gebhart/patrepeval huggingface dataset:
Identification of new target moleculesPTK2,TGFBR2andCD9overexpressed during advanced bone marrow remodelling in primary myelofibrosis (2009)

Primary myelofibrosis (PMF) is a myeloproliferative neoplasm characterized by remodelling of the bone marrow, including progressive myelofibrosis and exaggerated angiogenesis. Advanced PMF frequently shows a full-blown fibre meshwork, which avoids aspiration of cells, and the expression profile of genes related to stroma pathology at this stage remains largely undetermined. We investigated bone marrow core biopsies in PMF showing various degrees of myelofibrosis by custom-made low density arrays (LDA) representing target genes with designated roles in synthesis of extracellular matrix, matrix remodelling, cellular adhesion and motility. Among a set of 11 genes up-regulated in advanced stages of PMF (P < or = 0.01) three candidates, PTK2 protein tyrosine kinase 2 (PTK2), transforming growth factor beta type II receptor (TGFBR2) and motility-related protein-1 (CD9 molecule, CD9), were investigated in more detail. PTK2, TGFBR2 and CD9 were significantly overexpressed in larger series of advanced PMF stages (P < or = 0.01 respectively). Endothelial cells of the increased microvessel network in PMF could be identified as a predominant source for PTK2, TGFBR2 and CD9. CD9 also strongly identified activated fibroblasts in advanced myelofibrosis. We conclude that PTK2, TGFBR2 and CD9 represent new target molecules involved in bone marrow remodelling of PMF and warrant further investigation for potential targeted therapy.
Exposure to Diazinon Alters In Vitro Retinogenesis: Retinospheroid Morphology, Development of Chicken Retinal Cell Types, and Gene Expression (2005)

Developing embryos are more vulnerable than adults to acute cholinergic intoxication by anticholinesterases, including organophosphorus pesticides. These agents affect the process of neural development itself, leading to permanent deficits in the architecture of the nervous system. Recent evidence on direct roles of acetylcholinesterase (AChE) on neuronal differentiation provides additional grounds for investigating the developmental toxicity of anticholinesterases. Therefore, the effect of the organophosphate diazinon on the development of chick retinal differentiation was studied by an in vitro reaggregate approach. Reaggregated spheres from dissociated retinal cells of the E6 chick embryo were produced in rotation culture. During the whole culture period of 10 days, experimental cultures were supplemented with different concentrations of the pesticide, from 20 to 120 microM diazinon. The pesticide-treated spheres were reduced in size, and their outer surface was irregular. More importantly, inner structural distortions could be easily traced because the structure of control spheroids can be well characterized by a histotypical arrangement of laminar parts homologous to the normal retina. Acetylcholinesterase activity in diazinon-treated spheres was reduced when compared with controls. As a dramatic effect of exposure to the pesticide, inner plexiform layer (IPL)-like areas in spheroids were not distinguishable anymore. Similarly, photoreceptor rosettes and Müller radial glia were strongly decreased, whereas apoptosis was stimulated. The expression of transcripts for choline-acetyltransferase and muscarinic receptors was affected, revealing an effect of diazinon on the cholinergic system. This further proves the significance of cholinesterases and the cholinergic system for proper nervous system development and shows that further studies of debilitating diazinon actions on development are necessary.
Codon usage patterns inEscherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogasterandHomo sapiens; a review of the considerable within-species diversity (1988)

