cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4516751.v1
title: Morphology of diverse radiodontan head sclerites from the early Cambrian Chengjiang Lagerstätte, south-west China

description: Recorded in exceptionally preserved Lagerstätten, the radiodontans (including anomalocaridids) are cosmopolitan, soft-bodied, stem-group euarthropods that inhabited Palaeozoic seas. They are notable for their unique morphology, peculiar ecology and basal position in euarthropod evolution. The early Cambrian Chengjiang Lagerstätte has yielded some of the oldest radiodontans, including three unquestionable taxa – <i>Anomalocaris saron</i> Hou <i>et al</i>., 1995, <i>Amplectobelua symbrachiata</i> Hou <i>et al</i>., 1995 and <i>Lyrarapax unguispinus</i> Cong <i>et al</i>., 2014 – based on articulated specimens. However, recent discoveries of the Burgess Shale <i>Hurdia</i> Walcott, 1912 and the Fezouata <i>Aegirocassis benmoulae</i> Van Roy <i>et al</i>., 2015 highlight the presence of another radiodontan group (Hurdiidae) characterized by a tripartite head sclerite complex consisting of one central element and a pair of lateral elements. Here, we describe six morphotypes of possible hurdiid head sclerite elements from the Chengjiang Lagerstätte, some of which are closely associated with other typical radiodontan body parts. These, recognized as central elements, include two new species of the same new genus, <i>Tauricornicaris latizonae</i> gen. et sp. nov. and <i>T</i>. <i>oxygonae</i> gen. et sp. nov., and a former bivalved euarthropod, <i>Zhenghecaris shankouensis</i> Vannier <i>et al</i>., 2006. Another three unnamed sclerite elements are identified as lateral elements. These sclerite elements from Chengjiang provide detailed anatomy, such as mammillary tubercles and soft-tissue reticulate structure, to help understand the morphology and biology of all hurdiid head sclerites. A common single dorsal plate in <i>Anomalocaris saron</i> and <i>Amplectobelua symbrachiata</i> is confirmed. Although the morphologically diverse central and lateral elements of the Hurdiidae and the conserved dorsal plate of the Anomalocarididae + Amplectobeluidae reflect a major distinction in radiodontan body plans, they share a fundamental structure of double layers of cuticle. The Chengjiang specimens not only clarify the morphology and biology of the radiodontan head sclerites in general, but also illuminate the diversity and disparity of radiodontans in their early evolutionary history. http://zoobank.org/urn:lsid:zoobank.org:pub:D0590390-A85A-493A-8529-B2DF64D91169
DOI: 10.5281/zenodo.3761784
title: Measurement data evaluating stream processing on HPC systems

description: Measurement data evaluating different setups and options for stream processing on the Cori supercomputer at NERSC. To access the data, download the files and use the following commands: <pre><code>cat stream_hpc.tar.gz_part_* &gt; stream_hpc.tar.gz tar xzf stream_hpc.tar.gz</code></pre>
DOI: 10.6084/m9.figshare.4516739
title: High temperature and pressure influence the interdomain orientation of Nip7 proteins from <i>P. abyssi</i> and <i>P. furiosus</i>: MD simulations

description: Interactions between protein domains and their position and movement relative to each other are essential for the stability and normal functioning of a protein molecule. Features of the movement of domains may define the mechanism of enzymatic reactions. Therefore, the description of this motion is an important task in the analysis of the structures and functions of multidomain proteins. In the current work, we investigated the influence of pressure and temperature on changes in the movement of the two domains of the protein Nip7, expressed by deep-water (<i>Pyrococcus abyssi</i>) and shallow-water (<i>Pyrococcus furiosus</i>) archaea. The results of the present study show that the interdomain interfaces of the Nip7 proteins of <i>P. abyssi</i> and <i>P. furiosus</i> are formed by stable hydrophobic interactions. It was shown that high pressure and high temperature significantly changed the orientation of domains in Nip7 proteins which perhaps was connected with functional features of these domains. It was found that increasing the pressure significantly changed the angle of rotation of these domains, to a greater extent in the shallow-water protein, while an increase in temperature slightly reduced the angle of rotation of these domains. Moreover, the results suggest that the type of motion of the domains under study is similar to shear motion.
DOI: 10.6084/m9.figshare.4516739.v1
title: High temperature and pressure influence the interdomain orientation of Nip7 proteins from <i>P. abyssi</i> and <i>P. furiosus</i>: MD simulations

