gebhart/patrepeval huggingface dataset:
Characterization of low viscosity polymer solutions for microchip electrophoresis of non-denatured proteins on plastic chips (2011)

In this paper, we study characteristics of polymers (methylcellulose, hypromellose ((hydroxypropyl)methyl cellulose), poly(vinylpyrrolidone), and poly(vinyl alcohol)) with different chemical structures for microchip electrophoresis of non-denatured protein samples in a plastic microchip made of poly(methyl methacrylate) (PMMA). Coating efficiency of these polymers for controlling protein adsorption onto the channel surface of the plastic microchip, wettability of the PMMA surface, and electroosmotic flow in the PMMA microchannels in the presence of these polymers were compared. Also relative electrophoretic mobility of protein samples in solutions of these polymers was studied. We showed that when using low polymer concentrations (lower than the polymer entanglement point) where the sieving effect is substantially negligible, the interaction of the samples with the polymer affected the electrophoretic mobility of the samples. This effect can be used for achieving better resolution in microchip electrophoresis of protein samples.
A Genomic and Expression Compendium of the ExpandedPEBPGene Family from Maize (2007)

The phosphatidylethanolamine-binding proteins (PEBPs) represent an ancient protein family found across the biosphere. In animals they are known to act as kinase and serine protease inhibitors controlling cell growth and differentiation. In plants the most extensively studied PEBP genes, the Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) genes, function, respectively, as a promoter and a repressor of the floral transition. Twenty-five maize (Zea mays) genes that encode PEBP-like proteins, likely the entire gene family, were identified and named Zea mays CENTRORADIALIS (ZCN), after the first described plant PEBP gene from Antirrhinum. The maize family is expanded relative to eudicots (typically six to eight genes) and rice (Oryza sativa; 19 genes). Genomic structures, map locations, and syntenous relationships with rice were determined for 24 of the maize ZCN genes. Phylogenetic analysis assigned the maize ZCN proteins to three major subfamilies: TFL1-like (six members), MOTHER OF FT AND TFL1-like (three), and FT-like (15). Expression analysis demonstrated transcription for at least 21 ZCN genes, many with developmentally specific patterns and some having alternatively spliced transcripts. Expression patterns and protein structural analysis identified maize candidates likely having conserved gene function of TFL1. Expression patterns and interaction of the ZCN8 protein with the floral activator DLF1 in the yeast (Saccharomyces cerevisiae) two-hybrid assay strongly supports that ZCN8 plays an orthologous FT function in maize. The expression of other ZCN genes in roots, kernels, and flowers implies their involvement in diverse developmental processes.
Alkol Tüketimi ve Sosyo-Demografik Değişkenlerin Alkol Tüketimi Üzerine Etkisi (2008)

Alkol kullanımı ve buna bağlı sorunlar son yıllarda hem dünyada hem de ülkemizde önemli ölçüde artış göstermiştir. Bu çalışmanın amacı, alkol tüketimi üzerinde sosyo-demografik değişkenlerin etkisini belirlemektir. Bu amaç için gerekli veriler, Devlet İstatistik Enstitüsü tarafından yapılan 2003 yılı hanehalkı anket verilerinden elde edilmiştir. Elde edilen verilerde hanehalkı reisi temel olarak alınmış, sosyo-demografik değişkenlerin alkol tüketiminde etkili olup olmadığı gözlenmiştir. Çalışmada hanehalkının alkol harcaması kategorik bağımlı değişken olarak ele alınmış ve bu değişkenler üzerinde etkili olan diğer faktörler ekonometrik modeller aracılığı ile tahmin edilip yorumlanmıştır. Elde edilen sonuçlara göre, hanehalkı reisinin yası, eğitim durumu, oturduğu konut tipi, sigara kullanıp kullanmaması, meslek durumu, aylık geliri, çalıştığı yerin iş statüsü ve sağlık sigortasına sahip olup olmaması alkol tüketimi üzerinde etkisi olan temel faktörler olarak ortaya çıkmıştır.
Reduced Neutrophil Chemotaxis and Infiltration Contributes to Delayed Resolution of Cutaneous Wound Infection with Advanced Age (2013)