The genetic code is degenerate, but alternative synonymous codons are generally not used with equal frequency. Since the pioneering work of Grantham's group it has been apparent that genes from one species often share similarities in codon frequency; under the "genome hypothesis" there is a species-specific pattern to codon usage. However, it has become clear that in most species there are also considerable differences among genes. Multivariate analyses have revealed that in each species so far examined there is a single major trend in codon usage among genes, usually from highly biased to more nearly even usage of synonymous codons. Thus, to represent the codon usage pattern of an organism it is not sufficient to sum over all genes as this conceals the underlying heterogeneity. Rather, it is necessary to describe the trend among genes seen in that species. We illustrate these trends for six species where codon usage has been examined in detail, by presenting the pooled codon usage for the 10% of genes at either end of the major trend. Closely-related organisms have similar patterns of codon usage, and so the six species in Table 1 are representative of wider groups. For example, with respect to codon usage, Salmonella typhimurium closely resembles E. coli, while all mammalian species so far examined (principally mouse, rat and cow) largely resemble humans.
Prothrombin Is a Cofactor for the Binding of Factor XI to the Platelet Surface and for Platelet-Mediated Factor-XI Activation by Thrombin (2007)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionProthrombin Is a Cofactor for the Binding of Factor XI to the Platelet Surface and for Platelet-Mediated Factor-XI Activation by ThrombinFrank A. Baglia and Peter N. WalshCite this: Biochemistry 2007, 46, 44, 12886–12887Publication Date (Web):October 11, 2007Publication History Published online11 October 2007Published inissue 1 November 2007https://pubs.acs.org/doi/10.1021/bi701501khttps://doi.org/10.1021/bi701501kcorrectionACS PublicationsCopyright © 2007 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views683Altmetric-Citations7LEARN 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 PDF (15 KB) Get e-Alertsclose Get e-Alerts
Electrochemical Tuning of Electronic Structure of Single-Walled Carbon Nanotubes: In-situ Raman and Vis-NIR Study (2001)

The population of valence-band electronic states of single-walled carbon nanotubes (SWCNTs) was tuned electrochemically in acetonitrile electrolyte solution. In dry and oxygen-free solution, the electrochemistry of SWCNTs is controlled by capacitive charging. Reversible changes of intensity and frequency of the Raman spectra can be monitored during cyclic voltammetry at low scan rates. Electrochemical charging of SWCNTs can be also traced via reversible bleaching of the electronic transitions in the vis-NIR region. An aprotic medium offers a broader electrochemical window for tuning of electronic properties of SWCNTs. Electrochemical charging of SWCNTs in an aprotic electrolyte solution allows easy and precise control of the electronic structure of SWCNTs. In addition to commercial SWCNTs, a material made from gas-phase catalytic decomposition of CO by the HiPco process was also studied. Selective quenching of vis-NIR and Raman spectra is a useful tool to the analysis of tubes of varying diameter and helicity.
Continuous Ventricular Volume Assessment for Diagnosis and Pacemaker Control (1984)

Stroke volume measurements made by a catheter-based, right ventricular, intracardiac impedance system at rest and during upright bicycle ergometry were found to compare favorably with measurements made by acetylene rebreathing (r = 0.96, n = 13) and by radionuclide ventriculography (r = 0.96, n = 13) in a 46-year-old male pacemaker-dependent subject. The impedance information was then used to control the ventricular pacing rate during bicycle exercise, utilizing an algorithm that attempts to maintain a constant stroke volume. This resulted in a 23% increase in cardiac output accompanied by a 70% decrease in stroke volume as compared to the values measured during the same exercise at 70 pulses per minute (ppm).
Corneal Power Determination After Previous Corneal Refractive Surgery for Intraocular Lens Calculation (2003)

To avoid underestimation of intraocular lens power after cataract surgery in the eyes that had previously undergone myopic corneal refractive surgery, the measured corneal power must be corrected. Although correction factors may be calculated for cases after PRK and LASIK, there are no universal and absolutely reliable methods to determine corneal power in these cases. More than one accessible method should be used, and the lowest, most reliable data should be used.
Structure–Activity Relationships of Antitubercular Nitroimidazoles. 3. Exploration of the Linker and Lipophilic Tail of ((S)-2-Nitro-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazin-6-yl)-(4-trifluoromethoxybenzyl)amine (6-Amino PA-824). (2011)

