cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1471677.v1
title: Estrogen receptor alpha (ESR1) gene amplification is frequent in breast cancer. Subsequent Supplementary Video Clip S1+S2

description: <strong>Estrogen receptor alpha (ESR1) gene amplification is frequent in breast cancer. Subsequent Supplementary Material.</strong> Frederik Holst & Christian Ruiz The supplementary material refers to: Holst, F., Stahl, P.R., Ruiz, C., et al. Estrogen receptor alpha (ESR1) gene amplification s frequent in breast cancer. Nature Genetics 39, 655-660 (2007). Subsequent Supplementary Figures S1-S7 Illustration of the different Affymetrix 10K SNP array gene copy number data analysis methods and regarding segmented <em>ESR1</em> copy number profiles of 22 breast cancers. A photo documentation of ESR1 FISH analysis signal appearance (figures 5A-C + 7A-C) of tumors with <em>ESR1</em> amplification by SNP GeneChip analysis is added. DOI: http://dx.doi.org/10.6084/m9.figshare.1470035 Subsequent Supplementary Video Clips S1+S2 The video clips document FISH analysis as performed for results documented in regarding subsequent supplementary figures 5A-C + 7A-C. DOI: http://dx.doi.org/10.6084/m9.figshare.1471677 Subsequent Supplementary Optical Dataset S1 The optical dataset consists of 94 photographs documenting appearance of <em>ESR1</em> FISH analysis signals of 20 out of 22 tumors regarding SNP GeneChip analysis illustrated in subsequent supplementary figures S1-S3 and S4+S6. The 94 photographs are separated into 1-10 figures per tumor including up to three z-stacks per figure. DOI: http://dx.doi.org/10.6084/m9.figshare.1470130 <strong>Methods References</strong> Ruiz, C. Doctoral Thesis, Universität Basel (2006). Moelans, C.B., Holst, F., Hellwinkel, O., Simon, R. & van Diest, P.J. ESR1 Amplification in Breast Cancer by Optimized RNase FISH: Frequent but Low-Level and Heterogeneous. PLoS One 8, e84189 (2013). Holst, F. FISH Analysis of ESR1 Amplification in Breast Cancer - A Video Illustration. DOI: http://dx.doi.org/10.6084/m9.figshare.1471765 (2015).
DOI: 10.6084/m9.figshare.1471677.v3
title: Estrogen receptor alpha (ESR1) gene amplification is frequent in breast cancer. Subsequent Supplementary Video Clip S1+S2

description: <strong>Estrogen receptor alpha (<em>ESR1</em>) gene amplification is frequent in breast cancer. Subsequent Supplementary Material.</strong> Frederik Holst & Christian Ruiz The supplementary material refers to: Holst, F., Stahl, P.R., Ruiz, C., et al. Estrogen receptor alpha (<em>ESR1</em>) gene amplification s frequent in breast cancer. Nature Genetics 39, 655-660 (2007). Subsequent Supplementary Figures S1-S7 Illustration of the different Affymetrix 10K SNP array gene copy number data analysis methods and regarding segmented <em>ESR1</em> copy number profiles of 22 breast cancers. A photo documentation of ESR1 FISH analysis signal appearance (figures 5A-C + 7A-C) of tumors with <em>ESR1</em> amplification by SNP GeneChip analysis is added. DOI: http://dx.doi.org/10.6084/m9.figshare.1470035 Subsequent Supplementary Video Clips S1+S2 The video clips document FISH analysis as performed for results documented in regarding subsequent supplementary figures 5A-C + 7A-C. DOI: http://dx.doi.org/10.6084/m9.figshare.1471677 Subsequent Supplementary Optical Dataset S1 The optical dataset consists of 94 photographs documenting appearance of <em>ESR1</em> FISH analysis signals of 20 out of 22 tumors regarding SNP GeneChip analysis illustrated in subsequent supplementary figures S1-S3 and S4+S6. The 94 photographs are separated into 1-10 figures per tumor including up to three z-stacks per figure. DOI: http://dx.doi.org/10.6084/m9.figshare.1470130 <strong>Methods References</strong> Ruiz, C. Doctoral Thesis, Universität Basel (2006). Moelans, C.B., Holst, F., Hellwinkel, O., Simon, R. & van Diest, P.J. <em>ESR1</em> Amplification in Breast Cancer by Optimized RNase FISH: Frequent but Low-Level and Heterogeneous. PLoS One 8, e84189 (2013). Holst, F. FISH Analysis of <em>ESR1</em> Amplification in Breast Cancer - A Video Illustration. DOI: http://dx.doi.org/10.6084/m9.figshare.1471765 (2015).
DOI: 10.6084/m9.figshare.1471677.v2
title: Estrogen receptor alpha (ESR1) gene amplification is frequent in breast cancer. Subsequent Supplementary Video Clip S1+S2

