gebhart/patrepeval huggingface dataset:
RECESSIVE UAA SUPPRESSORS OF THE YEAST SACCHAROMYCES CEREVISIAE (1982)

Recessive lysine-independent revertants were isolated from a psi + haploid strain of the yeast Saccharomyces cerevisiae containing one of the leucine-inserting UAA suppressors, SUP29, and various UAA mutations including lys1-1. The majority of the revertants were found to have recessive suppressors in addition to the pre-existing SUP29 mutation. The recessive suppressors were able to suppress only a very limited number of UAA mutations, and none of the UAG mutations thus far examined. The recessive inefficient UAA suppressors were assigned to three complementation groups, sup111, sup112, and sup113. A high incidence of gene conversion was observed for an allele of sup111. An antisuppressor acting on sup111, but not detectably on SUP29, was inadvertently obtained during the course of the study. Interactions between SUP29, sup111 and the antisuppressor asu12 were studied.
Assay of alanine:glyoxylate aminotransferase in human liver by its serine: glyoxylate aminotransferase activity (2009)

We have examined assay methods and conditions for human liver alanine:glyoxylate aminotransferase (AGT). This enzyme shows not only the AGT activity but also serine:pyruvate and serine: glyoxylate aminotransferase (SPT and SGT) activities. In the assay of AGT activity using crude enzyme preparations, there is the complication that glutamate:glyoxylate aminotransferase (GGT) also contributes to AGT activity, but at present no other enzyme is known to catalyze transamination between L-serine and glyoxylate or pyruvate. Therefore, an assay for AGT using its SGT activity was investigated in which hydroxypyruvate formed from L-serine in the enzymic reaction with glyoxylate was determined by lactate dehydrogenase (LDH) in the presence of tris(hydroxym ethyl)aminomethane (Tris) at pH 8.4. A possible obstacle to this assay is that pyruvate formed from L-serine by serine dehydratase (SDH) interferes with SGT assay as an additional substrate of LDH and AGT. However, the SDH activity in human liver is very low, and by performing the SGT reaction in the presence and absence of glyoxylate the SGT activity was represented as the glyoxylate-dependent hydroxypyruvate formation from L-serine. There was a combined good correlation between the AGT, SGT and SPT activities, and the activity ratio, AGT : SGT : SPT was about 1.0 : 0.17 : 0.13.
Performance analysis of relief and mRMR algorithm combination for selecting features in lupus Genome-Wide Association Study (2011)

This paper describes research on the use of feature selection techniques to find correlation between single-nucleotide-polymorphism (SNP) in genes with the lupus disease in Genome-Wide Association (GWA) study. Feature selection is the process of selecting features that are correlated and discarding features that have no correlation in data mining. In this research, feature selection techniques will be applied on 262, 264 SNPs. SNP is a variation of nitrogen base pairs in human DNA. SNP number is very large so we needed feature selection techniques when performing data mining. Various feature selection techniques have been proposed with different accuracy for different types of data. This research uses a combination of Relief and minimal-redundancy-maximal relevance (mRMR) algorithms as a feature selection method. Classification methods, including decision tree, SVM, and Naive Bayes, are applied to the selected SNPs. We compare the results with Chi-Squared Test which is used commonly in GWA. We also compare the results with composer of feature selection algorithms: Max-Relevance (Mutual Information), Relief, and mRMR. We found that the combination algorithm does not yield in good performance for selecting SNPs in genome-wide association study with lupus disease. We also found that mRMR algorithm gives best result for selecting feature which gives very good classification accuracy.
Encapsulated fish oil enriched in α‐tocopherol alters plasma phospholipid and mononuclear cell fatty acid compositions but not mononuclear cell functions (2000)

Supplementation of the diet with 3.2 g EPA plus DHA per day markedly alters plasma phospholipid and PBMC fatty acid compositions. The lack of effect of FO upon PBMC functions may relate to the level of alpha-tocopherol included in the supplements.
Extracellular acidosis increases neuronal cell calcium by activating acid-sensing ion channel 1a (2004)

