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Scientific Data

Enrico Lunghi, Fabio Cianferoni, Filippo Ceccolini, Manuela Mulargia, Roberto Cogoni, Benedetta Barzaghi, Lorenzo Cornago, Domenico Avitabile, Michael Veith, Raoul Manenti, Gentile Francesco Ficetola, Claudia Corti
The availability of data on the feeding habits of species of conservation value may be of great importance to develop analyses for both scientific and management purposes. Stomach flushing is a harmless technique that allowed us to collect extensive data on the feeding habits of six Hydromantes species. Here, we present two datasets originating from a three-year study performed in multiple seasons (spring and autumn) on 19 different populations of cave salamanders. The first dataset contains data of the stomach content of 1,250 salamanders, where 6,010 items were recognized; the second one reports the size of the intact prey items found in the stomachs...
May 15, 2018: Scientific Data
Adam Collins, Alan Huett
We present a high-content screen (HCS) for the simultaneous analysis of multiple phenotypes in HeLa cells expressing an autophagy reporter (mcherry-LC3) and one of 224 GFP-fused proteins from the Crohn's Disease (CD)-associated bacterium, Adherent Invasive E. coli (AIEC) strain LF82. Using automated confocal microscopy and image analysis (CellProfiler), we localised GFP fusions within cells, and monitored their effects upon autophagy (an important innate cellular defence mechanism), cellular and nuclear morphology, and the actin cytoskeleton...
May 15, 2018: Scientific Data
Rainer Kujala, Christoffer Weckström, Richard K Darst, Miloš N Mladenović, Jari Saramäki
Various public transport (PT) agencies publish their route and timetable information with the General Transit Feed Specification (GTFS) as the standard open format. Timetable data are commonly used for PT passenger routing. They can also be used for studying the structure and organization of PT networks, as well as the accessibility and the level of service these networks provide. However, using raw GTFS data is challenging as researchers need to understand the details of the GTFS data format, make sure that the data contain all relevant modes of public transport, and have no errors...
May 15, 2018: Scientific Data
Sarah A M Perryman, Nathalie I D Castells-Brooke, Margaret J Glendining, Keith W T Goulding, Malcolm J Hawkesford, Andy J Macdonald, Richard J Ostler, Paul R Poulton, Christopher J Rawlings, Tony Scott, Paul J Verrier
The electronic Rothamsted Archive, e-RA ( provides a permanent managed database to both securely store and disseminate data from Rothamsted Research's long-term field experiments (since 1843) and meteorological stations (since 1853). Both historical and contemporary data are made available via this online database which provides the scientific community with access to a unique continuous record of agricultural experiments and weather measured since the mid-19th century. Qualitative information, such as treatment and management practices, plans and soil information, accompanies the data and are made available on the e-RA website...
May 15, 2018: Scientific Data
Li-Xuan Qin, Huei-Chung Huang, Liliana Villafania, Magali Cavatore, Narciso Olvera, Douglas A Levine
We set out to demonstrate the logistic feasibility of careful experimental design for microarray studies and its level of scientific benefits for improving the accuracy and reproducibility of data inference. Towards this end, we conducted a study of microRNA expression using endometrioid endometrial tumours (n=96) and serous ovarian tumours (n=96) that were primary, untreated, and collected from 2000 to 2012 at Memorial Sloan Kettering Cancer Center. The same set of tumour tissue samples were profiled twice using the Agilent microRNA microarrays: once under an ideal experimental condition with balanced array-to-sample allocation and uniform handling; a second time by mimicking typical practice, with arrays assigned in the order of sample collection and processed by two technicians in multiple batches...
May 15, 2018: Scientific Data
C Wade Ross, Lara Prihodko, Julius Anchang, Sanath Kumar, Wenjie Ji, Niall P Hanan
Hydrologic soil groups (HSGs) are a fundamental component of the USDA curve-number (CN) method for estimation of rainfall runoff; yet these data are not readily available in a format or spatial-resolution suitable for regional- and global-scale modeling applications. We developed a globally consistent, gridded dataset defining HSGs from soil texture, bedrock depth, and groundwater. The resulting data product-HYSOGs250m-represents runoff potential at 250 m spatial resolution. Our analysis indicates that the global distribution of soil is dominated by moderately high runoff potential, followed by moderately low, high, and low runoff potential...
