gebhart/patrepeval huggingface dataset:
Purification and Characterization of Two Isoenzymes of DL-Glycerol-3-phosphatase from Saccharomyces cerevisiae (1996)

The existence of specific dl-glycerol-3-phosphatase (EC 3.1.3.21) activity in extracts of Saccharomyces cerevisiae was confirmed by examining strains lacking nonspecific acid and alkaline phosphatase activities. During purification of the glycerol-3-phosphatase, two isozymes having very similar molecular weights were isolated by gel filtration and anion exchange chromatography. By microsequencing of trypsin-generated peptides the corresponding genes were identified as previously sequenced open reading frames of unknown function. The two genes, GPP1 (YIL053W) and GPP2 (YER062C) encode proteins that show 95% amino acid identity and have molecular masses of 30.4 and 27.8 kDa, respectively. The intracellular concentration of Gpp2p increases in cells subjected to osmotic stress, while the production of Gpp1p is unaffected by changes of external osmolarity. Both isoforms have a high specificity for dl-glycerol-3-phosphate, pH optima at 6.5, and KmG3P in the range of 3-4 mM. The osmotic induction of Gpp2p is blocked in cells that are defective in the HOG-mitogen-activated protein kinase pathway, indicating that GPP2 is a target gene for this osmosensing signal transduction pathway. Together with DOG1 and DOG2, encoding two highly homologous enzymes that dephosphorylate 2-deoxyglucose-6-phosphate, GPP1 and GPP2 constitute a new family of genes for low molecular weight phosphatases.
Cancer cachexia prevention via physical exercise: molecular mechanisms (2012)

Cancer cachexia is a debilitating consequence of disease progression, characterised by the significant weight loss through the catabolism of both skeletal muscle and adipose tissue, leading to a reduced mobility and muscle function, fatigue, impaired quality of life and ultimately death occurring with 25-30 % total body weight loss. Degradation of proteins and decreased protein synthesis contributes to catabolism of skeletal muscle, while the loss of adipose tissue results mainly from enhanced lipolysis. These mechanisms appear to be at least, in part, mediated by systemic inflammation. Exercise, by virtue of its anti-inflammatory effect, is shown to be effective at counteracting the muscle catabolism by increasing protein synthesis and reducing protein degradation, thus successfully improving muscle strength, physical function and quality of life in patients with non-cancer-related cachexia. Therefore, by implementing appropriate exercise interventions upon diagnosis and at various stages of treatment, it may be possible to reverse protein degradation, while increasing protein synthesis and lean body mass, thus counteracting the wasting seen in cachexia.
Synthesis and central nervous system depressant activity of new piperazine derivatives and related compounds. II (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and central nervous system depressant activity of new piperazine derivatives and related compounds. IID. J. Vadodaria, Chimanlal V. Deliwala, S. S. Mandrekar, and U. K. ShethCite this: J. Med. Chem. 1969, 12, 5, 860–865Publication Date (Print):September 1, 1969Publication History Published online1 May 2002Published inissue 1 September 1969https://pubs.acs.org/doi/10.1021/jm00305a033https://doi.org/10.1021/jm00305a033research-articleACS PublicationsRequest reuse permissionsArticle Views99Altmetric-Citations17LEARN 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
Molecular cloning of the gene for the yeast homolog (ACB) of diazepam binding inhibitor/endozepine/acyl-CoA-binding protein. (1992)