Acid-sensing ion channel (ASIC) 1a subunit is expressed in synapses of central neurons where it contributes to synaptic plasticity. However, whether these channels can conduct Ca(2+) and thereby raise the cytosolic Ca(2+) concentration, [Ca(2+)](c), and possibly alter neuronal physiology has been uncertain. We found that extracellular acidosis opened ASIC1a channels, which provided a pathway for Ca(2+) entry and elevated [Ca(2+)](c) in wild-type, but not ASIC1(-/-), hippocampal neurons. Acid application also raised [Ca(2+)](c) and evoked Ca(2+) currents in heterologous cells expressing ASIC1a. Although ASIC2a is also expressed in central neurons, neither ASIC2a homomultimeric channels nor ASIC1a/2a heteromultimers showed H(+)-activated [Ca(2+)](c) elevation or Ca(2+) currents. Because extracellular acidosis accompanying cerebral ischemia contributes to neuronal injury, we tested the effect of acidosis on cell death measured as lactate dehydrogenase release. Eliminating ASIC1a from neurons or treating ASIC1a-expressing cells with the ASIC blocker amiloride attenuated acidosis-induced cell injury. These results indicate that ASIC1a provides a non-voltage-gated pathway for Ca(2+) to enter neurons. Thus, it may provide a target for modulation of [Ca(2+)](c).
Clinical Trial Designs for Predictive Biomarker Validation: One Size Does Not Fit All (2009)

Traditionally, anatomic staging systems have been used to provide predictions of individual patient outcome and, to a lesser extent, guide the choice of treatment in cancer patients. With targeted therapies, biomarkers have the potential for providing added value through an integrated approach to prediction using the genetic makeup of the tumor and the genotype of the patient for treatment selection and patient management. Specifically, biomarkers can aid in patient stratification (risk assessment), treatment response identification (surrogate markers), or differential diagnosis (identifying individuals who are likely to respond to specific drugs). In this study, we explore two major topics in relation to the design of clinical trials for predictive marker validation. First, we discuss the appropriateness of an enrichment (i.e., targeted) vs. an unselected design through case studies focusing on the clinical question(s) at hand, the strength of the preliminary evidence, and assay reproducibility. Second, we evaluate the efficiency (total number of events and sample size) of two unselected predictive marker designs for validation of a marker under a wide range of clinically relevant scenarios, exploring the impact of the prevalence of the marker and the hazard ratios for the treatment comparisons. The review and evaluation of these designs represents an essential step toward the goal of personalized medicine because we explicitly seek to explore and evaluate the methodology for the clinical validation of biomarker guided therapy.
Differential Interactions of Thrombospondin-1, -2, and -4 with CD47 and Effects on cGMP Signaling and Ischemic Injury Responses (2008)

Thrombospondin-1 regulates nitric oxide (NO) signaling in vascular cells via CD47. Because CD47 binding motifs are conserved in the C-terminal signature domains of all five thrombospondins and indirect evidence has implied CD47 interactions with other family members, we compared activities of recombinant signature domains of thrombospondin-1, -2, and -4 to interact with CD47 and modulate cGMP signaling. Signature domains of thrombospondin-2 and -4 were less active than that of thrombospondin-1 for inhibiting binding of radiolabeled signature domain of thrombospondin-1 or SIRPalpha (signal-regulatory protein) to cells expressing CD47. Consistent with this binding selectivity, the signature domain of thrombospondin-1 was more potent than those of thrombospondin-2 or -4 for inhibiting NO-stimulated cGMP synthesis in vascular smooth muscle cells and downstream effects on cell adhesion. In contrast to thrombospondin-1- and CD47-null cells, primary vascular cells from thrombospondin-2-null mice lack enhanced basal and NO-stimulated cGMP signaling. Effects of endogenous thrombospondin-2 on NO/cGMP signaling could be detected only in thrombospondin-1-null cells. Furthermore, tissue survival of ischemic injury and acute recovery of blood flow in thrombospondin-2-nulls resembles that of wild type mice. Therefore, thrombospondin-1 is the dominant regulator of NO/cGMP signaling via CD47, and its limiting role in acute ischemic injury responses is not shared by thrombospondin-2.
Thermoresponsive Glasses: Temperature-Controlled Rapid Swelling and Deswelling of Silica-Based Sol-Gels (2001)

