gebhart/patrepeval huggingface dataset:
Protein kinase C phosphorylates two of the four known syndecan cytoplasmic domains in vitro. (1995)

The transmembrane heparan sulfate proteoglycans of the syndecan family are implicated to participate in several cellular reactions which are dependent on protein kinase C. We have used an in vitro assay to assess whether any of the Peptides corresponding to the complete cytoplasmic domains of rat syndecans 1 through 4 were used as substrates for the enzyme. The syndecan-2 (fibroglycan) and syndecan-3 (N-syndecan) peptides were both found to be phosphorylated by protein kinase C with Kms of 15 +/- 3 microM and 85 +/- 25 microM, respectively, while the syndecan-1 and -4 peptides were not phosphorylated under the conditions used. The sites of in vitro phosphorylation for syndecans-2 and -3 were localized to ser-197 and ser-339, respectively. Thus, among 13 available sites (serines and threonines) in the four peptides, two were selectively modified by the enzyme. The specificity and the kinetics of the reactions indicate that the cytoplasmic domains of syndecan-2 and -3 are likely to be physiological substrates for protein kinase C.
Tyrosine kinase inhibition of multiple angiogenic growth factor receptors improves survival in mice bearing colon cancer liver metastases by inhibition of endothelial cell survival mechanisms. (2001)

Redundant mechanisms mediate colon cancer angiogenesis. Targeting multiple angiogenic factors simultaneously may improve survival of mice with colon cancer metastases. BALB/c mice underwent splenic injection with CT-26 colon cancer cells to generate liver metastases and received administration of either vehicle alone or a tyrosine kinase inhibitor for vascular endothelial growth factor, basic fibroblast growth factor, and platelet-derived growth factor receptors (SU6668). Mice were sacrificed when they became moribund as determined by a blinded observer. In a parallel experiment, groups of mice were sacrificed at earlier time points to better define the kinetics of the effect of SU6668 on angiogenic parameters over time. SU6668 increased median survival by 58% (P < 0.001) and led to a progressive increase in tumor cell and endothelial cell apoptosis that increased over time. In addition, pericyte vessel coverage and tumor vascularity were significantly decreased in mice treated with SU6668. Based on current knowledge of endothelial cell survival, these data suggest that SU6668 may prevent tumor endothelial cell survival directly (vascular endothelial growth factor) and indirectly (pericyte coverage) by affecting endothelial cell survival mechanisms.
Mosaicplasty for the Treatment of Articular Defects of the Knee and Ankle (2001)

Efficacious treatment of full-thickness cartilage defects of the weightbearing surfaces is a multi-faceted challenge for the orthopaedic surgeon. Autologous osteochondral transplantation represents one solution: to bring about a hyaline or hyalinelike repair of the defected area. The current authors discuss the experimental background and their 8 years of clinical experience with the autologous osteochondral mosaicplasty. Several series of animal studies and subsequent clinical practice have confirmed the survival of the transplanted hyaline cartilage. Hyaline cartilage and fibrocartilage fill the donor sites located on the nonweightbearing surfaces and surfaces that bear less weight. Clinical scores, imaging techniques, control arthroscopies, histologic examination of biopsy samples, and cartilage stiffness measurements were used to evaluate the clinical outcomes and quality of the transplanted cartilage. According to these investigations, femoral condylar implantations have shown good to excellent results in 92%, tibial resurfacing in 88%, patellar and/or trochlear mosaicplasties in 81%, and talar procedures in 94% of patients. The Bandi score showed long-term donor site disturbances in 3% of patients. Fifty-eight of the 68 control arthroscopies had good gliding surfaces, histologically-proven survival of the transplanted hyaline cartilage, and fibrocartilage covering of the donor sites. In the entire series, there were four deep infections and 34 painful hemarthroses after surgery. A multicentric, comparative, prospective evaluation of 413 arthroscopic resurfacing procedures (mosaicplasty, Pridie drilling, abrasion arthroplasty, and microfracture cases in homogenized subgroups) showed that mosaicplasty gave a more favorable clinical outcome in the long-term followup, than the other three techniques. Intermediate-term evaluation of the femoral condylar implantations (3-6-years followup) and talar mosaicplasties (3-7-years followup) confirmed the durability of the early results. From these encouraging results from an increasingly large series and similar results from other centers, it seems that autologous osteochondral mosaicplasty may be a viable alternative treatment of localized full-thickness cartilage damage of the weightbearing surfaces of the knee and other weightbearing synovial joints.
Optimization of the scintillation detector in a combined 3D megavoltage CT scanner and portal imager (1998)

