We have discussed the connection between anxiety and physiological and psychological functioning, or its connection with the areas of family, religion, social life and behavior, as well as the cultural side, childhood, pregnancy and many others.
Application of a Heme-Binding Protein Eluted from Encapsulated Biomaterials to the Catalysis of Enantioselective Oxidation (2014)

A protein complex (PX) eluted from an encapsulated pea protein (PP) under aeration can be used as two types of biocatalysts: a polyethylene glycol (PEG) (1000/4000 = 2/1)-aggregated PX (AGPX) and a glutaraldehyde (GA)/compound-modified PX (CMPX). These biocatalysts have the following functional activities: AGPX can catalyze the oxidation of rac-1-(6-methoxynaphthalen-2-yl)ethanol (rac-1) to the corresponding ketone (∼95% chemical yield) via the selective oxidation of (S)-(+)-1, leaving highly enantiopure (R)-(−)-1 (>99% ee; ∼50% chemical yield); CMPX can catalyze the kinetic resolution of (S)-(+)-1 ((S)-naproxen precursor, >99% ee, ∼50% chemical yield) via the selective oxidation of (R)-(−)-1 to the corresponding ketone. Both reactions occur in the absence of an added cofactor (e.g., NAD(P)) in aqueous media. The specific activities of AGPX and CMPX were determined to be 0.8 ± 0.03 mU (mean ± SD) and 0.6 ± 0.02 mU (mean ± SD), respectively, and the exact nature of the species engaged in the key reaction was consistent with that of a heme-binding protein (HBP), on the basis of an N-terminal sequence comparison, which showed 93% similarity with a 20.853 kDa hemophore HasA gene product [Pseudomonas fluorescens Pf-5, a plant commensal bacterium]. PP-HBP can be regenerated via successive asymmetric catalytic events using an incorporated iron electron-transfer system (Fe2+ ⇄ Fe3+) in the presence of oxygen, a process seemingly similar to that utilized by hemoglobin. The use of a raw biomaterial as a PX-catalytic system with an incorporated redox cofactor for asymmetric oxidation overcomes the apparent difficulties in working with pure dehydrogenase enzyme/redox cofactor systems for biotransformation.
Adiponectin deficiency suppresses ABCA1 expression and ApoA‐I synthesis in the liver (2007)

Plasma high density lipoprotein (HDL)-cholesterol levels are inversely correlated with the incidence of cardiovascular diseases. HDL is mainly assembled in the liver through the ATP-binding cassette transporter (ABCA1) pathway. In humans, plasma HDL-cholesterol levels are positively correlated with plasma adiponectin (APN) concentrations. Recently, we reported that APN enhanced apolipoprotein A-I (apoA-I) secretion and ABCA1 expression in HepG2 cells. In the present study, we investigated HDL assembly in APN-knockout (KO) mice. The apoA-I protein levels in plasma and liver were reduced in APN-KO mice compared with wild-type-mice. The ABCA1 expression in liver was also decreased in APN-KO mice. APN deficiency might cause the impaired HDL assembly by decreasing ABCA1 expression and apoA-I synthesis in the liver.
Notch Inhibition Promotes Human Embryonic Stem Cell-Derived Cardiac Mesoderm Differentiation (2008)

Abstract The roles of Notch signaling in cardiac differentiation from murine embryonic stem cells have been well documented. We investigated whether Notch signaling plays a similar role in human embryonic stem cells (hESCs). Although, as previously reported, blocking Notch signaling via the addition of γ-secretase inhibitor (GSI) alone failed to affect hESC differentiation, we found that GSI plus reduced-volume culture medium (GSI/RVCM) accelerated mesodermal differentiation. GSI/RVCM conditions simultaneously suppressed commitment toward neuroectodermal lineages. Furthermore, sustained inhibition of Notch signaling further enhanced differentiation into cardiac mesoderm. Spontaneous beating activity was typically observed from 12 days after initiation of GSI treatment in RVCM. Moreover, hESC-derived cardiomyocytes expressed connexin 43 and possessed spontaneous calcium oscillations and cardiomyocyte beats coupled to neonatal rat cardiomyocytes when cocultured. These findings strongly suggest a distinct role for Notch signaling in the induction and specification of hESC-derived cardiac mesoderm in vitro. Disclosure of potential conflicts of interest is found at the end of this article.
Immunogenic Activity of a Ribosomal Fraction Obtained from Mycobacterium tuberculosis (1965)

