cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.806849
title: Population Genomics Of Sussex Lhm Drosophila Melanogaster

description: Input data, code, output data, summary plots, and run logs for investigation of the population genetics of the Drosophila melanogaster Sussex LHM sample.

For output graphs, see popgen_plots.png

Input data are 'plink binary' format.

Code is a unix/linux shell script containing commands for Plink to perform population genetic tests.

The two R scripts contain i. a short command for making a subpopulation file, ii. commands for plotting the output data. Both are initated in the shell script.

Platform and version information are available in the log files. Other information available in the shell and R scripts.

Broad observations are that the allele frequency disibribution is normal except a few humps around MAF 0.2-0.3 in the autosomes.

Linkage disequilbrium, on average, levels-out after ~200bp but there can still be some at distances of 300Kb.

The population appears to be divided into four genetically distinct groups (on the IBD-PCA scatter plot), with Fst analysis indicating that this is caused by genetic variation around the centromeres. This is possibly caused by historic admixture, and low centromeric recombination.
description: {"references": ["Gilks WP et al (2016) Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample  F1000Research 2016, 5:2644 doi: 10.12688/f1000research.9912.3"]}
DOI: 10.5281/zenodo.806863
title: Pre-Processed B-Cell Receptor Amplicon Sequencing Data From Srr1842411

description: An example dataset containing B-cell receptor (BCR) gene sequences. This dataset is intended to be used for testing software tools developed to annotate (i.e. map Variable, Diversity and Joining segments) and perform clonal analysis of BCR sequencing data.

<strong>Sequencing:</strong>

Libraries prepared using 5'RACE from PBMCs of a healthy donor. Input molecules were tagged with unique molecular identifiers (UMIs). Sequencing was ran on MiSeq , 300+300bp reads.

<strong>Contents:</strong>

The dataset contains both raw sequencing reads and high-quality consensus sequences assembled using unique molecular tagging (UMI) approach. Consensus assembly corrects for sequencing errors and eliminates sequencing artifacts.


	age_ig_s7_R1.fastq.gz and age_ig_s7_R2.fastq.gz contain raw reads
	age_ig_s7_R1.t10.cf.fastq.gz and age_ig_s7_R2.t10.cf.fastq.gz contain consensus sequences


All files contain an UMI tag sequence in their header, in form UMI:NNNN:QQQQ where N is the base character and Q is the quality character (for assembled consensuses the total number of reads is given instead of Q string).

Note that consensus sequences were assembled using only raw sequences that correspond to UMI tags supported by at least 10 sequencing reads. That means that consensus sequence files contain a subset of all UMI tags found in raw sequences. Thus, if one wants to assess software performance on raw sequencing reads using assembled consensus sequences as a high-quality data standard, raw sequencing reads should be filtered to contain only those UMI tags that are present in consensus sequence file.

<strong>Citations:</strong>

The whole dataset was used to benchmark MiXCR software and was originally referenced in Bolotin DA, et al. MiXCR: software for comprehensive adaptive immunity profiling Nature methods 12(5):380-381, 2015.

Data pre-processing was carried out using MIGEC software, Shugay M et al. Towards error-free profiling of immune repertoires. Nature Methods 11(6):653-655, 2014.

<strong>Contributors:</strong>

The dataset was generated in Prof. Chudakov lab (Adaptive Immunity Group in Masaryk University, Brno and Genomics of Adaptive Immunity Lab in Institute of Bioorganic Chemistry, Moscow). Sample preparation and sequencing was performed by Dr. Olga Britanova and Dr. Maria Turchaninova. Raw sequencing reads were pre-processed and uploaded by Dr. Mikhail Shugay.
DOI: 10.5281/zenodo.806848
title: Population Genomics Of Sussex Lhm Drosophila Melanogaster

description: Input data, code, output data, summary plots, and run logs for investigation of the population genetics of the Drosophila melanogaster Sussex LHM sample.

For output graphs, see popgen_plots.png

Input data are 'plink binary' format.

Code is a unix/linux shell script containing commands for Plink to perform population genetic tests.

The two R scripts contain i. a short command for making a subpopulation file, ii. commands for plotting the output data. Both are initated in the shell script.

Platform and version information are available in the log files. Other information available in the shell and R scripts.

Broad observations are that the allele frequency disibribution is normal except a few humps around MAF 0.2-0.3 in the autosomes.

