gebhart/patrepeval huggingface dataset:
Residues Y179 and H101 of a Hydrophobic Patch of Factor VII Are Involved in Activation by Factor Xa (2001)

We studied factor Xa activation of human factor VII in hopes of identifying factor VII residues, not adjacent to the cleavage site, involved in this interaction. We made eight factor VIIs with single mutations (N100A, H101A, D102Q, L144A, R147A, Y179A, D186A, and F256A) and two factor VIIs with multiple mutations [MM3 (L144A/R147A/D186A) and MM4 (N100A/H101A/Y179A/F256A)]. Residues in MM3 have previously been identified as affecting factor X activation, and the residues of MM4 are located at a hydrophobic patch of factor VII on the opposite side of the catalytic domain from those in MM3. Only H101A, Y179A, and MM4 were activated significantly more slowly than the wild type. Results of our kinetic analyses showed that the catalytic efficiency of factor Xa for activation of factor VII was 176- and 234-fold higher than that for H101A andY179A, respectively. All the mutants with measurable activity had affinities for tissue factor similar to those of the wild type. The activated hydrophobic patch residues, except N100A, which is adjacent to one of the catalytic residues, had normal activities toward both a small peptide substrate and factor X. The rest of the activated mutants (except D102Q with no activity) had reduced activities toward the small substrate (except R147A) and factor X. We conclude that factor VII activation by factor Xa and factor VIIa's catalytic interaction with factor X involve different regions in the catalytic domain, and residues H101 and Y179, part of an aromatic hydrophobic patch, are specifically involved in factor Xa activation of factor VII.
Biotransformations of Acyclic Terpenoids, (±)-trans-Nerolidol and Geranylacetone, by Glomerella cingulata (1996)

Microbial transformations of (±)-trans-nerolidol and geranylacetone were carried out with a plant pathogenic fungus, Glomerella cingulata. (±)-trans-Nerolidol and geranylacetone were hydrated at a remote double bond as the main metabolic pathway. A large amount of (E)-3,7,11-trimethyl-1,6-dodecadiene-3,11-diol and small amount of (E)-3,7,11-trimethyl-1,6-dodecadiene-3,10,11-triol were obtained from (±)-trans-nerolidol. Geranylacetone was transformed to (E)-10-hydroxy-6,10-dimethyl-5-undecen-2-one as the major metabolite. (E)-9,10-Dihydroxy-6,10-dimethyl-5-undecen-2-one, (E)-6,10-dimethyl-5,9-undecadien-2-ol, (E)-6,10-dimethyl-5-undecene-2,9,10-triol, and (E)-6,10-dimethyl-5-undecene-2,10-diol were also obtained from geranylacetone. The structures of metabolic products were determined by spectroscopic data. Keywords: Biotransformation; microbial transformation; Glomerella cingulata; plant pathogenic fungus; (±)-trans-nerolidol; geranylacetone
miR-21 as an Independent Biochemical Recurrence Predictor and Potential Therapeutic Target for Prostate Cancer (2012)

Positive miR-21 expression was associated with poor biochemical recurrence-free survival and predicted the risk of biochemical recurrence in patients with prostate cancer after radical prostatectomy. Accordingly gene therapy using miR-21 inhibition strategies may prove useful for prostate cancer therapy.
Expression and selective inhibition of the constitutive and inducible forms of human cyclo-oxygenase (1995)

The enzyme cyclo-oxygenase catalyses the oxygenation of arachidonic acid, leading to the formation of prostaglandins. Recently two forms of cyclo-oxygenase have been described: a constitutive (COX-1) enzyme present in most cells and tissues, and an inducible (COX-2) isoenzyme observed in many cells in response to pro-inflammatory cytokines. Constitutive and inducible forms of human cyclo-oxygenase (hCOX-1 and hCOX-2) were cloned and expressed in insect cells, utilizing a baculovirus expression system. hCOX-1 had a specific activity of 18.8 mumol of O2/mg with a Km of 13.8 microM for arachidonate and Vmax. of 1500 nmol of O2/nmol of enzyme, whereas hCOX-2 had a specific activity of 12.2 mumol of O2/mg with a Km of 8.7 microM for arachidonate and a Vmax. of 1090 nmol of O2/nmol of enzyme. Indomethacin inhibited both hCOX-1 and hCOX-2, whereas NS-398 and Dup-697 selectively inhibited hCOX-2. Both NS-398 and Dup-697 exhibited time-dependent inactivation of hCOX-2, as did indomethacin on both enzymes. The competitive inhibitor of hCOX-1, mefenamic acid, also displayed competitive inhibition of hCOX-2. These results demonstrate the ability to generate selective non-steroidal anti-inflammatory drugs (NSAIDs), which could provide useful improvement therapeutically in the treatment of chronic inflammatory disease.
Expression of common housekeeping genes is affected by disease in human hepatitis C virus-infected liver (2010)

