cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5319589.v2
title: Bayesian Dimensionality Reduction With PCA Using Penalized Semi-Integrated Likelihood

description: We discuss the problem of estimating the number of principal components in principal components analysis (PCA). Despite the importance of the problem and the multitude of solutions proposed in literature, it comes as a surprise that there does not exist a coherent asymptotic framework, which would justify different approaches depending on the actual size of the dataset. In this article, we address this issue by presenting an approximate Bayesian approach based on Laplace approximation and introducing a general method of developing criteria for model selection, called PEnalized SEmi-integrated Likelihood (PESEL). Our general framework encompasses a variety of existing approaches based on probabilistic models, like the Bayesian Information Criterion for Probabilistic PCA (PPCA), and enables the construction of new criteria, depending on the size of the dataset at hand and additional prior information. Specifically, we apply PESEL to derive two new criteria for datasets where the number of variables substantially exceeds the number of observations, which is out of the scope of currently existing approaches. We also report results of extensive simulation studies and real data analysis, which illustrate the desirable properties of our proposed criteria as compared to state-of-the-art methods and very recent proposals. Specifically, these simulations show that PESEL-based criteria can be quite robust against deviations from the assumptions of a probabilistic model. Selected PESEL-based criteria for the estimation of the number of principal components are implemented in the R package <i>pesel</i>, which is available on github (<i>https://github.com/psobczyk/pesel</i>). Supplementary material for this article, with additional simulation results, is available online. The code to reproduce all simulations is available at <i>https://github.com/psobczyk/pesel_simulations</i>.
DOI: 10.6084/m9.figshare.5319589.v1
title: Bayesian dimensionality reduction with PCA using penalized semi-integrated likelihood

description: We discuss the problem of estimating the number of principal components in Principal Components Analysis (PCA). Despite the importance of the problem and the multitude of solutions proposed in literature, it comes as a surprise that there does not exist a coherent asymptotic framework which would justify different approaches depending on the actual size of the data set. In this paper we address this issue by presenting an approximate Bayesian approach based on Laplace approximation and introducing a general method of developing criteria for model selection, called PEnalized SEmi-integrated Likelihood (PESEL). Our general framework encompasses a variety of existing approaches based on probabilistic models, like the Bayesian Information Criterion for Probabilistic PCA (PPCA), and enables the construction of new criteria, depending on the size of the data set at hand and additional prior information. Specifically, we apply PESEL to derive two new criteria for data sets where the number of variables substantially exceeds the number of observations, which is out of the scope of currently existing approaches. We also report results of extensive simulation studies and real data analysis, which illustrate the desirable properties of our proposed criteria as compared to state-of-the-art methods and very recent proposals. Specifically, these simulations show that PESEL-based criteria can be quite robust against deviations from the assumptions of a probabilistic model. Selected PESEL-based criteria for the estimation of the number of principal components are implemented in the R package <i>pesel</i>, which is available on github (https://github.com/psobczyk/pesel).
DOI: 10.6084/m9.figshare.5319523
title: Leading indicators of mosquito-borne disease elimination

description: Data and code to reproduce figures from O'Regan et al 2016. See "README.txt" for file details.<br><br>O'Regan SM, Lillie JW, and Drake JM. 2016. Leading indicators of mosquito-borne disease elimination. Theoretical Ecology 9(3):269-286. doi: 10.1007/s12080-015-0285-5
DOI: 10.6084/m9.figshare.5319514
title: sub-012 V1 h5 file

description: Data file contains data for expanded V1 region. Data types are 1. per-voxel percent signal change time-courses for 6 runs2. per-voxel percent signal change time-courses for 6 runs, leave-one-out median - name of the array refers to the file that was left out3. per-voxel percent signal change time-course, grand average over runs (median)4. parameters of pRF fits per run (leave-one-out)5. parameters of pRF fits all runs 6. design matrix of the experiment, [100,100,462] = pixels by pixels by time points, i.e. this constitutes a binary movie of what was on the screen on each sample point in the data.<br># indices into prf output array:# 0: X (position, degrees of visual angle from fixation)# 1: Y (position, degrees of visual angle from fixation)# 2: s (size, standard deviation of gauss)# 3: n (nonlinearity power)# 4: a (amplitude)# 5: b (baseline, intercept value)# 6: rsq# 7: #<br>Github repo for analysis code on this dataset: https://github.com/tknapen/decode_encode<br>The voxel size of these recordings is 2mm isotropic, and the sample duration (TR) is 0.945 s. pRF fits were done using a CSS model implemented in Popeye, using a standard HRF shape.<br>
DOI: 10.6084/m9.figshare.5319490
title: Effects on Alcohol Consumption and Alcohol Related Harm of a Community-Based Prevention Intervention With National Support in Sweden

