cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1409463
title: Visual processing of informative multipoint correlations arises primarily in V2

description: Supplementary files for eLife article "Visual processing of informative multipoint correlations arises primarily in V2" (2015, eLife 4:e06604, doi: 10.7554/eLife.06604). <strong>Source code 1. </strong>Custom software written in MATLAB. All computations were done with custom software written in MATLAB (The MathWorks, Inc. MA). In Source code 1, we provide the source code we used for smoothed firing rate computations, computation of the MCDI, statistics, and plotting. Note, though, that much of this code is tied to the specifics of our file formats, naming conventions, etc., and that locfit, used for smoothed firing rate computations, should be downloaded from http://cran.r-project.org/web/packages/locfit/index.html, and compiled for the target system. As mentioned above, spike-sorting was done with Klustakwik and Klusters; these packages can be downloaded from http://klustakwik.sourceforge.net/ (Klustakwik) and http://neurosuite.sourceforge.net/ (Klusters), and then compiled for the target system.
DOI: 10.6084/m9.figshare.1409464.v1
title: GI interactions under the flood condition

description: A conceptual diagram of SuDS/GI functions under the flood condition
DOI: 10.6084/m9.figshare.1409470.v1
title: Human-Machine Interface based on Electrocutaneous Menu

description: Repository for the paper Gonzalez-Vargas J, Dosen S, Amsuess S, Yu W, Farina D. "Human-Machine Interface based on Electrocutaneous Menu" PLOS ONE.
DOI: 10.6084/m9.figshare.1409463.v1
title: Visual processing of informative multipoint correlations arises primarily in V2

description: Supplementary files for eLife article "Visual processing of informative multipoint correlations arises primarily in V2" (2015, eLife 4:e06604, doi: 10.7554/eLife.06604). <strong>Source code 1. </strong>Custom software written in MATLAB. All computations were done with custom software written in MATLAB (The MathWorks, Inc. MA). In Source code 1, we provide the source code we used for smoothed firing rate computations, computation of the MCDI, statistics, and plotting. Note, though, that much of this code is tied to the specifics of our file formats, naming conventions, etc., and that locfit, used for smoothed firing rate computations, should be downloaded from http://cran.r-project.org/web/packages/locfit/index.html, and compiled for the target system. As mentioned above, spike-sorting was done with Klustakwik and Klusters; these packages can be downloaded from http://klustakwik.sourceforge.net/ (Klustakwik) and http://neurosuite.sourceforge.net/ (Klusters), and then compiled for the target system.
DOI: 10.6084/m9.figshare.1409470.v3
title: Human-Machine Interface based on Electrocutaneous Menu

description: Repository for the paper Gonzalez-Vargas J, Dosen S, Amsuess S, Yu W, Farina D. "Human-Machine Interface based on Electrocutaneous Menu" PLOS ONE.
DOI: 10.6084/m9.figshare.1409447
title: Gaussian Job Archive for C14H22Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1409470.v2
title: Human-Machine Interface based on Electrocutaneous Menu

description: Repository for the paper Gonzalez-Vargas J, Dosen S, Amsuess S, Yu W, Farina D. "Human-Machine Interface based on Electrocutaneous Menu" PLOS ONE.
DOI: 10.6084/m9.figshare.1409447.v1
title: Gaussian Job Archive for C14H22Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1409460.v1
title: Estrogen Withdrawal, Increased Breast Cancer Risk and the KRAS-variant

