gebhart/patrepeval huggingface dataset:
Regulatory Sequences of the Mouse Villin Gene That Efficiently Drive Transgenic Expression in Immature and Differentiated Epithelial Cells of Small and Large Intestines (1999)

Villin is an early marker of epithelial cells from the digestive and urogenital tracts. Indeed villin is expressed in the stem cells and the proliferative cells of the intestinal crypts. To investigate the underlying molecular mechanisms and particularly those responsible for the restricted tissue specificity, a large genomic region of the mouse villin gene has been analyzed. A 9-kilobase (kb) regulatory region of the mouse villin gene (harboring 3.5 kb upstream the transcription start site and 5.5 kb of the first intron) was able to promote transcription of the LacZ reporter gene in the small and large intestines of transgenic mice, in a transmissible manner, and thus efficiently directed subsequent beta-galactosidase expression in epithelial cells along the entire crypt-villus axis. In the kidney, the transgene was also expressed in the epithelial cells of the proximal tubules but is likely sensitive to the site of integration. A construct lacking the first intron restricted beta-galactosidase expression to the small intestine. Thus, the 9-kb genomic region contains the necessary cis-acting elements to recapitulate the tissue-specific expression pattern of the endogenous villin gene. Hence, these regulatory sequences can be used to target heterologous genes in immature and differentiated epithelial cells of the small and/or large intestinal mucosa.
2P1-R18 A proposition of the method to avoid overturning of the vehicle inverted pendulum in ascending and descending stairs(Wheeled Robot/Tracked Vehicle (3)) (2013)

In this study, we reveal the fact that the passenger's movement on the vehicle inverted pendulum in going up and down stairs cause the movement of wheels and the overturning happens. To avoid the overturning, we add the slider control depending on the passenger's mass position to the controller. In case the new controller is insufficient in safety, we suggest the additional ways. One way is the append of new actuator which prevent wheels from moving. The other way is the change of the gain on feedback control in accordance with the passenger's mass velocity and acceleration. Additionally, we consider the method of ascending and descending stairs to fulfill the safety and comfort.
Contact Lenses for Drug Delivery (2009)

The majority of ocular medications are delivered to the eye topically, often in the form of a solution, or eye drop. Contact lenses could potentially also be used to deliver medications to the eye. Recently, progress has been made in developing a drug-eluting contact lens. Different designs have been proposed and several offer the hope of expanding the therapeutic armamentarium for eye care providers.
A Rapid and Improved Method to Generate Recombinant Dengue Virus Vaccine Candidates (2016)

Dengue is one of the most important mosquito-borne infections accounting for severe morbidity and mortality worldwide. Recently, the tetravalent chimeric live attenuated Dengue vaccine Dengvaxia® was approved for use in several dengue endemic countries. In general, live attenuated vaccines (LAV) are very efficacious and offer long-lasting immunity against virus-induced disease. Rationally designed LAVs can be generated through reverse genetics technology, a method of generating infectious recombinant viruses from full length cDNA contained in bacterial plasmids. In vitro transcribed (IVT) viral RNA from these infectious clones is transfected into susceptible cells to generate recombinant virus. However, the generation of full-length dengue virus cDNA clones can be difficult due to the genetic instability of viral sequences in bacterial plasmids. To circumvent the need for a single plasmid containing a full length cDNA, in vitro ligation of two or three cDNA fragments contained in separate plasmids can be used to generate a full-length dengue viral cDNA template. However, in vitro ligation of multiple fragments often yields low quality template for IVT reactions, resulting in inconsistent low yield RNA. These technical difficulties make recombinant virus recovery less efficient. In this study, we describe a simple, rapid and efficient method of using LONG-PCR to recover recombinant chimeric Yellow fever dengue (CYD) viruses as potential dengue vaccine candidates. Using this method, we were able to efficiently generate several viable recombinant viruses without introducing any artificial mutations into the viral genomes. We believe that the techniques reported here will enable rapid and efficient recovery of recombinant flaviviruses for evaluation as vaccine candidates and, be applicable to the recovery of other RNA viruses.
Nanostructure Formation through β-Sheet Self-Assembly in Silk-Based Materials (2001)