A novel silica sol-gel that swells or shrinks rapidly by changing its hydration state upon temperature variation is described. The swelling–deswelling (see Figure) is reversible and the kinetics of the bulk transition are fast. The effects of preparation technique and structural variation on the thermal shrinkage properties are discussed.
Surface Tension-Driven Self-Folding Polyhedra (2007)

We discuss finite element simulations and experiments involving the surface tension-driven self-folding of patterned polyhedra. Two-dimensional (2D) photolithographically patterned templates folded spontaneously when solder hinges between adjacent faces were liquefied. Minimization of interfacial free energy of the molten solder with the surrounding fluidic medium caused the solder to ball up, resulting in a torque that rotated adjacent faces and drove folding. The simulations indicate that the folding process can be precisely controlled, has fault tolerance, and can be used to fold polyhedra composed of a variety of materials, ranging in size from the millimeter scale down to the nanometer scale. Experimentally, we have folded metallic, arbitrarily patterned polyhedra ranging in size from 2 mm to 15 microm.
Mast cells in the gastrointestinal tract. (1995)

The morphology and functions of gastrointestinal mast cells (MCs) under physiological and pathological conditions were described. Special attention was paid to the MCs origin, differentiation and morphological and biochemical aspects of their degranulation. Mast cells are important component of normal architecture of the gastrointestinal tract. Many substances released from MCs during degranulation are biologically active and mediate numerous processes: blood flow regulation, epithelial and endothelial permeability, mucosal secretion, gastrointestinal tract motility, immunological events related to the antigens of various origin, angiogenesis, cancer development. Thus MC is often considered as an important agent in pathogenesis of many gastrointestinal diseases. The gastrointestinal diseases which was described in this paper are following: bacterial and parasitic infections, peptic ulcer, ulcerative colitis, Leśniowski-Crohn's disease, inflammatory polyps, intestinal graft-versus-host reaction, neoplastic tumors, mastocytosis, intestinal ischemia.
Molecular orbital theory of the electronic structure of organic compounds. VIII. Geometries, energies, and polarities of C3 hydrocarbons (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular orbital theory of the electronic structure of organic compounds. VIII. Geometries, energies, and polarities of C3 hydrocarbonsL. Radom, W. A. Lathan, W. J. Hehre, and J. A. PopleCite this: J. Am. Chem. Soc. 1971, 93, 21, 5339–5342Publication Date (Print):October 1, 1971Publication History Published online1 May 2002Published inissue 1 October 1971https://pubs.acs.org/doi/10.1021/ja00750a005https://doi.org/10.1021/ja00750a005research-articleACS PublicationsRequest reuse permissionsArticle Views438Altmetric-Citations361LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Solid-State 13C NMR Assignment of Carbon Resonances on Metallic and Semiconducting Single-Walled Carbon Nanotubes (2010)

Solid-state 13C NMR spectroscopy was used to investigate the chemical shift of nanotube carbons on m- and s-SWNTs (metallic and semiconducting single-walled nanotubes) for samples with widely varying s-SWNT content, including samples highly enriched with nearly 100% m- and s-SWNTs. High-resolution 13C NMR was found to be a sensitive probe for m- and s-SWNTs in mixed SWNT samples with diameters of ∼1.3 nm. The two highly enriched m- and s-SWNT samples clearly exhibited features for m- and s-SNWT 13C nuclei (∼123 and 122 ppm, respectively) and were successfully fit with a single Gaussian, while five mixed samples required two Gaussians for a satisfactory fit.
Hemodynamic Effects of Di-Sec-Butyl Phenol, an Anesthetic Substituted Phenol (2005)

Dose- and age-related hemodynamic effects were determined for an anesthetic substituted phenol, 2,6-di-sec-butyl phenol (DSB). DSB, 7.5 mg/kg, induced hypnosis in young rabbits and increased mean blood pressure to 170 +/- 14% and heart rate to 150 +/- 21% of control values. In elderly rabbits, 7.5 mg/kg DSB induced hypnosis, had no effect on blood pressure, but increased the heart rate to 130 +/- 2% of control. After ganglionic blockade with hexamethonium, 7.5 mg/kg DSB caused a decline in mean blood pressure (71 +/- 5% of control) without change in heart rate. DSB increased norepinephrine release from SH-SY5Y cells, a human neuroblastoma cell line (5.4 +/- 1.7% vs. 3.5 +/- 0.3%). DSB produced age-dependent elevation of mean blood pressure in rabbits, probably by causing release of catecholamines from the sympathetic nervous system.
Design of Agonistic Altered Peptides for the Robust Induction of CTL Directed towards H-2Db in Complex with the Melanoma-Associated Epitope gp100 (2009)

