271 research outputs found

    Standards for plant synthetic biology: A common syntax for exchange of DNA parts

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    © 2015 New Phytologist Trust. Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering

    The Open-Access European Prevention of Alzheimer's Dementia (EPAD) MRI dataset and processing workflow

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    The European Prevention of Alzheimer Dementia (EPAD) is a multi-center study that aims to characterize the preclinical and prodromal stages of Alzheimer's Disease. The EPAD imaging dataset includes core (3D T1w, 3D FLAIR) and advanced (ASL, diffusion MRI, and resting-state fMRI) MRI sequences. Here, we give an overview of the semi-automatic multimodal and multisite pipeline that we developed to curate, preprocess, quality control (QC), and compute image-derived phenotypes (IDPs) from the EPAD MRI dataset. This pipeline harmonizes DICOM data structure across sites and performs standardized MRI preprocessing steps. A semi-automated MRI QC procedure was implemented to visualize and flag MRI images next to site-specific distributions of QC features - i.e. metrics that represent image quality. The value of each of these QC features was evaluated through comparison with visual assessment and step-wise parameter selection based on logistic regression. IDPs were computed from 5 different MRI modalities and their sanity and potential clinical relevance were ascertained by assessing their relationship with biological markers of aging and dementia. The EPAD v1500.0 data release encompassed core structural scans from 1356 participants 842 fMRI, 831 dMRI, and 858 ASL scans. From 1356 3D T1w images, we identified 17 images with poor quality and 61 with moderate quality. Five QC features - Signal to Noise Ratio (SNR), Contrast to Noise Ratio (CNR), Coefficient of Joint Variation (CJV), Foreground-Background energy Ratio (FBER), and Image Quality Rate (IQR) - were selected as the most informative on image quality by comparison with visual assessment. The multimodal IDPs showed greater impairment in associations with age and dementia biomarkers, demonstrating the potential of the dataset for future clinical analyses

    Using Parahydrogen Induced Polarization to Study Steps in the Hydroformylation Reaction.

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    A range of iridium complexes, Ir(η3-C3H5)(CO)(PR2R’)2 (1a-1e) [where 1a, PR2R’ = PPh3, 1b P(p-tol)3, 1c PMePh2, 1d PMe2Ph and 1e PMe3] were synthesized and their reactivity as stoichiometric hydroformylation precursors studied. Para-hydrogen assisted NMR spectroscopy detected the following intermediates: Ir(H)2(η3-C3H5)(CO)(PR2R’) (2a-e), Ir(H)2(η1-C3H5)(CO)(PR2R’)2 (4d-e), Ir(H)2(η1-C3H5)(CO)2(PR2R’) (10a-e), Ir(H)2(CO-C3H5)(CO)2(PR2R’) (11a-c), Ir(H)2(CO-C3H7)(CO)2(PR2R’) (12a-c) and Ir(H)2(CO-C3H5)(CO)(PR2R’)2 (13d-e). Some of these species exist as two geometric isomers according to their multinuclear NMR characteristics. The NMR studies suggest a role for the following 16 electron species in these reactions: Ir(η3-C3H5)(CO)(PR2R’), Ir(η1-C3H5)(CO)(PR2R’)2, Ir(η1-C3H5)(CO)2(PR2R’), Ir(CO-C3H5)(CO)2(PR2R’), Ir(CO-C3H7)(CO)2(PR2R’) and Ir(CO-C3H5)(CO)(PR2R’)2. Their role is linked to several 18 electron species in order to confirm the route by which hydroformylation and hydrogenation proceeds

    Observation of Cosmic Ray Anisotropy with Nine Years of IceCube Data

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    Design of an Efficient, High-Throughput Photomultiplier Tube Testing Facility for the IceCube Upgrade

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    Multi-messenger searches via IceCube’s high-energy neutrinos and gravitational-wave detections of LIGO/Virgo

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    We summarize initial results for high-energy neutrino counterpart searches coinciding with gravitational-wave events in LIGO/Virgo\u27s GWTC-2 catalog using IceCube\u27s neutrino triggers. We did not find any statistically significant high-energy neutrino counterpart and derived upper limits on the time-integrated neutrino emission on Earth as well as the isotropic equivalent energy emitted in high-energy neutrinos for each event
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