gebhart/patrepeval huggingface dataset:
True optical resolution beyond the Rayleigh limit achieved by standing wave illumination (2000)

During the last decade, various efforts have been undertaken to enhance the resolution of optical microscopes, mostly because of their importance in biological sciences. Herein, we describe a method to increase the resolution of fluorescence microscopy by illuminating the specimen with a mesh-like interference pattern of a laser source and electronic postprocessing of the images. We achieve 100-nm optical resolution, an improvement by a factor of more than 2 compared with standard fluorescence microscopy and of 1.5 compared with confocal scanning.
Transmission line Inductor Modeling and Design for Millimeter Wave Circuits in Digital CMOS Process (2007)

A pH-range inductor is necessary in millimeter wave integrated circuit design. Such small inductors can be designed as a small transmission line with a special structure. The quality factor of this inductor is the most important design issue, especially in CMOS process. This work proposes a simple and accurate model, developed for design and optimization of such inductors. This model comprises the resistive loss, dielectric loss and eddy current loss to predict the quality factor of the inductor. A shield layer composed of thin lines in poly-silicon and active layer has been introduced and its effect in quality factor has been investigated. We have developed a simple design and optimization package in MATLAB to design this type of inductors for STMicroelectronics 90 nm digital CMOS process. To evaluate the proposed model we have used the 3D-MoM simulation in ADS.
Using Marine Natural Products to Discover a Protease that Catalyzes Peptide Macrocyclization of Diverse Substrates (2009)

Small N-C terminally cyclic ribosomal peptides are common in nature, yet the mechanisms underlying their biosyntheses remain largely unknown. We recently identified candidate peptide cyclase genes in the metagenomes of marine animals. Here we report that PatG, a protease discovered in this analysis, cleaves variables, short peptides out of a precursor protein, and cyclizes these peptides in vivo and in vitro.
Flow cytometric detection of specific RNAs in native human cells with quenched autoligating FRET probes (2005)

We describe the use of modified fluorescent-labeled oligonucleotide probes in the sequence-specific detection of messenger RNAs in live human cells. To make this detection possible, we developed a previously undescribed probe design that combines earlier quenched autoligation chemistry with a previously undescribed fluorescence resonance energy transfer (FRET) strategy to lower background signals. The probe pairs consisted of a nucleophilic 3'-phosphorothioate probe carrying a Cy5 FRET acceptor, and an electrophilic probe containing the combination of a 5' end electrophile/quencher and a fluorescein FRET donor. Probes were introduced to HL-60 cells by use of the streptolysin O pore-forming peptide. Signals from three different messenger RNAs, as well as 28S ribosomal RNA, could be detected and quantitated by flow cytometry. Probes targeted to ribosomal sequences and beta-actin mRNA also could be detected over background by confocal fluorescence microscopy. Varying the target site and probe backbone chemistry were found to have large effects on signal. The data suggest that quenched autoligating probes may be of general utility as biological tools in following localization, transcription, and processing of eukaryotic cellular messages and may have applications in diagnostic or prognostic analysis of disease-related RNAs in human tissues.
Generation of α-1,3-galactosyltransferase knocked-out transgenic cloned pigs with knocked-in five human genes (2016)

