gebhart/patrepeval huggingface dataset:
Characterization of Proteolytic Fragments of Bacteriophage T7 DNA Ligase (1996)

Treatment of T7 DNA ligase with a range of proteases generates two major fragments which are resistant to further digestion. These fragments, of molecular weight 16 and 26 kDa, are derived from the N- and C-termini of the protein, respectively. The presence of ATP or a non-hydrolysable analogue, ADPNP, during limited proteolysis greatly reduces the level of digestion. The N-terminal 16 kDa region of the intact T7 ligase is labelled selectively in the presence of [α-32P]ATP, confirming that it contains the active site lysine residue. In common with the intact enzyme, the C-terminal portion of the protein retains the ability to band shift DNA fragments of various lengths, implicating it in DNA binding. It can also inhibit ligation by the intact protein, apparently by competing for target sites on DNA. We conclude that the N-terminal region, which contains the putative active site lysine, plays a role in the transfer of AMP from the enzyme-adenylate complex to the 5′ phosphate at the nick site, while the C-terminal 26 kDa fragment appears to position the enzyme at the target site on DNA.
High-throughput cell manipulation using ultrasound fields (2005)

A method is presented for high-throughput cell manipulation that is capable of trapping and transporting biological cells in liquid using acoustic forces in an ultrasound field. The authors applied this technique for concentrating several cell types such as HeLa cells and human mesencymal stem cells. More than 90% of the cells were successfully concentrated into desired patterns. They also investigated cell viability in ultrasound fields and found little adverse effect. This work demonstrates that ultrasonic cell manipulation is suitable for being integrated into lab-on-a-chip systems for trapping and transporting large numbers of cells rapidly and is promising in cell fractioning.
Thymocyte binding to human thymic epithelial cells is inhibited by monoclonal antibodies to CD-2 and LFA-3 antigens. (1987)

With the use of cultured human thymic epithelial (TE) cells, we have previously shown that thymocytes bind to TE cells in suspension in a rosette-forming assay. To identify cell surface molecules involved in human TE-thymocyte rosette formation, we assayed a large panel of monoclonal antibodies for their ability to inhibit rosette formation. We found anti-CD-2 (LFA-2, T11), and anti-LFA-3 antibodies all inhibited binding of TE cells to thymocytes. By using indirect immunofluorescence assays, we determined that cultured TE cells were 90% LFA-3 positive and CD-2 negative, whereas thymocytes were 10% LFA-3 positive and 98% CD-2 positive. Pretreatment of TE cells with anti-LFA-3 but not anti-LFA-2 inhibited TE-thymocyte binding. In contrast, pretreatment of thymocytes with anti-CD-2 but not anti-LFA-3 antibodies inhibited TE-thymocyte binding. Thus TE cell-thymocyte binding is blocked by antibodies to the CD-2 (T11) antigen on thymocytes and by an antibody to the LFA-3 antigen on TE cells. Because the CD-2 antigen has been implicated in T cell activation, these data suggest that a natural ligand for T cell activation via the CD-2 molecule is present on human thymic epithelial cells.
ASIC clock distribution using a phase locked loop (PLL) (2002)

Transferring data between ASIC chips at frequencies above 40 MHz requires special on-chip circuitry in current sub-micron technologies. Phase locked loops can provide clock skew management in ASIC devices to help compensate for clock tree insertion delays and process, temperature and voltage variations allowing maximum multi-chip system performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In vitro and in vivo activity of R547: a potent and selective cyclin-dependent kinase inhibitor currently in phase I clinical trials (2006)

