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https://www.readbyqxmd.com/read/28448065/construction-of-a-map-based-reference-genome-sequence-for-barley-hordeum-vulgare-l
#1
Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao-Qi Zhang, Roberto A Barrero, Qisen Zhang, Lin Li, Micha Bayer, Daniel Bolser, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz-Amatriaín, Rachid Ounit, Steve Wanamaker, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Dharanya Sampath, Darren Heavens, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K McCooke, Cong Tan, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse A Poland, Matthew I Bellgard, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Peter Langridge, Gary J Muehlbauer, Paul Kersey, Matthew D Clark, Mario Caccamo, Alan H Schulman, Matthias Platzer, Timothy J Close, Mats Hansson, Guoping Zhang, Ilka Braumann, Chengdao Li, Robbie Waugh, Uwe Scholz, Nils Stein, Martin Mascher
Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. 'Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C)...
April 27, 2017: Scientific Data
https://www.readbyqxmd.com/read/28440808/automated-and-manual-patch-clamp-data-of-human-induced-pluripotent-stem-cell-derived-dopaminergic-neurons
#2
Denise Franz, Hervør Lykke Olsen, Oliver Klink, Jan Gimsa
Human induced pluripotent stem cells can be differentiated into dopaminergic neurons (Dopa.4U). Dopa.4U neurons expressed voltage-gated NaV and KV channels and showed neuron-like spontaneous electrical activity. In automated patch clamp measurements with suspended Dopa.4U neurons, delayed rectifier K(+) current (delayed KV) and rapidly inactivating A-type K(+) current (fast KV) were identified. Examination of the fast KV current with inhibitors yielded IC50 values of 0.4 mM (4-aminopyridine) and 0.1 mM (tetraethylammonium)...
April 25, 2017: Scientific Data
https://www.readbyqxmd.com/read/28440795/multimodal-chest-surface-motion-data-for-respiratory-and-cardiovascular-monitoring-applications
#3
Ghufran Shafiq, Kalyana Chakravarthy Veluvolu
Chest surface motion is of significant importance as it contains information of respiratory and cardiac systems together with the complex coupling between these two systems. Chest surface motion is not only critical in radiotherapy, but also useful in personalized systems for continuous cardiorespiratory monitoring. In this dataset, a multimodal setup is employed to simultaneously acquire cardiorespiratory signals. These signals include high-density trunk surface motion (from 16 distinct locations) with VICON motion capture system, nasal breathing from a thermal sensor, respiratory effort from a strain belt and electrocardiogram in lead-II configuration...
April 25, 2017: Scientific Data
https://www.readbyqxmd.com/read/28440794/se-sad-serial-femtosecond-crystallography-datasets-from-selenobiotinyl-streptavidin
#4
Chun Hong Yoon, Hasan DeMirci, Raymond G Sierra, E Han Dao, Radman Ahmadi, Fulya Aksit, Andrew L Aquila, Alexander Batyuk, Halilibrahim Ciftci, Serge Guillet, Matt J Hayes, Brandon Hayes, Thomas J Lane, Meng Liang, Ulf Lundström, Jason E Koglin, Paul Mgbam, Yashas Rao, Theodore Rendahl, Evan Rodriguez, Lindsey Zhang, Soichi Wakatsuki, Sébastien Boutet, James M Holton, Mark S Hunter
We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity between biotin and streptavidin where the sulfur atom in the biotin molecule (C10H16N2O3S) is substituted with selenium. The dataset was collected at three different transmissions (100, 50, and 10%) using a serial sample chamber setup which allows for two sample chambers, a front chamber and a back chamber, to operate simultaneously...
April 25, 2017: Scientific Data
https://www.readbyqxmd.com/read/28440791/a-curated-database-of-cyanobacterial-strains-relevant-for-modern-taxonomy-and-phylogenetic-studies
#5
Vitor Ramos, João Morais, Vitor M Vasconcelos
The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references...