description: The <i>KRAS</i>-variant is a biologically functional, microRNA binding site variant, which predicts increased cancer risk especially for women. Because external exposures, such as chemotherapy, differentially impact the effect of this mutation, we evaluated the association of estrogen exposures, breast cancer (BC) risk and tumor biology in women with the <i>KRAS-</i>variant. Women with BC (<i>n</i>=1712), the subset with the <i>KRAS-</i>variant (<i>n=</i>286) and <i>KRAS-</i>variant unaffected controls (<i>n</i>=80) were evaluated, and hormonal exposures, <i>KRAS-</i>variant status, and pathology were compared. The impact of estrogen withdrawal on transformation of isogenic normal breast cell lines with or without the <i>KRAS-</i>variant was studied. Finally, the association and presentation characteristics of the <i>KRAS-</i>variant and multiple primary breast cancer (MPBC) were evaluated. <i>KRAS-</i>variant BC patients were more likely to have ovarian removal pre-BC diagnosis than non-variant BC patients (p=0.033). In addition, <i>KRAS-</i>variant BC patients also appeared to have a lower estrogen state than <i>KRAS-</i>variant unaffected controls, with a lower BMI (p&lt;0.001). Finally, hormone replacement therapy (HRT) discontinuation in <i>KRAS-</i>variant patients was associated with a diagnosis of triple negative BC (p&lt;0.001). Biologically confirming our clinical findings, acute estrogen withdrawal led to oncogenic transformation in <i>KRAS-</i>variant positive isogenic cell lines. Finally, <i>KRAS-</i>variant BC patients had greater than an 11-fold increased risk of presenting with MPBC compared to non-variant patients (45.39% vs 6.78%, OR 11.44 [3.42-37.87], p&lt;0.001). Thus, estrogen withdrawal and a low estrogen state appear to increase BC risk and to predict aggressive tumor biology in women with the <i>KRAS-</i>variant, who are also significantly more likely to present with multiple primary breast cancer.
DOI: 10.6084/m9.figshare.1409445
title: Correction: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

description: Supplementary File for eLife correction article "Correction: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting" (2014, <em>eLife</em> <strong>3</strong>:e03198, doi: 10.7554/eLife.03198). <strong>Supplementary file 1.</strong> A summary of the changes to Figure 1-source data 5. The cells where the null hypothesis is not rejected (e.g. RT-PCR amplicon sequencing data does not disagree with mRNA-seq data) are shaded green. There are 49 instances where the null hy_spothesis was originally rejected but now is not, and 10 instances where the null hypothesis was not rejected originally but now is.
DOI: 10.6084/m9.figshare.1409460.v2
title: Estrogen withdrawal, increased breast cancer risk and the KRAS-variant

description: The <i>KRAS</i>-variant is a biologically functional, microRNA binding site variant, which predicts increased cancer risk especially for women. Because external exposures, such as chemotherapy, differentially impact the effect of this mutation, we evaluated the association of estrogen exposures, breast cancer (BC) risk and tumor biology in women with the <i>KRAS</i>-variant. Women with BC (<i>n</i> = 1712), the subset with the <i>KRAS</i>-variant (<i>n</i> = 286) and <i>KRAS</i>-variant unaffected controls (<i>n</i> = 80) were evaluated, and hormonal exposures, <i>KRAS</i>-variant status, and pathology were compared. The impact of estrogen withdrawal on transformation of isogenic normal breast cell lines with or without the <i>KRAS</i>-variant was studied. Finally, the association and presentation characteristics of the <i>KRAS</i>-variant and multiple primary breast cancer (MPBC) were evaluated. <i>KRAS</i>-variant BC patients were more likely to have ovarian removal pre-BC diagnosis than non-variant BC patients (p = 0.033). In addition, <i>KRAS</i>-variant BC patients also appeared to have a lower estrogen state than <i>KRAS</i>-variant unaffected controls, with a lower BMI (<i>P</i> &lt; 0.001). Finally, hormone replacement therapy (HRT) discontinuation in <i>KRAS</i>-variant patients was associated with a diagnosis of triple negative BC (<i>P</i> &lt; 0.001). Biologically confirming our clinical findings, acute estrogen withdrawal led to oncogenic transformation in <i>KRAS</i>-variant positive isogenic cell lines. Finally, <i>KRAS</i>-variant BC patients had greater than an 11-fold increased risk of presenting with MPBC compared to non-variant patients (45.39% vs 6.78%, OR 11.44 [3.42–37.87], <i>P</i> &lt; 0.001). Thus, estrogen withdrawal and a low estrogen state appear to increase BC risk and to predict aggressive tumor biology in women with the <i>KRAS</i>-variant, who are also significantly more likely to present with multiple primary breast cancer.
DOI: 10.6084/m9.figshare.1409445.v1
title: Correction: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