The cyclin-dependent protein kinases are key regulators of cell cycle progression. Aberrant expression or altered activity of distinct cyclin-dependent kinase (CDK) complexes results in escape of cells from cell cycle control, leading to unrestricted cell proliferation. CDK inhibitors have the potential to induce cell cycle arrest and apoptosis in cancer cells, and identifying small-molecule CDK inhibitors has been a major focus in cancer research. Several CDK inhibitors are entering the clinic, the most recent being selective CDK2 and CDK4 inhibitors. We have identified a diaminopyrimidine compound, R547, which is a potent and selective ATP-competitive CDK inhibitor. In cell-free assays, R547 effectively inhibited CDK1/cyclin B, CDK2/cyclin E, and CDK4/cyclin D1 (K(i) = 1-3 nmol/L) and was inactive (K(i) > 5,000 nmol/L) against a panel of >120 unrelated kinases. In vitro, R547 effectively inhibited the proliferation of tumor cell lines independent of multidrug resistant status, histologic type, retinoblastoma protein, or p53 status, with IC(50)s </= 0.60 mumol/L. The growth-inhibitory activity is characterized by a cell cycle block at G(1) and G(2) phases and induction of apoptosis. R547 reduced phosphorylation of the cellular retinoblastoma protein at specific CDK phosphorylation sites at the same concentrations that induced cell cycle arrest, suggesting a potential pharmacodynamic marker for clinical use. In vivo, R547 showed antitumor activity in all of the models tested to date, including six human tumor xenografts and an orthotopic syngeneic rat model. R547 was efficacious with daily oral dosing as well as with once weekly i.v. dosing in established human tumor models and at the targeted efficacious exposures inhibited phosphorylation of the retinoblastoma protein in the tumors. The selective kinase inhibition profile and the preclinical antitumor activity of R547 suggest that it may be promising for development for use in the treatment of solid tumors. R547 is currently being evaluated in phase I clinical trials.
Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8) (2006)

Ubiquitin-specific protease 8 (USP8) hydrolyzes mono and polyubiquitylated targets such as epidermal growth factor receptors and is involved in clathrin-mediated internalization. In 1182 residues, USP8 contains multiple domains, including coiled-coil, rhodanese, and catalytic domains. We report the first high-resolution crystal structures of these domains and discuss their implications for USP8 function. The amino-terminal domain is a homodimer with a novel fold. It is composed of two five-helix bundles, where the first helices are swapped, and carboxyl-terminal helices are extended in an antiparallel fashion. The structure of the rhodanese domain, determined in complex with the E3 ligase NRDP1, reveals the canonical rhodanese fold but with a distorted primordial active site. The USP8 recognition domain of NRDP1 has a novel protein fold that interacts with a conserved peptide loop of the rhodanese domain. A consensus sequence of this loop is found in other NRDP1 targets, suggesting a common mode of interaction. The structure of the carboxyl-terminal catalytic domain of USP8 exhibits the conserved tripartite architecture but shows unique traits. Notably, the active site, including the ubiquitin binding pocket, is in a closed conformation, incompatible with substrate binding. The presence of a zinc ribbon subdomain near the ubiquitin binding site further suggests a polyubiquitin-specific binding site and a mechanism for substrate induced conformational changes.
Secretion of chondroitin sulfate from embryonic epidermal cells in Xenopus laevis. (1993)

We examined proteoglycans (PGs) in amphibian epidermal cells by immunofluorescence microscopy. Immunoelectron microscopy with pre- and post-embedding methods, combined with HRP- or gold-conjugated secondary antibody, revealed ultrastructural localization of glycosaminoglycans (GAGs). Embryonic epidermis secretion granules in Xenopus laevis contained chondroitin 6-sulfate and unsulfated chondroitin. Immature secretion granules were also labeled with anti-chondroitin 6-sulfate and anti-chondroitin. A step-wise digestion experiment on chondroitinase ABC revealed that fine filaments in the secretion granules were chondroitin sulfate chains. Inhibition experiments with brefeldin A revealed that the life of a secretion granule was 5-10 hr, suggesting that GAG secretion from embryonic epidermis is routed through a regulated pathway.
Characterization of a chemically modified plant cell culture expressed human α-Galactosidase-A enzyme for treatment of Fabry disease (2014)