Recent progress in genetic manipulation of pigs designated for xenotransplantation ha6s shown considerable promise on xenograft survival in primates. However, genetic modification of multiple genes in donor pigs by knock-out and knock-in technologies, aiming to enhance immunological tolerance against transplanted organs in the recipients, has not been evaluated for health issues of donor pigs. We produced transgenic Massachusetts General Hospital piglets by knocking-out the α-1,3-galactosyltransferase (GT) gene and by simultaneously knocking-in an expression cassette containing five different human genes including, DAF, CD39, TFPI, C1 inhibitor (C1-INH), and TNFAIP3 (A20) [GT<sup>-(DAF/CD39/TFPI/C1-INH/TNFAIP3)/+</sup>] that are connected by 2A peptide cleavage sequences to release individual proteins from a single translational product. All five individual protein products were successfully produced as determined by western blotting of umbilical cords from the newborn transgenic pigs. Although gross observation and histological examination revealed no significant pathological abnormality in transgenic piglets, hematological examination found that the transgenic piglets had abnormally low numbers of platelets and WBCs, including neutrophils, eosinophils, basophils, and lymphocytes. However, transgenic piglets had similar numbers of RBC and values of parameters related to RBC compared to the control littermate piglets. These data suggest that transgenic expression of those human genes in pigs impaired hematopoiesis except for erythropoiesis. In conclusion, our data suggest that transgenic expression of up to five different genes can be efficiently achieved and provide the basis for determining optimal dosages of transgene expression and combinations of the transgenes to warrant production of transgenic donor pigs without health issues.
Formulation, inflammation, and RNA sensing impact the immunogenicity of self-amplifying RNA vaccines (2022)

To be effective, RNA vaccines require both <i>in situ</i> translation and the induction of an immune response to recruit cells to the site of immunization. These factors can pull in opposite directions with the inflammation reducing expression of the vaccine antigen. We investigated how formulation affects the acute systemic cytokine response to a self-amplifying RNA (saRNA) vaccine. We compared a cationic polymer (pABOL), a lipid emulsion (nanostructured lipid carrier, NLC), and three lipid nanoparticles (LNP). After immunization, we measured serum cytokines and compared the response to induced antibodies against influenza virus. Formulations that induced a greater cytokine response induced a greater antibody response, with a significant correlation between IP-10, MCP-1, KC, and antigen-specific antibody titers. We then investigated how innate immune sensing and signaling impacted the adaptive immune response to vaccination with LNP-formulated saRNA. Mice that lacked MAVS and are unable to signal through RIG-I-like receptors had an altered cytokine response to saRNA vaccination and had significantly greater antibody responses than wild-type mice. This indicates that the inflammation induced by formulated saRNA vaccines is not solely deleterious in the induction of antibody responses and that targeting specific aspects of RNA vaccine sensing might improve the quality of the response.
Expressed protein ligation (2004)

The introduction of noncanonical amino acids and biophysical probes into peptides and proteins, and total or segmental isotopic labelling has the potential to greatly aid the determination of protein structure, function and protein-protein interactions. To obtain a peptide as large as possible by solid-phase peptide synthesis, native chemical ligation was introduced to enable synthesis of proteins of up to 120 amino acids in length. After the discovery of inteins, with their self-splicing properties and their application in protein synthesis, the semisynthetic methodology, expressed protein ligation, was developed to circumvent size limitation problems. Today, diverse expression vectors are available that allow the production of N- and C-terminal fragments that are needed for ligation to produce large amounts and high purity protein(s) (protein alpha-thioesters and peptides or proteins with N-terminal Cys). Unfortunately, expressed protein ligation is still limited mainly by the requirement of a Cys residue. Of course, additional Cys residues can be introduced into the sequence by site directed mutagenesis or synthesis, however, those mutations may disturb protein structure and function. Recently, alternative ligation approaches have been developed that do not require Cys residues. Accordingly, it is theoretically possible to obtain each modified protein using ligation strategies.
Thrombotic microangiopathy: new insights (2010)

In HUS/TTP the kidney shows characteristic vascular changes due to endothelial damage, that is, TMA, which should be clinically and morphologically differentiated from other diseases. Recent genetic and molecular studies have shed more light on the pathogenesis of TMA in atypical HUS, that is, disturbances of various aspects of the complement system, and in TTP, that is, von Willebrand factor regulation by ADAMTS13, which are also helpful in the differential diagnosis.
'Gadolinium' as an Alternative to Iodinated Contrast Media for X-Ray Angiography in Patients With Severe Allergy (2005)

