gebhart/patrepeval huggingface dataset:
ECM dependent and integrin mediated tumor cell migration of human glioma and melanoma cell lines under serum-free conditions. (1997)

Collagen IV, laminin and fibronectin are constituents of the cerebral extracellular matrix (ECM), which is critical in glioma cell invasion. The aim of the present study was to evaluate the integrin dependent cell-matrix interactions of two tumors with different invasive properties under matrixfree conditions. Two human glioma (GaMG, U373) and melanoma (MV3, BLM) cell lines were grown in serum free medium. Immunofluorescence microscopy of collagen IV, laminin, and fibronectin was performed. The adhesion of monolayer cells and their migration out of multicellular spheroids was quantified for these ECM components. Integrin chains known to act as laminin receptors were blocked by specific antibodies in additional migration assays. All cell lines expressed all the ECM components under serum free conditions. Tumor cell adhesion and migration in both glioma and melanoma cell lines was increased by all the ECM components, laminin being the strongest promotor of migration. However, migration was dose dependent in gliomas, whereas melanomas revealed a dose optimum of 10 micrograms/ml laminin. Antibodies against alpha 3 integrins significantly reduced migration on laminin in all cell lines, anti-beta 1 in all cell lines except U373. Anti-alpha 2 in BLM showed a strong effect, anti-alpha 6 was a stronger inhibitor in glioma than in melanoma cells. Integrins are functionally involved in tumor cell locomotion on laminin. The blocking of laminin related integrin chains markedly reduces cell motility in a varying manner between the cell lines. Moreover, different cell lines utilize different integrins as the laminin receptor.
Anti-CD69 Autoantibodies Cross-React with Low Density Lipoprotein Receptor-Related Protein 2 in Systemic Autoimmune Diseases (2001)

We investigated whether autoantibodies to CD69, one of the earliest markers of lymphocyte activation, exist in the sera of patients with systemic autoimmune disease. Serum samples were obtained from patients with rheumatoid arthritis (RA), systemic lupus erythematosus, and Behcet's disease, and were tested for the presence of anti-CD69 autoantibodies by ELISA and Western blotting using rCD69 fusion proteins. IgG-type autoantibodies to CD69 were detected in the sera of 38.3% of the RA patients, 14.5% of the systemic lupus erythematosus patients, and 4.0% of the patients with Behcet's disease. Among those with RA, the anti-CD69 autoantibody-positive patients had a higher serum level of rheumatoid factors and a more accelerated erythrocyte sedimentation rate than the anti-CD69 autoantibody-negative patients. Further, the predominant epitope on the CD69 molecule to which most of the anti-CD69 autoantibody-positive serum samples exclusively reacted, was mapped at the C terminus of CD69. Of interest, this epitope is homologous to a stretch of amino acids in the protein sequence of low-density lipoprotein receptor-related protein 2 (LRP2), which is a receptor for multiple ligands including beta-very low density lipoprotein and is also an autoantigen responsible for Heymann nephritis in rats. The anti-CD69 autoantibody cross-reacted to LRP2 through the homologous amino acid sequence. To our knowledge, this is the first evidence of the existence of anti-CD69 autoantibodies. This autoantibody may modulate the function of CD69- and LRP2-expressing cells.
Mechanistic Role of an NS4A Peptide Cofactor with the Truncated NS3 Protease of Hepatitis C Virus:  Elucidation of the NS4A Stimulatory Effect via Kinetic Analysis and Inhibitor Mapping (1997)