April 25, 2017: Scientific Data
https://www.readbyqxmd.com/read/28440790/large-scale-modeled-contemporary-and-future-water-temperature-estimates-for-10774-midwestern-u-s-lakes
#6
Luke A Winslow, Gretchen J A Hansen, Jordan S Read, Michael Notaro
Climate change has already influenced lake temperatures globally, but understanding future change is challenging. The response of lakes to changing climate drivers is complex due to the nature of lake-atmosphere coupling, ice cover, and stratification. To better understand the diversity of lake responses to climate change and give managers insight on individual lakes, we modelled daily water temperature profiles for 10,774 lakes in Michigan, Minnesota, and Wisconsin for contemporary (1979-2015) and future (2020-2040 and 2080-2100) time periods with climate models based on the Representative Concentration Pathway 8...
April 25, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398357/a-resource-for-assessing-information-processing-in-the-developing-brain-using-eeg-and-eye-tracking
#7
Nicolas Langer, Erica J Ho, Lindsay M Alexander, Helen Y Xu, Renee K Jozanovic, Simon Henin, Agustin Petroni, Samantha Cohen, Enitan T Marcelle, Lucas C Parra, Michael P Milham, Simon P Kelly
We present a dataset combining electrophysiology and eye tracking intended as a resource for the investigation of information processing in the developing brain. The dataset includes high-density task-based and task-free EEG, eye tracking, and cognitive and behavioral data collected from 126 individuals (ages: 6-44). The task battery spans both the simple/complex and passive/active dimensions to cover a range of approaches prevalent in modern cognitive neuroscience. The active task paradigms facilitate principled deconstruction of core components of task performance in the developing brain, whereas the passive paradigms permit the examination of intrinsic functional network activity during varying amounts of external stimulation...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398352/x-ray-computed-tomography-library-of-shark-anatomy-and-lower-jaw-surface-models
#8
Pepijn Kamminga, Paul W De Bruin, Jacob Geleijns, Martin D Brazeau
The cranial diversity of sharks reflects disparate biomechanical adaptations to feeding. In order to be able to investigate and better understand the ecomorphology of extant shark feeding systems, we created a x-ray computed tomography (CT) library of shark cranial anatomy with three-dimensional (3D) lower jaw reconstructions. This is used to examine and quantify lower jaw disparity in extant shark species in a separate study. The library is divided in a dataset comprised of medical CT scans of 122 sharks (Selachimorpha, Chondrichthyes) representing 73 extant species, including digitized morphology of entire shark specimens...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398351/a-database-of-global-marine-commercial-small-scale-illegal-and-unreported-fisheries-catch-1950-2014
#9
Reg A Watson
Global fisheries landings data from a range of public sources was harmonised and mapped to 30-min spatial cells based on the distribution of the reported taxa and the fishing fleets involved. This data was extended to include the associated fishing gear used, as well as estimates of illegal, unregulated and unreported catch (IUU) and discards at sea. Expressed as catch rates, these results also separated small-scale fisheries from other fishing operations. The dataset covers 1950 to 2014 inclusive. Mapped catch allows study of the impacts of fisheries on habitats and fauna, on overlap with the diets of marine birds and mammals, and on the related use of fuels and release of greenhouse gases...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398335/high-coverage-methylation-data-of-a-gene-model-before-and-after-dna-damage-and-homologous-repair
#10
Antonio Pezone, Giusi Russo, Alfonso Tramontano, Ermanno Florio, Giovanni Scala, Rosaria Landi, Candida Zuchegna, Antonella Romano, Lorenzo Chiariotti, Mark T Muller, Max E Gottesman, Antonio Porcellini, Enrico V Avvedimento
