gebhart/patrepeval huggingface dataset:
Reconstruction and Functional Characterization of the Human Mitochondrial Metabolic Network Based on Proteomic and Biochemical Data (2004)

Diverse datasets including genomic, proteomic, isotopomer, and DNA sequence variation are becoming available for human mitochondria. Thus there is a need to integrate these data within an in silico modeling framework where mitochondrial biology and related disorders can be studied and analyzed. This paper reports a reconstruction and characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. The 189 reactions included in this reconstruction are both elementally and charge-balanced and are assigned to their respective cellular compartments (mitochondrial, cytosol, or extracellular). The capabilities of the reconstructed network to fulfill three metabolic functions (ATP production, heme synthesis, and mixed phospholipid synthesis) were determined. Network-based analysis of the mitochondrial energy conversion process showed that the overall ATP yield per glucose is 31.5. Network flexibility, characterized by allowable variation in reaction fluxes, was evaluated using flux variability analysis and analysis of all of the possible optimal flux distributions. Results showed that the network has high flexibility for the biosynthesis of heme and phospholipids but modest flexibility for maximal ATP production. A subset of all of the optimal network flux distributions, computed with respect to the three metabolic functions individually, was found to be highly correlated, suggesting that this set may contain physiological meaningful fluxes. Examinations of optimal flux distributions also identified correlated reaction sets that form functional modules in the network.
Isolation and characterization of recombinant mitochondrial 4-aminobutyrate aminotransferase. (1993)

4-Aminobutyrate aminotransferase, which catalyzes the conversion of 4-aminobutyrate to succinic semialdehyde, is a key enzyme of the 4-aminobutyrate shunt. The amino acid sequence predicted from the cDNA sequence shows that the precursor protein consists of the mature enzyme of 473 amino acid residues and an amino-terminal segment of 27 amino acids (Kwon, O. S., Park, J., and Churchich, J. E. (1992) J. Biol. Chem. 267, 7215-7216). A recombinant 4-aminobutyrate aminotransferase has been expressed in Escherichia coli using pETIId as expression vector. The protein has been purified and characterized as a dimer (2 x 55 kDa). NH2-terminal sequence analysis has revealed the presence of an extra amino-terminal segment (signal peptide) predicted from the cDNA sequence. The isolated precursor of 4-aminobutyrate aminotransferase contains pyridoxal 5-phosphate and exhibits catalytic activity (18 units/mg) comparable to that of the mature enzyme (20 units/mg). The presequence peptide of the precursor of mitochondrial 4-aminobutyrate aminotransferase does not interfere with the folding and functional properties of the mature moiety of the aminotransferase.
MicroRNAs 125a and 455 Repress Lipoprotein-Supported Steroidogenesis by Targeting Scavenger Receptor Class B Type I in Steroidogenic Cells (2012)

We sought to identify and characterize microRNA (miRNAs) that posttranscriptionally regulate the expression of scavenger receptor class B type I (SR-BI) and SR-BI-linked selective high-density lipoprotein (HDL) cholesteryl ester (CE) transport and steroidogenesis. Four miRNAs (miRNA-125a, miRNA-125b, miRNA-145, and miRNA-455) with a potential to regulate SR-BI were identified in silico and validated by quantitative real-time PCR (qRT-PCR), Western blot analysis, and SR-BI 3' untranslated region (UTR) reporter assays. In vitro treatment of primary rat granulosa cells and MLTC-1 cells with cyclic AMP (cAMP) or in vivo treatment of rat adrenals with adrenocorticotropic hormone (ACTH) decreased the expression of miRNA-125a, miRNA-125b, and miRNA-455 and reciprocally increased SR-BI expression. Using luciferase constructs containing the 3' untranslated region of SR-BI combined with miRNA overexpression and mutagenesis, we have provided evidence that steroidogenic SR-BI is a direct target of miRNA-125a and miRNA-455. Moreover, the transfection of Leydig tumor cells with precursor miRNA 125a (pre-miRNA-125a) or pre-miRNA-455 resulted in the suppression of SR-BI at both the transcript and protein levels and reduced selective HDL CE uptake and HDL-stimulated progesterone production. Transfection of liver Hepa 1-6 cells with pre-miRNA-125a significantly reduced SR-BI expression and its selective transport function. In contrast, overexpression of miRNA-145 did not affect SR-BI expression or selective HDL CE uptake mediated by SR-BI in steroidogenic cell lines. These data suggest that a trophic hormone and cAMP inversely regulate the expression of SR-BI and miRNA-125a and miRNA-455 in steroidogenic tissues/cells and that both miRNA-125a and miRNA-455, by targeting steroidogenic SR-BI, negatively regulate selective HDL CE uptake and HDL CE-supported steroid hormone production.
Identification of a common gene signature for type II cytokine–associated myeloid cells elicited in vivo in different pathologic conditions (2006)