Fabry disease is an X-linked recessive disorder caused by the loss of function of the lysosomal enzyme α-Galactosidase-A. Although two enzyme replacement therapies (ERTs) are commercially available, they may not effectively reverse some of the Fabry pathology. PRX-102 is a novel enzyme for the therapy of Fabry disease expressed in a BY2 Tobacco cell culture. PRX-102 is chemically modified, resulting in a cross-linked homo-dimer. We have characterized the in-vitro and in-vivo properties of PRX-102 and compared the results with the two commercially produced α-Galactosidase-A enzymes. Results show that PRX-102 has prolonged in-vitro stability in plasma, after 1 h incubation it retains 30% activity compared with complete inactivation of the commercial enzymes. Under lysosomal-like conditions PRX-102 maintains over 80% activity following 10 days of incubation, while commercial enzymes become inactive after 2 days. Pharmacokinetic profile of PRX-102 measured in male Fabry mice shows a 10 fold increase in t1/2 in mice (581 min) compared to approved drugs. The enzyme has significantly different kinetic parameters to the alternative ERTs available (p-value < 0.05, one way ANOVA), although these differences do not indicate any significant biochemical variations. PRX-102 is uptaken to primary human Fabry fibroblasts. The repeat administration of the enzyme to Fabry mice caused significant reduction (p-value < 0.05) of Gb3 in various tissues (the measured residual content was 64% in kidney, liver was cleaned, 23% in heart, 5.7% in skin and 16.2% in spleen). PRX-102 has a relatively simple glycosylation pattern, characteristic to plants, having mainly tri-mannose structures with the addition of either α(1–3)-linked fucose or β(1–2)-linked xylose, or both, in addition to various high mannose structures, while agalsidase beta has a mixture of sialylated glycans in addition to high mannose structures. This study concludes that PRX-102 is equivalent in functionality to the current ERTs available, with superior stability and prolonged circulatory half-life. Therefore we propose that PRX-102 is a promising alternative for treatment of Fabry disease.
Electrical characterization of GaN p-n junctions with and without threading dislocations (1998)

The effect of dislocations on the electrical characteristics of GaN p-n junctions has been examined through current–voltage measurements. Lateral epitaxial overgrowth (LEO) was used to produce areas of low dislocation density in close proximity to areas with the high dislocation density typical for growth on sapphire. A comparison of p-n diodes fabricated in each region reveals that reverse-bias leakage current is reduced by three orders of magnitude on LEO GaN. Temperature-dependent measurements on the LEO diodes indicate that the remaining leakage current in these devices is associated with a deep trap level.
Silver dressings improve diabetic wound healing without reducing bioburden. (2013)

The results demonstrate improved healing and reduced bioburden in normal wounds with silver dressings. In contrast, silver dressings improved healing in diabetic wounds despite no effect on bioburden, suggesting silver may have beneficial effects in addition to its antimicrobial properties.
Identification of Aldolase as a Target Antigen in Alzheimer’s Disease (2005)

Alzheimer's disease (AD) is the most common human neurodegenerative disease, leading to progressive cognitive decline and eventually death. The prevailing paradigm on the pathogenesis of AD is that abnormally folded proteins accumulate in specific brain areas and lead to neuronal loss via apoptosis. In recent years it has become evident that an inflammatory and possibly autoimmune component exists in AD. Moreover, recent data demonstrate that immunization with amyloid-beta peptide is therapeutically effective in AD. The nature of CNS Ags that are the target of immune attack in AD is unknown. To identify potential autoantigens in AD, we tested sera IgG Abs of AD patients in immunoblots against brain and other tissue lysates. We identified a 42-kDa band in brain lysates that was detected with >50% of 45 AD sera. The band was identified by mass spectrometry to be aldolase A. Western blotting with aldolase using patient sera demonstrated a band of identical size. The Ab reactivity was verified with ELISAs using aldolase. One of 25 elderly control patients and 3 of 30 multiple sclerosis patients showed similar reactivity (p < 0.002). In enzymatic assays, anti-aldolase positive sera were found to inhibit the enzyme's activity, and the presence of the substrate (fructose 1,6-diphosphate) enhanced Ab binding. Immunization of rats and mice with aldolase in complete Freund's adjuvant was not pathogenic. These findings reveal an autoimmune component in AD, point at aldolase as a common autoantigen in this disease, and suggest a new target for potential immune modulation.
Results of phase III trial of rh-endostatin (YH-16) in advanced non-small cell lung cancer (NSCLC) patients (2005)

