gebhart/patrepeval huggingface dataset:
Sec5 and Exo84 Foster Oncogenic Ras-Mediated Tumorigenesis (2010)

The genes encoding the Ras family of small GTPases are mutated to yield constitutively active GTP-bound oncogenic proteins in one third of all human cancers. Oncogenic Ras binds to and activates a number of proteins that promote tumorigenic phenotypes, including the family of Ral guanine nucleotide exchange factors (RalGEF). Activated RalGEFs convert the Ral family of small GTPases, composed of RalA and RalB, from an inactive GDP-bound state to an active GTP-bound state. As both RalA and RalB have been implicated in a variety of tumorigenic phenotypes, we sought to determine which proteins downstream of Rals promote transformation and tumorigenesis. Here, we report that shRNA-mediated knockdown of the Ral effector proteins Sec5 and Exo84, but less so in the case of RalBP1, reduced oncogenic RalGEF-mediated transformation and oncogenic Ras-driven tumorigenic growth of human cells. These results suggest that Rals promote oncogenic Ras-mediated tumorigenesis through, at least in part, Sec5 and Exo84.
Highly conducting, soluble, and environmentally-stable poly(3-alkylthiophenes) (1986)

Homopolymers and copolymers of 3-alkylthiophenes incorporating alkyl groups equal to or greater than butyl in size can be handled in solution and form highly conducting, environmentally-stable compositions on doping.
Isolation of Listeria monocytogenes small-plaque mutants defective for intracellular growth and cell-to-cell spread (1990)

To dissect the regulatory and structural requirements for Listeria monocytogenes intracellular growth and cell-to-cell spread, we designed a protocol based on transposon mutagenesis and the isolation of mutants which form small plaques in monolayers of mouse L2 cell fibroblasts. Two different transposable elements were used to generate libraries of insertion mutants: Tn916 and a derivative of Tn917-lac, Tn917-LTV3. Ten classes of mutants were isolated and evaluated for growth and cell-to-cell spread in J774 mouse macrophagelike cells, Henle 407 human epithelial cells, and mouse bone marrow-derived macrophages. Mutants were also evaluated for secretion of hemolysin and phospholipase (assayed by egg yolk opacity) and association with F-actin in the cytoplasm of cells, using NBD-phallacidin staining. The ten classes of mutants included (i) mutants showing abortive intracellular and extracellular growth; (ii) mutants showing abortive intracellular growth; (iii) rough mutants; (iv) mutants showing greatly reduced hemolysin and phospholipase secretion but showing normal growth in cells and little or no association with F-actin; (v) mutants with mutations mapping to an open reading frame (ORF) adjacent to hlyA and referred to as ORF U, lacking phospholipase activity, and with 50% normal hemolysin activity; (vi) mutants with reduced secretion of both hemolysin and phospholipase; (vii) nonhemolytic mutants with mutations mapping to the structural gene, hlyA; (viii) mutants with 25% normal hemolysin secretion and absolutely no association with F-actin; (ix) mutants with mutations mapping to ORF U, lacking phospholipase activity, and with normal hemolysin activity; and (x) mutants showing a mixed-plaque morphology but normal for all other parameters.
Practical Aspects of the Ligand-Binding and Enzymatic Properties of Human Serum Albumin. (2002)

