gebhart/patrepeval huggingface dataset:
Continuous medium exchange and optically induced electroporation of cells in an integrated microfluidic system (2015)

Optically induced electroporation (OIE) is a promising microfluidic-based approach for the electroporation of cell membranes. However, previously proposed microfluidic cell-electroporation devices required tedious sample pre-treatment steps, specifically, periodic media exchange. To enable the use of this OIE process in a practical protocol, we developed a new design for a microfluidic device that can perform continuous OIE; i.e., it is capable of automatically replacing the culture medium with electroporation buffers. Integrating medium exchanges on-chip with OIE minimises critical issues such as cell loss and damage, both of which are common in traditional, centrifuge-based approaches. Most importantly, our new system is suitable for handling small or rare cell populations. Two medium exchange modules, including a micropost array railing structure and a deterministic lateral displacement structure, were first adopted and optimised for medium exchange and then integrated with the OIE module. The efficacy of these integrated microfluidic systems was demonstrated by transfecting an enhanced green fluorescent protein (EGFP) plasmid into human embryonic kidney 293T cells, with an efficiency of 8.3%. This result is the highest efficiency reported for any existing OIE-based microfluidic system. In addition, successful co-transfections of three distinct plasmids (EGFP, DsRed and ECFP) into cells were successfully achieved. Hence, we demonstrated that this system is capable of automatically performing multiple gene transfections into mammalian cells. A microfluidic device offers a more streamlined approach for introducing foreign genes into mammalian cells. So-called ‘lab-on-a-chip’ systems could simplify and improve the efficiency of many biological techniques by employing microscale channels and valves to precisely control the movement of fluids, cells and reagents. Researchers led by Gwo-Bin Lee of National Tsing Hua University, Hsinchu, have devised such a system to manage the targeted genetic modification of cultured cells via a process known as electroporation. Lee and colleagues constructed microfluidic devices that employ polymeric structures to direct a continuously flowing stream of cells out of their culture medium and into a specialized module for light-induced electroporation. Their approach achieves remarkable efficiency in introducing individual genes into human cells, and the researchers were even able to use their device to deliver three different plasmids simultaneously.
Grammar Sharing Techniques for Rule-Based Multilingual NLP Systems (2007)

Proceedings of the 16th Nordic Conference &#13;\nof Computational Linguistics NODALIDA-2007.&#13;\nEditors: Joakim Nivre, Heiki-Jaan Kaalep, Kadri Muischnek and Mare Koit.&#13;\nUniversity of Tartu, Tartu, 2007.&#13;\nISBN 978-9985-4-0513-0 (online)&#13;\nISBN 978-9985-4-0514-7 (CD-ROM)&#13;\npp. 253-260.
Analysis of the effects of viscosity, volume, and temperature in photopolymer material for holographic applications (2013)

In recent work carried out, we introduced the developments made to the Non-local Photo-polymerization Driven Diffusion model, and illustrate some of the useful trends, which the model predicts and then analyse their implications on photopolymer improvement. The model was improved in its physicality through the inclusion of viscosity effects (changes in fractional free volume), multiple components and their photo-kinetic and photo-physical behaviour, and free space vacuoles. In this paper, we further explore this model to provide a more rigorous and informed basis for predicting the behaviours of photopolymer materials in both photo-chemical and photo-physical sides. Such improvements include a) the analysis of the effects of viscosity on the refractive index modulation, b) the effects of the introduction of free space holes, e.g. the volumetric changes, and c) an examination of the effects of local temperatures and various concentration ratios to optimise material performance.
A Field Case Study of Inter-well Chemical Tracer Test (2015)

