cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3792210.v1
title: <i>Papahu</i>-like fossil dolphin from Kaikoura, New Zealand, helps to fill the Early Miocene gap in the history of Odontoceti

description: An early Miocene dolphin (ZMT 73: partial skull and ear bones) from Kaikoura, New Zealand, is the sister taxon to the previously named Early Miocene <i>Papahu taitapu.</i> The new specimen, although insufficient to justify a new species name, includes an informative squamosal and periotic that help move the <i>Papahu</i> clade from the stem Odontoceti to either the Platanistoidea, or to become the sister taxon to the Ziphiidae+Eurhinodelphinidae+Delphinida. The fossils usefully add to the taxonomic and structural diversity of Cetacea during the important but poorly known Early Miocene.
DOI: 10.6084/m9.figshare.3792204
title: SpyTag/SpyCatcher cyclization enhances the thermostability of firefly luciferase

description: SpyTag can spontaneously form a covalent isopeptide bond with its protein partner SpyCatcher. Firefly luciferase from <i>Photinus pyralis</i> was cyclized <i>in vivo</i> by fusing SpyCatcher at the N terminus and SpyTag at the C terminus. Circular LUC was more thermostable and alkali-tolerant than the wild type, without compromising the specific activity. Structural analysis indicated that the cyclized LUC increased the thermodynamic stability of the structure and remained more properly folded at high temperatures when compared with the wild type. We also prepared an N-terminally and C-terminally shortened form of the SpyCatcher protein and cyclization using this truncated form led to even more thermostability than the original form. Our findings suggest that cyclization with SpyTag and SpyCatcher is a promising and effective strategy to enhance thermostability of enzymes.
DOI: 10.6084/m9.figshare.3792204.v1
title: SpyTag/SpyCatcher cyclization enhances the thermostability of firefly luciferase

description: SpyTag can spontaneously form a covalent isopeptide bond with its protein partner SpyCatcher. Firefly luciferase from <i>Photinus pyralis</i> was cyclized <i>in vivo</i> by fusing SpyCatcher at the N terminus and SpyTag at the C terminus. Circular LUC was more thermostable and alkali-tolerant than the wild type, without compromising the specific activity. Structural analysis indicated that the cyclized LUC increased the thermodynamic stability of the structure and remained more properly folded at high temperatures when compared with the wild type. We also prepared an N-terminally and C-terminally shortened form of the SpyCatcher protein and cyclization using this truncated form led to even more thermostability than the original form. Our findings suggest that cyclization with SpyTag and SpyCatcher is a promising and effective strategy to enhance thermostability of enzymes.
DOI: 10.6084/m9.figshare.3792180
title: Usability vs. Purity: How UCSF and Duke Enabled Data Reuse by Going Beyond Linked Data

description: Presenters: Julia Trimmer, Anirvan Chatterjee, Eric Meeks, Richard Outten and Brian Turner<br><br>Duke and UCSF have come up with ways to make their research networking platforms indispensable at their institutions, winning friends and allies, and strengthening the case for renewed funding. Others can do this too — but only if we retrofit VIVO, Profiles, and other platforms with simple data reuse mechanisms. In this session, we’ll talk about techniques for developers, traffic growth on downstream sites, and researcher engagement. We’ll look at examples of sites that consume VIVO and Profiles data and talk about what it’s like to share data across nearly 50 local websites and apps.<br>
DOI: 10.6084/m9.figshare.3792117
title: Variance in plant nutritive traits reduces insect herbivore performance (dataset)

description: Data and metadata from Wetzel, W. C., H. M. Kharouba, M. Robinson, M. Holyoak, & R. Karban. 2016. Variance in plant nutritive traits reduces insect herbivore performance. Nature. doi: 10.1038/nature20140
DOI: 10.6084/m9.figshare.3792117.v1
title: Data and metadata from Wetzel et al. 2016. Nature. doi: 10.1038/nature20140