Biomolecular Bombyx mori silk-based multiblock copolymers of poly(ethylene oxide)(PEO) and GlyAlaGlyAla prepared by step-growth polymerization based on a modular chemical method have been found to self-assemble into nanostructures. Solid-state 13C NMR, solid-state FTIR, and powder X-ray diffraction provided evidence for the β-sheet self-assembly. The overall β-sheet content was as high as 90%. The building blocks had significant impact on the solid-state structure of the resulting polymer. Longer PEO spacers lowered the tendency to self-assemble into antiparallel β-sheets and implicated the existence of PEO-sequestered isolated β-sheets. Differential scanning calorimetry, transmission electron microscopy, and atomic force microscopy confirmed nanostructure formation and microphase separation. The microphase-separated morphology of the polymers contained 20−50 nm peptide domains dispersed in a continuous PEO phase on which was superimposed a 100−150 nm superstructure due to the polymers' polydispersity and multiblock character. Instron measurements suggested that mechanical properties could be modulated by manipulating the building blocks.
Preparation and Characterization of the Skutterudite-Related Phase Ru0.5Pd0.5 Sb3 (1995)

A new skutterudite phase Ru0.5Pd0.5 Sb3 was prepared. It adds to the many materials with the skutterudite structure that have shown a good potential for thermoelectric applications. Single- phase polycrystalline samples were prepared and characterized by x-ray analysis, electron probe microanalysis, density, sound velocity, thermal expansion coefficient, and differential thermal analysis measurements.
Consequences of mutations within the C terminus of the <i>FHL1</i> gene (2009)

As a consequence of C terminal FHL1 gene mutations, the X-linked myopathy characterized by postural muscle atrophy (XMPMA) phenotype and morphotype with cytoplasmic bodies are found. In the spectrum of FHL1opathies, the preserved FHL1C protein is likely responsible for the moderate XMPMA phenotype compared with the more severe reducing body myopathy/scapuloperoneal myopathy phenotype.
Lightweight security solution for Host-based mobility &amp; multi-homing protocols (2010)

Host-based mobility and multi-homing protocols allow hosts to change their location or network interface during ongoing sessions in a cost-efficient, technology-agnostic manner. Since these solutions enjoy resurgence with the rise in mobile internet traffic, they are faced with the problem of providing sufficient security without impairing the economical benefits. We present a lightweight security solution to protect such protocols against redirection- and DoS attacks. Our solution combines methods of weak authentication with proof of session ownership. We discuss how this solution creates a level of protection that requires more (sometimes significantly more) effort to break than conducting corresponding attacks using the existing Internet signaling protocols.
Flexible, large-area metamaterials fabricated on thin silicon nitride membranes (2008)

We present terahertz metamaterials fabricated on large-area, free-standing thin (les1 mum) silicon nitride membranes with the aim of reducing dielectric losses, enhancing metamaterial sensing capabilities, and enabling flexible and conformable designs.
In-memory computing on a photonic platform (2019)

Collocated data processing and storage are the norm in biological computing systems such as the mammalian brain. As our ability to create better hardware improves, new computational paradigms are being explored beyond von Neumann architectures. Integrated photonic circuits are an attractive solution for on-chip computing which can leverage the increased speed and bandwidth potential of the optical domain, and importantly, remove the need for electro-optical conversions. Here we show that we can combine integrated optics with collocated data storage and processing to enable all-photonic in-memory computations. By employing nonvolatile photonic elements based on the phase-change material, Ge<sub>2</sub>Sb<sub>2</sub>Te<sub>5</sub>, we achieve direct scalar and matrix-vector multiplication, featuring a novel single-shot <i>Write</i>/<i>Erase</i> and a drift-free process. The output pulse, carrying the information of the light-matter interaction, is the result of the computation. Our all-optical approach is novel, easy to fabricate and operate, and sets the stage for development of entirely photonic computers.
Pop-Up LightField (2004)

In this article, we present an image-based modeling and rendering system, which we call pop-up light field, that models a sparse light field using a set of coherent layers. In our system, the user specifies how many coherent layers should be modeled or popped up according to the scene complexity. A coherent layer is defined as a collection of corresponding planar regions in the light field images. A coherent layer can be rendered free of aliasing all by itself, or against other background layers. To construct coherent layers, we introduce a Bayesian approach, coherence matting, to estimate alpha matting around segmented layer boundaries by incorporating a coherence prior in order to maintain coherence across images. We have developed an intuitive and easy-to-use user interface (UI) to facilitate pop-up light field construction. The key to our UI is the concept of human-in-the-loop where the user specifies where aliasing occurs in the rendered image. The user input is reflected in the input light field images where pop-up layers can be modified. The user feedback is instant through a hardware-accelerated real-time pop-up light field renderer. Experimental results demonstrate that our system is capable of rendering anti-aliased novel views from a sparse light field.
Determinants of Corticotropin Releasing Factor. Receptor Selectivity of Corticotropin Releasing Factor Related Peptides. (2005)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionDeterminants of Corticotropin Releasing Factor. Receptor Selectivity of Corticotropin Releasing Factor Related Peptides.Adam W. Mazur, Feng Wang, Michelle Tscheiner, Elizabeth Donnelly, and Robert J. IsfortCite this: J. Med. Chem. 2005, 48, 23, 7502Publication Date (Web):November 10, 2005Publication History Published online10 November 2005Published inissue 1 November 2005https://pubs.acs.org/doi/10.1021/jm058274qhttps://doi.org/10.1021/jm058274qcorrectionACS PublicationsCopyright © 2005 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views226Altmetric-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 PDF (17 KB) Get e-Alertsclose Get e-Alerts
Antisense Inhibition of Membrane-Bound Human Interleukin-5 Receptor-α Chain Does Not Affect Soluble Receptor Expression and Induces Apoptosis in TF-1 Cells (2000)