Genome-wide methylation analysis is limited by its low coverage and the inability to detect single variants below 10%. Quantitative analysis provides accurate information on the extent of methylation of single CpG dinucleotide, but it does not measure the actual polymorphism of the methylation profiles of single molecules. To understand the polymorphism of DNA methylation and to decode the methylation signatures before and after DNA damage and repair, we have deep sequenced in bisulfite-treated DNA a reporter gene undergoing site-specific DNA damage and homologous repair...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398334/diffraction-data-of-core-shell-nanoparticles-from-an-x-ray-free-electron-laser
#11
Xuanxuan Li, Chun-Ya Chiu, Hsiang-Ju Wang, Stephan Kassemeyer, Sabine Botha, Robert L Shoeman, Robert M Lawrence, Christopher Kupitz, Richard Kirian, Daniel James, Dingjie Wang, Garrett Nelson, Marc Messerschmidt, Sébastien Boutet, Garth J Williams, Elisabeth Hartmann, Aliakbar Jafarpour, Lutz M Foucar, Anton Barty, Henry Chapman, Mengning Liang, Andreas Menzel, Fenglin Wang, Shibom Basu, Raimund Fromme, R Bruce Doak, Petra Fromme, Uwe Weierstall, Michael H Huang, John C H Spence, Ilme Schlichting, Brenda G Hogue, Haiguang Liu
X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398302/a-distribution-and-taxonomic-reference-dataset-of-geranium-in-the-new-world
#12
Carlos Aedo, Francisco Pando
Geranium L. is a genus of over 350 species distributed throughout most of the world, except in lowland tropical areas. It is the largest genus of the Geraniaceae and is represented in the New World by 137 species. This dataset includes 8,937 records that covers the genus Geranium the New World, providing an updated, taxonomically consistent and a sound geographical distribution of the 137 species of Geranium in America. Specimens from 128 herbaria were reviewed. These were supplemented by others collected during nine field trips, which allowed better knowledge of the variability of characters within populations, and refining species distribution ranges...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398292/the-contemporary-distribution-of-trypanosoma-cruzi-infection-in-humans-alternative-hosts-and-vectors
#13
Annie J Browne, Carlos A Guerra, Renato Vieira Alves, Veruska Maia da Costa, Anne L Wilson, David M Pigott, Simon I Hay, Steve W Lindsay, Nick Golding, Catherine L Moyes
Chagas is a potentially fatal chronic disease affecting large numbers of people across the Americas and exported throughout the world through human population movement. It is caused by the Trypanosoma cruzi parasite, which is transmitted by triatomine vectors to humans and a wide range of alternative host species. The database described here was compiled to allow the risk of vectorial transmission to humans to be mapped using geospatial models. The database collates all available records, published since 2003, for prevalence and occurrence of infection in humans, vectors and alternative hosts, and links each record to a defined time and location...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398290/a-geographically-diverse-collection-of-418-human-gut-microbiome-pathway-genome-databases
#14
Aria S Hahn, Tomer Altman, Kishori M Konwar, Niels W Hanson, Dongjae Kim, David A Relman, David L Dill, Steven J Hallam
Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398289/a-high-throughput-molecular-data-resource-for-cutaneous-neurofibromas
#15
Sara J C Gosline, Hubert Weinberg, Pamela Knight, Thomas Yu, Xindi Guo, Nripesh Prasad, Angela Jones, Shristi Shrestha, Braden Boone, Shawn E Levy, Salvatore La Rosa, Justin Guinney, Annette Bakker
Neurofibromatosis type 1 (NF1) is a genetic disorder with a range of clinical manifestations such as widespread growth of benign tumours called neurofibromas, pain, learning disorders, bone deformities, vascular abnormalities and even malignant tumours. With the establishment of the Children's Tumour Foundation biobank, neurofibroma samples can now be collected directly from patients to be analysed by the larger scientific community. This work describes a pilot study to characterize one class of neurofibroma, cutaneous neurofibromas, by molecularly profiling of ~40 cutaneous neurofibromas collected from 11 individual patients...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398288/spatiotemporal-historical-datasets-at-micro-level-for-geocoded-individuals-in-five-swedish-parishes-1813-1914
#16
Finn Hedefalk, Patrick Svensson, Lars Harrie
