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Scientific Data

Laura Jones, Maria Pureza Laudiano-Dray, Kimberley Whitehead, Madeleine Verriotis, Judith Meek, Maria Fitzgerald, Lorenzo Fabrizi
We present a dataset of cortical, behavioural, and physiological responses following a single, clinically required noxious stimulus in a neonatal sample. Cortical activity was recorded from 112 neonates (29-47 weeks gestational age at study) using a 20-channel electroencephalogram (EEG), which was time-locked to a heel lance. This data is linked to pain-related behaviour (facial expression), physiology (heart rate, oxygenation) and a composite clinical score (Premature Infant Pain Profile, PIPP). The dataset includes responses to non-noxious sham and auditory controls...
November 13, 2018: Scientific Data
Vadim Yapiyev, Charles P Gilman, Tolganay Kabdullayeva, Akmaral Suleimenova, Aizhan Shagadatova, Azat Duisembay, Sanzhar Naizabekov, Saule Mussurova, Kamilya Sydykova, Ilyas Raimkulov, Ilyas Kabimoldayev, Ainagul Abdrakhmanova, Symbat Omarkulova, Dastan Nurmukhambetov, Aliya Kudarova, Daniyar Malgazhdar, Christian Schönbach, Vassilis Inglezakis
Kazakhstan's soil properties have yet to be comprehensively characterized. We sampled 40 sites consisting of ten major soil types at spring (wet) and late-summer (dry) seasons. The sample locations range from semi-arid to arid with an annual mean air temperature from 1.2 to 10.7 °C and annual precipitation from less than 200 to around 400 mm. Overall topsoil total (STC), organic (SOC), and inorganic (SIC) carbon did not change significantly between spring and late summer. STC and SOC show a wave like pattern from north to south with two maxima in northern and southern Kazakhstan and one minimum in central Kazakhstan...
November 13, 2018: Scientific Data
Santosh Lamichhane, Linda Ahonen, Thomas Sparholt Dyrlund, Heli Siljander, Heikki Hyöty, Jorma Ilonen, Jorma Toppari, Riitta Veijola, Tuulia Hyötyläinen, Mikael Knip, Matej Orešič
Early prediction and prevention of type 1 diabetes (T1D) are currently unmet medical needs. Previous metabolomics studies suggest that children who develop T1D are characterised by a distinct metabolic profile already detectable during infancy, prior to the onset of islet autoimmunity. However, the specificity of persistent metabolic disturbances in relation T1D development has not yet been established. Here, we report a longitudinal plasma lipidomics dataset from (1) 40 children who progressed to T1D during follow-up, (2) 40 children who developed single islet autoantibody but did not develop T1D and (3) 40 matched controls (6 time points: 3, 6, 12, 18, 24 and 36 months of age)...
November 13, 2018: Scientific Data
Jason L Brown, Daniel J Hill, Aisling M Dolan, Ana C Carnaval, Alan M Haywood
High-resolution, easily accessible paleoclimate data are essential for environmental, evolutionary, and ecological studies. The availability of bioclimatic layers derived from climatic simulations representing conditions of the Late Pleistocene and Holocene has revolutionized the study of species responses to Late Quaternary climate change. Yet, integrative studies of the impacts of climate change in the Early Pleistocene and Pliocene - periods in which recent speciation events are known to concentrate - have been hindered by the limited availability of downloadable, user-friendly climatic descriptors...
November 13, 2018: Scientific Data
Yu Leng Phua, Andrew Clugston, Kevin Hong Chen, Dennis Kostka, Jacqueline Ho
MicroRNAs (miRNAs) are small non-coding RNAs that are essential for the regulation of gene expression and play critical roles in human health and disease. Here we present comprehensive miRNA profiling data for mouse nephrogenic mesenchymal progenitors, a population of cells enriched for nephron progenitors that give rise to most cell-types of the nephron, the functional unit of the kidney. We describe a miRNA expression in nephrogenic mesenchymal progenitors, with 162 miRNAs differentially expressed in progenitors when compared to whole kidney...
November 13, 2018: Scientific Data
Nita Bharti, Andrew J Tatem
Dynamic measures of human populations are critical for global health management but are often overlooked, largely because they are difficult to quantify. Measuring human population dynamics can be prohibitively expensive in under-resourced communities. Satellite imagery can provide measurements of human populations, past and present, to complement public health analyses and interventions. We used anthropogenic illumination from publicly accessible, serial satellite nighttime images as a quantifiable proxy for seasonal population variation in five urban areas in Niger and Nigeria...