Our results indicate that liver disease affects the expression of common HKGs and that β-glucuronidase and splicing factor arginine/serine-rich 4 are the most stable HKGs from this group for studies of gene expression in HCV-infected human liver.
Accumulation of the β amyloid precursor protein at sites of ischemic injury in rat brain (1993)

We used various antibodies to the beta amyloid precursor protein (APP) of Alzheimer's disease to study changes in the cellular distribution of APP in experimental ischemic brain injury. In contrast to sham operated controls, rats with repeated reversible occlusions of one middle cerebral artery showed striking APP reactivity in astrocytic processes in perifocal regions and white matter tracts. Dystrophic axons and neurons with accumulated APP were also evident in the ipsilateral neocortex and hippocampus. Such changes were also apparent in rats subjected to partial forebrain ischemia by bilateral occlusion of the carotid arteries. Our studies suggest that focal ischemic insults or chronic hypoperfusion leads to increased accumulation of APP in surviving brain cells that may pertain to enhanced beta amyloid deposition in Alzheimer's disease.
Agrobacterium-mediated transformation of rice and stable inheritance of bar gene (2003)

Herbicideresistant bar gene was incorporated into rice genome via Agrobacteriummediated transformation using the embryogenic calli induced from 072,Xiushui 11 and ZH9905.The transgenic nature of transformants was confirmed by PCR and Southern hybridization. Integration of both genes was confirmed by PCR and Southern hybridization. High herbicide resistance of transgenic plants was evident from spraying test with Basta. The foreign bar gene was inherited and segregation ratio in some R1 progeny was 3∶1.Agronomic traits of transgenic R1 plants were similar to those of parents' varieties,but their fertilify decreased.
Reproducible and efficient murine CNS gene delivery using a microprocessor-controlled injector (1998)

To develop a reproducible gene transfer method for the murine CNS we evaluated delivery of various gene vehicles using mechanical or manual stereotaxic intracranial inoculation. A microprocessor controlled microsyringe pump (The World Precision Instruments/UltraMicroPump) programmable for volume, rate and syringe size and designed to dispense nanoliter and picoliter volumes was compared to a standard manual deliver method. Gene transfer efficiency of two viral vectors, two synthetic cationic lipid molecules, and naked DNA were evaluated in mice injected unilaterally in two brain regions. Animals received 1 microl over 10 min. of either HSVlac (1 x 10(5) b.f.u), AdLac (1 x 10(5) p.f.u), Tfx-10 or Tfx-20 (2.6 microg DNA in 2.0 microl Tfx; 1:1 charge ratio of DNA to liposome), or naked DNA (HSVlac plasmid, 10 microg/microl). After 4 days, animals from each group were perfused and tissue prepared for X-gal histochemical detection of beta-galactosidase expression. Blue cells were observed in the HSV, Adenovirus, and Tfx-20 groups only at the injection site in animals injected using the UMP. Animals injected manually exhibited fewer blue cells and positive cells were not restricted to the injection site. To quantify expression, tissue punches harvested from the injection sites as well as other brain regions were analyzed using a chemiluminescent reporter assay to detect beta-galactosidase (Galacto-Light). These data indicated increased activity in all animals injected with a lacZ containing vector via the UMP as compared to manual delivery: A 41% increase in the expression levels of beta-gal in HSVlac infected animals (p = 0.0029); a 29% increase in Adlac infected animals (p = 0.01); a 56% increase in Tfx-10 transduced animals (p = 0.04); a 24% increase in Tfx-20 transduced animals (p = 0.01); and a 69% increase in naked DNA gene transfer (p = 0.05). Total beta-galactosidase activity was greatest in HSVlac infected mice followed by Adlac > Tfx-20 > Tfx-10 = naked DNA.
Development potential of rifalazil (2003)