Infection by hepatitis C viruses (HCVs) is a serious medical problem with no broadly effective treatment available for the progression of chronic hepatitis. The catalytic activity of a viral serine protease located in the N-terminal one-third of nonstructural protein 3 (NS3) is required for polyprotein processing at four site-specific junctions. The three-dimensional crystal structure of the NS3-NS4A co-complex [Kim, J. L., Morgenstern, K. A., Lin, C., Fox, T., Dwyer, M. D., Landro, J. A., Chambers, S. P., Markland, W., Lepre, C. A., O'Malley, E. T., Harbeson, S. L., Rice, C. M., Murcko, M. A., Caron, P. R., & Thomson, J. A. (1996) Cell 87, 343-355] delineates a small hydrophobic region within the 54-residue NS4A protein that intercalates with and makes extensive contacts to the core of the protease. The current investigation addresses the mechanism of NS3 protease catalytic activation by NS4A utilizing a small synthetic NS4A peptide (residues 1678-1691 of the virus polyprotein sequence) and the recombinantly expressed protease domain of NS3. The addition of NS4A dramatically increased NS3 kcat and kcat/Km catalytic parameters when measured against small peptide substrates representing the different site-specific junctions of the polyprotein. The catalytic effect of natural and non-natural amino acid substitutions at the P1 position in a 5A/5B peptide substrate was investigated. NS3-NS4A demonstrated a marked catalytic preference for the cysteine residue commonly found in authentic substrates. The pH dependence of the NS3 hydrolysis reaction is not affected by the presence of NS4A. This result suggests that NS4A does not change the pKa values of the active site residues of NS3 protease. A steady state kinetic analysis was performed and indicated that the binding of NS4A and the peptide substrate occurs in an ordered fashion during the catalytic cycle, with NS4A binding first. Two distinct kinetic classes of peptidyl inhibitors based upon the 5A/5B cleavage site were identified. An NS4A-independent class is devoid of prime residues. A second class of inhibitors is NS4A-dependent and contains a natural or non-natural cyclic amino acid substituted for the commonly found P1' residue serine. These inhibitors display an up to 80-fold increase in affinity for NS3 protease in the presence of NS4A. Sequential truncation of prime and P residues from this inhibitor class demonstrated the fact that the P4' and P1' residues are crucial for potent inhibition. The selectivity of this NS4A effect is interpreted using a model of the 5A/5B decapeptide substrate bound to the active site of the NS3-NS4A structure.
Design and Evaluation of a High-Frequency LTCC Inductor Substrate for a Three-Dimensional Integrated DC/DC Converter (2012)

High operating frequency and integration technique are two main approaches to achieve high power density for the switching mode power supply. The emerging gallium nitride (GaN)-based power device enables a multimegahertz high-efficiency point-of-load (POL) converter with high current capability. The low-temperature cofire ceramic (LTCC)-based integration technique successfully extends the three-dimensional (3-D) integrated POL module from the low current level to the high current level (>10 A). This paper presents the low-profile LTCC inductor substrate design and evaluation for a multimegahertz 3-D integrated POL converter with large output current. The detailed study about the impact of frequency on the LTCC inductor shows that the high frequency not only shrinks the volume of the inductor, but also simplifies the inductor structure. The comparison between the LTCC inductor and the discrete inductor demonstrates that the LTCC inductor dramatically boosts the converter light-load efficiency due to its nonlinear inductance. Because of the low-profile design, the power density of the single-phase POL module with LTCC inductor achieves 1.1 kW/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> at 5 MHz. The performance of the LTCC inductor can be further improved by the inverse coupling, which results in more than 40% core thickness and core loss reduction. Therefore, the power density of a two-phase integrated POL module is pushed to 1.5 kW/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , which is around ten times of the power density of state-of-the-art industry products with the same current level.
Personalized Therapy (2017)

Adoptive cell therapy using endogenous T cells involves the ex vivo isolation and expansion of antigen-specific T cells from the peripheral blood and is uniquely suited for validating and translating antigen discovery. Endogenous T-cell therapy does not require accessible tumor as a source of infiltrating T cells and is free of regulatory and logistical constraints associated with engineering T cells. Candidate epitope peptides identified through antigen discovery may be rapidly implemented as targets in clinical trials of endogenous T-cell therapy and even incorporated as an "ad hoc" approach to personalized treatment when autologous tumor is available. Several first-in-human studies using a uniform population of antigen-specific T cells defined by phenotype and specificity have provided a means to confirm candidate antigens as potential tumor rejection antigens and to evaluate the reasons for success or failure using as a "transferrable cellular biomarker" the adoptively transferred T cells.
Meningococcal C Polysaccharide Vaccine Induces Immunologic Hyporesponsiveness in Adults That Is Overcome by Meningococcal C Conjugate Vaccine (2000)