The (S)-2-nitro-6-(4-(trifluoromethoxy)benzyloxy)-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine named PA-824 (1) has demonstrated antitubercular activity in vitro and in animal models and is currently in clinical trials. We synthesized derivatives at three positions of the 4-(trifluoromethoxy)benzylamino tail, and these were tested for whole-cell activity against both replicating and nonreplicating Mycobacterium tuberculosis (Mtb). In addition, we determined their kinetic parameters as substrates of the deazaflavin-dependent nitroreductase (Ddn) from Mtb that reductively activates these pro-drugs. These studies yielded multiple compounds with 40 nM aerobic whole cell activity and 1.6 μM anaerobic whole cell activity: 10-fold improvements over both characteristics from the parent molecule. Some of these compounds exhibited enhanced solubility with acceptable stability to microsomal and in vivo metabolism. Analysis of the conformational preferences of these analogues using quantum chemistry suggests a preference for a pseudoequatorial orientation of the linker and lipophilic tail.
Identification of Highly Expressed Genes in Peripheral Blood T Cells from Patients with Atopic Dermatitis (2002)

The upregulated genes identified in this work may serve as useful markers for moderate to severe AD as opposed to normal or mild AD and also as markers indicating progression to more severe AD. Further functional characterization will provide a better understanding of the pathophysiology of circulating T cells in AD.
A Classification-Based Surrogate-Assisted Evolutionary Algorithm for Expensive Many-Objective Optimization (2018)

Surrogate-assisted evolutionary algorithms (SAEAs) have been developed mainly for solving expensive optimization problems where only a small number of real fitness evaluations are allowed. Most existing SAEAs are designed for solving low-dimensional single or multiobjective optimization problems, which are not well suited for many-objective optimization. This paper proposes a surrogate-assisted many-objective evolutionary algorithm that uses an artificial neural network to predict the dominance relationship between candidate solutions and reference solutions instead of approximating the objective values separately. The uncertainty information in prediction is taken into account together with the dominance relationship to select promising solutions to be evaluated using the real objective functions. Our simulation results demonstrate that the proposed algorithm outperforms the state-of-the-art evolutionary algorithms on a set of many-objective optimization test problems.
Comparison of biodistribution profile of monoclonal antibodies nanoparticles and aptamers in rats with breast cancer (2016)

The use of monoclonal antibodies and aptamers is growing every single day, as the use of nanoparticle systems. Although most of the products are under investigation, there are a few commercialized products available at the market, for human consume. In this study, we have compared three formulations (aptamer anti-MUC1, monoclonal antibody – Trastuzumab and monoclonal antibodies nanoparticles – PLA/PVA/MMT trastuzumab) to identify their profile as also to understand their behavior into an alive biological system. In this direction the radiolabeling of the products were done and they were all tested in animals (in vivo) in two conditions: healthy rats and breast cancer induced animals. The results showed that the nanoparticle has the better biodistribution profile, followed by the aptamer. We conclude that more studies and a global effort to elucidate the biological behavior of drugs and especially nano-drugs are necessary.
10-MB/s multi-level programming of Gb-scale flash memory enabled by new AG-AND cell technology (2003)

This paper describes the first exhaustive study of a multi-level flash memory cell that achieves a programming throughput of over 10 MB/s. We reveal that increasing the individual cell programming speed (2 /spl mu/s), reducing the distribution in cell programming speeds (1.2 V), and reducing the inter-floating gate coupling to reduce Vth shift (0.15 V) are required. These three specifications are achieved by a new AG-AND cell technology consisting of self-aligned isolated punch-through stopper (SAIPTS) and U-shaped floating. This results in multilevel programming faster than 10 MB/s for the first time.
Small Pulmonary Nodules: Volumetrically Determined Growth Rates Based on CT Evaluation (2000)

CT volumetric measurements are highly accurate for determining volume and are useful in assessing growth of small nodules and calculating their doubling times.
The datacycle architecture for very high throughput database systems (1987)