description: Supplementary File for eLife correction article "Correction: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting" (2014, <em>eLife</em> <strong>3</strong>:e03198, doi: 10.7554/eLife.03198). <strong>Supplementary file 1.</strong> A summary of the changes to Figure 1-source data 5. The cells where the null hypothesis is not rejected (e.g. RT-PCR amplicon sequencing data does not disagree with mRNA-seq data) are shaded green. There are 49 instances where the null hy_spothesis was originally rejected but now is not, and 10 instances where the null hypothesis was not rejected originally but now is.
DOI: 10.6084/m9.figshare.1409460
title: Estrogen withdrawal, increased breast cancer risk and the KRAS-variant

description: The <i>KRAS</i>-variant is a biologically functional, microRNA binding site variant, which predicts increased cancer risk especially for women. Because external exposures, such as chemotherapy, differentially impact the effect of this mutation, we evaluated the association of estrogen exposures, breast cancer (BC) risk and tumor biology in women with the <i>KRAS</i>-variant. Women with BC (<i>n</i> = 1712), the subset with the <i>KRAS</i>-variant (<i>n</i> = 286) and <i>KRAS</i>-variant unaffected controls (<i>n</i> = 80) were evaluated, and hormonal exposures, <i>KRAS</i>-variant status, and pathology were compared. The impact of estrogen withdrawal on transformation of isogenic normal breast cell lines with or without the <i>KRAS</i>-variant was studied. Finally, the association and presentation characteristics of the <i>KRAS</i>-variant and multiple primary breast cancer (MPBC) were evaluated. <i>KRAS</i>-variant BC patients were more likely to have ovarian removal pre-BC diagnosis than non-variant BC patients (p = 0.033). In addition, <i>KRAS</i>-variant BC patients also appeared to have a lower estrogen state than <i>KRAS</i>-variant unaffected controls, with a lower BMI (<i>P</i> &lt; 0.001). Finally, hormone replacement therapy (HRT) discontinuation in <i>KRAS</i>-variant patients was associated with a diagnosis of triple negative BC (<i>P</i> &lt; 0.001). Biologically confirming our clinical findings, acute estrogen withdrawal led to oncogenic transformation in <i>KRAS</i>-variant positive isogenic cell lines. Finally, <i>KRAS</i>-variant BC patients had greater than an 11-fold increased risk of presenting with MPBC compared to non-variant patients (45.39% vs 6.78%, OR 11.44 [3.42–37.87], <i>P</i> &lt; 0.001). Thus, estrogen withdrawal and a low estrogen state appear to increase BC risk and to predict aggressive tumor biology in women with the <i>KRAS</i>-variant, who are also significantly more likely to present with multiple primary breast cancer.
DOI: 10.6084/m9.figshare.1409460.v4
title: Estrogen withdrawal, increased breast cancer risk and the KRAS-variant

