cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4569673.v1
title: Biogeographic scenarios for the diversification of a widespread Neotropical species, <i>Glossophaga soricina</i> (Chiroptera: Phyllostomidae)

description: In order to contribute to the understanding of the effect of geological and climatic changes on species diversification in the Neotropics, we employed molecular techniques to study the population dynamics of the glossophagine bat <i>Glossophaga soricina</i>, a widespread species in the Neotropical region. We aimed to assess the dispersal and distribution of mtDNA lineages of <i>G. soricina</i> and evaluate the possible effect of vicariant events in the population history and dynamics. <i>Glossophaga soricina</i> presented two main highly supported mtDNA lineages, which diverged between ∼2.4 and 5 million years ago, probably following a vicariant event caused by the Andes final uplift. The lower sea level during Pleistocene glaciations also made possible the occupation of Jamaica after an event of dispersion over the Caribbean Sea, although past climatic fluctuations had little effect over population dynamics of <i>G. soricina</i>. Our results corroborate the idea that the Andes uplift played an important role in the evolution of Neotropical biodiversity. In this context we suggest that geographic events causing large scale environmental disjunction, such as the uplift of mountains, are more likely to restrict gene flow amongst populations of tolerant species with broad geographic range than local climate driven environmental changes.
DOI: 10.6084/m9.figshare.4569634
title: OCC triplestore of all the data, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) triplestore (Blazegraph, https://www.blazegraph.com/, licensed in GPLv2) containing all the data of the corpus, and 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-triplestore<br><br>Please execute "run.sh" for running the triplestore, and use "stop.sh" for stopping it.<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.4569649
title: MCPIP1, alias Regnase-1 binds and cleaves mRNA of C/EBPβ.

description: These are dataset underlying the findings in the manuscript.
DOI: 10.6084/m9.figshare.4569634.v1
title: OCC triplestore of all the data, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) triplestore (Blazegraph, https://www.blazegraph.com/, licensed in GPLv2) containing all the data of the corpus, and 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-triplestore<br><br>Please execute "run.sh" for running the triplestore, and use "stop.sh" for stopping it.<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.4569649.v1
title: MCPIP1, alias Regnase-1 binds and cleaves mRNA of C/EBPβ.

description: These are dataset underlying the findings in the manuscript.
DOI: 10.6084/m9.figshare.4569598
title: OCC dataset of all the responsible agents, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about responsible agents, 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.4569616
title: OCC dataset of all the resource embodiments, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about resource embodiments, 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.4569619
title: OCC provenance data of all the provenance agents shared by the whole corpus, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) provenance data about provenance agents shared by the whole OCC, 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.4569598.v1
title: OCC dataset of all the responsible agents, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about responsible agents, 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.4569616.v1
title: OCC dataset of all the resource embodiments, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about resource embodiments, 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.4568251
title: Card from Emile Zuckerkandl noting acceptance of paper

description: Acceptance post card for paper in the Journal of Molecular Evolution
DOI: 10.6084/m9.figshare.4568251.v1
title: Card from Emile Zuckerkandl noting acceptance of paper

description: Acceptance post card for paper in the Journal of Molecular Evolution
DOI: 10.6084/m9.figshare.4568005
title: Visualizing Type II Error in Normality Tests

description: A skewed exponential power distribution, with parameters defining kurtosis and skewness, is introduced as a way to visualize Type II error in normality tests. By varying these parameters a mosaic of distributions is built, ranging from double exponential to uniform or from positive to negative exponential; the normal distribution is a particular case located in the center of the mosaic. Using a sequential color scheme, a different color is assigned to each distribution in the mosaic depending on the probability of committing a Type II error. This graph gives a visual representation of the power of the performed test. This way of representing results facilitates the comparison of the power of various tests and the influence of sample size. A script to perform this graphical representation, programmed in the R statistical software, is available online as supplementary material.
DOI: 10.6084/m9.figshare.4568002
title: Optimal Whitening and Decorrelation