description: <strong>Estrogen receptor alpha (<em>ESR1</em>) gene amplification is frequent in breast cancer. Subsequent Supplementary Material.</strong> Frederik Holst & Christian Ruiz The supplementary material refers to: Holst, F., Stahl, P.R., Ruiz, C., et al. Estrogen receptor alpha (<em>ESR1</em>) gene amplification s frequent in breast cancer. Nature Genetics 39, 655-660 (2007). Subsequent Supplementary Figures S1-S7 Illustration of the different Affymetrix 10K SNP array gene copy number data analysis methods and regarding segmented <em>ESR1</em> copy number profiles of 22 breast cancers. A photo documentation of ESR1 FISH analysis signal appearance (figures 5A-C + 7A-C) of tumors with <em>ESR1</em> amplification by SNP GeneChip analysis is added. DOI: http://dx.doi.org/10.6084/m9.figshare.1470035 Subsequent Supplementary Video Clips S1+S2 The video clips document FISH analysis as performed for results documented in regarding subsequent supplementary figures 5A-C + 7A-C. DOI: http://dx.doi.org/10.6084/m9.figshare.1471677 Subsequent Supplementary Optical Dataset S1 The optical dataset consists of 94 photographs documenting appearance of <em>ESR1</em> FISH analysis signals of 20 out of 22 tumors regarding SNP GeneChip analysis illustrated in subsequent supplementary figures S1-S3 and S4+S6. The 94 photographs are separated into 1-10 figures per tumor including up to three z-stacks per figure. DOI: http://dx.doi.org/10.6084/m9.figshare.1470130 <strong>Methods References</strong> Ruiz, C. Doctoral Thesis, Universität Basel (2006). Moelans, C.B., Holst, F., Hellwinkel, O., Simon, R. & van Diest, P.J. <em>ESR1</em> Amplification in Breast Cancer by Optimized RNase FISH: Frequent but Low-Level and Heterogeneous. PLoS One 8, e84189 (2013). Holst, F. FISH Analysis of <em>ESR1</em> Amplification in Breast Cancer - A Video Illustration. DOI: http://dx.doi.org/10.6084/m9.figshare.1471765 (2015).
DOI: 10.6084/m9.figshare.1471639
title: Examining the origin of European weather systems during changes in the NAO, ENSO, and the Solar cycle

description: A repository relating to a study of the how the origin of European synoptic types varies with extremes of ENSO, the NAO, stratospheric aerosols, and the Solar cycle. They study is published in the <b>Royal Society Open Science</b> journal, DOI: 10.1098/rsos.150320. http://rsos.royalsocietypublishing.org/content/3/2/150320#sec-13<b>Data Sources </b>Hess Brezowsky Großwetterlagen weather types, a subjective classification of synoptic-scale weather using meteorological sites across Germany, originally from Hess, Paul and Brezowsky, Helmuth, Großwetterlagen Europas 1881-1992. 4., vollständig neu bearbeitete Auﬂage, Ber. Dt. Wetterd. 113, 1993, 5.Sunspot data from the World Data Centre SILSO (http://sidc.be/silso/home), Royal Observatory of Belgium, Brussels.Stratospheric aerosol data from NASA (http://data.giss.nasa.gov/modelforce/strataer).MEI (ENSO) data from NOAA (http://www.esrl.noaa.gov/psd/enso/mei.ext/), credit Dr Klaus Wolter.NAO data from CRU (http://www.cru.uea.ac.uk/timo/datapages/naoi.htm/).
DOI: 10.6084/m9.figshare.1471638
title: Queens University Belfast APC Payments August 2014 - March 2015

description: This spreadsheet contains details of article processing charges (APCs) paid by Queens University Belfast during the period 1 August 2014 to 31 March 2015.
DOI: 10.6084/m9.figshare.1471648.v1
title: new fileset