Advanced age is associated with alterations in innate and adaptive immune responses, which contribute to an increased risk of infection in elderly patients. Coupled with this immune dysfunction, elderly patients demonstrate impaired wound healing with elevated rates of wound dehiscence and chronic wounds. To evaluate how advanced age alters the host immune response to cutaneous wound infection, we developed a murine model of cutaneous Staphylococcus aureus wound infection in young (3-4 mo) and aged (18-20 mo) BALB/c mice. Aged mice exhibit increased bacterial colonization and delayed wound closure over time compared with young mice. These differences were not attributed to alterations in wound neutrophil or macrophage TLR2 or FcγRIII expression, or age-related changes in phagocytic potential and bactericidal activity. To evaluate the role of chemotaxis in our model, we first examined in vivo chemotaxis in the absence of wound injury to KC, a neutrophil chemokine. In response to a s.c. injection of KC, aged mice recruited fewer neutrophils at increasing doses of KC compared with young mice. This paralleled our model of wound infection, where diminished neutrophil and macrophage recruitment was observed in aged mice relative to young mice despite equivalent levels of KC, MIP-2, and MCP-1 chemokine levels at the wound site. This reduced leukocyte accumulation was also associated with lower levels of ICAM-1 in wounds from aged mice at early time points. These age-mediated defects in early neutrophil recruitment may alter the dynamics of the inflammatory phase of wound healing, impacting macrophage recruitment, bacterial clearance, and wound closure.
Digital analysis of the expression levels of multiple colorectal cancer-related genes by multiplexed digital-PCR coupled with hydrogel bead-array (2011)

To digitally analyze expression levels of multiple genes in one reaction, we proposed a method termed as 'MDHB' (Multiplexed Digital-PCR coupled with Hydrogel Bead-array). The template for bead-based emulsion PCR (emPCR) was prepared by reverse transcription using sequence-tagged primers. The beads recovered from emPCR were immobilized with hydrogel to form a single-bead layer on a chip, and then decoded by gene-specific probe hybridization and Cy3-dUTP based primer extension reaction. The specificity of probe hybridization was improved by using electrophoresis to remove mismatched probes on the bead's surface. The number of positive beads reflects the abundance of expressed genes; the expression levels of target genes were normalized to a housekeeping gene and expressed as the number ratio of green beads to red beads. The discrimination limit of MDHB is 0.1% (i.e., one target molecule from 1000 background molecules), and the sensitivity of the method is below 100 cells when using the β-actin gene as the detection target. We have successfully employed MDHB to detect the relative expression levels of four colorectal cancer (CRC)-related genes (c-myc, COX-2, MMP7, and DPEP1) in 8 tissue samples and 9 stool samples from CRC patients, giving the detection rates of 100% and 77%, respectively. The results suggest that MDHB could be a potential tool for early non-invasive diagnosis of CRC.
Estrogen‐mediated neuroprotection against β‐amyloid toxicity requires expression of estrogen receptor α or β and activation of the MAPK pathway (2002)

It is well documented that estrogen can activate rapid signaling pathways in a variety of cell types. These non-classical effects of estrogen have been reported to be important for cell survival after exposure to a variety of neurotoxic insults. Since direct evidence of the ability of the estrogen receptors (ERs) alpha and/or beta to mediate such responses is lacking, the hippocampal-derived cell line HT22 was stably transfected with either ERalpha (HTERalpha) or ERbeta (HTERbeta). In HTERalpha and HTERbeta cells, but not untransfected cells, an increase in ERK2 phosphorylation was measured within 15 min of 17beta-estradiol treatment. The ER antagonist ICI 182, 780 (1 microm) and the MEK inhibitor, PD98059 (50 microm) blocked this increase in ERK2 phosphorylation. Treatment of HT22, HTERalpha and HTERbeta cells with the beta-amyloid peptide (25-35) (10 micro m) resulted in a significant decrease in cell viability. Pre-treatment for 15 min with 10 nm 17beta-estradiol resulted in a 50% increase in the number of living cells in HTERalpha and HTERbeta cells, but not in HT22 cells. Finally, ICI 182, 780 and PD98059 prevented 17beta-estradiol-mediated protection. This study demonstrates that both ERalpha and ERbeta can couple to rapid signaling events that mediate estrogen-elicited neuroprotection.
The isolation of angiotensin-converting enzyme cDNA. (1988)