Diazepam binding inhibitor (DBI)/endozepine (EP)/acyl-CoA-binding protein (ACBP) is a small, highly conserved protein which has been independently isolated and characterized from different species using several different biological systems. To further investigate the structural and functional properties of this protein, we have cloned the homologous gene for DBI/EP/ACBP from the budding yeast Saccharomyces cerevisiae. The yeast gene contains no introns and encodes a polypeptide of 87 amino acids (including the initiating methionine), identical in length to the human gene product with 48% conservation of amino acid residues. The most highly conserved domain consists of 7 contiguous residues which are identical in all known protein species from yeast, birds, and mammals. This domain has previously been shown to constitute the hydrophobic binding site on DBI/EP/ACBP for acyl-CoA esters and is located within the second helical region of the molecule. Major and minor mRNA species of approximately 520 and 740 nucleotides, respectively, were detected in exponentially growing yeast. Sequences similar to those implicated in the regulation of fatty acid synthesis and beta-oxidation in yeast were detected in the promoter region of the gene. The presence of a highly conserved DBI/EP/ACBP gene in a primitive organism such as yeast provides support for the basic biological role of DBI/EP/ACBP as an acyl-CoA-binding protein and suggests that many of the biological functions attributed to it in higher organisms may result from its ability to interact with acyl-CoA. Hence, we have designated the yeast gene as ACB, for acyl-CoA-binding protein.
Solid-State Photodecarbonylation of Diphenylcyclopropenone:  A Quantum Chain Process Made Possible by Ultrafast Energy Transfer (2008)

It has been reported that electronic excitation of diphenylcyclopropenone (DPCP) into the second excited state (S2) results in an adiabatic ring-opening process within 200 fs to give an excited product with a lifetime of ca. 8 ps in S2. Knowing that energy transfer in crystals may occur within 1−2 ps, we recognized that the conditions could be right for a quantum chain process with the excited-state product sensitizing a neighboring ground-state reactant to set up a domino effect. In agreement with that, we discovered that excitation or macroscopic crystals result in a remarkably efficient reaction to give diphenylacetylene as a polycrystalline powder by a process that releases a great deal of mechanical energy. By taking advantage of nanocrystalline suspensions and using dicumyl ketone as an internal actinometer and after accounting for differences in absorbance at the irradiation wavelength, we were able to establish that the quantum yield of the reaction for DPCP was ΦDPCP = 3.30 ± 0.35, which is well above unity and consistent with a remarkable quantum chain process.
Microanalysis of enzyme digests of hyaluronan and chondroitin/dermatan sulfate by fluorophore-assisted carbohydrate electrophoresis (FACE) (2000)

Hyaluronan and chondroitin/dermatan sulfate are glycosaminoglycans that play major roles in the biomechanical properties of a wide variety of tissues, including cartilage. A chondroitin/dermatan sulfate chain can be divided into three regions: (1) a single linkage region oligosaccharide, through which the chain is attached to its proteoglycan core protein, (2) numerous internal repeat disaccharides, which comprise the bulk of the chain, and (3) a single nonreducing terminal saccharide structure. Each of these regions of a chondroitin/dermatan sulfate chain has its own level of microheterogeneity of structure, which varies with proteoglycan class, tissue source, species, and pathology. We have developed rapid, simple, and sensitive protocols for detection, characterization and quantitation of the saccharide structures from the internal disaccharide and nonreducing terminal regions of hyaluronan and chondroitin/dermatan sulfate chains. These protocols rely on the generation of saccharide structures with free reducing groups by specific enzymatic treatments (hyaluronidase/chondroitinase) which are then quantitatively tagged though their free reducing groups with the fluorescent reporter, 2-aminoacridone. These saccharide structures are further characterized by modification through additional enzymatic (sulfatase) or chemical (mercuric ion) treatments. After separation by fluorophore-assisted carbohydrate electrophoresis, the relative fluorescence in each band is quantitated with a cooled, charge-coupled device camera for analysis. Specifically, the digestion products identified are (1) unsaturated internal Deltadisaccharides including DeltaDiHA, DeltaDi0S, DeltaDi2S, DeltaDi4S, DeltaDi6S, DeltaDi2,4S, DeltaDi2,6S, DeltaDi4,6S, and DeltaDi2,4,6S; (2) saturated nonreducing terminal disaccharides including DiHA, Di0S, Di4S and Di6S; and (3) nonreducing terminal hexosamines including glcNAc, galNAc, 4S-galNAc, 6S-galNAc, and 4, 6S-galNAc.
Complement and Kidney Disease (2006)

