gebhart/patrepeval huggingface dataset:
Immunodominant T-cell epitopes of rubella virus structural proteins defined by synthetic peptides (1993)

Sets of overlapping synthetic peptides containing predicted T-cell epitope motifs were designed from the murine monoclonal antibody-defined map of linear B-cell epitope domains within each of the structural proteins of rubella virus (RV). The peptides represented well-defined subsequences of two capsid domains (C1 to C29 and C64 to C97), of a domain of glycoprotein E1 containing neutralizing determinants (E1(202) to E1(283), and of a domain of glycoprotein E2 (E2(31) to E2(105). With the exception of peptides representing C64 to C97, each set of peptides stimulated varied but individually specific lymphoproliferative responses in peripheral blood mononuclear cells from 25 to 50% of a representatively large number of normal, RV-immune human donors with diverse human leukocyte antigen (HLA) backgrounds. Responses were mediated by CD4+ T cells in association with HLA class II antigens, though lymphoproliferative responses to a given peptide were usually not HLA-DR allele specific. Correlation analysis of responses to overlapping peptides suggests that there is an immunodominant T-proliferative epitope within C14 to C29 recognized by approximately 50% of the donor population. However, limiting-dilution analysis indicated much variability between individuals in lymphocyte recognition of this T-cell determinant, even within similar HLA-DR contexts. Thus, the fine specificity of relatively immunodominant T-cell epitopes may vary from individual to individual. Synthetic peptides with predicted T-cell motifs have proved to be useful probes of the molecular determinants of cellular immunity to RV and should expand the rational basis for the design of synthetic RV vaccines.
A bilayered living skin construct (APLIGRAF®) accelerates complete closure of hard‐to‐heal venous ulcers (1999)

The efficacy of a bilayered, living skin construct (APLIGRAF(R) [Graftskin]) was evaluated in patients (n = 120) with hard- to-heal venous leg ulcers of greater than 1 year's duration. The study was prospective, randomized, and controlled. Patients received Graftskin plus compression therapy, or standard compression therapy (active control). Patients were evaluated for frequency and time to complete (100%) wound closure. Treatment with Graftskin was significantly more effective than active control in the percentage of patients healed by 6 months (47% vs. 19%; p < 0.005) and the median time to complete wound closure (p < 0.005). Analysis with multivariate regression methods, adjusting for factors generally thought to influence wound healing (duration, baseline area, depth, location, fibrinous wound bed, and infection), showed that patients treated with Graftskin were twice as likely to achieve complete wound closure by 6 months (p < 0.005), and over 60% more effective in achieving wound closure than active control (p < 0.01). These data indicate that Graftskin is an effective treatment for venous ulcers of greater than 1 year's duration.
ZeroG: Overground gait and balance training system (2011)

A new overground body-weight support system called ZeroG has been developed that allows patients with severe gait impairments to practice gait and balance activities in a safe, controlled manner. The unloading system is capable of providing up to 300 lb of static support and 150 lb of dynamic (or constant force) support using a custom-series elastic actuator. The unloading system is mounted to a driven trolley, which rides along an overhead rail. We evaluated the performance of ZeroG's unloading system, as well as the trolley tracking system, using benchtop and human-subject testing. Average root-mean-square and peak errors in unloading were 2.2 and 7.2 percent, respectively, over the range of forces tested while trolley tracking errors were less than 3 degrees, indicating the system was able to maintain its position above the subject. We believe training with ZeroG will allow patients to practice activities that are critical to achieving functional independence at home and in the community.
Pathophysiology of Cancer-Related Fatigue (2008)

Cancer-related fatigue (CRF) is influenced and modulated by a number of critical factors, and the mechanism that is both necessary and sufficient to induce development of severe fatigue in patients with cancer has not yet been identified. Specific research efforts to understand the factors that may contribute to CRF development have been made, including studies of the direct effects of tumor burden, the effects of cancer treatment, and other pathophysiologic and psychosocial conditions. Compelling new hypotheses regarding CRF pathophysiology have been proposed, such as the pro-inflammatory hypothesis, the serotonin hypothesis, the vagal-afferent-activation hypothesis, the anemia hypothesis, and the adenosine triphosphate hypothesis; some of these have been tested in both animal models and humans and some in animals only. Gaining an understanding of the specific mechanisms related to the development of fatigue in patients with cancer and survivors requires further investigation. Pathophysiologic research in CRF could be applied in the clinic to improve CRF diagnosis and to enable administration of mechanism-driven interventions. A targeted intervention study with CRF as a primary end point also would be useful.
<sup>13</sup>C NMR Quantitative Spectrometric Data-Activity Relationship (QSDAR) Models of Steroids Binding the Aromatase Enzyme (2001)

