gebhart/patrepeval huggingface dataset:
Functional genomics identifies novel genes essential for clear cell renal cell carcinoma tumor cell proliferation and migration (2014)

Currently there is a lack of targeted therapies that lead to long-term attenuation or regression of disease in patients with advanced clear cell renal cell carcinoma (ccRCC). Our group has implemented a high-throughput genetic analysis coupled with a high-throughput proliferative screen in order to investigate the genetic contributions of a large cohort of overexpressed genes at the functional level in an effort to better understand factors involved in tumor initiation and progression. Patient gene array analysis identified transcripts that are consistently elevated in patient ccRCC as compared to matched normal renal tissues. This was followed by a high-throughput lentivirus screen, independently targeting 195 overexpressed transcripts identified in the gene array in four ccRCC cell lines. This revealed 31 'hits' that contribute to ccRCC cell proliferation. Many of the hits identified are not only presented in the context of ccRCC for the first time, but several have not been previously linked to cancer. We further characterize the function of a group of hits in tumor cell invasion. Taken together these findings reveal pathways that may be critical in ccRCC tumorigenicity, and identifies novel candidate factors that could serve as targets for therapeutic intervention or diagnostic/prognostic biomarkers for patients with advanced ccRCC.
Reactions of cyclic β-keto esters and other enol derivatives with 3-acetoxyamino-2-isopropylquinazolin-4(3H)-one: further oxidation of the cyclic α-(3,4-dihydro-2-isopropyl-4-oxoquinazolin-3-yl)amino ketones with lead tetraacetate leading to ring-expansion (in dichloromethane) and ring-cleavage (in methanol) (1995)

The cyclic β-keto esters 12, 20, 22, 26, the β-diketone 28 and the enol silyl ethers 24 and 30 have been converted in 60–77% yields into the corresponding α-(oxoquinazolinyl)amino cyclic ketone derivatives 16, 21, 23, 29, 27, 25 and 31, respectively, by reaction with 3-acetoxyamino-2-isopropylquinazolin-4(3H)-one 11. Further oxidation of some of these products with lead tetraacetate gives products whose nature depends on the solvent used; in dichloromethane, 16, 21 and 25, which contain 5-membered ring ketones, give ring-expanded products 32, 38 and 39, respectively whereas, in methanol, ring-cleavage of 16, 25 and 27 occurs to give imino-esters 41, 44 and 42/43, respectively. Ring-expansion of 23, 27 and 31, which contain 6-membered ring ketones, does not occur and the only isolated product in each case is the benzoxazinone 40. A mechanism which accounts for this dependence on the solvent is presented: radical intermediates do not appear to be implicated.
Expression of Helicobacter pylori urease genes in Escherichia coli grown under nitrogen-limiting conditions (1992)

Helicobacter pylori produces a potent urease that is believed to play a role in the pathogenesis of gastroduodenal diseases. Four genes (ureA, ureB, ureC, and ureD) were previously shown to be able to achieve a urease-positive phenotype when introduced into Campylobacter jejuni, whereas Escherichia coli cells harboring these genes did not express urease activity (A. Labigne, V. Cussac, and P. Courcoux, J. Bacteriol. 173:1920-1931, 1991). Results that demonstrate that H. pylori urease genes could be expressed in E. coli are presented in this article. This expression was found to be dependent on the presence of accessory urease genes hitherto undescribed. Subcloning of the recombinant cosmid pILL585, followed by restriction analyses, resulted in the cloning of an 11.2-kb fragment (pILL753) which allowed the detection of urease activity (0.83 +/- 0.39 mumol of urea hydrolyzed per min/mg of protein) in E. coli cells grown under nitrogen-limiting conditions. Transposon mutagenesis of pILL753 with mini-Tn3-Km permitted the identification of a 3.3-kb DNA region that, in addition to the 4.2-kb region previously identified, was essential for urease activity in E. coli. Sequencing of the 3.3-kb DNA fragment revealed the presence of five open reading frames encoding polypeptides with predicted molecular weights of 20,701 (UreE), 28,530 (UreF), 21,744 (UreG), 29,650 (UreH), and 19,819 (UreI). Of the nine urease genes identified, ureA, ureB, ureF, ureG, and ureH were shown to be required for urease expression in E. coli, as mutations in each of these genes led to negative phenotypes. The ureC, ureD, and ureI genes are not essential for urease expression in E. coli, although they belong to the urease gene cluster. The predicted UreE and UreG polypeptides exhibit some degree of similarity with the respective polypeptides encoded by the accessory genes of the Klebsiella aerogenes urease operon (33 and 92% similarity, respectively, taking into account conservative amino acid changes), whereas this homology was restricted to a domain of the UreF polypeptide (44% similarity for the last 73 amino acids of the K. aerogenes UreF polypeptide). With the exception of the two UreA and UreB structural polypeptides of the enzyme, no role can as yet be assigned to the nine proteins encoded by the H. pylori urease gene cluster.
Integrated transcriptome and proteome data: The challenges ahead (2004)

