gebhart/patrepeval huggingface dataset:
High‐efficiency gene targeting in hexaploid wheat using <scp>DNA</scp> replicons and <scp>CRISPR</scp> /Cas9 (2016)

The ability to edit plant genomes through gene targeting (GT) requires efficient methods to deliver both sequence-specific nucleases (SSNs) and repair templates to plant cells. This is typically achieved using Agrobacterium T-DNA, biolistics or by stably integrating nuclease-encoding cassettes and repair templates into the plant genome. In dicotyledonous plants, such as Nicotinana tabacum (tobacco) and Solanum lycopersicum (tomato), greater than 10-fold enhancements in GT frequencies have been achieved using DNA virus-based replicons. These replicons transiently amplify to high copy numbers in plant cells to deliver abundant SSNs and repair templates to achieve targeted gene modification. In the present work, we developed a replicon-based system for genome engineering of cereal crops using a deconstructed version of the wheat dwarf virus (WDV). In wheat cells, the replicons achieve a 110-fold increase in expression of a reporter gene relative to non-replicating controls. Furthermore, replicons carrying CRISPR/Cas9 nucleases and repair templates achieved GT at an endogenous ubiquitin locus at frequencies 12-fold greater than non-viral delivery methods. The use of a strong promoter to express Cas9 was critical to attain these high GT frequencies. We also demonstrate gene-targeted integration by homologous recombination (HR) in all three of the homoeoalleles (A, B and D) of the hexaploid wheat genome, and we show that with the WDV replicons, multiplexed GT within the same wheat cell can be achieved at frequencies of ~1%. In conclusion, high frequencies of GT using WDV-based DNA replicons will make it possible to edit complex cereal genomes without the need to integrate GT reagents into the genome.
Capillary Electrophoresis–Electrospray Ionization Mass Spectrometry of Amino Acids, Peptides, and Proteins (2004)

Separation in capillary electrophoresis (CE) is based on the movement of charged compounds inside a background electrolyte under an applied potential. Because the mechanism of separation of CE differs from that of conventional high-performance liquid chromatography (HPLC), where separation is based on the analyte's hydrophobic properties, CE is often used as a complementary technique to HPLC. In addition, because CE is performed in narrow capillaries at atmospheric pressure, it is used as an alternative to HPLC, capable of handling small sample volumes while providing shorter analysis times with higher efficiency. For the analysis of amino acid, protein, and peptide mixtures in small volume samples such as in single cells, CE has rapidly evolved as a preferred separation technique. The combination of a high-efficiency separation technique, such as CE, with mass spectrometry (MS) detection provides a powerful system for the analysis of complex biological mixtures. In this chapter, a theoretical and practical approach to achieving high-performance CE-MS is discussed and the utility of CE-MS for the analysis of amino acids, peptides, and proteins is demonstrated.
600 GHz Imaging Radar with 2 cm Range Resolution (2007)

We report the first submillimeter-wave imaging system that has radar ranging capabilities. By frequency-modulating the K-band synthesizers of a single-pixel 630 GHz scanning vector imager and applying a distortion compensation technique in software, we have achieved a range resolution of approximately 2 cm for targets at a range of several meters. Relief images of test objects obtained with our system demonstrate that three-dimensional THz imaging of scanned targets is feasible using a room temperature, all solid-state approach.
Differential expression of a gene encoding an acidic dehydrin in chilling sensitive and freezing tolerant gramineae species (1994)

We have characterized a new wheat cold-regulated cDNA clone, Wcor410, that accumulates to equivalent levels in root, crown and leaf tissues during cold acclimation. The Wcor410 cDNA contains an ORF encoding a dehydrin-like glutamate-rich protein of 28 kDa with a pI of 5.1. However, the acidic nature, the absence of the glycine-rich repeat and of the conserved N-terminal region, DEYGNP, suggest that Wcor410 belongs to a different subgroup of the D11 protein family. Northern analysis showed that this gene is expressed only in freezing tolerant gramineae, whereas Southern analysis showed that the Wcor410 gene is present in all monocot species tested. The presence of freezing tolerance-associated genes in sensitive species such as rice and corn is interesting. Characterization of the regulatory factors controlling these genes may help to establish an appropriate strategy to improve freezing tolerance.
Perspectives of Stem Cell-Derived Microglia for Medicine (2011)