Abstract Tracers are increasingly being used as effective reservoir monitoring and surveillance (M&amp;S) tool in the oil and gas industry. They can qualitatively or quantitatively gauge how fluid flows through the reservoir. Tracer surveys, conducted either as interwell tests or single-well tests, are one of the enabling technologies that can be deployed to investigate reservoir flow performance, reservoir connectivity, residual oil saturation and reservoir properties that control displacement processes, particularly in improved oil recovery (IOR) and enhanced oil recovery (EOR) operations. An inter-well chemical tracer test (IWCTT) was designed and implemented in a carbonate field with a diffuse fracture network on peripheral water-flood to determine reservoir connectivity, water breakthrough times, and fluid saturations. The reservoir is heterogeneous with layers of high to low permeability limestone with porosity a range of 20-30%, and interspersed with patchy layers of dolomites and a very competent anhydrite seal. The IWCTT was conducted on a very mature part of the field near the peripheral water injectors to determine the effectiveness of infill injector wells. Four distinct tracers were injected into four individual injectors and the residuals were monitored in four “paired” producers. This paper reviews the complete design and implementation of the test, operational issues, and the analyses and interpretation of the results. The breakthrough times of the tracers are reported and interwell connectivity between the paired and cross-paired injectors and producers are analyzed. Tracers were detected in three of the paired producers, albeit at different breakthrough times. One tracer was also detected in a cross-paired producer. The tracer results were modeled using the current reservoir simulation model with fairly good matches. The tracer data were then used to fine tune the current reservoir simulation model. The IWCTT has been very effective in analyzing well interconnectivity in the reservoir and has led to better reservoir description and an improved dynamic simulation model. Plans for further implementation of this important M&amp;S tool will also be shared.
Novel drug classes: entry inhibitors [enfuvirtide, chemokine (C–C motif) receptor 5 antagonists] (2009)

The rapid pace of scientific discovery and pharmaceutical development has led to the release of several novel and well tolerated antiretroviral agents, with activity against resistant isolates. Entry inhibitors remain a critical therapeutic option for treatment-experienced patients. Providers need to be familiar with these agents, and future drug development should be encouraged.
A Synthetic Peptide Ligand of Neural Cell Adhesion Molecule (NCAM), C3d, Promotes Neuritogenesis and Synaptogenesis and Modulates Presynaptic Function in Primary Cultures of Rat Hippocampal Neurons (2003)

The neural cell adhesion molecule (NCAM) plays a key role in morphogenesis of the nervous system and in remodeling of neuronal connections accompanying regenerative and cognitive processes. Recently, a new synthetic ligand of NCAM, the C3-peptide, which binds to the NCAM IgI module, has been identified by means of combinatorial chemistry (Rønn, L. C. B, Olsen, M., Ostergaard, S., Kiselyov, V., Berezin, V., Mortensen, M. T., Lerche, M. H., Jensen, P. H., Soroka, V., Saffell, J. L., Doherty, P., Poulsen, F. M., Bock, E., Holm, A., and Saffells, J. L. (1999) Nat. Biotechnol. 17, 1000-1005). In vitro, the dendrimeric form of C3, termed C3d, disrupts NCAM-mediated cell adhesion, induces neurite outgrowth, and triggers intracellular signaling cascades similar to those activated by homophilic NCAM binding. The peptide may therefore be expected to regulate regeneration and synaptic plasticity. Here we demonstrate that in primary cultures of hippocampal neurons: 1) C3d induces a sustained neuritogenic response, the neuritogenic activity of the compound being dependent on the dose, starting time, and duration of peptide application; 2) the peptide triggers the neuritogenic response by forming an adhesive substratum necessary for NCAM-mediated neurite formation and elongation; 3) C3d promotes synapse formation; and 4) C3d modulates the presynaptic function, causing a transient increase of the function at low (2 and 5 microm) doses and a reduction when applied at a higher concentration (10 microm). The effect of the peptide is dependent on the activation of the fibroblast growth factor receptor. We suggest that C3d may constitute a useful lead for the development of compounds for treatment of various neurodegenerative disorders.
Heme oxygenase–carbon monoxide signalling pathway in atherosclerosis: anti-atherogenic actions of bilirubin and carbon monoxide? (1999)

