gebhart/patrepeval huggingface dataset:
Glycosylation and thermodynamic versus kinetic stability of horseradish peroxidase (1998)

The influence of N-linked glycans on the stability of glycoproteins has been studied using horseradish peroxidase isoenzyme C (HRP), which contains eight asparagine-linked glycans. HRP was deglycosylated (d-HRP) with trifluoromethanesulfonic acid and purified to an enzymatically active homogeneous protein containing (GlcNAc)2 glycans. The thermal stability of HRP and d-HRP at pH 6.0, measured by residual activity, was indistinguishable and showed transition midpoints at 57 degrees C, whereas the unfolding in guanidinium chloride at pH 7.0, 23 degrees C was 2-3-fold faster for d-HRP than for HRP. The results are compatible with a glycan-induced decrease in the dynamic fluctuation of the polypeptide chain.
Explosively-driven magnetohydrodynamic (MHD) generator studies (2002)

Plasma jet generators have been designed and tested which used an explosive driver and shocktube with a rectangular cross section that optimize the flow velocity and electrical conductivity. The latest in a series of designs has been tested using a reactive load to diagnose the electrical properties of the MHD generator/electromagnet combination. The results of these tests indicate that the plasma jet/MHD generator design does generate a flow velocity greater than 25 km/s and produces several gigawatts of pulsed power in a very small package size. A larger, new generator design is also presented.
Migration of implanted markers for image‐guided lung tumor stereotactic ablative radiotherapy (2013)

The purpose of this study was to quantify postimplantation migration of percutaneously implanted cylindrical gold seeds ("seeds") and platinum endovascular embolization coils ("coils") for tumor tracking in pulmonary stereotactic ablative radiotherapy (SABR). We retrospectively analyzed the migration of markers in 32 consecutive patients with computed tomography scans postimplantation and at simulation. We implanted 147 markers (59 seeds, 88 coils) in or around 34 pulmonary tumors over 32 procedures, with one lesion implanted twice. Marker coordinates were rigidly aligned by minimizing fiducial registration error (FRE), the root mean square of the differences in marker locations for each tumor between scans. To also evaluate whether single markers were responsible for most migration, we aligned with and without the outlier causing the largest FRE increase per tumor. We applied the resultant transformation to all markers. We evaluated migration of individual markers and FRE of each group. Median scan interval was 8 days. Median individual marker migration was 1.28 mm (interquartile range [IQR] 0.78-2.63 mm). Median lesion FRE was 1.56 mm (IQR 0.92-2.95 mm). Outlier identification yielded 1.03 mm median migration (IQR 0.52-2.21 mm) and 1.97 mm median FRE (IQR 1.44-4.32 mm). Outliers caused a mean and median shift in the centroid of 1.22 and 0.80 mm (95th percentile 2.52 mm). Seeds and coils had no statistically significant difference. Univariate analysis suggested no correlation of migration with the number of markers, contact with the chest wall, or time elapsed. Marker migration between implantation and simulation is limited and unlikely to cause geometric miss during tracking.
Control of Retinal Ganglion Cell Positioning and Neurite Growth: Combining 3D Printing with Radial Electrospun Scaffolds (2016)

Retinal ganglion cells (RGCs) are responsible for the transfer of signals from the retina to the brain. As part of the central nervous system, RGCs are unable to regenerate following injury, and implanted cells have limited capacity to orient and integrate in vivo. During development, secreted guidance molecules along with signals from extracellular matrix and the vasculature guide cell positioning, for example, around the fovea, and axon outgrowth; however, these changes are temporally regulated and are not the same in the adult. Here, we combine electrospun cell transplantation scaffolds capable of RGC neurite guidance with thermal inkjet 3D cell printing techniques capable of precise positioning of RGCs on the scaffold surface. Optimal printing parameters are developed for viability, electrophysiological function and, neurite pathfinding. Different media, commonly used to promote RGC survival and growth, were tested under varying conditions. When printed in growth media containing both brain-derived neurotrophic factor (BDNF) and ciliary neurotrophic factor (CNTF), RGCs maintained survival and normal electrophysiological function, and displayed radial axon outgrowth when printed onto electrospun scaffolds. These results demonstrate that 3D printing technology may be combined with complex electrospun surfaces in the design of future retinal models or therapies.
Notes on the Cell Biology of Tissue Factor (1996)