description: Minimum-energy crossing points (MECP) between potential energy surfaces with different spin multiplicities are important in non-radiative relaxation of excited states, analysis of phosphorescent materials and for the study of "spin-forbidden" reactions. Harvey et al. described an algorithm that you can use to find MECP using any theory level, in J.N.Harvey, M.Aschi, H.Schwarz, W.Koch (1998) <br>The Singlet and Triplet State of Phenyl Cation. A Hybrid Approach for Locating Minimum Energy Crossing Points between Non-interacting Potential Energy Surfaces. Theor. Chem. Acc. (1998) 99, 95 Prof. Harvey kindly provided me with the code, which I have aapted for use with the output from the quantum-chemistry program Firefly (Alex Granovsky, Moscow State University, http://classic.chem.msu.su/gran/gamess/index.html) mecp requires output and punch <br>files from two calculations of the same system, with the same coordinates, but different<br> spin multiplicities. These files MUST be named as: First.out and First.dat (for the first spin multiplicity, i.e. that with the HIGHER energy )<br>Second.out and Second.dat (for the second spin multiplicity)<br><br><br>mecp produces several output files: results.txt (geometries, graidents, energies, etc...)<br>results.xyz (geometries in xyz format)<br>new_geom.txt (the next geometry in the MECP optimization)<br>new_grad.txt (computed gradient - output only when BFGS update is selected)<br>hessian.txt (computed hessian - output only when BFGS update is selected)<br>vec1.txt (orbitals for the first state, taken from First.dat)<br>vec2.txt (orbitals for the second state, taken from Second.dat)<br><br><br>new_geom.txt, vec1.txt and vec2.txt must be combined in order to build input files <br>(First.txt and Second,txt) for a new round of computation. The easiest way to do this<br> is to have all other input commands in separate files (e.g. First_temp.txt and Second_temp.txt), <br>and concatenate them as needed.<br><br><br><br><br><br><br>In the first paper I published using MECP (Silva & Ramos (2007), J. Phys. Chem. B,111, 12883-12887), I found that in my system the MECP <br>geometry in gas phase was quite different from the one in solution. It is therefore STRONGLY recommended that spin-forbidden reactions in solution be studied in the presence of implicit or explicit solvent models.<br><br><br> DISCLAIMER: The programs were built for my personal use. My programming skills are limited (to say the least) and I am sure that a good programmer would be able to make them much more user-friendly.
DOI: 10.6084/m9.figshare.1471629
title: Automated detection of foot contacts, aerial phases, and visibility of bird

description: These codes were written by Daniel Hasse and were used, in combination with other methods, to perform an automated large-scale study (over one million frames) on the fluctuations of the CoM’s mechanical energy in several bird species (quail, oystercatcher, northern lapwing, pigeon, and avocet) during treadmill locomotion. see Andrada, E. et al. Mixed gaits in small avian terrestrial locomotion. Sci. Rep. 5, 13636; doi: 10.1038/srep13636 (2015). for more information events.R includes: Touch-down detection: we found that when the pixel values of the leg of every frame are projected onto the x-axis, the obtained 1D-curve display at TD a maximal bimodality. We measured the bimodality value of the 1D-curve by comparing it to a normal distribution of same mean and variance using histogram intersection distance. Frames in which a TD event occurs are then found by identifying all local maxima of the bimodality score over all frames (Andrada et. al., Mixed gaits in avian locomotion, in review, Fig. 5). Aerial phase: for each frame of a trial, we computed the minimum distance between the lowest point of the legs and the bottom of the image. Afterwards, a threshold was used to classify each frame as "aerial phase" or "stance phase" based on its leg height. For each sequence, the threshold was estimated automatically in such a way that only frames in which the legs are substantially higher than the median leg height are classified as "aerial phase" (Andrada et. al., Mixed gaits in avian locomotion, in review. Supplementary Information, Fig. S1). visibility.R includes: Visibility: to account for cases in which the birds left the field of view, for every frame of each trial we computed the number of pixels in which the bird is visible ('bird-pixels'). % of congruity was computed, only when the measured number of bird-pixel during all frames of a stance phase was higher than 80% of the maximal computed number of bird-pixels of the complete trial.
DOI: 10.6084/m9.figshare.1471639.v3
title: Examining the origin of European weather systems during changes in the NAO, ENSO, and the Solar cycle

description: A repository relating to a study of the how the origin of European synoptic types varies with extremes of ENSO, the NAO, stratospheric aerosols, and the Solar cycle. They study is published in the <b>Royal Society Open Science</b> journal, DOI: 10.1098/rsos.150320. http://rsos.royalsocietypublishing.org/content/3/2/150320#sec-13<b>Data Sources </b>Hess Brezowsky Großwetterlagen weather types, a subjective classification of synoptic-scale weather using meteorological sites across Germany, originally from Hess, Paul and Brezowsky, Helmuth, Großwetterlagen Europas 1881-1992. 4., vollständig neu bearbeitete Auﬂage, Ber. Dt. Wetterd. 113, 1993, 5.Sunspot data from the World Data Centre SILSO (http://sidc.be/silso/home), Royal Observatory of Belgium, Brussels.Stratospheric aerosol data from NASA (http://data.giss.nasa.gov/modelforce/strataer).MEI (ENSO) data from NOAA (http://www.esrl.noaa.gov/psd/enso/mei.ext/), credit Dr Klaus Wolter.NAO data from CRU (http://www.cru.uea.ac.uk/timo/datapages/naoi.htm/).
DOI: 10.6084/m9.figshare.1471629.v1
title: Automated detection of foot contacts, aerial phases, and visibility of bird