Atherosclerosis is a major contributor to cardiovascular disease, and genetic disorders of lipoprotein metabolism are recognized risk factors in atherogenesis. The gaseous monoxides nitric oxide (NO) and carbon monoxide (CO), generated within the blood vessel wall, have been identified as important cellular messengers involved in the regulation of vascular smooth muscle tone. Microsomal heme oxygenases degrade heme to biliverdin and CO, and the cytosolic enzyme biliverdin reductase then catalyzes reduction of biliverdin to bilirubin, both powerful chain-breaking antioxidants. Two principal isozymes of heme oxygenase have been identified, a constitutive isoform HO-2 (M(r) approximately 34,000) and an inducible isoform HO-1 (M(r) approximately 32,000), which is expressed at a low basal level in vascular endothelial and smooth muscle cells and is induced by heavy metals, oxidative stress, inflammatory mediators and oxidized low density lipoproteins. Although NO and CO modulate intracellular cGMP levels, platelet aggregation and smooth muscle relaxation, CO has a much lower affinity for soluble guanylyl cyclase than NO. Decreased production or sensitivity to NO in atherosclerosis may be compensated for by an induction of HO-1, with bilirubin acting as a cellular antioxidant and CO as a vasodilator. This review examines the evidence that oxidized low density lipoproteins (LDL), hypoxia and pro-inflammatory cytokines induce HO-1 expression and activity in vascular endothelial and smooth muscle cells, and evaluates the anti-atherogenic potential of the heme oxygenase signalling pathway.
Fractionation, phosphorylation and ligation on oligonucleotide microchips to enhance sequencing by hybridization (1997)

Oligonucleotide microchips are manufactured by immobilizing presynthesized oligonucleotides within 0.1 x 0.1 x 0.02 mm or 1 x 1 x 0.02 mm polyacrylamide gel pads arranged on the surface of a microscope slide. The gel pads are separated from each other by hydrophobic glass spacers and serve as a kind of 'microtest tube' of 200 pl or 20 nl volume, respectively. Fractionation of single-stranded DNAs is carried out by their hybridization with chip pads containing immobilized 10mers. DNA extracted separately from each pad is transferred onto a sequencing chip and analyzed thereon. The chip, containing a set of 10mers, was enzymatically phosphorylated, then hybridized with DNA and ligated in a site-directed manner with a contiguously stacked 5mer. Several cycles of successive hybridization-ligation of the chip-bound 10mers with different contiguously stacked 5mers and hybridized with DNA were carried out to sequence DNA containing tetranucleotide repeats. Combined use of these techniques show significant promise for sequence comparison of homologous regions in different genomes and for sequence analysis of comparatively long DNA fragments or DNA containing internal repeats.
Dendritic Cell Vaccines for Cancer Immunotherapy (1999)

Human tumors express a number of protein antigens that can be recognized by T cells, thus providing potential targets for cancer immunotherapy. Dendritic cells (DCs) are rare leukocytes that are uniquely potent in their ability to present antigens to T cells, and this property has prompted their recent application to therapeutic cancer vaccines. Isolated DCs loaded with tumor antigen ex vivo and administered as a cellular vaccine have been found to induce protective and therapeutic anti-tumor immunity in experimental animals. In pilot clinical trials of DC vaccination for patients with non-Hodgkin's lymphoma and melanoma, induction of anti-tumor immune responses and tumor regressions have been observed. Additional trials of DC vaccination for a variety of human cancers are under way, and methods for targeting tumor antigens to DCs in vivo are also being explored. Exploitation of the antigen-presenting properties of DCs thus offers promise for the development of effective cancer immunotherapies.
Membrane Raft Association of CD47 Is Necessary for Actin Polymerization and Protein Kinase C θ Translocation in Its Synergistic Activation of T Cells (2001)

CD47 is a ubiquitously expressed membrane protein with an extracellular Ig domain and a multiple membrane-spanning domain that can synergize with antigen to induce interleukin (IL)-2 secretion by T lymphocytes. Ligation of CD47 induced actin polymerization and increased protein kinase Ctheta (PKCtheta) association with the cytoskeleton independent of antigen receptor ligation, but ligation of mutant forms of the molecule missing either the Ig domain or the multiple membrane-spanning domain did not. Simultaneous ligation of CD47 and CD3 led to additive effects on F-actin and synergistic effects on PKCtheta cytoskeletal association. Disruption of membrane rafts by removal of cholesterol with cyclodextrin blocked CD47-induced actin polymerization, and mutant forms of CD47 that localized poorly to rafts failed to effect cytoskeletal rearrangement. However, raft association alone was not sufficient, because a raft-localized CD47 Ig domain bound to the membrane by a glycan phosphoinositol anchor was unable to induce actin polymerization. A mutant form of CD47 without its Ig domain that did not induce actin polymerization or localize to rafts still enhanced T cell receptor (TCR)-dependent tyrosine phosphorylation of PLCgamma and associated Ca(2+) signaling but did not augment IL-2 secretion. Thus, CD47 synergy with TCR to increase [Ca(2+)](i) is independent of actin and rafts but is insufficient to explain CD47 cooperation with TCR in IL-2 synthesis. Full synergy with TCR requires CD47 localization to membrane rafts where ligation leads to TCR-independent signals causing actin polymerization and PKCtheta translocation.
Reflectance spectroscopy for diagnosis of epithelial precancer: model-based analysis of fiber-optic probe designs to resolve spectral information from epithelium and stroma (2005)