Linkage disequilbrium, on average, levels-out after ~200bp but there can still be some at distances of 300Kb.

The population appears to be divided into four genetically distinct groups (on the IBD-PCA scatter plot), with Fst analysis indicating that this is caused by genetic variation around the centromeres. This is possibly caused by historic admixture, and low centromeric recombination.
description: {"references": ["Gilks WP et al (2016) Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample  F1000Research 2016, 5:2644 doi: 10.12688/f1000research.9912.3"]}
DOI: 10.1285/i20398573v2n2p64
title: Title Page
DOI: 10.5281/zenodo.807748
title: Cmip5 P50 Analysis V1.0 For Tuna Species: Source Data

description: <strong>Model results and data used to make future projections of the effects of climate change on the physiology of tuna in the global ocean</strong>

-------------------------------------------------

<strong>Description:</strong>

Coupled Model Intercomparison Project Phase 5 (CMIP5) model results were downloaded from here:<br>
https://esgf-node.llnl.gov/search/cmip5/

World Ocean Atlas (WOA) 2009 data were downloaded from here:<br>
https://www.nodc.noaa.gov/OC5/WOA09/netcdf_data.html

The model results and data should only be used to reproduce the analysis described in this publication:

Mislan, K. A. S., C. A. Deutsch, R. W. Brill, J. P. Dunne, and J. L. Sarmiento. (2017) Projections of climate driven changes in tuna vertical habitat based on species-specific differences in blood oxygen affinity. Global Change Biology.

<strong>The Zenodo archive of the code is here:<br>
https://doi.org/10.5281/zenodo.808742</strong>

 

-------------------------------------------------

<strong>Instructions:</strong>

Download the tar.gz file, unzip, and put the folders in the data folder of the CMIP5_p50_tuna code.
DOI: 10.1285/i20398573v2n2p100
title: Joint programme Council of Europe / European Union "Pro- moting freedom, professionalism and pluralism of the media in the South Caucasus and Moldova"

description: While free and independent media, sometimes qualified as the "forth estate", is a pillar of civil society, the European Union (EU) is rather absent from media development in democratizing countries. In its Strategy Paper 2011-2013, the European Instrument for Democracy and Human Rights does not mention the media as an explicit objective. Despite the poor situation of media in the South Caucasus, the EU is quite discreet in this sector of democracy promotion within the Armenia, Azeri and Georgian civil societies. It co-funds with the Council of Europe the joint programme "Promoting freedom, professionalism and pluralism of the media in South Caucasus and Moldova", which started on January 1, 2011 and will run until December 31, 2012. The implementation of the programme is entirely under the responsibility of the Council of Europe, an organisation which lacks the EU institutional incentives to influence the governments in the South Caucasus. Can the Council of Europe / European Union Joint programme SC-MLD-Media II have any impact on the media situation in South Caucasus, or do the realities on the field prevent any efficient implementation?
DOI: 10.1285/i20398573v2n2p66
title: Index
DOI: 10.1285/i20398573v2n2p67
title: Continuity and change in national parties' strategies of adaptation to European integration

description: How have national parties adapted their strategies of competition and behaviour to use, handle, and manage the European issue in domestic political competition? This article outlines the principal elements of continuity and change in the ways national party organisations have strategically adapted to the increasing significance of European integration in West European party systems over the last twenty years. It contests the arguments of a gradual europeanisation and rising progress of euroscepticism. It shows that the likelihood of politicisation over European matters occurring has been very dependent on the arena and the context considered. Few changes have occurred regarding the consensual and relatively positive treatment of the European Union (EU) in national newspapers, the very limited saliency of EU-related debates in national electoral campaigns and the tendency of mainstream parties to converge rather than diverge on the ways they frame the EU. Conflicts over EU matters are not typical, nor are they inherently on the increase: they remain the exception rather than the rule.
DOI: 10.1285/i20398573v2n2p82
title: Democracy in Europe: a tale of two crises

description: This article addresses the issue of the relationship between 'the market' and democracy in the European Union from a critical political economy perspective. It argues that the way the European Union institutions and national governments are attempting to solve the current economic and financial problems of the Eurozone enhances the trend towards 'new constitutionalist' arrangement that were already present. A detailed analysis of the reforms is proposed, as well as an historical perspective on the relationship between 'the market' and democracy that has characterised Western political economies. The recent reforms of EU economic governance are thus seen as furthering the insulation of socio-economic policy-making from public's electoral accountability.
DOI: 10.1285/i20398573v2n2p97
title: European Union Monitoring Mission in Georgia (EUMM) - a redundant mission?
DOI: 10.5281/zenodo.807747
title: Cmip5 P50 Analysis V1.0 For Tuna Species: Source Data

description: <strong>Model results and data used to make future projections of the effects of climate change on the physiology of tuna in the global ocean</strong>

