cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4560607
title: Evolution of the diatoms: IX. Two datasets resolving monophyletic Classes of diatoms are used to explore the validity of adding short clone library sequences to the analysis

description: A previous study of available diatom sequences tested the value of multiple outgroups in analyses of the 18S ribosomal RNA gene aimed at recovering the three diatom Classes (Coscinodiscophyceae, Mediophyceae, Bacillariophyceae) as monophyletic groups. Of the 34 datasets tested in that study, three recovered these Classes and two of these are explored here in more detail. The major differences between these two datasets were the number of outgroups, the number of nucleotides selected for the analysis and the addition to the dataset of short clone library sequences, primarily from raphid pennate taxa. The addition of short sequences resulted in a smaller dataset in terms of total nucleotides analysed because of the filter selected in the ARB program to generate the final dataset for phylogenetic analysis. The 50% parsimony filter selects a base for the final dataset if that position is parsimony-informative in at least 50% of the sequences chosen for the analysis. Thus, with short sequences, fewer bases are available for selection in the final dataset. A final dataset with fewer nucleotides is produced from the original alignment than from a similar one with no filter applied. If no filter is applied, then a final dataset is produced with all full-length sequences. From these analyses, it was determined that the addition of short clone library sequences recovered sister relationships for certain raphid diatoms that go against conventional wisdom with regard to valve morphology. Thus, the smaller database caused some of the groupings to be unnatural. It was determined that the optimal resolution of the taxa in these datasets resulted from using only full length sequences and selected multiple outgroups. Results obtained from the reduced dataset would be a cause for concern with next generation sequencing in which short amplicons are used to identify taxa.
DOI: 10.6084/m9.figshare.4560649.v1
title: Impact of predator diversity treatments on aphid prey density

description: Predator density and diversity were manipulated in a field cage experiment. <br><br>The data uploaded is the mean numbers and standard deviation of aphids (<i>R. padi</i>) at predator introduction and at the end of experiment 12 days later. <br><br>we had:<br>- Three low diversity treatments: carabid <i>P. melanariu</i>s, ladybird larvae <i>(C. septempunctata)</i>, lacewing larvae (<i>C. carnea</i>)<br>- A high diversity treatment using a subsitutive design <br>
DOI: 10.6084/m9.figshare.4560658.v1
title: OCC dataset of all the bibliographic resources, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about bibliographic resources, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.</pre>
DOI: 10.6084/m9.figshare.4560568
title: OCC dataset of all the bibliographic entries, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about bibliographic entries, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.</pre>
DOI: 10.6084/m9.figshare.4560604
title: minimal_data_set.zip

description: File minimal_data_set.zip contains compressed excel files with numerical data extracted from the simulation trajectories after data processing, for figures 2, 5, 6, 7, 8 and table 1 as well as text files for figures 3, 4, 10, 11 and 12.<br>PLOS One submitted manuscript PONE-D-16-27127R2 with title: Frequency Dependent Non- Thermal Effects of Oscillating Electric Fields in the Microwave Region on the Properties of a Solvated Lysozyme System: a Molecular Dynamics Study<br>
DOI: 10.6084/m9.figshare.4560607.v1
title: Evolution of the diatoms: IX. Two datasets resolving monophyletic Classes of diatoms are used to explore the validity of adding short clone library sequences to the analysis

description: A previous study of available diatom sequences tested the value of multiple outgroups in analyses of the 18S ribosomal RNA gene aimed at recovering the three diatom Classes (Coscinodiscophyceae, Mediophyceae, Bacillariophyceae) as monophyletic groups. Of the 34 datasets tested in that study, three recovered these Classes and two of these are explored here in more detail. The major differences between these two datasets were the number of outgroups, the number of nucleotides selected for the analysis and the addition to the dataset of short clone library sequences, primarily from raphid pennate taxa. The addition of short sequences resulted in a smaller dataset in terms of total nucleotides analysed because of the filter selected in the ARB program to generate the final dataset for phylogenetic analysis. The 50% parsimony filter selects a base for the final dataset if that position is parsimony-informative in at least 50% of the sequences chosen for the analysis. Thus, with short sequences, fewer bases are available for selection in the final dataset. A final dataset with fewer nucleotides is produced from the original alignment than from a similar one with no filter applied. If no filter is applied, then a final dataset is produced with all full-length sequences. From these analyses, it was determined that the addition of short clone library sequences recovered sister relationships for certain raphid diatoms that go against conventional wisdom with regard to valve morphology. Thus, the smaller database caused some of the groupings to be unnatural. It was determined that the optimal resolution of the taxa in these datasets resulted from using only full length sequences and selected multiple outgroups. Results obtained from the reduced dataset would be a cause for concern with next generation sequencing in which short amplicons are used to identify taxa.
DOI: 10.6084/m9.figshare.4560568.v1
title: OCC dataset of all the bibliographic entries, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about bibliographic entries, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.</pre>
DOI: 10.6084/m9.figshare.4560604.v1
title: minimal_data_set.zip

