gebhart/patrepeval huggingface dataset:
Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae (2016)

Genome-scale metabolic models (GEMs) can be used to evaluate genotype-phenotype relationships and their application to microbial strain engineering is increasing in popularity. Some of the algorithms used to simulate the phenotypes of mutant strains require the determination of a wild-type flux distribution. However, the accuracy of this reference, when calculated with flux balance analysis, has not been studied in detail before. Here, the wild-type simulations of selected GEMs for <i>Saccharomyces cerevisiae</i> have been analysed and most of the models tested predicted erroneous fluxes in central pathways, especially in the pentose phosphate pathway. Since the problematic fluxes were mostly related to areas of the metabolism consuming or producing NADPH/NADH, we have manually curated all reactions including these cofactors by forcing the use of NADPH/NADP<sup>+</sup> in anabolic reactions and NADH/NAD<sup>+</sup> for catabolic reactions. The curated models predicted more accurate flux distributions and performed better in the simulation of mutant phenotypes.
Current Surgical Therapy (1992)

Current surgical therapy , Current surgical therapy , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
The development of packet data communications in the ISDN (1989)

As a circuit-switched network the ISDN inherently supports circuit-switched data services. But an increasing number of Information Technology applications involve short interactive transactions for which packet switching is the natural choice. Integrated access to packet mode services is therefore an important element of service integration in the ISDN. Following a brief historical perspective and review of the current arrangements and standards for supporting packet mode services in the ISDN, the authors discuss how packet mode services are likely to develop in the ISDN during the next few years, how these may be supported, and what the outstanding issues are. >
NMNAT1 inhibits axon degeneration via blockade of SARM1-mediated NAD+ depletion (2016)

Overexpression of the NAD<sup>+</sup> biosynthetic enzyme NMNAT1 leads to preservation of injured axons. While increased NAD<sup>+</sup> or decreased NMN levels are thought to be critical to this process, the mechanism(s) of this axon protection remain obscure. Using steady-state and flux analysis of NAD<sup>+</sup> metabolites in healthy and injured mouse dorsal root ganglion axons, we find that rather than altering NAD<sup>+</sup> synthesis, NMNAT1 instead blocks the injury-induced, SARM1-dependent NAD<sup>+</sup> consumption that is central to axon degeneration.
Nanoscale nuclear architecture for cancer diagnosis beyond pathology via spatial-domain low-coherence quantitative phase microscopy (2010)

Definitive diagnosis of malignancy is often challenging due to limited availability of human cell or tissue samples and morphological similarity with certain benign conditions. Our recently developed novel technology-spatial-domain low-coherence quantitative phase microscopy (SL-QPM)-overcomes the technical difficulties and enables us to obtain quantitative information about cell nuclear architectural characteristics with nanoscale sensitivity. We explore its ability to improve the identification of malignancy, especially in cytopathologically non-cancerous-appearing cells. We perform proof-of-concept experiments with an animal model of colorectal carcinogenesis-APC(Min) mouse model and human cytology specimens of colorectal cancer. We show the ability of in situ nanoscale nuclear architectural characteristics in identifying cancerous cells, especially in those labeled as "indeterminate or normal" by expert cytopathologists. Our approach is based on the quantitative analysis of the cell nucleus on the original cytology slides without additional processing, which can be readily applied in a conventional clinical setting. Our simple and practical optical microscopy technique may lead to the development of novel methods for early detection of cancer.
The Impact of Leachate Recirculation On Municipal Solid Waste Landfill Operating Characteristics (1996)

Landfill bioreactor technology offers important advantages in the management and treatment of municipal solid waste, including accelerated waste stabilization rates, enhanced gas production, facilitated leachate management, volume reduction and minimized long-term liability. These advantages have been documented in laboratory-, pilot- and full-scale investigations. Although challenges remain in implementing the technology, bioreactor landfills are designed and operated with increasing frequency. © 1996 ISWA
Lipopolysaccharide modulates cyclooxygenase-2 transcriptionally and posttranscriptionally in human macrophages independently from endogenous IL-1 beta and TNF-alpha. (1999)