description: Data and metadata from Wetzel, W. C., H. M. Kharouba, M. Robinson, M. Holyoak, & R. Karban. 2016. Variance in plant nutritive traits reduces insect herbivore performance. Nature. doi: 10.1038/nature20140
DOI: 10.6084/m9.figshare.3792117.v2
title: Variance in plant nutritive traits reduces insect herbivore performance (dataset)

description: Data and metadata from Wetzel, W. C., H. M. Kharouba, M. Robinson, M. Holyoak, & R. Karban. 2016. Variance in plant nutritive traits reduces insect herbivore performance. Nature. doi: 10.1038/nature20140
DOI: 10.6084/m9.figshare.3792000.v2
title: Random Codes

description: Diverse codes in Matlab. No wheel re-invented here, but it might help users save 15 minutes here and there.<br>- linReg.m: Performs simple linear regression between X and Y using least square fit and tests the null hypothesis of non-significant slope at the alpha significance level.- cmpTrends.m: Compares the significance of the difference between two trends from two independent datasets.<br>
DOI: 10.6084/m9.figshare.3792000.v3
title: Random Codes

description: Diverse codes in Matlab. No wheel re-invented here, but it might help users save 15 minutes here and there.<br>- linReg.m: Performs simple linear regression between X and Y using least square fit and tests the null hypothesis of non-significant slope at the alpha significance level.- cmpTrends.m: Compares the significance of the difference between two trends from two independent datasets.<br>
DOI: 10.15129/29ade4d6-6603-4a70-a807-0c8889751f07
title: Data for: "The effect of chirality on the compression of 2-(2-Oxo-1-pyrrolidinyl) butyramide: A Tale of Two Crystals" article

description: Data for characterization of S-enantiomer (levetiracetam) and racemic compound (etiracetam) of 2-(2-Oxo-1-pyrrolidinyl) butyramide by increasing pressure. The data was collected through single-crystal X-ray diffraction and Raman Spectroscopy. The single-crystal X-ray diffraction images are in the format .sfrm (Bruker program) and can be read in APEX software. The PIXEL data has been generated using Gaussian software (.gjf files) and PIXEL (.mlc, .pri files); the latter can be viewed in a text editor. The Raman spectroscopy data are in the .l6S format (LabSpec 6 program) and also .txt format that can be viewed using any data analysis software. The modification of single-crystal X-ray file names from the original names to those represented in the article is explained in .xlsx files visible in the main folder. The naming used in the PIXEL calculation follows those represented in the article.
DOI: 10.6084/m9.figshare.3791973
title: CAST Alignments and Scores for Terminally Differentiated Cells at selected time points from 200 to 400 minutes of embryogenesis.

description: For more information on CAST alignments, please see: Alicea, B. and Gordon, R. (2016). Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development Via Differentiation Trees of Embryos. Biology, 5(3), 33.
DOI: 10.6084/m9.figshare.3791973.v1
title: CAST Alignments and Scores for Terminally Differentiated Cells at selected time points from 200 to 400 minutes of embryogenesis.

description: For more information on CAST alignments, please see: Alicea, B. and Gordon, R. (2016). Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development Via Differentiation Trees of Embryos. Biology, 5(3), 33.
DOI: 10.6084/m9.figshare.3791970
title: Colored chart showing the emergence of terminally differentiated cells in <i>C. elegans</i> from 200 to 400 minutes of embryogenesis.

