cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5616415
title: Avian Colour Gamut

description: A data set of colour spectra of birds collected from the Natural History Museum ornithology study collection at Tring. The data covers &gt;300 species distributed across the avian phylogeny.<br>Consists of four files:<br>AvianColourGamut_SpecMetadata.csv - contains details of species/specimens measured<br>ColourGamut_BriefDataCollectionMethods.docx - overview of data collection methods<br><br>SpectrasuiteSettings.txt - software settings for spectrasuite<br><br>Spectra.zip - data archive of individual spectrasuite format files
DOI: 10.6084/m9.figshare.5616427.v1
title: Demo datasets for fMLC and DiVE

description: The "small" dataset contains ~4000 ITS yeast sequences, checked and validated by the specialists at the Westerdijk Fungal Biodiversity Institute. This dataset were analyzed and released in Vu D. et al. 2016. The "large" dataset contains ~350K ITS fungal sequences downloaded from GenBank (https://www.ncbi.nlm.nih.gov/) which was used in Vu D. et al. 2014 to evaluate the speed of MLC. The smallest dataset is the Fusarium dataset of only 85 Actin sequences from 14 species.The embedded files (in .json format) of the datasets can be uploaded directly from https://nlesc.github.io/DiVE/ for a quick inspection. Manual for DiVE is at https://github.com/NLeSC/DiVE .
DOI: 10.6084/m9.figshare.5616439.v1
title: Americas Data.xlsx

description: The data presented here is analysed in 'Why does freshwater fish species richness differ between Atlantic and Pacific drainages of the Americas?' to be published in Journal of Biogeography. A detailed description of the procedures is described there.<br>
DOI: 10.6084/m9.figshare.5616412.v1
title: Dataset for: <i>Lactobacillus reuteri </i>strains protect epithelial barrier integrity of IPEC-J2 monolayers from the detrimental effect of Enterotoxigenic <i>Escherichia coli</i> (ETEC).

description: <i>Lactobacillus reuteri</i> is an inhabitant of the gastrointestinal (GI) tract of mammals and birds and several strains of this species are known to be effective probiotics. The mechanisms by which <i><i>L. reuteri</i></i> confers its health-promoting effects are far from being fully understood, but protection of the mucosal barrier is thought to be important. Leaky gut is a state of abnormal intestinal permeability with implications for the pathophysiology of various gastrointestinal disorders. Enterotoxigenic<i><i> Escherichia coli </i></i>(ETEC) can invade the intestinal mucosa and induce changes in barrier function by producing enterotoxin or by direct invasion of the intestinal epithelium.Our hypothesis was that<i> L. reuteri </i>can protect the mucosal barrier, and the goal of the study was to challenge this hypothesis by monitoring the protective effect of <i>L. reuteri </i>strains on epithelial dysfunction caused by ETEC. This study examined the potential of <i><i>Lactobacillus reuteri</i></i> to attenuate the effect of ETEC strain 853/67 on mucosal permeability. Using an infection model based on the porcine intestinal cell line IPEC-J2, it was demonstrated that pre-treatment of the cells with human-derived <i>L. reuteri </i>strains (ATCC PTA 6475, DSM 17938 and 1563F) and a rat strain (R2LC) reduced the detrimental effect of ETEC in a dose-dependent manner, as monitored by permeability of FITC-dextran and transepithelial electrical resistance (TEER). Moreover, the results revealed that ETEC up-regulated pro-inflammatory cytokines IL-6 and TNFα and decreased expression of the shorter isoform of ZO-1 (187 kDa) and E-cadherin. In contrast, pre-treatment with<i> L. reuteri</i> DSM 17938 and 1563F downregulated expression of IL-6 and TNFα, and led to an increase in production of the longer isoform of ZO-1 (195 kDa) and maintained E-cadherin expression. Interestingly, expression of ZO-1 (187 kDa) was preserved only when the infected cells were pre-treated with strain 1563F. These findings demonstrate that <i><i>L. reuteri</i></i> strains exert a protective effect against ETEC-induced mucosal integrity disruption.
DOI: 10.6084/m9.figshare.5616418.v2
title: Discrete and Continuous encoding in RL

description: Illustration of the differences in observation and Q-values encoding between a tabular and a neural network implementation of a Q-learning algorithm.<br>
DOI: 10.6084/m9.figshare.5616367
title: Supporting Code for The shape of the contact-density function matters when modelling disease transmission in fluctuating populations