Widespread use of meningococcal AC polysaccharide (MACP) vaccines has raised concerns about induction of hyporesponsiveness to C polysaccharide. Whether meningococcal C conjugate (MCC) vaccine overcomes any immunologic refractoriness following MACP vaccination in adults was investigated. University students vaccinated 6 months previously with MACP vaccine were randomized to receive MACP or MCC vaccine, and antibody responses were compared with those of previously unvaccinated students receiving MACP or MCC vaccine. In students primed with MACP vaccine, MCC vaccine induced significantly higher IgG and serum bactericidal antibody levels than did a second dose of MACP vaccine. Responses to a second dose of MACP vaccine were significantly lower than to the first dose. Previous receipt of MACP vaccine reduced serum bactericidal antibody but not IgG responses to MCC vaccine compared with those in previously unvaccinated students. This confirms that MACP vaccine induces immunologic hyporesponsiveness to C polysaccharide in adults, but this can be overcome with MCC vaccine. Repeated vaccination with MACP vaccine may be ineffective, and MCC vaccines should provide better long-term protection.
The dual role of factor VII in blood coagulation. Initiation and inhibition of a proteolytic system by a zymogen. (1982)

Factor W, a single-chain zymogen, is known to be unusually active with respect to ester hydrolysis and inhibition by diisopropylfluorophosphate (DFP).Assays of coagulant activity have shown the zymogen to contain 1-2% of the activity of its two-chain derivative enzyme, Factor VII,.This activity could be inherent in the zymogen or due to contamination with Factor VII.. To distinguish between these possibilities and to confirm the activity of the zymogen, we show the following: 1) Factor W inhibits the activation of 3H-labeled Factor M by Factor W, when tissue factor is limiting, indicating that enzyme and zymogen compete for the cofactor.In contrast, when tissue factor is in excess, the activities are additive.2) Diisopropylphosphoryl derivatives of Factor W and Factor VII, both inhibit the radioassay for Factor W,-tissue factor, the KlIz of inhibition being 2.8 k 0.4 and 2.0 k0.2 m, respectively.3) The rate of incorporation of r3H]DFP by these proteins is insensitive to trace contamination; pseudo-first order rate constants were calculated for the incorporation of 2 ~l l ~ DFP into Factor VI1 and Factor VII,.These were 0.032 k 0.001 min" and 0.130 k 0.003 min", respectively.Inhibition rates of the coagulant activity of the two proteins were also determined in 2 m M DFP.The inhibition kinetics and the rate constants of incorporation were used to calculate the intrinsic coagulant activity of the zymogen.It was nearly 0.8% that of the enzyme.4) Factor W was rendered virtually free of Factor VII. by incubation with 2 m DFP for over 6 half-lives of Factor VII,.At this point, Factor W had approximately 0.8% the activity of the enzyme.Further, the coagulant activity decayed with the rate constant of the zymogen, 0.033 2 0.003 min-'.We also explored the recent proposal that a ternary complex of tissue factor with Factor VI1 and Factor X, (Morrison-Silverberg, S.
Treatment of atopic dermatitis with alpha 1-proteinase inhibitor. (1992)

Alpha 1-proteinase inhibitor (alpha 1-PI), a serine protease inhibitor, was tested for its efficacy for the treatment of recalcitrant atopic dermatitis. Atopic dermatitis affects both children and adults and has no established etiology. We hypothesized that during inflammation there is an excess of serine proteases and a deficiency of their naturally occurring inhibitors at the local site of tissue injury, even though there is a normal serum level of serine protease inhibitors. This pilot study consisted of a nonblinded trial using alpha 1-PI at a concentration of 20 mg/mL in an aqueous solution in an alternate day schedule in conjunction with a 1% cream of alpha 1-PI (Stage I) and a 5% cream of alpha 1-PI for maintenance therapy (Stage II). Before enrollment in this trial all six patients failed to respond to high potency topical steroids. Safety was gauged by careful clinical monitoring of subjective complaints, objective findings of erythema, edema, and serial measurements of blood chemistries and complete blood counts. Wound healing was documented by serial photography. Written informed consent was obtained from each patient. All six patients showed significant clinical improvement within 6 to 21 days of initiation of alternate day therapy. Alpha 1-PI stopped pain, pruritus, and promoted tissue healing without scarring in all six patients. No adverse side effects of therapy were documented by clinical history, physical examination, or by blood studies after 120 days of therapy. Atopic dermatitis may be one example where inflammation is due to an imbalance of serine proteases and their naturally occurring inhibitors.(ABSTRACT TRUNCATED AT 250 WORDS)
Immunofluorescence versus ELISA for the detection of antinuclear antigens (2002)