Angiotensin-converting enzyme (ACE) is an Zn(II)-containing dipeptidyl carboxypeptidase that converts angiotensin I to the potent vasoconstrictor, angiotensin II. Using oligonucleotide probes based on the amino acid sequence of mouse kidney ACE, cDNA encoding this protein has been isolated. One cDNA, ACE.31, encodes the N-terminal 332 amino acids of mouse ACE, a portion of the protein containing a putative 34-amino acid leader sequence and the N terminus of the mature protein. Northern analyses with cloned ACE cDNA revealed that both mouse kidney and lung express two ACE mRNAs, one of 4900 and another of 4150 bases. Southern analysis suggests that cDNA ACE.31 is the product of a single gene, and thus these data add evidence to the hypothesis that the converting enzymes produced by epithelial and endothelial cells are identical.
Assessing fear of hypoglycemia in children with Type 1 diabetes and their parents (2011)

This article summarizes the literature on fear of hypoglycemia in pediatric Type 1 diabetes and the assessment of this fear in both children with Type 1 diabetes and their parents. The most common instrument for assessing fear of hypoglycemia in this population is the children's and parent's versions of the Hypoglycemia Fear Survey (HFS), although studies using other assessment measures are also reviewed. Studies using this survey have identified variables contributing to fear of hypoglycemia in children with Type 1 diabetes and their parents, such as history of frequent or traumatic hypoglycemia, as well as trait anxiety. In addition to this summary of the literature, new data are presented supporting the reliability of hypoglycemic fear assessment in younger children and comparing fear of hypoglycemia in children in different age groups (6-18 years old) and their parents. Also reviewed are studies investigating the relationship between fear of hypoglycemia and diabetes control, which have yielded inconsistent results. Given the potential importance of fear of hypoglycemia in pediatric diabetes, there has been limited research in this area.
Generative communication in Linda (1985)

Generative communication is the basis of a new distributed programming langauge that is intended for systems programming in distributed settings generally and on integrated network computers in particular. It differs from previous interprocess communication models in specifying that messages be added in tuple-structured form to the computation environment, where they exist as named, independent entities until some process chooses to receive them. Generative communication results in a number of distinguishing properties in the new language, Linda, that is built around it. Linda is fully distributed in space and distributed in time; it allows distributed sharing, continuation passing, and structured naming. We discuss these properties and their implications, then give a series of examples. Linda presents novel implementation problems that we discuss in Part II. We are particularly concerned with implementation of the dynamic global name space that the generative communication model requires.
Catalytic oxidations with air for clean and selective transformations of polyols (1995)

Oxidations of polyols of commercial interest currently performed via stoichiometric oxidations with mineral acids or via enzymatic processes can be advantageously replaced by oxidation with air on metal supported catalysts. Thus, glyoxal solutions are oxidized to glyoxylic acid under controlled pH on active charcoal supported, platinum catalysts with a selectivity better than 70% at nearly total conversion. Factors limiting the diffusion of reactants and products in the catalyst are detrimental to the selectivity because any increase of the contact time favors the oxidation into oxalic acid. Glucose is oxidized into gluconate with a 99.3% yield on a Pd/C catalyst prepared by ion-exchange provided bismuth atoms are deposited on the Pd particles. A mechanism is proposed whereby bismuth acts as a cocatalyst preventing the oxygen poisoning of palladium.
Identification of Oligo-N-glycolylneuraminic Acid Residues in Mammal-derived Glycoproteins by a Newly Developed Immunochemical Reagent and Biochemical Methods (1998)

The occurrence of the alpha2-->8-linked oligomeric form of N-glycolylneuraminic acid (oligo-Neu5Gc) residues in mammalian glycoproteins was unequivocally demonstrated using a newly developed anti-oligo/poly-Neu5Gc monoclonal antibody as well as by chemical and biochemical methods. First, the antibody, designated mAb.2-4B, which specifically recognized oligo/poly-Neu5Gc with a degree of polymerization of >2, was developed by establishing a hybridoma cell line from P3U1 myeloma cells fused with splenocytes from an MRL autoimmune mouse immunized with dipalmitoylphosphatidylethanolamine-conjugated oligo/poly-Neu5Gc. Second, oligo-Neu5Gc was shown to occur in glycoproteins derived from pig spleen by Western blot analysis using mAb.2-4B, which was also confirmed by fluorometric high performance liquid chromatographic analysis of the product of periodate oxidation/reduction/acid hydrolysis of the purified glycopeptide fractions and by TLC and 600-MHz 1H NMR spectroscopic analysis of their mild acid hydrolysates. Finally, the ubiquitous occurrence of oligo-Neu5Gc chains as glycoproteinaceous components in Wistar rat tissue was immunochemically indicated. This is the first example demonstrating the diversity in oligo/poly-Sia structure in mammalian glycoproteins, where only poly-N-acetylneuraminic acid is known to occur. Such diversity in oligo/poly-Sia structure also implicates a diverged array of biological functions of this glycan unit in glycoproteins.
The Impact of Glycosylation on the Biological Function and Structure of Human Immunoglobulins (2006)