Reflectance spectroscopy is a promising technology for detection of epithelial precancer. Fiber-optic probes that selectively collect scattered light from both the epithelium and the underlying stroma are likely to improve diagnostic performance of in vivo reflectance spectroscopy by revealing diagnostic features unique to each layer. We present Monte Carlo models with which to evaluate fiber-optic probe geometries with respect to sampling depth and depth resolution. We propose a probe design that utilizes half-ball lens coupled source and detector fibers to isolate epithelial scattering from stromal scattering and hence to resolve spectral information from the two layers. The probe is extremely compact and can provide easy access to different organ sites.
Stress induced defects and transistor leakage for shallow trench isolated SOI (1999)

Anomalous leakage currents are observed for shallow trench isolated SOI transistors. The leakage effect is caused by stress induced dislocations in the device silicon islands. These dislocations are observed using cross-sectional TEM analysis. For the shallow trench isolation process employed, the leakage is most pronounced on SIMOX wafers when the buried oxide thickness is scaled down to 100 nm. Limiting fabrication stresses to a minimum is critical for eliminating this leakage defect and in obtaining a robust, high yielding SOI STI process.
Identification of Large Fullerenes Formed during the Growth of Single-Walled Carbon Nanotubes in the HiPco Process (2003)

Iron-catalyzed, gas-phase disproportionation of carbon monoxide under high pressures is known to produce single-walled carbon nanotubes (SWNT) in high yields. Small amounts of nontubular nanocarbons and iron encapsulated-graphitic shelled nanoparticles are produced concomitantly. Differences in the oxidation kinetics among the SWNT, nontubular carbon, and iron core−graphitic shell nanoparticles have been exploited as a tool for the quantitative determination of high-molecular-weight nontubular, carbon products. The nontubular carbon materials were eliminated by selective oxidation wherein the raw material was subjected to increasing oxidation thresholds followed by acid leaching in an aqueous or gas−solid reaction. Relative concentrations of nontubular nanocarbons in differentially oxidized samples were determined employing laser desorption ionization-mass spectrometry (LDI-MS) with C60 and bismuth triphenyl as internal markers. The identity of the nontubular carbon was examined by nondestructive extraction through fluorination in a gas−solid reaction followed by LDI-MS and electron microscopic and polarized Raman spectroscopies. The extracted nontubular carbon was found to be comprised predominantly of large, closed-shell carbon structures spanning the range of C120 to C400.
Protein and RNA of Human Telomerase as Targets for Modified Oligonucleotides (1999)

Chimeric oligodeoxynucleotides containing phosphorothioate and N3'-->P5' phosphoramidate linkages were synthesized. These oligomers show a high inhibitory activity against human telomerase.
Quilt Packaging: High-Density, High-Speed Interchip Communications (2007)

ldquoQuilt packagingrdquo (QP), a new superconnect paradigm for interchip communication, is presented. QP uses conducting nodules that protrude from the vertical facets of integrated circuits to effect a dense, fast, and reduced-power method of interfacing multiple die together within a package or on a multichip module. The concept of QP is presented along with a discussion of advantages over traditional system-on-chip and other system-in-package technologies. A process flow and results of chip fabrication are detailed. Simulations show expected signal propagation between adjacent die of greater than 200 GHz, and measurements of interconnected chips confirming low losses and resonance-free operation to at least 40 GHz have been achieved.
2D-DIGE: Comparative Proteomics of Cellular Signalling Pathways (2009)