The recent availability of platform technologies for high throughput proteome analysis has led to the emergence of integrated messenger RNA and protein expression data. The Pearson correlation coefficients for these data range from 0.46 to 0.76. In these integrated studies, serial analyses of gene expression and DNA microarrays have been used to quantify the transcriptome, while proteome analysis has been based on two-dimensional gel electrophoresis, isotope coded affinity tags and multidimensional protein identification technology. This paper provides a comprehensive review of the analytical techniques used in these studies and explores the extent to which the choice of experimental methodology can bias the correlation or the ability to detect proteins.
Cyanide Utilization and Degradation by Microorganisms (2007)

Various microorganisms can produce (cyanogenesis) or degrade cyanide. They degrade cyanide either to detoxify it, or to use it as a source of nitrogen for growth. Significant amounts of cyanide are formed as a secondary metabolite by a wide range of fungi and a few bacteria by decarboxylation of glycine. When cyanide has been formed by the snow mould fungus it is degraded by conversion to carbon dioxide and ammonia via an unknown pathway. In contrast, cyanogenic bacteria either do not further catabolize cyanide or they convert it into beta-cyanoalanine by addition to cysteine or O-acetylserine. Several non-cyanogenic fungi that are pathogens of cyanogenic plants are known to degrade cyanide by hydration to formamide by the enzyme cyanide hydratase. Such fungi can be immobilized and used in packed-cell columns to continuously detoxify cyanide. ICI Biological Products Business market a preparation of spray-dried fungal mycelia, 'CYCLEAR', to detoxify industrial wastes. Novo Industri have also introduced a cyanidase preparation to convert cyanide directly into formate and ammonia. Bacteria have been isolated that use cyanide as a source of nitrogen for growth. Because cyanide, as KCN or NaCN, is toxic for growth, the bacteria (Pseudomonas fluorescens) have to be grown in fed-batch culture with cyanide as the limiting nutrient. Cyanide is converted to carbon dioxide and ammonia (which is then assimilated) by an NADH-linked cyanide oxygenase system.
Interactive Global Illumination (2002)