Some patients cannot undergo coronary angiography (CAG) because of the adverse effects of contrast media. In the present study gadolinium, (gadodiamide hydrate: Gd DTPA-BMA) commonly used for magnetic resonance imaging (MRI), was used as the contrast agent for diagnostic CAG in 3 patients with severe allergy to iodine or iodinated contrast agents. The indications for CAG were recurrent chest pain, evaluation of peri-operative risk of gastric cancer and abdominal aortic aneurysm, and evaluation of graft patency after coronary artery bypass grafting. The procedure was well tolerated by each patient and the amount of the gadolinium-based contrast media did not exceed 40 ml, which is twice the volume used for MRI. The images were of fair quality. In patients with allergy to iodinated contrast media, CAG with gadolinium-based contrast media is an alternative technique for evaluating coronary artery disease.
Innate recognition of bacteria by a macrophage cytosolic surveillance pathway (2002)

Host recognition of bacterial pathogens is a critical component of the immune response. Intracellular bacterial pathogens are able to evade the humoral immune system by residing within the host cell. Here we show the existence of an innate host surveillance mechanism in macrophages that specifically distinguishes bacteria in the cytosol from bacteria in the vacuole. Recognition of Gram-positive and Gram-negative bacterial products by this surveillance system results in transcription of the ifnb gene. The activation of cytosol-specific signaling is associated with translocation of NF-κB into the nucleus and phosphorylation of the p38 mitogen-activated protein (MAP) kinase. Activation of the p38 kinase is required for the induction of gene expression by the cytosolic surveillance pathway. Our studies suggest that infection by intracellular bacterial pathogens results in an immune response distinct from that of infection by extracellular bacterial pathogens.
Gastric preconditioning induced by short ischemia: the role of prostaglandins, nitric oxide and adenosine. (2001)

1) gastric ischemic preconditioning represents one of the most powerful protective intervention against the mucosal damage induced by severe I/R as well as by topical mucosal irritants in the stomach; 2) this protection, involving several mediators such as PG derived from COX-1 and COX-2, NO originating from NO-synthase and adenosine, appear to play a key mechanism of gastric ischemic preconditioning.
Laser Beam Splitting by Diffractive Optics (2004)

Recent advances in diffractive optics theory and technology have made it possible to design programmable, multichannel optical systems based on diffraction gratings, lenslet arrays and digital holography algorithms. Spot array generation, multiple and multifocal imaging, matched filtering, laser beam mode selection and simultaneous contour shaping are among the most promising applications of diffractive beam splitting.
Rod-Derived Cone Viability Factor for Treating Blinding Diseases: From Clinic to Redox Signaling (2010)

The identification of one mechanism that causes vision loss in inherited degenerative retinal disorders revealed a new signaling molecule that represents a potential therapy for these currently untreatable diseases. This protein, called rod-derived cone viability factor (RdCVF), maintains the function and consequently the viability of cone photoreceptor cells in the retina; mice that lack this factor exhibit a progressive loss of photoreceptor cells. The gene encoding RdCVF also encodes, by differential splicing, a second product that has characteristics of a thioredoxin-like enzyme and protects both photoreceptor cells and, more specifically, its interacting protein partner, the tau protein, against oxidative damage. This signaling pathway potentially links environmental insults to an endogenous neuroprotective response.
Ab initioestimate of temperature dependence of electrical conductivity in a model amorphous material: Hydrogenated amorphous silicon (2007)

We present an ab initio calculation of the dc conductivity of amorphous silicon and hydrogenated amorphous silicon. The Kubo-Greenwood formula is used to obtain the dc conductivity, by thermal averaging over extended dynamical simulation. Its application to disordered solids is discussed. The conductivity is computed for a wide range of temperatures and doping is explored in a naive way by shifting the Fermi level. We observed the Meyer-Neldel rule for the electrical conductivity with ${E}_{\mathrm{MNR}}=0.06\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ and a temperature coefficient of resistance close to experiment for $a\text{\ensuremath{-}}\mathrm{Si}:\mathrm{H}$. In general, experimental trends are reproduced by these calculations, and this suggests the possible utility of the approach for modeling carrier transport in other disordered systems.
A Novel Strategy by the Action of Ricin that Connects Phenotype and Genotype without Loss of the Diversity of Libraries (2002)