Determining the presence and specificity of antinuclear antigens (ANA) is a challenge to a laboratory involved in the diagnosis of connective tissue disease (CTD). The immunofluorescent technique (IF), once considered the gold standard, is more and more displaced by ELISA. ELISA can be fully automated and the interpretation does not require the extensive experience needed in IF. However, literature in which both techniques are compared does not give unequivocal conclusions that ELISA indeed performs better. The clue as to which technique is best in the cascade testing of ANA, is given by its clinical value, not only by its technical and logistic performance. Selective test ordering is strongly recommended to increase the predictive value of these tests. The pros and cons of both techniques are discussed.
Downregulating Viral Gene Expression: Codon Usage Bias Manipulation for the Generation of Novel Influenza A Virus Vaccines (2015)

Vaccination represents the best option to protect humans against influenza virus. However, improving the effectiveness of current vaccines could better stifle the health burden caused by viral infection. Protein synthesis from individual genes can be downregulated by synthetically deoptimizing a gene's codon usage. With more rapid and affordable nucleotide synthesis, generating viruses that contain genes with deoptimized codons is now feasible. Attenuated, vaccine-candidate viruses can thus be engineered with hitherto uncharacterized properties. With eight gene segments, influenza A viruses with variably recoded genomes can produce a spectrum of attenuation that is contingent on the gene segment targeted and the number of codon changes. This review summarizes different targets and approaches to deoptimize influenza A virus codons for novel vaccine generation.
In vivo behavior of epoxy-crosslinked porcine heart valve cusps and walls (2000)

Calcification limits the long-term durability of xenograft glutaraldehyde-crosslinked heart valves. In this study, epoxy-crosslinked porcine aortic valve tissue was evaluated after subcutaneous implantation in weanling rats. Non-crosslinked valves and valves crosslinked with glutaraldehyde or carbodiimide functioned as control. Epoxy-crosslinked valves had somewhat lower shrinkage temperatures than the crosslinked controls, and within the series also some macroscopic and microscopic differences were obvious. After 8 weeks implantation, cusps from non-crosslinked valves were not retrieved. The matching walls were more degraded than the epoxy- and control-crosslinked walls. This was observed from the higher cellular ingrowth with fibroblasts, macrophages, and giant cells. Furthermore, non-crosslinked walls showed highest numbers of lymphocytes, which were most obvious in the capsules. Epoxy- and control-crosslinked cusps and walls induced lower reactions. Calcification, measured by von Kossa-staining and by Ca-analysis, was always observed. Crosslinked cusps calcified more than walls. Of all wall samples, the non-crosslinked walls showed the highest calcification. It is concluded that epoxy-crosslinked valve tissue induced a foreign body and calcification reaction similar to the two crosslinked controls. Therefore, epoxy-crosslinking does not represent a solution for the calcification problem of heart valve bioprostheses.
Efficient Production ofl-Lactic Acid by Metabolically EngineeredSaccharomyces cerevisiaewith a Genome-Integratedl-Lactate Dehydrogenase Gene (2005)

