cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4507490
title: Supplementary data for 'Comparison of sparse biclustering algorithms for gene expression datasets'

description: <strong>Motivation:</strong> Gene clustering and sample clustering are commonly used to find patterns in gene expression datasets. However, in heterogeneous samples (e.g. different tissues or disease states), genes may cluster differently. Biclustering algorithms aim to solve this issue by performing sample clustering and gene clustering simultaneously. Existing reviews of biclustering algorithms have yet to include a number of more recent algorithms and have based comparisons on simplistic simulated datasets without specific evaluation of biclusters in real datasets, using less robust metrics. <br> <strong>Results:</strong> In this study we compared four classes of sparse biclustering algorithms on a range of simulated and real datasets. In particular we use a knockout mouse RNA-seq dataset to evaluate each algorithm’s ability to simultaneously cluster genes and cluster samples. We found that Bayesian algorithms with strict sparsity constraints had high accuracy on the simulated datasets and didn't require any post-processing, but were considerably slower than other algorithm classes. We assessed whether non-negative matrix factorisation algorithms can be repurposed for biclustering and found that, although the raw output was poor, after using a sparsity-inducing post-processing procedure we introduce, one such algorithm was one of the most highly ranked on real datasets. We also exhibit the limitations of biclustering algorithms by varying the complexity of simulated datasets. The algorithms generally struggled on simulated datasets with a large number of implanted factors, or with a large number of genes. In real datasets, the algorithms rarely returned clusters containing samples from multiple tissues, which highlights the need for further thought in the design and analysis of multi-tissue studies to avoid differences between tissues dominating the analysis. <br> Code to run the analysis is available at https://github.com/nichollskc/biclust_comp, including wrappers for each algorithm, implementations of evaluation metrics, and code to simulate datasets and perform pre- and post-processing.
DOI: 10.5281/zenodo.4507546
title: 20200623-DOLA

description: Experiment design <br><b>Agent adapt ontologies to agree on decision taking.</b><br>Hypothesis: <b>['Success rate converges to 1', ' Improve the average accuracy at the end of the experiment', ' Agents do not necessarily converge to the same ontology']</b><br>Experimental setting: <b>Agents learn decision trees (transformed into ontologies); get income from environment; adapt by splitting their leaf nodes.</b><br><br><b>Variables</b><br>independent variables: <b>['numberOfAgents', 'numberOfFeatures', 'numberOfClasses', 'ratio', 'sampleRatio']</b><br>dependent variables: <b>['ssrate', 'accuracy', 'distance']</b><br><br>link: http://sake.re/20200623-DOLA
DOI: 10.5281/zenodo.4507545
title: 20200623-DOLA

description: Experiment design <br><b>Agent adapt ontologies to agree on decision taking.</b><br>Hypothesis: <b>['Success rate converges to 1', ' Improve the average accuracy at the end of the experiment', ' Agents do not necessarily converge to the same ontology']</b><br>Experimental setting: <b>Agents learn decision trees (transformed into ontologies); get income from environment; adapt by splitting their leaf nodes.</b><br><br><b>Variables</b><br>independent variables: <b>['numberOfAgents', 'numberOfFeatures', 'numberOfClasses', 'ratio', 'sampleRatio']</b><br>dependent variables: <b>['ssrate', 'accuracy', 'distance']</b><br><br>link: http://sake.re/20200623-DOLA
DOI: 10.5281/zenodo.4507599
title: Scientific and vernacular names of miombo woody species identified in the Gilé National Park and surroundings in Mozambique

description: The Gilé National Park (GNAP) is located in the northeastern part of Zambezia province in Mozambique. Species names were recorded from local field guide in Lomwe language during floristic inventories. Inventories were carried out in mature Miombo forest and Miombo regeneration areas during the dry seasons in 2015, 2016 and 2019, inside the GNAP (core area and buffer zone) and in the surroundings of the GNAP. Correspondences in scientific name were then carried out using determinations with field identification guides and with the checklist of the vernacular names of vascular plants in Mozambique (de Koning, 1993).
DOI: 10.5281/zenodo.4115903
title: Scientific and vernacular names of miombo woody species identified in the Gilé National Park and surroundings in Mozambique

description: The Gilé National Park (GNAP) is located in the northeastern part of Zambezia province in Mozambique. Species names were recorded from local field guide in Lomwe language during floristic inventories. Inventories were carried out in mature Miombo forest and Miombo regeneration areas during the dry seasons in 2015, 2016 and 2019, inside the GNAP (core area and buffer zone) and in the surroundings of the GNAP. Correspondences in scientific name were then carried out using determinations with field identification guides and with the checklist of the vernacular names of vascular plants in Mozambique (de Koning, 1993).
DOI: 10.6073/pasta/b20f6e5679dde30e6376215dc3d2a8af
title: Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Lakes 2001 - 2004