description: Whitening, or sphering, is a common preprocessing step in statistical analysis to transform random variables to orthogonality. However, due to rotational freedom there are infinitely many possible whitening procedures. Consequently, there is a diverse range of sphering methods in use, for example based on principal component analysis (PCA), Cholesky matrix decomposition and zero-phase component analysis (ZCA), among others. Here we provide an overview of the underlying theory and discuss five natural whitening procedures. Subsequently, we demonstrate that investigating the cross-covariance and the cross-correlation matrix between sphered and original variables allows to break the rotational invariance and to identify optimal whitening transformations. As a result we recommend two particular approaches: ZCA-cor whitening to produce sphered variables that are maximally similar to the original variables, and PCA-cor whitening to obtain sphered variables that maximally compress the original variables.
DOI: 10.6084/m9.figshare.4568002.v1
title: Optimal Whitening and Decorrelation

description: Whitening, or sphering, is a common preprocessing step in statistical analysis to transform random variables to orthogonality. However, due to rotational freedom there are infinitely many possible whitening procedures. Consequently, there is a diverse range of sphering methods in use, for example based on principal component analysis (PCA), Cholesky matrix decomposition and zero-phase component analysis (ZCA), among others. Here we provide an overview of the underlying theory and discuss five natural whitening procedures. Subsequently, we demonstrate that investigating the cross-covariance and the cross-correlation matrix between sphered and original variables allows to break the rotational invariance and to identify optimal whitening transformations. As a result we recommend two particular approaches: ZCA-cor whitening to produce sphered variables that are maximally similar to the original variables, and PCA-cor whitening to obtain sphered variables that maximally compress the original variables.
DOI: 10.6084/m9.figshare.4568005.v1
title: Visualizing Type II Error in Normality Tests

description: A skewed exponential power distribution, with parameters defining kurtosis and skewness, is introduced as a way to visualize Type II error in normality tests. By varying these parameters a mosaic of distributions is built, ranging from double exponential to uniform or from positive to negative exponential; the normal distribution is a particular case located in the center of the mosaic. Using a sequential color scheme, a different color is assigned to each distribution in the mosaic depending on the probability of committing a Type II error. This graph gives a visual representation of the power of the performed test. This way of representing results facilitates the comparison of the power of various tests and the influence of sample size. A script to perform this graphical representation, programmed in the R statistical software, is available online as supplementary material.
DOI: 10.6084/m9.figshare.4567948
title: Photolytic changes in the morphology of porphyrin-phthalocyanine nanostructures (P-PcNs) in the presence of platinum and gold salts

description: Porphyrin-phthalocyanine nanostructures (P-PcNs) have been fabricated by electrostatic self-assembly of two oppositely charged molecules. The negatively charged molecule, meso-tetra-(4-phenylsulphonate)porphyrin (HT) and the positively charged species; {1,(4)-tetrakis-[(N-methyl(3-pyridyloxy) phthlocyaninato] chloro gallium(III)} sulphate, {2,(3)-tetrakis-[(N-methyl{(2-mercaptopyridine) phthalocyaninato} hydroxy manganese(III)} sulphate, {1,(4)-tetrakis-[(N-methyl-(3-pyridyloxy) phthalocyaninato] chloro indium(III)} sulphate, {2,3-octakis-{[(N-methyl-2-mercaptopyridine) phthalocyaninato] acetato manganese(III)} sulphate, {2,(3)-tetrakis-[(N-methyl(3-pyridyloxy) phthlocyaninato] choro gallium(III)} sulphate, {2,3-octakis-[(N-methy-3-pyridyloxy) phthalocyaninato] chloro indium(III)} sulphate, and {2,(3)-tetrakis-[(N-methyl (3-pyridyloxy) phthalocyaninato] chloro indium(III)} sulphate. Transmission electron microscopic (TEM) images showed that the formed nanostructures ranged from nanosheets to nanorods and nanotubes. The UV-Vis spectra confirmed that the molecules formed J-aggregates. The P-PcNs were exposed to incandescence light in the presence of platinum and gold salts. It was observed that the presence of platinum salts resulted in the destruction of the P-PcNs with possible formation of a Pt-Pc complex. While with the gold salt, the structures of P-PcNs were not only retained but were also enhanced to longer nanorods and nanofibers with the formation of gold nanoparticles.
DOI: 10.6084/m9.figshare.4567945
title: Source data for manuscript figures