Recent work with approaches like recombinant mutants and X-ray crystallography has given much new information about the ligand-binding properties of human serum albumin (HSA). The information increases the understanding of this unique transport and depot protein and could give a structural basis for the possible construction of therapeutic agents with altered HSA-binding properties. A tabulation of high-affinity binding sites for both endogenous and exogenous compounds has been made; it could be useful for the above-mentioned purpose, but it could also be of value when trying to predict potential drug interactions at the protein-binding level. Drug displacement is not always a complication to therapy; it can be used to increase the biological effect of a drug. However, due to rebinding at other sites, the increase in the free concentration of a displaced ligand can be less than expected. Drugs and drug metabolites can also interact covalently with HSA; thiol-containing drugs often bind to the single free cysteine residue of HSA, and glucuronidated drugs react irreversibly with other residues of the protein. Reversible binding of ligands is often stereospecific, and therefore immobilized HSA can be used to separate drug isomers. Albumin-containing dialysates are useful for extracorporeal removal of endogenous toxins and in the treatment of drug overdoses. HSA has different types of hydrolytic activities, which also can be stereospecific. The esterase-like property seems especially useful in converting prodrugs to active drugs in plasma.
Quinoline Analogs of Podophyllotoxin. I. Preliminary Experiments. Syntheses of Some 4-Phenylquinoline Derivatives1 (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuinoline Analogs of Podophyllotoxin. I. Preliminary Experiments. Syntheses of Some 4-Phenylquinoline Derivatives1EDWARD A. FEHNELCite this: J. Org. Chem. 1958, 23, 3, 432–434Publication Date (Print):March 1, 1958Publication History Published online1 May 2002Published inissue 1 March 1958https://pubs.acs.org/doi/10.1021/jo01097a029https://doi.org/10.1021/jo01097a029research-articleACS PublicationsRequest reuse permissionsArticle Views134Altmetric-Citations3LEARN 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
A role for the MHC class I‐like Mill molecules in nutrient metabolism and wound healing (2008)

MHC class I family members serve multiple functions beyond antigen presentation. We provide insight into the structure, expression and function of the Mill subfamily. This family includes two surface glycoproteins, Mill1 and Mill2. Protein sequences for Mill1 and Mill2 are most highly related to the NKG2D ligands, MICA and MICB, but neither of them bound to NKG2D. Computer-based protein modelling indicated that hereditary haemochromatosis protein (HFE), a molecule involved in iron uptake, was most similar. Mill1 and Mill2 were observed on cycling thymocytes, proliferating smooth muscle cells and fibroblasts. Using soluble Mill proteins, we found evidence for a soluble ligand in serum. Like HFE, the Mill family may be involved in nutrient metabolism. Skin was one of the only three organs found to express transcripts for both Mill1 and Mill2. Addition of antibodies specific for Mill2 to wounded skin enhanced healing. Our results suggest a role for the Mill proteins in cellular metabolism, with possible therapeutic significance.
Comparison of Percutaneous Coronary Intervention and Coronary Artery Bypass Grafting After Acute Myocardial Infarction Complicated by Cardiogenic Shock (2005)

Among SHOCK trial patients randomized to emergency revascularization, those treated with CABG had a greater prevalence of diabetes and worse coronary disease than those treated with PCI. However, survival rates were similar. Emergency CABG is an important component of an optimal treatment strategy in patients with cardiogenic shock, and should be considered a complementary treatment option in patients with extensive coronary disease.
FLAIR diffusion-tensor MR tractography: comparison of fiber tracking with conventional imaging. (2005)

Despite the reduction of signal-to-noise ratio and longer imaging times, FLAIR improved tractography by eliminating CSF partial volume effects.
Protein Analysis in Cerebrospinal Fluid (1993)

Analyses of the cerebrospinal fluid (CSF) to determine the blood-CSF barrier function and to detect intrathecal IgG production are used in the diagnosis of neurological and psychiatric diseases. Therefore, accurate reference values for these parameters are of utmost importance. However, current reference values are based on ‘reference groups’ consisting of patients with psychiatric and/or neurological symptoms but without positive clinical findings and on groups of young students. The present study presents reference values for CSF proteins in a large sample (n = 105) of healthy individuals, with a large age-span (18-88 years of age). The parameter for the determination of the blood CSF barrier function, the CSF/serum (CSF/S) albumin ratio, was found to show an increasing variability in individuals over 45 years of age, suggesting a less stable blood-CSF barrier function than in younger individuals. The upper reference limit for the CSF/S albumin ratio was 6.8 for individuals under 45 years of age and 10.2 for individuals over 45 years of age. The IgG index, a dimensionless quotient for the determination of intrathecal IgG production, showed only a minor correlation with age and had an upper reference limit of 0.63.
Radiofrequency Catheter Ablation of Ventricular Tachycardia Guided by Nonsurgical Epicardial Mapping in Chronic Chagasic Heart Disease (1999)