description: The study lakes selected for the "cross-lake comparison" segment of the Biocomplexity Project include 62 lakes located in Vilas County, Wisconsin. The lakes were chosen to represent a range of positions on gradients of both human development and landscape position.
DOI: 10.17632/6yws5g4tmf.1
title: Data for: ROBUST DESIGNS FOR DOSE-RESPONSE STUDIES: MODEL AND LABELLING ROBUSTNESS

description: Matlab code used in the preparation of ROBUST DESIGNS FOR DOSE-RESPONSE STUDIES: MODEL AND LABELLING ROBUSTNESS
DOI: 10.17632/7bh3by8tv2.1
title: Data for: Modeling the evolution of drinking behavior: A Statistical Physics perspective

description: Density of risk drinkers for Brazil, during the window of time 2009 to 2019.
DOI: 10.6084/m9.figshare.13238870
title: DIAMOND v2 suppl. benchmark 2 query FASTA

description: FASTA file of query DNA sequences used for the DIAMOND v2.0 supplementary benchmark 2.
DOI: 10.6084/m9.figshare.13238870.v1
title: DIAMOND v2 suppl. benchmark 2 query FASTA

description: FASTA file of query DNA sequences used for the DIAMOND v2.0 supplementary benchmark 2.
DOI: 10.6084/m9.figshare.13202921
title: DIAMOND v2 suppl. benchmark 1 query FASTA

description: FASTA file of query DNA sequences used for the DIAMOND v2.0 supplementary benchmark 1.
DOI: 10.6084/m9.figshare.13202939
title: DIAMOND v2 suppl. benchmark 1 query file SCOP annotation

description: Annotation of supplementary benchmark 1 query DNA sequences with SCOP domains generated using BLASTX. TSV file containing 7 columns: Accession of SCOP domain, NCBI protein accession, alignment bit score, SCOP class, SCOP fold, SCOP superfamily, SCOP family
DOI: 10.6084/m9.figshare.13238876
title: DIAMOND v2 suppl. benchmark 2 query file SCOP annotation

description: Annotation of supplementary benchmark 2 query DNA sequences with SCOP domains generated using BLASTX. TSV file containing 7 columns: Accession of SCOP domain, NCBI protein accession, alignment bit score, SCOP class, SCOP fold, SCOP superfamily, SCOP family
DOI: 10.6084/m9.figshare.13202852
title: DIAMOND v2 benchmark query FASTA (shuffled)

description: FASTA file of query protein sequences used for the DIAMOND v2.0 benchmark (non-annotated ranges shuffled).
DOI: 10.6084/m9.figshare.13202939.v1
title: DIAMOND v2 suppl. benchmark 1 query file SCOP annotation

description: Annotation of supplementary benchmark 1 query DNA sequences with SCOP domains generated using BLASTX. TSV file containing 7 columns: Accession of SCOP domain, NCBI protein accession, alignment bit score, SCOP class, SCOP fold, SCOP superfamily, SCOP family
DOI: 10.6084/m9.figshare.13238876.v1
title: DIAMOND v2 suppl. benchmark 2 query file SCOP annotation

description: Annotation of supplementary benchmark 2 query DNA sequences with SCOP domains generated using BLASTX. TSV file containing 7 columns: Accession of SCOP domain, NCBI protein accession, alignment bit score, SCOP class, SCOP fold, SCOP superfamily, SCOP family
DOI: 10.6084/m9.figshare.13202921.v1
title: DIAMOND v2 suppl. benchmark 1 query FASTA

description: FASTA file of query DNA sequences used for the DIAMOND v2.0 supplementary benchmark 1.
DOI: 10.5281/zenodo.4453850
title: Classical Syriac Genitive Constructions

description: The data is sourced from the 92-page historical manuscript, <em>The Chronicle of Joshua the Stylite</em> [5th c. A.D] (Wright, 1882). A total of 116 tokens are included, collected via a method of random sampling. Each token corresponds to a full genitive construction: appositional (including compound nominals), periphrastic or double. Each token is transcribed in Syriac, transliterated, translated and glossed for word-class, noun features and genitive type. The dataset is not quality-checked; manuscript source pages for each token is provided to facilitate ease of validatation.
DOI: 10.5281/zenodo.4453849
title: Classical Syriac Genitive Constructions