Microglia, the resident immune cells of the central nervous system (CNS), are responsible for the innate brain immune defence. The exact origin of microglia is still unclear, but several reports suggest that microglia are of myeloid origin (Chan et al., 2007). They appear for the first time at an early embryonic state in the neuroepithelium and populate the brain from the blood in a second perinatal phase. Under pathological conditions or infections, microglia migrate to the affected tissue. On site, they change their phenotype to a proinflammatory cell type, release cytotoxic molecules such as reactive oxygen species to fight against microbes or clear tissue debris after sterile injury. Microglia also phagocyte oncogenically transformed brain cells and are able to activate additional immune cells. Proinflammatory microglial cells are also involved in the progression of neurodegenerative diseases. Research on microglia is mainly performed on primary cells. However, only a limited amount of murine or human microglial cells can be obtained from the brain tissue, thus complicating investigations of drug screenings or new cell therapy approaches that are requiring a high number of cells. For this reason, stem cell-derived microglia represent a useful tool for further studies to elucidate the role of microglia in diseases and therapeutical approaches. Data from others and our laboratory show that microglial precursor cell lines can be obtained from mouse embryonic stem cells or human induced pluripotent stem cells via a neural differentiation protocol. Human microglial cell lines open new alternatives for drug screening, combating cancer and regenerative approaches for neurological diseases.
The effect of high dietary eicosapentaenoic acid supplementation in leukemic mice (2013)

Current chemotherapies for treatment of chronic myelogenous leukemia (CML) do not eliminate leukemic stem cells (LSCs), leading to relapse of the disease. Discovery of alternative therapies to target LSCs is essential for elimination of the disease. We have recently reported on the endogenous production of increased levels of a novel anti‐inflammatory cyclopentenone prostaglandin Δ 12 ‐ prostaglandin J3 (Δ 12 ‐PGJ3), by macrophages cultured with eicosapentaenoic acid (EPA). The levels of EPA used in our studies reflect the doses prescribed by the FDA. To effectively translate these studies, we report here the endogenous production of Δ 12 ‐PGJ3 in mice on high EPA using LC‐MS/MS. Furthermore, we report the effect of high EPA on progression of leukemia and the ability of endogenous metabolites to target the LSCs in a CML model where the hematopoietic stem cells expressing the fusion oncoprotein Bcr‐Abl are transplanted into such mice. Pathways of apoptosis activated by Δ 12 ‐PGJ3 will be discussed. Grant Funding Source : NIH RO1 CA 175576–01
Noninvasive Measurement of Renal Hemodynamic Functions Using Gadolinium-Enhanced Magnetic Resonance Imaging (1994)

Katzberg RW, Dumoulin CL, Buonocore MA, Opsahl LR, Darrow RD, Morris TW. Noninvasive measurement of renal hemodynamic functions using gadolinium-enhanced magnetic resonance imaging. Invest Radiol 1994;29:S123–S126.
<title>Optimum wavelengths for measurement of blood hemoglobin content and tissue hydration by NIR spectrophotometry</title> (1996)

This paper examines non-invasive methods for absolute determination of the hemoglobin content of arterial blood and the water content of skin. Both methods are based on diffuse reflectance spectrophotometry in the near-infrared band (800 - 1600 nm). Separation of blood and background tissue spectra is accomplished by a technique similar to pulse oximetry, with the added feature that the set of measurement wavelengths is chosen to be sensitive to both hemoglobin and water concentration in the blood. Regressions performed on a simulated tissue spectra suggest that {1060, 1160, 1200 and 1320 nm} is an optimal set of wavelengths for measurement of tissue hydration and {1040, 1120, 1140 and 1200 nm} is an optimal set of wavelengths for measurement of hemoglobin content under typical measurement conditions. A simple in vitro tissue phantom whose optical properties can be altered in a controlled manner was developed to test the feasibility of the methods. Measurements were made with a custom-designed NIR spectrophotometer.
Advances in the Detection & Repair of Flash-Eye Defects in Digital Images - A Review of Recent Patents (2012)