A parametric study is described leading to the optimization of a custom-made scintillation detector with a relatively high quantum efficiency (QE) for megavoltage photons and light output toward a remote lens. This detector allows low-dose portal imaging and continuous cone-beam megavoltage CT acquisition. The EGS4 Monte Carlo code was used to simulate the x-ray and electron transport in the detector. A Monte Carlo model of optical photon transport in a detector element was devised and used as well as various irradiation experiments on scintillators. Different detector materials and configurations were compared in terms of the optical photon irradiance on the lens from on- and off-axis detector elements and the practical constraints regarding detector construction and weight. Effects of scintillator material, detector element size, crystal coating type, and reflectivity, combinations of different coatings on detector faces, scintillator doping level, and crystal transparency were studied. With scintillator thickness adjusted to give an 18% x-ray QE at 6 MV, the light output of CsI(Tl) was at least eight times higher than ZnWO4, BGO and NE118 plastic. Further, CsI(Tl) showed the smallest decrease in QE going from 6 to 24 MV. The off-axis reduction in emittance from the periphery of the detector was relatively small with a slight dependence on the type and reflectivity of the coating and the crystal thickness for a fixed detector element cross section. Light output was more strongly dependent on the reflectivity of lambertian coatings than specular ones. For a fixed detector element cross section, optimum coating type depended on crystal thickness. Typical CsI(Tl) crystals showed a relatively small variation in light output with changes in optical attenuation length. The optimum detector element was found to be CsI(Tl) coated on five faces with TiO2-loaded epoxy resin offering about a ten-fold improvement in light output per incident photon compared to typical metal/phosphor screens.
Growth of undulating Si0.5Ge0.5 layers for photodetectors at λ=1.55 μm (1999)

Si 0.5 Ge 0.5 /Si multiquantum-well structures are grown using a production-compatible ultrahigh vacuum chemical vapor deposition system. The structures are designed in order to obtain dislocation-free undulating strained layers used as the absorbing layers in photodetector structures. The Si/SiGe/Si stack on a silicon-on-insulator wafer is used as the waveguiding layer. Transmission electron microscopy and photoluminescence are used to characterize the undulating layers. A photoluminescence emission corresponding to the band edge “no phonon” transition is measured at a wavelength beyond 1.55 μm. Preliminary data from metal–semiconductor–metal photodetectors fabricated with this material show a responsivity of approximately 0.1 A/W at the telecommunication wavelength of λ=1.55 μm.
Early lymphocyte expansion is severely impaired in interleukin 7 receptor-deficient mice. (1994)

Interleukin 7 (IL-7) stimulates the proliferation of B cell progenitors, thymocytes, and mature T cells through an interaction with a high affinity receptor (IL-7R) belonging to the hematopoietin receptor superfamily. We have further addressed the role of IL-7 and its receptor during B and T cell development by generating mice genetically deficient in IL-7R. Mutant mice display a profound reduction in thymic and peripheral lymphoid cellularity. Analyses of lymphoid progenitor populations in IL-7R-deficient mice define precisely those developmental stages affected by the mutation and reveal a critical role for IL-7R during early lymphoid development. Significantly, these studies indicate that the phase of thymocyte expansion occurring before the onset of T cell receptor gene rearrangement is critically dependent upon, and mediated by the high affinity receptor for IL-7.
Quantitative Evaluation of Factor VIII in Factor VIII Products. (2004)