description: These codes were written by Daniel Hasse and were used, in combination with other methods, to perform an automated large-scale study (over one million frames) on the fluctuations of the CoM’s mechanical energy in several bird species (quail, oystercatcher, northern lapwing, pigeon, and avocet) during treadmill locomotion. see Andrada, E. et al. Mixed gaits in small avian terrestrial locomotion. Sci. Rep. 5, 13636; doi: 10.1038/srep13636 (2015). for more information events.R includes: Touch-down detection: we found that when the pixel values of the leg of every frame are projected onto the x-axis, the obtained 1D-curve display at TD a maximal bimodality. We measured the bimodality value of the 1D-curve by comparing it to a normal distribution of same mean and variance using histogram intersection distance. Frames in which a TD event occurs are then found by identifying all local maxima of the bimodality score over all frames (Andrada et. al., Mixed gaits in avian locomotion, in review, Fig. 5). Aerial phase: for each frame of a trial, we computed the minimum distance between the lowest point of the legs and the bottom of the image. Afterwards, a threshold was used to classify each frame as "aerial phase" or "stance phase" based on its leg height. For each sequence, the threshold was estimated automatically in such a way that only frames in which the legs are substantially higher than the median leg height are classified as "aerial phase" (Andrada et. al., Mixed gaits in avian locomotion, in review. Supplementary Information, Fig. S1). visibility.R includes: Visibility: to account for cases in which the birds left the field of view, for every frame of each trial we computed the number of pixels in which the bird is visible ('bird-pixels'). % of congruity was computed, only when the measured number of bird-pixel during all frames of a stance phase was higher than 80% of the maximal computed number of bird-pixels of the complete trial.
DOI: 10.6084/m9.figshare.1471638.v2
title: Queens University Belfast APC Payments August 2014 - March 2015

description: This spreadsheet contains details of article processing charges (APCs) paid by Queens University Belfast during the period 1 August 2014 to 31 March 2015.
DOI: 10.6084/m9.figshare.1471639.v2
title: Does Europe's wind respond to either ENSO or the Solar cycle?

description: A repository relating to a study of European synoptic weather types.
DOI: 10.6084/m9.figshare.1471638.v1
title: Queens University Belfast APC Payments August 2014 - March 2015

description: This spreadsheet contains details of article processing charges (APCs) paid by Queens University Belfast during the period 1 August 2014 to 31 March 2015.
DOI: 10.6084/m9.figshare.1471586
title: Enduring Schooling : Against Noise, and in the Service of the Remix

description: Enduring Schooling : Against Noise, and in the Service of the Remix Nikolina Nedeljkov Candidate in the PhD Program in English The Graduate Center, The City University of New York The article was published in Genero: Journal of Feminist Theory and Cultural Studies. Eds. Katarina Lončarević, Marina Simić, and Daša Duhaček. Issue 18. Belgrade: Women’s Studies Center, 2014. 65-88. Print. It was also presented at “THE NEXUS”: First TC interdisciplinary studies conference in collaboration with Cultural Studies, Film and Education Research Academy, and Cultural Formations, Teachers College, Columbia University (10/2013).
DOI: 10.6084/m9.figshare.1471586.v1
title: Enduring Schooling : Against Noise, and in the Service of the Remix

description: Enduring Schooling : Against Noise, and in the Service of the Remix Nikolina Nedeljkov Candidate in the PhD Program in English The Graduate Center, The City University of New York The article was published in Genero: Journal of Feminist Theory and Cultural Studies. Eds. Katarina Lončarević, Marina Simić, and Daša Duhaček. Issue 18. Belgrade: Women’s Studies Center, 2014. 65-88. Print. It was also presented at “THE NEXUS”: First TC interdisciplinary studies conference in collaboration with Cultural Studies, Film and Education Research Academy, and Cultural Formations, Teachers College, Columbia University (10/2013).
DOI: 10.6084/m9.figshare.1471586.v3
title: Enduring Schooling : Against Noise, and in the Service of the Remix