Rifalazil represents a new generation of ansamycins that contain a unique four-ring structure. Originally rifalazil was developed as a therapeutic agent to replace rifampin as part of a multiple drug regimen in the treatment of tuberculosis. As a result of its superior antimicrobial activity and high intracellular levels, rifalazil has potential to treat indications caused by the intracellular pathogen, Chlamydia trachomatis, which causes non-gonococcal urethritis and cervicitis, often leading to pelvic inflammatory disease. Rifalazil also has potential to treat the related microorganism, Chlamydia pneumoniae, which may be involved in chronic inflammatory processes thought to be partly responsible for atherosclerosis. Due to its favourable antimicrobial spectrum and other positive attributes, rifalazil may also prove valuable in the treatment of gastric ulcer disease, caused by Helicobacter pylori, and antibiotic-associated colitis, the result of toxin production following the growth of Clostridium difficile in the colon. The potential value of rifalazil in the treatment of these indications will be assessed in human clinical trials.
A complete system for controlled access television (1990)

The author sets out to provide an overview of conditional access systems using Eurocypher access control. BSB (British Satellite Broadcasting) have in place fully operational customer management and Eurocypher conditional access systems. The systems architecture outlined provides for sophisticated control and reliable operation of conditionally accessed subscription television services. It provides all the functions and features required to support the continued operation and growth of BSB for the future. The Eurocypher systems are capable of being configured in ways which allow support for many programmers in complex multinational and multichannel environments, and with the provision of appropriate data collection systems can also support additional features such as impulse pay per view. >
Gastric emptying of liquids and solids evaluated by acetaminophen test in diabetic patients with and without autonomic neuropathy. (1992)

A delayed gastric emptying of solids but not of liquids has been recorded in diabetic patients with autonomic neuropathy by radionuclide labelled test meals. Acetaminophen test (rate of acetaminophen absorption after ingestion of 1500 mg of the drug) has been previously validated for quantitative indirect measurement of gastric emptying. In the present study we measured gastric emptying of liquid and solid meals by acetaminophen test in 14 insulin-requiring diabetic patients (7 with and 7 without autonomic neuropathy) and 14 healthy subjects, matched for age, sex, BMI and blood pressure. All values recorded after liquid meal were not significantly different in the three groups of subjects. After solid meal, the mean area under the plasma acetaminophen concentration-time curve was significantly lower in neuropathic diabetic patients vs control subjects (p less than 0.05), and the emptying index (peak time/peak plasma concentration ratio) was significantly higher in neuropathic diabetic patients vs non-neuropathic diabetic patients (p less than 0.01) and vs control subjects (p less than 0.05). These results confirm a delayed gastric emptying of solids but not of liquids in diabetic patients with autonomic neuropathy, and indicate that acetaminophen test may be proposed as simple, safe and noninvasive test for quantitative assessment of gastric emptying in diabetic patients.
Antibodies against the myelin oligodendrocyte glycoprotein and the myelin basic protein in multiple sclerosis and other neurological diseases: a comparative study (1999)

In experimental animal models of multiple sclerosis demyelinating antibody responses are directed against the myelin oligodendrocyte glycoprotein (MOG). We have investigated whether a similar antibody response is also present in multiple sclerosis patients. Using the recombinant human extracellular immunoglobulin domain of MOG (MOG-Ig) we have screened the sera and CSFs of 130 multiple sclerosis patients, 32 patients with other inflammatory neurological diseases (OIND), 30 patients with other non-inflammatory neurological diseases (ONND) and 10 patients with rheumatoid arthritis. We report that 38% of multiple sclerosis patients are seropositive for IgG antibodies to MOG-Ig compared with 28% seropositive for anti-myelin basic protein (MBP). In contrast, OIND are characterized by similar frequencies of serum IgG antibody responses to MOG-Ig (53%) and MBP (47%), whereas serum IgG responses to MOG-Ig are rare in ONND (3%) and rheumatoid arthritis (10%). Anti-MBP IgG antibodies, however, are a frequent finding in ONND (23%) and rheumatoid arthritis (60%). Our results provide clear evidence that anti-MOG-Ig antibodies are common in CNS inflammation. However, in OIND these antibody responses are transient, whereas they persist in multiple sclerosis. We demonstrate that the serum anti-MOG-Ig response is already established in early multiple sclerosis (multiple sclerosis-R0; 36%). In later multiple sclerosis stages frequencies and titres are comparable with early multiple sclerosis. In contrast, the frequency of anti-MBP antibodies is low in multiple sclerosis-R0 (12%) and increases during disease progression in relapsing-remitting (32%) and chronic progressive multiple sclerosis (40%), thus suggesting that anti-MBP responses accumulate over time. Finally we provide evidence for intrathecal synthesis of IgG antibodies to MOG-Ig in multiple sclerosis.
Medical Image Databases: A Content-based Retrieval Approach (1997)