Red-eye and flash-eye defects in still photography continue to cause problems for digital imaging devices. New variants of flash-eye defects have appeared as cameras and cameras sub-systems get smaller in size. This paper reviews a wide range of the more recently patented techniques that have been applied to solve various problems associated with red and non-red flash-eye, particularly solutions which are implemented in the camera. The use of in-camera metadata, multiple images of the same scene and adaptation of image acquisition conditions to improve red-eye detection and correction are explained. Four principle categories of flash-eye defect are identified and techniques are outlined to deal with each of these. The use of face, eye and scene metadata obtained within the camera is also considered. In particular data obtained regarding indoor/outdoor scenes, partial face regions, eye orientation and gaze and pupil size can all assist with some difficult cases of flash-eye defect. Some advanced techniques to improve the correction and reconstruction of eye regions are also considered. Keywords: Embedded image processing, flash-eye defects, redeye detection, redeye correction, Connected Red Segments, Simple Filter Set, Eye-Glint for Detection, Camera red-eye filter, Camera Metadata, Image Filtering
Transparent Ceramics: Magnesium Aluminate Spinel (2005)

Abstract : There is a need for high-strength, rugged materials that transmit in the visible and mid-infrared (0.4 to 5 microns) wavelength region. These materials are needed for applications requiring transparent armor, including next-generation high-speed missiles and pods, as well as protection against improvised explosive devices (IED).
Reduction of NO sub x emissions from gasoline engines (1992)

This patent describes in combination, a spark-ignition internal combustion engine, a supply of liquid fuel for the operation of the engine, and an exhaust gas catalyst for controlling the amount of pollutants released to the environment via the engine exhaust after the exhaust has contacted the catalyst. It comprises the fuel contains at least one fuel-soluble cyclopentadienyl manganese tricarbonyl compound in an amount equivalent to up to 1/32 gram of manganese per gallon of fuel; and the NO{sub x} control activity of the catalyst has been enhanced by prior operation of the engine on fuel containing at least one fuel-soluble cyclopentadienyl manganese tricarbonyl compound in an amount equivalent to up to 1.32 gram of manganese per gallon of fuel; such that there is a reduction in the quantity of nitrogen oxides in the exhaust emitted during the operation of the engine.
Two‐Photon Fluorescent Probes for Bioimaging (Eur. J. Org. Chem. 17/2012) (2012)

Abstract The cover picture shows the advantage of two‐photon absorption (upper fluorescence in the cuvette), which is highly localized in three‐dimensional space, in contrast to conventional or one‐photon absorption (lower fluorescence in the cuvette), in deep tissue imaging as shown in a tumor derived from HeLa cells (upper right) with efficient two‐photon absorbing fluorescent dyes such as that pictured in the upper left. Details are presented in the Microreview by S. Yao and K. D. Belfield on p. 3199 ff. magnified image
Low pressure nickel hydrogen cell. [uses rare earth intermetallic hydride capable of absorbing and desorbing hydrogen in response to pressure changes] (1974)

An improved rechargeable power cell comprises a sealed container which includes a first electrode means comprising an oxidizing agent, a second electrode means comprising a catalyst mounted on a conductive support (the catalyst being a material capable of dissociating molecular hydrogen to monatomic hydrogen), an alkaline electrolyte, electrolyte retaining means disposed between the first and second electrode means, and a supply of hydrogen in the container. The improvement comprises a hexagonal rare earth intermetallic hydride disposed within the container out of contact with the electrolyte. The intermetallic hydride is a material capable of absorbing and desorbing hydrogen in response to changes in pressure.
Accurate process-hotspot detection using critical design rule extraction (2012)

In advanced fabrication technology, the sub-wavelength lithography gap causes unwanted layout distortions. Even if a layout passes design rule checking (DRC), it still might contain process hotspots, which are sensitive to the lithographic process. Hence, process-hotspot detection has become a crucial issue. In this paper, we propose an accurate process-hotspot detection framework. Unlike existing DRC-based works, we extract only critical design rules to express the topological features of hotspot patterns. We adopt a two-stage filtering process to locate all hotspots accurately and efficiently. Compared with state-of-the-art DRC-based works, our results show that our approach can reach 100% success rate with significant speedups.
Synthesis of a Homogeneously Porous Solid Oxide Matrix with Tunable Porosity and Pore Size (2012)