This paper presents datasets that enable historical longitudinal studies of micro-level geographic factors in a rural setting. These types of datasets are new, as historical demography studies have generally failed to properly include the micro-level geographic factors. Our datasets describe the geography over five Swedish rural parishes, and by linking them to a longitudinal demographic database, we obtain a geocoded population (at the property unit level) for this area for the period 1813-1914. The population is a subset of the Scanian Economic Demographic Database (SEDD)...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28398286/a-database-of-marine-phytoplankton-abundance-biomass-and-species-composition-in-australian-waters
#17
Claire H Davies, Alex Coughlan, Gustaaf Hallegraeff, Penelope Ajani, Linda Armbrecht, Natalia Atkins, Prudence Bonham, Steve Brett, Richard Brinkman, Michele Burford, Lesley Clementson, Peter Coad, Frank Coman, Diana Davies, Jocelyn Dela-Cruz, Michelle Devlin, Steven Edgar, Ruth Eriksen, Miles Furnas, Christel Hassler, David Hill, Michael Holmes, Tim Ingleton, Ian Jameson, Sophie C Leterme, Christian Lønborg, James McLaughlin, Felicity McEnnulty, A David McKinnon, Margaret Miller, Shauna Murray, Sasi Nayar, Renee Patten, Sarah A Pausina, Tim Pritchard, Roger Proctor, Diane Purcell-Meyerink, Eric Raes, David Rissik, Jason Ruszczyk, Anita Slotwinski, Kerrie M Swadling, Katherine Tattersall, Peter Thompson, Paul Thomson, Mark Tonks, Thomas W Trull, Julian Uribe-Palomino, Anya M Waite, Rouna Yauwenas, Anthony Zammit, Anthony J Richardson
No abstract text is available yet for this article.
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28350394/long-term-growth-data-of-escherichia-coli-at-a-single-cell-level
#18
Yu Tanouchi, Anand Pai, Heungwon Park, Shuqiang Huang, Nicolas E Buchler, Lingchong You
Long-term, single-cell measurement of bacterial growth is extremely valuable information, particularly in the study of homeostatic aspects such as cell-size and growth rate control. Such measurement has recently become possible due to the development of microfluidic technology. Here we present data from single-cell measurements of Escherichia coli growth over 70 generations obtained for three different growth conditions. The data were recorded every minute, and contain time course data of cell length and fluorescent intensity of constitutively expressed yellow fluorescent protein...
March 28, 2017: Scientific Data
https://www.readbyqxmd.com/read/28350387/the-global-avian-invasions-atlas-a-database-of-alien-bird-distributions-worldwide
#19
Ellie E Dyer, David W Redding, Tim M Blackburn
The introduction of species to locations where they do not naturally occur (termed aliens) can have far-reaching and unpredictable environmental and economic consequences. Therefore there is a strong incentive to stem the tide of alien species introduction and spread. In order to identify broad patterns and processes of alien invasions, a spatially referenced, global dataset on the historical introductions and alien distributions of a complete taxonomic group is required. Here we present the Global Avian Invasions Atlas (GAVIA)-a new spatial and temporal dataset comprising 27,723 distribution records for 971 alien bird species introduced to 230 countries and administrative areas spanning the period 6000BCE-AD2014...
March 28, 2017: Scientific Data
https://www.readbyqxmd.com/read/28350385/molecular-phenotypic-and-sample-associated-data-to-describe-pluripotent-stem-cell-lines-and-derivatives
#20
Kenneth Daily, Shannan J Ho Sui, Lynn M Schriml, Phillip J Dexheimer, Nathan Salomonis, Robin Schroll, Stacy Bush, Mehdi Keddache, Christopher Mayhew, Samad Lotia, Thanneer M Perumal, Kristen Dang, Lorena Pantano, Alexander R Pico, Elke Grassman, Diana Nordling, Winston Hide, Antonis K Hatzopoulos, Punam Malik, Jose A Cancelas, Carolyn Lutzko, Bruce J Aronow, Larsson Omberg
The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols, monitor genetic stability, and evaluate self-renewal and differentiation potential. To accomplish these goals, 57 stem cell lines from 10 laboratories were differentiated to 7 different states, resulting in 248 analyzed samples...
March 28, 2017: Scientific Data
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