The evolutionary trend toward a database-driven public communications network has motivated research into database architectures capable of executing thousands of transactions per second. In this paper we introduce the Datacycle architecture, an attempt to exploit the enormous transmission bandwidth of optical systems to permit the implementation of high throughput multiprocessor database systems. The architecture has the potential for unlimited query throughput, simplified data management, rapid execution of complex queries, and efficient concurrency control. We describe the logical operation of the architecture and discuss implementation issues in the context of a prototype system currently under construction.
Quantitation of glycolysis and skeletal muscle glycogen synthesis in humans (1993)

We measured the net rates of skeletal muscle glycogen synthesis and glycolysis (conversion of [3-3H]glucose to 3H2O) in healthy overnight-fasted volunteers. Two studies were performed. In study 1, seven subjects participated in two paired infusions under basal conditions of either [2-3H]glucose (H2) or [3-3H]glucose (H3). Total glucose uptake (Rd) and rates of whole body 3H2O formation (3H2O Ra) were measured. With H2, Rd and 3H2O Ra were similar. With H3, 3H2O Ra, equal to glycolysis, was 65% of Rd. In study 2, six different subjects underwent a 3-h, 40 mU.m-2 x min-1 euglycemic insulin clamp. [6,6-2H2]glucose was infused throughout and H3 was infused during the last hour of the study. Open muscle biopsies were obtained at 150 and 180 min. Glycogen synthesis was assessed by three independent means: 1) direct measurement, as 3H disintegrations per minute in isolated muscle glycogen per plasma H3 specific activity; 2) extrapolation from the activity of glycogen synthase assayed in the presence of the concentrations of glucose 6-phosphate and UDP-glucose measured in the biopsy; and 3) the difference between Rd and glycolysis. Despite a wide range in Rd [24.5-58.8 mumol.kg fat-free mass (FFM)-1 x min-1] and glycolysis (14.2-26.1), the three methods yielded similar results of 20.0 +/- 3.9, 22.5 +/- 3.7, and 20.6 +/- 3.7 mumol.kg FFM-1 x min-1 and correlated highly with each other (r2 = 0.92-0.96). Our results (study 1) indicate that the rate of plasma tritiated water formation reflects the intracellular detritiation of tritiated glucose. Under hyperinsulinemic conditions (study 2) the net rate of muscle glycogen synthesis can be accurately estimated from the glycogen synthase activity and from the difference between total glucose uptake and glycolysis. Thus, at high physiological plasma insulin concentrations resulting in submaximal stimulation of muscle glycogen synthesis, the latter can be accurately measured in humans.
Mechanism of Cyclization of Pyridine Nucleotides by Bovine Spleen NAD+ Glycohydrolase (1996)

We have shown that bovine spleen NAD+ glycohydrolase (EC), purified to homogeneity, is a multifunctional enzyme. A time-dependent formation of cADPR from NAD+ that did not exceed 1.5-2% of the reaction products was measurable. The cyclase activity of this enzyme was, however, best evidenced by its transformation of NGD+ into cyclic GDP-ribose (cGDPR). The formation of the cyclic compound could be monitored spectroscopically (UV and fluorescence) and by high-performance liquid chromatography; the product ratio of cGDPR/GDP-ribose was 2:1. Bovine spleen NAD+ glycohydrolase is also able to hydrolyze cADPR (Muller-Steffner et al. (1994) Biochem. Biophys. Res. Commun. 204, 1279-1285); the kinetic parameters (V/Km) measured exclude, however, the possibility that cADPR is a kinetically competent reaction intermediate in the transformation of NAD+ into ADP-ribose. Experimental data indicating that NAD+ glycohydrolase-catalyzed hydrolysis and methanolysis of NA(G)D+ occurred at the expense of the formation of the cyclic compounds are in favor of a reaction mechanism involving the partitioning of a common oxocarbenium reaction intermediate between the different acceptors. Thus E.A(G)DP-ribosyl oxocarbenium intermediate can react according to i) intramolecular processes with the positions N-1 of adenine and N-7 of guanine to give cA(G)DPR as reaction products, and ii) intermolecular reactions with water (formation of A(G)DP-ribose) and methanol (formation of methyl A(G)DP-ribose). We attribute the marked difference in yield of cADPR and cGDPR to the intrinsic reactivity (nucleophilicity and positioning) of the purine N-positions that are involved in the cyclization reactions within the E.A(G)DP-ribosyl oxocarbenium complexes.
DNA Immunization of Newborn Mice with a Plasmid-Expressing Nucleoprotein of Influenza Virus (1996)