description: Supporting Code
DOI: 10.6084/m9.figshare.5616403
title: Pitch, yaw and roll (torsion) of left and right eyes during yaw optokinesis

description: The pitch, yaw and roll (torsion) of the left and right eyes of 17 mantis shrimp during yaw optokinesis experiments.<br>Pose.mat contains six 17 x 6 cell matlab matrix [17 rows = individuals, 6 columns = trials]Data in each are as follows: - LP [left eye pitch] - RP [right eye pitch]<br> - LY [left eye yaw] - RY [right eye yaw] - LR [left eye roll (torsion)] - RR [right eye roll (torsion)](all in degrees)Data sampling at 0.2 s (50fps)<br>Speed.mat contains one 17 x 6 cell matlab matrix [17 rows = individuals, 6 columns = trials]Data in the speed matrix is the speed (degrees/s) of the rotating drum in each trial (6) for each individual (17).<br>Dir.mat contains one 17 x 6 cell matlab matrix [17 rows = individuals, 6 columns = trials]Data in the dir matrix is the direction (1=clockwise / -1=anticlockwise) of the rotating drum in each trial (6) for each individual (17).<br><br>
DOI: 10.6084/m9.figshare.5616403.v1
title: Pitch, yaw and roll (torsion) of left and right eyes during yaw optokinesis

description: The pitch, yaw and roll (torsion) of the left and right eyes of 17 mantis shrimp during yaw optokinesis experiments.<br>Pose.mat contains six 17 x 6 cell matlab matrix [17 rows = individuals, 6 columns = trials]Data in each are as follows: - LP [left eye pitch] - RP [right eye pitch]<br> - LY [left eye yaw] - RY [right eye yaw] - LR [left eye roll (torsion)] - RR [right eye roll (torsion)](all in degrees)Data sampling at 0.2 s (50fps)<br>Speed.mat contains one 17 x 6 cell matlab matrix [17 rows = individuals, 6 columns = trials]Data in the speed matrix is the speed (degrees/s) of the rotating drum in each trial (6) for each individual (17).<br>Dir.mat contains one 17 x 6 cell matlab matrix [17 rows = individuals, 6 columns = trials]Data in the dir matrix is the direction (1=clockwise / -1=anticlockwise) of the rotating drum in each trial (6) for each individual (17).<br><br>
DOI: 10.6084/m9.figshare.5616367.v1
title: Supporting Code for The shape of the contact-density function matters when modelling disease transmission in fluctuating populations

description: Supporting Code
DOI: 10.6084/m9.figshare.5616310
title: North_Atlantic_Alaska_Siberia_Regional_time_series

description: These three regional time seris were calculated and used in the study published by Nicolle et al. (2017). The methods used to calculate the records are available in the paper. The study is a contribution to the PAGES 2k Network (through the Arctic 2k working group).<br><br>Nicolle, M., Debret, M., Massei, N., Colin, C., deVernal, A., Divine, D., Werner, J. P., Hormes, A., Korhola, A., and Linderholm, H. W.: Climate variability in subarctic area for the last two millennia, Clim. Past Discuss., https://doi.org/10.5194/cp-2017-33, in review, 2017.<br>
DOI: 10.17045/sthlmuni.5616304
title: Open data: Cascade and no-repetition rules are comparable controls for the auditory frequency mismatch negativity in oddball tasks