description: source data in CSV format used to generate figures<br>
DOI: 10.6084/m9.figshare.4567999.v1
title: Statistical Considerations in Demonstrating CMC Analytical Similarity for a Biosimilar Product

description: Demonstration of analytical similarity between a reference product and a biosimilar product is required as part of the biosimilarity approval process. A statistical two one-sided test (TOST) based on the difference of means proposed in the literature and recommended by the FDA for Tier 1 quality attributes is demonstrated to have a type I error rate greater than the specified level, which cannot be corrected by increasing sample size. In this paper, an alternative TOST based on the effect size is demonstrated to maintain the desired type I error rate, and in some situations, provide greater power than the TOST based on the mean difference. Results are demonstrated both analytically and with computer simulations. An example with calculations is provided in the paper.
DOI: 10.6084/m9.figshare.4567939
title: Yersinia pestis acetyltransferase-mediated dual acetylation at the serine and lysine residues enhances the auto-ubiquitination of ubiquitin ligase MARCH8 in human cells

description: Lysine acetylation is known as a post translational modification (PTM) by histone acetyltransferases (HAT) that modifies histones and non-histone proteins to regulate gene expression. Serine acetylation, however, is reported in mammalian hosts by serine acetyltransferase of Yersinia pestis (YopJ) during infection. The protein target and cellular function of bacterial YopJ in mammalian systems are not fully addressed. Here we report dual acetylation at the serine and lysine residues by transiently expressed serine acetyltransferase YopJ mimicking Y. pestis infection in HeLa cells. Using shotgun proteomics followed by label-free quantification, we demonstrate an increase of dual acetylation in YopJ transfected human cells, including 10 Ser- (YopJ/non-YopJ 1.3-fold, p = 0.02) and 8 Lys- (YopJ/non-YopJ 3.5-fold, p = 0.00003) acetylation sites. Specifically, YopJ expression augments acetylation of membrane-associated E3 ubiquitin ligase MARCH8 at the serine residue Sac44, Sac71 and Sac253, and the lysine residue Kac247 and Kac252. YopJ-mediated Ser- and Lys-acetylation of MARCH8 is further confirmed by Western blotting using the specific antibodies against MARCH8 Sac71 and pan-acetyl lysine. Functional study demonstrates that YopJ-mediated Ser- and Lys-acetylation affects the auto-ubiquitination of MARCH8. The mutant C172A of YopJ previously shown to abolish the acetyltransferase activity also reduces Ser- and Lys-acetylation and diminishes the auto-ubiquitination of MARCH8. In support, MARCH8 is indeed acetylated at serine and lysine <i>in vitro</i> by purified YopJ but the activity is reduced by the C172A mutant in YopJ. Our study provides evidence that bacterial serine acetyltransferase YopJ mediates Ser- and Lys-acetylation and affects auto-ubiquitination of ubiquitin ligase MARCH8 in human cells.
DOI: 10.6084/m9.figshare.4567999.v2
title: Statistical Considerations in Demonstrating CMC Analytical Similarity for a Biosimilar Product

description: Demonstration of analytical similarity between a reference product and a biosimilar product is required as part of the biosimilarity approval process. A statistical two one-sided test (TOST) based on the difference of means proposed in the literature and recommended by the FDA for Tier 1 quality attributes is demonstrated to have a Type I error rate greater than the specified level, which cannot be corrected by increasing sample size. In this article, an alternative TOST based on the effect size is demonstrated to maintain the desired Type I error rate, and in some situations, provide greater power than the TOST based on the mean difference. Results are demonstrated both analytically and with computer simulations. An example with calculations is provided in the article. Supplementary materials for this article are avalilable online.
DOI: 10.6084/m9.figshare.4567927
title: Wee1 and Cdc25 are controlled by conserved PP2A-dependent mechanisms in fission yeast

