Find research datasets worth reusing

opencc-by-4.0Mar 2020View details →

KALI: calibration and validation results

The presented .zip archive consists of calibration and validation results we obtained while investigating the effect of calibration data length on the performance of different hydrological models. For more information, please visit our GitHub repository at <a href="https://github.com/hydrogo/KALI">https://github.com/hydrogo/KALI</a>.

opencc-by-4.0Apr 2009View details →

Figure 5. Dorsal habitus, P in The Platycerus (Coleoptera, Lucanidae) of California, with the recognition of Platycerus cribripennis Van Dyke as a valid species

Figure 5. Dorsal habitus, P. oregonensis male.

opencc-by-4.0Apr 2009View details →

Figure 4. Dorsal habitus, P in The Platycerus (Coleoptera, Lucanidae) of California, with the recognition of Platycerus cribripennis Van Dyke as a valid species

Figure 4. Dorsal habitus, P. marginalis male.

opencc-by-4.0Apr 2009View details →

Figure 3. Dorsal habitus, P in The Platycerus (Coleoptera, Lucanidae) of California, with the recognition of Platycerus cribripennis Van Dyke as a valid species

Figure 3. Dorsal habitus, P. cribripennis male.

opencc-zeroMay 2020View details →

Data from: Validation of serum neurofilaments as prognostic & potential pharmacodynamic biomarkers for ALS

Objective. Identify preferred neurofilament assays, and clinically validate serum NfL and pNfH as prognostic and potential pharmacodynamic biomarkers relevant to ALS therapy development. Methods. Prospective, multi-center, longitudinal observational study of patients with ALS (n=229), primary lateral sclerosis (PLS, n=20) and progressive muscular atrophy (PMA, n=11). Biological specimens were collected, processed and stored according to strict standard operating procedures (SOPs) 1. Neurofilament assays were performed in a blinded manner by independent contract research organizations (CROs). Results. For serum NfL and pNfH measured using the Simoa assay, there were no missing data (i.e. both technical replicates below the lower limit of detection were not encountered). For the Iron Horse and Euroimmun pNfH assays, such missingness was encountered in ~4% and ~10% of serum samples respectively. Mean coefficients of variation (CVs) for pNfH in serum and CSF were ~4-5% and ~2-3% respectively in all assays. Baseline NfL concentration, but not pNfH, predicted the future ALSFRS-R slope and survival. Incorporation of baseline serum NfL into mixed effects models of ALSFRS-R slopes yields an estimated sample size saving of ~8%. Depending on the method used to estimate effect size, use of serum NfL (and perhaps pNfH) as pharmacodynamic biomarkers, instead of the ALSFRS-R slope, yields significantly larger sample size savings. Conclusions. Serum NfL may be considered a clinically validated prognostic biomarker for ALS. Serum NfL (and perhaps pNfH), quantified using the Simoa assay, have potential utility as pharmacodynamic biomarkers of treatment effect.

opencc-by-4.0Jun 2020View details →

Dataset used for PARASOL/GRASP aerosol products validation with AERONET and comparison with MODIS

Dataset used for PARASOL/GRASP aerosol products validation with AERONET and comparison with MODIS  1. PARASOL/GRASP vs. AERONET for 2005-2013 <ul> <li>AOD at 443, 490, 550, 565, 670, 865 and 1020 nm</li> <li>AE (440/870)</li> <li>AODF and AODC at 550 nm</li> <li>SSA at 440, 675, 870, and 1020 nm</li> <li>AAOD at 550 nm</li> </ul> 2. PARASOL/GRASP, PARASOL/Operational, MODIS (DT, DB and MAIAC) vs. AERONET for year 2008 <ul> <li>AOD 550 nm</li> <li>AE (440/670) and AE (440/870)</li> <li>AODF and AODC 550 nm</li> </ul> 3. Inter-comparison of daily 0.1 degree grided PARASOL and MODIS aerosol products for year 2008 <ul> <li>Daily 0.1 x 0.1 degree grided PARASOL and MODIS AOD 550 nm for 2008 <ul> <li>PARASOL/HP; PARASOL/Models; MODIS/DT; MODIS/DB; MODIS/MAIAC</li> </ul> </li> </ul>   Please follow the data policy of each data source: PARASOL/GRASP: GRASP-OPEN (<a href="https://www.grasp-open.com/products/">https://www.grasp-open.com/products/</a>) PARASOL/Operational: ICARE (<a href="http://www.icare.univ-lille1.fr">http://www.icare.univ-lille1.fr</a>) MODIS/DT and DB C6 MYD04_L2: ICARE (<a href="http://www.icare.univ-lille1.fr">http://www.icare.univ-lille1.fr</a>) MODIS/MAIAC MAC19A2: NASA LAADS (<a href="https://ladsweb.modaps.eosdis.nasa.gov">https://ladsweb.modaps.eosdis.nasa.gov</a>) AERONET: <a href="http://www.aeronet.gsfc.nasa.gov">http://www.aeronet.gsfc.nasa.gov</a>   Details can be found in manuscript: Chen, C., O. Dubovik, D. Fuertes, P. Litvinov, T. Lapyonok, A. Lopatin, F. Ducos, Y. Derimian, M. Herman, D. Tanré, L. A. Remer, A. Lyapustin, A. M. Sayer, R. C. Levy, N. C. Hsu, J. Descloitres, L. Li, B. Torres, Y. Karol, M. Herrera, M. Herreras., M. Aspetsberger, M. Wanzenboeck, L. Bindreiter, D. Marth, A. Hangler, and Federspiel C., Validation of GRASP algorithm product from POLDER/PARASOL data and assessment of multi-angular polarimetry potential for aerosol monitoring, submitted to ESSD, <a href="https://essd.copernicus.org/preprints/essd-2020-224/">https://essd.copernicus.org/preprints/essd-2020-224/</a>, 2020.

