gebhart/patrepeval huggingface dataset:
Hydrodynamics of a DNA molecule in a flow field (1997)

The hydrodynamics of a single, fluorescing, DNA molecule held at one end by 'optical tweezers' and subjected to a uniform flow are compared with Monte Carlo simulations that account for the molecule's entropic elasticity, Brownian motion, and hydrodynamic drag. Using self-diffusion data and analytic expressions to obtain the drag in the limits of the undeformed coil and of the fully stretched thread, the predicted chain stretching and mass distribution are in quantitative agreement with measurements. The results explain the success of the nonlinear elastic 'dumbbell' model in predicting the rheological properties of dilute polymer solutions.
Cerebral Microhemorrhage (2006)

When cerebral microhemorrhages are diagnosed on MRI, conclusions regarding their significance and associated risks should be made based on the population examined. Further studies to characterize the associated risks of cerebral microhemorrhages in different stroke populations are needed to use this new imaging marker in therapeutic decisions.
Direct antidiabetic effect of leptin through triglyceride depletion of tissues (1997)

Leptin is currently believed to control body composition largely, if not entirely, via hypothalamic receptors that regulate food intake and thermogenesis. Here we demonstrate direct extraneural effects of leptin to deplete fat content of both adipocytes and nonadipocytes to levels far below those of pairfed controls. In cultured pancreatic islets, leptin lowered triglyceride (TG) content by preventing TG formation from free fatty acids (FFA) and by increasing FFA oxidation. In vivo hyperleptinemia, induced in normal rats by adenovirus gene transfer, depleted TG content in liver, skeletal muscle, and pancreas without increasing plasma FFA or ketones, suggesting intracellular oxidation. In islets of obese Zucker Diabetic Fatty rats with leptin receptor mutations, leptin had no effect in vivo or in vitro. The TG content was approximately 20 times normal, and esterification capacity was increased 3- to 4-fold. Thus, in rats with normal leptin receptors but not in Zucker Diabetic Fatty rats, nonadipocytes and adipocytes esterify FFA, store them as TG, and later oxidize them intracellularly via an "indirect pathway" of intracellular fatty acid metabolism controlled by leptin. By maintaining insulin sensitivity and preventing islet lipotoxicity, this activity of leptin may prevent adipogenic diabetes.
Inhibition of Cell Proliferation by a Unique Lysophosphatidic Acid, PHYLPA, Isolated from Physarum polycephalum: Signaling Events of Antiproliferative Action by PHYLPA. (1993)

The unique Physarum lysophosphatidic acid, PHYLPA, having a cyclopropane in the fatty acid moiety and a cyclic phosphate at C-2 and C-3 positions of the glycerol (16), inhibited proliferation of human fibroblast cells, TIG-3 and TIG-7, which were cultured in a chemically defined (serum-free) medium. The cells at S- and M-phases proceeded to G2- and G1-phases, respectively, and most of cells were arrested at G1- or G2- phase during PHYLPA treatment. The growth was recovered when PHYLPA was removed from the medium. In the presence of serum, PHYLPA did not show obvious inhibitory effects, indicating the existence of a factor(s) which neutralizes the antiproliferative activity of PHYLPA. PHYLPA elicited an increase in 3', 5' -cyclic adenosine monophosphate (cAMP) in a biphasic fashion in fibroblast cells. It also elicited inositol phosphate accumulation, as well as a transient rise in cytoplasmic free Ca2+ ion.
Biological impediments to monoclonal antibody–based cancer immunotherapy (2004)

The ability of antibodies to exploit antigenic differences between normal and malignant tissues and to exact a variety of antitumor responses offers significant advantages to conventional forms of therapy. Several monoclonal antibodies (mAb) have already proved to be relatively well tolerated and effective for the treatment of many different malignant diseases. However, mAbs must overcome substantial obstacles to reach antigens presented on target cells to be of therapeutic value. Intravenously administered antibodies must avoid host immune response and contend with low or heterogeneous expression of antigen on tumor cells. Antibodies must also overcome significant physical barriers en route to a solid tumor mass, including the vascular endothelium, stromal barriers, high interstitial pressure, and epithelial barriers. Here we review the application and evolution of mAbs as effective forms of treatment, with particular attention to the barriers and impediments to successful treatment and discuss strategies to overcome these barriers and improve the efficacy of mAb-based therapy.
Chronic, multisite, multielectrode recordings in macaque monkeys (2003)