We report a case of a 63-year-old women with Chagas' disease and recurrent, syncopal VT treated by RF catheter ablation in whom endocardial application of RF energy was guided by nonsurgical epicardial mapping. The procedure was undertaken in the electrophysiology laboratory under deep anesthesia. VT was interrupted after 2.4 seconds of application and rendered noninducible afterwards. Two weeks after the procedure, a distinct morphology VT was induced by programmed ventricular stimulation, and the patient was started on amiodarone, remaining asymptomatic 12 months after the procedure.
Pain Recognition Using Artificial Neural Network (2006)

Facial expressions are a key index of emotion. To make use of the information afforded by facial expression for emotion science and clinical practice, reliable, valid, and efficient methods of measurement are critical. Enabling computer systems to recognize facial expressions and infer emotions from them is a challenging research topic. In this paper, we present an efficient video analysis technique for recognition of a specific expression, pain, from human faces. We employ an automatic face detector and facial feature tracker for face detection and feature extraction respectively. The face detector uses skin color modeling approach. For pain recognition, location and shape features of the detected faces are computed. These features are then used as inputs to the artificial neural network which uses standard error backpropagation algorithm for classification of painful and painless faces
Pore Structures and Microstructures of Silica Gel Monoliths at Different Stages of Sintering (1988)

The pore structures and microstructures of silica gel monoliths derived from the polycondensation of tetramethoxysilane (TMOS) in basic pH were characterized after various stages of sintering, using N{sub 2} gas adsorption-desorption, mercury porosimetry, and TEM. Gels dried by supercritical drying, i.e., aerogels and gels dried slowly in air have different pore structures and sinter with contrasting results when heat-treated under identical conditions. The air-dried gels do not sinter to full density and exhibit bloating on heating to high temperatures (1,100{degree}C), whereas under the same condition aerogels sinter to dense, transparent glass without bloating. Transmission electron microscopy shows that the microstructure of gels is composed of 5- to 10-nm primary spherical particles which clustered to form large (100 nm) spherical aggregates loosely bound to each other. In aerogels, two types of porosity exit: macroporosity and ultraporosity.
Tyrosine Phosphorylation of Paxillin and Focal Adhesion Kinase during Insulin-like Growth Factor-I-stimulated Lamellipodial Advance (1997)

In the current studies, we examined whether focal adhesion kinase (FAK) and paxillin play a role in insulin-like growth factor-I (IGF-I)-stimulated morphological changes in neuronal cells. In SH-SY5Y human neuroblastoma cells, 10 nM IGF-I enhanced the extension of lamellipodia within 30 min. Scanning electron microscopy and staining with rhodamine-phalloidin showed that these lamellipodia displayed ruffles, filopodia, and a distinct meshwork of actin filaments. Immunofluorescent staining identified focal concentrations of FAK, paxillin, and phosphotyrosine within the lamellipodia. Immunoprecipitation experiments revealed that FAK and paxillin are tyrosine-phosphorylated during IGF-I-stimulated lamellipodial extension. Maximal phosphorylation of FAK and paxillin was observed 15-30 min after the addition of 10 nM IGF-I, whereas maximal IGF-I receptor phosphorylation occurred within 5 min. FAK, paxillin, and IGF-I receptor tyrosine phosphorylation had similar concentration-response curves and were inhibited by the receptor blocking antibody alphaIR-3. These results indicate that FAK and paxillin are tyrosine-phosphorylated during IGF-I-stimulated lamellipodial advance and suggest that the tyrosine phosphorylation of these two proteins helps mediate IGF-I-stimulated cell and growth cone motility. These responses contrast directly with recent reports showing insulin-stimulated dephosphorylation of FAK and paxillin.
Masked fake face detection using radiance measurements (2009)

This research presents a novel 2D feature space where real faces and masked fake faces can be effectively discriminated. We exploit the reflectance disparity based on albedo between real faces and fake materials. The feature vector used consists of radiance measurements of the forehead region under 850 and 685 nm illuminations. Facial skin and mask material show linearly separable distributions in the feature space proposed. By simply applying Fisher's linear discriminant, we have achieved 97.78% accuracy in fake face detection. Our method can be easily implemented in commercial face verification systems.
Liposuction and Lipoinjection Treatment for Congenital and Acquired Lipodystrophies in Children (2009)