Porous ceramics are a technologically important branch of functional materials for a variety of physical and chemical systems. The properties of porous ceramics depend critically on porosity, pore morphology, pore size, and distribution. In this study, we demonstrate the synthesis of a homogeneously porous samarium‐doped cerium ( Ce 0.8 Sm 0.2 O 1.9 , SDC ) matrix with tunable porosity and pore size via sacrificial template method. The study explicitly shows that the porosity and pore size of the resultant porous matrix can be controlled by the volume fraction of sacrificial material NiO and sintering temperature, along with the mono‐mode pore distribution produced by molecular‐level mixing of co‐precipitating SDC and NiO . The demonstrated sacrificial template methodology provides an alternative means of tailoring properties of a porous ceramic for particular applications in catalysis, fuel cells, and gas separation membranes.
Perfluorinated Brønsted 'Superacids': Powerful Catalysts for the Preparation of Vitamin E (2004)

The key-step in the industrial synthesis of (all-rac)-?-tocopherol (synthetic vitamin E) is the condensation reaction of trimethylhydroquinone with the C20 building block isophytol. For this Friedel-Crafts-type reaction, perfluorinated NH- and CH-acidic compounds (perfluoroalkyl(aryl)sulfonyl imides and methides) have been applied as excellent catalysts, preferably in biphasic solvent systems.
Structural Features of Dilute Acid Pretreated <i>Acacia mangium</i> and Impact of Sodium Sulfite Supplementation on Enzymatic Hydrolysis (2016)

Lignocellulosic biomasses (LCB) differ in their chemical composition and cell wall architecture from one another and within the same LCB due to varying geographical conditions. Thus, pretreatment parameters need optimization for recovery of sugars across different biomasses. In the current study, Acacia mangium has been investigated at bench scale for its potential as a feedstock for fermentable sugar production. Attempts were first made to target hydrolysis of hemicellulose using dilute acid (DA) as a catalyst. Pretreatment at temperature of 160 °C, residence time of 30 min and H2SO4 concentration of 2% (w/w) yielded highest overall saccharification efficiency (50%) corresponding to a glucan conversion in enzymatic hydrolysis (57.8%). Further enhancement in glucan conversion and reduction in the formation of inhibitors was brought about by using sodium sulfite (SS). It was observed that SS caused a significant increase in overall sugar recovery. Interestingly, the order in which SS and DA were added to the pretreatment medium was an important strategy to improve enzymatic saccharification. The condition (SS→DA) where sodium sulfite (SS) was added right in the beginning along with the biomass followed by dilute acid (DA) addition at the desired temperature was more effective in improving the glucan conversion yield (77.0%). Highest BET surface area of SS→DA residue (3.7 m2/g) among all the pretreated residues is one of the factors contributing to this high conversion yield. To get further insight into the basis for improved saccharification, cellulase adsorption studies were conducted. The results showed that the solid residue obtained by SS→DA despite having the lowest maximum adsorption capacity (σmax) resulted into highest saccharification yield which was supported by its highest affinity constant (Ka = 0.25 mL/mg) for the enzyme. Among the pretreated residual solids, SS→DA residue showed lignin modification and cellulose peak alterations by FT-IR spectroscopy and increased surface area by BET measurement revealing implication in improved enzymatic saccharification and overall sugar recovery.
Development of a TaqMan assay for the six major genotypes of hepatitis C virus: Comparison with commercial assays (2007)