Abstract Several factor VIII products, recombinant and natural, have been used for hemophilia A treatment worldwide. Typically, two activity-based assays (factor Xase and aPTT) are used for the assessment of factor VIII concentration in these products. Frequently, the results are dependent upon the assay and its modifications in different laboratories. In this study, we evaluated five pharmacologic factor VIII products (three lots of each) in three activity-based assays and in two immunoassays for the concentration and activity of factor VIII protein. Two factor VIII products were plasma-derived (Immunate and Hemofil M) and three were recombinant; two of these contained full-length factor VIII (Recombinate and Kogenate) and one was B-domainless (ReFacto). Albumin-free full-length recombinant factor VIII was used as a standard in all assays. In the factor Xase assay, all recombinant factor VIII products and Immunate at 1U/ml (indicated by manufacturer) showed activity similar to that of 0.7nM (1U/ml) standard, whereas activity of Hemofil M was 64–68% of the standard. In the aPTT assay both full-length recombinant products and Hemofil M displayed activity similar to the standard, whereas Immunate had increased (142% of standard) and ReFacto decreased (83% of standard) activity. In synthetic plasma, all three recombinant products had standard-like activity, whereas Hemofil M and Immunate were slightly more active than standard. The ELISA immunoassay revealed that the factor VIII protein content in Recombinate, Kogenate and Hemofil M corresponded to the units assigned by manufacturers (1.4–1.6x1012U/mol vs1.4x1012U/mol calculated for standard), whereas the specific activity of Immunate was 50% of that expected (0.7x1012U/mol). In contrast, the specific activity of ReFacto was almost 3-fold that of full-length factor VIII (4.0x1012U/mol). The data of this study indicate that: 1) factor VIII activity estimated in different assays gives dissimilar results; 2) the specific activity of factor VIII in various factor VIII products is different and, as a consequence, administration of an equal factor VIII activity in U/ml means the administration of different amounts of factor VIII protein.
Implementation and performance of a femtosecond laser mask repair system in manufacturing (1998)

Current laser based tools for removing Cr defects are fundamentally limited due to the thermal nature of ablation carried out with nanosecond pulses. Conversely, ablation carried out with femtosecond pulses of light removes Cr in a non-thermal process. As a result, the problems of metal splatter, haze, reduced transmission and pitting of the underlying quartz common to nanosecond ablation are virtually nonexistent with femtosecond ablation of Cr. In this paper we describe a femtosecond pulsed laser mask repair system which is presently operating successfully in a manufacturing environment.
A Synthesis of Acetamidines (2011)

The condensation of primary amine with N,N-dimethylacetamide dimethyl acetal yields a mixture of acetamidine and imidate ester. The product distribution in this reaction depends on the temperature, solvent, and structure of the primary amine. It is possible to suppress the formation of imidate ester by performing the reaction in the presence of excess dimethyl amine, yielding acetamidine as the exclusive product. For acetamidines that cannot be purified either by crystallization or distillation, this new method is necessary for the generation of pure acetamidines in good yields.
Integrative Software Design for Reliability: Beyond Models and Defect Prediction (2012)

The prevalence of software as an integral part of almost anything is commonplace today among the products, systems, applications, services and/or solutions with which we all interact. Software reliability directly impacts both the user experience and field operating costs. A key challenge is for the product developer to accurately predict and improve software field reliability in terms of attributes such as outage frequency and duration, prior to software delivery. Unfortunately, the actual field performance data does not often correlate with the predictions. Markov analysis and software reliability growth models are necessary key steps, but are insufficient to fully address customer-perceived reliability issues. Can we make better use of field performance data to improve our predictive models and tune our test strategies from one release to the next? In this paper, we describe an integrative software reliability framework that attempts to close the gap between expectations, predictions, and the actual behavior of systems by leveraging key best-in-class practices, tools, and techniques for software reliability analysis, modeling and predicting software field performance in terms of outage frequency/duration; tracking and monitoring test defect data and defects “not fixed” in subsequent releases over the software lifecycle, and validating prediction results with the actual field data. The proposed approach is designed to achieve customer expectations for software reliability and help assure the delivery of highly reliable software products. © 2012 Alcatel-Lucent.
Proliferation of early human myeloid precursors induced by interleukin- 1 and recombinant soluble CD23 (1990)