description: File minimal_data_set.zip contains compressed excel files with numerical data extracted from the simulation trajectories after data processing, for figures 2, 5, 6, 7, 8 and table 1 as well as text files for figures 3, 4, 10, 11 and 12.<br>PLOS One submitted manuscript PONE-D-16-27127R2 with title: Frequency Dependent Non- Thermal Effects of Oscillating Electric Fields in the Microwave Region on the Properties of a Solvated Lysozyme System: a Molecular Dynamics Study<br>
DOI: 10.15131/shef.data.4560562
title: Data for paper: Proton radiation effect on InAs avalanche photodiodes

description: The files correspond to experimental results in paper: “Proton radiation effect on InAs avalanche photodiodes” DOI: 10.1364/OE.25.002818. <br> There are two types of files: -.PNG, which corresponds to the figures -.CSV, which are raw data in figures The work in this paper mainly focus on the experimental study of proton radiation effects on performance parameters of InAs APDs, whose sensitivity extends from visible light to ~ 3.5 mm. This is the first report demonstrating a comprehensive study of radiation damage effect on InAs APDs. The data consists of pre- and post-radiation results from InAs avalanche photodiodes: dark current, responsivity and avalanche gain. Three irradiation energies (10.0, 31.4, and 58.8 MeV) and four fluences (10<sup>9</sup> to 10<sup>11</sup> p/cm<sup>2</sup>) were tested. At the harshest irradiation condition (10.0 MeV energy and 10<sup>11</sup> p/cm<sup>2</sup> fluence) the APDs’ avalanche gain and leakage current showed a measurable degradation. However, the responsivity of the APDs was unaffected under all conditions tested. More details about these data/figures can be found in README file.
DOI: 10.6084/m9.figshare.4560547
title: OCC dataset of all the agent roles, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about author roles, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.</pre>
DOI: 10.15131/shef.data.4560562.v1
title: Data for paper: Proton radiation effect on InAs avalanche photodiodes

description: The files correspond to experimental results in paper: “Proton radiation effect on InAs avalanche photodiodes” DOI: 10.1364/OE.25.002818. <br> There are two types of files: -.PNG, which corresponds to the figures -.CSV, which are raw data in figures The work in this paper mainly focus on the experimental study of proton radiation effects on performance parameters of InAs APDs, whose sensitivity extends from visible light to ~ 3.5 mm. This is the first report demonstrating a comprehensive study of radiation damage effect on InAs APDs. The data consists of pre- and post-radiation results from InAs avalanche photodiodes: dark current, responsivity and avalanche gain. Three irradiation energies (10.0, 31.4, and 58.8 MeV) and four fluences (10<sup>9</sup> to 10<sup>11</sup> p/cm<sup>2</sup>) were tested. At the harshest irradiation condition (10.0 MeV energy and 10<sup>11</sup> p/cm<sup>2</sup> fluence) the APDs’ avalanche gain and leakage current showed a measurable degradation. However, the responsivity of the APDs was unaffected under all conditions tested. More details about these data/figures can be found in README file.
DOI: 10.6084/m9.figshare.4560541
title: A model for the ergosterol biosynthetic pathway in <i>Chlamydomonas reinhardtii</i>

description: Ergosterol and 7-dehydroporiferasterol are the predominant sterols in the membranes of the alga <i>Chlamydomonas reinhardtii</i> Dangeard. Ergosterol is primarily found in most fungi, which produce their end-product sterols by way of the intermediate lanosterol. In contrast, plants rarely make ergosterol and plant sterols are made via the intermediate cycloartenol. The cycloartenol-lanosterol bifurcation has been used as a means to evolutionarily categorize species based on their sterol production. Use of bioinformatics has revealed that the green alga, <i>C. reinhardtii</i> is probably producing sterols using a pathway very similar to that of higher plants. The <i>Chlamydomonas</i> genome was searched for genes that encoded proteins exhibiting high similarity to sterol biosynthetic proteins in the higher plant <i>Arabidopsis thaliana</i> or the yeast <i>Saccharomyces cerevisiae</i>. Genes with the greatest similarity were chosen and annotated. To establish whether these genes were expressed, the presence of their transcripts was determined and quantitative RT-PCR was performed. It was observed that many of the transcripts coordinately increased in abundance after deflagellation, which induces an increase in membrane biosynthesis. This work demonstrates that <i>C. reinhardtii</i> has all of the genes necessary for the biosynthesis of ergosterol and 7-dehydroporiferasterol and that this alga uses the higher plant pathway to make a sterol normally associated with fungi. Evidence is also presented that other organisms commonly known as algae, including chlorophytes, haptophytes, rhodophytes, bacillariophytes, a phaeophyte and a cryptomonad, are likely to utilize the same biosynthetic pathway, making sterols via a cycloartenol intermediate.
DOI: 10.6084/m9.figshare.4560541.v1
title: A model for the ergosterol biosynthetic pathway in <i>Chlamydomonas reinhardtii</i>