description: Interactions between protein domains and their position and movement relative to each other are essential for the stability and normal functioning of a protein molecule. Features of the movement of domains may define the mechanism of enzymatic reactions. Therefore, the description of this motion is an important task in the analysis of the structures and functions of multidomain proteins. In the current work, we investigated the influence of pressure and temperature on changes in the movement of the two domains of the protein Nip7, expressed by deep-water (<i>Pyrococcus abyssi</i>) and shallow-water (<i>Pyrococcus furiosus</i>) archaea. The results of the present study show that the interdomain interfaces of the Nip7 proteins of <i>P. abyssi</i> and <i>P. furiosus</i> are formed by stable hydrophobic interactions. It was shown that high pressure and high temperature significantly changed the orientation of domains in Nip7 proteins which perhaps was connected with functional features of these domains. It was found that increasing the pressure significantly changed the angle of rotation of these domains, to a greater extent in the shallow-water protein, while an increase in temperature slightly reduced the angle of rotation of these domains. Moreover, the results suggest that the type of motion of the domains under study is similar to shear motion.
DOI: 10.6084/m9.figshare.4516826.v3
title: How to save time and reduce frustration when writing manuscripts by using customised Captions to manage the numbering, citation and renaming of Supplementary Materials

description: Different journals have different in-house styles. For example, some journals have no limit to the number of Figures allowed in a manuscript whereas others are more restrictive but allow Supplementary Information: however, whereas some journals allow inclusion of “Extended Data” (Nature), other journals preclude any form of “Supplemental Information” (<i>e.g.</i>, Journal of Neuroscience), whilst others allow “Supplemental Information” (Cell) or “Supplementary Information” (Science). Collectively, researchers waste thousands of hours when re-submitting manuscripts to different journals because they have to convert one type of Caption Label into another type and then usually have to manually re-number each item in the text. This manuscript describes a simple method for writing a manuscript which saves time, money and frustration. I show how to generate customised Caption Labels (<i>e.g.</i>, “Extended Data”, “Supplementary Figure”, “Supplementary Note” or “Supplemental Table”). Each type of Caption Label is numbered automatically according to its order in the text (<i>e.g.</i>, “Supplementary Video 1”). I show how to convert one type of Caption Label to another (<i>e.g.</i>, turn all “Extended Data” into conventional “Figures”). Finally, I show how one can insert, delete or re-order material using cut-and-paste such that all the numbering (in Figure Legends and in the main body of the text) is updated automatically with two clicks. This method works in Microsoft Word and also in Open Office. The Figures and additional material for a manuscript can be converted into a different format in a few minutes. This method should help researchers save thousands of hours and tax dollars.
DOI: 10.6084/m9.figshare.4516745.v1
title: Supplement to "Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in Zambezian region."

description: Lists of specimens used for <i>CYTB</i> phylogeny, distribution maps, divergence dating, species distribution modelling and morphometric analysis as well as the list of records upon which delimitation of <i>A. ineptus</i> is based.
DOI: 10.6084/m9.figshare.4516724
title: biorxiv Document Editing v13.docx

description: Different journals have different in-house styles. For example, some journals have no limit to the number of Figures allowed in a manuscript whereas others are more restrictive but allow Supplementary Information: however, whereas some journals allow inclusion of “Extended Data” (Nature journals), other journals preclude any form of “Supplemental Information” (<i>e.g.</i>, Journal of Neuroscience), whilst others allow “Supplemental Information” (Cell) or “Supplementary Information” (Science). Collectively, researchers waste thousands of hours when re-submitting manuscripts to different journals because they have to convert one type of Caption Label into another type and then usually have to manually re-number each item in the text. This manuscript describes a simple method for writing a manuscript which saves time, money and frustration. I show how to generate customised Caption Labels (<i>e.g.</i>, “Extended Data”, “Supplementary Figure”, “Supplementary Note” or “Supplemental Table”). Each type of Caption Label is numbered automatically according to its order in the text (<i>e.g.</i>, “Supplementary Video 1”). I show how to convert one type of Caption Label to another (<i>e.g.</i>, turn all “Extended Data” into conventional “Figures”). Finally, I show how one can insert, delete or re-order material using cut-and-paste such that all the numbering (in Figure Legends and in the main body of the text) is updated automatically with two clicks. This method works in Microsoft Word and also in Open Office. The Figures and additional material for a manuscript can be converted into a different format in a few minutes. This method should help researchers save thousands of hours and tax dollars.
DOI: 10.6084/m9.figshare.4516745.v3
title: Material used in "Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion."