Compared with type I cytokine-associated myeloid (M1) cells, the molecular repertoire and mechanisms underlying functional properties of type II cytokine-associated myeloid (M2) cells are poorly characterized. Moreover, most studies have been limited to in vitro-elicited M2 cells. Here, comparative gene expression profiling of M1 and M2 cells, elicited in murine models of parasitic infections and cancer, yielded a common signature for in vivo-induced M2 populations independent of disease model, mouse strain, and organ source of cells. Some of these genes, such as cadherin-1, selenoprotein P, platelet-activating factor acetylhydrolase, and prosaposin, had not been documented as associated with M2. Overall, the common signature genes provide a molecular basis for a number of documented or suggested properties of M2, including immunomodulation, down-regulation of inflammation, protection against oxidative damage, high capacity for phagocytosis, and tissue repair. Interestingly, several common M2 signature genes encode membrane-associated markers that could be useful for the identification and isolation of M2. Some of these genes were not induced by IL-4/IL-13 or IL-10 under various in vitro settings and thus were missed in approaches based on in vitro-activated cells, validating our choice of in vivo models for expression profiling of myeloid cells.
Dynamic modeling and control of hybrid electric vehicle powertrain systems (1998)

This paper describes the mathematical modeling, analysis, and simulation of a dynamic automatic manual layshaft transmission and dry clutch combination powertrain model, and corresponding coordinated control laws synthesized using a conventional SI ICE powerplant-alternator combination, a dry clutch and manual transmission/differential, variable field alternator, brakes, and complete vehicle longitudinal dynamics with tire-road interface characterization. The conventional power train model is validated using experimental test data confirming accurate emulation of dynamic components of the pre-hybridized vehicle. In addition, the development of dynamic series and parallel hybrid electric vehicle (HEV) powertrain models and corresponding coordinated control laws are described. A discussion of the key issues associated with coordinated control law development is provided. Simulations of the dynamic behavior of two types of series HEVs are shown.
An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations (2020)

Multisystem Inflammatory Syndrome in Children (MIS-C) associated with Coronavirus Disease 2019 (COVID-19) is a newly recognized condition in which children with recent SARS-CoV-2 infection present with a constellation of symptoms including hypotension, multiorgan involvement, and elevated inflammatory markers. These symptoms and the associated laboratory values strongly resemble toxic shock syndrome, an escalation of the cytotoxic adaptive immune response triggered upon the binding of pathogenic superantigens to MHCII molecules and T cell receptors (TCRs). Here, we used structure-based computational models to demonstrate that the SARS-CoV-2 spike (S) exhibits a high-affinity motif for binding TCR, interacting closely with both the α- and β-chains variable domains' complementarity-determining regions. The binding epitope on S harbors a sequence motif unique to SARS-CoV-2 (not present in any other SARS coronavirus), which is highly similar in both sequence and structure to bacterial superantigens. Further examination revealed that this interaction between the virus and human T cells is strengthened in the context of a recently reported rare mutation (D839Y/N/E) from a European strain of SARS-CoV-2. Furthermore, the interfacial region includes selected residues from a motif shared between the SARS viruses from the 2003 and 2019 pandemics, which has intracellular adhesion molecule (ICAM)-like character. These data suggest that the SARS-CoV-2 S may act as a superantigen to drive the development of MIS-C as well as cytokine storm in adult COVID-19 patients, with important implications for the development of therapeutic approaches.
Neue Therapieansätze bei Cystischer Fibrose (2008)

Abstract Cystische Fibrose ist mit einer Inzidenz von 1/2.500 bis 1/1.600 die häufigste autosomal‐rezessive Erbkrankheit in Mittel‐ und Nord‐Europa. Ungefähr jeder Zwanzigste ist Träger eines defekten Allels. Mutiert ist dabei das CFTR‐Gen ( Cystic Fibrosis Conductance Transmembrane Regulator ), das sich auf Chromosom 7 befindet.
Investigation of Electrochemically Mediated Atom Transfer Radical Polymerization (2013)

Electrochemically mediated atom transfer radical polymerization (eATRP) of n-butyl acrylate was systematically investigated using diminished catalyst concentrations (≤300 parts per million) under a variety of formulations and electrochemical conditions. Critical polymerization parameters, including the applied potential, catalyst concentration, and ligand, were explored and correlated with polymerization rates, polymer properties, and currents during the eATRP process. Additional electrochemical methods were explored to improve the feasibility of eATRP under galvanostatic conditions. Copper electrodeposition and stripping experimentation proved to be an effective strategy for catalyst recycling allowing sequential controlled polymerizations to be possible utilizing one catalyst charge.
Folding and Finding RNA Secondary Structure (2010)

Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed.
Stem cell differentiation requires a paracrine pathway in the heart (2002)

Members of the transforming growth factor beta1 (TGF-beta) superfamily--namely, TGF-beta and BMP2--applied to undifferentiated murine embryonic stem cells up-regulated mRNA of mesodermal (Brachyury) and cardiac specific transcription factors (Nkx2.5, MEF2C). Embryoid bodies generated from stem cells primed with these growth factors demonstrated an increased potential for cardiac differentiation with a significant increase in beating areas and enhanced myofibrillogenesis. In an environment of postmitotic cardiomyocytes, stem cells engineered to express a fluorescent protein under the control of a cardiac promoter differentiated into fluorescent ventricular myocytes beating in synchrony with host cells, a process significantly enhanced by TGF-beta or BMP2. In vitro, disruption of the TGF-beta/BMP signaling pathways by latency-associated peptide and/or noggin prevented differentiation of stem cells. In fact, only host cells that secrete a TGF-beta family member induced a cardiac phenotype in stem cells. In vivo, transplantation of stem cells into heart also resulted in cardiac differentiation provided that TGF-beta/BMP2 signaling was intact. In infarcted myocardium, grafted stem cells differentiated into functional cardiomyocytes integrated with surrounding tissue, improving contractile performance. Thus, embryonic stem cells are directed to differentiate into cardiomyocytes by signaling mediated through TGF-beta/BMP2, a cardiac paracrine pathway required for therapeutic benefit of stem cell transplantation in diseased heart.
Stabilizing GAN Training with Multiple Random Projections (2017)

Training generative adversarial networks is unstable in high-dimensions as the true data distribution tends to be concentrated in a small fraction of the ambient space. The discriminator is then quickly able to classify nearly all generated samples as fake, leaving the generator without meaningful gradients and causing it to deteriorate after a point in training. In this work, we propose training a single generator simultaneously against an array of discriminators, each of which looks at a different random low-dimensional projection of the data. Individual discriminators, now provided with restricted views of the input, are unable to reject generated samples perfectly and continue to provide meaningful gradients to the generator throughout training. Meanwhile, the generator learns to produce samples consistent with the full data distribution to satisfy all discriminators simultaneously. We demonstrate the practical utility of this approach experimentally, and show that it is able to produce image samples with higher quality than traditional training with a single discriminator.
Design, Synthesis, and Biological Evaluation of C9- and C2-Substituted Pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidines as New A2Aand A3Adenosine Receptors Antagonists (2003)

In the past few years, our group has been involved in the development of A(2A) and A(3) adenosine receptor antagonists which led to the synthesis of SCH58261 (5-amino-7-(2-phenylethyl)-2-(2-furyl)pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine, 61), potent and very selective at the A(2A) receptor subtype, and N(8)-substituted-pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidines-N(5)-urea or amide (MRE series, b), very selective at the human A(3) adenosine receptor subtype. We now describe a large series of C(9)- and C(2)-substituted pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidines to represent an extension of structure-activity relationship work on this class of tricyclic compounds. The introduction of a substituent at 9 position of the tricyclic antagonistic structure led to retention of receptor affinity but a loss of selectivity in respect to the lead compounds b, N(8)-substituted-pirazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidines-N(5)-urea or -amide. The substitution of the furanyl moiety of compound 61, necessary for receptor binding, with a phenyl or a substituted aromatic ring (compounds 5a-d, 6-8), caused a complete loss of the affinity at all the adenosine receptor subtypes, demonstrating that the furanyl ring is a necessary structural element to guarantee interaction with the adenosine receptor surface. The introduction of an ethoxy group at the ortho position of the aromatic ring to mimic the oxygen of the furan (compound 5c, 5-amino-7-(2-phenylethyl)-2-(2-ethoxyphenyl)pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine) did not enhance affinity. The introduction of the cycloaminomethyl function by Mannich reaction at the 5' position of the furanyl ring of 61 and the C(9)-substituted compound 41 (5-amino-8-methyl-9-methylsulfanyl-2-(2-furyl)-pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine) resulted in complete water solubility but a loss of receptor affinity. We can conclude that modifications or substitutions at the furanyl ring are not allowed and the introduction of a substituent at the 9-position of the core pyrazolo-triazolo-pyrimidine structure caused a severe loss of selectivity, probably due to an increased steric hindrance of the radical introduced.
γ-carboxyglutamate-containing proteins and the vitamin K-dependent carboxylase (1990)