description: Open data for "cascade and no-repetition rules are comparable controls for the auditory frequency mismatch negativity in oddball tasks" by Stefan Wiens, Malina Szychowska, Rasmus Eklund, and Erik van Berlekom<br><br>bayesfactor.zip contains the bayes factor analyses of the main data. some files were generated with aladins r scripts (https://doi.org/10.17045/sthlmuni.4981154). the r-files can be run with r (https://www.r-project.org/), and the jasp-files can be opened with jasp (https://jasp-stats.org/). <br><br>bayesfactor_ruhnau_2012.zip contains the bayes factor analyses of the ruhnau et al. (2012) data. the "computing_bf_for_ruhnau_2012.pdf" explains the analyses. some files were generated with aladins r scripts (https://doi.org/10.17045/sthlmuni.4981154). the r-files can be run with r (https://www.r-project.org/). <br><br>bdf.zip contains the raw eeg data files that were recorded with a biosemi system (www.biosemi.com). the files can be opened in matlab with the fieldtrip toolbox. http://www.fieldtriptoolbox.org/<br><br>fieldtrip.zip contains all the matlab scripts that were used to process the erp data with the toolbox fieldtrip. http://www.fieldtriptoolbox.org/<br><br>fieldtrip_mat.zip contains the final, preprocessed individual data files. they can be opened with matlab.<br><br>figures.zip contains extra erp figures. for example, it contains the grand mean erps for the good subjects (n=26) and all subjects (n=40).<br><br>logfiles.zip contains the behavioral logfiles from the main task.<br><br>no_repetition_sound_order_simulation.zip contains the r script to simulate tone order for a random task without the no-repetition rule. see the publication for an explanation. the r-files can be opened with r (https://www.r-project.org/).<br><br>osf.zip contains the protocol and the matlab scripts that we preregistered at open science framework (osf).<br><br>MMN3.py is the python script for the main task. It needs python (https://www.python.org/) and psychopy (http://www.psychopy.org/)
DOI: 10.6084/m9.figshare.5616256
title: Thermomechanical effects caused by martensite formation in powder metallurgy FeMnSiCrNi shape memory alloys

description: Supplemental Video material for the invited paper, by Pricop et al., for the Special Issue RoPM&AM 2017 of the journal Powder Metallurgy
DOI: 10.17045/sthlmuni.5616304.v1
title: Open data: Cascade and no-repetition rules are comparable controls for the auditory frequency mismatch negativity in oddball tasks

description: Open data for "cascade and no-repetition rules are comparable controls for the auditory frequency mismatch negativity in oddball tasks" by Stefan Wiens, Malina Szychowska, Rasmus Eklund, and Erik van Berlekom<br><br>bayesfactor.zip contains the bayes factor analyses of the main data. some files were generated with aladins r scripts (https://doi.org/10.17045/sthlmuni.4981154). the r-files can be run with r (https://www.r-project.org/), and the jasp-files can be opened with jasp (https://jasp-stats.org/). <br><br>bayesfactor_ruhnau_2012.zip contains the bayes factor analyses of the ruhnau et al. (2012) data. the "computing_bf_for_ruhnau_2012.pdf" explains the analyses. some files were generated with aladins r scripts (https://doi.org/10.17045/sthlmuni.4981154). the r-files can be run with r (https://www.r-project.org/). <br><br>bdf.zip contains the raw eeg data files that were recorded with a biosemi system (www.biosemi.com). the files can be opened in matlab with the fieldtrip toolbox. http://www.fieldtriptoolbox.org/<br><br>fieldtrip.zip contains all the matlab scripts that were used to process the erp data with the toolbox fieldtrip. http://www.fieldtriptoolbox.org/<br><br>fieldtrip_mat.zip contains the final, preprocessed individual data files. they can be opened with matlab.<br><br>figures.zip contains extra erp figures. for example, it contains the grand mean erps for the good subjects (n=26) and all subjects (n=40).<br><br>logfiles.zip contains the behavioral logfiles from the main task.<br><br>no_repetition_sound_order_simulation.zip contains the r script to simulate tone order for a random task without the no-repetition rule. see the publication for an explanation. the r-files can be opened with r (https://www.r-project.org/).<br><br>osf.zip contains the protocol and the matlab scripts that we preregistered at open science framework (osf).<br><br>MMN3.py is the python script for the main task. It needs python (https://www.python.org/) and psychopy (http://www.psychopy.org/)
DOI: 10.6084/m9.figshare.5616256.v1
title: Thermomechanical effects caused by martensite formation in powder metallurgy FeMnSiCrNi shape memory alloys

description: Supplemental Video material for the invited paper, by Pricop et al., for the Special Issue RoPM&AM 2017 of the journal Powder Metallurgy
DOI: 10.6084/m9.figshare.5616250.v1
title: Dataset for: Tumor-adjacent tissue co-expression profile analysis reveals pro-oncogenic ribosomal gene signature for prognosis of resectable hepatocellular carcinoma

