gebhart/patrepeval huggingface dataset:
Biologically active vascular endothelial growth factor as a bacterial recombinant glutathione S‐transferase fusion protein (2006)

Human VEGF121 (vascular endothelial growth factor isoform 121) was produced as a recombinant fusion protein with GST (glutathione S-transferase) in Escherichia coli. After affinity purification with glutathione, the GST-VEGF121 fusion protein preparation was used to obtain antibodies in mice against commercial hrVEGF (human recombinant VEGF) through immunization. It was also employed successfully to select specific antihuman VEGF antibody fragments of human origin employing phage-display technology. The fusion protein preparation was separated in monomeric, dimeric and oligomeric forms using size-exclusion chromatography. The dimers were recognized by a soluble VEGF receptor 2-Fc chimaera, and stimulated the growth of human umbilical-vein endothelial cells in vitro in a similar fashion to a commercial hrVEGF. The presence of GST in the fusion protein apparently did not affect the correct assembly of dimers and display of residues critical for receptor recognition. The two-step purification method reported in the present paper involves no laborious renaturalization methods, yields 10 mg/l of the mixture of different aggregation states after affinity chromatography, and 5 mg/l of the biologically active dimer after gel filtration, thus providing a source of material for the development of new anti-angiogenic therapeutic molecules.
Noise-Enhanced Performance for an Optimal Bayesian Estimator (2004)

A novel instance of a stochastic resonance effect, under the form of a noise-improved performance, is shown to be possible for an optimal Bayesian estimator. Estimation of the frequency of a periodic signal corrupted by a phase noise is considered. The optimal Bayesian estimator, achieving the minimum of the mean square estimation error, is explicitly derived. Conditions are exhibited where this minimal error is reduced when the noise level is raised, over some ranges, where this occurs essentially with non-Gaussian noise, in the tested configurations. These results contribute a new step in the exploration of stochastic resonance and its potentialities for signal processing.
AMPK Activation by Metformin Promotes Survival of Dormant ER+ Breast Cancer Cells (2020)

AMPK has context-dependent effects in cancer, cautioning against the widespread use of an AMPK activator across disease settings. The development of therapeutics targeting fat metabolism is warranted in ER<sup>+</sup> breast cancer.
A plate-based high-throughput assay for virus stability and vaccine formulation (2012)

Standard methods for assessing the thermal stability of viruses can be time consuming and rather qualitative yet such data is a necessary requisite for vaccine formulation. In this study a novel plate-based thermal scanning assay for virus particle stability has been developed (PaSTRy: Particle Stability Thermal Release Assay). Two environment-sensitive fluorescent dyes, with non-overlapping emission spectra and different affinities, are used to accrue simultaneously independent data for the overall stability of the virus capsid, as judged by the exposure of the genome, and for capsid protein stability according to the exposure of hydrophobic side chains which are normally buried. This offers a fast and efficient high-throughput method to optimise vaccine formulation and to investigate the processes of virus uncoating.
VADE: a Virtual Assembly Design Environment (1999)

Virtual Assembly Design Environment (VADE) resulted from a research and development project started in 1995, sponsored by the National Institute of Standards and Technology (NIST). The main purpose of this project was to explore the potential and the technical challenges in using VR technologies for design and manufacturing by creating a VE for assembly planning and evaluation. In this article, we describe the overall system, the important features, and examples of using VADE. We also discuss the benefits and limitations of virtual assembly systems. In addition, we compare virtual assembly and automated assembly planning systems.
Protein kinase C isoforms: Multi-functional regulators of cell life and death (2009)

The protein kinase C (PKC) family consists of 10 related serine/threonine protein kinases some of which are critical regulators of cell proliferation, survival and cell death. While early studies relied on broad spectrum chemical activators or inhibitors of this family, the generation of isoform specific tools has greatly facilitated our understanding of the contribution of specific PKC isoforms to cell proliferation and apoptosis. These studies suggest that PKC-alpha, PKC-epsilon, and the atypical PKC's, PKC-lambda/iota and PKC-zeta, preferentially function to promote cell proliferation and survival, while the novel isoform, PKC-delta is an important regulator of apoptosis. The essential role of this kinase family in both cell survival and apoptosis suggests that specific isoforms may function as molecular sensors, promoting cell survival or cell death depending on environmental cues. Given their central role in cell and tissue homeostasis, it is not surprising that the expression or activity of some of these kinases is altered in human diseases, particularly cancer.
Machine learning approaches for prediction of linear B‐cell epitopes on proteins (2006)