Binding of human interleukin-5 (HuIL-5) to its membrane-anchored receptor (IL-5R) triggers multiple signaling pathways, cellular proliferation, and maturational responses, as well as protection from apoptosis. In contrast, soluble forms of the HuIL-5R have been shown to inhibit IL-5 signaling and, therefore, may represent naturally occurring negative regulators of IL-5 function. Because of the central role of IL-5 in promoting eosinophilia and airway hyperresponsiveness in animal models of asthma, antisense oligonucleotides specific either for the membrane form alone or for sequences shared between both the membrane and soluble forms of the HuIL-5Ralpha ligand binding chain were designed. The activities of these oligonucleotides were characterized in IL-5R-expressing erythroleukemic TF-1 cells. Herein we report that an antisense oligonucleotide targeted to a sequence unique to the alternatively spliced membrane-bound form of the HuIL-5Ralpha chain has been developed that selectively inhibits membrane, but not soluble, mRNA isoform expression. Both this membrane-specific oligonucleotide and an antisense oligonucleotide targeted to sequence common to both membrane and soluble isoforms were found to potently suppress cell surface IL-5Ralpha levels and IL-5-mediated cell survival by inducing apoptosis similar to IL-5 withdrawal. Thus, these oligonucleotides represent unique genetic agents with therapeutic potential for diseases with an eosinophilic component.
Inhibition of autoantibody binding to platelet glycoprotein IIb/IIIa by anti-idiotypic antibodies in intravenous gammaglobulin (1989)

Intravenous immunoglobulin (IVIgG) causes an acute rise in the platelet count in the majority of patients with chronic immune thrombocytopenic purpura (ITP) but the mechanism(s) of action is still unknown. We evaluated the ability of three different IVIgG preparations to inhibit the in vitro binding of autoantibody to platelet glycoprotein (GP) IIb/IIIa. ITP plasma, known to contain anti-GPIIb/IIIa antibodies, was incubated overnight with either IVIgG or bovine serum albumin (BSA) followed by measurement of the autoantibody titer. Binding of autoantibody from eight ITP patients was inhibited by IVIgG in proportion to the IVIgG concentration. Using 3.2% IVIgG, compatible with therapeutic concentrations expected in vivo, mean inhibition of autoantibody binding ranged from 20.2% to 41.3%. No inhibition by IVIgG of alloantibody binding to the same or different molecules was detected (five patients with anti-GPIIb/IIIa and two with anti-HLA alloantibodies). F(ab')2 fragments of IVIgG also inhibited the binding of both plasma autoantibodies and purified anti-GPIIb/IIIA autoantibodies prepared by elution from antigen affinity columns. A portion of the anti-idiotypic antibodies could be adsorbed from IVIgG using insolubilized, purified anti-GPIIb/IIIa autoantibody. These results show that IVIgG preparations from normal donors contain anti-idiotypic antibodies directed against idiotypes located on GPIIb/IIIa autoantibodies but do not have anti-idiotypes to platelet alloantibodies against the same or different molecules. The importance of these anti-idiotypic antibodies in the therapeutic response to IVIgG remains to be established.
Altering the Self-Association and Stability of Insulin by Amino Acid Replacement (1993)

We have manipulated the amino acid sequence of insulin to speed the absorption rate from the subcutaneous injection site and to improve the storage stability. The self-association of insulin was shown to be particularly sensitive to amino acid changes in the C-terminus of the B chain. The self-association of insulin was completely abolished in some analogs, which resulted in the biological effect of faster absorption rates from the subcutaneous injection site. The storage stability of Zn-free insulin was shown to be limited by the lability of the disulfide bonds. The maintenance of the native state of insulin was shown to be important in protecting the disulfides, indicating that the storage stability of insulin is under the thermodynamic control of the conformational equilibria. The storage stability of these insulin analogs differed by 100-fold.
An Energy Packet Switch for Digital Power Grids (2018)