description: <i>Background</i>: In order to strengthen local alcohol prevention work in Sweden the Swedish government has for the past almost 15 years commissioned the Public Health Agency of Sweden to initiate a series of community-based alcohol prevention projects. The latest of these, labeled local development with ambitions (LUMA), included 25 municipalities in Sweden. <i>Objectives</i>: Aim of this study is to examine if LUMA municipalities that received financial support, with requirements, increased local alcohol prevention and if alcohol consumption and harm declined. <i>Methods</i>: Twenty-five Swedish municipalities that received financial support aiming to strengthen local alcohol preventing activities (intervention group) were compared to municipalities that did not receive such support (control group, <i>N</i> = 224), before, during, and after the intervention period. Two composite measures of policy and activity were created and used. The composite activity measure includes seven activity indicators and the composite policy measure includes six policy indicators. Harm measures have been selected based on several recommended indicators for monitoring alcohol, tobacco, and other drugs in Sweden. A fixed effects model was used to analyze data. <i>Results</i>: The results reveal that prevention activities increased and several alcohol-related harm indicators were reduced in intervention municipalities (LUMA) compared with in control municipalities. <i>Conclusions</i>: It seems as if financial support, combined with specific requirements and support from the regional and national level, can stimulate local alcohol prevention activities and have a significant effect on alcohol consumption and alcohol-related harm. Similar evaluations in other countries would be of great value for assessing the generalizability of findings.
DOI: 10.6084/m9.figshare.5319568.v1
title: Summary of data used to build the article "Multi-scale characterization of joint surface roughness".

description: The following dataset contains all surface measurements dataset related to the article "Multi-scale characterization of joint surface roughness". The IGSN reference is IEBNB0001. Sample description: The following data set summarize surface measurements on a fresh joint surface present in the active Klieve quarry, southern Münsterland, western Germany (51°34’30’’N, 8°18’00’’E). The joint was developed at less than 1 km depth in Turonian glauconitic. Sampling for microscopic characterization were realized on a loose part from the main block. Surface elevation measurements of the plumose structure were performed with a LiDAR terrestrial scanner FARO<sup>® </sup>Focus3D X330, then processed using software SCENE<sup>®</sup> to obtain a referenced 3D point cloud of the joint surface. The 3D point cloud is provided in xyz format in the file “LiDAR data coordinates” directly after extraction from SCENE<sup>® </sup>software. The authors provide a file “raw_data_LiDAR_measurement” which may be used as a first start with data scaled as a 2D surface. The three files for microscopic characterization are provided as raw data as extracted from Keyence software. _A jpegfile "together_V2" which allows a clear identification of selected measured surface location and a photo of the joint surface. Coating of iron-hydroxides and of quartz only on the central part are observed on the joint surface. However, they are very thin and mimic the plumose structure. Hackles and ridges, revealed by surface measurements, have been identified during in-situ observations. _ LiDAR data coordinates.xyz: LiDAR cloud of points after exportation in x,y,z format. Be careful: axis have to be changed. First column corresponds to X direction. Third column corresponds to Y direction. Second column corresponds to Z direction and elevation are inversed (lower values are the maximum values). Unit are in meters. _ A file "raw_data_LiDAR_measurement" following the merging of four scans by use of LiDAR technology. Units are in meters, these raws data have not been filtered. Users are free to follow the method proposed in the article"Multi-scale characterization of joint surface roughness" to process data. Element size is 0.49 mm. _ A file "im100X.mat" containing the surface measurement by use of Keyence microscope at 100X magnification. Unit are in micrometers. Element size is 8.46 µm. _ A file " im200X.mat " containing the surface measurement by use of Keyence microscope at 200X magnification. Unit are in micrometers. Element size is 5.15 µm. _ A file " im500X.mat " containing the surface measurement by use of Keyence microscope at 500X magnification. Unit are in micrometers. Element size is 2.1 µm.
DOI: 10.6084/m9.figshare.5319490.v1
title: Effects on Alcohol Consumption and Alcohol Related Harm of a Community-Based Prevention Intervention With National Support in Sweden