Identification and characterization of antigenic determinants on proteins has received considerable attention utilizing both, experimental as well as computational methods. For computational routines mostly structural as well as physicochemical parameters have been utilized for predicting the antigenic propensity of protein sites. However, the performance of computational routines has been low when compared to experimental alternatives. Here we describe the construction of machine learning based classifiers to enhance the prediction quality for identifying linear B-cell epitopes on proteins. Our approach combines several parameters previously associated with antigenicity, and includes novel parameters based on frequencies of amino acids and amino acid neighborhood propensities. We utilized machine learning algorithms for deriving antigenicity classification functions assigning antigenic propensities to each amino acid of a given protein sequence. We compared the prediction quality of the novel classifiers with respect to established routines for epitope scoring, and tested prediction accuracy on experimental data available for HIV proteins. The major finding is that machine learning classifiers clearly outperform the reference classification systems on the HIV epitope validation set.
Design and modeling of the 600 V IGBT with emitter ballast resistor (2002)

Summary form only given. Device performance of IGBT's has been improved rapidly in recent years, particularly regarding the trade-off between its on-state voltage and switching loss. Another important performance trade-off is between its on-state voltage and short-circuit withstanding capability. A short-circuit condition occurs when an IGBT is fully turned on and the collector-emitter voltage remains high. Since the IGBT experiences both high current and voltage simultaneously, the power dissipation becomes excessive even during a short time period. The IGBT may be destroyed through a latch-up failure mode or simply due to the excessive heat generated in the device. In this paper, a new IGBT structure with emitter ballast resistor is investigated to improve the trade-off between the on-state voltage and the short circuit withstanding capability. IGBTs with voltage and current ratings of 600 V and 5 A have been designed and fabricated to conduct this study. The IGBTs demonstrate excellent switching speed with a typical turn-off fall time of 150 ns. The 3-dimensional semiconductor device simulator DAVINCI is used to model this new design. Both experimental and simulation results are discussed.
Proteinated Elemental Selenium Potentiates Anti-Tumor Effect of Ionizing Radiation and Chemotherapeutic Agents but Is Only Minimally Affected by Drug Resistance Mechanisms. (2004)

Abstract Elemental selenium generated by the photobleaching of selone photosensitizers combined with serum albumin and lipoproteins to generate conjugates that were highly cytotoxic to leukemia and selected solid tumor cells but well tolerated by normal CD34-positive hematopoietic cells. Selenium-protein conjugates were internalized by an endocytotic mechanism and localized in lysosomes. Internalized conjugates caused an extremely rapid and extensive (up to 80% in 1 hour) depletion of intracellular glutathione (GSH), the oxidation of 2′,7′-dichlorofluorescin, a loss of plasma membrane asymmetry, a breakdown of mitochondrial potential, and the activation of several caspases. Additive or synergistic anti-tumor effects were obtained when Se-protein conjugates were used in combination with ionizing radiation, melphalan, amifostine, 4-hydroperoxycyclophosphamide, edelfosine, buthionine sulfoximine, or moderate doses of arsenic (III) oxide. For example, pretreatment with a nontoxic dose of amifostine enhanced the depletion of L1210 leukemia cells from 7 log to 12 log (depletions in excess of 6 log estimated from linear extrapolations of survival curves) while the yield of normal CD34-positive cells remained at 100%. Antagonistic interactions were obtained with simultaneously applied cisplatin or very high doses of arsenic (III) oxide. The antagonistic interaction with cisplatin probably reflected a competition of cisplatin and selenium for the same binding site at or near cysteine-34 of albumin. Melphalan-resistant L1210/L-PAM1 leukemia cells (elevated intracellular GSH) were more sensitive to Se-protein conjugates than wild-type cells because of an unexpected increase in conjugate uptake by mutant cells. Cisplatin-resistant H69/CDDP cells (elevated GSH, metallothioneine, glutathione-S-transferase-pi) were slightly more sensitive than wild-type cells. Cisplatin-resistant PC14/CDDP cells (reduced drug uptake) and adriamycin-resistant HL-60/ADR cells (MRP-mediated efflux) were slightly less sensitive than the corresponding wild-type cells. In the latter cases, the reduced sensitivity of mutant tumor cells correlated with reduced conjugate uptake and/or higher intracellular GSH levels. Taken together, the above results suggest that compounds modeled after our Se-protein conjugates may prove useful for the systemic therapy of leukemia and selected solid tumors. Supported by CA77387, MACC Fund, Children’s Hospital Foundation, and Wisconsin Breast Cancer Showhouse for a Cure.
Relations Among Speech, Language, and Reading Disorders (2008)

In this article, we critically review the evidence for overlap among three developmental disorders, namely speech sound disorder (SSD), language impairment (LI), and reading disability (RD), at three levels of analysis: diagnostic, cognitive, and etiological. We find that while overlap exists at all three levels, it varies by comorbidity subtype, and the relations among these three disorders are complex and not fully understood. We evaluate which comorbidity models can be rejected or supported as explanations for why and how these three disorders overlap and what new data are needed to better define their relations.
Thin-Film Cryotrons: Part I-Properties of Thin Superconducting Films (1960)