Figure 1: Scene with complete global illumination computed at 1 fps (640 × 480 on 16 dual-AthlonMP 1800+ PCs) while the book and glass ball are moved by a user. Note the changing soft shadows, the caustics from the glass ball, the reflections in the window, and especially the color bleeding effects on the walls due to indirect illumination. Interactive graphics has been limited to simple direct illumination that commonly results in an artificial appearance. A more realistic appearance by simulating global illumination effects has been too costly to compute at interactive rates. In this paper we describe a new Monte Carlo-based global illumination algorithm. It achieves performance of up to 10 frames per second while arbitrary changes to the scene may be applied interactively. The performance is obtained through the effective use of a fast, distributed ray-tracing engine as well as a new interleaved sampling technique for parallel Monte Carlo simulation. A new filtering step in combination with correlated sampling avoids the disturbing noise artifacts common to Monte Carlo methods. CR Categories: I.3.7 [Computer Graphics]: Three-Dimensional
Mutation of Tyrosine Residues Involved in the Alkylation Half Reaction of Epoxide Hydrolase from Agrobacterium radiobacter AD1 Results in Improved Enantioselectivity (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTMutation of Tyrosine Residues Involved in the Alkylation Half Reaction of Epoxide Hydrolase from Agrobacterium radiobacter AD1 Results in Improved EnantioselectivityRick Rink, Jeffrey H. Lutje Spelberg, Roland J. Pieters, Jaap Kingma, Marco Nardini, Richard M. Kellogg, Bauke W. Dijkstra, and Dick B. JanssenView Author Information Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands Cite this: J. Am. Chem. Soc. 1999, 121, 32, 7417–7418Publication Date (Web):July 30, 1999Publication History Received17 February 1999Published online30 July 1999Published inissue 1 August 1999https://pubs.acs.org/doi/10.1021/ja990501ohttps://doi.org/10.1021/ja990501orapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views381Altmetric-Citations59LEARN 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 SUBJECTS:Ethers,Genetics,Monomers,Peptides and proteins,Stereoselectivity Get e-Alerts
Perfil antropométrico de alunos de dança de salão: uma análise comparativa (2012)

Introduction: Currently the dance hall has been widely publicized, either by the media as the appeal that it promotes socialization for the visitors. Objective: This study aimed to ascertain the anthropometric profile of students who do ballroom dancing, compared to sedentary individuals. Materials, Methods and Results: For the study, a population of 22 (n = 22) subjects. 11 individuals GD (average 70.42 kg, SD 9.46) and 11 GS (average 74.15 kg, SD 9.89). Submitted to CC values for GD group (mean 92.68 cm, SD 11.14 cm) and GS (average 94.05 cm, SD 10.59 cm) in the analysis for the RCQ groups pointed GD (average 0.88 and SD 0.12) and GS (mean 0.86, SD 0.07), IMC GD (mean 28.36 kg/m2, SD 3.19), GS (mean 28.75 kg/m2, SD 4, 12) IC, GD (mean 1.27, SD 0.13),GS (mean 1.27 and SD 0.19). was used for hypothesis testing, the t-student test simple independent, with p &lt;0.05 as the minimum level of significance and Chi square and odds ratio (OR) with a score of 95% to analyze the relationship between overweight by IMC in Groups and the relationship between sedentary lifestyle and practicing ballroom dancing. Conclusion: It refers to the results obtained by anthropometric protocols was found that no significant differences between groups, indicating that ballroom dancing does not promote significant changes in body composition.
Cloning and Expression of a Queen Pheromone-Binding Protein in the Honeybee: an Olfactory-Specific, Developmentally Regulated Protein (1999)

Odorant-binding proteins (OBPs) are small abundant extracellular proteins thought to participate in perireceptor events of odor-pheromone detection by carrying, deactivating, and/or selecting odor stimuli. The honeybee queen pheromone is known to play a crucial role in colony organization, in addition to drone sex attraction. We identified, for the first time in a social insect, a binding protein called antennal-specific protein 1 (ASP1), which binds at least one of the major queen pheromone components. ASP1 was characterized by cDNA cloning, expression in Pichia pastoris, and pheromone binding. In situ hybridization showed that it is specifically expressed in the auxiliary cell layer of the antennal olfactory sensilla. The ASP1 sequence revealed it as a divergent member of the insect OBP family. The recombinant protein presented the exact characteristics of the native protein, as shown by mass spectrometry, and N-terminal sequencing and exclusion-diffusion chromatography showed that recombinant ASP1 is dimeric. ASP1 interacts with queen pheromone major components, opposite to another putative honeybee OBP, called ASP2. ASP1 biosynthetic accumulation, followed by nondenaturing electrophoresis during development, starts at day 1 before emergence, in concomitance with the functional maturation of olfactory neurons. The isobar ASP1b isoform appears simultaneously to ASP1a in workers, but only at approximately 2 weeks after emergence in drones. Comparison of in vivo and heterologous expressions suggests that the difference between ASP1 isoforms might be because of dimerization, which might play a physiological role in relation with mate attraction.
Endogenous glucose production is inhibited by the adipose-derived protein Acrp30 (2001)