A paradigm is described for recording the activity of single cortical neurons from awake, behaving macaque monkeys. Its unique features include high-density microwire arrays and multichannel instrumentation. Three adult rhesus monkeys received microwire array implants, totaling 96–704 microwires per subject, in up to five cortical areas, sometimes bilaterally. Recordings 3–4 weeks after implantation yielded 421 single neurons with a mean peak-to-peak voltage of 115 ± 3 μV and a signal-to-noise ratio of better than 5:1. As many as 247 cortical neurons were recorded in one session, and at least 58 neurons were isolated from one subject 18 months after implantation. This method should benefit neurophysiological investigation of learning, perception, and sensorimotor integration in primates and the development of neuroprosthetic devices.
Pluripotent Stem Cells Induced from Mouse Somatic Cells by Small-Molecule Compounds (2013)

Pluripotent stem cells can be induced from somatic cells, providing an unlimited cell resource, with potential for studying disease and use in regenerative medicine. However, genetic manipulation and technically challenging strategies such as nuclear transfer used in reprogramming limit their clinical applications. Here, we show that pluripotent stem cells can be generated from mouse somatic cells at a frequency up to 0.2% using a combination of seven small-molecule compounds. The chemically induced pluripotent stem cells resemble embryonic stem cells in terms of their gene expression profiles, epigenetic status, and potential for differentiation and germline transmission. By using small molecules, exogenous "master genes" are dispensable for cell fate reprogramming. This chemical reprogramming strategy has potential use in generating functional desirable cell types for clinical applications.
Safe sorting of GFP‐transduced live cells for subsequent culture using a modified FACS Vantage (1999)

Background: A stream-in-air cell sorter enables rapid sorting to a high purity, but it is not well suited for sorting of infectious material due to the risk of airborne spread to the surroundings. Methods: A FACS Vantage cell sorter was modified for safe use with potentially HIV infected cells. Safety tests with bacteriophages were performed to evaluate the potential spread of biologically active material during cell sorting. Cells transduced with a retroviral vector carrying the gene for GFP were sorted on the basis of their GFP fluorescence, and GFP expression was followed during subsequent culture. Results: The bacteriophage sorting showed that the biologically active material was confined to the sorting chamber. A failure mode simulating a nozzle blockage resulted in detectable droplets inside the sorting chamber, but no droplets could be detected when an additional air suction from the sorting chamber had been put on. The GFP transduced cells were sorted to 99% purity. Cells not expressing GFP at the time of sorting did not turn on the gene during subsequent culture. Un-sorted cells and cells sorted to be positive for GFP showed a decrease in the fraction of GFP positive cells during culture. Conclusions: Sorting of live infected cells can be performed safely and with no deleterious effects on vector expression using the modified FACS Vantage instrument. Cytometry 37: 284–290, 1999. © 1999 Wiley-Liss, Inc.
CD19-antigen specific nanoscale liposomal formulation of a SYK P-site inhibitor causes apoptotic destruction of human B-precursor leukemia cells (2014)

We report the anti-leukemic potency of a unique biotargeted nanoscale liposomal nanoparticle (LNP) formulation of the spleen tyrosine kinase (SYK) P-site inhibitor C61. C61-loaded LNP were decorated with a murine CD19-specific monoclonal antibody directed against radiation-resistant CD19-receptor positive aggressive B-precursor acute lymphoblastic leukemia (ALL) cells. The biotargeted C61-LNP were more potent than untargeted C61-LNP and consistently caused apoptosis in B-precursor ALL cells. The CD19-directed C61-LNP also destroyed B-precursor ALL xenograft cells and their leukemia-initiating in vivo clonogenic fraction. This unique nanostructural therapeutic modality targeting the SYK-dependent anti-apoptotic blast cell survival machinery shows promise for overcoming the clinical radiochemotherapy resistance of B-precursor ALL cells.
Expression and characterization of an antibody binding specificity joined to insulin-like growth factor 1: potential applications for cellular targeting. (1990)