Research Article| March 15 1990 γ-carboxyglutamate-containing proteins and the vitamin K-dependent carboxylase C Vermeer C Vermeer 1Department of Biochemistry, University of Limburg, P.O. Box 616, 6200 MD Maastricht, The Netherlands Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8728 Print ISSN: 0264-6021 © 1990 London: The Biochemical Society1990 Biochem J (1990) 266 (3): 625–636. https://doi.org/10.1042/bj2660625 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation C Vermeer; γ-carboxyglutamate-containing proteins and the vitamin K-dependent carboxylase. Biochem J 15 March 1990; 266 (3): 625–636. doi: https://doi.org/10.1042/bj2660625 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1990 London: The Biochemical Society1990 Article PDF first page preview Close Modal You do not currently have access to this content.
A tool to improve pre-selection for deep brain stimulation in patients with Parkinson’s disease (2010)

Determining the eligibility of patients with Parkinson's disease (PD) for deep brain stimulation (DBS) can be challenging for general (non-specialised) neurologists. We evaluated the use of an online screening tool (Stimulus) that aims to support appropriate referral to a specialised centre for the further evaluation of DBS. Implementation of the tool took place via an ongoing European multicentre educational programme, currently completed in 15 DBS centres with 208 referring neurologists. Use of the tool in daily practice was monitored via an online data capture programme. Selection decisions of patients referred with the assistance of the Stimulus tool were compared to those of patients outside the screening programme. Three years after the start of the programme, 3,128 patient profiles had been entered. The intention for referral was made for 802 patients and referral intentions were largely in accordance with the tool recommendations. Follow-up at 6 months showed that actual referral took place in only 28%, predominantly due to patients' reluctance to undergo brain surgery. In patients screened with the tool and referred to a DBS centre, the acceptance rate was 77%, significantly higher than that of the unscreened population (48%). The tool showed a sensitivity of 99% and a specificity of 12% with a positive and negative predictive value of 79 and 75%, respectively. The Stimulus tool is useful in assisting general neurologists to identify appropriate candidates for DBS consideration. The principal reason for not referring potentially eligible patients is their reluctance to undergo brain surgery.
Lymphocyte surface thiol levels (2003)

Recent studies have implicated reduced thiols (cysteine -SH) in the function of individual cell surface proteins. Studies presented here demonstrate that the overall level of reduced thiols on cell surface molecules differs on individual subsets of peripheral blood mononuclear cells and that these levels can be manipulated in vitro by altering the level of intracellular glutathione (iGSH). To quantitate cell surface thiols, we have developed a Hi-D (11-color) fluorescence-activated cell sorter method in which we covalently couple a fluorescent molecule, Alexa-maleimide, to free (reduced) -SH groups on proteins or other molecules exposed on the cell surface (exofacial membrane). In addition, to reveal changes in cell surface thiol levels in response to various in vitro treatments, we used a pair of fluorescent Alexa dyes with distinct excitation and emission spectra to stain the cells before and after treatments. These in vitro studies demonstrate that decreasing iGSH, by specifically inhibiting its synthesis, decreases cell surface molecule thiols (csm-SH) and that preventing loss of iGSH also prevents loss of csm-SH. However, examination of peripheral blood mononuclear cell subsets tested immediately after isolation from healthy or HIV-infected subjects failed to reveal a similar relationship between internal iGSH and csm-SH. Although there is a relatively wide variation between individuals in both csm-SH and iGSH, there is no correlation between median iGSH and csm-SH compared for 22 healthy and 36 HIV-infected subjects. Collectively, our findings indicate that local environment plays a greater role in determining the redox status of cell surface molecules than the internal redox status of the cells.
MeV energy ion implantation and its device applications in InP (2002)

MeV energy Si, S, Be, B, Fe, and Co implantations were performed in the energy range 0.4-20 MeV to obtain buried/thick n- or p- or high-resistance layers in InP. The first four range statistics have been established for these dopants in this energy range. Optimum annealing conditions have been established. Electron concentrations as high as 2 /spl times/ 10/sup 18/ cm/sup -3/ have been obtained. B, Fe, and Co implantations gave high resistivity layers. The usefulness of MeV implantation was demonstrated in the fabrication of vertical positive-intrinsic-negative (PIN) and varactor diodes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Real-Time Pattern Recognition Based Myoelectric Control Usability Study Implemented in a Virtual Environment (2007)

Pattern recognition based myoelectric control systems have been well researched; however very few systems have been implemented in a clinical environment. Although classification accuracy or classification error is the metric most often reported to describe how well these control systems perform, very little work research has been conducted to relate this measure to the usability of the system. This work presents a virtual clothespin usability test to assess the performance of pattern recognition based myoelectric control systems. The results suggest that users can complete the virtual task in reasonable time frames when using systems with high classification accuracies. Additionally, results indicate that a clinically-supported classifier training approach (inclusion of the transient potion of contraction signals) may reduce classification accuracy but increase real-time performance.