A quantitative real-time PCR assay was developed that detects genomic RNA from reference strains representing the six major genotypes of hepatitis C virus (HCV) with equal sensitivity and accurately measured HCV RNA in JFH1 HCV-infected Huh7.5 cells. The method is indirectly calibrated to the first international (WHO 96/790) HCV standard preparation and has a linear dynamic range of 10(2.6)-10(6.5) IU/ml. In addition, the inter- and intra-assay precision were approximately 3% CV and <2% CV, respectively. Comparison with results obtained by commercially available HCV RNA Nucleic Acid Technology kits (Versant HCV RNA 3.0 b-DNA and Amplicor HCV Monitor), that also employ the WHO standard, allowed validation of the TaqMan assay against all major HCV genotypes. Both commercial methods detected HCV RNA over a wide dynamic range, but showed a consistent difference of about 0.3 log10 when evaluating samples of different HCV genotypes. The genome titers obtained with the three methods correlated with the infectivity titers previously determined for the HCV reference strains. TaqMan assays have become an essential tool to follow viral load in clinical samples and cell culture-based experiments and this technology offers significant advantages in linear dynamic range, sensitivity and customization.
Experimental Model of Hepatic Fibrosis Following Repeated Periportal Necrosis Induced by Allylalcohol (2000)

Hepatic fibrosis can be sufficiently induced by repetitive intraperitoneal injection of 0.62 mmol/kg of allylalcohol twice a week for 8 weeks. This simple model of hepatic fibrosis, in which TGFbeta1 is overexpressed at the transcriptional level, may be useful in the study of patients who have predominantly periportal necrosis and fibrosis.
Organic superconductors: structural aspects and design of new materials (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganic superconductors: structural aspects and design of new materialsJack M. Williams, Mark A. Beno, Hau H. Wang, Peter C. W. Leung, Thomas J. Emge, Urs Geiser, and K. Douglas CarlsonCite this: Acc. Chem. Res. 1985, 18, 9, 261–267Publication Date (Print):September 1, 1985Publication History Published online1 May 2002Published inissue 1 September 1985https://pubs.acs.org/doi/10.1021/ar00117a001https://doi.org/10.1021/ar00117a001research-articleACS PublicationsRequest reuse permissionsArticle Views592Altmetric-Citations189LEARN 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
Design of Protease Activated Optical Contrast Agents That Exploit a Latent Lysosomotropic Effect for Use in Fluorescence-Guided Surgery (2015)

There is a need for new molecular-guided contrast agents to enhance surgical procedures such as tumor resection that require a high degree of precision. Cysteine cathepsins are highly up-regulated in a wide variety of cancers, both in tumor cells and in the tumor-supporting cells of the surrounding stroma. Therefore, tools that can be used to dynamically monitor their activity in vivo could be used as imaging contrast agents for intraoperative fluorescence image guided surgery (FGS). Although multiple classes of cathepsin-targeted substrate probes have been reported, most suffer from overall fast clearance from sites of protease activation, leading to reduced signal intensity and duration in vivo. Here we describe the design and synthesis of a series of near-infrared fluorogenic probes that exploit a latent cationic lysosomotropic effect (LLE) to promote cellular retention upon protease activation. These probes show tumor-specific retention, fast activation kinetics, and rapid systemic distribution. We demonstrate that they are suitable for detection of diverse cancer types including breast, colon and lung tumors. Most importantly, the agents are compatible with the existing, FDA approved, da Vinci surgical system for fluorescence guided tumor resection. Therefore, our data suggest that the probes reported here can be used with existing clinical instrumentation to detect tumors and potentially other types of inflammatory lesions to guide surgical decision making in real time.
Biometric recognition of conjunctival vasculature using GLCM features (2011)

Besides the iris, conjunctival vasculature may also be used for ocular biometric recognition. Conjunctival vessel patterns can be easily observed in the visible spectrum and can compensate for off-angle or otherwise occluded iridial texture. In this paper, classification of conjunctival vasculature using Gray Level Co-occurrence Matrix (GLCM) is studied. Statistical features of GLCM, i.e., contrast, correlation, energy and homogeneity, were used in conjunction with Fisher linear discriminant analysis and regularized neural network classifiers in order to recognize textures arising from conjunctival vessels. Match score level fusion of Fisher LDA and neural networks provided the best results, resulting in a test set equal error rate (EER) and area under receiver operating characteristics curve (ROC AUC) of 13.97% and 0.9333, respectively. These figures improved to 11.9% and 0.9504 after fusion of LDA and neural network match scores.