description: Molecular markers are not used in the determination of prognosis and treatment for HCC patients. We proposed that the identification of the common pro-oncogenic pathways in primary tumor (PT) and adjacent non-malignant tissues (AT) predicting HCC patient risks result in the HCC marker discovery. We examined the genome-wide mRNA expression profiles of paired PT and AT samples from 321 HCC patients. The workflow integrated differentially expressed gene selection, gene ontology enrichment, computational classification, survival predictions, image analysis and experimental validation methods. We developed a 24-ribosomal gene-based HCC classifier (RGC), which are prognostically significant in both PT and AT. The RGC gene overexpression in PT was associated with a poor prognosis in the training (HR=8.2, p=9.4E-06) and cross-cohort validation (HR=2.63, p=0.004) datasets. The multivariate survival analysis demonstrated the significant and independent prognostic value of the RGC. The RGC displayed a significant prognostic value in AT of the training (HR=5.0, p=0.03) and cross-validation (HR=1.9, p=0.03) HCC groupsconfirming the accuracy and robustness of RGC. Our experimental and bioinformatics analyses suggested a key role for c-MYC in the pro-oncogenic pattern of ribosomal biogenesis co-regulation in PT and AT. Microarray, qRT-PCR and quantitative immunohistochemical studies of the PT showed that DKK1 in PT is the perspective biomarker for poor HCC outcomes. The common co-transcriptional patterns of ribosome biogenesis genes in PT and AT from HCC patients suggests a new scalable prognostic system, supported by the model of tumor-like metabolic redirection/assimilation in non-malignant AT. The RGC, comprising 24 ribosomal genes, is introduced as a robust and reproducible prognostic model for stratifying HCC patient risks. The adjacent non-malignant liver tissue alone or in combination with HCC tissue biopsy could be an important target to develop predictive and monitoring strategies and evidence-based therapeutic interventions to reduce the risk of post-surgery relapse of HCC patients.
DOI: 10.6084/m9.figshare.5616256.v3
title: Thermomechanical effects caused by martensite formation in powder metallurgy FeMnSiCrNi shape memory alloys

description: Supplemental Video material for the invited paper, by Pricop et al., for the Special Issue RoPM&AM 2017 of the journal Powder Metallurgy
DOI: 10.6084/m9.figshare.5616256.v2
title: Thermomechanical effects caused by martensite formation in powder metallurgy FeMnSiCrNi shape memory alloys

description: Supplemental Video material for the invited paper, by Pricop et al., for the Special Issue RoPM&AM 2017 of the journal Powder Metallurgy
DOI: 10.6084/m9.figshare.5616208
title: PLA Figure 2 Positive Series

description: The second set of images provided is a set of photomicrographs acquired on methanol fixed T47D breast cancer cells and subjected to proximity ligation assays using antibodies to detect interactions between CDK2 and Cyclin E1 and counter stained with ToPro3/DAPI (nuclei) and Phalloidin (cytoplasm)
DOI: 10.6084/m9.figshare.5616205
title: PLA Figure 2 Negative Series

description: The second set of images provided is a set of photomicrographs acquired on methanol fixed T47D breast cancer cells and subjected to proximity ligation assays using antibodies to detect interactions between CDK2 and Cyclin E1 and counter stained with ToPro3/DAPI (nuclei) and Phalloidin (cytoplasm).
DOI: 10.6084/m9.figshare.5616208.v1
title: PLA Figure 2 Positive Series

description: The second set of images provided is a set of photomicrographs acquired on methanol fixed T47D breast cancer cells and subjected to proximity ligation assays using antibodies to detect interactions between CDK2 and Cyclin E1 and counter stained with ToPro3/DAPI (nuclei) and Phalloidin (cytoplasm)
DOI: 10.4225/03/5a126aae4cd89
title: Annual estimates of gross domestic product : Australian colonies/states 1861-1976/77

description: The annual estimates of Gross Domestic Product are presented for three sequential sub-periods:1861-1938/391939/40-1947/481948/49-1976/77.There is a summary table for each sub-period and each colony/state giving annual estimates of GDP in current prices and GDP in constant prices by industrial sector and shares of industrial sectors in GDP in current prices. These summary tables appear in Microsoft Excel files which are linked in turn to supplementary tables showing the composition of certain of the industrial sectors.<br>1. A detailed account of the methods of estimation for each colony/state is contained in Microsoft Word files. These files are located in the directory …\Methods. With some adjustment, the basic approach is to replicate the methods of estimation for the GDP of Australia as a whole made by N. G. Butlin in Australian Domestic Product, Investment and Overseas Borrowing 1861-1938/39 (Cambridge University Press, 1962).<br>2. The results and detailed calculations are available in worksheets. The file …\Data\Index.xls contains links to a master worksheet for each state which in turn has links to constructed time series of the various components of GDP.<br><br>Contributor: Monash University. Faculty of Business and Economics. Department of Economics.<br>Copyright 2009. W. A. Sinclair<br>
DOI: 10.6084/m9.figshare.5616205.v1
title: PLA Figure 2 Negative Series