Two-dimensional (2-D) gel electrophoresis concerted with protein identification by mass spectrometry (MS) is an extremely powerful method for comparative expression profiling of complex protein samples such as cell lysates. The highly resolutive 2-D electrophoresis allows the separation of heterogeneous protein samples on the basis of isoelectric point (pI), molecular mass (Mr), solubility, and relative abundance ((1) J Biol Chem 250: 4007-4021, 1975; (2) Electrophoresis 14: 1067-1073, 1993). Consequently, it provides a comprehensive view of a proteome state ((3) Electrophoresis 21: 1037-1053, 2000), where variations in protein expression levels, isoforms, or post-translational modifications (e.g. phosphorylation) can be highlighted and investigated ((4) Electrophoresis 21: 2196-2208, 2000). Furthermore, this allows the identification of biological markers that characterize a specific physiological or pathological background of a cell or a tissue ((5) Proteomics 1: 397-408, 2001; (6) J Bacteriol 179: 7595-7599, 1997). In this way one can compare the effects of a stimulus or drug on cells or tissue, or more importantly, analyse the effects of disease on the expression level of proteins. Relatively recently, conventional 2-D gel electrophoresis has been combined with protein labelling strategies using up to three different fluorescent dyes to allow comparative analysis of different protein samples within a single 2-D gel platform. In this technique, termed differential in-gel electrophoresis (DIGE), samples are labelled separately then combined and run on the same 2D gel minimizing experimental variation and greatly facilitating spot matching. When three CyDyes (Cy2, Cy3, and Cy5) have been used, three images of the gel are captured then superposed to localize the differentially regulated spots on the 2-D gel using image analysis software. This is an extremely powerful tool in comparative proteomics as these dyes provide a linear response to protein concentration up to five orders of magnitude and great sensitivity with detection down to 125 pg of a single protein, which is less than needed for MS identification. In this chapter, we describe the basic methods for protein labelling, optimization of the isoelectrofocusing parameters for the first dimension (where proteins are separated according to their isoelectric point (pI)), sodium-dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) separation for the second dimension (based on molecular weight (MW)), and different post-staining protocols of the 2-D gel and protein preparation for mass spectrometry identification.
Combination Treatment with Erlotinib and Pertuzumab against Human Tumor Xenografts Is Superior to Monotherapy (2005)

In many solid tumors, overexpression of human epidermal growth factor receptors (e.g., HER1/EGFR and HER2) correlates with poor prognosis. Erlotinib (Tarceva) is a potent HER1/EGFR tyrosine kinase inhibitor. Pertuzumab (Omnitarg), a novel HER2-specific, recombinant, humanized monoclonal antibody, prevents heterodimerization of HER2 with other HERs. Both mechanisms disrupt signaling pathways, resulting in tumor growth inhibition. We evaluated whether inhibition of both mechanisms is superior to monotherapy in tumor cell lines expressing different HER levels. Human non-small cell lung cancer (NSCLC) cells (Calu-3: HER1/EGFR 0+, HER2 3+; QG56: HER1/EGFR 2-3+, HER2 0+) and breast cancer cells (KPL-4: HER1/EGFR 2-3+, HER2 3+) were implanted into BALB/c nu/nu mice and severe combined immunodeficient beige mice, respectively. Tumor-bearing mice (n = 12 or 15 per group) were treated with vehicle (Captisol or buffer), erlotinib (orally, 50 mg/kg/d), pertuzumab (i.p. 6 mg/kg/wk with a 2-fold loading dose), or erlotinib and pertuzumab for 20 (QG56), 27 (KPL-4), or 49 (Calu-3) days. Drug monotherapy had antitumor activity in all models. Tumor volume treatment-to-control ratios (TCR) with erlotinib were 0.36 (Calu-3), 0.79 (QG56), and 0.51 (KPL-4). Pertuzumab TCR values were 0.42, 0.51, and 0.64 in Calu-3, QG56, and KPL-4 models, respectively. Combination treatment resulted in additive (QG56: TCR 0.39; KPL-4: TCR 0.38) or greater than additive (Calu-3: TCR 0.12) antitumor activity. Serum tumor markers for NSCLC (Cyfra 21.1) and breast cancer (soluble HER2) were markedly inhibited by combination treatment (80-97% in Calu-3 and QG56; 92% in KPL-4), correlating with decreased tumor volume. Overall, erlotinib and pertuzumab are active against various human xenograft models, independently of HER1/EGFR or HER2 expression. A combination of these HER-targeted agents resulted in additive or greater than additive antitumor activity.