7138 Background: Endostar (rh-endostatin, YH-16) is a new recombinant human endostatin developed by Medgenn Co. Ltd. Pre-clinical study indicates that it can inhibit tumor endothelial cell proliferation, angiogenesis, and tumor growth. Phase I and Phase II studies revealed that Endostar was effective as single agent with good tolerance in clinical use. This study is to compare the response rate, median time to progression (TTP), clinical benefit, and safety in patients with advanced NSCLC, treated with Endostar plus vinorelbine and cisplatin (NP) or placebo plus NP. Methods: 493 histology or cytology confirmed stage IIIB and IV NSCLC patients, life expectancy >3 months, and WHO performance status 0–2 patients were entered in a double-blind, placebo-controlled, prospectively randomized trial after stratification, either Arm A: NP plus Endostar (n=326; vinorelbine 25mg/m2 on day 1 and 5, cisplatin 30mg/ m2 on days 2 to 4, Endostar 7.5 mg/ m2 on days 1 to 14) or Arm B: NP plus placebo (n=167; vinorelbine 25mg/m2 on day 1 and day5, cisplatin 30mg/ m2 on days 2 to 4, 0.9% sodium-chloride 3.75 ml on days 1 to 14) every 3 weeks for 2–6 cycles, according to the response after the second cycles, i.e. CR,PR,SD continue to receive treatment; while PD stop treatment. The response and adverse effects were evaluated by an Independent Experts Evaluation Committee (IEEC) before open the code. Results: Of the 486 assessable patients, overall response rates were 35.4% in Arm A and 19.5% in Arm B (P=.0003). The median TTP were 6.3 and 3.6 months for Arm A and B respectively (P<.001). The clinical benefit rates were 73.3% in Arm A and 64.0% in Arm B (P=.035). Grade 3/4 neutropenia, anemia, nausea/vomiting were 28.5%, 3.4%, 8.0% respectively in Arm A, as compared with 28.2%, 3.0%, 6.6% in Arm B(P>.05). There were 2 treatment-related death in Arm A and 1 in Arm B (P>.05). Conclusion: The addition of Endostar to NP regimen resulted in significant and clinically meaningful improvement in response rate, median TTP, and clinical benefit rate compared with NP alone in advanced NSCLC patients. Recombinant rh-Endostatin in combination with chemotherapy showed a synergic activity and a favorable toxic profile in advanced cancer patients. No significant financial relationships to disclose.
La biologie moléculaire au service de la virologie médicale quotidienne1. Principes méthodologiques (1997)

Les methodes de biologie moleculaire, en etant capables de detecter quelques copies de genome, permettent de determiner de nouveaux parametres pour repondre aux objectifs de la virologie quotidienne moderne de diagnostic, de pronostic, de mesure de la charge virale et de detection des resistances aux antiviraux en complement ou en association avec la culture cellulaire et la recherche des antigenes et des anticorps. Les techniques, basees sur la connaissance des genomes et de la replication intracellulaire des virus et sur l'utilisation des outils du genie genetique, comportent l'hybridation moleculaire (dot-blot, southern-blot, hybridation en phase liquide, hybridation in situ), l'amplification enzymatique (PCR, PCR nichee, RT-PCR, NASBA, ADNb, PCR in situ, PCR multiplex), la quantification des genomes (PCR ou RT-PCR quantitative, NASBA, ADNb) et le genotypage (types viraux, mutants, variants). La revelation des fragments genomiques extraits, natifs ou amplifies avec un nucleotide marque (dUTP biotine ou dUTP digoxigenine), est effectuee par electrophorese en gel suivie d'hybridation ou en microplaques par test colorimetrique enzymatique ou en biochimioluminescence.
Evaluation of Monoclonal Antifibrin Antibodies by Their Binding to Human Blood Clots (1987)