Five quantitative spectroscopic data-activity relationships (QSDAR) models for 50 steroidal inhibitors binding to aromatase enzyme have been developed based on simulated (13)C nuclear magnetic resonance (NMR) data. Three of the models were based on comparative spectral analysis (CoSA), and the two other models were based on comparative structurally assigned spectral analysis (CoSASA). A CoSA QSDAR model based on five principal components had an explained variance (r(2)) of 0.78 and a leave-one-out (LOO) cross-validated variance (q(2)) of 0.71. A CoSASA model that used the assigned (13)C NMR chemical shifts from a steroidal backbone at five selected positions gave an r(2) of 0.75 and a q(2) of 0.66. The (13)C NMR chemical shifts from atoms in the steroid template position 9, 6, 3, and 7 each had correlations greater than 0.6 with the relative binding activity to the aromatase enzyme. All five QSDAR models had explained and cross-validated variances that were better than the explained and cross-validated variances from a five structural parameter quantitative structure-activity relationship (QSAR) model of the same compounds. QSAR modeling suffers from errors introduced by the assumptions and approximations used in partial charges, dielectric constants, and the molecular alignment process of one structural conformation. One postulated reason that the variances of QSDAR models are better than the QSAR models is that (13)C NMR spectral data, based on quantum mechanical principles, are more reflective of binding than the QSAR model's calculated electrostatic potentials and molecular alignment process. The QSDAR models provide a rapid, simple way to model the steroid inhibitor activity in relation to the aromatase enzyme.
Convolutional Neural Networks for Classification of Malware Assembly Code (2017)

Traditional signature-based methods have started becoming inadequnate to deal with next generation malware which utilize sophisticated obfuscation (polymorphic and metamorphic) techniques to evade detection. Recently, research efforts have been conducted on malware detection and classification by applying machine learning techniques. Despite them, most methods are build on shallow learning architectures and rely on the extraction of hand-crafted features. In this paper, based on assembly language code extracted from disassembled binary files and embedded into vectors, we present a convolutional neural network architecture to learn a set of discriminative patterns able to cluster malware files amongst families. To demonstrate the suitability of our approach we evaluated our model on the data provided by Microsoft for the BigData Innovators Gathering 2015 Anti-Malware Prediction Challenge. Experiments show that the method achieves competitive results without relying on the manual extraction of features and is resilient to the most common obfuscation techniques.
A new cross-diamond search algorithm for fast block matching motion estimation (2003)

In order to fit the small cross-center-biased characteristic of the real world video sequences, an improved version of the well-known cross diamond search algorithm is proposed in this paper. The new algorithm uses a small cross-shaped search patterns in the first two steps to speedup the motion estimation of stationary and quasi-stationary blocks. Experimental results show that this new cross-diamond search algorithm could achieve much higher computational reduction as compared with Diamond Search (DS) and Cross Diamond Search (CDS) while similar prediction accuracy is maintained, and it is especially suitable for videoconferencing sequences.
Three-Mode Dual-Frequency Two-Edge Modulation Scheme for Four-Switch Buck–Boost Converter (2009)

Four-switch buck-boost (FSBB) converter features low-voltage stress across the power switches and positive output voltage. They have two active power switches and two synchronous rectifiers, so two freedoms, i.e., the duty cycles of the two active switches, are available to regulate the output voltage. This paper proposes a two-edge modulation (TEM), in which the two active switches are trailing-edge and leading-edge modulated, respectively. Thus, the inductor current ripple can be reduced. Furthermore, a 3-mode TEM is derived to reduce the root-mean-square value of the inductor current to reduce the conduction loss. The line range is divided into three regions, and FSBB operates at boost, buck-boost, and buck modes in the lower, medium, and higher input voltage regions, respectively. At buck and boost modes, only two switches are high-frequency switched, so that the total switching loss is reduced. In the buck-boost mode, the inductor current ripple is very low compared with other two modes. Hence, the switching frequency is lowered to reduce the switching loss. The 3-mode TEM can achieve high efficiency over the line range, which is verified by a 48-V (36-75 V) input, 48-V @ 6.25-A output prototype. The measured efficiency is higher than 96.5% over the line range and the efficiency at the nominal input voltage is 97.8%.
Genes of variola and vaccinia viruses necessary to overcome the host protective mechanisms (1993)