The pathogenesis of septicemia can be triggered by LPS, a potent stimulus for PG synthesis. The enzyme cyclooxygenase (COX) is a rate-limiting step in PG production. COX exists as two isoforms: COX-1, which is constitutively expressed in most cell types, and COX-2, which is inducible by LPS and cytokines in a variety of cells. In this study we determined the role of the proinflammatory cytokines IL-1 beta and TNF-alpha released by LPS-stimulated U937 human macrophages in the regulation of COX-2. Macrophages exposed to LPS showed a rapid and sustained expression of COX-2 mRNA and protein for up to 48 h, whereas PGE2 production was notably enhanced only after 12 h. LPS increased COX-2 gene transcription and activation of the transcription factor NF-kappa B in a transient manner. LPS-treated macrophages produced high levels of TNF-alpha and moderate amounts of IL-1 beta protein. However, neutralizing Abs against these cytokines had no effect on COX-2 mRNA and protein expression, nor did they affect the stability of COX-2 mRNA. Interestingly, in the presence of LPS or exogenous IL-1 beta, COX-2 transcripts were stabilized, and actinomycin D inhibited their degradation. Only when LPS or IL-1 beta was removed did COX-2 mRNA decay with a t1/2 of >/=5 h. In contrast, dexamethasone promoted a faster decay of the LPS-induced COX-2 transcripts (t1/2 = 2.5 h). These results clearly demonstrate that LPS can regulate COX-2 at both transcriptional and posttranscriptional levels independently from endogenous IL-1 beta and TNF-alpha in human macrophages.
Evidence for a bidomain structure of constitutive cerebellar nitric oxide synthase. (1994)

Nitric oxide synthase (NOS) catalyzes the NADPH-dependent, Ca2+/calmodulin-dependent formation of NO and citrulline from L-arginine and molecular oxygen. The localization of the heme-binding consensus sequence in the NH2-terminal half of NOS and of the binding sequences for nucleotides (FMN and FAD) in the COOH-terminal half suggests a bidomain structure. In addition, the presence of a putative calmodulin-binding sequence between the heme- and flavin-binding domains of the enzyme suggests a role for calmodulin in modulating a spatial orientation of these domains that is required for catalytic activity. First, to determine the effects of calmodulin and the functionality of the separated domains, Ca2+/calmodulin binding-induced conformational changes in NOS were measured by fluorescence quenching, from which a binding constant of approximately 1 nM for calmodulin was calculated. Second, electron transport to various artificial acceptors was measured. The addition of Ca2+/calmodulin increased cytochrome c reduction from 10-15-fold while stimulating the rate of 2,6-dichlorophenolindophenol and ferricyanide reduction only slightly, if at all. Calmodulin stimulation of NOS results in NADPH-mediated cytochrome c reduction, which is sensitive to superoxide dismutase, and the reduction of acetylated cytochrome c, which is only weakly reducible by unstimulated NOS. Thus, this stimulated activity is presumably superoxide anion-mediated. Third, limited proteolysis of NOS in the absence of calmodulin resulted in a time-dependent increase in cytochrome c reductase activity, which was not inhibitable by superoxide dismutase, and a decrease in catalysis of NO formation. SDS-polyacrylamide gel electrophoresis analysis of the tryptic digest demonstrated the formation of approximately 89- and approximately 79-kDa fragments. Sequence analysis of the peptides confirmed that trypsin cleaves the enzyme in the putative calmodulin-binding region beginning with Ala728. This region was protected from proteolysis by the addition of Ca2+/calmodulin. The separated NH2-terminal domain exhibited the characteristic spectrum of bound heme, while the COOH-terminal domain showed the characteristic spectrum of bound flavins. Other cleavage patterns were obtained in the presence of calmodulin. The data demonstrate that the heme- and flavin-binding domains of NOS can be isolated in functionally intact forms.
The syntheses and structures of lithium phosphinimide and phosphinimine complexes (2003)

The preparation and structures of [Li(µ-NPt-Bu 3 )] 4 1, [Li(µ-Cl)(HNPt-Bu 3 )] 4 2, and [Li(µ-Cl)(HNPPh 3 )] 4 3 are described. The structure of 1 stands in contrast to that of the only other known Li-phosphinimide derivative, [Li(µ-NPPh 3 )] 6 . The impact of the steric bulk on the aggregation and the geometries of the Li 4 N 4 and Li 4 Cl 4 cores are considered and discussed.Key words: lithium compounds, phosphinimine, phosphinimide, P-N ligands.
Steroidal Glycosides from the Fresh Stem of Stephanotis lutchuensis var. japonica (Asclepiadaceae). Chemical Structures of Stephanosides K-Q. (1996)