Immunogenicity of tumor-associated antigens (TAA) is often weak because many TAA are autoantigens for which the T-cell repertoire is sculpted by tolerance mechanisms. Substitutions at main anchor positions to increase the complementarity between the peptide and the MHC class I (MHC-I) binding cleft constitute a common procedure to improve binding capacity and immunogenicity of TAA. However, such alterations are tailored for each MHC-I allele and may recruit different CTL specificities through conformational changes in the targeted peptides. Comparative analysis of substituted melanoma-differentiation antigen gp100 in complex with H-2D(b) revealed that combined introduction of glycine and proline residues at the nonanchor positions 2 and 3, respectively, resulted in an agonistic altered peptide with dramatically enhanced binding affinity, stability, and immunogenicity of this TAA. Peptide vaccination using the p2Gp3P-altered peptide version of gp100 induced high frequencies of melanoma-specific CTL in the endogenous CD8+ repertoire. Crystal structure analysis of MHC/peptide complexes revealed that the conformation of the modified p2Gp3P-peptide was similar to the wild-type peptide, and indicated that this mimotope was stabilized through interactions between peptide residue p3P and the tyrosine residue Y159 that is conserved among most known MHC-I molecules throughout mammalian species. Our results may provide an alternative approach to enhance MHC stabilization capacity and immunogenicity of low-affinity peptides for induction of robust tumor-specific CTL.
Wireless Body Area Network Protocols (2018)

Wireless body area networks (WBANs) differ from other types of wireless networks in some important aspects, related to, for example, dynamics and energy constraints. This chapter focuses on communication of sensor nodes deployed on or in a human body with a particular wireless device on the body to deliver the sensed data. It discusses architectures and protocols for such communication, considering the requirements, constraints, and challenges associated with these networks. Several types of biosensors may be used in a WBAN, based on the application requirements and the conditions of the person wearing the WBAN. Different sensors are likely to have different data sampling rates and precisions. Literature on WBANs describes several medium access control and data propagation protocols for communication within WBANs. The quality of wireless links in WBANs changes due to the movements of the human body. In particular, the link quality between some nodes on the body fluctuates periodically in some postures.
CGX1037 is a novel PKC isoform delta selective inhibitor in platelets (2014)

Platelets upon activation change their shape, aggregate and secrete alpha and dense granule contents among which ADP acts as a feedback activator. Different Protein Kinase C (PKC) isoforms have specific non-redundant roles in mediating platelet responses including secretion and thrombus formation. Murine platelets lacking specific PKC isoforms have been used to evaluate the isoform specific functions. Novel PKC isoform δ has been shown to play an important role in some pathological processes. Lack of specific inhibitors for PKCδ has restricted analysis of its role in various cells. The current study was carried out to evaluate a novel small molecule PKCδ inhibitor, CGX1037 in platelets. Platelet aggregation, dense granule secretion and western blotting experiments were performed to evaluate CGX1037. In human platelets, CGX1037 inhibited PAR4-mediated phosphorylation on PKD2, a PKCδ-specific substrate. Pre-treatment of human or murine platelets with CGX1037 inhibited PAR4-mediated dense granule secretion whereas it potentiated GPVI-mediated dense granule secretion similar to the responses observed in murine platelets lacking PKCδ· Furthermore, pre-treatment of platelets from PKCδ(-/-) mice with CGX1037 had no significant additive effect on platelet responses suggesting the specificity of CGX1037. Hence, we show that CGX1037 is a selective small molecule inhibitor of PKCδ in platelets.
METALLOPURPURINS and LIGHT: EFFECT ON TRANSPLANTABLE RAT BLADDER TUMORS and MURINE SKIN (1990)