To create antibody molecules with improved functional properties, a growth factor (insulin-like growth factor 1, IGF1) was used to replace the constant region of a chimeric mouse-human IgG3 anti-dansyl antibody. The chimeric heavy chain was expressed with an anti-dansyl-specific chimeric kappa light chain. The IgG3-IGF1 chimeric protein retained its specificity for the antigen dansyl. The chimeric proteins bound to the IGF1 receptors of the human lymphoblast IM-9, albeit with reduced affinity, and elicited some of the same biologic effects (increased glucose and amino acid uptake) in human KB cells as did human IGF1, but with reduced specific activity. The reduced affinity and biologic activity may result from several things: the presence of the unprocessed IGF1 moiety, the large size of the IgG3-IGF1 chimeric protein (160 kDa) compared with IGF1 (7 kDa), and three amino acid substitutions in rat IGF1 compared with human IGF1, which may lead to decreased affinity for the human IGF1 receptor. The chimeric proteins show that it is feasible to produce a new family of immunotherapeutic molecules targeted to growth factor receptors.
Asymmetric alkylation of amide anions. Product analysis by GLC using cholesteryl cinnamate, a liquid crystal phase (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric alkylation of amide anions. Product analysis by GLC using cholesteryl cinnamate, a liquid crystal phasePhilip E. Sonnet and Robert R. HeathCite this: J. Org. Chem. 1980, 45, 15, 3137–3139Publication Date (Print):July 1, 1980Publication History Published online1 May 2002Published inissue 1 July 1980https://pubs.acs.org/doi/10.1021/jo01303a046https://doi.org/10.1021/jo01303a046research-articleACS PublicationsRequest reuse permissionsArticle Views842Altmetric-Citations72LEARN 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
Two Solutions of Soil Moisture Sensing with RFID for Landslide Monitoring (2018)

Two solutions for UHF RFID tags for soil moisture sensing were designed and are described in this paper. In the first, two conventional tags (standard transponders) are employed: one, placed close to the soil surface, is the sensor tag, while the other, separated from the soil, is the reference for system calibration. By transmission power ramps, the tag's turn-on power levels are measured and correlated with soil condition (dry or wet). In the second solution, the SL900A chip, which supports up to two external sensors and an internal temperature sensor, is used. An interdigital capacitive sensor was connected to the transponder chip and used for soil moisture measurement. In a novel design for an UHF RFID tag the sensor is placed below the soil surface, while the transponder and antenna are above the soil to improve communication. Both solutions are evaluated practically and results show the presence of water in soil can be remotely detected allowing for their application in landslide monitoring.
Lossless Video Coding Using Variable Block-Size Mc And 3D Prediction Optimized For Each Frame (2004)

Publication in the conference proceedings of EUSIPCO, Viena, Austria, 2004
A neutral amino acid change in segment IIS4 dramatically alters the gating properties of the voltage-dependent sodium channel. (1990)

Sodium channels encoded by the rat IIA cDNA clone [Auld, V. J., Goldin, A. L., Krafte, D. S., Marshall, J., Dunn, J., Catterall, W. A., Lester, H. A., Davidson, N. & Dunn, R. J. (1988) Neuron 1, 449-461] differ at seven amino acid residues from those encoded by the rat II cDNA [Noda, M., Ikeda, T., Kayano, T., Suzuki, H., Takeshima, H., Kurasaki, M., Takahashi, H. & Numa, S. (1986) Nature (London) 320, 188-192]. When expressed in Xenopus oocytes, rat IIA channels display a current-voltage relationship that is shifted 20-25 mV in the depolarizing direction relative to channels expressed from rat II cDNA or rat brain poly(A)+ mRNA. By modifying each variant residue in rat IIA to the corresponding residue in rat II, we demonstrate that a single Phe----Leu substitution at position 860 in the S4 segment of domain II is sufficient to shift the current-voltage relationship to that observed for channels expressed from rat brain poly(A)+ RNA or rat II cDNA. Rat genomic DNA encodes leucine but not phenylalanine at position 860, indicating that the phenylalanine at this position in rat IIA cDNA likely results from reverse transcriptase error.
Generation of a Murine Monoclonal Antibody Specific for N -Glycolylneuraminic Acid-Containing Gangliosides That Also Recognizes Sulfated Glycolipids (1995)