The structural elucidation of seven related oxypregnane-oligoglycosides stephanosides K (1), L (2), M (3), N (4), O (5), P (6), and Q (7) from the fresh stem of Stephanotis lutchuensis var. japonica (Asclepiadaceae) was achieved through on a detailed study of their high-field 1H- and 13C-NMR spectra. The results show that all the sugars are beta (1-->4)-linked. The aglycones of stephanosides K, M, and O, and stephanosides L, N, and P were identified as 12-O-cinnamoyl-20-O-(E)-2-methyl-2-butenoyl, and 12-O-cinnamoyl-20-O-nicotinoyl derivatives of (20S)-pregn-6-ene-3 beta,5 alpha,8 beta,12 beta,14 beta,17 beta,20-heptaol, respectively. The aglycone of stephanoside Q was 12-O-cinnamoyldeacetylmetaplexigenin (kidjoranin).
Statistical Timing Analysis with Extended Pseudo-Canonical Timing Model (2005)

State of the art statistical timing analysis (STA) tools often yield less accurate results when timing variables become correlated due to global source of variations and path reconvergence. To the best of our knowledge, no good solution is available for dealing both types of correlations simultaneously. In this paper, we present a novel extended pseudo-canonical timing model to retain and evaluate both types of correlation during statistical timing analysis with minimum computation cost. Also, an intelligent pruning method is introduced to enable trade-off runtime with accuracy. Tested with ISCAS benchmark suites, our method shows both high accuracy and high performance. For example, on the circuit c6288, our distribution estimation error shows 15/spl times/ accuracy improvement compared with previous approaches.
Chitosan-based thermosensitive hydrogel as a promising ocular drug delivery system: Preparation, characterization, and<i>in vivo</i>evaluation (2011)

The purpose of this study was to evaluate the feasibility of in situ thermosensitive hydrogel based on chitosan in combination with disodium α-d-Glucose 1-phosphate (DGP) for ocular drug delivery system. Aqueous solution of chitosan/DGP underwent sol-gel transition as temperature increased which was flowing sol at room temperature and then turned into non-flowing hydrogel at physiological temperature. The properties of gels were characterized regarding gelation time, gelation temperature, and morphology. The sol-to-gel phase transition behaviors were affected by the concentrations of chitosan, DGP and the model drug levocetirizine dihydrochloride (LD). The developed hydrogel presented a characteristic of a rapid release at the initial period followed by a sustained release and remarkably enhanced the cornea penetration of LD. The results of ocular irritation demonstrated the excellent ocular tolerance of the hydrogel. The ocular residence time for the hydrogel was significantly prolonged compared with eye drops. The drug-loaded hydrogel produced more effective anti-allergic conjunctivitis effects compared with LD aqueous solution. These results showed that the chitosan/DGP thermosensitive hydrogel could be used as an ideal ocular drug delivery system in terms of the suitable sol-gel transition temperature, mild pH environment in the hydrogel as well as the organic solvent free.
Synthesis of chloroisoxazoline amino-acids (1976)

The addition of chloronitrile oxide to the nitronate salts of αβ-unsaturated-α-nitrocrotonic esters yields the 3-chloroisoxazoline adducts, in an efficient reaction; further transformations convert these into the free aminoderivatives which are members of a class of biologically interesting amino-acids.
Composition of Phospholipid Fatty Acids in Red Blood Cell Membranes of Patients in Intensive Care Units: Effects of Different Intakes of Soybean Oil, Medium‐Chain Triglycerides, and Black‐Currant Seed Oil (1992)