description: The data is sourced from the 92-page historical manuscript, <em>The Chronicle of Joshua the Stylite</em> [5th c. A.D] (Wright, 1882). A total of 116 tokens are included, collected via a method of random sampling. Each token corresponds to a full genitive construction: appositional (including compound nominals), periphrastic or double. Each token is transcribed in Syriac, transliterated, translated and glossed for word-class, noun features and genitive type. The dataset is not quality-checked; manuscript source pages for each token is provided to facilitate ease of validatation.
DOI: 10.5281/zenodo.4507584
title: Oceanographic data collected within the Pacific Arctic Ocean by the Russia and China cruises in the summer of 2016

description: An Arctic expedition was carried out by Russian vessel <em>R/V Akademik M.A. Lavrentyev</em> in the East Siberia Sea and Chukchi Sea from 24 August to 16 September. Total 57 temperature-salinity profiles were collected. Among of them, 45 profiles were obtained using a SBE-911 plus Conductivity, Temperature, Depth (CTD) sensor with temperature and salinity accuracies of 0.001°C and 0.003, respectively, and 12 profiles using expendable CTDs (XCTDs) with temperature and salinity accuracies of 0.02°C and 0.04, respectively. At the same time, another expedition was carried out by Chinese icebreaker R/V <em>Xuelong</em> around the Chukchi Plateau. Total 72 temperature-salinity profiles were collected by the same type of CTD sensor as that of the Russian expedition in the Arctic Ocean.
DOI: 10.5281/zenodo.4507583
title: Oceanographic data collected within the Pacific Arctic Ocean by the Russia and China cruises in the summer of 2016

description: An Arctic expedition was carried out by Russian vessel <em>R/V Akademik M.A. Lavrentyev</em> in the East Siberia Sea and Chukchi Sea from 24 August to 16 September. Total 57 temperature-salinity profiles were collected. Among of them, 45 profiles were obtained using a SBE-911 plus Conductivity, Temperature, Depth (CTD) sensor with temperature and salinity accuracies of 0.001°C and 0.003, respectively, and 12 profiles using expendable CTDs (XCTDs) with temperature and salinity accuracies of 0.02°C and 0.04, respectively. At the same time, another expedition was carried out by Chinese icebreaker R/V <em>Xuelong</em> around the Chukchi Plateau. Total 72 temperature-salinity profiles were collected by the same type of CTD sensor as that of the Russian expedition in the Arctic Ocean.
DOI: 10.6084/m9.figshare.12624281.v1
title: DIAMOND v2 benchmark query file SCOP annotation

description: Annotation of benchmark query protein sequences with SCOP domains generated using SWIPE. TSV file containing 7 columns: Accession of SCOP domain, NCBI protein accession, alignment bit score, SCOP class, SCOP fold, SCOP superfamily, SCOP family<br>
DOI: 10.6084/m9.figshare.13238780
title: DIAMOND v2 benchmark protein database FASTA (non-annotated ranges shuffled)

description: Contains protein sequences from the September 2019 release of UniRef50 that were annotated with SCOP domains, non-annotated ranges are shuffled.<br>
DOI: 10.6084/m9.figshare.12624320.v1
title: DIAMOND v2 benchmark database SCOP annotation

description: Annotation of UniRef50 sequences with SCOP domains generated using SWIPE. TSV file containing 7 columns: Accession of SCOP domain, accession of UniRef50 sequence, alignment bit score, SCOP class, SCOP fold, SCOP superfamily, SCOP family
DOI: 10.6084/m9.figshare.13238780.v1
title: DIAMOND v2 benchmark protein database FASTA (non-annotated ranges shuffled)

description: Contains protein sequences from the September 2019 release of UniRef50 that were annotated with SCOP domains, non-annotated ranges are shuffled.<br>
DOI: 10.6084/m9.figshare.12624281
title: DIAMOND v2 benchmark query file SCOP annotation

description: Annotation of benchmark query protein sequences with SCOP domains generated using SWIPE. TSV file containing 7 columns: Accession of SCOP domain, NCBI protein accession, alignment bit score, SCOP class, SCOP fold, SCOP superfamily, SCOP family<br>
DOI: 10.6084/m9.figshare.12624320
title: DIAMOND v2 benchmark database SCOP annotation

description: Annotation of UniRef50 sequences with SCOP domains generated using SWIPE. TSV file containing 7 columns: Accession of SCOP domain, accession of UniRef50 sequence, alignment bit score, SCOP class, SCOP fold, SCOP superfamily, SCOP family
DOI: 10.17632/tpcdk4km8f.1
title: Data for: Modeling rare earth elements binding to humic acids with Model VII