description: Lists of specimens used for <i>CYTB</i> phylogeny, distribution maps, divergence dating, species distribution modelling and morphometric analysis as well as the list of records upon which delimitation of <i>A. ineptus</i> is based.
DOI: 10.6084/m9.figshare.4516721
title: Structure and interactions of RecA: plasticity revealed by molecular dynamics simulations

description: Eleven independent simulations, each involving three consecutive molecules in the RecA filament, carried out on the protein from <i>Mycobacterium tuberculosis</i>, <i>Mycobacterium smegmatis</i> and <i>Escherichia coli</i> and their Adenosine triphosphate (ATP) complexes, provide valuable information which is complementary to that obtained from crystal structures, in addition to confirming the robust common structural framework within which RecA molecules from different eubacteria function. Functionally important loops, which are largely disordered in crystal structures, appear to adopt in each simulation subsets of conformations from larger ensembles. The simulations indicate the possibility of additional interactions involving the P-loop which remains largely invariant. The phosphate tail of the ATP is firmly anchored on the loop while the nucleoside moiety exhibits substantial structural variability. The most important consequence of ATP binding is the movement of the ‘switch’ residue. The relevant simulations indicate the feasibility of a second nucleotide binding site, but the pathway between adjacent molecules in the filament involving the two nucleotide binding sites appears to be possible only in the mycobacterial proteins.
DOI: 10.6084/m9.figshare.4516745.v2
title: Material used in "Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion."

description: Lists of specimens used for <i>CYTB</i> phylogeny, distribution maps, divergence dating, species distribution modelling and morphometric analysis as well as the list of records upon which delimitation of <i>A. ineptus</i> is based.
DOI: 10.6084/m9.figshare.4516721.v1
title: Structure and interactions of RecA: plasticity revealed by molecular dynamics simulations