Intraperitoneal injection of purified recombinant Acrp30 lowers glucose levels in mice. To gain insight into the mechanism(s) of this hypoglycemic effect, purified recombinant Acrp30 was infused in conscious mice during a pancreatic euglycemic clamp. In the presence of physiological hyperinsulinemia, this treatment increased circulating Acrp30 levels by approximately twofold and stimulated glucose metabolism. The effect of Acrp30 on in vivo insulin action was completely accounted for by a 65% reduction in the rate of glucose production. Similarly, glucose flux through glucose-6-phosphatase (G6Pase) decreased with Acrp30, whereas the activity of the direct pathway of glucose-6-phosphate biosynthesis, an index of hepatic glucose phosphorylation, increased significantly. Acrp30 did not affect the rates of glucose uptake, glycolysis, or glycogen synthesis. These results indicate that an acute increase in circulating Acrp30 levels lowers hepatic glucose production without affecting peripheral glucose uptake. Hepatic expression of the gluconeogenic enzymes phosphoenolpyruvate carboxykinase and G6Pase mRNAs was reduced by more than 50% following Acrp30 infusion compared with vehicle infusion. Thus, a moderate rise in circulating levels of the adipose-derived protein Acrp30 inhibits both the expression of hepatic gluconeogenic enzymes and the rate of endogenous glucose production.
Acellular and cellular high-density, collagen-fibril constructs with suprafibrillar organization (2016)

Collagen is used extensively for tissue engineering due to its prevalence in connective tissues and its role in defining tissue biophysical and biological signalling properties. However, traditional collagen-based materials fashioned from atelocollagen and telocollagen have lacked collagen densities, multi-scale organization, mechanical integrity, and proteolytic resistance found within tissues in vivo. Here, highly interconnected low-density matrices of D-banded fibrils were created from collagen oligomers, which exhibit fibrillar as well as suprafibrillar assembly. Confined compression then was applied to controllably reduce the interstitial fluid while maintaining fibril integrity. More specifically, low-density (3.5 mg mL(-1)) oligomer matrices were densified to create collagen-fibril constructs with average concentrations of 12.25 mg mL(-1) and 24.5 mg mL(-1). Control and densified constructs exhibited nearly linear increases in ultimate stress, Young's modulus, and compressive modulus over the ranges of 65 to 213 kPa, 400 to 1.26 MPa, and 20 to 150 kPa, respectively. Densification also increased construct resistance to collagenase degradability. Finally, this process was amenable to creating high-density cellularized tissues; all constructs maintained high cell viability (at least 97%) immediately following compression as well as after 1 day and 7 days of culture. This method, which integrates the suprafibrillar assembly capacity of oligomers and controlled fluid reduction by confined compression, supports the rational and scalable design of a broad range of collagen-fibril materials and cell-encapsulated tissue constructs for tissue engineering applications.
Dual-electron-injector-structure electrically alterable read-only-memory modeling studies (1981)

The threshold voltage shift of various dual-electron-injector structures (DEIS's) which are composed of chemically vapor-deposited (CVD) stacks of Si-rich SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , and Si-rich SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> incorporated into floating polycrystalline-silicon-gate electrically alterable read-only memories (EAROM's) has been studied as a function of write/erase voltages, write/erase times, and the initial charge state of the floating poly-Si gate and compared, to a simple physical model for a variety of different device structures. This model depends on the interface limited (Si-rich-SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> -SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> interfaces) enhanced current injection observed for the dual-electron-injector stacks at moderate gate voltages for both voltage polarities, the changing electric fields in the SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> layers as the floating polycrystalline silicon gate electrode is charged or discharged, and the voltage-dependent capacitance of the dual-electron-injector stack. Good agreement is observed between the experimental data and this model. This model will be the starting point in designing more complicated device arrays for nonvolatile memory applications.
The Development and Use of a Coiled-Tubing Simulation for Horizontal Applications (1991)