Complement and kidney disease , Complement and kidney disease , کتابخانه دیجیتال جندی شاپور اهواز
Second-strand synthesis is a rate-limiting step for efficient transduction by recombinant adeno-associated virus vectors (1996)

The ability of recombinant adeno-associated virus (AAV) to transduce cells with a marker gene in vitro was found to be substantially increased by the presence of adenovirus. Transfection experiments with adenovirus genomic DNA suggest that this increase is not facilitated by adenovirus-mediated viral uptake but is instead dependent on adenovirus gene expression. Using various adenovirus mutants, we were able to map this function to early-region E4 open reading frame 6. Plasmid expression of open reading frame 6 protein in cells infected with recombinant AAV increased transduction between 100- and 1,000-fold. The increase in transduction was not dependent on the recombinant AAV gene cassette but instead appeared to involve an immediate early step of the AAV life cycle. Chemical and physical agents that have been shown to induce helper-free replication of wild-type AAV were also able to stimulate recombinant AAV transduction, suggesting that the phenomenon might affect AAV DNA replication. Further experiments showed that viral uncoating was not affected and that the rate-limiting step involved synthesis of a second strand on the single-stranded genomic AAV DNA. These data suggest that the adenovirus E4 region, as well as chemical and physical agents, can play an essential role in an immediate-early step of the AAV life cycle, specifically in second-strand synthesis, and have important implications for the use of AAV vectors in gene therapy protocols.
An integrated PC-based characterization system for optical waveguides (1995)

This paper reports an automatic instrument developed for characterization of optical waveguides. A specially designed waveguide excitation unit offers a flexible platform for measurement of optical waveguide characteristics like number of propagating modes, mode field intensity distribution, the refractive index profiles, waveguide geometry, attenuation, and dispersion. Further, the availability of attachments like filters, polarizers, chopper, intensity profiler, and CCD camera make the instrument flexible enough for a variety of other experiments also. The instrument is PC controlled and assisted by user friendly menu-driven software. A large number of waveguides have been analyzed using the setup. These results are also presented in the paper.
The 19 S Proteasomal Subunit POH1 Contributes to the Regulation of c-Jun Ubiquitination, Stability, and Subcellular Localization (2006)

The AP1 (activator protein 1) transcription factor, c-Jun, is an important regulator of cell proliferation, differentiation, survival, and death. Its activity is regulated both at the level of transcription and post-translationally through phosphorylation, sumoylation, and targeted degradation. The degradation of c-Jun by the ubiquitin proteasome pathway has been well established. Here, we report that POH1, a subunit of the 19 S proteasome lid with a recently described deubiquitinase activity, is a regulator of c-Jun. Ectopic expression of POH1 in HEK293 cells decreased the level of c-Jun ubiquitination, leading to significant accumulation of the protein and a corresponding increase in AP1-mediated gene expression. The stabilization also correlated with a redistribution of c-Jun in the nucleus. These effects were reduced by mutation of a cysteine residue in the Mpr1 pad1 N-terminal plus motif of POH1 (Cys-120) and appeared to be selective for c-Jun, because POH1 had no effect on other proteasomal substrates. Our results identify a novel mechanism of c-Jun regulation in mammalian cells.
A review of polymers as multifunctional excipients in drug dosage form technology (2015)

In the article, groups of multifunctional polymers used in drug dosage form technology were classified and evaluated. These compounds, in addition to their basic function as excipients, may have additional properties, e.g. stimuli sensitivity, enzyme inhibition, intestinal epithelium penetration enhancement, efflux pump inhibition, taste-masking, pharmacological activity and the ability to interact with enzymes responsible for drug metabolism. While classifying specific groups of multifunctional polymers, special emphasis was placed on the advantages of using them when designing new drug. Such advantages include, i.a., increasing substance bioavailability, improving substance stability during formulation and the possibility of obtaining forms of controlled or localized release to a specific site in the organism.
Expression of NAD(P)H: quinone oxidoreductase and glutathione S-transferases α and π in human renal cell carcinoma and in kidney cancer-derived cell lines (1994)