description: Rare earth elements-copper competition for humic acid binding
DOI: 10.15454/gyqeuw/tnftfl
title: RepereD.stl

description: :unav
DOI: 10.15454/gyqeuw/6txdik
title: 01_platform.xml

description: :unav
DOI: 10.15454/gyqeuw/x92tzo
title: needle.rom

description: :unav
DOI: 10.15454/gyqeuw/2m64qb
title: APPLE_3_post.stl

description: :unav
DOI: 10.15454/gyqeuw/br0r4z
title: Ball.stl

description: :unav
DOI: 10.15454/gyqeuw/aglflp
title: 01_platform.png

description: :unav
DOI: 10.15454/gyqeuw/ndunas
title: Descender.stl

description: :unav
DOI: 10.15454/gyqeuw/hogewy
title: Clip.stl

description: :unav
DOI: 10.15454/gyqeuw/o5ercp
title: nut.stl

description: :unav
DOI: 10.15454/gyqeuw/tensqg
title: Base.stl

description: :unav
DOI: 10.15454/gyqeuw/tvka5n
title: Schematic.pdf

description: :unav
DOI: 10.15454/gyqeuw/p14apd
title: Compoments for motorised frame.docx

description: :unav
DOI: 10.15454/gyqeuw/6cb7dt
title: needle.png

description: :unav
DOI: 10.15454/gyqeuw/fw1xoz
title: RepereC.stl

description: :unav
DOI: 10.15454/gyqeuw/gm68hg
title: Coagulator.png

description: :unav
DOI: 10.15454/gyqeuw/mgblag
title: Coagulator.stl

description: :unav
DOI: 10.15454/gyqeuw/kioi6w
title: Arduino code.ino

description: :unav
DOI: 10.15454/gyqeuw/5t3r1r
title: Base.stl

description: :unav
DOI: 10.15454/gyqeuw/dtywva
title: APPLE_1_post.stl

description: :unav
DOI: 10.15454/gyqeuw/lo8x41
title: 01_platform.rom

description: :unav
DOI: 10.15454/gyqeuw/c7tw5l
title: Knob.stl

description: :unav
DOI: 10.15454/gyqeuw/ci8vdx
title: RepereB.stl

description: :unav
DOI: 10.15454/gyqeuw/mkzbdj
title: Descender.xml

description: :unav
DOI: 10.15454/gyqeuw/cv700t
title: Descender.rom

description: :unav
DOI: 10.15454/gyqeuw/eggqbs
title: Thickness piece.stl

description: :unav
DOI: 10.15454/gyqeuw/mvp0ks
title: Ball.stl

description: :unav
DOI: 10.15454/gyqeuw/exuxa7
title: Part 2.stl

description: :unav
DOI: 10.15454/gyqeuw/quj07x
title: Cap.stl

description: :unav
DOI: 10.15454/gyqeuw/gkkzih
title: needle.xml

description: :unav
DOI: 10.15454/gyqeuw/zcgopb
title: Coagulator.rom

description: :unav
DOI: 10.15454/gyqeuw/yzjyfu
title: APPLE_2_post.stl

description: :unav
DOI: 10.15454/gyqeuw/rlyglv
title: Part 3.stl

description: :unav
DOI: 10.15454/gyqeuw/p1wfqq
title: needle.stl

description: :unav
DOI: 10.15454/gyqeuw/pqbedo
title: Holder Luer.stl

description: :unav
DOI: 10.15454/gyqeuw/sm357o
title: Coagulator.xml

description: :unav
DOI: 10.15454/gyqeuw/yi83gq
title: APPLE_6_post.stl

description: :unav
DOI: 10.15454/gyqeuw/vyuxxz
title: Descender.png

description: :unav
DOI: 10.15454/gyqeuw/fnb7ss
title: Mobile piece V2.stl

description: :unav
DOI: 10.15454/gyqeuw/jkqlnb
title: Ventricules.stl

description: :unav
DOI: 10.15454/gyqeuw/ll36ra
title: Contents.docx

description: :unav
DOI: 10.15454/gyqeuw/5lvxza
title: Supporting pole.stl

description: :unav
DOI: 10.15454/gyqeuw
title: Supplemental data for "Open-source 3D printable frameless stereotactic system for young and adult pigs"

description: This dataset includes as a zip archive all the tools related to the paper entitled "Open-source 3D printable frameless stereotactic system for young and adult pigs"
DOI: 10.17028/rd.lboro.13656215
title: Data for Enhanced bio-production from CO<sub>2</sub> by Microbial electrosynthesis (MES) with Continuous operational mode