description: The second set of images provided is a set of photomicrographs acquired on methanol fixed T47D breast cancer cells and subjected to proximity ligation assays using antibodies to detect interactions between CDK2 and Cyclin E1 and counter stained with ToPro3/DAPI (nuclei) and Phalloidin (cytoplasm).
DOI: 10.17608/k6.auckland.5616193
title: Bent FRP anchors dataset

description: Data set of 32 specimens
DOI: 10.17608/k6.auckland.5616193.v1
title: Bent FRP anchors dataset

description: Data set of 32 specimens
DOI: 10.6084/m9.figshare.5616160
title: Database of Biodiversity Offsetting Projects

description: This database lists the biodiversity offsetting projects used in Sonter et al. 2018. The Methods section of the paper describes how projects were identified, reviewed and analysed. WebTable 1 shows the information sources used to collect data on each project and WebTable 2 defines the project variables collected for review. <br><br>For further details, see: Sonter et al. (2018) "Biodiversity offsets forest opportunities to mitigate impacts on ecosystem services", Frontiers in Ecology and the Environment. DOI: XX.<br>
DOI: 10.6084/m9.figshare.5616142
title: IHC Figure 1 Model 1 Treated Photomicrographs

description: The first set of photomicrographs provided depict the lungs from mice bearing human breast cancer cell line xenografts subjected to DAB+ immune-histochemistry using antibodies to either anti-human high molecular weight cytokeratin (MDA-MB-468 cells, model 1) or anti-human Vimentin (MDA-MB-231 cells, model 2), a technique that was used to quantify metastatic deposits in the lungs.
DOI: 10.6084/m9.figshare.5616160.v1
title: Database of Biodiversity Offsetting Projects

description: This database lists the biodiversity offsetting projects used in Sonter et al. 2018. The Methods section of the paper describes how projects were identified, reviewed and analysed. WebTable 1 shows the information sources used to collect data on each project and WebTable 2 defines the project variables collected for review. <br><br>For further details, see: Sonter et al. (2018) "Biodiversity offsets forest opportunities to mitigate impacts on ecosystem services", Frontiers in Ecology and the Environment. DOI: XX.<br>
DOI: 10.6084/m9.figshare.5616136
title: Diversity, systematics, and evolution of Cynodonteae inflorescences (Chloridoideae – Poaceae)

description: The species of the Cynodonteae tribe show great morphological diversity in their reproductive structures. Previous studies where inflorescences were comparatively analysed in the context of phylogeny have shown that although grass inflorescences seem to be excessively variable, there are certain aspects of inflorescences that store relevant information on the evolution and systematics in Poaceae. We have analysed and compared the inflorescence structures of species belonging to the Hilariinae, Monanthochloinae, Scleropogoninae, and Muhlenbergiinae subtribes. Considering the most relevant morphological characters, the most recurrent types of inflorescences in the lineage were determined by means of a principal coordinates analysis. To understand the evolution of inflorescence morphology, ancestral reconstructions of inflorescence characters were performed using the Bayesian inference method. The results obtained demonstrate that the processes of homogenization and truncation might account for the diversity observed in adult inflorescences. Five different types of inflorescences were identified out of 36 theoretical possibilities. Amongst these, inflorescence type 1 (panicle of spikelets, with a terminal spikelet, non-homogenized, and bearing third- or higher-order branches) was found to be the most frequent in the studied group. Ancestral reconstructions of morphological characters allowed us to suggest that the ancestor of the group might have had an inflorescence with the form of a raceme of spikelets, non-truncated and bearing first-order branches. More complex inflorescences bearing no terminal spikelets and having branches of higher order might have diverged this lineage.
DOI: 10.6084/m9.figshare.5616142.v1
title: IHC Figure 1 Model 1 Treated Photomicrographs

description: The first set of photomicrographs provided depict the lungs from mice bearing human breast cancer cell line xenografts subjected to DAB+ immune-histochemistry using antibodies to either anti-human high molecular weight cytokeratin (MDA-MB-468 cells, model 1) or anti-human Vimentin (MDA-MB-231 cells, model 2), a technique that was used to quantify metastatic deposits in the lungs.