description: <i>Background</i>: In order to strengthen local alcohol prevention work in Sweden the Swedish government has for the past almost 15 years commissioned the Public Health Agency of Sweden to initiate a series of community-based alcohol prevention projects. The latest of these, labeled local development with ambitions (LUMA), included 25 municipalities in Sweden. <i>Objectives</i>: Aim of this study is to examine if LUMA municipalities that received financial support, with requirements, increased local alcohol prevention and if alcohol consumption and harm declined. <i>Methods</i>: Twenty-five Swedish municipalities that received financial support aiming to strengthen local alcohol preventing activities (intervention group) were compared to municipalities that did not receive such support (control group, <i>N</i> = 224), before, during, and after the intervention period. Two composite measures of policy and activity were created and used. The composite activity measure includes seven activity indicators and the composite policy measure includes six policy indicators. Harm measures have been selected based on several recommended indicators for monitoring alcohol, tobacco, and other drugs in Sweden. A fixed effects model was used to analyze data. <i>Results</i>: The results reveal that prevention activities increased and several alcohol-related harm indicators were reduced in intervention municipalities (LUMA) compared with in control municipalities. <i>Conclusions</i>: It seems as if financial support, combined with specific requirements and support from the regional and national level, can stimulate local alcohol prevention activities and have a significant effect on alcohol consumption and alcohol-related harm. Similar evaluations in other countries would be of great value for assessing the generalizability of findings.
DOI: 10.6084/m9.figshare.5319523.v1
title: Leading indicators of mosquito-borne disease elimination

description: Data and code to reproduce figures from O'Regan et al 2016. See "README.txt" for file details.<br>
DOI: 10.6084/m9.figshare.5319460
title: NBDA code from Social learning in otters

description: This R script contains the code to run NBDAs on the smooth-coated otter data
DOI: 10.6084/m9.figshare.5319463
title: Data from Social learning in otters

description: This file contains the raw data used for all analyses
DOI: 10.6084/m9.figshare.5319514.v1
title: sub-012 V1 h5 file

description: Data file contains data for expanded V1 region. Data types are 1. per-voxel percent signal change time-courses for 6 runs2. per-voxel percent signal change time-courses for 6 runs, leave-one-out median - name of the array refers to the file that was left out3. per-voxel percent signal change time-course, grand average over runs (median)4. parameters of pRF fits per run (leave-one-out)5. parameters of pRF fits all runs 6. design matrix of the experiment, [100,100,462] = pixels by pixels by time points, i.e. this constitutes a binary movie of what was on the screen on each sample point in the data.<br># indices into prf output array:# 0: X (position, degrees of visual angle from fixation)# 1: Y (position, degrees of visual angle from fixation)# 2: s (size, standard deviation of gauss)# 3: n (nonlinearity power)# 4: a (amplitude)# 5: b (baseline, intercept value)# 6: rsq# 7: #<br>Github repo for analysis code on this dataset: https://github.com/tknapen/decode_encode<br>The voxel size of these recordings is 2mm isotropic, and the sample duration (TR) is 0.945 s. pRF fits were done using a CSS model implemented in Popeye, using a standard HRF shape.<br>
DOI: 10.6084/m9.figshare.5319523.v3
title: Leading indicators of mosquito-borne disease elimination

description: Data and code to reproduce figures from O'Regan et al 2016. See "README.txt" for file details.<br><br>O'Regan SM, Lillie JW, and Drake JM. 2016. Leading indicators of mosquito-borne disease elimination. Theoretical Ecology 9(3):269-286. doi: 10.1007/s12080-015-0285-5
DOI: 10.6084/m9.figshare.5319457
title: Data Sets from Responses of neurogenesis and neuroplasticity related genes to elevated CO<sub>2</sub> levels in the brain of three teleost species