Purpurins are modified chlorins with photodynamic properties. Their strong absorption in the red region of the visible spectrum makes them candidates for use in photodynamic cancer therapy. A series of metal derivatives of the free base purpurins have been synthesized and shown to cause tumor necrosis in transplantable tumors when exposed to visible light. In the following set of experiments, the effects of two metallo-derivatives (tin and zinc) of two purpurins, octaethylpurpurin (NT2) and etiopurpurin (ET2), and light on the N-[4-(5-nitro-2-furyl)-2-thiazolyl] formamide transplantable tumors in Fischer CDF(F344)/CrlBr rats were studied. The photodynamic activity was assessed by a short term assay using tumor dry weight 12 days after purpurin-PDT as a criterion of response. From these experiments it appears that SnET2 greater than SnNT2 greater than ZnET2 greater than ZnNT2 in photodynamic activity. SnET2 was further characterized by attempting to determine the time interval after systemic injection at which maximum therapeutic effect occurred. These studies shown that 24 h after metallopurpurin injection was the optimum time for treatment of tumors with visible light. In a final set of experiments, the effect of solar light on the skin of hairless mice injected with SnET2 was found to be much less injurious than with hematoporphyrin derivative.
Tsg101, a homologue of ubiquitin-conjugating (E2) enzymes, binds the L domain in HIV type 1 Pr55 Gag (2001)

Ubiquitination appears to be involved in virus particle release from infected cells. Free ubiquitin (Ub), as well as Ub covalently bound to a small fraction of p6 Gag, is detected in mature HIV particles. Here we report that the p6 region in the Pr55(Gag) structural precursor polyprotein binds to Tsg101, a putative Ub regulator that is involved in trafficking of plasma membrane-associated proteins. Tsg101 was found to interact with Gag in (i) a yeast two-hybrid assay, (ii) in vitro coimmunoprecipitation by using purified Pr55(Gag) and rabbit reticulocyte lysate-synthesized Tsg101, and (iii) in vivo in the cytoplasm of COS cells transfected with gag. The PTAPP motif [or late (L) domain] within p6, which is required for release of mature virus from the plasma membrane, was the determinant for binding Pr55(Gag). The N-terminal region in Tsg101, which is homologous to the Ubc4 class of Ub-conjugating (E2) enzymes, was the determinant of interaction with p6. Mutation of Tyr-110 in Tsg101, present in place of the active-site Cys that binds Ub in E2 enzymes, and other residues unique to Tsg101, impaired p6 interaction, indicating that features that distinguish Tsg101 from active E2 enzymes were important for binding the viral protein. The results link L-domain function in HIV to the Ub machinery and a specific component of the cellular trafficking apparatus.
Purification and characterization of acharan sulfate lyases, two novel heparinases, from Bacteroides stercoris HJ‐15 (2001)

Two novel acharan sulfate lyases (ASL1 and ASL2: no EC number) have been purified from Bacteroides stercoris HJ-15 which was isolated from human intestinal bacteria with glycosaminoglycan (GAG) degrading enzymes. These enzymes were purified to apparent homogeneity by a combination of QAE-cellulose, DEAE-cellulose, carboxymethyl-Sephadex C-50, hydroxyapatite and HiTrap SP Sephadex C-25 column chromatography with the final specific activity of 50.5 and 76.7 micromol.min-1.mg-1, respectively. Both acharan sulfate lyases are single subunits of 83 kDa by SDS/PAGE and gel filtration. ASL1 showed optimal activity at pH 7.2 and 45 degrees C. ASL1 activity was inhibited by Cu2+, Ni2+ and Co2+, but ASL2 activity was inhibited by Cu2+, Ni2+and Pb2. Both enzymes were slightly inhibited by some agents that modify histidine and cysteine residues, but activated by reducing agents such as DL-dithiothreitol and 2-mercaptoethanol. Both purified bacteroidal acharan sulfate lyases acted to the greatest extent on acharan sulfate, and to a lesser extents on heparan sulfate and heparin. They did not act on de-O-sulfated acharan sulfate. These findings suggest that the biochemical properties of these purified acharan sulfate lyases are different from those of the previously purified heparin lyases, but these enzymes belong to heparinase II.