-------------------------------------------------

<strong>Description:</strong>

Coupled Model Intercomparison Project Phase 5 (CMIP5) model results were downloaded from here:<br>
https://esgf-node.llnl.gov/search/cmip5/

World Ocean Atlas (WOA) 2009 data were downloaded from here:<br>
https://www.nodc.noaa.gov/OC5/WOA09/netcdf_data.html

The model results and data should only be used to reproduce the analysis described in this publication:

Mislan, K. A. S., C. A. Deutsch, R. W. Brill, J. P. Dunne, and J. L. Sarmiento. (2017) Projections of climate driven changes in tuna vertical habitat based on species-specific differences in blood oxygen affinity. Global Change Biology.

<strong>The Zenodo archive of the code is here:<br>
https://doi.org/10.5281/zenodo.808742</strong>

 

-------------------------------------------------

<strong>Instructions:</strong>

Download the tar.gz file, unzip, and put the folders in the data folder of the CMIP5_p50_tuna code.
DOI: 10.1285/i20398573v2n2p103
title: The EU-Russia partnership: a new context

description: The EU–Russia summit that took place on June 4 in St Petersburg met expectations for two reasons. Firstly, expectations prior to the summit were low: nobody was under any illusion that the summit would result in a radical breakthrough. Secondly, the biannual EU–Russia summits tend to produce symbolic rather than practical outcomes.
DOI: 10.5281/zenodo.800529
title: Mri Raw Data: Se Measurement Of The Knee Of A Healthy Volunteer (8 Channel Coil)

description: SE measurement of the knee of a healthy volunteer Sequence parameters:

TR 1800ms<br>
TE 18ms<br>
Matrix Size 192x192<br>
In Plane Resolution 0.78mmx0.78mm<br>
Slice Thickness 2mm<br>
3T System<br>
8 channel knee coil<br>
Florian Knoll (florian.knoll@tugraz.at) Date: 2.2.2011

Acknowledgements to Tobias Block and Martin Uecker for their support with the in vivo radial spin echo data.
description: Supported by the Austrian Science Fund (FWF) under grant SFB F32 (SFB
"Mathematical Optimization and Applications in Biomedical Sciences").
description: {"references": ["Knoll, F., Clason, C., Bredies, K., Uecker, M. and Stollberger, R. (2012), Parallel imaging with nonlinear reconstruction using variational penalties. Magn. Reson. Med., 67: 34\u201341. doi:10.1002/mrm.22964", "Zhang, S.; Block, K.T.; Frahm, J. (2010), Magnetic resonance imaging in real time: advances using radial FLASH. Journal of Magnetic Resonance Imaging 31:101-109", "Uecker, M.; Zhang, S.; Frahm, J. (2010),\u00a0Nonlinear inverse reconstruction for real-time MRI of the human heart using undersampled radial FLASH. Magnetic Resonance in Medicine 63:1456-1462"]}
DOI: 10.5517/ccdc.csd.cc1nrf72
title: CCDC 1541854: Experimental Crystal Structure Determination

description: Related Article: Kai-Stephan Feichtner, Thorsten Scherpf, Viktoria H. Gessner|2018|Organometallics|37|645|doi:10.1021/acs.organomet.7b00254
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1nrf83
title: CCDC 1541855: Experimental Crystal Structure Determination

description: Related Article: Kai-Stephan Feichtner, Thorsten Scherpf, Viktoria H. Gessner|2018|Organometallics|37|645|doi:10.1021/acs.organomet.7b00254
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1nrf94
title: CCDC 1541856: Experimental Crystal Structure Determination