ABSTRACT Thorough analysis of the many circulation parame- ters and force conditions experienced with coiled tubing has helped to improve job efficiency and eliminated many of the operating difficulties experienced in the past. The arrival of horizontal well technology has pro- duced the need for more diversity and greater reliability from coiled tubing. Many standard completion and work-over operations now require the use of coiled tubing in order to gain access to the horizontal sections. Using recognized correlations for all of the circulation parame- ters involved, and incorporating them into a set of force balance equations, a completely interactive model has been constructed to analyze flow conditions and tubing force effects and predict the outcome of coiled tubing operations. This paper will describe some of the concepts used to develop a coiled tubing simulator, its operating fea- tures and a few horizontal well examples to demonstrate its capability.
Distinct domains within Mash1 and Math1 are required for function in neuronal differentiation versus neuronal cell-type specification (2004)

Many members of the basic helix-loop-helix (bHLH) family of transcription factors play pivotal roles in the development of a variety of tissues and organisms. We identify activities for the neural bHLH proteins Mash1 and Math1 in inducing neuronal differentiation, and in inducing the formation of distinct dorsal interneuron subtypes in the chick neural tube. Although both factors induce neuronal differentiation, each factor has a distinct activity in the type of dorsal interneuron that forms, with overexpression of Math1 increasing dI1 interneurons, and Mash1 increasing dI3 interneurons. Math1 and Mash1 function as transcriptional activators for both of these functions. Furthermore, we define discrete domains within the bHLH motif that are required for these different activities in neural development. Helix 1 of the Mash1 HLH domain is necessary for Mash1 to be able to promote neuronal differentiation, and is sufficient to confer this activity to the non-neural bHLH factor MyoD. In contrast, helix 2 of Math1, and both helix 1 and 2 of Mash1, are the domains required for the neuronal specification activities of these factors. The requirement for distinct domains within the HLH motif of Mash1 and Math1 for driving neuronal differentiation and cell-type specification probably reflects the importance of unique protein-protein interactions involved in these functions.
The mRNA coding for the secreted protease transin is expressed more abundantly in malignant than in benign tumors. (1986)

Transin RNA is a 1.9-kilobase RNA transcript induced by oncogenes in rat embryo fibroblast cell lines. We show that RNA species complementary to a cloned transin cDNA are present in mouse skin squamous cell carcinomas induced by a classical initiation-promotion protocol but not in premalignant, benign papillomas or in normal epidermis. A single application of a tumor promoting phorbol ester to normal epidermis elicits a transient increase in these RNA levels. Transin RNA encodes a secreted protease, an activity consistent with a functional role for enhanced expression of transin RNA in the progression of benign, encapsulated tumors to malignant, invasive carcinomas.
Survival Benefit of High-Dose Therapy in Poor-Risk Aggressive Non-Hodgkin’s Lymphoma: Final Analysis of the Prospective LNH87–2 Protocol—A Groupe d’Etude des Lymphomes de l’Adulte Study (2000)

On the basis of the final analysis of this prospectively treated series of patients, retrospectively analyzed on the basis of the International Prognostic Index, we hypothesize that HDT benefits patients at higher risk who achieve complete remission after induction treatment.
Panic disorder across the life span: a differential diagnostic approach to treatment resistance. (1997)

There has been significant progress over the past 30 years in our understanding of the treatment of panic disorder. There are now several different classes of pharmacological treatments, as well as cognitive-behavioral treatments that have been shown to have efficacy in treating panic disorder. Despite the increase in the knowledge base, many patients are only partially responsive or unresponsive to initial treatment efforts. A differential diagnostic approach to reviewing possible causes for treatment failure is presented. These causes include coexisting psychiatric disorders, unrecognized medical factors, environmental stressors, and others. Additionally, a review of factors specifically related to elderly and to very young treatment-resistant panic disorder patients is presented, along with some suggestions for evaluation and treatment. Based on the limited literature and clinical experience, practical clinical suggestions for approaching identified factors are presented.