An Empirical Validation of Cognitive Complexity as a Measure of Source Code Understandability - Data, Code and Documentation

Release version of the data, code and documentation used in and generated by our data analysis and literature search to ensure reproducibility, repeatability, and transparency, to be published alongside our paper "An Empirical Validation of Cognitive Complexity as a Measure of Source Code Understandability".

opencc-zeroJul 2020View details →

Data from: The island syndrome hypothesis is only partially validated in two rodent species in an inland-island system

According to the island syndrome and island rule hypotheses, island isolation and reduced area lead to phenotypic shifts in ecologically relevant traits in insular populations compared to mainland ones. These hypotheses have been built up with oceanic islands in mind or islands where isolation is high and colonization rate relatively limited. This set of hypotheses, however, may not be applicable to other inland-island systems or recently fragmented landscapes. We investigated how island life leads to phenotypic changes in two rodent metapopulations: deer mice and red-backed voles in a fragmented system on a river in Canada. From 2013 to 2016, we sampled 454 deer mice and 665 red-backed voles spread across 10 islands and six mainland sites on river shores. We compared body mass, tail and hindfoot length, exploration, and reaction towards predators, between individuals from island and mainland sites, and assessed the role of connectivity, isolation and area of islands. Insular individuals from both species were less aggressive towards potential predators and insular mice were more thorough explorers compared to mainland ones. Male mice were heavier and juvenile mice had longer tails on islands. However, contrary to expectations, we found negative relationships between aggressiveness and juvenile exploration score with patch connectivity for mice. Island connectivity significantly affected tail length of mice through a concave relationship. Finally, vole aggressiveness and exploration of male mice were positively correlated to island isolation. Our study supports only partially the predictions of the island syndrome hypothesis. It provides empirical evidence that inland-island life can modify traits in deer mice, but less so in red-backed voles in a non-oceanic system. It also raises questions about the direct causal factors of these changes in a naturally fragmented landscape, and urges for more predictive models about phenotypic/genetic divergence among populations in natural and artificial fragmented landscapes.

Reproducible Validation and Replication Studies in Nanoscale Physics (repro results plots - Ellis et al., 2016)

This archive contains the Jupyter notebooks needed to reproduce the figures of the paper that are related to the  Validation results and replication of Ellis et al. 2016. For further information direct to the README.md file.

Reproducible Validation and Replication Studies in Nanoscale Physics (problem datasets for Rockstuhl et al. 2005 replication)

Problem folders including all the input files necessary to reproduce the computations of the results related to Rockstuhl et al. 2005 on the paper: Reproducible Validation and Replication Studies in Nanoscale Physics

Codes used to identify hospital complications in validation of Charlson comorbidity index ICD-10 for the US

Codes used to identify hospital complications in validation of Charlson comorbidity index ICD-10 for the US.

Code list used to generate cohorts in ICD-10 CCI US validation study

Code list used to generate cohorts in validating the Charlson comorbidity index (CCI) for ICD-10 in the United States.

opencc-zeroDec 2019View details →

Data from: RapidRat: development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management

Invasive alien species (IAS) are among the main causes of global biodiversity loss. Invasive brown (Rattus norvegicus) and black (R. rattus) rats, in particular, are leading drivers of extinction on islands, especially in the case of seabirds where >50% of all extinctions have been attributed to rat predation. Eradication is the primary form of invasive rat management, yet this strategy has resulted in a ~10-38% failure rate on islands globally. Genetic tools can help inform IAS management, but such applications to date have been largely reactive, time-consuming, and costly. Here, we developed a Genotyping-in-Thousands by sequencing (GT-seq) panel for rapid species identification and population assignment of invasive brown and black rats (RapidRat) in Haida Gwaii, an archipelago comprising ~150 islands off the central coast of British Columbia, Canada. We constructed an optimized panel of 443 single nucleotide polymorphisms (SNPs) using previously generated double-digest restriction-site associated DNA (ddRAD) genotypic data (27,686 SNPs) from brown (n=295) and black rats (n=241) sampled throughout Haida Gwaii. The informativeness of this panel for identifying individuals to species and island of origin was validated relative to the ddRAD results; in all comparisons, admixture coefficients and population assignments estimated using RapidRat were consistent. To demonstrate application, 20 individuals from novel invasions of three islands (Agglomerate, Hotspring, Ramsay) were genotyped using RapidRat, all of which were confidently assigned (>98.5% probability) to Faraday and Murchison Islands as putative source populations. These results indicated that a previous eradication on Hotspring Island was conducted at an inappropriate geographic scale; future management should expand the eradication unit to include neighboring islands to prevent re-invasion. Overall, we demonstrated that RapidRat is an effective tool for managing invasive rat populations in Haida Gwaii and provided a clear framework for GT-seq panel development for informing biodiversity conservation in other systems.

opencc-zeroAug 2020View details →

Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

Background The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.

opencc-by-4.0Sep 2020View details →

Edge turbulence in ISTTOK: a multi-code fluid validation

Experimental data from ISTTOK, simulation outputs from GBS, BOUT++/Hermes, and HESEL, and processing scripts used in a paper to be submitted to PPCF.

opencc-by-4.0Sep 2020View details →

Validation Data for WinProp and NYUSIM

Validation of WinProp and NYUSIM ================================ This archive contains simulation data the same scenario that is used in the measurement campaign published in [1-3]. The directories correspond to the respective simulators that have been used.