May 15, 2018: Scientific Data
Hungyen Chen, Ching-Yi Chen, Kwang-Tsao Shao
Long-term time series datasets with consistent sampling methods are rather rare, especially the ones of non-target coastal fishes. Here we described a long-term time series dataset of fish collected by trammel net fish sampling and observed by an underwater diving visual census near the thermal discharges at two nuclear power plants on the northern coast of Taiwan. Both experimental and control stations of these two investigations were monitored four times per year in the surrounding seas at both plants from 2000 to 2017...
May 8, 2018: Scientific Data
Julia Schmale, Silvia Henning, Bas Henzing, Helmi Keskinen, Karine Sellegri, Jurgita Ovadnevaite, Aikaterini Bougiatioti, Nikos Kalivitis, Iasonas Stavroulas, Anne Jefferson, Minsu Park, Patrick Schlag, Adam Kristensson, Yoko Iwamoto, Kirsty Pringle, Carly Reddington, Pasi Aalto, Mikko Äijälä, Urs Baltensperger, Jakub Bialek, Wolfram Birmili, Nicolas Bukowiecki, Mikael Ehn, Ann Mari Fjæraa, Markus Fiebig, Göran Frank, Roman Fröhlich, Arnoud Frumau, Masaki Furuya, Emanuel Hammer, Liine Heikkinen, Erik Herrmann, Rupert Holzinger, Hiroyuki Hyono, Maria Kanakidou, Astrid Kiendler-Scharr, Kento Kinouchi, Gerard Kos, Markku Kulmala, Nikolaos Mihalopoulos, Ghislain Motos, Athanasios Nenes, Colin O'Dowd, Mikhail Paramonov, Tuukka Petäjä, David Picard, Laurent Poulain, André Stephan Henry Prévôt, Jay Slowik, Andre Sonntag, Erik Swietlicki, Birgitta Svenningsson, Hiroshi Tsurumaru, Alfred Wiedensohler, Cerina Wittbom, John A Ogren, Atsushi Matsuki, Seong Soo Yum, Cathrine Lund Myhre, Ken Carslaw, Frank Stratmann, Martin Gysel
This corrects the article DOI: 10.1038/sdata.2017.3.
May 8, 2018: Scientific Data
(no author information available yet)
No abstract text is available yet for this article.
May 8, 2018: Scientific Data
Sarala M Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A McMurry, Niall Beard, Rafael Jimenez, Jeffrey S Grethe, Henning Hermjakob, Maryann E Martone, Tim Clark
Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier, providing global uniqueness. Such "compact identifiers" have been widely used in biomedical informatics to support global resource identification with local identifier assignment...
May 8, 2018: Scientific Data
Kamal Choudhary, Qin Zhang, Andrew C E Reid, Sugata Chowdhury, Nhan Van Nguyen, Zachary Trautt, Marcus W Newrock, Faical Yannick Congo, Francesca Tavazza
We perform high-throughput density functional theory (DFT) calculations for optoelectronic properties (electronic bandgap and frequency dependent dielectric function) using the OptB88vdW functional (OPT) and the Tran-Blaha modified Becke Johnson potential (MBJ). This data is distributed publicly through JARVIS-DFT database. We used this data to evaluate the differences between these two formalisms and quantify their accuracy, comparing to experimental data whenever applicable. At present, we have 17,805 OPT and 7,358 MBJ bandgaps and dielectric functions...
May 8, 2018: Scientific Data
Zhiqiang Hu, Wensheng Wang, Zhichao Wu, Chen Sun, Min Li, Jinyuan Lu, Binying Fu, Jianxin Shi, Jianlong Xu, Jue Ruan, Chaochun Wei, Zhikang Li
Genomic diversity within a species genome is the genetic basis of its phenotypic diversity essential for its adaptation to environments. The big picture of the total genetic diversity within Asian cultivated rice has been uncovered since the sequencing of 3,000 rice genomes, including the SNP data publicly available in the SNP-Seek database. Here we report other aspects of the genetic diversity, including rice sequences assembled from over 3,000 accessions but absent in the Nipponbare reference genome, structural variations (SVs) and gene presence/absence variations (PAVs) in 453 accessions with sequencing depth over 20x...
May 2, 2018: Scientific Data
Guido Petretto, Shyam Dwaraknath, Henrique P C Miranda, Donald Winston, Matteo Giantomassi, Michiel J van Setten, Xavier Gonze, Kristin A Persson, Geoffroy Hautier, Gian-Marco Rignanese
The knowledge of the vibrational properties of a material is of key importance to understand physical phenomena such as thermal conductivity, superconductivity, and ferroelectricity among others. However, detailed experimental phonon spectra are available only for a limited number of materials, which hinders the large-scale analysis of vibrational properties and their derived quantities. In this work, we perform ab initio calculations of the full phonon dispersion and vibrational density of states for 1521 semiconductor compounds in the harmonic approximation based on density functional perturbation theory...