description: Ergosterol and 7-dehydroporiferasterol are the predominant sterols in the membranes of the alga <i>Chlamydomonas reinhardtii</i> Dangeard. Ergosterol is primarily found in most fungi, which produce their end-product sterols by way of the intermediate lanosterol. In contrast, plants rarely make ergosterol and plant sterols are made via the intermediate cycloartenol. The cycloartenol-lanosterol bifurcation has been used as a means to evolutionarily categorize species based on their sterol production. Use of bioinformatics has revealed that the green alga, <i>C. reinhardtii</i> is probably producing sterols using a pathway very similar to that of higher plants. The <i>Chlamydomonas</i> genome was searched for genes that encoded proteins exhibiting high similarity to sterol biosynthetic proteins in the higher plant <i>Arabidopsis thaliana</i> or the yeast <i>Saccharomyces cerevisiae</i>. Genes with the greatest similarity were chosen and annotated. To establish whether these genes were expressed, the presence of their transcripts was determined and quantitative RT-PCR was performed. It was observed that many of the transcripts coordinately increased in abundance after deflagellation, which induces an increase in membrane biosynthesis. This work demonstrates that <i>C. reinhardtii</i> has all of the genes necessary for the biosynthesis of ergosterol and 7-dehydroporiferasterol and that this alga uses the higher plant pathway to make a sterol normally associated with fungi. Evidence is also presented that other organisms commonly known as algae, including chlorophytes, haptophytes, rhodophytes, bacillariophytes, a phaeophyte and a cryptomonad, are likely to utilize the same biosynthetic pathway, making sterols via a cycloartenol intermediate.
DOI: 10.6084/m9.figshare.4560526
title: Main analysis data files (participant no/run no)

description: Main analysis data files (prts & sdm) for each participant and each run
DOI: 10.6084/m9.figshare.4560547.v1
title: OCC dataset of all the author roles, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about author roles, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.</pre>
DOI: 10.6084/m9.figshare.4560523
title: Parametric analysis - Experience questionnaire - sdm files (participant no/run no)

description: Sdm files for each participant and each of their 6 runs for parametric analysis based on the 'Sensorimotor Experience' questionnaire.
DOI: 10.6084/m9.figshare.4560523.v1
title: Parametric analysis - Experience questionnaire - sdm files

description: Sdm files for each participant and each of their 6 runs for parametric analysis based on the 'Sensorimotor Experience' questionnaire.
DOI: 10.6084/m9.figshare.4560505
title: Common and specific genes and peripheral biomarkers in children and adults with attention-deficit/hyperactivity disorder

description: <b>Objectives:</b> Elucidating the biological mechanisms involved in attention-deficit/hyperactivity disorder (ADHD) has been challenging. Relatively unexplored is the fact that these mechanisms can differ with age. <b>Methods:</b> We present an overview on the major differences between children and adults with ADHD, describing several studies from genomics to metabolomics performed in ADHD children and in adults (cADHD and aADHD, respectively). A systematic search (up until February 2016) was conducted. <b>Results:</b> From a PRISMA flow-chart, a total of 350 and 91 genomics and metabolomics studies were found to be elligible for cADHD and aADHD, respectively. For children, associations were found for genes belonging to dopaminergic (SLC6A3, DRD4 and MAOA) and neurodevelopmental (LPHN3 and DIRAS2) systems and OPRM1 (Yates corrected <i>P</i> = 0.016; OR = 2.27 95%CI: 1.15–4.47). Studies of adults have implicated circadian rhythms genes, HTR2A, MAOB and a more generic neurodevelopmental/neurite outgrowth network (BCHE, SNAP25, BAIAP2, NOS1/NO, KCNIP4 and SPOCK3; Yates corrected <i>P</i> = 0.007; OR = 3.30 95%CI: 1.33–8.29). In common among cADHD and aADHD, the most significant findings are for oxidative stress proteins (MAD, SOD, PON1, ARES, TOS, TAS and OSI), and, in the second level, DISC1, DBH, DDC, microRNA and adiponectin. <b>Conclusions:</b> Through a convergent functional genomics, this review contributes to clarification of which genetic/biological mechanisms differ with age. The effects of some genes do not change throughout the lifetime, whereas others are linked to age-specific stages. Additional research and further studies are needed to generate firmer conclusions that might someday be useful for predicting the remission and persistence of the disorder. Despite the limitations, some of these genes/proteins could be potential useful biomarkers to discriminate cADHD from aADHD.
DOI: 10.6084/m9.figshare.4560502
title: Lithium response in bipolar disorders and core clock genes expression