November 13, 2018: Scientific Data
Zhiying Li, Jiabin Wang, Yunliu Fu, Yu Gao, Hunzhen Lu, Li Xu
Anthurium andraeanum is a popular tropical ornamental plant. Its spathes are brilliantly coloured due to variable anthocyanin contents. To examine the mechanisms that control anthocyanin biosynthesis, we sequenced the spathe transcriptomes of 'Albama', a red-spathed cultivar of A. andraeanum, and 'Xueyu', its anthocyanin-loss mutant. Both long reads and short reads were sequenced. Long read sequencing produced 805,869 raw reads, resulting in 83,073 high-quality transcripts. Short read sequencing produced 347...
November 13, 2018: Scientific Data
Arun Pal, Hannes Glaß, Marcel Naumann, Nicole Kreiter, Julia Japtok, Ronny Sczech, Andreas Hermann
Neurodegenerative diseases pose a complex field with various neuronal subtypes and distinct differentially affected intra-neuronal compartments. Modelling of neurodegeneration requires faithful in vitro separation of axons and dendrites, their distal and proximal compartments as well as organelle tracking with defined retrograde versus anterograde directionality. We use microfluidic chambers to achieve compartmentalization and established high throughput live organelle imaging at standardized distal and proximal axonal readout sites in iPSC-derived spinal motor neuron cultures from human amyotrophic lateral sclerosis patients to study trafficking phenotypes of potential disease relevance...
November 13, 2018: Scientific Data
Dai Fei Elmer Ker, Sungeun Eom, Sho Sanami, Ryoma Bise, Corinne Pascale, Zhaozheng Yin, Seung-Il Huh, Elvira Osuna-Highley, Silvina N Junkers, Casey J Helfrich, Peter Yongwen Liang, Jiyan Pan, Soojin Jeong, Steven S Kang, Jinyu Liu, Ritchie Nicholson, Michael F Sandbothe, Phu T Van, Anan Liu, Mei Chen, Takeo Kanade, Lee E Weiss, Phil G Campbell
Phase contrast time-lapse microscopy is a non-destructive technique that generates large volumes of image-based information to quantify the behaviour of individual cells or cell populations. To guide the development of algorithms for computer-aided cell tracking and analysis, 48 time-lapse image sequences, each spanning approximately 3.5 days, were generated with accompanying ground truths for C2C12 myoblast cells cultured under 4 different media conditions, including with fibroblast growth factor 2 (FGF2), bone morphogenetic protein 2 (BMP2), FGF2 + BMP2, and control (no growth factor)...
November 13, 2018: Scientific Data
Long-Hai Zou, Xiao Wan, Hua Deng, Bao-Qiang Zheng, Bai-Jun Li, Yan Wang
The regulation of crassulacean acid metabolism (CAM) pathway has recently become a topic of intensive research and has been explored in terms of several aspects, including phylogenetics, genomics, and transcriptomics. Orchidaceae, which contains approximately 9,000 CAM species, is one of the largest lineages using this special photosynthetic pathway. However, no comprehensive transcriptomic profiling focused on CAM regulation in orchid species had previously been performed. In this report, we present two Illumina RNA-seq datasets, including a total of 24 mature leaf samples with 844...
November 13, 2018: Scientific Data
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November 6, 2018: Scientific Data
Katie Irving, Mathias Kuemmerlen, Jens Kiesel, Karan Kakouei, Sami Domisch, Sonja C Jähnig
Hydrological variables are among the most influential when analyzing or modeling stream ecosystems. However, available hydrological data are often limited in their spatiotemporal scale and resolution for use in ecological applications such as predictive modeling of species distributions. To overcome this limitation, a regression model was applied to a 1 km gridded stream network of Germany to obtain estimated daily stream flow data (m3 s-1 ) spanning 64 years (1950-2013). The data are used as input to calculate hydrological indices characterizing stream flow regimes...
November 6, 2018: Scientific Data
Josh Hooker, Gregory Duveiller, Alessandro Cescatti
Air temperature at 2 m above the land surface is a key variable used to assess climate change. However, observations of air temperature are typically only available from a limited number of weather stations distributed mainly in developed countries, which in turn may often report time series with missing values. As a consequence, the record of air temperature observations is patchy in both space and time. Satellites, on the other hand, measure land surface temperature continuously in both space and time. In order to combine the relative strengths of surface and satellite temperature records, we develop a dataset in which monthly air temperature is predicted from monthly land surface temperature for the years 2003 to 2016, using a statistical model that incorporates information on geographic and climatic similarity...
November 6, 2018: Scientific Data
Tiago R Simões, Michael W Caldwell, Mateusz Tałanda, Massimo Bernardi, Alessandro Palci, Oksana Vernygora, Federico Bernardini, Lucia Mancini, Randall L Nydam
Understanding the origin and early evolution of squamates has been a considerable challenge given the extremely scarce fossil record of early squamates and their poor degree of preservation. In order to overcome those limitations, we conducted high-resolution X-ray computed tomography (CT) studies on the fossil reptile Megachirella wachtleri (Middle Triassic, northern Italy), which revealed an important set of features indicating this is the oldest known fossil squamate in the world, predating the previous oldest record by ca...
