cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.706329.v1
title: Virtual Proteomics: Inferring global protein activity profiles by network based analysis of gene expression signatures

description: This file contains all the normalized datasets and R-scripts used in the "Virtual Proteomics: Inferring global protein activity profiles<br>by network based analysis of gene expression signatures" manuscript by Mariano J. Alvarez, Yao Shen, B. Belinda Ding, B. Hilda Ye and Andrea Califano.
DOI: 10.6084/m9.figshare.706347.v2
title: Extinction risk and evolution of a quantitative trait in a variable environment with increasing frequency of extreme events

description: Data and code for "Extinction risk and evolution of a quantitative trait in a variable environment with increasing frequency of extreme events" ######### the file ext.RDS can be loaded in R by typing ext.df = readRDS("ext.RDS") after having moved the file to you current directory ######## In the data set ext.RDS, I included the following variables and outcomes of simulations: sel - strength of selection cat.freq - probability of occurrence of point extremes pop.ext10.rand - mean population size in the "sampling window" addvar.mean.10.rand. - mean additive genetic variance in the "sampling window" meanopt - directional trend mut - mutation amplitude mean.pheno - mean phenotype at the end of simulation time (interesting for replicates in which ext = 1) cat.bef - number of point extremes in the five years before extinction (interesting for replicates in which ext = 1) ext_year - extinction time (299 for replicates that persisted up to the end of simulation time) ext - extinct (1) or not (0) ############# For some of the analyses and plots in Vincenzi Point Extremes.r, the full dataset is required Please download sum.ris1.RDS and sum.ris2.RDS and move them to the current directory of R Then: sum.ris1 = readRDS("sum.ris1.RDS") sum.ris2 = readRDS("sum.ris2.RDS") sum.ris = c(sum.ris1,sum.ris2) rm(list=c("sum.ris1","sum.ris2")) The list sum.ris contains some of the measured variables for all the 25 600 replicates. In particular: extinct - pop going extinct or not<br>addvar - additive genetic variance at each time step<br>phenvar - phenotypic variance at each time step<br>yearextinct - year of extinction (299 if not extinct)<br>phenomean - phenotypic mean at each time step<br>sdopt - increase in variability of the optimum<br>meanopt - directional trend<br>selstrength - strength of selection<br>mutalfa - mutation amplitude<br>fitness.mean - mean fitness at each time step<br>optimum - optimum at each time step<br>popsize.post - population size after mortality at each time step Please write to simon.vincenz@gmail.com in the case help or clarifications are needed
DOI: 10.6084/m9.figshare.705877
title: Body cross-section of the flying snake Chrysopelea paradisi

description: This file bundle contains the geometry of the body cross-section of a flying snake Chrysopelea paradisi, in its flying configuration. We provide the coordinates of the boundary, a gnuplot script to plot the cross-section and a PDF of the output plot. The snake geometry was used in the CFD analysis of the flying snake using the cuIBM code for incompressible Navier-Stokes. The results are part of a publication recently submitted for peer-review, of which the preprint can be found at: http://arxiv.org/abs/1309.2969 The README file explains how to run the script to plot the cross-section geometry and gives reference to the other file bundles for our paper, titled "Lift and Wakes of Flying Snakes." The geometry used in this dataset and plot were obtained previously by J. J. Socha, and appeared in: "Gliding Flight in Chrysopelea: Turning a snake into a wing", J. J. Socha, Integrative and Comparative Biology, Vol. 51(6): 969–982 (2011).
DOI: 10.6084/m9.figshare.705883
title: Lift and drag coefficient versus angle of attack for a flying snake cross-section

description: Plots of the lift coefficient and drag coefficient of a flying snake cross-section, obtained from two-dimensional simulations using an immersed boundary method (cuIBM). We provide PDF files of the final plots, as they will appear in our paper "Lift and Wakes of Flying Snakes," submitted for peer review. The preprint of the paper is found at: http://arxiv.org/abs/1309.2969 The file bundle also includes the data set and the plotting scripts. The README file explains how to run the plotting scripts, as well as describing other file bundles that are released as supplementary materials for our paper. The data and figures are here shared under CC-BY, and will be thus referenced in the Figure captions in the paper.
DOI: 10.6084/m9.figshare.705863
title: "Insectivore" mammal skulls, dorsal view