description: Emergence of Terminally Differentiated Cells in each cell type class, relative to the 400 minutes of embryogenesis. be 200 to 300 minute period is sampled at 5-minute intervals, while the 300 to 400 minute period is sampled at 30-minute intervals. Bottom of figure is labeled with the corresponding developmental stages and images of the embryo during select times.<br>Data sources:[A] Cell Lineage and Timing Data, Nikhil Bhatla @ WormWeb.<br>[B] Annotations of Terminally Differentiated Cells. Stephen Larson & Mark Watts @ PyOpenWorm. OpenWorm Foundation.<br>References:[1] Picture for 200 minute embryo (beginning of Gastrulation). Hartwell, L.H., Hood, L., Goldberg, M.L., Reynolds, A.E., and Silver, L.M. Genetics: from genes to genomes. 4th Edition. Genetic Portrait C, Caenorhabditis elegans: Genetic Portrait of a Simple Multicellular Animal. http://highered.mheducation.com/sites/dl/free/007352526x/387004/Reference_C.pdf Accessed on August 27, 2016.<br>[2] Pictures of Closure of Ventral Cleft and Dorsal Intercalation. Figure 3 in Epithelial System Hypodermis (Epidermis), WormAtlas. http://www.wormatlas.org/hermaphrodite/hypodermis/mainframe.htm Accessed on August 26, 2016.<br>[3] Pictures of Comma Stage embryo and Embryogenesis Stage Information. Figure 1 in Chisholm, A.D. and Hardin, J. Epidermal Morphogenesis, WormBook. http://www.wormbook.org/chapters/www_epidermalmorphogenesis/epidermalmorphogenesis.html Accessed on August 27, 2016.
DOI: 10.6084/m9.figshare.3791970.v3
title: Colored chart showing the emergence of terminally differentiated cells in <i>C. elegans</i> from 200 to 400 minutes of embryogenesis.

description: Emergence of Terminally Differentiated Cells in each cell type class, relative to the 400 minutes of embryogenesis. be 200 to 300 minute period is sampled at 5-minute intervals, while the 300 to 400 minute period is sampled at 30-minute intervals. Bottom of figure is labeled with the corresponding developmental stages and images of the embryo during select times.<br>Data sources:[A] Cell Lineage and Timing Data, Nikhil Bhatla @ WormWeb.<br>[B] Annotations of Terminally Differentiated Cells. Stephen Larson & Mark Watts @ PyOpenWorm. OpenWorm Foundation.<br>References:[1] Picture for 200 minute embryo (beginning of Gastrulation). Hartwell, L.H., Hood, L., Goldberg, M.L., Reynolds, A.E., and Silver, L.M. Genetics: from genes to genomes. 4th Edition. Genetic Portrait C, Caenorhabditis elegans: Genetic Portrait of a Simple Multicellular Animal. http://highered.mheducation.com/sites/dl/free/007352526x/387004/Reference_C.pdf Accessed on August 27, 2016.<br>[2] Pictures of Closure of Ventral Cleft and Dorsal Intercalation. Figure 3 in Epithelial System Hypodermis (Epidermis), WormAtlas. http://www.wormatlas.org/hermaphrodite/hypodermis/mainframe.htm Accessed on August 26, 2016.<br>[3] Pictures of Comma Stage embryo and Embryogenesis Stage Information. Figure 1 in Chisholm, A.D. and Hardin, J. Epidermal Morphogenesis, WormBook. http://www.wormbook.org/chapters/www_epidermalmorphogenesis/epidermalmorphogenesis.html Accessed on August 27, 2016.
DOI: 10.6084/m9.figshare.3791970.v2
title: Colored chart showing the emergence of terminally differentiatied cells in <i>C. elegans</i> from 200 to 400 minutes of embryogenesis.

description: Emergence of Terminally Differentiated Cells in each cell type class, relative to the 400 minute point in embryogenesis.<br>References:Picture for 200 minute embryo (beginning of Gastrulation). Hartwell, L.H., Hood, L., Goldberg, M.L., Reynolds, A.E., and Silver, L.M. Genetics: from genes to genomes. 4th Edition. Genetic Portrait C, Caenorhabditis elegans: Genetic Portrait of a Simple Multicellular Animal. http://highered.mheducation.com/sites/dl/free/007352526x/387004/Reference_C.pdf Accessed on August 27, 2016.<br>Pictures of Closure of Ventral Cleft and Dorsal Intercalation. Figure 3 in Epithelial System Hypodermis (Epidermis), WormAtlas. http://www.wormatlas.org/hermaphrodite/hypodermis/mainframe.htm Accessed on August 26, 2016.<br>Pictures of Comma Stage embryo and Embryogenesis Stage Information. Figure 1 in Chisholm, A.D. and Hardin, J. Epidermal Morphogenesis, WormBook. http://www.wormbook.org/chapters/www_epidermalmorphogenesis/epidermalmorphogenesis.html Accessed on August 27, 2016.<br>Cell Lineage and Timing Data, Nikhil Bhatla @ WormWeb.<br>Annotations of Terminally Differentiated Cells. Stephen Larson & Mark Watts @ PyOpenWorm. OpenWorm Foundation.
DOI: 10.6084/m9.figshare.3790617
title: Are views towards egg farming associated with egg consumers' purchasing habits?