Information contained in medical images differs considerably from that residing in alphanumeric format. The difference can be attributed to four characteristics: (1) the semantics of medical knowledge extractable from images is imprecise; (2) image information contains form and spatial data, which are not expressible in conventional language; (3) a large part of image information is geometric; (4) diagnostic inferences derived from images rest on an incomplete, continuously evolving model of normality. This paper explores the differentiating characteristics of text versus images and their impact on design of a medical image database intended to allow content-based indexing and retrieval. One strategy for implementing medical image databases is presented, which employs object-oriented iconic queries, semantics by association with prototypes, and a generic schema.
A Theoretical Model of Erosion and Macromolecular Drug Release from Biodegrading Microspheres (1997)

A theoretical model is outlined for predicting the time evolution of total mass, mean molecular weight, and drug release for the case of a spherical bulk-eroding microsphere, prepared by a double emulsification procedure and containing a hydrophilic drug, such as a protein or peptide. Explicit analytical formulae are derived for calculating the time evolution of measurable macroscopic characteristics, such as drug release or mean molecular weight. Microsphere hydration, polymer erosion, and drug release phases are each described. Results indicate that polymer degradation by only random-chain scission or only end scission (or unzipping) cannot explain experimentally observed kinetics of particle mass loss and molecular weight change; thus, a combined model (incorporating both random and end scission) is proposed. A general methodology for determining the microscopic transport coefficients (such as polymer degradation rate constant or drug diffusion coefficient) from erosion and release data is outlined. This paradigm is applied to the specific case of 50:50 poly(D,L-lactic-co-glycolic acid (PLGA) microspheres encapsulating glycoprotein 120 (gp 120), a candidate AIDS vaccine. Predictions permit comparisons with experimental data for mean weight- and number-averaged molecular weights, as well as for mass loss and protein release. Other comparisons are made with data appearing in the literature for release of tetanus toxoid from PLA and PLGA microspheres of variable molecular weight. Agreement between theory and experiment is observed.
Characterization of room temperature induced apoptosis in HL‐60 (1997)

We found that exposure to room temperature (RT/21 degrees C) causes apoptosis in HL-60 cells. Here we characterized RT-induced apoptosis in HL-60. After exposure to RT, apoptosis starts within 6 h and more than 80% of the cells underwent apoptosis within 20 h. All cells, however, were committed to apoptosis after 16 h and no viable cells could be recovered. The caspase-1 inhibitor (YVAD-CHO) effectively blocked apoptosis, whereas the caspase-3 inhibitor (DEVD-CHO) did not. About 20% of newly obtained early passage HL-60 cells (passage 10) also underwent apoptosis by RT treatment. These data suggest that some population in HL-60 which responds to RT with apoptosis became dominant during passaging.
Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor. (1989)

Binding of U2 small nuclear ribonucleoprotein (snRNP) to the pre-mRNA branch site is an early step in spliceosome assembly and appears to commit a pre-mRNA to the splicing pathway. We have shown previously that this ATP-dependent binding requires a non-rnRNP factor, U2 snRNP auxiliary factor (U2AF), in addition to U2 snRNP. In this report we have identified U2AF, purified it to homogeneity, and characterized its biochemical properties. Purified U2AF comprises roughly equimolar quantities of two polypeptides, approximately 65 kDa and approximately 35 kDa, which appear to be associated. Measured by ultraviolet crosslinking, the 65-kDa polypeptide binds specifically to the polypyrimidine tract/3' splice site region. U2AF binds rapidly at 4 degrees C in the absence of ATP and remains associated with the pre-mRNA following U2 snRNP binding. Thus, the simple binding of U2AF initiates mammalian spliceosome assembly by facilitating the ATP-dependent binding of U2 snRNP.
Characterization of the promoter for vascular cell adhesion molecule-1 (VCAM-1). (1992)