Youmans, Anne S. (Northwestern University Medical School, Chicago, Ill.), and Guy P. Youmans. Immunogenic activity of a ribosomal fraction obtained from Mycobacterium tuberculosis. J. Bacteriol. 89:1291-1298. 1965.-The highly immunogenic particulate fraction obtained from mechanically ruptured cells of the H37Ra strain of Mycobacterium tuberculosis was suspended and centrifuged at 20,360 x g. The supernatant liquid from this centrifugation was centrifuged at 56,550 x g to remove the larger particles, and the supernatant liquid from this was centrifuged at 144,000 x g to obtain a ribosomal fraction. The sediments from the first two centrifugations were highly immunogenic, but the ribosomal fraction showed only slight capacity to immunize mice. However, when the ribosomal fraction was mixed with Freund's incomplete adjuvant, the immunogenic activity was equivalent to the particulate fraction from which it was prepared. To test the hypothesis that some membranous substance in the particulate fraction was acting as an adjuvant for the smaller particles in the ribosomal fraction, portions of the particulate fraction were treated separately with each of the membrane-disrupting agents, sodium deoxycholate, sodium lauryl sulfate, and 1 m sodium chloride. The treated materials were then centrifuged at 144,000 x g, and the sediments were tested for immunogenicity both with and without the addition of Freund's incomplete adjuvant. Without the adjuvant, the immunizing activities were very weak or absent; with the adjuvant, they were equivalent to that of the particulate fraction from which they were prepared. Other factors which have been found to damage or destroy membranes, such as freezing and thawing, and heat, also significantly decreased the immunogenic activity of the particulate fraction unless it was incorporated into Freund's incomplete adjuvant. The larger particles which sedimented at 56,550 x g were also treated with sodium lauryl sulfate and sodium chloride. Again, immunogenicity was greatly reduced but was fully restored by use of Freund's incomplete adjuvant. The data suggest, then, that the immunizing component of the particulate fraction is a substance (ribosomal?) which sediments at 144,000 x g, but for maximal immunizing activity a labile, possibly membranous, moiety of the mycobacterial cell, which has the properties of an adjuvant, is required.
Suggested Correlation between the Visible Photoluminescence and the Fourier Transform Infrared Spectrum of a Porous Silicon Surface (1997)

The FTIR spectrum for a heavily oxidized porous silicon (PS) surface is considered. It is suggested that a portion of this spectrum be reassigned to the SiO stretch frequency of a surface bound-silanone-based silicon oxyhydride consistent also with the 18O2/16O2 isotopic labeling of the FTIR spectrum and with matrix isolation infrared spectra for silanone, silanoic acid, and silicic acid. Within the framework of this assignment the FTIR spectrum, the photoluminescence excitation spectrum, and the visible photoluminescence spectrum of PS correlate well with a surface-bound silanone-based silicon oxyhydride fluorophor.
Understanding Transport at the Acid-Alkaline Interface of Bipolar Membranes (2016)

The combination of cation exchange membrane (CEM) and anion exchange membrane (AEM) electrolytes to form of a hybrid, or bipolar membrane (BPM) electrolyte, can have unique advantages for electrochemical systems including fuel cells, electrolyzers, electrodialysis, and photovoltaic solar-to-fuel devices. However, a major challenge for this approach is the development of a stable and active interfacial region (i.e., junction) that adjoins the CEM and AEM layers. Moreover, a fundamental understanding of transport at the CEM-AEM junction is lacking. Therefore, the present study focuses on the theoretical development and analysis of the nature of the BPM interface. A Poisson-Nernst-Planck (PNP) theory is formalized and applied to a representative BPM interface. The findings are reported in terms of bias (i.e., overpotential) in a galvanic device with respect to CEM and AEM material requirements. Specific attention is paid to our interests in the application of the BPM to a fuel cell device with an acidic (CEM) anode and alkaline (AEM) cathode. We demonstrate that a BPM with an acidic CEM anode and alkaline AEM cathode must promote a trap-assisted type of recombination mechanism under forward bias. Without such a mechanism, large overpotentials are needed to drive ionic recombination processes.
Conjugate Chemistry and Cellular Processing of EGF-Dextran (1999)

Conjugates with specific binding to the epidermal growth factor receptor, EGFR, of interest for radionuclide based imaging and therapy were prepared using mouse epidermal growth factor, mEGF, and dextran. In one type of conjugate, mEGF was coupled to dextran by reductive amination in which the free amino group on the mEGF N-terminal reacted with the aldehyde group on the reductive end of dextran. The end-end coupled conjugate could be further activated by the cyanopyridinium agent CDAP, thereby introducing tyrosines to the dextran part. In the other type of conjugate, the cyanylating procedure using CDAP was applied, first to activate dextran and then allowing for the amino terminus of mEGF to randomly attach to the dextran. In the latter case, radionuclide-labelled tyrosines or glycines could be added in the same conjugation step. All types of mEGF-dextran conjugates had EGFR-specific binding since the binding could be displaced by an excess of non-radioactive mEGF. The conjugates were to a large extent internalized in the test cells and the associated radioactivity was retained intracellularly for different times depending on both the type of cells and conjugate applied. Different intracellular 'traffic routes' for the radionuclides are discussed as well as applications for both imaging and therapy.
Interleukin 6 gene transfection into Lewis lung carcinoma tumor cells suppresses the malignant phenotype and confers immunotherapeutic competence against parental metastatic cells. (1992)