description: Related Article: Kai-Stephan Feichtner, Thorsten Scherpf, Viktoria H. Gessner|2018|Organometallics|37|645|doi:10.1021/acs.organomet.7b00254
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.14457/tu.the.2015.309
title: การศึกษาการใช้ประโยชน์ที่ดินที่เหมาะสม บริเวณอำเภอเมืองชลบุรี

description: คอนโดมิเนียม เดอะโอเชี่ยน ตั้งอยู่ใจกลางอำเภอเมืองชลบุรี และสามารถเข้าถึงได้ทางถนนสุขุมวิท พื้นที่โครงการมีขนาด 4-2-35 ไร่ มีทั้งหมด 916 ยูนิต จำนวน 42 ชั้น ราคาเริ่มตั้งแต่ยูนิตละ 3 ล้านถึง 10 ล้านบาท โปรเจคนี้มีความคุ้มค่าในการลงทุน มีมาตรฐานความเป็นอยู่ที่ดี มีความทันสมัยและหรูหรา นอกจากนี้ยังอยู่ใกล้แหล่งการค้า โรงพยาบาล โรงเรียน สถานที่ราชการ นิคมอุตสาหกรรมรอบๆโครงการระดับรายได้ครัวเรือนของลูกค้ากลุ่มเป้าหมายอยุ่ที่ 400,000 บาทต่อเดือน โดยกลุ่มลูกค้าเป้าหมายจะเป็นนักลงทุนทั้งไทยและต่างชาติ และผู้ประกอบการท้องถิ่นNet Present Value (NPV) ของโครงการอยู่ที่ 415,292,761.68 บาท และ Internal Rate of Return (IRR) อยู่ที่ 13.79% ซึ่งสูงกว่าที่คาดไว้ โดยผลลัพธ์นี้แสดงให้เห็นว่าโปรเจคนี้มีศักยภาพในการลงทุน ในแง่ของการตลาด การเงิน กฏหมาย และกายภาพ
DOI: 10.5281/zenodo.800528
title: Mri Raw Data: Se Measurement Of The Knee Of A Healthy Volunteer (8 Channel Coil)

description: SE measurement of the knee of a healthy volunteer Sequence parameters:

TR 1800ms<br>
TE 18ms<br>
Matrix Size 192x192<br>
In Plane Resolution 0.78mmx0.78mm<br>
Slice Thickness 2mm<br>
3T System<br>
8 channel knee coil<br>
Florian Knoll (florian.knoll@tugraz.at) Date: 2.2.2011

Acknowledgements to Tobias Block and Martin Uecker for their support with the in vivo radial spin echo data.
description: Supported by the Austrian Science Fund (FWF) under grant SFB F32 (SFB
"Mathematical Optimization and Applications in Biomedical Sciences").
description: {"references": ["Knoll, F., Clason, C., Bredies, K., Uecker, M. and Stollberger, R. (2012), Parallel imaging with nonlinear reconstruction using variational penalties. Magn. Reson. Med., 67: 34\u201341. doi:10.1002/mrm.22964", "Zhang, S.; Block, K.T.; Frahm, J. (2010), Magnetic resonance imaging in real time: advances using radial FLASH. Journal of Magnetic Resonance Imaging 31:101-109", "Uecker, M.; Zhang, S.; Frahm, J. (2010),\u00a0Nonlinear inverse reconstruction for real-time MRI of the human heart using undersampled radial FLASH. Magnetic Resonance in Medicine 63:1456-1462"]}
DOI: 10.5517/ccdc.csd.cc1p76pt
title: CCDC 1556066: Experimental Crystal Structure Determination

description: Related Article: Brian W. Skelton, Stephen G. Pyne|2017|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1p7479
title: CCDC 1555990: Experimental Crystal Structure Determination

description: Related Article: Brian W. Skelton, Stephen G. Pyne|2017|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1p79cl
title: CCDC 1556149: Experimental Crystal Structure Determination