Tissue factor is both a trigger of blood coagulation and a true receptor inducing an intracellular signal upon binding of its ligand factor VII to its extracellular parts. When induced in endothelial cells more than 75% of tissue factor antigen was found on the apical side of the cell.
First genomic sequence of a human Ig variable λ gene belonging to subgroup I. Functional genes, pseudogenes and vestigial sequences are interspersed in the IGLV locus (1989)

Journal Article First genomic sequence of a human Ig variable λ gene belonging to subgroup I. Functional genes, pseudogenes and vestigial sequences are interspersed in the IGLV locus Get access D. Alexandre, D. Alexandre Laboratoire d'Immunogènètique MolèculaireURA CNRS 199, Universitè des Sciences et Techniques du Languedoc, Place E. Bataillon 34060. Montpellier cedex 1. France Search for other works by this author on: Oxford Academic PubMed Google Scholar P. Chuchana, P. Chuchana Laboratoire d'Immunogènètique MolèculaireURA CNRS 199, Universitè des Sciences et Techniques du Languedoc, Place E. Bataillon 34060. Montpellier cedex 1. France Search for other works by this author on: Oxford Academic PubMed Google Scholar F. Brockly, F. Brockly Laboratoire d'Immunogènètique MolèculaireURA CNRS 199, Universitè des Sciences et Techniques du Languedoc, Place E. Bataillon 34060. Montpellier cedex 1. France Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Blancher, A. Blancher Laboratoire d'Immunogènètique MolèculaireURA CNRS 199, Universitè des Sciences et Techniques du Languedoc, Place E. Bataillon 34060. Montpellier cedex 1. France Search for other works by this author on: Oxford Academic PubMed Google Scholar G. Lefranc, G. Lefranc Laboratoire d'Immunogènètique MolèculaireURA CNRS 199, Universitè des Sciences et Techniques du Languedoc, Place E. Bataillon 34060. Montpellier cedex 1. France Search for other works by this author on: Oxford Academic PubMed Google Scholar M.-P. Lefranc M.-P. Lefranc Laboratoire d'Immunogènètique MolèculaireURA CNRS 199, Universitè des Sciences et Techniques du Languedoc, Place E. Bataillon 34060. Montpellier cedex 1. France Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 10, 25 May 1989, Page 3975, https://doi.org/10.1093/nar/17.10.3975 Published: 25 May 1989 Article history Received: 21 April 1989 Published: 25 May 1989
Replication and amplification of defective interfering particle RNAs of vesicular stomatitis virus in cells expressing viral proteins from vectors containing cloned cDNAs (1990)

Replication and amplification of RNA genomes of defective interfering (DI) particles of vesicular stomatitis virus (VSV) depend on the expression of viral proteins and have until now been attained only in cells coinfected with helper VSV. In the work described in this report, we used a recombinant vaccinia virus-T7 RNA polymerase expression system to synthesize individual VSV proteins in cells transfected with plasmid DNAs that contain cDNA copies of the VSV genes downstream of the T7 RNA polymerase promoter. In this way, we were able to examine the ability of VSV proteins, individually and in combination, to support DI particle RNA replication. VSV proteins were synthesized soon after transfection in amounts that depended on the amount of input plasmid DNA and at rates that remained constant for at least 16 h after transfection. When cells expressing the nucleocapsid protein (N), the phosphoprotein (NS), and the large polymerase protein (L) of VSV were superinfected with the DI particles, rapid and efficient replication and amplification of DI particle RNA was observed. Omission of any one of the three viral proteins abrogated the replication. The maximum levels of DI particle RNA replication that were achieved in the system exceeded those seen with wild-type helper VSV by 8- to 10-fold and were observed at molar L:NS:N protein ratios of approximately 1:200:200. This replication system can be used for analysis of structure-function relationships of VSV proteins that are involved in RNA replication and has potential for use in the identification of RNA sequences in the viral genome that control transcription and replication of VSV RNA.
A pilot study comparing the purity, functionality and isoform composition of alpha-1-proteinase inhibitor (human) products (2005)

Zemaira demonstrated greater purity compared with Aralast and Prolastin. Prolastin had more inactive A1-PI than Zemaira or Aralast. Isoform ratios appeared to be altered in Aralast. The results from this pilot study warrant further investigation.
Inhibition of the TGF-β receptor I kinase promotes hematopoiesis in MDS (2008)