description: Photographs of dorsal views of "insectivore" mammal skulls (Afrosoricida, Erinaceomorpha, Soricomorpha and Notoryctemorphia) from the American Museum of Natural History (AMNH) and the Smithsonian Institute (SI). I can provide a list of the species identities corresponding to each specimen ID number. Alternatively, species may be identified by searching the online museum databases for the specimen ID number. I photographed the skulls on a flat plane relative to the camera and the scale bar has 1mm as the smallest demarcation. Images are grey scale TIF files labelled with the museum specimen ID number, the specimen identity (<strong>cr</strong>anial) and view (<strong>d</strong>orsa<strong>l</strong>) along with the date that I took the photograph. Some specimens were photographed three times, re-positioning the skull in between each picture. They are labelled with the same museum specimen number and then _1A, _2A and _3A to indicate that they are replicate pictures of the same skull. These photos form part of my research on morphological diversity in tenrecs compared to other mammal groups
DOI: 10.6084/m9.figshare.705892.v2
title: Tracking Software Contributions

description: The challenges and enablers of tracking software contributions as a research output.
DOI: 10.6084/m9.figshare.705877.v1
title: Body cross-section of the flying snake Chrysopelea paradisi

description: This file bundle contains the geometry of the body cross-section of a flying snake Chrysopelea paradisi, in its flying configuration. We provide the coordinates of the boundary, a gnuplot script to plot the cross-section and a PDF of the output plot. The snake geometry was used in the CFD analysis of the flying snake using the cuIBM code for incompressible Navier-Stokes. The results are part of a publication recently submitted for peer-review, of which the preprint can be found at: http://arxiv.org/abs/1309.2969 The README file explains how to run the script to plot the cross-section geometry and gives reference to the other file bundles for our paper, titled "Lift and Wakes of Flying Snakes." The geometry used in this dataset and plot were obtained previously by J. J. Socha, and appeared in: "Gliding Flight in Chrysopelea: Turning a snake into a wing", J. J. Socha, Integrative and Comparative Biology, Vol. 51(6): 969–982 (2011).
DOI: 10.6084/m9.figshare.705863.v2
title: "Insectivore" mammal skulls, dorsal view

description: Photographs of dorsal views of "insectivore" mammal skulls (Afrosoricida, Erinaceomorpha, Soricomorpha and Notoryctemorphia) from the American Museum of Natural History (AMNH) and the Smithsonian Institute (SI). I can provide a list of the species identities corresponding to each specimen ID number. Alternatively, species may be identified by searching the online museum databases for the specimen ID number. I photographed the skulls on a flat plane relative to the camera and the scale bar has 1mm as the smallest demarcation. Images are grey scale TIF files labelled with the museum specimen ID number, the specimen identity (<strong>cr</strong>anial) and view (<strong>d</strong>orsa<strong>l</strong>) along with the date that I took the photograph. Some specimens were photographed three times, re-positioning the skull in between each picture. They are labelled with the same museum specimen number and then _1A, _2A and _3A to indicate that they are replicate pictures of the same skull. These photos form part of my PhD research on morphological convergent evolution among tenrecs and other "insectivore" mammal species.
DOI: 10.6084/m9.figshare.705883.v1
title: Lift and drag coefficient versus angle of attack for a flying snake cross-section

description: Plots of the lift coefficient and drag coefficient of a flying snake cross-section, obtained from two-dimensional simulations using an immersed boundary method (cuIBM). We provide PDF files of the final plots, as they will appear in our paper "Lift and Wakes of Flying Snakes," submitted for peer review. The preprint of the paper is found at: http://arxiv.org/abs/1309.2969 The file bundle also includes the data set and the plotting scripts. The README file explains how to run the plotting scripts, as well as describing other file bundles that are released as supplementary materials for our paper. The data and figures are here shared under CC-BY, and will be thus referenced in the Figure captions in the paper.
DOI: 10.6084/m9.figshare.705863.v3
title: "Insectivore" mammal skulls, dorsal view