NAD(P)H:quinone oxidoreductase (NQOR) and glutathione S-transferases (GST) are enzymes of interest in cell defence and drug resistance. Relative levels of NQOR mRNA in renal cell carcinomas were 28 +/- 24% (n = 21) of those in non-neoplastic tissue and the enzyme activity decreased from 41 +/- 39 to 18 +/- 27 mU/mg protein (n = 23). In three of the cases, there was no measurable NQOR enzyme activity at all, indicating a polymorphism in the population for this gene. Relative GST-alpha mRNA levels in the tumours were on average 6 +/- 6% (n = 22) of the control value, whereas for GST-pi mRNA smaller decreases as well as increases were found in the tumours as compared to control tissue, but, on average, the level remained unchanged. Overall GST activity measured with CDNB as a substrate was 152 +/- 157 mU/mg protein in tumour tissue and 342 +/- 177 mU/mg protein in non-neoplastic tissue (n = 23). In all kidney tumour-derived cell lines NQOR mRNA was strongly expressed and on a per protein basis NQOR activity was about 10-fold higher than in the kidney tumour samples. GST-pi but not GST-alpha mRNA was also present. Total GST enzyme activities in these cell lines were similar to those in kidney tumour samples. HepG2 cells exhibited expression of NQOR and GST-alpha; GST-pi was not detectable. NQOR activity in HepG2 was about four-fold higher than in kidney-derived cell lines. Thus, NQOR and GST-alpha are both down-regulated in renal carcinoma, but their expression diverges in carcinoma cell lines.
8,16,24,32,40,48-Hexamethoxy[2.6]metacyclophane-1,9,17,25,33,41-hexayne: a novel near-planar ammonium-selective ionophore (2001)

The titled cyclophane (cyclic [6]metaphenylacetylene) with six methoxy groups inside the cavity has a nearly planar carbon framework, forms open-channel structures in the crystal, and exhibits an ammonium-selective ionophoric property in spite of the considerably large cavity.
Rheology of Milk Protein Gels and Protein-Stabilized Emulsion Gels Cross-Linked with Transglutaminase (1996)

Oscillatory shear measurements have been used to investigate the rheological properties of enzymically cross-linked milk protein gels at neutral pH with and without emulsion droplets. A Ca2+-independent transglutaminase extracted from microorganisms was used as the enzyme source. Storage and loss moduli are presented for gels formed from enzyme-treated β-lactoglobulin solutions (13 and 14 wt % protein) and β-lactoglobulin-stabilized emulsions (7−9 wt % protein, 32.5 wt % oil). The frequency dependence of the small-deformation elastic moduli of the enzyme-treated gels is weaker than for the equivalent heat-set β-lactoglobulin gels (90 °C for 30 min), and the strain dependence of the elastic moduli of the enzyme-treated gels is of opposite sign to that of the heat-set gels at large deformations. These differences in rheological behavior are consistent with a network consisting of permanent covalent cross-links for the enzyme-induced gels and predominantly physical cross-links for the heat-set gels. Thermal processing after enzyme treatment is very effective in making a strong gel from either a β-lactoglobulin solution or a β-lactoglobulin-stabilized emulsion. Lecithin addition to the β-lactoglobulin-stabilized emulsion gel before enzyme treatment was found to have a weakly positive effect on the gel strength arising from lecithin−protein complexation. When β-lactoglobulin was replaced with sodium caseinate, the rate and extent of enzyme-induced cross-linking was found to increase substantially. Keywords: Emulsion gel; transglutaminase; β-lactoglobulin; sodium caseinate; enzymic cross-linking; thermal denaturation; rheology; lecithin−protein interaction
DNA Block Copolymer Micelles – A Combinatorial Tool for Cancer Nanotechnology (2008)