MDS is characterized by ineffective hematopoiesis that leads to peripheral cytopenias. Development of effective treatments has been impeded by limited insight into pathogenic pathways governing dysplastic growth of hematopoietic progenitors. We demonstrate that smad2, a downstream mediator of transforming growth factor-beta (TGF-beta) receptor I kinase (TBRI) activation, is constitutively activated in MDS bone marrow (BM) precursors and is overexpressed in gene expression profiles of MDS CD34(+) cells, providing direct evidence of overactivation of TGF-beta pathway in this disease. Suppression of the TGF-beta signaling by lentiviral shRNA-mediated down-regulation of TBRI leads to in vitro enhancement of hematopoiesis in MDS progenitors. Pharmacologic inhibition of TBRI (alk5) kinase by a small molecule inhibitor, SD-208, inhibits smad2 activation in hematopoietic progenitors, suppresses TGF-beta-mediated gene activation in BM stromal cells, and reverses TGF-beta-mediated cell-cycle arrest in BM CD34(+) cells. Furthermore, SD-208 treatment alleviates anemia and stimulates hematopoiesis in vivo in a novel murine model of bone marrow failure generated by constitutive hepatic expression of TGF-beta1. Moreover, in vitro pharmacologic inhibition of TBRI kinase leads to enhancement of hematopoiesis in varied morphologic MDS subtypes. These data directly implicate TGF-beta signaling in the pathobiology of ineffective hematopoiesis and identify TBRI as a potential therapeutic target in low-risk MDS.
Structure from stereo vision using unsynchronized cameras for simultaneous localization and mapping (2005)

This paper presents a system for automatic reconstruction of 3D structure using two unsynchronized cameras. Three images are acquired sequentially from the left, right, and again from the left camera. A virtual image from the left camera synchronized with the right image is created by interpolating matching points of interest (SIFT features) in the two left images. Both geometric and probabilistic criteria are used to select the correct set of matching features amongst the three views. In an indoor environment, the method typically results in 3D structure with approximately 200 feature points, with a median 3D accuracy of 1.6 cm when the average depth is 3 m and the robot has moved 1-2 cm between each image acquisition.
Development of a Cancer-Targeted Tissue-Specific Promoter System (2004)

Present cancer gene therapy using proapoptotic genes has had limited success because the therapy is prone to cause side effects as a result of the lack of tissue and cancer specificity. To target cancer cells without damaging normal cells, we have designed a novel dual promoter system in which a tissue-specific transcription system under the control of a cancer-specific promoter drives expression of a therapeutic gene. The applicability of this system was demonstrated by adapting it to target lung cancer. We termed this lung cancer system TTS (TTF1 gene under the control of human telomerase reverse transcriptase promoter and human surfactant protein A1 promoter). The TTS system showed much higher promoter activity in lung cancer cells compared with other kinds of cancer and normal lung cells, including stem cells. Moreover, insertion of negative glucocorticoid responsive elements in the system allows it to be drug controllable. The approaches that we have used could be adapted to target other types of cancer. We report a novel cancer-targeted tissue-specific dual promoter system designed for gene therapy.
IL-23 Production by Cosecretion of Endogenous p19 and Transgenic p40 in Keratin 14/p40 Transgenic Mice: Evidence for Enhanced Cutaneous Immunity (2003)

p40, the common subunit of the proinflammatory cytokines IL-12 and IL-23, is produced by resident skin cells. Whereas the in vivo effects of IL-12 are well established, little is known about the role of IL-23 in cutaneous immune responses. In this study we show that p40 transgenic (TG) mice constitutively produce IL-23 (p19/p40), but not IL-12 (p35/p40), in basal keratinocytes by cosecretion of TG p40 with endogenous p19. Repeated injections of rIL-23 in littermate (LM) mice result in an inflammatory skin disease similar to that of p40 TG mice, confirming the proinflammatory activity of IL-23. Furthermore, IL-23 secretion by p40 TG keratinocytes induces elevated numbers of Langerhans cells (LC) with a marked up-regulation of costimulatory molecules, indicating advanced maturation of keratin 14 (K14)/p40 LC when compared with LM LC. At the functional level, freshly isolated K14/p40 LC greatly exceeded LC from LM animals in their capacity to stimulate allogeneic T cell proliferation. To assess whether IL-23 regulates cutaneous immune responses in vivo, we used an allogeneic skin transplantation model. Full thickness skin grafts from K14/p40 donors (H-2(q)) transplanted across a MHC class I and class II barrier onto BALB/c (H-2(d)) recipients were rejected in a significantly accelerated fashion (mean survival time: 8.8 days) when compared with skin grafts from non-TG LM (H-2(q)) (mean survival time: 10.7 days, p < 0.01). Based on these results we propose that IL-23-induced changes of LC may be an important mechanism in directing the outcome of cutaneous immune responses.
A detector tree of boosted classifiers for real-time object detection and tracking (2003)