Immunoglobulins are the major secretory products of the adaptive immune system. Each is characterized by a distinctive set of glycoforms that reflects the wide variation in the number, type, and location of their oligosaccharides. In a given physiological state, glycoform populations are reproducible; therefore, disease-associated alterations provide diagnostic biomarkers (e.g., for rheumatoid arthritis) and contribute to disease pathogenesis. The oligosaccharides provide important recognition epitopes that engage with lectins, endowing the immunoglobulins with an expanded functional repertoire. The sugars play specific structural roles, maintaining and modulating effector functions that are physiologically relevant and can be manipulated to optimize the properties of therapeutic antibodies. New molecular models of all the immunoglobulins are included to provide a basis for informed and critical discussion. The models were constructed by combining glycan sequencing data with oligosaccharide linkage and dynamics information from the Glycobiology Institute experimental database and protein structural data from "The Protein Data Bank."
Decreased type 1 iodothyronine deiodinase expression might be an early and discrete event in thyroid cell dedifferentation towards papillary carcinoma (2005)

These findings suggest that thyroid cell dedifferentiation promotes changes in D1 gene expression by pretranscriptional mechanisms and indicate that decreased D1 expression might be an early and discrete event in thyroid cell dedifferentiation towards papillary thyroid carcinoma.
Induction of alpha-smooth muscle actin expression in cultured human brain pericytes by transforming growth factor-beta 1. (1994)

Pericytes are cells localized at the abluminal side of the microvascular endothelium and completely enveloped by a basement membrane. Pericytes have close contact with endothelial cells and are probably involved in the regulation of endothelial cell functions. Previous studies suggested a role for pericytes in microvascular proliferation in tumors. To study this cell type, we isolated human brain pericytes from microvessel segments derived from autopsy brain tissue. These cells were characterized in vitro using a panel of monoclonal antibodies. Human brain pericytes were reactive with monoclonal antibodies directed against the high molecular weight-melanoma associated antigen and intercellular adhesion molecule-1, but only a minority of the cells expressed alpha-smooth muscle actin (alpha-SMA, 0 to 10%) or vascular cell adhesion molecule-1 (10 to 50%). In histologically normal human brain microvessels in situ, pericytes consistently lacked staining for these four markers. Tissue with microvascular proliferation, however, showed a marked pericyte staining for both alpha-SMA and high molecular weight-melanoma associated antigen. The expression of alpha-SMA in vitro could be slightly up-regulated by incubation with serum-containing medium. An increase in alpha-SMA expression up to 40% of the total cell population was seen when pericytes were treated with transforming growth factor-beta 1, whereas basic fibroblast growth factor slightly inhibited alpha-SMA expression. Incubation with other factors (platelet-derived growth factor-AA, heparin, interferon-gamma, tumor necrosis factor-alpha) had no effect on the alpha-SMA expression at all. Transforming growth factor-beta 1 thus induces smooth muscle-like differentiation in pericytes in vitro and might play a role in the activation of pericytes during angiogenesis in vivo.
Fluorescence Studies of the Binding of the Polyene Antibiotics Filipin III, Amphotericin B, Nystatin, and Lagosin to Cholesterol (1972)