We propose the design of an energy packet switch for forwarding and delivery of energy in digital power grids in this paper. The proposed switch may receive energy from one or multiple power sources, store and forward it in the form of energy packets to requesting loads connected to one or multiple ports of the switch. Energy packets carry discrete amounts of energy for a finely controlled supply. Loads receive discrete amounts of energy through packets rather than a continuing and discretionary energy flow. Using energy packets may help manage the delivery of power in a more reliable, robust, and economical form than that used by the present power grid. The control and management of the proposed switch are based on a request-grant protocol. The switch uses a data network for the transmission of these requests and grants. The energy packet switch may be the centerpiece for creating infrastructure in the realization of the digital power grid. The design of the energy packet switch is based on shared supercapacitors to shape and manage discretization of energy. We introduce the design and analysis of the electrical properties of the proposed switch and describe the procedure used in the switch to determine the amount of energy transmitted to requesting loads.
Cross-reactive neutralizing human survivor monoclonal antibody BDBV223 targets the ebolavirus stalk (2019)

Three Ebolavirus genus viruses cause lethal disease and lack targeted therapeutics: Ebola virus, Sudan virus and Bundibugyo virus. Monoclonal antibody (mAb) cocktails against the surface glycoprotein (GP) present a potential therapeutic strategy. Here we report two crystal structures of the antibody BDBV223, alone and complexed with its GP2 stalk epitope, an interesting site for therapeutic/vaccine design due to its high sequence conservation among ebolaviruses. BDBV223, identified in a human survivor of Bundibugyo virus disease, neutralizes both Bundibugyo virus and Ebola virus, but not Sudan virus. Importantly, the structure suggests that BDBV223 binding interferes with both the trimeric bundle assembly of GP and the viral membrane by stabilizing a conformation in which the monomers are separated by GP lifting or bending. Targeted mutagenesis of BDBV223 to enhance SUDV GP recognition indicates that additional determinants of antibody binding likely lie outside the visualized interactions, and perhaps involve quaternary assembly or membrane-interacting regions.
EuroFlow-Based Flowcytometric Diagnostic Screening and Classification of Primary Immunodeficiencies of the Lymphoid System (2019)

Guidelines for screening for primary immunodeficiencies (PID) are well-defined and several consensus diagnostic strategies have been proposed. These consensus proposals have only partially been implemented due to lack of standardization in laboratory procedures, particularly in flow cytometry. The main objectives of the EuroFlow Consortium were to innovate and thoroughly standardize the flowcytometric techniques and strategies for reliable and reproducible diagnosis and classification of PID of the lymphoid system. The proposed EuroFlow antibody panels comprise one orientation tube and seven classification tubes and corresponding databases of normal and PID samples. The 8-color 12-antibody PID Orientation tube (PIDOT) aims at identification and enumeration of the main lymphocyte and leukocyte subsets; this includes naïve pre-germinal center (GC) and antigen-experienced post-GC memory B-cells and plasmablasts. The seven additional 8(-12)-color tubes can be used according to the EuroFlow PID algorithm in parallel or subsequently to the PIDOT for more detailed analysis of B-cell and T-cell subsets to further classify PID of the lymphoid system. The Pre-GC, Post-GC, and immunoglobulin heavy chain (IgH)-isotype B-cell tubes aim at identification and enumeration of B-cell subsets for evaluation of B-cell maturation blocks and specific defects in IgH-subclass production. The severe combined immunodeficiency (SCID) tube and T-cell memory/effector subset tube aim at identification and enumeration of T-cell subsets for assessment of T-cell defects, such as SCID. In case of suspicion of antibody deficiency, PIDOT is preferably directly combined with the IgH isotype tube(s) and in case of SCID suspicion (e.g., in newborn screening programs) the PIDOT is preferably directly combined with the SCID T-cell tube. The proposed ≥8-color antibody panels and corresponding reference databases combined with the EuroFlow PID algorithm are designed to provide fast, sensitive and cost-effective flowcytometric diagnosis of PID of the lymphoid system, easily applicable in multicenter diagnostic settings world-wide.
Photonic burst switching (pbs) architecture for hop and span-constrained optical networks (2003)

The paper presents a new architecture, called photonic burst switching (PBS), with variable time slot provisioning, supporting high-speed bursty data transmission within hop and span-constrained networks. First, the edge and switching node architecture for in-band and out-of-band signaling is defined with optical switch fabric performance parameters. Second, the edge router regions of operation for burst assembly are studied via simulations. Third, we introduce: (i) a GMPLS-based PBS software architecture in terms of control and data plane operations that is extended to enable the PBS optical interfaces with software building blocks for edge and switching nodes; (ii) an adaptive PBS MAC layer functionality and framing of multiple generic payloads. The integration of the proposed PBS network architecture with low-cost optical switching fabrics and GMPLS-based software architecture should provide the means for robust and efficient optical transport of bandwidth-demanding applications within enterprise networks.