description: Eleven independent simulations, each involving three consecutive molecules in the RecA filament, carried out on the protein from <i>Mycobacterium tuberculosis</i>, <i>Mycobacterium smegmatis</i> and <i>Escherichia coli</i> and their Adenosine triphosphate (ATP) complexes, provide valuable information which is complementary to that obtained from crystal structures, in addition to confirming the robust common structural framework within which RecA molecules from different eubacteria function. Functionally important loops, which are largely disordered in crystal structures, appear to adopt in each simulation subsets of conformations from larger ensembles. The simulations indicate the possibility of additional interactions involving the P-loop which remains largely invariant. The phosphate tail of the ATP is firmly anchored on the loop while the nucleoside moiety exhibits substantial structural variability. The most important consequence of ATP binding is the movement of the ‘switch’ residue. The relevant simulations indicate the feasibility of a second nucleotide binding site, but the pathway between adjacent molecules in the filament involving the two nucleotide binding sites appears to be possible only in the mycobacterial proteins.
DOI: 10.5281/zenodo.4012368
title: Ontolex-lemon and TIAD versions of Apertium Kazakh-Russian dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: (c) 2012 Алина Рустамовна Мансурова (c) 2014 Ilnar Salimzyanov
DOI: 10.5281/zenodo.4012367
title: Ontolex-lemon and TIAD versions of Apertium Kazakh-Russian dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: (c) 2012 Алина Рустамовна Мансурова (c) 2014 Ilnar Salimzyanov
DOI: 10.5281/zenodo.4012362
title: Ontolex-lemon and TIAD versions of Apertium Icelandic-Swedish dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: 2010-2013, Tihomir Rangelov 2011-2013, Francis M. Tyers 2013, Kevin Brubeck Unhammer 2013, Trond Trosterud 2014, Tino Didriksen
DOI: 10.5281/zenodo.4012361
title: Ontolex-lemon and TIAD versions of Apertium Icelandic-Swedish dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: 2010-2013, Tihomir Rangelov 2011-2013, Francis M. Tyers 2013, Kevin Brubeck Unhammer 2013, Trond Trosterud 2014, Tino Didriksen
DOI: 10.5281/zenodo.4012359
title: Ontolex-lemon and TIAD versions of Apertium Icelandic-English dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: 2009-2010, Jim O'Regan 2009-2011, Hlynur Sigurþórsson , Háskólinn í Reykjavík 2009-2011, Hrafn Loftsson , Háskólinn í Reykjavík 2009-2011, Martha Dís Brandt , Háskólinn í Reykjavík 2009-2014, Francis M. Tyers 2009-2014, Kevin Brubeck Unhammer 2009, Jacob Nordfalk 2009, Pminervini 2010-2011, Trond Trosterud 2011, Ólafur Waage 2012, Anthony J. Bentley
DOI: 10.5281/zenodo.4012358
title: Ontolex-lemon and TIAD versions of Apertium Icelandic-English dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: 2009-2010, Jim O'Regan 2009-2011, Hlynur Sigurþórsson , Háskólinn í Reykjavík 2009-2011, Hrafn Loftsson , Háskólinn í Reykjavík 2009-2011, Martha Dís Brandt , Háskólinn í Reykjavík 2009-2014, Francis M. Tyers 2009-2014, Kevin Brubeck Unhammer 2009, Jacob Nordfalk 2009, Pminervini 2010-2011, Trond Trosterud 2011, Ólafur Waage 2012, Anthony J. Bentley
DOI: 10.5281/zenodo.4012354
title: Ontolex-lemon and TIAD versions of Apertium Indonesian-Malay (individual language) dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: 2012-2018, Francis M. Tyers 2018, Marc Riera Irigoyen 2012-2016, Kevin Brubeck Unhammer 2012, Raymond HS 2012, Septina Dian Larasati
DOI: 10.5281/zenodo.4012353
title: Ontolex-lemon and TIAD versions of Apertium Indonesian-Malay (individual language) dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: 2012-2018, Francis M. Tyers 2018, Marc Riera Irigoyen 2012-2016, Kevin Brubeck Unhammer 2012, Raymond HS 2012, Septina Dian Larasati
DOI: 10.5281/zenodo.4012350
title: Ontolex-lemon and TIAD versions of Apertium French-Spanish dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: (c) 2007 Eleka Ingenieritza Linguistikoa S.L. Prompsit Language Engineering S.L. 2012 Bernard Chardonneau
DOI: 10.5281/zenodo.4012349
title: Ontolex-lemon and TIAD versions of Apertium French-Spanish dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: (c) 2007 Eleka Ingenieritza Linguistikoa S.L. Prompsit Language Engineering S.L. 2012 Bernard Chardonneau
DOI: 10.6084/m9.figshare.12081147.v20
title: Data for research on "Effect of plate length on subduction kinematics and slab geometry: Insights from buoyancy-driven analog subduction models".