The interactions of filipin III, amphotericin B, nystatin, and lagosin with sterols in aqueous suspension and in vesicles were followed by fluorescence excitation spectra and by measurement of polarized fluorescence intensities. The equilibrium constants for association of the polyene antibiotics with aqueous suspensions of cholesterol follow the order filipin III > amphotericin B > nystatin > lagosin, in agreement with the order reported for the extent of damage these antibiotics cause in natural and model membranes. Fluorescence polarization measurements show that hydrophobic forces are primarily responsible for the formation of the complexes. Filipin III undergoes a large enhancement in fluorescence polarization on binding to aqueous suspensions of cholesterol and epi-cholesterol, and to vesicles of lecithin-cholesterol, lecithin-beta-cholestanol, and lecithinergosterol. Small increases in polarization occur on interaction of filipin III with vesicles derived from lecithin and epi-cholesterol, thiocholesterol, and androstan-3beta-ol. Amphotericin B undergoes a relatively constant enhancement in fluorescence polarization on interaction with the various lecithin-sterol vesicles used and does not display the selectivity exhibited by filipin III. It is suggested that filipin III serves as a probe of lecithin-sterol interaction.
Antioxidative Effects of a Processed Grain Food. (1994)

Antioxidant biofactor: AOB is a unique processed grain food. It is a yellow-green powder. It contains the following extracts: germ extracts, soybean, rice bran, tear grass, sesame, wheat, citron, green tea, green leaf extract, and malted rice. These materials were slowly roasted under a powdered oure at less than 60 degrees C and fermented with Aspergillus oryzae over 3 days to transform each ingredient into low molecular weight substances. These conditions were different by each material, environmental humidity and temperature. It probably contains a variety of substances having antioxidant activity including flavonoids, alpha-tocopherol, vitamin C, and tannins. We investigated its antioxidative properties using electron spin resonance (ESR) and autoxidation of rat brain homogenates. The superoxide, hydroxyl radical, and the stable free radical, diphenyl-p-picrylhydrazyl (DPPH) radical scavenging activity of AOB was investigated using ESR spectrometry. In an in vitro study, a suspension of AOB was added directly to a superoxide generating system (hypoxanthine-xanthine oxidase; HX/XO) and investigated using 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) as a spin trapping agent. At final concentrations of 0.01, 0.05, and 0.1 mg/ml, AOB dose-dependent scavenging activity was observed as 0.103, 0.619, and 1.369 U/ml, respectively. A concentration of 1.0 mg/ml completely scavenged DMPO-OOH signals; 1.0 mg/ml of AOB inhibited the DMPO-OH signal generated by Fenton's reaction, but its inhibitory effect was not competitive, and was inhibition of the Fenton's reaction. 1.0, 3.0, and 5.0 mg/ml of AOB were significantly inhibited the DPPH radical. In an in vivo study, rats were fed AOB orally at doses of 1 or 5 g/day for 24 h or for 3 days and the superoxide scavenging activity was measured in plasma. With the administration of 1 g/day for 3 days, the superoxide scavenging activity was about 1.8 times that of the control group fed a basal diet; 1.5 times the control with 5 g/day for 1 day, and 2.6 times the control with 5 g/day for 3 days, all of which represented significant increases in superoxide scavenging activity. AOB strongly inhibited the autoxidation of rat brain homogenates in vitro in a dose-dependent manner. However, each ingredient before roast and fermentation little inhibited lipid peroxidation. Roasting and fermentation with A. oryzae way be important to transform each ingredient into low molecular weight substances. Therefore, it was suggested that AOB possesses strong antioxidant and free radical scavenging activities.
The effect of age on the development and outcome of adult sepsis* (2005)

The incidence of sepsis is disproportionately increased in elderly adults, and age is an independent predictor of mortality. Compared with younger sepsis patients, elderly nonsurvivors of sepsis die earlier during hospitalization and elderly survivors more frequently require skilled nursing or rehabilitative care after hospitalization. These findings have implications for patient care and health care resource prioritization and provide insights for expanded scientific investigations and potential patient interventions.
<title>Self-location for indoor navigation of autonomous vehicles</title> (1998)

Accurate position estimation is a fundamental requirement for mobile robot navigation. The positioning problem consists of keeping in real-time a reliable estimate of the robot location with respect to a reference frame in the environment. A fast landmark-based position estimation method is presented in this paper. The technique combines orientation of the mobile robot from a heading sensor (a compass) with observations of landmarks from a vision sensor (a CCD camera). Knowing the position of the landmarks in a fixed coordinate system and the orientation of the optical axis of the camera it's possible to recover the robot position by simple geometric considerations. The experiments made in our laboratory demonstrate the reliability of the method and suggest its applicability in the context of autonomous robot navigation.