The P3 murine monoclonal antibody (MAb) was generated by immunizing BALB/c mice with NeuGcGM3 included into liposomes. The specificity of this MAb was defined by an enzyme-linked immunosorbent assay and immunostaining on thin-layer chromatograms. P3 MAb binds to NeuGc-containing gangliosides and was shown also to react with sulfated glycolipids. A preliminary immunohistochemical study showed that the P3 MAb was able to recognize antigens expressed in human breast tumors.
Surface display of a massively variable lipoprotein by a Legionella diversity-generating retroelement (2013)

Diversity-generating retroelements (DGRs) are a unique family of retroelements that confer selective advantages to their hosts by facilitating localized DNA sequence evolution through a specialized error-prone reverse transcription process. We characterized a DGR in Legionella pneumophila, an opportunistic human pathogen that causes Legionnaires disease. The L. pneumophila DGR is found within a horizontally acquired genomic island, and it can theoretically generate 10(26) unique nucleotide sequences in its target gene, legionella determinent target A (ldtA), creating a repertoire of 10(19) distinct proteins. Expression of the L. pneumophila DGR resulted in transfer of DNA sequence information from a template repeat to a variable repeat (VR) accompanied by adenine-specific mutagenesis of progeny VRs at the 3'end of ldtA. ldtA encodes a twin-arginine translocated lipoprotein that is anchored in the outer leaflet of the outer membrane, with its C-terminal variable region surface exposed. Related DGRs were identified in L. pneumophila clinical isolates that encode unique target proteins with homologous VRs, demonstrating the adaptability of DGR components. This work characterizes a DGR that diversifies a bacterial protein and confirms the hypothesis that DGR-mediated mutagenic homing occurs through a conserved mechanism. Comparative bioinformatics predicts that surface display of massively variable proteins is a defining feature of a subset of bacterial DGRs.
Patient-Based Transcriptome-Wide Analysis Identify Interferon and Ubiquination Pathways as Potential Predictors of Influenza A Disease Severity (2014)

The attenuation of interferon and ubiquitination pathways may associate with the clinical outcomes of influenza patients.
A voltage sensing approach for a maximum power tracking in integrated photovoltaic applications (2009)

The main aim of this paper is the analysis and experimental evaluation of the performance of a photovoltaic power plant controlled by a dedicated algorithm. This is devoted to the search of the maximum power point during the energy conversion of the photovoltaic panels. The proposed approach uses a control strategy that does not requires the current sensing, which is a main cause of noises, errors and delays during the step by step detection of the working point. Modeling of both the power source and the switching converter is a key step for the implementation of the voltage sensing tracking routine. The proposed algorithm has been implemented in a 8-bit microcontroller. A SEPIC converter topology is the core of the experimental workbench that has been realized with 100 W as rated power. The experimental analyses show a very low noise in the signal sensing and a very fast response of the whole system. This is able to reach suitable working points in less than 100 ms after the a perturbation occurred. The achieved results led to consider this set-up appropriate for a system that is composed by a PV module and an integrated DC-DC converter.
Characterization of a second protein (CM2) encoded by RNA segment 6 of influenza C virus (1997)