Low affinity Fc epsilon receptors (Fc epsilon RII/CD23) or their soluble fragments have various biologic effects on B- and T-cell lineages. In this study, we have assessed the effect of recombinant soluble CD23 (rsCD23) on the proliferation of human bone marrow (BM)-derived myeloid precursors with or without recombinant interleukin-1 (rIL-1) addition. Non-adherent CD2- or CD34+ BM cell subsets were used as target cells. Our results show that rsCD23 in synergy with rIL-1 displays an interleukin-3-like activity as it promotes the proliferation of multipotential marrow precursors. This effect was abolished by anti-CD23 addition to these cultures, but was not affected by anti-IL-3 monoclonal antibody. Furthermore, sequential study indicates that rIL-1 induces bone marrow cell responsiveness to rsCD23.
Thin locks (1998)

Language-supported synchronization is a source of serious performance problems in many Java programs. Even single-threaded applications may spend up to half their time performing useless synchronization due to the thread-safe nature of the Java libraries. We solve this performance problem with a new algorithm that allows lock and unlock operations to be performed with only a few machine instructions in the most common cases. Our locks only require a partial word per object, and were implemented without increasing object size. We present measurements from our implementation in the JDK 1.1.2 for AIX, demonstrating speedups of up to a factor of 5 in micro-benchmarks and up to a factor of 1.7 in real programs.
Heterologous protein production and delivery systems for Lactococcus lactis. (2003)

Lactic acid bacteria (LAB), widely used in the food industry, are present in the intestine of most animals, including humans. The potential use of these bacteria as live vehicles for the production and delivery of heterologous proteins of vaccinal, medical or technological interest has therefore been extensively investigated. Lactococcus lactis, a LAB species, is a potential candidate for the production of biologically useful proteins. Several delivery systems have been developed to target heterologous proteins to a specific cell location (i.e., cytoplasm, cell wall or extracellular medium). A promising application of L. lactis is its use as an antigen delivery vehicle, for the development of live mucosal vaccines. The expression of heterologous proteins and antigens as well as the various delivery systems developed in L. lactis, and its use as an oral vaccine carrier are discussed.
Carbamylated erythropoietin ameliorates the metabolic stress induced in vivo by severe chronic hypoxia (2006)

Ischemia and chronic hypoxia (CH) trigger a variety of adverse effects arising from metabolic stress that injures cells. In response to reduced O2, hypoxia-inducible factor 1alpha (HIF-1alpha) activates erythropoietin (Epo) as well as many other target genes that counteract the effects of O2 deficiency. Epo produced by the kidney stimulates erythrocyte production, leading to decreased HIF-1alpha production by improved tissue O2 delivery. However, Epo is produced by many other tissues, and it is currently unclear to what extent, if any, locally produced Epo modulates HIF-1alpha expression. Derivatives of Epo that possess tissue-protective activities but do not stimulate erythropoiesis [e.g., carbamylated Epo (CEpo)] are useful tools with which to determine whether exogenous Epo modulates HIF-1alpha in the absence of changes in hemoglobin concentration. We compared the effects of CH (6.5% O2 for 10 days) with or without CEpo administered by daily s.c. injection (10 microg/kg of body weight). CEpo administration did not alter the survival rate, weight loss, or increased hemoglobin concentration associated with CH. Therefore, CEpo does not directly suppress HIF-mediated erythropoiesis. CEpo does, however, prevent CH-induced neuronal increases of HIF-1alpha and Epo receptor-associated immunoreactivity (a measure of stress) while reducing the apoptotic index. In contrast, the myocardium did not exhibit increased HIF-1alpha expression during CH, although CEpo did reduce the apoptotic index. These observations therefore demonstrate that CEpo administration reduces the metabolic stress caused by severe CH, resulting in improved cellular survival independent of erythrocyte production.
Analyte Gradient-Surface Plasmon Resonance:  A One-Step Method for Determining Kinetic Rates and Macromolecular Binding Affinities (2000)