November 6, 2018: Scientific Data
Fabien Dutreux, Corinne Da Silva, Léo d'Agata, Arnaud Couloux, Elise J Gay, Benjamin Istace, Nicolas Lapalu, Arnaud Lemainque, Juliette Linglin, Benjamin Noel, Patrick Wincker, Corinne Cruaud, Thierry Rouxel, Marie-Hélène Balesdent, Jean-Marc Aury
Leptosphaeria maculans and Leptosphaeria biglobosa are ascomycete phytopathogens of Brassica napus (oilseed rape, canola). Here we report the complete sequence of three Leptosphaeria genomes (L. maculans JN3, L. maculans Nz-T4 and L. biglobosa G12-14). Nz-T4 and G12-14 genome assemblies were generated de novo and the reference JN3 genome assembly was improved using Oxford Nanopore MinION reads. The new assembly of L. biglobosa showed the existence of AT rich regions and pointed to a genome compartmentalization previously unsuspected following Illumina sequencing...
November 6, 2018: Scientific Data
Matthew P Salomon, Javier I J Orozco, James S Wilmott, Parvinder Hothi, Ayla O Manughian-Peter, Charles S Cobbs, Richard A Scolyer, Dave S B Hoon, Diego M Marzese
Brain metastases (BM) are one the most lethal and poorly managed clinical complications in cancer patients. These secondary tumors represent the most common intracranial neoplasm in adults, most frequently originating from lung cancer, breast cancer, and cutaneous melanoma. In primary brain tumors, such as gliomas, recent advances in DNA methylation profiling have allowed for a comprehensive molecular classification. Such data provide prognostic information, in addition to helping predict patient response to specific systemic therapies...
November 6, 2018: Scientific Data
Ji Yeon Kim, Hye Young Lim, Sang Eon Shin, Hyo Kyeong Cha, Jeong-Han Seo, Suel-Kee Kim, Seong Hwan Park, Gi Hoon Son
Sarcophaga peregrina (flesh fly) is a frequently found fly species in Palaearctic, Oriental, and Australasian regions that can be used to estimate minimal postmortem intervals important for forensic investigations. Despite its forensic importance, the genome information of S. peregrina has not been fully described. Therefore, we generated a comprehensive gene expression dataset using RNA sequencing and carried out de novo assembly to characterize the S. peregrina transcriptome. We obtained precise sequence information for RNA transcripts using two different methods...
November 6, 2018: Scientific Data
Marina Sirota, Cristel G Thomas, Rebecca Liu, Maya Zuhl, Payal Banerjee, Ronald J Wong, Cecele C Quaintance, Rite Leite, Jessica Chubiz, Rebecca Anderson, Joanne Chappell, Mara Kim, William Grobman, Ge Zhang, Antonis Rokas, Sarah K England, Samuel Parry, Gary M Shaw, Joe Leigh Simpson, Elizabeth Thomson, Atul J Butte
Preterm birth, or the delivery of an infant prior to 37 weeks of gestation, is a significant cause of infant morbidity and mortality. In the last decade, the advent and continued development of molecular profiling technologies has enabled researchers to generate vast amount of 'omics' data, which together with integrative computational approaches, can help refine the current knowledge about disease mechanisms, diagnostics, and therapeutics. Here we describe the March of Dimes' Database for Preterm Birth Research (http://www...
November 6, 2018: Scientific Data
Xiawei Jiang, Wenhong Liu, Beiwen Zheng
Because of poor differentiation among the members of genus Comamonas using phenotypic methods, human infections caused by C. kerstersii are sporadically reported in the literature. Here, we represent the first complete genome sequence of C. kerstersii 8943, which caused peritonitis in a patient with continuous ambulatory peritoneal dialysis (CAPD). The complete genome with no gaps was obtained using third-generation Pacific Biosciences (PacBio) RSII sequencing system with single-molecule real-time (SMRT) analysis...
November 6, 2018: Scientific Data
Ehsan Raei, Mohammad Reza Nikoo, Amir AghaKouchak, Omid Mazdiyasni, Mojtaba Sadegh
Heatwaves are extended periods of unusually high temperatures with significant societal and environmental impacts. Despite their significance, there is not a generalized definition for heatwaves. In this paper, we introduce a multi-method global heatwave and warm-spell data record and analysis toolbox (named GHWR). In addition to a comprehensive long-term global data record of heatwaves, GHWR allows processing and extracting heatwave records for any location efficiently. We use traditional constant temperature threshold methods, as well as spatially and temporally localized threshold approaches to identify heatwaves...
October 30, 2018: Scientific Data
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