description: A survey regarding knowledge, values and attitudes of Latin Americans towards egg farming
DOI: 10.6084/m9.figshare.3790617.v1
title: Attitudes of Latin Americans towards egg farming

description: A survey regarding knowledge, values and attitudes of Latin Americans towards egg farming
DOI: 10.6084/m9.figshare.3790617.v3
title: Are views towards egg farming associated with egg consumers' purchasing habits?

description: A survey regarding knowledge, values and attitudes of Latin Americans towards egg farming
DOI: 10.6084/m9.figshare.3790617.v2
title: Attitudes of Latin Americans towards egg farming

description: A survey regarding knowledge, values and attitudes of Latin Americans towards egg farming
DOI: 10.6084/m9.figshare.3790611
title: Irrigated Area Maps for India

description: <b>New Version!! -- Please use the updated data located at:</b><br><b>https://figshare.com/articles/Remotely_sensed_irrigated_area_mapping_in_India_for_2000-2015/4012635</b><br>Irrigated area maps for India for the period of 2000-2015. Each file (2000-2001.tiff) contains irrigated area maps with values 0 and 1 representing non irrigated and irrigated areas, respectively.<br><br>
DOI: 10.6084/m9.figshare.3790602
title: 2015_Audiencia publica.pdf

description: This paper anchors on the premise that all organization facing physical limit, economic, social, ethical and political about their impacts related biophysical environment. The objective of this paper is to verify if the public hearing, on the environmental impact activities, promotes a space for the practice of environmental citizenship. For that, far-up approach will use the inductive method, focused in field research, combined with bibliographic procedures. It concludes that the public hearing, in this case, denies spaces for the environmental citizenship.
DOI: 10.6084/m9.figshare.3790602.v1
title: 2015_Audiencia publica.pdf

description: This paper anchors on the premise that all organization facing physical limit, economic, social, ethical and political about their impacts related biophysical environment. The objective of this paper is to verify if the public hearing, on the environmental impact activities, promotes a space for the practice of environmental citizenship. For that, far-up approach will use the inductive method, focused in field research, combined with bibliographic procedures. It concludes that the public hearing, in this case, denies spaces for the environmental citizenship.
DOI: 10.6084/m9.figshare.3790599
title: 2016_Efetividade das políticas ambientais.pdf

description: The contemporary socioenvironmental crisis emerged as a result of unsuccessful attempts to achieve sustainable development. Its factors and consequences must be understood in order to effect change. This work was developed based on a literature review of books, articles, journals, and the legislation, among other sources. The aim was to reflect on the interplay between man, the Law and the environment in the current socioenvironmental crisis, to assess the effectiveness of environmental policies. Environmental Law influences modern legal thought with the idea of mainstreaming environmental standards, especially with the principles of protection, participation and education. In general, the current Brazilian environmental policies are marked by compartmentalization, fragmentation and a consequent lack of universality. The cause of this inefficiency is a truncated historical construction, marked by a lack of environmental education, and founded on an individualistic instrumental rationality and a very small popular participation in the decisions made.
DOI: 10.6084/m9.figshare.3790599.v1
title: 2016_Efetividade das políticas ambientais.pdf