A novel one-step method for determining kinetic rates and equilibrium binding affinities, termed analyte gradient-surface plasmon resonance (AG-SPR) is described. A gradient maker or HPLC pump system is used to produce a gradient so that, under continuous-flow conditions, the concentration of analyte passing over the sensor surface increases linearly with time. The rate at which analyte binds to the immobilized receptors is measured by monitoring the change in the surface plasmon resonance minimum as the analyte concentration increases. Kinetic rates are determined by fitting the data to a modified version of the previously described two-compartment model (Schuck, P.; Minton, A. P. Anal. Biochem. 1996, 240, 262-272). Numerical simulations indicate that AG-SPR results in accurate estimates of both kinetic rates and equilibrium affinities regardless of the intrinsic kinetics of the interaction and can be used for systems under mass transport limitations. Simulations also indicate that AG-SPR can be used to characterize interactions that do not obey pseudo-first-order kinetics due to the presence of a heterogeneous receptor population. Experimentally, the interaction of cytochrome c with cytochrome b5 immobilized on a negatively charged monolayer has been characterized by AG-SPR, and both the specific and the nonspecific interactions were quantitatively analyzed. This new technique is advantageous over traditional SPR methods because it eliminates the need for surface regeneration and is significantly faster than traditional titration experiments.
Sideswipe removal via null steering (1992)

Abstract Null steering refers to the removal (or zeroing) of interferences at specified dips by creating receiving patterns with nulls that are aligned on the interferences. This type of beamforming is more effective than forming a simple crossline array and can be applied to both multistreamer and swath data for reducing out-of-plane interferences (sideswipe, boat interference, etc.) that corrupt two-dimensional (2-D) data (the desired signal). Many beamforming techniques lead to signal cancellation when the interferences are correlated with the desired signal. However, a beamforming technique that has been developed is effective in the presence of signal correlated interferences. The technique can be effectively extended to prestack and poststack seismic data.The number of interferences and their dips are identified by a visual examination of the plotted data. This information can be used to design filters that are applied to the total data set. The resulting 2-D data set is free from the crossline interferences with the inline 2-D data remaining unaltered.Model and real data comparisons between null steering and simple crossline array summation show that: (1) null steering significantly attenuates crossline interference, and (2) 2-D inline data, masked by sideswipe, can be revealed once sideswipe is attenuated by null steering. The real data examples show the identification and effective attenuation of interferences that could easily be interpreted as inline 2-D data: (1) an apparent steeply dipping event, and (2) an apparent flat 'bright spot.'
Apoptosis-resistant E1B-19K-expressing NS/0 myeloma cells exhibit increased viability and chimeric antibody productivity under perfusion culture conditions (1999)

We have shown previously that recombinant NS/0 myelomas expressing sufficient amounts of E1B-19K were resistant to apoptosis occurring in the late phase of batch culture and under stressful conditions such as cultivation in glutamine-free medium or following heat shock. However, no significant increase in monoclonal antibodies (MAb) was observed during the prolonged stationary phase of these batch cultures. Here, we show that E1B-19K can enhance cell survival and improve MAb productivity in high cell density perfusion culture. Typically, lymphoid cells grown under steady state in perfusion exhibit decreasing viabilities with concomitant accumulation of apoptotic cells. By modulating the ability of these cells to resist to induction of apoptosis in low nutrient environment, a 3-fold decrease in specific death rate from 0.22 day-1 for NS/0 control to 0.07 day-1 for E1B-19K cells was achieved, resulting in a significant improvement in cell viability throughout perfusion. E1B-19K cells at the perfusion plateau phase also exhibited a 3-fold reduction in specific growth rate concomitant with a lower percentage of S and higher percentage of G1 phase cells. This was associated with a 40% decrease in specific oxygen consumption rate, likely related to a reduction in the specific consumption rates of limiting nutrient(s). Expression of E1B-19K consequently had a significant impact on the steady-state viable cell density, allowing maintenance of 11.5 x 10(6) E1B-19K cells/mL versus 5.9 x 10(6) control NS/0 cells/mL for the same amount of fresh medium brought into the system (half a volume per day). Whereas MAb concentrations found in perfusion culture of control NS/0 myelomas were almost 3-fold higher than those found in batch culture; in the case of E1B-19K-expressing myelomas, the MAb concentration in perfusion was more than 7-fold higher than in batch. This was attributable to the 2-fold increase in viable cell plateau and to a 40% increase in the perfusion to batch ratio of specific MAb productivity (2.2-fold for E1B-19K myelomas versus 1.6-fold for NS/0 control).