To investigate the influence of interleukin 6 (IL-6) production on malignancy of tumor cells we transfected cells of the high-metastatic, low-immunogenic D122 clone of the Lewis lung carcinoma with a mammalian expression vector containing the human IL-6 complementary DNA. In vitro, IL-6 positive transfectants showed growth inhibition that was directly correlated with the levels of IL-6 production. The in vitro growth arrest did not seem to be a function of an autocrine system mediated via the secreted human IL-6 acting on the tumor cell surface receptors since neutralizing antibodies to human IL-6 did not prevent the growth inhibition. Neither did exogenous human recombinant IL-6 affect the growth of D122 cells. In vivo, IL-6 positive transfectants showed reduction of tumorigenicity and significant suppression of metastatic competence in syngeneic, immunocompetent mice. In mature T-cell deficient nude mice, the IL-6 transfectants showed some arrest of local growth but no suppression of lung metastasis. It seems therefore that the reduction of metastatic competence of IL-6 transfectants is primarily a function of stimulation by the transfectants of host T-cell immune responses. Immunization with inactivated high-positive IL-6 transfectants induced high levels of anti-tumor cytotoxic T-lymphocytes and protected mice against metastatic growth of a subsequent graft of parental tumor cells. Moreover, reduction of metastatic growth of parental highly metastatic D122 cells was also achieved when immunization of mice was begun after establishment of the primary parental tumors. Thus, inactivated IL-6 transfectants were effective when used as a cellular vaccine for experimental immunotherapy of metastasis.
Energetics of folding subtilisin BPN' (1992)

Subtilisin is an unusual example of a monomeric protein with a substantial kinetic barrier to folding and unfolding. Here we document for the first time the in vitro folding of the mature form of subtilisin. Subtilisin was modified by site-directed mutagenesis to be proteolytically inactive, allowing the impediments to folding to be systematically examined. First, the thermodynamics and kinetics of calcium binding to the high-affinity calcium A-site have been measured by microcalorimetry and fluorescence spectroscopy. Binding is an enthalpically driven process with an association constant (Ka) equal to 7 x 10(6) M-1. Furthermore, the kinetic barrier to calcium removal from the A-site (23 kcal/mol) is substantially larger than the standard free energy of binding (9.3 kcal/mol). The kinetics of calcium dissociation from subtilisin (e.g., in excess EDTA) are accordingly very slow (t1/2 = 1.3 h at 25 degrees C). Second, to measure the kinetics of subtilisin folding independent of calcium binding, the high-affinity calcium binding site was deleted from the protein. At low ionic strength (I = 0.01) refolding of this mutant requires several days. The folding rate is accelerated almost 100-fold by a 10-fold increase in ionic strength, indicating that part of the free energy of activation may be electrostatic. At relatively high ionic strength (I = 0.5) refolding of the mutant subtilisin is complete in less than 1 h at 25 degrees C. We suggest that part of the electrostatic contribution to the activation free energy for folding subtilisin is related to the highly charged region of the protein comprising the weak ion binding site (site B).(ABSTRACT TRUNCATED AT 250 WORDS)
Food Processing and Maillard Reaction Products: Effect on Human Health and Nutrition (2015)

Maillard reaction produces flavour and aroma during cooking process; and it is used almost everywhere from the baking industry to our day to day life to make food tasty. It is often called nonenzymatic browning reaction since it takes place in the absence of enzyme. When foods are being processed or cooked at high temperature, chemical reaction between amino acids and reducing sugars leads to the formation of Maillard reaction products (MRPs). Depending on the way the food is being processed, both beneficial and toxic MRPs can be produced. Therefore, there is a need to understand the different types of MRPs and their positive or negative health effects. In this review we have summarized how food processing effects MRP formation in some of the very common foods.
Distribution of α2-adrenoceptor mRNAs in the rat lumbar spinal cord in normal and axotomized rats (1999)

Using riboprobe in situ hybridization we have studied the distribution of alpha2A-, alpha2B- and alpha2c-adrenoceptor (AR) mRNAs in the lumbar spinal cord in normal rats and after peripheral axotomy. A strong alpha2A- and alpha2C AR mRNA labelling was found in motoneurons and other cells in the ventral horns. In the dorsal horns strong alpha2A-AR mRNA labelling was found in all layers and in the lateral spinal nucleus, whereas alpha2C-AR mRNA was found in lower numbers of cells in various layers. The alpha2B-AR mRNA signal was only detected in some small cells superficially in the dorsal horn. With regard to axotomy only a marginal effect was observed for alpha2C-AR mRNA in the ventral horn. The results suggest that alpha2-ARs are involved both in sensory and motor processing.