Background: The purpose of this clinical study was to establish liposuction and lipoinjection as a noncosmetic procedure in children to correct lipodystrophies. Methods: Liposuction, fat injection, or a combination of both was performed on 30 patients between 1994 and 2006 at Roberto del Rio Hospital or Clinica Alemana, Santiago, Chile. Liposuction was indicated in patients with excessive amounts of fatty tissue or tumor-like swelling. Combined liposuction and lipoinjection was performed on patients with deficit and excess in soft tissues. Lipoinjection was used for patients with soft-tissue insufficiencies. Samples of fat obtained by liposuction were submitted to histopathologic examination. Traditional tumescent technique was used for liposuction. The supernatant obtained by simple filtration was used for fat injection. Short- and long-term postoperative follow-up included registration of complications and assessment of aesthetic and functional outcome. The kappa test was used for statistical analysis. Results: Thirty patients, nine boys and 21 girls, were operated on, with an average age of 11 years (range, 4 to 17 years). A total of 43 procedures were performed: 27 liposuctions, 10 lipoinjections, and six combined procedures. Average hospital stay was 1.1 days. Of a total 20 patients who underwent liposuction, six required revision. Histopathologic study showed 19 lipomatoses and one lipoblastomatosis. Cosmetic outcomes based on Strasser scale were as follows: six excellent, 19 good, four mediocre, and one poor. Conclusions: Liposuction and lipoinjection as sole or combined procedures are safe methods for the pediatric population. They are well tolerated, with a low rate of complications and satisfactory aesthetic results.
Mutations in the Isocitrate Dehydrogenase Genes IDH1 and IDH2 in Tumors (2012)

Heterozygous hotspot mutations in isocitrate dehydrogenases (IDH) IDH1 or IDH2 are frequently observed in specific types of cartilaginous tumors, gliomas, and leukemias. Mutant IDH enzyme loses its normal activity to convert isocitrate into α-ketoglutarate (αKG) and instead acquires the ability to reduce αKG to D-2-hydroxyglutarate. Through direct competition with αKG, accumulation of the oncometabolite D-2-hydroxyglutarate in IDH mutated tumors results in inhibition of αKG-dependent dioxygenases involved in DNA and histone demethylation. Apart from epigenetic alterations, perturbations in the tricarboxylic acid cycle (depletion of intermediates) and activation of the intricately linked hypoxia signaling pathway are apparent in IDH mutated cells. As molecular details are being unraveled, the emerging concept is that IDH mutations result in tumor formation by epigenetic alterations that affect gene expression and result in inhibition of cellular differentiation. Activation of hypoxic stress signaling reprograms cellular energy metabolism and promotes anabolic processes and angiogenesis, thus, providing an advantage to promote neoplastic growth.
Anti-Inflammatory and Antiatherogenic Role of BMP Receptor II in Endothelial Cells (2013)

These results suggest that BMPRII is a critical, anti-inflammatory, and antiatherogenic protein that is commonly targeted by multiple pro- and antiatherogenic factors. BMPRII may be used as a novel diagnostic and therapeutic target in atherosclerosis.
Composition of peptidoglycans in Bacteroidaceae: determination and distribution of lanthionine (1982)

Peptidoglycans of organisms belonging to the strictly anaerobic family Bacteroidaceae were investigated for the presence of lanthionine. Different procedures for the quantitation of lanthionine were compared. Performic acid and peroxide oxidation procedures on 35S-labeled peptidoglycan from Fusobacterium nucleatum Fev1 resulted in low yields of cysteic acid (42 and 60%, respectively) and many other additional unidentified oxidation products. Lanthionine was, however, recovered in high yield (89% or more) from acid hydrolysates of unoxidized peptidoglycans. Lanthionine was found exclusively in some species of Fusobacterium, in particular F. nucleatum, F. necrophorum, F. russi, and F. gonidiaformans, for which lanthionine may be ascribed a function as a taxonomic marker. Peptidoglycans of these bacteria are thus proposed to belong to a new chemotype, assigned A1 delta. One strain of Fusobacterium, F. mortiferum VPI 0473 contained both lanthionine and diaminopimelic acid in about equal proportions. Species of F.plauti had a composition atypic of gram-negative cells. Chemotypic differences were also indicated among the species of Bacteroides investigated. Thus, some species contained lysine and not diaminopimelic acid as the major dibasic amino acid (e.g., F. asaccharolyticus). It is concluded that peptidoglycans of gram-negative organisms constitute a somewhat more heterogeneous group than hitherto assumed.
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media (2010)