description: The <i>KRAS</i>-variant is a biologically functional, microRNA binding site variant, which predicts increased cancer risk especially for women. Because external exposures, such as chemotherapy, differentially impact the effect of this mutation, we evaluated the association of estrogen exposures, breast cancer (BC) risk and tumor biology in women with the <i>KRAS</i>-variant. Women with BC (<i>n</i> = 1712), the subset with the <i>KRAS</i>-variant (<i>n</i> = 286) and <i>KRAS</i>-variant unaffected controls (<i>n</i> = 80) were evaluated, and hormonal exposures, <i>KRAS</i>-variant status, and pathology were compared. The impact of estrogen withdrawal on transformation of isogenic normal breast cell lines with or without the <i>KRAS</i>-variant was studied. Finally, the association and presentation characteristics of the <i>KRAS</i>-variant and multiple primary breast cancer (MPBC) were evaluated. <i>KRAS</i>-variant BC patients were more likely to have ovarian removal pre-BC diagnosis than non-variant BC patients (p = 0.033). In addition, <i>KRAS</i>-variant BC patients also appeared to have a lower estrogen state than <i>KRAS</i>-variant unaffected controls, with a lower BMI (<i>P</i> &lt; 0.001). Finally, hormone replacement therapy (HRT) discontinuation in <i>KRAS</i>-variant patients was associated with a diagnosis of triple negative BC (<i>P</i> &lt; 0.001). Biologically confirming our clinical findings, acute estrogen withdrawal led to oncogenic transformation in <i>KRAS</i>-variant positive isogenic cell lines. Finally, <i>KRAS</i>-variant BC patients had greater than an 11-fold increased risk of presenting with MPBC compared to non-variant patients (45.39% vs 6.78%, OR 11.44 [3.42–37.87], <i>P</i> &lt; 0.001). Thus, estrogen withdrawal and a low estrogen state appear to increase BC risk and to predict aggressive tumor biology in women with the <i>KRAS</i>-variant, who are also significantly more likely to present with multiple primary breast cancer.
DOI: 10.6084/m9.figshare.1409432
title: WSCG 2015 dataset

description: WSCG 2015 dataset
DOI: 10.6084/m9.figshare.1409460.v3
title: Estrogen withdrawal, increased breast cancer risk and the KRAS-variant

description: The <i>KRAS</i>-variant is a biologically functional, microRNA binding site variant, which predicts increased cancer risk especially for women. Because external exposures, such as chemotherapy, differentially impact the effect of this mutation, we evaluated the association of estrogen exposures, breast cancer (BC) risk and tumor biology in women with the <i>KRAS</i>-variant. Women with BC (<i>n</i> = 1712), the subset with the <i>KRAS</i>-variant (<i>n</i> = 286) and <i>KRAS</i>-variant unaffected controls (<i>n</i> = 80) were evaluated, and hormonal exposures, <i>KRAS</i>-variant status, and pathology were compared. The impact of estrogen withdrawal on transformation of isogenic normal breast cell lines with or without the <i>KRAS</i>-variant was studied. Finally, the association and presentation characteristics of the <i>KRAS</i>-variant and multiple primary breast cancer (MPBC) were evaluated. <i>KRAS</i>-variant BC patients were more likely to have ovarian removal pre-BC diagnosis than non-variant BC patients (p = 0.033). In addition, <i>KRAS</i>-variant BC patients also appeared to have a lower estrogen state than <i>KRAS</i>-variant unaffected controls, with a lower BMI (<i>P</i> &lt; 0.001). Finally, hormone replacement therapy (HRT) discontinuation in <i>KRAS</i>-variant patients was associated with a diagnosis of triple negative BC (<i>P</i> &lt; 0.001). Biologically confirming our clinical findings, acute estrogen withdrawal led to oncogenic transformation in <i>KRAS</i>-variant positive isogenic cell lines. Finally, <i>KRAS</i>-variant BC patients had greater than an 11-fold increased risk of presenting with MPBC compared to non-variant patients (45.39% vs 6.78%, OR 11.44 [3.42–37.87], <i>P</i> &lt; 0.001). Thus, estrogen withdrawal and a low estrogen state appear to increase BC risk and to predict aggressive tumor biology in women with the <i>KRAS</i>-variant, who are also significantly more likely to present with multiple primary breast cancer.
DOI: 10.6084/m9.figshare.1409430
title: Gaussian Job Archive for C14H22Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1409432.v1
title: WSCG 2015 dataset

description: WSCG 2015 dataset
DOI: 10.6084/m9.figshare.1409428
title: Gaussian Job Archive for C14H22Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1409429
title: Gaussian Job Archive for C14H22Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1409427
title: Methods S2

description: A static HTML representation of the code that was used to create all the analyses in this study. <strong>nbviewer</strong>: http://goo.gl/KzFAvj
DOI: 10.6084/m9.figshare.1409428.v1
title: Gaussian Job Archive for C14H22Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1409429.v1
title: Gaussian Job Archive for C14H22Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1409424
title: Figure S1. Loci statistics boxplots for data derived from [1].