Vascular cell adhesion molecule-1 (VCAM-1) was first identified as a protein that appears on the surface of endothelial cells after exposure to inflammatory cytokines. Through interaction with its integrin counter receptor VLA-4, VCAM-1 mediates cell-cell interactions important for immune function. We have cloned and begun characterization of the promoter for the VCAM-1 gene. In a series of transfection assays into human umbilical vein endothelial cells (HUVECs), we find that silencers between positions -1.641 kilobases and -288 base pairs restrict promoter activity, and that treatment with tumor necrosis factor-alpha overcomes this inhibition and activates the promoter through two NF kappa B sites located at positions -77 and -63 base pairs of the VCAM-1 gene. This responsiveness appears cell-specific since constructs containing the VCAM-1 NF kappa B sites are not responsive to tumor necrosis factor alpha in the T-cell line Jurkat. The two VCAM-1 NF kappa B sites, which differ slightly in their sequence, form distinct complexes in gel retardation assays, suggesting that they interact with different NF kappa B-site binding proteins. The distribution of these proteins could then control activity of the NF kappa B sites. We conclude that the pattern of VCAM-1 expression in HUVECs is controlled by a combination of these silencers and NF kappa B sites.
AZT inhibit telomerase activity of squamous cell carcinoma of tongue (2002)

Purpose:To study the effect of inhibition of telomerase activity and cell cycle by transcriptase telomerase inhibitors (3′ azido 3′ deoxythymidine, AZT) on squamous cell carcinoma of tongue in vitro.Methods:Human squmous cell carcinoma of tongue cell line Tca8113 was used as target cell. Telomerase activity was determined by TRAP PCR ELISA in untreated and treated Tca8113 by AZT, cell cycle phases were analyzed by flow cytometry. Results:Telomerase activity of Tca8113 was significantly inhibited when treated with AZT, and the effect of inhibition was dose dependant (rate of telomerase activity treated with AZT in 0.3, 0.6, 1.0, 1.5mol 10 -1 was 0.69 0.03, 0.61 0.08, 0.53 0.11, 0.50 0.02 respectively, rate of telomerase activity treated without AZT was 0.76 0.06). Cell cycle of treated Tca8113 was changed with marked increase in G 2 /M phase compared with untreated Tca8113 (62.8% vs 19.7%, P 0.05). Conclusions:The results indicated that AZT can effectively inhibit telomerase activity of tumor cells. AZT could be potentially used in anti tongue cancer or as an auxiliary method in cancer treatment.
Characterization of Nutrient-Induced Dispersion in Pseudomonas aeruginosa PAO1 Biofilm (2004)

The processes associated with early events in biofilm formation have become a major research focus over the past several years. Events associated with dispersion of cells from late stage biofilms have, however, received little attention. We demonstrate here that dispersal of Pseudomonas aeruginosa PAO1 from biofilms is inducible by a sudden increase in carbon substrate availability. Most efficient at inducing dispersal were sudden increases in availability of succinate > glutamate > glucose that led to approximately 80% reductions in surface-associated biofilm biomass. Nutrient-induced biofilm dispersion was associated with increased expression of flagella (fliC) and correspondingly decreased expression of pilus (pilA) genes in dispersed cells. Changes in gene expression associated with dispersion of P. aeruginosa biofilms were studied by using DNA microarray technology. Results corroborated proteomic data that showed gene expression to be markedly different between biofilms and newly dispersed cells. Gene families that were upregulated in dispersed cells included those for flagellar and ribosomal proteins, kinases, and phage PF1. Within the biofilm, genes encoding a number of denitrification pathways and pilus biosynthesis were also upregulated. Interestingly, nutrient-induced dispersion was associated with an increase in the number of Ser/Thr-phosphorylated proteins within the newly dispersed cells, and inhibition of dephosphorylation reduced the extent of nutrient-induced dispersion. This study is the first to demonstrate that dispersal of P. aeruginosa from biofilms can be induced by the addition of simple carbon sources. This study is also the first to demonstrate that dispersal of P. aeruginosa correlates with a specific dispersal phenotype.
Perpendicular recording media using phase-separated AlSi films (2005)

We have developed perpendicular recording media with nanosized cylindrical Co particles. The diameter and period of these particles are less than 10 and 12 nm, respectively. Al cylinders were grown in an a-Si matrix during AlSi film deposition due to the eutectic phase separation. The Al cylinders can be removed by chemical etching to form nanoporous templates. The pores were filled with Co by electrodeposition method via a metal underlayer as an electrode. These films show perpendicular anisotropy with Hc of 4.1 kOe.