description: The contemporary socioenvironmental crisis emerged as a result of unsuccessful attempts to achieve sustainable development. Its factors and consequences must be understood in order to effect change. This work was developed based on a literature review of books, articles, journals, and the legislation, among other sources. The aim was to reflect on the interplay between man, the Law and the environment in the current socioenvironmental crisis, to assess the effectiveness of environmental policies. Environmental Law influences modern legal thought with the idea of mainstreaming environmental standards, especially with the principles of protection, participation and education. In general, the current Brazilian environmental policies are marked by compartmentalization, fragmentation and a consequent lack of universality. The cause of this inefficiency is a truncated historical construction, marked by a lack of environmental education, and founded on an individualistic instrumental rationality and a very small popular participation in the decisions made.
DOI: 10.6084/m9.figshare.3790578
title: Domestication of grain crops

description: Dataset for the article - 'How did the domestication of Fertile Crescent grain crops increase their yields?', Preece et al., 2016. <br>Domestication_data1.csv: Provides data for INDIVIDUAL PLANTS from Yield Experiments, for comparison of traits between crops and their progenitors, using lme and lmekin functions in R. <br>Domestication_data2.csv: Trait data from Yield Experiments as SPECIES MEANS, for use in pgls analysis and in decomposition of variance analyses. <br>Domestication_data_growth_analysis: Data from Growth Analysis Experiment showing mass measured at 6 harvests. <br>combined tree-grass.leg.tre: Phylogenetic tree for species in dataset, in tre format.<br>cp_grass_matkndhf_final.tre: Phylogenetic tree for grass species only.
DOI: 10.6084/m9.figshare.3790578.v1
title: Domestication of grain crops

description: Dataset for the article - 'How did the domestication of Fertile Crescent grain crops increase their yields?', Preece et al., 2016. <br>Domestication_data1.csv: Provides data for INDIVIDUAL PLANTS from Yield Experiments, for comparison of traits between crops and their progenitors, using lme and lmekin functions in R. <br>Domestication_data2.csv: Trait data from Yield Experiments as SPECIES MEANS, for use in pgls analysis and in decomposition of variance analyses. <br>Domestication_data_growth_analysis: Data from Growth Analysis Experiment showing mass measured at 6 harvests. <br>combined tree-grass.leg.tre: Phylogenetic tree for species in dataset, in tre format.<br>cp_grass_matkndhf_final.tre: Phylogenetic tree for grass species only.
DOI: 10.6084/m9.figshare.3785277
title: Spatial and temporal distributions in the Barents Sea cod fishery (The CAb-ABe model)

description: Data material and procedures for the estimation of model parameters.
DOI: 10.6084/m9.figshare.3785277.v2
title: New draft item

description: Data material and procedures for the estimation of model parameters.
DOI: 10.6084/m9.figshare.3785277.v3
title: New draft item

description: Data material and procedures for the estimation of model parameters.
DOI: 10.6084/m9.figshare.3784821.v4
title: Introduction to Fisheries Economics

description: Text book in fisheries economics and Mathematica programming.<br>EARLY DRAFT<br><br><br>
DOI: 10.6084/m9.figshare.3784821.v5
title: Introduction to Fisheries Economics

description: Text book in fisheries economics and Mathematica programming.<br>EARLY DRAFT<br><br><br>
DOI: 10.6084/m9.figshare.3784821.v7
title: Introduction to Fisheries Economics

description: Text book in fisheries economics and Mathematica programming.<br>EARLY DRAFT<br><br><br>
DOI: 10.6084/m9.figshare.3784821.v8
title: Introduction to Fisheries Economics

description: Text book in fisheries economics and Mathematica programming.<br>EARLY DRAFT<br><br><br>
DOI: 10.6084/m9.figshare.3784821.v9
title: Introduction to Fisheries Economics

description: Text book in fisheries economics and Mathematica programming.<br>EARLY DRAFT<br><br><br>
DOI: 10.6084/m9.figshare.3784821.v10
title: Introduction to Fisheries Economics