description: This raw data is used to support the paper published in Faraday Discussions: https://doi.org/10.1039/D0FD00132E.
DOI: 10.17028/rd.lboro.13656215.v1
title: Data for Enhanced bio-production from CO<sub>2</sub> by Microbial electrosynthesis (MES) with Continuous operational mode

description: This raw data is used to support the paper published in Faraday Discussions: https://doi.org/10.1039/D0FD00132E.
DOI: 10.5281/zenodo.4270365
title: Dataset for "Nanoscale Confinement of Skyrmions in FeGe Device shapes"

description: <strong>Dataset for "Confinement of Skyrmions in Nanoscale FeGe Device Structures"</strong> This dataset comprises of the data from the simulation part of the study of the paper "Confinement of Skyrmions in Nanoscale FeGe Device Structures." In this study, a series of five FeGe nanostructures were milled by Focused Ion Beam (FIB) lithography, into two 'blocks' and three 'dumbbells' in order to investigate the formation of skyrmions around a geometric constriction. The experimental samples were imaged by way of Lorentz Transmission Electron Microscopy (LTEM). Simulations were then performed in order to help understand the physics of skyrmion formation within these samples. <strong><em>Prerequisites</em></strong> In order to run the scripts contained in the subfolders, the following are needed: An installation of MuMax 3.10 (https://mumax.github.io/download.html). In order to set this up, you must first install the NVidia graphics drivers appropriate to your system, and the CUDA libraries. Python &gt; 3.6 A number of Python dependencies which are specified in the requirements.txt file in the root directory. Once Python is installed, we recommend installing these via a virtualenv: <pre><code class="language-bash">virtualenv env source env/bin/activate python -m pip install -r requirements.txt</code></pre> <em><strong>Dataset Details</strong></em> This dataset consists of the following tar.xz archives: <em>preprocessing.tar.xz </em>- A small preprocessing library and script for converting experimental TEM images into a 'mask' that can be used for forming a simulation mesh. To run these, run the following command: <pre><code class="language-bash">tar xf preprocessing.tar.xz cd preprocessing python generate-masks.py</code></pre> <em>simulation-scripts.tar.xz</em> - This contains five folders labelled B1, B2 and D1, D2 and D3 representing the five different sample types. In each folder is the MuMax simulation script used for this study, along with the cropped final mask image which is used in the simulation script. To rerun each part of the study (please note that the run time is several weeks per script on current hardware), for e.g. for the B1 sample you can do the following: <pre><code class="language-bash">tar xf simulation-scripts.tar.xz cd simulation-scripts/B1/ mumax3 B1.mx3</code></pre> <em>B1.tar.xz, B2.tar.xz, D1.tar.xz, D2.tar.xz, D3.tar.xz - </em>These archives contain the simulation results for each of the five samples in OVF format. They can be extracted into the simulation-scripts folder to allow the postprocessing analysis to be repeated. <em>postprocessing.tar.xz </em>- This archive contains a postprocessing script which calculates the projection of the magnetisation in the z-direction from the simulation output data. To run this, run the simulations, or download the results archives and place the extracted files into the simulation-scripts folder and then run: <pre><code class="language-bash">tar xf postprocessing.tar.xz cd postprocessing python postprocess.py</code></pre> <br>
DOI: 10.17188/1758962
title: Materials Data on NaFeAsO4F by Materials Project

description: NaFeAsO4F crystallizes in the monoclinic C2/c space group. The structure is three-dimensional. Na1+ is bonded in a 7-coordinate geometry to six O2- and one F1- atom. There are a spread of Na–O bond distances ranging from 2.45–2.78 Å. The Na–F bond length is 2.25 Å. Fe3+ is bonded to four O2- and two equivalent F1- atoms to form FeO4F2 octahedra that share corners with two equivalent FeO4F2 octahedra and corners with four equivalent AsO4 tetrahedra. The corner-sharing octahedral tilt angles are 40°. There are two shorter (2.00 Å) and two longer (2.04 Å) Fe–O bond lengths. Both Fe–F bond lengths are 1.99 Å. As5+ is bonded to four O2- atoms to form AsO4 tetrahedra that share corners with four equivalent FeO4F2 octahedra. The corner-sharing octahedra tilt angles range from 40–54°. All As–O bond lengths are 1.73 Å. There are two inequivalent O2- sites. In the first O2- site, O2- is bonded in a 4-coordinate geometry to two equivalent Na1+, one Fe3+, and one As5+ atom. In the second O2- site, O2- is bonded in a 3-coordinate geometry to one Na1+, one Fe3+, and one As5+ atom. F1- is bonded in a distorted trigonal planar geometry to one Na1+ and two equivalent Fe3+ atoms.