Specific small deletions within the rpoC gene encoding the β'-subunit of RNA polymerase (RNAP) are found repeatedly after adaptation of Escherichia coli K-12 MG1655 to growth in minimal media. Here we present a multiscale analysis of these mutations. At the physiological level, the mutants grow 60% faster than the parent strain and convert the carbon source 15-35% more efficiently to biomass, but grow about 30% slower than the parent strain in rich medium. At the molecular level, the kinetic parameters of the mutated RNAP were found to be altered, resulting in a 4- to 30-fold decrease in open complex longevity at an rRNA promoter and a ∼10-fold decrease in transcriptional pausing, with consequent increase in transcript elongation rate. At a genome-scale, systems biology level, gene expression changes between the parent strain and adapted RNAP mutants reveal large-scale systematic transcriptional changes that influence specific cellular processes, including strong down-regulation of motility, acid resistance, fimbria, and curlin genes. RNAP genome-binding maps reveal redistribution of RNAP that may facilitate relief of a metabolic bottleneck to growth. These findings suggest that reprogramming the kinetic parameters of RNAP through specific mutations allows regulatory adaptation for optimal growth in new environments.
The immunological barriers to xenotransplantation. (1996)

There is an increasing interest in the potential clinical application of xenotransplantation. This interest derives in part from the need to identify a more abundant source of organs for transplantation and in part from rapid progress in understanding the cellular and molecular changes that contribute to hyperacute and acute vascular xenograft rejection. Recent areas of progress in understanding the immunological hurdles to xenotransplantation include the characterization of xenoreactive antibodies and the antigens they recognize, the role of complement regulatory proteins in immune recognition, the mechanism of complement activation in a xenograft, and the pathophysiologic changes in endothelial cells caused by the activation of complement.
Purification and properties of the major nuclease from mitochondria of Saccharomyces cerevisiae. (1988)

The vast majority of nuclease activity in yeast mitochondria is due to a single polypeptide with an apparent molecular weight of 38,000. The enzyme is located in the mitochondrial inner membrane and requires non-ionic detergents for solubilization and activity. A combination of heparin-agarose and Cibacron blue-agarose chromatography was employed to purify the nuclease to approximately 90% homogeneity. The purified enzyme shows multiple activities: 1) RNase activity on single-stranded, but not double-stranded RNA, 2) endonuclease activity on single- and double-stranded DNA, and 3) a 5'-exonuclease activity on double-stranded DNA. Digestion products with DNA contain 5'-phosphorylated termini. Antibody raised against an analogous enzyme purified from Neurospora crassa (Chow, T. Y. K., and Fraser, M. (1983) J. Biol. Chem. 258, 12010-12018) inhibits and immunoprecipitates the yeast enzyme. This antibody inhibits 90-95% of all nuclease activity present in solubilized mitochondria, indicating that the purified nuclease accounts for the bulk of mitochondrial nucleolytic activity. Analysis of a mutant strain in which the gene for the nuclease has been disrupted supports this conclusion and shows that all detectable DNase activity and most nonspecific RNase activity in the mitochondria is due to this single enzyme.
Model Selection for Multivariate Regression in Small Samples (1994)

We develop a small-sample criterion (AICc) for selecting multivariate regression models. This criterion adjusts the Akaike information criterion to be an exact unbiased estimator for the expected Kullback-Leibler information. A small-sample comparison shows that AICC provides better model order choices than other available model selection methods. Data from an agricultural experiment are analyzed.