We developed a metabolically engineered yeast which produces lactic acid efficiently. In this recombinant strain, the coding region for pyruvate decarboxylase 1 (PDC1) on chromosome XII is substituted for that of the l-lactate dehydrogenase gene (LDH) through homologous recombination. The expression of mRNA for the genome-integrated LDH is regulated under the control of the native PDC1 promoter, while PDC1 is completely disrupted. Using this method, we constructed a diploid yeast transformant, with each haploid genome having a single insertion of bovine LDH. Yeast cells expressing LDH were observed to convert glucose to both lactate (55.6 g/liter) and ethanol (16.9 g/liter), with up to 62.2% of the glucose being transformed into lactic acid under neutralizing conditions. This transgenic strain, which expresses bovine LDH under the control of the PDC1 promoter, also showed high lactic acid production (50.2 g/liter) under nonneutralizing conditions. The differences in lactic acid production were compared among four different recombinants expressing a heterologous LDH gene (i.e., either the bovine LDH gene or the Bifidobacterium longum LDH gene): two transgenic strains with 2microm plasmid-based vectors and two genome-integrated strains.
Amplification of IgG VH and VL (Fab) from single human plasma cells and B cells (2000)

Amplification of human immunoglobulin has many potential applications such as analysis of clonality, isolation of immunogenic antigens and antigen-specific immunotherapy. Here we describe a method for amplification of human immunoglobulin heavy and light chains from single B lymphocytes or plasma cells. Cells are isolated by FACS, and Ig is amplified by semi-nested RT-PCR. The method is versatile, sensitive and reliable: it provides appropriately paired heavy and light chains, requiring as little as 2 days to produce amplified Fab DNA from human tissues.
A phase Ib/II study testing the safety and efficacy of combined inhibition of the AKT/PI3K and AR signaling pathways in castration-resistant prostate cancer: GDC-0068 or GDC-0980 with abiraterone acetate versus abiraterone acetate. (2012)

TPS2616 Background: Loss of PTEN, leading to activation of the AKT/PI3K pathway is frequent and associated with poor prognosis in prostate cancer. In addition, AR and AKT/PI3K cross-regulate by reciprocal feedback and combined inhibition of both pathways resulted in improved preclinical efficacy. This study is designed to evaluate the effect of combined inhibition of AR pathway (with abiraterone) and AKT/PI3K pathway (with either GDC-0068 or GDC-0980). GDC-0068 is a potent, selective ATP-competitive inhibitor of AKT1, 2, and 3. Preclinical studies showed that cell and tumor models with PTEN loss are more likely to be sensitive to GDC-0068. GDC-0068 was generally well tolerated in phase I and a MTD of 600 mg daily was identified. GDC-0980 is a potent pan-inhibitor of Class I PI3K and inhibits wild-type and mutated p110α isoforms, as well as mTOR kinase. The recommended phase II dose (RP2D) for single-agent GDC-0980 is 40 mg daily. Methods: This study will enroll CRPC patients previously treated with docetaxel. In phase Ib, the RP2D will be determined separately for GDC-0068 and GDC-0980 in combination with abiraterone 1000 mg qd and prednisone 5mg bid. In phase II, patients will be randomized 1:1:1 to receive GDC-0068 + abiraterone, GDC-0980 + abiraterone, or placebo + abiraterone. The primary endpoint of phase II is PFS measured by PCWG2 in all patients and in patients with PTEN loss. Secondary endpoints include OS, PSA response rate, ORR, safety, Pharmacokinetics and biomarker analyses. The effect of each treatment on the number of circulating tumor cells will be assessed. Primary and secondary analyses will include all randomized patients and will be conducted according to assigned treatment arm. Kaplan-Meier methodology will be used to estimate median PFS for each arm. Up to 24 patients are planned to be enrolled in phase Ib; 240 patients (80 per arm) are planned for phase II. This study is open for accrual; to date 2 patients have been enrolled in phase Ib.
Rhabdomyosarcoma in Pediatric Patients (2001)

Rhabdomyosarcoma in Pediatric PatientsThe Good, the Bad, and the UnusualM. Beth McCarville1 2, Sheri L. Spunt3 4 and Alberto S. Pappo3 4Audio Available | Share
Dynamically resizable binary decision diagrams (2010)

We present the architecture of a new Ordered Binary Decision Diagram library that is designed from the ground up to be space efficient. The main novelty lies in the library's node structure, which is modified at run-time to closely follow the variations in size of the stored OBDDs. We compare the new library with existing OBDD libraries on ACM/SIGDA and industrial circuits and report significant performance and space gains.