description: Photographs of dorsal views of "insectivore" mammal skulls (Afrosoricida, Erinaceomorpha, Soricomorpha and Notoryctemorphia) from the American Museum of Natural History (AMNH) and the Smithsonian Institute (SI). I can provide a list of the species identities corresponding to each specimen ID number. Alternatively, species may be identified by searching the online museum databases for the specimen ID number. I photographed the skulls on a flat plane relative to the camera and the scale bar has 1mm as the smallest demarcation. Images are grey scale TIF files labelled with the museum specimen ID number, the specimen identity (<strong>cr</strong>anial) and view (<strong>d</strong>orsa<strong>l</strong>) along with the date that I took the photograph. Some specimens were photographed three times, re-positioning the skull in between each picture. They are labelled with the same museum specimen number and then _1A, _2A and _3A to indicate that they are replicate pictures of the same skull. These photos form part of my PhD research on morphological convergent evolution among tenrecs and other "insectivore" mammal species.
DOI: 10.6084/m9.figshare.705830.v1
title: Gaussian Job Archive for C8H10

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.705831.v1
title: Gaussian Job Archive for C8H10

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.705842.v1
title: Dynamics of Neuronal Models in Online Neuroevolution of Robotic Controllers

description: <strong>Dynamics of Neuronal Models in Online Neuroevolution of Robotic Controllers</strong>, by Fernando Silva, Luís Correia, and Anders Lyhne Christensen. To appear in: EPIA 2013. 16th Portuguese Conference on Artificial Intelligence. Springer-Verlag. <strong>Abstract: </strong>In this paper, we investigate the dynamics of different neuronal models on online neuroevolution of robotic controllers in multirobot systems.<br>We compare the performance and robustness of neural network-based controllers using summing neurons, multiplicative neurons, and a combination of the two.<br>We perform a series of simulation-based experiments in which a group of e-puck-like robots must perform an integrated navigation and obstacle avoidance task in environments of different complexity.<br>We show that multiplicative controllers and hybrid controllers maintain stable performance levels across tasks of different complexity.<br>We show that: (i)~summing controllers evolve diverse behaviours that vary qualitatively during task-execution, and that (ii)~multiplicative controllers lead to less diverse and more static behaviours that are maintained despite environmental changes.<br>Complementary, hybrid controllers exhibit both behavioural characteristics, and display superior generalisation capabilities in simple and complex tasks. <strong>Description of the dataset:</strong> The dataset contains a number of figures and .gv files that represent artificial neural networks used as evolved robotic controllers. For a given experimental setup (see the paper), each controller evolved is named as "S.R", where S represents the sample/run in which the controller was evolved, and R is the id of the robot. Networks are described in the following manner: - Ri denotes sensor i for robot detection, with i in [1:8] - Wi denotes sensor i for wall/obstacle detection, with i in [1:8] - E denotes the virtual energy level sensor - Hx denotes the hidden neuron H with id x - LW represents the output neuron that controls the robot's left wheel - RW represents the output neuron that controls the robot's right wheel
DOI: 10.6084/m9.figshare.705163
title: chc1 untreated vs 3-minute Zoloft treatment

description: Transmission electron microscopy dataset on <em>chc1</em> (clathrin heavy chain) mutant cells treated for 3 minutes with the antidepressant sertraline/Zoloft vs control cells.
DOI: 10.6084/m9.figshare.705842.v2
title: Dynamics of Neuronal Models in Online Neuroevolution of Robotic Controllers