description: <b>Objectives:</b> We examine whether the lithium response is associated with changes in the expression of core clock genes. <b>Methods:</b> The effect of a therapeutic concentration of lithium (1 mM) on the expression levels of 17 circadian genes was examined in lymphoblastoid cell lines (LCLs) derived from two well-characterized groups of bipolar disorder patients, defined as lithium non-responders (NR, <i>n</i> = 20) or excellent responders (ER, <i>n</i> = 16). Quantitative real-time PCR (qRT-PCR) was conducted at 2, 4 and 8 days (d2, d4 and d8) with and without lithium exposure. <b>Results:</b> At d2, in ER only, <i>BHLHE41</i>, <i>RORA</i>, <i>PER1</i>, <i>ARNTL</i>, <i>CRY2</i>, <i>BHLHE40</i> and <i>CSNK1D</i> were upregulated, whereas <i>NR1D1</i> was downregulated. At d4, in ER only, <i>CRY1</i> was downregulated. At d8, in NR only, <i>GSK3β</i> was upregulated and <i>DBP</i>, <i>TIMELESS</i> and <i>CRY1</i> were downregulated. Significant Group × Lithium interactions existed for <i>NR1D1</i> at d2 (<i>P</i> = 0.02), and <i>CRY1</i> at d4 (<i>P</i> = 0.02). Longitudinal analyses showed differential temporal evolutions between NR and ER (significant Time × Group interaction) for <i>PER3</i>, <i>NR1D1</i>, <i>DBP</i>, <i>RORA</i>, <i>CSNK1D and TIMELESS</i>; and a significant Time × Lithium interaction for <i>NR1D1</i>. Coexpression data analyses suggested distinct groups of circadian genes concurrently modulated by lithium. <b>Conclusions:</b> In LCLs, lithium influences expression of circadian genes with differences in amplitude and kinetics according to the patient’s lithium response status.
DOI: 10.6084/m9.figshare.4560505.v2
title: Common and specific genes and peripheral biomarkers in children and adults with attention-deficit/hyperactivity disorder

description: <b>Objectives:</b> Elucidating the biological mechanisms involved in attention-deficit/hyperactivity disorder (ADHD) has been challenging. Relatively unexplored is the fact that these mechanisms can differ with age. <b>Methods:</b> We present an overview on the major differences between children and adults with ADHD, describing several studies from genomics to metabolomics performed in ADHD children and in adults (cADHD and aADHD, respectively). A systematic search (up until February 2016) was conducted. <b>Results:</b> From a PRISMA flow-chart, a total of 350 and 91 genomics and metabolomics studies were found to be elligible for cADHD and aADHD, respectively. For children, associations were found for genes belonging to dopaminergic (SLC6A3, DRD4 and MAOA) and neurodevelopmental (LPHN3 and DIRAS2) systems and OPRM1 (Yates corrected <i>P</i> = 0.016; OR = 2.27 95%CI: 1.15–4.47). Studies of adults have implicated circadian rhythms genes, HTR2A, MAOB and a more generic neurodevelopmental/neurite outgrowth network (BCHE, SNAP25, BAIAP2, NOS1/NO, KCNIP4 and SPOCK3; Yates corrected <i>P</i> = 0.007; OR = 3.30 95%CI: 1.33–8.29). In common among cADHD and aADHD, the most significant findings are for oxidative stress proteins (MAD, SOD, PON1, ARES, TOS, TAS and OSI), and, in the second level, DISC1, DBH, DDC, microRNA and adiponectin. <b>Conclusions:</b> Through a convergent functional genomics, this review contributes to clarification of which genetic/biological mechanisms differ with age. The effects of some genes do not change throughout the lifetime, whereas others are linked to age-specific stages. Additional research and further studies are needed to generate firmer conclusions that might someday be useful for predicting the remission and persistence of the disorder. Despite the limitations, some of these genes/proteins could be potential useful biomarkers to discriminate cADHD from aADHD.