May 1, 2018: Scientific Data
Yongbo Liang, Mohamed Elgendi, Zhencheng Chen, Rabab Ward
A photoplethysmogram (PPG) contains a wealth of cardiovascular system information, and with the development of wearable technology, it has become the basic technique for evaluating cardiovascular health and detecting diseases. However, due to the varying environments in which wearable devices are used and, consequently, their varying susceptibility to noise interference, effective processing of PPG signals is challenging. Thus, the aim of this study was to determine the optimal filter and filter order to be used for PPG signal processing to make the systolic and diastolic waves more salient in the filtered PPG signal using the skewness quality index...
May 1, 2018: Scientific Data
Neil S Lagali, Stephan Allgeier, Pedro Guimarães, Reza A Badian, Alfredo Ruggeri, Bernd Köhler, Tor Paaske Utheim, Beatrice Peebo, Magnus Peterson, Lars B Dahlin, Olov Rolandsson
A dense nerve plexus in the clear outer window of the eye, the cornea, can be imaged in vivo to enable non-invasive monitoring of peripheral nerve degeneration in diabetes. However, a limited field of view of corneal nerves, operator-dependent image quality, and subjective image sampling methods have led to difficulty in establishing robust diagnostic measures relating to the progression of diabetes and its complications. Here, we use machine-based algorithms to provide wide-area mosaics of the cornea's subbasal nerve plexus (SBP) also accounting for depth (axial) fluctuation of the plexus...
April 24, 2018: Scientific Data
Valerio Barbarossa, Mark A J Huijbregts, Arthur H W Beusen, Hylke E Beck, Henry King, Aafke M Schipper
This corrects the article DOI: 10.1038/sdata.2018.52.
April 24, 2018: Scientific Data
Soledad Ceccarelli, Agustín Balsalobre, Paula Medone, María Eugenia Cano, Rodrigo Gurgel Gonçalves, Dora Feliciangeli, Darío Vezzani, Cristina Wisnivesky-Colli, David E Gorla, Gerardo A Marti, Jorge E Rabinovich
Trypanosoma cruzi, the causative agent of Chagas disease, is transmitted to mammals - including humans - by insect vectors of the subfamily Triatominae. We present the results of a compilation of triatomine occurrence and complementary ecological data that represents the most complete, integrated and updated database (DataTri) available on triatomine species at a continental scale. This database was assembled by collecting the records of triatomine species published from 1904 to 2017, spanning all American countries with triatomine presence...
April 24, 2018: Scientific Data
Tae Woong Whon, Won-Hyong Chung, Mi Young Lim, Eun-Ji Song, Pil Soo Kim, Dong-Wook Hyun, Na-Ri Shin, Jin-Woo Bae, Young-Do Nam
High-quality and high-throughput sequencing technologies are required for therapeutic and diagnostic analyses of human gut microbiota. Here, we evaluated the advantages and disadvantages of the various commercial sequencing platforms for studying human gut microbiota. We generated fecal bacterial sequences from 170 Korean subjects using the GS FLX+ (V1-4), Illumina MiSeq (V1-3, V3-4 and V4), and PacBio (V1-9) systems. Comparative analyses revealed that the PacBio data showed the weakest relationship with the reference whole-metagenome shotgun datasets...
April 24, 2018: Scientific Data
Yu Fang, James W Jawitz
Where do people live, and how has this changed over timescales of centuries? High-resolution spatial information on historical human population distribution is of great significance to understand human-environment interactions and their temporal dynamics. However, the complex relationship between population distribution and various influencing factors coupled with limited data availability make it a challenge to reconstruct human population distribution over timescales of centuries. This study generated 1-km decadal population maps for the conterminous US from 1790 to 2010 using parsimonious models based on natural suitability, socioeconomic desirability, and inhabitability...
April 24, 2018: Scientific Data
Georg E Kindermann, Ferdinand Kristöfel, Markus Neumann, Günter Rössler, Thomas Ledermann, Silvio Schueler
In 1892 a forest spacing experiment with four different spacing patterns was established with Norway spruce (Picea abies). From 1923 until 1997, when the stand was harvested, diameter, height and height to crown base of in total 4507 trees were measured up to 23 times. The original aim of the experiment during establishment was to analyse short term effects of different spacing patterns. The thinning regime followed state of the art forestry practises. During the observation time of more than 100 years, the individual observers and the measurement technology changed several times...
April 24, 2018: Scientific Data
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