description: The continuous increase of anthropogenic CO<sub>2</sub> in the atmosphere resulting in ocean acidification has been reported to affect brain function in some fishes. During adulthood, cell proliferation is fundamental for fish brain growth and for it to adapt in response to external stimuli, such as environmental changes. Here we report the first expression study of genes regulating neurogenesis and neuroplasticity in brains of three-spined stickleback (<i>Gasterosteus aculeatus</i>), cinnamon anemonefish (<i>Amphiprion melanopus</i>) and spiny damselfish (<i>Acanthochromis polyacanthus</i>) exposed to elevated CO<sub>2</sub>. The mRNA expression levels of the neurogenic differentiation factor (NeuroD) and doublecortin (DCX) were upregulated in three-spined stickleback exposed to high-CO<sub>2</sub> compared with controls, while no changes were detected in the other species. The mRNA expression levels of the proliferating cell nuclear antigen (PCNA) and the brain-derived neurotrophic factor (BDNF) remained unaffected in the high-CO<sub>2</sub> exposed groups compared to the control in all three species. These results indicate a species-specific regulation of genes involved in neurogenesis in response to elevated ambient CO<sub>2</sub> levels. The higher expression of NeuroD and DCX mRNA transcripts in the brain of high-CO<sub>2</sub> exposed three-spined stickleback, together with the lack of effects on mRNA levels in cinnamon anemonefish and spiny damselfish, indicate differences in coping mechanisms among fish in response to the predicted-future CO<sub>2</sub> level.
DOI: 10.6084/m9.figshare.5319457.v1
title: Data Sets from Responses of neurogenesis and neuroplasticity related genes to elevated CO<sub>2</sub> levels in the brain of three teleost species

description: The continuous increase of anthropogenic CO<sub>2</sub> in the atmosphere resulting in ocean acidification has been reported to affect brain function in some fishes. During adulthood, cell proliferation is fundamental for fish brain growth and for it to adapt in response to external stimuli, such as environmental changes. Here we report the first expression study of genes regulating neurogenesis and neuroplasticity in brains of three-spined stickleback (<i>Gasterosteus aculeatus</i>), cinnamon anemonefish (<i>Amphiprion melanopus</i>) and spiny damselfish (<i>Acanthochromis polyacanthus</i>) exposed to elevated CO<sub>2</sub>. The mRNA expression levels of the neurogenic differentiation factor (NeuroD) and doublecortin (DCX) were upregulated in three-spined stickleback exposed to high-CO<sub>2</sub> compared with controls, while no changes were detected in the other species. The mRNA expression levels of the proliferating cell nuclear antigen (PCNA) and the brain-derived neurotrophic factor (BDNF) remained unaffected in the high-CO<sub>2</sub> exposed groups compared to the control in all three species. These results indicate a species-specific regulation of genes involved in neurogenesis in response to elevated ambient CO<sub>2</sub> levels. The higher expression of NeuroD and DCX mRNA transcripts in the brain of high-CO<sub>2</sub> exposed three-spined stickleback, together with the lack of effects on mRNA levels in cinnamon anemonefish and spiny damselfish, indicate differences in coping mechanisms among fish in response to the predicted-future CO<sub>2</sub> level.
DOI: 10.6084/m9.figshare.5319463.v1
title: Data from Social learning in otters

description: This file contains the raw data used for all analyses
DOI: 10.6084/m9.figshare.5319523.v2
title: Leading indicators of mosquito-borne disease elimination

description: Data and code to reproduce figures from O'Regan et al 2016. See "README.txt" for file details.<br>
DOI: 10.6084/m9.figshare.5319460.v1
title: NBDA code from Social learning in otters

description: This R script contains the code to run NBDAs on the smooth-coated otter data
DOI: 10.6084/m9.figshare.5319436
title: Supplementary Table S7 from Ancient whales did not filter feed with their teeth