description: Related Article: Marilyn M. Olmstead, Jimmy U. Franco|2017|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.14458/dpu.the.2006.72
title: การพยายามกระทำความผิด : ศึกษาเฉพาะหลักเกณฑ์การแบ่งแยกระหว่างการลงมือกระทำความผิดกับการตระเตรียมกระทำความผิด /
DOI: 10.14458/dpu.the.2006.73
title: การปรับเปลี่ยนความผิดลหุโทษที่ไม่มีลักษณะเป็นความผิดอาญาโดยแท้ เป็นความผิดต่อกฎระเบียบของสังคม : ศึกษาเฉพาะความผิดลหุโทษในประมวลกฎหมายอาญา /
DOI: 10.14458/dpu.the.2006.74
title: การประเมินสภาพแวดล้อมอุตสาหกรรมภาพยนตร์ไทย ในเขตกรุงเทพมหานคร /
DOI: 10.14458/dpu.the.2006.75
title: การประกันตัวในคดีอาญา : ศึกษาเฉพาะกรณีการประกันภัยอิสรภาพ /
DOI: 10.5281/zenodo.807041
title: Skyrmions At The Edge: Confinement Effects In Fe/Ir(111)

description: We have employed spin-polarized scanning tunneling microscopy and Monte-Carlo simulations to investigate the effect of lateral confinement onto the nanoskyrmion lattice in Fe/Ir(111). We find a strong coupling of one diagonal of the square magnetic unit cell to the close-packed edges of Fe nanostructures. In triangular islands this coupling in combination with the mismatching symmetries of the islands and of the square nanoskyrmion lattice leads to frustration and triple-domain states. In direct vicinity to ferromagnetic NiFe islands, the surrounding skyrmion lattice forms additional domains. In this case a side of the square magnetic unit cell prefers a parallel orientation to the ferromagnetic edge. These experimental findings can be reproduced and explained by Monte-Carlo simulations. Here, the single-domain state of a triangular island is lower in energy, but nevertheless multi-domain states occur due to the combined effect of entropy and an intrinsic domain wall pinning arising from the skyrmionic character of the spin texture.
DOI: 10.5281/zenodo.807042
title: Skyrmions At The Edge: Confinement Effects In Fe/Ir(111)

description: We have employed spin-polarized scanning tunneling microscopy and Monte-Carlo simulations to investigate the effect of lateral confinement onto the nanoskyrmion lattice in Fe/Ir(111). We find a strong coupling of one diagonal of the square magnetic unit cell to the close-packed edges of Fe nanostructures. In triangular islands this coupling in combination with the mismatching symmetries of the islands and of the square nanoskyrmion lattice leads to frustration and triple-domain states. In direct vicinity to ferromagnetic NiFe islands, the surrounding skyrmion lattice forms additional domains. In this case a side of the square magnetic unit cell prefers a parallel orientation to the ferromagnetic edge. These experimental findings can be reproduced and explained by Monte-Carlo simulations. Here, the single-domain state of a triangular island is lower in energy, but nevertheless multi-domain states occur due to the combined effect of entropy and an intrinsic domain wall pinning arising from the skyrmionic character of the spin texture.
DOI: 10.5281/zenodo.807743
title: Asteroseismic Data Analysis: Foundations And Techniques

description: <strong>This site contains data needed to solve the Exercise sets in the book: "<em>Asteroseismic Data Analysis: Foundations and Techniques</em>".</strong>

The archive Basu_and_Chaplin_Data.tar.gz  contains the synthetic data.<br>
The file archive answers.pdf contains a PDF detailing the answers to the Exercise questions that are not open-ended.<br>
<br>
All data files are ASCII format.<br>
<br>
Here are some notes about the file formats, these can also be read in file README.txt:<br>
<br>
(1) Unless otherwise mentioned, the files with mode frequencies of modes have the format:<br>
l, n, frequency, Inl<br>
<br>
(2) Files with observed frequencies (or simulated observations) have the format<br>
l, n, frequency, uncertainty<br>
<br>
(3) Files in the archive freq_obs.tar have the formal<br>
l, frequency, uncertainty<br>
<br>
(4) Files Kernels_gs98_c2_rho.txt and Kernels_gs98_rho_c2.txt have the following information:<br>
<br>
Row 1: R, M<br>
Row 2: nr, (radius(i),i=1,nr)<br>
Row 3 onwards: l, n, frequency (kernel(i),i=1,nr)<br>
<br>
(5) The frequency files in the archives frequencies_ov[0-2].tar.gz have the following format<br>
<br>
l, n, frequency, Inl, np, ng<br>
<br>
(6) The rotational kernel files have the following format<br>
<br>
Row 1: R, M<br>
Row 2: nr, (radius(i),i=1, nr)<br>
Row 3 onwards: l, np, ng, frequency (kernel(i),i=1, nr)