Lower responsiveness and higher susceptibility to tolerance are the two main characteristics of neonatal immunity that limit the efficacy of conventional vaccines administered during this period. Based on the fact that DNA immunization of adult organisms is able to generate protective immune responses, we investigated the ability of a plasmid-(NPV1) encoding nucleoprotein (NP) of A/PR8/34 strain of influenza virus to generate a cellular immune response following intramuscular delivery in neonates. Newborn mice immunized with NPV1 plasmid developed significant cytotoxic immunity, comparable to the immune response displayed by adult mice injected with the same dose of plasmid. Furthermore, mice infected with influenza virus 1 month after completion of immunization showed a significant decrease of virus lung titer between day 3 and 7 after challenge, consistent with the protectivity conferred by specific cytotoxic immunity. Thus, mice immunized as neonates with NPV1 plasmid developed a protective cellular immune response, like the adult mice. Therefore, the strategy of DNA immunization may be considered for the purpose of human vaccination to prevent horizontally and vertically transmitted life-threatening infections in infants or children.
Asymmetric Aldol Reactions Using (S,S)-(+)-Pseudoephedrine-Based Amides:  Stereoselective Synthesis of α-Methyl-β-hydroxy Acids, Esters, Ketones, and 1,3-Syn and 1,3-Anti Diols (2000)

A very efficient method for performing stereoselective aldol reactions is reported. The reaction of (S, S)-(+)-pseudoephedrine-derived propionamide enolates with several aldehydes yielded exclusively one of the four possible diastereomers in good yields, although transmetalation of the firstly generated lithium enolate with a zirconium(II) salt, prior to the addition of the aldehyde, is necessary in order to achieve high syn selectivity. The so-formed syn-alpha-methyl-beta-hydroxy amides were transformed into other valuable chiral nonracemic synthons such as alpha-methyl-beta-hydroxyacids, esters, and ketones. Finally, a stereocontrolled reduction procedure starting from the so-obtained alpha-methyl-beta-hydroxy ketones has been developed allowing the synthesis of either 1,3-syn- or 1,3-anti-alpha-methyl-1,3-diols in almost enantiopure form by choosing the appropriate reaction conditions.
Pel, the protein that permits lambda DNA penetration of Escherichia coli, is encoded by a gene in ptsM and is required for mannose utilization by the phosphotransferase system. (1986)

Mannose uptake and phosphorylation in Escherichia coli is catalyzed by the phosphoenolpyruvate:glycose phosphotransferase system (PTS). The mannose-specific complex of the PTS, designated IIMan, comprises lipid and two membrane proteins, II-AMan and II-BMan. The proteins are encoded by ptsM, located at approximately equal to 40 minutes on the E. coli chromosome. A different genetic marker, pel, maps with ptsM, and is required for lambda DNA penetration of the cytoplasmic membrane. Earlier studies suggested that both pel function and II-BMan are encoded by the same gene, while a different gene (also in ptsM) encodes II-AMan. In the present studies, a ptsM clone, pCS13, was isolated from an E. coli HindIII gene bank in pBR322 and restored both mannose termentation and pel+ function to ptsM mutants defective in II-BMan. Subclones of pCS13 show that two distinct genes, manY and manZ, encode the pel+ function and the II-BMan protein, respectively; each gene may have its own promoter; whereas the protein encoded by manY (Pel) alone seems sufficient for lambda sensitivity, all three gene products are required for mannose fermentation, transport of the mannose analogue 2-deoxyglucose, and phosphorylation of the latter by cytoplasmic membranes. Thus, Pel is required for function of the IIMan complex. The efficiency of the complex may depend on the ratio of Pel to IIMan.