description: The origin of baleen whales (Mysticeti), the largest animals on Earth, is closely tied to their signature filter-feeding strategy. Unlike their modern relatives, archaic whales possessed a well-developed, heterodont adult dentition. How these teeth were used, and what role their function and subsequent loss played in the emergence of filter feeding, is an enduring mystery. In particular, it has been suggested that elaborate tooth crowns may have enabled stem mysticetes to filter with their postcanine teeth in a manner analogous to living crabeater and leopard seals, thereby facilitating the transition to baleen-assisted filtering. Here we show that the teeth of archaic mysticetes are as sharp as those of terrestrial carnivorans, raptorial pinnipeds and archaeocetes, and thus were capable of capturing and processing prey. By contrast, the postcanine teeth of leopard and crabeater seals are markedly blunter, and clearly unsuited to raptorial feeding. Our results suggest that mysticetes never passed through a tooth-based filtration phase, and that the use of teeth and baleen in early whales was not functionally connected. Continued selection for tooth sharpness in archaic mysticetes is best explained by a feeding strategy that included both biting and suction, similar to that of most living pinnipeds and, probably, early toothed whales (Odontoceti).
DOI: 10.6084/m9.figshare.5319439
title: R input file from Social learning in otters

description: This is the R input file to use in association with the NBDA code to conduct the Network-Based Diffusion Analysis
DOI: 10.6084/m9.figshare.5319439.v1
title: R input file from Social learning in otters

description: This is the R input file to use in association with the NBDA code to conduct the Network-Based Diffusion Analysis
DOI: 10.6084/m9.figshare.5319436.v1
title: Supplementary Table S7 from Ancient whales did not filter feed with their teeth

description: The origin of baleen whales (Mysticeti), the largest animals on Earth, is closely tied to their signature filter-feeding strategy. Unlike their modern relatives, archaic whales possessed a well-developed, heterodont adult dentition. How these teeth were used, and what role their function and subsequent loss played in the emergence of filter feeding, is an enduring mystery. In particular, it has been suggested that elaborate tooth crowns may have enabled stem mysticetes to filter with their postcanine teeth in a manner analogous to living crabeater and leopard seals, thereby facilitating the transition to baleen-assisted filtering. Here we show that the teeth of archaic mysticetes are as sharp as those of terrestrial carnivorans, raptorial pinnipeds and archaeocetes, and thus were capable of capturing and processing prey. By contrast, the postcanine teeth of leopard and crabeater seals are markedly blunter, and clearly unsuited to raptorial feeding. Our results suggest that mysticetes never passed through a tooth-based filtration phase, and that the use of teeth and baleen in early whales was not functionally connected. Continued selection for tooth sharpness in archaic mysticetes is best explained by a feeding strategy that included both biting and suction, similar to that of most living pinnipeds and, probably, early toothed whales (Odontoceti).
DOI: 10.6084/m9.figshare.5319388
title: CERES - Meyers, Bryan, et al. Nature Genetics. 2017.

description: Datasets used in CERES publication.Meyers, Bryan, et al. Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics. 2017.<br><br>External data:<br>CCLE_copynumber_2013-12-03.seg.txt<br>CCLE copy number data downloaded from https://data.broadinstitute.org/ccle_legacy_data/dna_copy_number/CCLE_copynumber_2013-12-03.seg.txt<br>CCLE_RNAseq_081117.rpkm.gctCCLE gene expression data downloaded from https://data.broadinstitute.org/ccle/CCLE_RNAseq_081117.rpkm.gct<br><br>ccle2maf_081117.txtCCLE mutation data downloaded from https://data.broadinstitute.org/ccle/ccle2maf_081117.txt<br><br>Achilles_v2.20.2_GeneSolutions.gct<br>RNAi DEMETER gene dependencies downloaded from https://portals.broadinstitute.org/achilles/datasets/12/download/Achilles_v2.20.2_GeneSolutions.gct<br>CCDS.current.txtCCDS gene annotations downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/archive/15/CCDS.current.txt<br>c2.all.v6.0.symbols.gmt MSigDB genesets downloaded from http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/6.0/c2.all.v6.0.symbols.gmt<br><br>avana_rs2.txt and gecko_rs2.txtDoench-Root scores for sgRNAs provided by authors of Doench, et al. Nat. Biotechnol. 2016. <br> wang_pool_normalized.counts.txtDownloaded from supplement of Wang, et al. Cell. 2017. <br>