description: Text book in fisheries economics and Mathematica programming.<br>EARLY DRAFT<br><br><br>
DOI: 10.6084/m9.figshare.3784821.v11
title: Introduction to Fisheries Economics

description: Text book in fisheries economics and Mathematica programming.<br>EARLY DRAFT<br><br><br>
DOI: 10.6084/m9.figshare.3784821.v22
title: Introduction to Fisheries Economics

description: Text book in fisheries economics and Mathematica programming.<br>EARLY DRAFT<br><br><br>
DOI: 10.6084/m9.figshare.3784029
title: Reduced kinase activity of polo kinase Cdc5 affects chromosome stability and DNA damage response in <i>S. cerevisiae</i>

description: Polo-like kinases (PLKs) control several aspects of eukaryotic cell division and DNA damage response. Remarkably, PLKs are overexpressed in several types of cancer, being therefore a marker of bad prognosis. As such, specific PLK kinase activity inhibitors are already used in clinical trials and the regulation of PLK activation is a relevant topic of cancer research. Phosphorylation of threonine residues in the T-loop of the kinase domain is pivotal for PLKs activation. Here, we show that T238A substitution in the T-loop reduces the kinase activity of Cdc5, the only PLK in <i>Saccharomyces cerevisiae</i>, with minor effect on cell growth in unperturbed conditions. However, the <i>cdc5</i>-T238A cells have increased rate of chromosome loss and gross chromosomal rearrangements, indicating altered genome stability. Moreover, the T238A mutation affects timely localization of Cdc5 to the spindle pole bodies and blocks cell cycle restart after one irreparable double-strand break. In cells responding to alkylating agent metylmethane sulfonate (MMS), the <i>cdc5</i>-T238A mutation reduces the phosphorylation of Mus81-Mms4 resolvase and exacerbates the MMS sensitivity of <i>sgs1</i>Δ cells that accumulate Holliday junctions. Of importance, the previously described checkpoint adaptation defective allele, <i>cdc5</i>-ad does not show reduced kinase activity, defective Mms4 phosphorylation and genetic interaction with <i>sgs1</i>Δ. Our data define the importance of regulating Cdc5 activity through T-loop phosphorylation to preserve genome integrity and respond to DNA damage.
DOI: 10.6084/m9.figshare.3784029.v2
title: Reduced kinase activity of polo kinase Cdc5 affects chromosome stability and DNA damage response in <i>S. cerevisiae</i>

description: Polo-like kinases (PLKs) control several aspects of eukaryotic cell division and DNA damage response. Remarkably, PLKs are overexpressed in several types of cancer, being therefore a marker of bad prognosis. As such, specific PLK kinase activity inhibitors are already used in clinical trials and the regulation of PLK activation is a relevant topic of cancer research. Phosphorylation of threonine residues in the T-loop of the kinase domain is pivotal for PLKs activation. Here, we show that T238A substitution in the T-loop reduces the kinase activity of Cdc5, the only PLK in <i>Saccharomyces cerevisiae</i>, with minor effect on cell growth in unperturbed conditions. However, the <i>cdc5</i>-T238A cells have increased rate of chromosome loss and gross chromosomal rearrangements, indicating altered genome stability. Moreover, the T238A mutation affects timely localization of Cdc5 to the spindle pole bodies and blocks cell cycle restart after one irreparable double-strand break. In cells responding to alkylating agent metylmethane sulfonate (MMS), the <i>cdc5</i>-T238A mutation reduces the phosphorylation of Mus81-Mms4 resolvase and exacerbates the MMS sensitivity of <i>sgs1</i>Δ cells that accumulate Holliday junctions. Of importance, the previously described checkpoint adaptation defective allele, <i>cdc5</i>-ad does not show reduced kinase activity, defective Mms4 phosphorylation and genetic interaction with <i>sgs1</i>Δ. Our data define the importance of regulating Cdc5 activity through T-loop phosphorylation to preserve genome integrity and respond to DNA damage.