A novel micelle platform consisting of amphiphilic DNA block copolymers is introduced for chemotherapeutic drug delivery, allowing combinatorial testing of the drug carrier system. Oligodeoxynucleotide modified targeting units are “clicked” into the micelle corona by hybridization, allowing perfect control of surface functionalities of the nanoparticle system. Cancer cells are efficiently killed when targeting units and chemotherapeutic act together within the DNA block copolymer aggregates. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2008/c0866_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Layered shortest path (LASH) routing in irregular system area networks (2002)

In recent years we have seen a growing interest in irregular network topologies for cluster interconnects. One problem related to such topologies is that the combination of shortest path and deadlock free routing is difficult. As a result of this the existing solutions for routing in irregular networks either guarantee shortest paths relative to some constraint (like up*/down*), or have to resort to deadlock recovery through non-minimal escape channels. In this paper we propose a method that guarantees shortest path routing and in-order delivery, and that uses virtual channels for deadlock avoidance. We present a theoretical upper bound on the number of virtual channels needed, and through extensive empirical testing we demonstrate that the actual number of virtual channels is very low even for large networks.
The current state of PDC bit technology (2010)

Part 1 of 3: Development and application of polycrystalline diamond compact bits have overcome complex challenges from the difficulty of reliably mounting PDC cutters in bit bodies to accelerated thermal wear.
Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma (2009)

Mass spectrometry-based multiple reaction monitoring (MRM) quantitation of proteins can dramatically impact the discovery and quantitation of biomarkers via rapid, targeted, multiplexed protein expression profiling of clinical samples. A mixture of 45 peptide standards, easily adaptable to common plasma proteomics work flows, was created to permit absolute quantitation of 45 endogenous proteins in human plasma trypsin digests. All experiments were performed on simple tryptic digests of human EDTA-plasma without prior affinity depletion or enrichment. Stable isotope-labeled standard peptides were added immediately following tryptic digestion because addition of stable isotope-labeled standard peptides prior to trypsin digestion was found to generate elevated and unpredictable results. Proteotypic tryptic peptides containing isotopically coded amino acids ([(13)C(6)]Arg or [(13)C(6)]Lys) were synthesized for all 45 proteins. Peptide purity was assessed by capillary zone electrophoresis, and the peptide quantity was determined by amino acid analysis. For maximum sensitivity and specificity, instrumental parameters were empirically determined to generate the most abundant precursor ions and y ion fragments. Concentrations of individual peptide standards in the mixture were optimized to approximate endogenous concentrations of analytes and to ensure the maximum linear dynamic range of the MRM assays. Excellent linear responses (r > 0.99) were obtained for 43 of the 45 proteins with attomole level limits of quantitation (<20% coefficient of variation) for 27 of the 45 proteins. Analytical precision for 44 of the 45 assays varied by <10%. LC-MRM/MS analyses performed on 3 different days on different batches of plasma trypsin digests resulted in coefficients of variation of <20% for 42 of the 45 assays. Concentrations for 39 of the 45 proteins are within a factor of 2 of reported literature values. This mixture of internal standards has many uses and can be applied to the characterization of trypsin digestion kinetics and plasma protein expression profiling because 31 of the 45 proteins are putative biomarkers of cardiovascular disease.
DynGEM: Deep Embedding Method for Dynamic Graphs (2018)

Embedding large graphs in low dimensional spaces has recently attracted significant interest due to its wide applications such as graph visualization, link prediction and node classification. Existing methods focus on computing the embedding for static graphs. However, many graphs in practical applications are dynamic and evolve constantly over time. Naively applying existing embedding algorithms to each snapshot of dynamic graphs independently usually leads to unsatisfactory performance in terms of stability, flexibility and efficiency. In this work, we present an efficient algorithm DynGEM based on recent advances in deep autoencoders for graph embeddings, to address this problem. The major advantages of DynGEM include: (1) the embedding is stable over time, (2) it can handle growing dynamic graphs, and (3) it has better running time than using static embedding methods on each snapshot of a dynamic graph. We test DynGEM on a variety of tasks including graph visualization, graph reconstruction, link prediction and anomaly detection (on both synthetic and real datasets). Experimental results demonstrate the superior stability and scalability of our approach.