This paper presents a novel tree classifier for complex object detection tasks together with a general framework for real-time object tracking in videos using the novel tree classifier. A boosted training algorithm with a clustering-and-splitting step is employed to construct branches in the nodes recursively, if and only if it improves the discriminative power compared to a single monolithic node classifier and has a lower computational complexity. A mouth tracking system that integrates the tree classifier under the proposed framework is built and tested on XM2FDB database. Experimental results show that the detection accuracy is equal or better than a single or multiple cascade classifier, while being computational less demanding.
Nonlinear Kinetics After High–Dose Omeprazole Caused by Saturation of Genetically Variable Cyp2c19 (1996)

Nonlinear kinetics of omeprazole and its metabolites were investigated after treatment with repeated high doses. Extensive metabolizers relating to cytochrome P450 2C19 (CYP2C19) activity received for 1 week either omeprazole at 40 mg/d (n = 14) or 60 mg/d omeprazole twice daily (n = 8). Five poor metabolizers (PMs) received 40 mg/d for 1 week. Comparison of omeprazole plasma kinetics between extensive metabolizers (EMs) and PMs after 40-mg treatment revealed a dominant role of CYP2C19 over cytochrome P450 3A CYP3A in omeprazole metabolism. Comparing the omeprazole doses of 40 mg and 60 mg in eight EMs on day 7 of treatment showed that CYP2C19-dependent plasma clearance of omeprazole and omeprazole sulfone was reduced from 19.0 to 8.4 L/h (P < .001) and from 19.8 to 9.2 L/h (P = .012), respectively. Similarly, formation half-life of 5'-hydroxyomeprazole increased from 0.58 to 1.45 hours (P = .025) with the higher dose. CYP3A-dependent metabolic routes remained unaffected. Thus, high-dose treatment with omeprazole uncovers saturation kinetics for CYP2C19 pathways in EMs, and CYP3A becomes the predominant enzyme of omeprazole elimination. Moreover, these individuals may be at risk for side effects due to high omeprazole concentrations if high-dose omeprazole treatment is combined with drugs inhibiting CYP3A activity.
Ganglioside‐Induced Neuritogenesis: Verification That Gangliosides Are the Active Agents, and Comparison of Molecular Species (1983)

Gangliosides were previously reported to induce neuritogenesis in primary neuronal cultures and in some neurally derived cell lines. Because isolated gangliosides usually contain variable quantities of peptides, we investigated the possibility that neurite-stimulating activity could be caused by these contaminants. Ganglioside preparations from bovine brain and other sources were subjected to a three-step purification procedure that eliminated at least 95% of the contaminating peptides. These purified preparations retained their capacity to induce extensive neurite growth in neuro-2A murine neuroblastoma. Proteolytic digestion and a number of additional procedures were used to reduce residual contamination further without loss of activity. Several crude ganglioside samples had negative effects on neurite development until freed of their inhibitory factors, which were derived from the tissue and/or introduced during laboratory operations. This was particularly evident for bovine white matter gangliosides whose activity increased in proportion to peptide removal. When carefully purified, virtually all of 11 different gangliosides tested were highly active, with the possible exception of GM4, which demonstrated only moderate activity in a limited number of tests. All of the neutral glycolipids tested, as well as sulfatides and free sialic acid, were inactive.
Silicon-on-Insulator Wafers with Buried Cavities (2006)

