Virtual outcrop geology comes of age: the application of consumer-grade virtual reality hardware and software to digital outcrop data analysis
Contributors: Thomas Seers, Ali Sheharyar
... In this work, the need for discipline specific analysis tools is addressed by harnessing a consumer grade virtual reality system (HTC Vive) and freeform 3D visual arts software package (Google Tilt Brush) to interactively interpret and analyze sedimentary and structural architecture (bedding contacts, faults, fractures) from digital outcrop models. Having generated these interpretations, users utilize a script library developed in the MATLABTM language to extract geologically useful data (e.g. orientation, length, intensity) from interactively generated 3D mesh patches output by Tilt Brush. Note that the submission contains the MATLAB code library, test data and presentation (.ppt) with videoed examples of Tilt Brush data input and interpretation.
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and prefrontal cortex across development and in schizophrenia. Collado-Torres et al, Neuron, 2019.
Contributors: Leonardo Collado-Torres, Emily E Burke, Amy Peterson, Joo Heon Shin, Richard Straub, Nina Rajpurohit, Stephen A Semick, William S Ulrich, BrainSeq Consortium, Amanda J Price
... This dataset contains the Supplementary Figures and Tables for the "Regional heterogeneity in gene expression, regulation and coherence in hippocampus and prefrontal cortex across development and in schizophrenia" article by Collado-Torres et al, Neuron, 2019. Please cite the original article as well as the data itself if appropriate. For clarifications about the figures or data, please contact us by creating an issue at https://github.com/LieberInstitute/brainseq_phase2/issues. Thank you!
The NAD-booster nicotinamide riboside potently stimulates hematopoiesis through increased mitochondrial clearance
Contributors: Olaia Naveiras
... It has been recently shown that increased oxidative phosphorylation, as reflected by increased mitochondrial activity, together with impairment of the mitochondrial stress response can severely compromise hematopoietic stem cell (HSC) regeneration. Here we show that the NAD+-boosting agent Nicotinamide Riboside (NR) reduces mitochondrial activity within HSCs through increased mitochondrial clearance, leading to increased asymmetric HSC divisions. NR dietary supplementation results in a significantly enlarged pool of progenitors, without concurrent HSC exhaustion, improves survival by 80%, and accelerates blood recovery after murine lethal irradiation and limiting-HSC transplantation. In immune-deficient mice, NR increased the production of human leucocytes from hCD34+ progenitors. Our work demonstrates for the first time a positive effect of NAD+ boosting strategies on the most primitive blood stem cells, establishes a novel link between HSC mitochondrial stress, mitophagy and stem cell fate decision, and unveils the potential of NR to improve recovery of patients suffering from hematological failure including post-chemo/radiotherapy.
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Pacer is a mediator of mTORC1 and GSK3-TIP60 signaling in regulation of autophagosome maturation and lipid metabolism
Contributors: Xiawei Cheng, Sun Qiming
... Molecular Cell D-18-00349-Original images of Western blot and microscopy images
Contributors: Philipp Keller
... Guide's software and data repository- compact version
Contributors: Philipp Keller
... Guide's software and data repository- full version
Contributors: Agnieszka Tudek
... A nuclear export block triggers the decay of newly synthesized polyadenylated RNA Agnieszka Tudek1, Manfred Schmid1, Marius Makaras1, J. David Barrass2, Jean D. Beggs2, Torben Heick Jensen1* 1Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark, 2Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK *corresponding author and lead contact: firstname.lastname@example.org Keywords: nuclear export of pA+ RNA, nuclear degradation of pA+ RNA, Mex67p, Nab2p, transcription. ABSTRACT Genomes are promiscuously transcribed necessitating mechanisms that facilitate the sorting of RNA for function or destruction. The polyA (pA) tail is one such distinguishing feature, which in the Saccharomyces cerevisiae nucleus is bound by the Nab2p protein, yielding transcript protection. As Nab2p also contacts the main nuclear export factor Mex67p, we asked whether transport kinetics contributes to RNA sorting. Indeed, 3’end sequencing of newly transcribed pA+ RNAs demonstrates that nuclear depletion of Mex67p elicits their instant and global decay. A similar phenotype is evident upon inactivation of other export factors and proportional to the amount of nuclear pA+ RNA. As RNA expression is partially rescued by Nab2p over-expression, we propose that an export-block out-titrates Nab2p onto nuclear retained pA+ RNA, reducing the pool of Nab2p available to protect new transcripts. More generally, we suggest that nuclear RNA decay, negotiated by Nab2p availability, aids in balancing cellular transcript supply with demand.
Dataset _ Interfacial control through ZnO nanorod growth on plasma-treated carbon fiber for multiscale reinforcement of carbon fiber/polyamide 6 composites
Contributors: Byeong-Joo Kim
... This data shows hydrothermal synthesis of ZnO nanorods on carbon fibers and entire raw data on analyses and mechanical testing of multiscale hybrid composites. Whole data is fully used for a paper prepared by Byeong-Joo Kim et al., "Interfacial control through ZnO nanorod growth on plasma-treated carbon fiber for multiscale reinforcement of carbon fiber/polyamide 6 composites" You can arrange the data using various software as shown below. Mechanical testing results : Origin or Excel XPS : Origin or CasaXPS AFM : Origin or Excel XRD : DIFFRAC. EVA or JADE EA : Origin or Excel
Contributors: Eduardo Fox, Meng Xu, Lei Wang, Li Chen, Yongyue Lu
... This is the supporting raw data and information behind the published paper "Speedy milking of fresh venom from Aculeate hymenopterans" by Fox et al. (2018), available at: https://www.sciencedirect.com/science/article/pii/S0041010118300990 It includes: - Draft version of the manuscript prior to submission; - Peer review details; - Raw chromatograms obtained for centrifuge-milked venoms of fire ants, two species of bees, one species of Asian hornet; - Raw chromatograms of internal and calibration standards; - Images and details on the identification of utilised insects; - Pictures obtained for the venoms extracted and utilised structures. Disclaimer: The presented method for venom extraction is extremely simple, and can be extended to other poisonous animal through simple adaptations. Such secretions can be highly dangerous. Responsible use of this technology is strongly recommended. Venom obtained via such method is to be used for legal, surveilled scientific purposes **only**.
CELL-REPORTS-D-17-02899R1, Rayman et al. "TIA-1 self-multimerization, phase separation, and recruitment into stress granules are dynamically regulated by Zn2+"
Contributors: Joseph Rayman
... These data files are associated with the following article: Rayman, J.B., Karl, K.A., and Kandel, E.R. (2018). TIA-1 self-multimerization, phase separation, and recruitment into stress granules are dynamically regulated by Zn2+. Cell Reports 22, 1-13.