description: For each locus, the plots illustrate the distributions of (from top to bottom) per-position entropy, per-position gap score [4], per position conservation score [4], sequence length and GC content. 1. Kawahara AY, Breinholt JW. Phylogenomics provides strong evidence for relationships of butterflies and moths. Proc R Soc B. 2014;281: 20140970. 2. Robinson DF, Foulds LR. Comparison of phylogenetic trees. Math Biosci. 1981;53: 131–147. 3. Kuhner MK, Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol. 1994;11: 459–468. 4. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25: 1972–1973.
DOI: 10.6084/m9.figshare.1409426
title: ReproPhylo: an environment for reproducible phylogenomics

description: Methods S1 in nbviewer: http://goo.gl/KzFAvj The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system, and does not require user intervention or configuration because the it stores the experimental workflow as a single, serialized Python object that contains explicit provenance and environment information. This ‘single file’ approach ensures the persistence of provenance across iterations of the analysis with changes automatically, managed by the version control program Git. ReproPhylo produces an extensive human-readable report, and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 python module, and is easily installed as a Docker image, with an IPython Notebook GUI, or as a slimmer version in a Galaxy distribution.
DOI: 10.6084/m9.figshare.1409430.v1
title: Gaussian Job Archive for C14H22Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1409424.v1
title: Figure S1. Loci statistics boxplots for data derived from [1].

description: For each locus, the plots illustrate the distributions of (from top to bottom) per-position entropy, per-position gap score [4], per position conservation score [4], sequence length and GC content. 1. Kawahara AY, Breinholt JW. Phylogenomics provides strong evidence for relationships of butterflies and moths. Proc R Soc B. 2014;281: 20140970. 2. Robinson DF, Foulds LR. Comparison of phylogenetic trees. Math Biosci. 1981;53: 131–147. 3. Kuhner MK, Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol. 1994;11: 459–468. 4. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25: 1972–1973.
DOI: 10.6084/m9.figshare.1409426.v4
title: ReproPhylo: an environment for reproducible phylogenomics

description: Methods S1 in nbviewer: http://goo.gl/KzFAvj The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system, and does not require user intervention or configuration because the it stores the experimental workflow as a single, serialized Python object that contains explicit provenance and environment information. This ‘single file’ approach ensures the persistence of provenance across iterations of the analysis with changes automatically, managed by the version control program Git. ReproPhylo produces an extensive human-readable report, and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 python module, and is easily installed as a Docker image, with an IPython Notebook GUI, or as a slimmer version in a Galaxy distribution.
DOI: 10.6084/m9.figshare.1409427.v1
title: Methods S1

description: A static HTML representation of the code that was used to create all the analyses in this study. <strong>nbviewer</strong>: http://goo.gl/KzFAvj
DOI: 10.6084/m9.figshare.1409426.v5
title: ReproPhylo: an environment for reproducible phylogenomics

description: Methods S1 in nbviewer: http://goo.gl/KzFAvj The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system, and does not require user intervention or configuration because the it stores the experimental workflow as a single, serialized Python object that contains explicit provenance and environment information. This ‘single file’ approach ensures the persistence of provenance across iterations of the analysis with changes automatically, managed by the version control program Git. ReproPhylo produces an extensive human-readable report, and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 python module, and is easily installed as a Docker image, with an IPython Notebook GUI, or as a slimmer version in a Galaxy distribution.
DOI: 10.6084/m9.figshare.1409427.v2
title: Methods S1

description: A static HTML representation of the code that was used to create all the analyses in this study. <strong>nbviewer</strong>: http://goo.gl/KzFAvj
DOI: 10.6084/m9.figshare.1409427.v4
title: Methods S2

description: A static HTML representation of the code that was used to create all the analyses in this study. <strong>nbviewer</strong>: http://goo.gl/KzFAvj