description: <strong>Dynamics of Neuronal Models in Online Neuroevolution of Robotic Controllers</strong>, by Fernando Silva, Luís Correia, and Anders Lyhne Christensen. To appear in: EPIA 2013. 16th Portuguese Conference on Artificial Intelligence. Springer-Verlag. <strong>Abstract: </strong>In this paper, we investigate the dynamics of different neuronal models on online neuroevolution of robotic controllers in multirobot systems.<br>We compare the performance and robustness of neural network-based controllers using summing neurons, multiplicative neurons, and a combination of the two.<br>We perform a series of simulation-based experiments in which a group of e-puck-like robots must perform an integrated navigation and obstacle avoidance task in environments of different complexity.<br>We show that multiplicative controllers and hybrid controllers maintain stable performance levels across tasks of different complexity.<br>We show that: (i)~summing controllers evolve diverse behaviours that vary qualitatively during task-execution, and that (ii)~multiplicative controllers lead to less diverse and more static behaviours that are maintained despite environmental changes.<br>Complementary, hybrid controllers exhibit both behavioural characteristics, and display superior generalisation capabilities in simple and complex tasks. <strong>Description of the dataset:</strong> The dataset contains a number of figures and .gv files that represent artificial neural networks used as evolved robotic controllers. For a given experimental setup (see the paper), each controller evolved is named as "S.R", where S represents the sample/run in which the controller was evolved, and R is the id of the robot. Networks are described in the following manner: - Ri denotes sensor i for robot detection, with i in [1:8] - Wi denotes sensor i for wall/obstacle detection, with i in [1:8] - E denotes the virtual energy level sensor - Hx denotes the hidden neuron H with id x - LW represents the output neuron that controls the robot's left wheel - RW represents the output neuron that controls the robot's right wheel
DOI: 10.6084/m9.figshare.705163.v1
title: chc1 untreated vs 3-minute Zoloft treatment

description: Transmission electron microscopy dataset on <em>chc1</em> (clathrin heavy chain) mutant cells treated for 3 minutes with the antidepressant sertraline/Zoloft vs control cells.
DOI: 10.6084/m9.figshare.705167.v1
title: Banca pentru Reconstrucţie şi Dezvoltare

description: BERD susţine dezvoltarea economică a ţărilor din centrul şi estul Europei.
DOI: 10.6084/m9.figshare.705154
title: Data sets and query script used in identifying FAM129B as a putative regulator of Wnt/β-catenin signaling using large-scale siRNA screen integrated with phosphoproteomic and bioinformatic analyses.

description: Data File 1. Results of a large-scale siRNA screen for Wnt/β-catenin signaling in HT1080 B/R cells. Column a contains the siRNA probe ID. Column b contains the ENTREZ gene ID. Coulnm D shows median percent enhancement or inhibition of BAR reporter relative to control siRNA. All data are normalized to constitutively expressed renilla. P-value calculated using student's T. if, for a given gene, all siRNA shows a twofold change in med(normFFluc) and a -logP &lt;=2, that gene is classified as a hit. Data File 2. Melanoma-associated genes identified by an NCBI gene search. Data File 3a. Protein target overlaps between the siRNA screen and the phosphoproteomic dataset. Column A contains the official gene symbol for protein target of associated peptide. If, for a given gene, all siRNA shows a twofold change in med(normFFluc) and a -logP &lt;=2, that gene is classified as a hit. Phosphoproteomic Hit defined as a 1.7-fold change in phosphosite intensity as described in Old WM et al. 2009. Gene previously associated with melanoma as identified by biopython code described in the Query Script. % control siRNA = median percent enhancement or inhibition of BAR reporter relative to control siRNA. All data are normalized to a viability marker. Data File 3b. Protein target overlaps between siRNA dataset and the bioinformatic enrichment. If, for a given gene, all siRNA shows a twofold change in med(normFFluc) and a -logP &lt;=2, that gene is classified as a hit. median percent enhancement or inhibition of BAR reporter relative to control siRNA. All data are normalized to constitutively expressed renilla. Query Script. Biopython script for identifying disease- or query-associated geneIDs.
DOI: 10.6084/m9.figshare.705153
title: Data showing positive regulation of Wnt/β-catenin signal transduction by FAM129B siRNA using transcriptional reporter assay, target gene expression, and apoptosis assay