description: Enduring Schooling : Against Noise, and in the Service of the Remix Nikolina Nedeljkov Candidate in the PhD Program in English The Graduate Center, The City University of New York The article was published in Genero: Journal of Feminist Theory and Cultural Studies. Eds. Katarina Lončarević, Marina Simić, and Daša Duhaček. Issue 18. Belgrade: Women’s Studies Center, 2014. 65-88. Print. It was also presented at “THE NEXUS”: First TC interdisciplinary studies conference in collaboration with Cultural Studies, Film and Education Research Academy, and Cultural Formations, Teachers College, Columbia University (10/2013).
DOI: 10.6084/m9.figshare.1470182
title: Orchestration Workbench Learner Survey

description: A learner survey to elicit feedback on the use of a prototype orchestration workbench within the classroom.
DOI: 10.6084/m9.figshare.1470180
title: Evolution 2015 tweets

description: The list of tweets with the hashtag #evol2015 retrieved on July 1st using Twitter's API.
DOI: 10.6084/m9.figshare.1470182.v1
title: Orchestration Workbench Learner Survey

description: A learner survey to elicit feedback on the use of a prototype orchestration workbench within the classroom.
DOI: 10.6084/m9.figshare.1470180.v1
title: Evolution 2015 tweets

description: The list of tweets with the hashtag #evol2015 retrieved on July 1st using Twitter's API.
DOI: 10.6084/m9.figshare.1470178
title: Brook Trout Distribution, Genetics, and Population Characteristics in the Driftless Area of Minnesota

description: The Driftless Area in southeastern Minnesota is on the southwestern edge of the native range of Brook Trout <i>Salvelinus fontinalis</i>. It was assumed that native Brook Trout were extirpated from this region in the early 1900s due to degraded stream conditions and stockings of eastern-origin Brook Trout and European Brown Trout <i>Salmo trutta</i>. Our objectives were to examine Brook Trout populations in the region to determine their spatial and genetic distribution and quantify population characteristics. Information on presence or absence of Brook Trout was gathered by electrofishing 174 streams in southeastern Minnesota. Brook Trout were present in 68% of coldwater streams compared with only in 3% in the early 1970s. The increase is likely due to increasing stream discharge throughout the Driftless Area, enabling recolonization or successful establishment of stocked populations. Streams with higher base flow discharge also had higher abundance, larger size at maturity, and larger Brook Trout present. Genetic data on 74 populations were analyzed to characterize genetic variation within populations, assess genetic structure among populations, and determine possible origins. Numerous populations were not associated with known hatchery sources but were primarily composed of geographic groupings that could represent remnant lineages. Although population characteristics were similar among genetic origins, potentially remnant populations should be given conservation priority because they have proven their ability to sustain themselves in this region. Management actions that emphasize maintaining or increasing stream base flows throughout the region will likely enhance remnant Brook Trout populations in the Driftless Area.Received July 25, 2014; accepted March 17, 2015
DOI: 10.6084/m9.figshare.1470178.v2
title: Brook Trout Distribution, Genetics, and Population Characteristics in the Driftless Area of Minnesota

description: The Driftless Area in southeastern Minnesota is on the southwestern edge of the native range of Brook Trout <i>Salvelinus fontinalis</i>. It was assumed that native Brook Trout were extirpated from this region in the early 1900s due to degraded stream conditions and stockings of eastern-origin Brook Trout and European Brown Trout <i>Salmo trutta</i>. Our objectives were to examine Brook Trout populations in the region to determine their spatial and genetic distribution and quantify population characteristics. Information on presence or absence of Brook Trout was gathered by electrofishing 174 streams in southeastern Minnesota. Brook Trout were present in 68% of coldwater streams compared with only in 3% in the early 1970s. The increase is likely due to increasing stream discharge throughout the Driftless Area, enabling recolonization or successful establishment of stocked populations. Streams with higher base flow discharge also had higher abundance, larger size at maturity, and larger Brook Trout present. Genetic data on 74 populations were analyzed to characterize genetic variation within populations, assess genetic structure among populations, and determine possible origins. Numerous populations were not associated with known hatchery sources but were primarily composed of geographic groupings that could represent remnant lineages. Although population characteristics were similar among genetic origins, potentially remnant populations should be given conservation priority because they have proven their ability to sustain themselves in this region. Management actions that emphasize maintaining or increasing stream base flows throughout the region will likely enhance remnant Brook Trout populations in the Driftless Area.Received July 25, 2014; accepted March 17, 2015