This paper, consisting of three parts, describes the thin-film cryotron. This device, constructed by vacuum deposition of layers of lead, tin and silicon monoxide, is considerably smaller and faster than its wire-wound predecessor. Part I describes the characteristics of evaporated superconductive films as they apply to cryotrons. Their current-carrying capacity has been found to be proportional to width and proportional to thickness when the film is thinner than twice the penetration depth. Thermal effects caused by poor heat transfer to the bath distort the data, and the use of quartz substrates and low duty cycle pulse measurements help to reduce this distortion. The function of a superconductive reflector or ground plane under a film is discussed. The current-carry ing capacity of such a film is increased because of effective cancella tion of the normal component of magnetic field.
Hydroboration with Haloborane/Trialkylsilane Mixtures (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydroboration with Haloborane/Trialkylsilane MixturesRaman Soundararajan and Donald S. MattesonCite this: Organometallics 1995, 14, 9, 4157–4166Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/om00009a018https://doi.org/10.1021/om00009a018research-articleACS PublicationsRequest reuse permissionsArticle Views1712Altmetric-Citations67LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Oxysterol Mixture in Hypercholesterolemia-Relevant Proportion Causes Oxidative Stress-Dependent Eryptosis (2014)

Oxysterols induce an oxidative stress-dependent eryptosis, involving calcium-independent mechanisms. Eryptotic activity of oxysterols may be relevant in vivo.
Low-Power Optimization by Smart Bit-Width Allocation in a SystemC-Based ASIC Design Environment (2007)

The modern era of embedded system design is geared toward the design of low-power systems. One way to reduce power in an application-specified integrated circuit (ASIC) implementation is to reduce the bit-width precision of its computation units. This paper describes algorithms to optimize the bit widths of fixed-point variables for low power in a SystemC-based ASIC design environment. We propose an optimal bit-width allocation algorithm for two variables and a greedy heuristic that works for any number of variables. The algorithms are used in the automation of converting floating-point SystemC programs into ASIC synthesizable SystemC programs. Expected inputs are profiled to estimate errors in the finite precision conversions. Experimental results for the tradeoffs between quantization error, power consumption, and hardware resources used are reported on a set of four SystemC benchmarks that are mapped onto a 0.18-mum ASIC cell library from Artisan Components. We demonstrate that it is possible to reduce the power consumption by 50% on the average by allowing roundoff errors to increase from 0.5% to 1%
Auto-evaluating System of Computer Hardware Experiment Based on Remote Hardware Platform (2015)

For the requirement of the Massive Open Online Courses, computer hardware experiment teaching should support online and massive experiment. This paper demonstrates the computer hardware online experiment system based on the real hardware experiment platform, and it can evaluate the experiment design automatically. This system explores an effective practice method for the massive online computer hardware experiment.
Transfer of nitroglycerine to hands during contact with commercial explosives. (1982)

The techniques of thin-layer chromatography, gas chromatography with electron capture detection, and gas chromatography/mass spectrometry were used to analyze hand swab extracts for the presence of nitroglycerine. Both the amount of nitroglycerine transferred to the hands after handling commercial explosives and its persistence were measured. Gas chromatography-electron capture detection was found to be the most accurate and sensitive technique for making such determinations, especially if the extract was partially purified by thin-layer chromatography prior to analysis. The lowest limit of detection was 10 ng of nitroglycerine, and residues could be detected over 20 h after handling the raw explosive.
Coupled Spin Torque Nano Oscillators for Low Power Neural Computation (2015)

We present coupled spin torque nano oscillators (STNOs) as electronic neurons for efficient brain-inspired computation. The coupled STNOs show two distinct outputs, depending on whether the frequencies are locked or not. The locking mechanisms are based on magnetic coupling or injection locking. The neuron firing threshold can be set by tuning the locking range of the coupled STNOs. We employ a crossbar array of programmable memory devices like memristors to implement electronic synapses that work seamlessly with the coupled STNOs for hardware implementation of neural networks. Results show that injection locking-based neuron model can be attractive from scaling point of view and computation like character recognition can be performed with energy consumption per neuron of ~1.8× and ~ 3× lower than the digital and the analog CMOS counterpart, respectively.
3 Patterning and Differentiation of the Vertebrate Spine (2009)