description: Data for Figure 2b. Measured β-catenin dependent firefly: constitutive renilla ratios for HT1080, A375, and A2058 reporter cells treated with the indicated conditions. Data for Figure 2c: Quantitative RT-PCR of β-catenin dependent Axin2 mRNA and housekeeping actin mRNA for HT1080, A375, and A2058 cells treated with the indicated conditions. Data for Figure 3a. Measured β-catenin dependent firefly: constitutive renilla ratios for A375 reporter cells treated with a dose curve of WNT3A or a single dose of WNT3A. Data for Figure 3b. Measured NFκB dependent firefly: constitutive renilla ratios for A375 reporter cells treated with a dose curve of TNFalpha or a single dose of TNFα . Data for Figure 4b. Quantitation of DAPI and TUNEL positive nuclei from A375 cells treated with WNT3A, PLX4720, and the control, FAM129B, or CTNNB1 siRNA.
DOI: 10.6084/m9.figshare.705154.v1
title: Data sets and query script used in identifying FAM129B as a putative regulator of Wnt/β-catenin signaling using large-scale siRNA screen integrated with phosphoproteomic and bioinformatic analyses.

description: Data File 1. Results of a large-scale siRNA screen for Wnt/β-catenin signaling in HT1080 B/R cells. Column a contains the siRNA probe ID. Column b contains the ENTREZ gene ID. Coulnm D shows median percent enhancement or inhibition of BAR reporter relative to control siRNA. All data are normalized to constitutively expressed renilla. P-value calculated using student's T. if, for a given gene, all siRNA shows a twofold change in med(normFFluc) and a -logP &lt;=2, that gene is classified as a hit. Data File 2. Melanoma-associated genes identified by an NCBI gene search. Data File 3a. Protein target overlaps between the siRNA screen and the phosphoproteomic dataset. Column A contains the official gene symbol for protein target of associated peptide. If, for a given gene, all siRNA shows a twofold change in med(normFFluc) and a -logP &lt;=2, that gene is classified as a hit. Phosphoproteomic Hit defined as a 1.7-fold change in phosphosite intensity as described in Old WM et al. 2009. Gene previously associated with melanoma as identified by biopython code described in the Query Script. % control siRNA = median percent enhancement or inhibition of BAR reporter relative to control siRNA. All data are normalized to a viability marker. Data File 3b. Protein target overlaps between siRNA dataset and the bioinformatic enrichment. If, for a given gene, all siRNA shows a twofold change in med(normFFluc) and a -logP &lt;=2, that gene is classified as a hit. median percent enhancement or inhibition of BAR reporter relative to control siRNA. All data are normalized to constitutively expressed renilla. Query Script. Biopython script for identifying disease- or query-associated geneIDs.
DOI: 10.6084/m9.figshare.704996
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.704886
title: An electrophysiological approach to study the Drosophila larval heart

description: This poster was presented in the 45th Annual Drosophila Research Conference (2004) held in Washington DC.
DOI: 10.6084/m9.figshare.704886.v1
title: An electrophysiological approach to study the Drosophila larval heart

description: This poster was presented in the 45th Annual Drosophila Research Conference (2004) held in Washington DC.
DOI: 10.6084/m9.figshare.704995.v1
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.704996.v1
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.704844.v1
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.704838
title: Navigating the statistical maze - ASM poster

description: Poster presented at the ASM in Denver, Colorado in May 2013, describing the Biostat Decision Tool, a user-friendly guide to help biologists analyse and present their data.
DOI: 10.6084/m9.figshare.704840
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.704841.v1
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.704838.v1
title: Navigating the statistical maze - ASM poster

description: Poster presented at the ASM in Denver, Colorado in May 2013, describing the Biostat Decision Tool, a user-friendly guide to help biologists analyse and present their data.
DOI: 10.6084/m9.figshare.704840.v1
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.704833.v1
title: Gaussian Job Archive for C10H14

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.704842.v1
title: Reproductive biology of sub- and low-arctic mosquitoes of the genus Ochlerotatus (Diptera: Culicidae)1

description: Incidence of facultative and obligate autogeny in species of mosquitoes of the genus <em>Ochlerotatus</em> at Baker Lake, Nunavut and Churchill, Manitoba, Canada.