We present a novel strategy for connection of phenotype and genotype in vitro that can be used for the selection of functional proteins even at room temperature. The strategy involves generation of a stable complex between a ribosome, an mRNA, and its translated protein, without removal of the termination codon, as a result of the action of the ricin A chain during translation. We demonstrate the potential selection capacity of this novel strategy by isolating such complexes that contain newly synthesized streptavidin and glutathione-S-transferase (GST) using appropriate ligands. The technique requires no transfection, no chemical synthesis, no ligation, and no removal of the termination codon. Thus our novel "Ribosome-Inactivation Display System (RIDS)" should provide, without loss of the pool population, a reliable, simple, and robust selection system for in vitro evolution of the properties of proteins in a predictable direction by a combination of randomization and appropriate selection strategies.
Efficient Clustering of Uncertain Data (2006)

We study the problem of clustering data objects whose locations are uncertain. A data object is represented by an uncertainty region over which a probability density function (pdf) is defined. One method to cluster uncertain objects of this sort is to apply the UK-means algorithm, which is based on the traditional K-means algorithm. In UK-means, an object is assigned to the cluster whose representative has the smallest expected distance to the object. For arbitrary pdf, calculating the expected distance between an object and a cluster representative requires expensive integration computation. We study various pruning methods to avoid such expensive expected distance calculation.
Development of a Low-Dielectric-Constant Polymer for the Fabrication of Integrated Circuit Interconnect (2000)

For faster, smaller, and higher performance integrated circuits, a low dielectric constant insulator is required to replace silicon dioxide. Here the properties of a new dielectric—SiLK resin, a solution of a low-molecular-weight aromatic thermosetting polymer—are reviewed and examples of its application in the fabrication of interconnect structures, such as the one shown in the Figure, are given.
Effect of velocity control on kinesthetic lung tumour localization (2008)

Restricted access during minimally invasive surgery precludes manual palpation, making the localization of lung tumours challenging. This paper investigates the force sensing performance that would allow an instrumented kinesthetic probe to localize tumours based on stiffness variations of the lung parenchyma. Agar injected into ex vivo porcine lungs produced a model approximating commonly encountered tumours. Using both constant and variable velocity approaches, force-deformation data were collected from multiple sites at various palpation depths, before and after the tumours were injected. Analysis showed an increase in force after the tumours were injected, ranging from 0.07 to 0.16 N at 7 mm. A constant palpation velocity minimized exponential stress decay at constant depths, facilitating easier comparisons between measurements. A sensing range of 0 to 2 N, with 0.01 N resolution should allow a kinesthetic palpation probe to resolve local tissue stiffness changes that suggest an underlying tumour.
Degeneration of the intervertebral disc. (2003)

The intervertebral disc is a cartilaginous structure that resembles articular cartilage in its biochemistry, but morphologically it is clearly different. It shows degenerative and ageing changes earlier than does any other connective tissue in the body. It is believed to be important clinically because there is an association of disc degeneration with back pain. Current treatments are predominantly conservative or, less commonly, surgical; in many cases there is no clear diagnosis and therapy is considered inadequate. New developments, such as genetic and biological approaches, may allow better diagnosis and treatments in the future.
Continuous Fixed Bed CO2 Adsorption: Breakthrough, Column Efficiency, Mass Transfer Zone (2020)