Analysis of variola virus nucleotide sequence revealed proteins belonging to several families which provide the virus with the possibility of overcoming the barriers of specific and non-specific host defence against viral infection. The complement-binding proteins, lymphokine-binding proteins, and serine protease inhibitors can be assigned to this type, as can the proteins providing the orthopoxviruses with resistance to interferon. The revealed differences between the genes (proteins) of variola and vaccinia viruses under study are discussed.
Workflow engine-driven universal product lifecycle management system framework for small and medium-size enterprises (2014)

PLM (product lifecycle management) is the management of the enterprise's products all the way across their lifecycles in the most effective way. However, at present, the PLM system in the market is not very appropriate to the small and medium-size enterprises. This paper presents a workflow engine-driven universal PLM system framework, which is constructed by four layers: client layer, application layer, business logic layer, data layer. The workflow engine-driven universal PLM system framework can be directly used as the PLM system, or can be used to customize the autonomy PLM system for the small and medium-size enterprises. The workflow engine-driven universal PLM system framework is implemented by Java enterprise edition and service-oriented architecture, which has the advantage of lightweight, cross-platform, and so on.
Hyaluronic Acid Modified Tantalum Oxide Nanoparticles Conjugating Doxorubicin for Targeted Cancer Theranostics (2015)

Theranostic tantalum oxide nanoparticles (TaOxNPs) of about 40 nm were successfully developed by conjugating functional molecules including polyethylene glycol (PEG), near-infrared (NIR) fluorescent dye, doxorubicin (DOX), and hyaluronic acid (HA) onto the surface of the nanoparticles (TaOx@Cy7-DOX-PEG-HA NPs) for actively targeting delivery, pH-responsive drug release, and NIR fluorescence/X-ray CT bimodal imaging. The obtained nanoagent exhibits good biocompatibility, high cumulative release rate in the acidic microenvironments, long blood circulation time, and superior tumor-targeting ability. Both in vitro and in vivo experiments show that it can serve as an excellent contrast agent to simultaneously enhance fluorescence imaging and CT imaging greatly. Most importantly, such a nanoagent could enhance the therapeutic efficacy of the tumor greatly and the tumor growth inhibition was evaluated to be 87.5%. In a word, multifunctional TaOx@Cy7-DOX-PEG-HA NPs can serve as a theranostic nanomedicine for fluorescence/X-ray CT bimodal imaging, remote-controlled therapeutics, enabling personalized detection, and treatment of cancer with high efficacy.
Fast allocation and deallocation of memory based on object lifetimes (1990)

Abstract Dynamic storage‐management algorithms are based either on object sizes or object lifetimes. Stack allocation, which is based on object lifetimes, is the most efficient algorithm, but severely restricts object lifetimes and creation times. Other algorithms based on object sizes, such as first fit and related algorithms, permit arbitrary lifetimes but cost more. More efficient variations capitalize on application‐specific characteristics. Quick fit, for example, is more efficient when there are only a few object sizes. This paper describes a simple algorithm that is very efficient when there are few object lifetimes. In terms of instructions executed per byte allocated, the algorithm is almost half the cost of quick fit and less than twice the cost of stack allocation. Space for all objects with the same lifetime is allocated from a list of large arenas, and the entire list is deallocated at once. An implementation in ANSI C is included.
Modeling and Extraction of Nanometer Scale Interconnects: Challenges and Opportunities (Invited) (2006)

We discuss interconnect parasitic extraction in the nanometer domain using the ITRS 2005 roadmap for future technology generations. Resistance becomes the dominant contribution for timing for local wires at 65 nm and beyond, a major qualitative change. For scaled wires, maintaining global wire routes within 1 clock period is expensive in terms of power consumption. An acceptable solution involves reverse scaling of global wires leading to RLC transmission line behavior which results in significant power savings. RLC transmission for scaled signal wires is otherwise negligible.
Review: Video-enhanced light microscopy and its applications in cell biology (1988)

The combination of novel optical microscopic techniques with advanced video and digital image-processing technology now permits dramatic improvements in the quality of light-microscope images. Such video-enhanced light microscopy has lead to a renaissance in the applications of the light microscope for the study of living cells in two important areas: the intensification of faint fluorescence images, permitting observation of fluorescently labelled cells under conditions of very low illuminating intensity; and the enhancement of extremely low contrast images generated by minute cellular structures, so that these may be clearly seen and their normal intracellular movements recorded. Application of both these aspects of video-enhanced light microscopy have recently led to major discoveries concerning the functioning of the living cell. In this review I discuss the equipment, procedures and image-processing principles employed in these applications, and describe and illustrate some of the spectacular results that have recently been obtained.
SEDAN: Secure and Efficient protocol for Data Aggregation in wireless sensor Networks (2007)