description: Data for research on "Effect of plate length on subduction kinematics and slab geometry: Insights from buoyancy-driven analog subduction models".
DOI: 10.5281/zenodo.4012345
title: Ontolex-lemon and TIAD versions of Apertium French-Catalan dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: (c) 2005, Universitat d'Alacant, (Transducens group) (c) 2007 Eleka Ingenieritza Linguistikoa S.L. Prompsit Language Engineering S.L. (c) 2009 Jimmy O'Regan 2017-2020, Hèctor Alòs i Font 2015-2018, Francis M. Tyers 2017-2018, Xavi Ivars 2017, Bernard Chardonneau 2017, Kevin Brubeck Unhammer
DOI: 10.5281/zenodo.4012344
title: Ontolex-lemon and TIAD versions of Apertium French-Catalan dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: (c) 2005, Universitat d'Alacant, (Transducens group) (c) 2007 Eleka Ingenieritza Linguistikoa S.L. Prompsit Language Engineering S.L. (c) 2009 Jimmy O'Regan 2017-2020, Hèctor Alòs i Font 2015-2018, Francis M. Tyers 2017-2018, Xavi Ivars 2017, Bernard Chardonneau 2017, Kevin Brubeck Unhammer
DOI: 10.5281/zenodo.4012341
title: Ontolex-lemon and TIAD versions of Apertium Basque-Spanish dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: (c) 2008, Prompsit Language Engineering (c) 2005--2008, Universitat d'Alacant (Transducens group) (c) 2005--2007, IXA research group / IXA ikerkuntza taldea (c) 2005--2007, TALP research group, Universitat Politècnica de Catalunya
DOI: 10.5281/zenodo.4012340
title: Ontolex-lemon and TIAD versions of Apertium Basque-Spanish dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: (c) 2008, Prompsit Language Engineering (c) 2005--2008, Universitat d'Alacant (Transducens group) (c) 2005--2007, IXA research group / IXA ikerkuntza taldea (c) 2005--2007, TALP research group, Universitat Politècnica de Catalunya
DOI: 10.6084/m9.figshare.4515845
title: Temporal expansion of annual crop classification layers for the CONUS using the C5 decision tree classifier

description: Crop cover maps have become widely used in a range of research applications. Multiple crop cover maps have been developed to suite particular research interests. The National Agricultural Statistics Service (NASS) Cropland Data Layers (CDL) are a series of commonly used crop cover maps for the conterminous United States (CONUS) that span from 2008 to 2013. In this investigation, we sought to contribute to the availability of consistent CONUS crop cover maps by extending temporal coverage of the NASS CDL archive back eight additional years to 2000 by creating annual NASS CDL-like crop cover maps derived from a classification tree model algorithm. We used over 11 million records to train a classification tree algorithm and develop a crop classification model (CCM). The model was used to create crop cover maps for the CONUS for years 2000–2013 at 250 m spatial resolution. The CCM and the maps for years 2008–2013 were assessed for accuracy relative to resampled NASS CDLs. The CCM performed well against a withheld test data set with a model prediction accuracy of over 90%. The assessment of the crop cover maps indicated that the model performed well spatially, placing crop cover pixels within their known domains; however, the model did show a bias towards the ‘Other’ crop cover class, which caused frequent misclassifications of pixels around the periphery of large crop cover patch clusters and of pixels that form small, sparsely dispersed crop cover patches.
DOI: 10.6084/m9.figshare.4515851
title: Nicotine affects protein complex rearrangement in <i>Caenorhabditis elegans</i> cells

description: Nicotine may affect cell function by rearranging protein complexes. We aimed to determine nicotine-induced alterations of protein complexes in <i>Caenorhabditis elegans</i> (<i>C. elegans</i>) cells, thereby revealing links between nicotine exposure and protein complex modulation. We compared the proteomic alterations induced by low and high nicotine concentrations (0.01 mM and 1 mM) with the control (no nicotine) <i>in vivo</i> by using mass spectrometry (MS)-based techniques, specifically the cetyltrimethylammonium bromide (CTAB) discontinuous gel electrophoresis coupled with liquid chromatography (LC)–MS/MS and spectral counting. As a result, we identified dozens of <i>C. elegans</i> proteins that are present exclusively or in higher abundance in either nicotine-treated or untreated worms. Based on these results, we report a possible network that captures the key protein components of nicotine-induced protein complexes and speculate how the different protein modules relate to their distinct physiological roles. Using functional annotation of detected proteins, we hypothesize that the identified complexes can modulate the energy metabolism and level of oxidative stress. These proteins can also be involved in modulation of gene expression and may be crucial in Alzheimer’s disease. The findings reported in our study reveal putative intracellular interactions of many proteins with the cytoskeleton and may contribute to the understanding of the mechanisms of nicotinic acetylcholine receptor (nAChR) signaling and trafficking in cells.
DOI: 10.6084/m9.figshare.4515842
title: SEBT & FPI EFA, normative data & relationship

description: Relationship between the Star Excursion Balance Test and Foot Posture Index.