The biochemical properties of a second protein (CM2) encoded by RNA segment 6 of influenza C virus were investigated. Three forms of CM2 with different electrophoretic mobilities (CM2(0), CM2a, and CM2b) were detected in infected cells by immunoprecipitation with antiserum to the glutathione S-transferase (GST)-CM2 fusion protein. Treatment of infected cells with tunicamycin and digestion of immunoprecipitated proteins with endoglycosidase H or peptide-N-glycosidase F suggested that a mannose-rich oligosaccharide core is added to unglycosylated CM2(0) (Mr, approximately 16,000) to form CM2a (Mr, approximately 18,000) and that the processing of the carbohydrate chain from the high-mannose type to the complex type converts CM2a into CM2b, which is heterogeneous in electrophoretic mobility (Mr, approximately 22,000 to 30,000). Labeling of infected cells with [3H]palmitic acid showed that CM2 is fatty acylated. The fatty acid bond was sensitive to treatment with hydroxylamine and mercaptoethanol, which indicates a labile thioester-type linkage. The CM2 protein was also found to form disulfide-linked dimers and tetramers on sodium dodecyl sulfate-polyacrylamide gels under nonreducing conditions. Trypsin treatment of infected cell surfaces as well as of microsome vesicles from infected cells followed by immunoprecipitation with antiserum to the GST fusion protein containing the 56 C-terminal amino acid residues of CM2 suggested that this C-terminal domain is intracellular and exposed to the cytoplasms of microsomes. Furthermore, evidence that a small amount of CM2 is incorporated into progeny virus particles was obtained by Western blot analysis. These results, altogether, suggest that CM2 is an integral membrane protein with biochemical properties similar to those of influenza A virus M2 and influenza B virus NB proteins.
A review of synergy concepts of nonlinear blending and dose-reduction profiles (2009)

This article presents a case-study review of synergy concepts of nonlinear blending and dose-reduction profiles. "Strong nonlinear blending" is a novel concept that provides a flexible paradigm for the assessment of combination drug synergy that is applicable to any shaped combination-drug dose-response surface; issues of varying relative potency, partial inhibitors, potentiation, or coalism pose no problems at all. Dose-reduction profiles are overlay plots created to show how much each drug can be reduced in amount and yet achieve the same efficacy as larger amounts of each drug used individually. This review applies these synergy concepts to two data sets from a previously published experiment. The previous publication had claimed a high degree of Loewe synergy for one of the data sets. However, a more penetrating analysis shows that with regard to strong nonlinear blending there is no reason to blend (for purposes of response enhancement) the two compounds studied. However, the dose-reduction profile plots show how Loewe synergy is present and provide further insight to the interaction of the two compounds (on the dose-concentration scale).
An efficient and flexible access control framework for Java programs in mobile terminals (2003)

The current Java Application Environment for mobile terminals provides a very restricted security mechanism which is known as "the sandbox model." Although 3rd Generation Partnership Project defines access control and permission framework of a Java program in the terminal as the security domain, the specification has problems such that implementation in the terminal becomes difficult because it requires content authentication for determining the domain. In order to solve the problems and increase flexibility of mobile software services, we propose an efficient and flexible access control framework for the Java program in the mobile terminal. This framework relates a security domain to a server and utilizes the server authentication in SSL in order to determine the domain which the program belong to. As a result, downloading the program and determining the domain becomes efficient. This framework is able to apply other information appliances.
Time-Predictable Embedded Software on Multi-Core Platforms: Analysis and Optimization (2014)

Multi-core architectures have recently gained popularity due to their high-performance and low-power characteristics. Most of the modern desktop systems are now equipped with multi-core processors. Despite the wide-spread adaptation of multi-core processors in desktop systems, using such processors in embedded systems still poses several challenges. Embedded systems are often constrained by several extra-functional aspects, such as time. Therefore, providing guarantees for time-predictable execution is one of the key requirements for embedded system designers. Multi-core processors adversely affect the time-predictability due to the presence of shared resources, such as shared caches and shared buses. In this contribution, we shall first discuss the challenges imposed by multi-core architectures in designing time-predictable embedded systems. Subsequently, we shall describe, in details, a comprehensive solution to guarantee time-predictable execution on multi-core platforms. Besides, we shall also perform a discussion of different techniques to provide an overview of the state-of-the-art solutions in this topic. Through this work, we aim to provide a solid background on recent trends of research towards achieving time-predictability on multi-cores. Besides, we also highlight the limitations of the state-of-the-art and discuss future research opportunities and challenges to accomplish time-predictable execution on multi-core platforms.