Fatty acid composition of phospholipids in red blood cell membranes was studied in 32 severely head-injured or cerebral stroke patients receiving enteral nutrition for 3 weeks. During this study the effects of three diets differing only by their lipid composition were investigated. The daily energy intake of each patient amounted to 2950 kilocalories, of which the lipid fraction represented 45.7%. Diet A contained only soybean oil, diet B consisted of a 50% soybean oil and 50% medium-chain triglycerides mixture, and diet C was an emulsion of 50% soybean oil, 42.5% medium-chain triglycerides, and 7.5% black-currant seed oil. Our results showed no biochemical signs of fatty acid deficiency in red blood cell membranes for the patients at the beginning of the study, after a comparison with a control group of 20 healthy adults. Inhibition of delta 6-desaturase activity on linoleic acid (C18:2 omega 6) after diet A was suggested by an increase of linoleic acid without a corresponding increase of dihomo-gamma-linolenic acid (C20:3 omega 6). Replacing 50% of soybean oil by with medium-chain triglycerides (diet B) prevented this enzyme inhibition. Supply of black-currant seed oil rich in gamma-linolenic (C18:3 omega 6) and stearidonic (C18:4 omega 3) acids (diet C) induced significant increases of dihomo-gamma-linolenic and eicosapentaenoic (C20:5 omega 3) acids, without influencing arachidonic acid (C20:4 omega 6) levels. This balance was evaluated through the ratio (C20:3 omega 6 + C20:5 omega 3)/C20:4 omega 6.
Structure and topic information in expository text overviews (2002)

The current wisdom on texts is that they should start by providing readers with an overview of the content (the topics discussed) and the structure (the relationship between the topics). However, in a recent paper Murray and McGlone (1997) reported that readers benefit from topic information but not from structural information provided in an overview of a very simple text. In the present experiments we ask whether these observations would be applicable to more complex texts in which structural information would be more important. Two experiments, which used a text with a complex hierarchical structure, replicated previous results on reading times. The second experiment also permitted us to rule out the effect of numerical signals in the text as the reason for the results.
Molecular cloning of the cDNAs encoding the feline B‐lymphocyte activation antigen B7–1 (CD80) and B7–2 (CD86) homologues which interact with human CTLA4‐Ig (2000)

We cloned the cDNAs encoding the feline homologues of B-lymphocyte activation antigens B7-1 (CD80) and B7-2 (CD86). We expressed recombinant feline CD80 and CD86 molecules by the baculovirus expression system, and demonstrated their binding ability to human CTLA4-murine immunoglobulin fusion protein.
Immunocytochemical localization of estrogen and progesterone receptor and prognosis in human primary breast cancer. (1990)

An immunocytochemical assay (ICA) for the measurement of estrogen receptor (ER) and progesterone receptor (PgR) has been evaluated in 426 human primary breast carcinomas. For estrogen receptor determination ER ICA was used. PgR ICA was performed using the monoclonal antibody KD 68. Assay results for progesterone receptor immunocytochemistry were in agreement (P less than 0.0001) with those of biochemical determination in 74%. Progesterone receptor positivity determined with a semiquantified approach based on intensity and heterogeneity of immunocytochemical staining correlated significantly with biochemically determined progesterone receptor levels (P = 0.0001). Survival data showed a significantly better overall survival for patients with either ER ICA- or PgR ICA-positive carcinomas (ER ICA, P less than 0.00001; PgR ICA, P = 0.004). Patients with both negative ER ICA and PgR ICA showed a poorer prognosis than patients with only one negative receptor. In ER ICA- and PgR ICA-positive carcinomas a trend could be found that patients whose carcinomas contained high numbers of receptor-positive tumor cells had a better survival. This study demonstrates that ER ICA and PgR ICA are strong prognostic indicators and that the proportion of steroid hormone receptor-positive tumor cells seems to be of clinical importance.
Oxidative Damage Linked to Neurodegeneration by Selective α-Synuclein Nitration in Synucleinopathy Lesions (2000)

Aggregated alpha-synuclein proteins form brain lesions that are hallmarks of neurodegenerative synucleinopathies, and oxidative stress has been implicated in the pathogenesis of some of these disorders. Using antibodies to specific nitrated tyrosine residues in alpha-synuclein, we demonstrate extensive and widespread accumulations of nitrated alpha-synuclein in the signature inclusions of Parkinson's disease, dementia with Lewy bodies, the Lewy body variant of Alzheimer's disease, and multiple system atrophy brains. We also show that nitrated alpha-synuclein is present in the major filamentous building blocks of these inclusions, as well as in the insoluble fractions of affected brain regions of synucleinopathies. The selective and specific nitration of alpha-synuclein in these disorders provides evidence to directly link oxidative and nitrative damage to the onset and progression of neurodegenerative synucleinopathies.
Pituitary Tumors (2004)