The primary goal of this study was to develop a method for evaluating fibrin-specific antibodies as thrombus detecting agents. The apparatus and assay conditions were chosen by testing antibody 64C5, which binds to the amino terminus of the fibrin beta chain, for its ability to bind to human blood clots. Using 125I-labeled antibody 64C5, the effects of antibody concentration, clot shape, clot mass, temperature, and flow rate were tested. Increased antibody binding was observed when antibody concentration, clot mass and temperature were increased. Under one set of conditions, six 125I-labeled monoclonal antifibrin antibodies (four specific for the beta chain, two specific for the alpha chain) were tested for their binding to retracted clots of human blood. Two radioiodinated antidigoxin antibodies were used as a control. Beta chain-specific antibody 59D8, which provided the highest level of binding to clot, bound 14-fold better than the control antidigoxin antibody. Neither alpha chain-specific antibody bound to clotted blood. To examine the in vivo relevance of the in vitro binding to clots, the uptake of antibody 64C5 was assessed for its binding to human fibrin clotted within the jugular vein of a rabbit. The correlation coefficient between in vitro and in vivo uptake as a function of clot weight was calculated to be 0.91. Thus, in vitro binding of monoclonal antifibrin antibodies to human blood clots was judged to be a realistic method for the comparison and selection of an ideal antifibrin antibody for detailed in vivo testing.
Identification of active-site cysteines in the conserved domain of PilD, the bifunctional type IV pilin leader peptidase/N-methyltransferase of Pseudomonas aeruginosa (1993)

PilD is a bifunctional enzyme responsible for cleavage of the leader peptides from the precursors of the type IV pilin and four proteins with type IV pilin-like amino termini that are required for extracellular protein secretion in Pseudomonas aeruginosa. Following cleavage, PilD also catalyzes the second major posttranslational modification of these proteins, namely the N-methylation of the amino-terminal phenylalanine residues of the mature polypeptides. In this report, we demonstrate that the enzymatic activities of PilD involve cysteine residues that lie within a cytoplasmic domain that shows a high degree of similarity to other proteins postulated to perform the same function in other bacterial species. Both activities are reduced in the presence of sulfhydryl-reactive reagents such as N-ethylmaleimide and p-chloromercuribenzoate. Mutagenesis of pilD resulting in specific amino acid substitutions in all of the Cys residues in PilD show that the 4 conserved cysteines in the cytoplasmic domain are required for full peptidase activity in vivo and for complete peptidase and methyltransferase activities in vitro. Conversely, substitution for a Cys residue in a membrane spanning domain had no effect on PilD activities in vivo or in vitro. Evidence suggests that the peptidase and methyltransferase sites of PilD are adjacent, with the Cys residues in the cytoplasmic domain important for methyl donor binding, as prior reaction of PilD with the S-adenosyl-L-methionine analogue sinefungin afforded complete protection of peptidase activity from inactivation with N-ethylmaleimide.
The monoclonal antibody directed to difucosylated type 2 chain (Fuc alpha 1 leads to 2Gal beta 1 leads to 4[Fuc alpha 1 leads to 3]GlcNAc; Y Determinant). (1983)

One of the monoclonal (AH-6) antibodies prepared by hybridoma technique against human gastric cancer cell line MKN74 was found to react with a series of glycolipids having the Y determinant (Fuc alpha 1 leads to 2Gal beta 1 leads to 4[Fuc alpha 1 leads to 3]GlcNAc). The structure of one such glycolipid isolated from human colonic cancer and from dog intestine was identified as lactodifucohexaosyl-ceramide (Fuc alpha 1 leads to 2Gal beta 1 leads to 4[Fuc alpha 1 leads to 3]GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc beta 1 leads to 1-ceramide; IV3,III3Fuc2nLc4Cer). The hapten glycolipid did not react with monoclonal antibodies directed to Lea, Leb, and X-hapten structures, and the AH-6 antibody did not react with the X-hapten ceramide pentasaccharide (Gal beta 1 leads to 4[Fuc alpha 1 leads to 3]GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc beta 1 leads to 1-ceramide), H1 glycolipid (Fuc alpha 1 leads to 2Gal beta 1 leads to 4GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc beta 1 leads to 1-ceramide), nor with glycolipids having the Leb (Fuc alpha 1 leads to 2Gal beta 1 leads to 3[Fuc alpha 1 leads 4]GlcNAc beta 1 leads to R) determinant. The antibody reacted with blood group O erythrocytes, but not with A erythrocytes. Immunostaining of thin layer chromatography with the monoclonal antibody AH-6 indicated that a series of glycolipids with the Y determinant is present in tumors and in O erythrocytes.