Energy is a scarce resource in Wireless Sensor Networks. Some studies show that more than 70% of energy is consumed in data transmission. Since most of the time, the sensed information is redundant due to geographically collocated sensors, most of this energy can be saved through data aggregation. Furthermore, data aggregation improves bandwidth usage. Unfortunately, while aggregation eliminates redundancy, it makes data integrity verification more complicated since the received data is unique. In this paper, we present a new protocol that provides secure aggregation for wireless sensor networks. Our protocol is based on a two hops verification mechanism of data integrity. Our solution is essentially different from existing solutions in that it does not require referring to the base station for verifying and detecting faulty aggregated readings, thus providing a totally distributed scheme to guarantee data integrity. We carried out simulations using TinyOS environment. Simulation results show that the proposed protocol yields significant savings in energy consumption while preserving data integrity.
Electrochemistry of Nonconjugated Proteins and Glycoproteins. Toward Sensors for Biomedicine and Glycomics (2015)

The present advances in biology are related to progress in genomics, proteomics, and other -omics, including glycomics, working with a large amount of data regarding human and other genomes, protein expression, post-translational modifications of proteins, as well as a great diversity of glycan composition in glycoproteins, etc. Genomics, proteomics, and glycomics are intimately connected with each other at various levels. In their exponential growth, they require new integrative technologies for highly parallel analysis of genes and proteins of entire organisms. The current experimental techniques applied in these fields have been reviewed in a number of articles.
Amplified DNA Sensing and Immunosensing by the Rotation of Functional Magnetic Particles (2003)

Amplified chemiluminescent detection of DNA-complementary DNA or of antigen-antibody interactions is accomplished in the presence of rotating functionalized magnetic particles.
Synthesis and Thermal Stability of 4-Substituted 1,2-Dithiolanes. (1988)

Synthese des composes du titre a partir de bis-hydroxymethyl malonate de diethyle et de [disodiothio-3,3 cyano-2] acrylamide; potentiels d'ionisation des composes synthetises
Closed-loop system for control of combustor pattern factor (2002)

A neural network (NN) controller was developed to control the exit temperature distribution in a small-scale liquid fueled combustor. Simple feedforward NN structures were developed and trained off-line to simulate the closed-loop system and optimize the training algorithm. The adaptive NN controller was trained online and its ability to control under different operating scenarios was assessed. Various training sets were used to determine accuracy when controlling to set points representing interpolated and extrapolated values. These tests revealed accuracies similar to those when controlling to set points included in the training set and indicated that the controller could develop accurate models of the combustor response even when trained with limited information. Combustor performance drift was simulated by introducing a baseline profile offset. The control system demonstrated the ability to quickly adapt and compensate for the offset, The successful implementation of this control system in gas turbine engines would result in an increased service life of hot section components and allow higher average combustor exit temperatures.
Additions and Corrections-Small Charged Rings. IV. Expansion of the Aziridinium Ring by Reaction with ALdehydes (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdditions and Corrections-Small Charged Rings. IV. Expansion of the Aziridinium Ring by Reaction with ALdehydesNelson Leonard, E Kiefer, and Leonard BradyCite this: J. Org. Chem. 1965, 30, 12, 4394Publication Date (Print):December 1, 1965Publication History Published online30 July 2002Published inissue 1 December 1965https://pubs.acs.org/doi/10.1021/jo01023a600https://doi.org/10.1021/jo01023a600research-articleACS PublicationsRequest reuse permissionsArticle Views23Altmetric-Citations-LEARN 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
Optimized protocols for the isolation of specific protein-binding peptides or peptoids from combinatorial libraries displayed on beads (2005)

Many methods have been published by which combinatorial libraries may be screened for compounds capable of manipulating the function(s) of a target protein. One of the simplest approaches is to identify compounds in a library that bind the protein of interest, since these binding events usually occur on functionally important surfaces of the protein. These protein-binding compounds could also be of utility as protein capture agents in the construction of protein-detecting microarrays or related analytical devices and as reagents for the affinity purification of proteins from complex mixtures. In this article, we provide optimized methods for screening libraries of molecules displayed on the beads on which they were synthesized. This is a particularly convenient format for library screening for laboratories with limited budgets and modest robotics capabilities.