One of the most striking features of the human spine is its periodic organization. This so-called “segmental” arrangement of the vertebrae along the anteroposterior body axis is established during embryonic development. Structures called somites, which contain the precursors of the vertebrae, form in a rhythmic fashion at the posterior end of the embryo during the process of somitogenesis. Somites are sequentially added to the growing axis, thus establishing the characteristic periodic pattern of the future vertebral column. The primary segmentation of the vertebrate embryo displayed by somitic organization also underlies much of the segmental organization of the body, including muscles, nerves, and blood vessels. In amniotes, somites are the major component of the paraxial mesoderm that form bilaterally along the nerve cord as a result of primitive streak and tail bud regression during body axis formation. Somites bud off from the anterior presomitic mesoderm (PSM) as epithelial spheres surrounding a core of mesenchymal cells called the somitocoele. The dorsal portion of the somite remains epithelial and forms the dermomyotome, which differentiates into muscle and dermis while its ventral moiety undergoes an epithelio-mesenchymal transition, leading to the formation of the sclerotome. The sclerotome gives rise to the skeletal elements of the vertebral column: the vertebrae, ribs, intervertebral disks, and tendons. Most of our understanding of amniote somitogenesis at the morphogenetic and molecular levels results from studies involving the chicken ( Gallus gallus ) and the mouse ( Mus musculus ). In this chapter, we essentially focus on the patterning and development of the spine in...
Models for count data with many zeros (1998)

Poisson regression models provide a standard framework for the analysis of count data. In practice, however, count data are often overdispersed relative to the Poisson distribution. One frequent manifestation of overdispersion is that the incidence of zero counts is greater than expected for the Poisson distribution and this is of interest because zero counts frequently have special status. For example, in counting disease lesions on plants, a plant may have no lesions either because it is resistant to the disease, or simply because no disease spores have landed on it. This is the distinction between structural zeros, which are inevitable, and sampling zeros, which occur by chance. In recent years there has been considerable interest in models for count data that allow for excess zeros, particularly in the econometric literature. These models complement more conventional models for overdispersion that concentrate on modelling the variance-mean relationship correctly. Application areas are diverse and have included manufacturing defects (Lambert, 1992), patent applications (Crepon & Duguet, 1997), road safety (Miaou, 1994), species abundance (Welsh et al., 1996; Faddy, 1998), medical consultations
Supplementation of plant-based diets for rainbow trout (Oncorhynchus mykiss) with macro-minerals and inositol (2009)

Replacement of fish meal with plant products in aquafeeds results in the elimination of dietary compounds which may be important for optimal growth and physiology. A study was conducted to determine if supplementation with macro-minerals and/or inositol would improve performance of rainbow trout (Oncorhynchus mykiss) fed a plant-based diet. Four iso-caloric and iso-nitrogenous diets (40 g kg−1 protein and 15 g kg−1 lipid) were formulated and consisted of a fish meal-based control diet (control) and three plant-based experimental diets. Plant-based diets were supplemented with either macro-minerals and inositol (+MM+I), no macro-minerals with inositol (−MM+I), and no macro-minerals and no inositol (−MM−I). Sodium chloride, potassium chloride and magnesium oxide were the sources used in the macro-mineral premix. There was no effect of diet on survival, but there was an effect of diet on weight gain, FCR, feed intake, HSI and nutrient retentions. Significant liver pathology was observed in trout fed plant-based diets without MM supplementation. Supplementation of MM and inositol significantly improved weight gain of trout fed a plant-based diet. Supplementation of MM and/or inositol also improved PRE and ERE. This study demonstrates the importance of supplementing these nutrients to trout fed fish meal free diets.
Productive Hepatitis C Virus Infection of Stem Cell-Derived Hepatocytes Reveals a Critical Transition to Viral Permissiveness during Differentiation (2012)

Primary human hepatocytes isolated from patient biopsies represent the most physiologically relevant cell culture model for hepatitis C virus (HCV) infection, but these primary cells are not readily accessible, display individual variability, and are largely refractory to genetic manipulation. Hepatocyte-like cells differentiated from pluripotent stem cells provide an attractive alternative as they not only overcome these shortcomings but can also provide an unlimited source of noncancer cells for both research and cell therapy. Despite its promise, the permissiveness to HCV infection of differentiated human hepatocyte-like cells (DHHs) has not been explored. Here we report a novel infection model based on DHHs derived from human embryonic (hESCs) and induced pluripotent stem cells (iPSCs). DHHs generated in chemically defined media under feeder-free conditions were subjected to infection by both HCV derived in cell culture (HCVcc) and patient-derived virus (HCVser). Pluripotent stem cells and definitive endoderm were not permissive for HCV infection whereas hepatic progenitor cells were persistently infected and secreted infectious particles into culture medium. Permissiveness to infection was correlated with induction of the liver-specific microRNA-122 and modulation of cellular factors that affect HCV replication. RNA interference directed toward essential cellular cofactors in stem cells resulted in HCV-resistant hepatocyte-like cells after differentiation. The ability to infect cultured cells directly with HCV patient serum, to study defined stages of viral permissiveness, and to produce genetically modified cells with desired phenotypes all have broad significance for host-pathogen interactions and cell therapy.
Monoclonal antibodies against epithelial antigens in laryngeal carcinomas (1988)

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