Secretory tumors can cause a variety of problems depending on the hormone that the tumor secretes.
On the Use of Microarchitecture-Driven Dynamic Voltage Scaling (2000)

This paper proposes microarchitecture-driven dynamic voltage scaling as a viable solution to power efficient architectures, with little or no performance penalty. The run-time behavior exhibited by common applications, with active periods, alternated with stall periods due to cache misses, is exploited to reduce the dynamic component of power consumption via selective voltage scaling. As it is shown by experimental results, up to 20% reduction in total energy consumption, 22% in average power and 14% in peak power have been achieved with less than 6% penalty in performance. The study shows that microarchitecture-driven dynamic voltage scaling can become an effective tool for energy reduction in high-performance processors. 1 Introduction Driven by the increased levels of complexity and emergence of mobile applications, power dissipation has become a critical design concern in recent years. In addition, power consumption has especially become important for designers of high-performanc...
Generation of a functional liver tissue mimic using adipose stromal vascular fraction cell-derived vasculatures (2013)

One of the major challenges in cell implantation therapies is to promote integration of the microcirculation between the implanted cells and the host. We used adipose-derived stromal vascular fraction (SVF) cells to vascularize a human liver cell (HepG2) implant. We hypothesized that the SVF cells would form a functional microcirculation via vascular assembly and inosculation with the host vasculature. Initially, we assessed the extent and character of neovasculatures formed by freshly isolated and cultured SVF cells and found that freshly isolated cells have a higher vascularization potential. Generation of a 3D implant containing fresh SVF and HepG2 cells formed a tissue in which HepG2 cells were entwined with a network of microvessels. Implanted HepG2 cells sequestered labeled LDL delivered by systemic intravascular injection only in SVF-vascularized implants demonstrating that SVF cell-derived vasculatures can effectively integrate with host vessels and interface with parenchymal cells to form a functional tissue mimic.
Identification of a locus, distinct from RDS-peripherin, for autosomal recessive retinitis pigmentosa on chromosome 6p (1994)

We performed a genomic search for linkage to autosomal recessive retinitis pigmentosa in a large pedigree obtained from the Dominican Republic using microsatellite markers. Regions of the genome known to contain genes for retinitis pigmentosa were preferentially tested. One of these regions, on chromosome 6p, which contains the gene for peripherin, gave positive lod scores. Use of a mononucleotide repeat polymorphism in the peripherin gene excluded this locus. Two- and multi-point analyses suggest that the most likely location for the disease gene is near D6S291, which is located approximately 20 centimorgans telomeric from peripherin.
Glycoprotein H of pseudorabies virus is essential for entry and cell-to-cell spread of the virus (1992)

To study the function of the envelope glycoprotein gH of pseudorabies virus, a gH null mutant was constructed. A premature translation termination codon was introduced in the gH gene by linker insertion mutagenesis, and a mutant virus was rescued by using a cell line that expresses the wild-type protein. Mutant virus isolated from complementing cells was unable to form plaques on noncomplementing cells, indicating that gH is essential in the life cycle of the virus. Immunological staining and electron microscopy showed that the mutant virus produced noninfectious progeny and was unable to spread from infected to uninfected cells by cell-cell fusion. Thus, similar to gH of herpes simplex virus, gH of pseudorabies virus is required for entry and cell-to-cell spread.
A Bayesian method for probable surface reconstruction and decimation (2006)

We present a Bayesian technique for the reconstruction and subsequent decimation of 3D surface models from noisy sensor data. The method uses oriented probabilistic models of the measurement noise and combines them with feature-enhancing prior probabilities over 3D surfaces. When applied to surface reconstruction, the method simultaneously smooths noisy regions while enhancing features such as corners. When applied to surface decimation, it finds models that closely approximate the original mesh when rendered. The method is applied in the context of computer animation where it finds decimations that minimize the visual error even under nonrigid deformations.