The increased levels of carbon dioxide in the environment have incited the search for breakthrough technologies to lessen its impact on climate. The CO2 capture from a mixture of CO2/N2 was studied using a molecular sieve (MS) and silica gel type-III. The breakthrough behavior was predicted as a function of temperature, superficial velocity, and CO2 partial pressure. The breakpoint time reduced significantly with increased temperature and increased superficial velocity. The CO2 adsorption capacity increased appreciably with decreased temperature and increased CO2 pressure. The saturation CO2 adsorption capacity from the CO2/N2 mixture reduced appreciably with increased temperature. The molecular sieve contributed to higher adsorption capacity, and the highest CO2 uptake of 0.665 mmol/g was realized for MS. The smaller width of the mass transfer zone and higher column efficiency of 87.5% for MS signify the efficient use of the adsorbent; this lowers the regeneration cost. The findings suggest that a molecular sieve is suitable for CO2 capture due to high adsorption performance owing to better adsorption characteristic parameters.
Humoral immune responses in CD40 ligand-deficient mice. (1994)

Individuals with X-linked hyper-IgM syndrome fail to express functional CD40 ligand (CD40L) and, as a consequence, are incapable of mounting protective antibody responses to opportunistic bacterial infections. To address the role of CD40L in humoral immunity, we created, through homologous recombination, mice deficient in CD40L expression. These mice exhibited no gross developmental deficiencies or health abnormalities and contained normal percentages of B and T cell subpopulations. CD40L-deficient mice did display selective deficiencies in humoral immunity; basal serum isotype levels were significantly lower than observed in normal mice, and IgE was undetectable. Furthermore, the CD40L-deficient mice failed to mount secondary antigen-specific responses to immunization with a thymus-dependent antigen, trinitrophenol-conjugated keyhole limpet hemocyanin (TNP-KLH). By contrast, the CD40L-deficient mice produced antigen-specific antibody of all isotypes except IgE in response to the thymus-independent antigen, DNP-Ficoll. These results underscore the requirement of CD40L for T cell-dependent antibody responses. Moreover, Ig class switching to isotypes other than IgE can occur in vivo in the absence of CD40L, supporting the notion that alternative B cell signaling pathways regulate responses to thymus-independent antigens.
Boron-Nitrogen Compounds. XV. Preparation of Vinylated Aminoboranes (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBoron-Nitrogen Compounds. XV. Preparation of Vinylated AminoboranesKurt Niedenzu, Peter Fritz, and John W. DawsonCite this: Inorg. Chem. 1964, 3, 5, 778–779Publication Date (Print):May 1, 1964Publication History Published online1 May 2002Published inissue 1 May 1964https://pubs.acs.org/doi/10.1021/ic50015a043https://doi.org/10.1021/ic50015a043research-articleACS PublicationsRequest reuse permissionsArticle Views42Altmetric-Citations6LEARN 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
Cutting Edge: TREM-Like Transcript-1, a Platelet Immunoreceptor Tyrosine-Based Inhibition Motif Encoding Costimulatory Immunoreceptor that Enhances, Rather than Inhibits, Calcium Signaling via SHP-2 (2004)

To date, immunoreceptor tyrosine-based inhibition motifs (ITIMs) have been shown to mediate inhibitory properties. We report a novel triggering receptor expressed on myeloid cells (TREM) family member, TREM-like transcript-1 (TLT1), which differs from the activating members because its cytoplasmic tail contains two ITIMs at Y245 and Y281. A TLT1 splice variant (TLT1sp) encodes a different cytoplasmic tail lacking ITIMs. Both isoforms are expressed in resting platelet alpha-granules, which are up-regulated to the cell surface following activation. TLT1 recruited Src homology 2 domain-containing tyrosine phosphatase (SHP)-2 to the "classical" ITIM (Y281) but not the "nonclassical" ITIM (Y245). In contrast to previously characterized ITIM receptors, TLT1 enhanced, rather than inhibited, FcepsilonRI-mediated calcium signaling in rat basophilic leukemia cells, a property dependent on the SHP-2 recruiting classical Y281 ITIM. Therefore, TLT1 represents a new costimulatory ITIM immunoreceptor and is the second ITIM-bearing receptor to be identified in platelets after platelet endothelial cell adhesion molecule-1.