Direct bonding and mechanical thinning of pre-etched silicon wafers have been studied for the fabrication of silicon-on-insulator (SOI) wafers with buried cavities. The thin Si diaphragm over the cavity is deflected downward during the grinding and polishing, as the thinning is carried out without supporting the diaphragm. The deflection causes thickness variation for the Si diaphragm that can also be observed as a hill on the wafer surface after thinning. The results show that the thickness variation of the Si diaphragm increases with increasing cavity size and with decreasing SOI layer thickness. After grinding the measured hill height was about for a -thick Si diaphragm over a cavity. The hill height was reduced to less than when a small supporting column was placed under the diaphragm. With polishing the hill height was further reduced to . It appears that mechanical thinning of the bonded wafers with pre-etched cavities is a viable method for various applications.
Monoclonal antibodies in the treatment of non-Hodgkin's lymphoma: recent results and future prospects. (1997)

The availability of monoclonal antibodies with well-defined specificities to lymphoma-associated antigens promises to open new therapeutic opportunities in the treatment of patients with non-Hodgkin's lymphoma. Monoclonal antibodies against lineage-specific surface markers such as CD19, CD20 or CD22 have been generated and employed in native or modified forms in clinical phase I/II trials. Modified versions such as toxin-conjugated antibodies or antibodies with dual specificities (bispecific antibodies) were introduced to enhance the cytotoxicity of monoclonal antibodies since native antibodies were not able to induce long-lasting remissions in patients with advanced disease although responses were seen and side-effects were usually mild. Future efforts should concentrate on patients with minimal residual disease employing genetically engineered antibody fragments.
Acetylation genotype and phenotype in patients with systemic lupus erythematosus. (2006)

Acetylation polymorphism appears not to be an important risk factor in SLE.
Mechanism of action of Escherichia coli exonuclease III (1989)

Exonuclease III is the major apurinic/apyrimidinic (AP) endonuclease of Escherichia coli, accounting for more than 80% of the total cellular AP endonuclease activity. We have shown earlier that the endonucleolytic activity of exonuclease III is able to hydrolyze the phosphodiester bond 5' to the urea N-glycoside in a duplex DNA [Kow, Y. W., & Wallace, S. S. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 8354-8358]. Therefore, we were interested in studying the mechanism of action of the endonucleolytic activity of exonuclease III by preparing DNA containing different base lesions as well as chemically modified AP sites. When AP sites were converted to O-alkylhydroxylamine residues, exonuclease III was able to hydrolyze the phosphodiester bond 5' to O-alkylhydroxylamine residues. The apparent Km for different O-alkylhydroxylamine residues was not affected by the particular O-alkylhydroxylamine residue substituted; however, the apparent Vmax decreased as the size of the residue increased. On the basis of a study of the substrate specificity of exonuclease III, a modification of the Weiss model for the mechanism of action of exonuclease III is presented. Furthermore, a temperature study of exonucleolytic activity of exonuclease III in the presence of Mg2+ showed discontinuity in the Arrhenius plot. However, no discontinuity was observed when the reaction was performed in the presence of Ca2+. Similarly, no discontinuity was observed for the endonucleolytic activity of exonuclease III, in the presence of either Ca2+ or Mg2+. These data suggest that, in the presence of Mg2+, exonuclease III, in the presence of either Ca2+ or Mg2+.(ABSTRACT TRUNCATED AT 250 WORDS)
A hypo‐osmotic medium to disaggregate tumor cell clumps into viable and clonogenic single cells for the human tumor stem cell clonogenic assay (1983)

A hypo-osmolar medium and tissue processing technique is described which is useful for disaggregation of residual human tumor cell clumps persisting after mechanical or enzymatic treatment of solid tumors and malignant effusions. The addition of the hypo-osmolar procedure to the standard methods for disaggregation increased the viable single cell yield in solid tumors by 47% and in malignant effusions by 67%. In 5 of the 26 solid tumor specimens tested in the human tumor stem cell assay, clonogenic single cells were obtained with the hypo-osmolar procedure, whereas no growth was observed using standard methods. Overall, the success rate for clonogenicity increased from 46% to 65% for the 26 solid tumors, with the major improvement occurring in ovarian cancer. Clonogenicity was obtained in 80% of malignant effusions both by standard methods and the hypo-osmolar techniques. The increased total yield of clonogenic cells obtained with this procedure enhances the opportunity for experimental versatility and in vitro drug testing.