description: Wee1 and Cdc25 are conserved regulators of mitosis. Wee1 is a kinase that delays mitosis via inhibitory phosphorylation of Cdk1, while Cdc25 is a phosphatase that promotes mitosis by removing the inhibitory phosphorylation. Although Wee1 and Cdc25 are conserved proteins, it has remained unclear whether their functions and regulation are conserved across diverse species. Here, we analyzed regulation of Wee1 and Cdc25 in fission yeast. Both proteins undergo dramatic cell cycle-dependent changes in phosphorylation that are dependent upon PP2A associated with the regulatory subunit Pab1. The mechanisms that control Wee1 and Cdc25 in fission yeast appear to share similarities to those in budding yeast and vertebrates, which suggests that there may be common mechanisms that control mitotic entry in all eukaryotic cells.
DOI: 10.6084/m9.figshare.4567999.v3
title: Statistical Considerations in Demonstrating CMC Analytical Similarity for a Biosimilar Product

description: Demonstration of analytical similarity between a reference product and a biosimilar product is required as part of the biosimilarity approval process. A statistical two one-sided test (TOST) based on the difference of means proposed in the literature and recommended by the FDA for Tier 1 quality attributes is demonstrated to have a type I error rate greater than the specified level, which cannot be corrected by increasing sample size. In this paper, an alternative TOST based on the effect size is demonstrated to maintain the desired type I error rate, and in some situations, provide greater power than the TOST based on the mean difference. Results are demonstrated both analytically and with computer simulations. An example with calculations is provided in the paper.
DOI: 10.6084/m9.figshare.4567927.v1
title: Wee1 and Cdc25 are controlled by conserved PP2A-dependent mechanisms in fission yeast

description: Wee1 and Cdc25 are conserved regulators of mitosis. Wee1 is a kinase that delays mitosis via inhibitory phosphorylation of Cdk1, while Cdc25 is a phosphatase that promotes mitosis by removing the inhibitory phosphorylation. Although Wee1 and Cdc25 are conserved proteins, it has remained unclear whether their functions and regulation are conserved across diverse species. Here, we analyzed regulation of Wee1 and Cdc25 in fission yeast. Both proteins undergo dramatic cell cycle-dependent changes in phosphorylation that are dependent upon PP2A associated with the regulatory subunit Pab1. The mechanisms that control Wee1 and Cdc25 in fission yeast appear to share similarities to those in budding yeast and vertebrates, which suggests that there may be common mechanisms that control mitotic entry in all eukaryotic cells.
DOI: 10.6084/m9.figshare.4567999.v4
title: Statistical Considerations in Demonstrating CMC Analytical Similarity for a Biosimilar Product

description: Demonstration of analytical similarity between a reference product and a biosimilar product is required as part of the biosimilarity approval process. A statistical two one-sided test (TOST) based on the difference of means proposed in the literature and recommended by the FDA for Tier 1 quality attributes is demonstrated to have a Type I error rate greater than the specified level, which cannot be corrected by increasing sample size. In this article, an alternative TOST based on the effect size is demonstrated to maintain the desired Type I error rate, and in some situations, provide greater power than the TOST based on the mean difference. Results are demonstrated both analytically and with computer simulations. An example with calculations is provided in the article. Supplementary materials for this article are avalilable online.
DOI: 10.6084/m9.figshare.4567999.v5
title: Statistical Considerations in Demonstrating CMC Analytical Similarity for a Biosimilar Product

description: Demonstration of analytical similarity between a reference product and a biosimilar product is required as part of the biosimilarity approval process. A statistical two one-sided test (TOST) based on the difference of means proposed in the literature and recommended by the FDA for Tier 1 quality attributes is demonstrated to have a type I error rate greater than the specified level, which cannot be corrected by increasing sample size. In this paper, an alternative TOST based on the effect size is demonstrated to maintain the desired type I error rate, and in some situations, provide greater power than the TOST based on the mean difference. Results are demonstrated both analytically and with computer simulations. An example with calculations is provided in the paper.
DOI: 10.6084/m9.figshare.4567999.v6
title: Statistical Considerations in Demonstrating CMC Analytical Similarity for a Biosimilar Product

description: Demonstration of analytical similarity between a reference product and a biosimilar product is required as part of the biosimilarity approval process. A statistical two one-sided test (TOST) based on the difference of means proposed in the literature and recommended by the FDA for Tier 1 quality attributes is demonstrated to have a Type I error rate greater than the specified level, which cannot be corrected by increasing sample size. In this article, an alternative TOST based on the effect size is demonstrated to maintain the desired Type I error rate, and in some situations, provide greater power than the TOST based on the mean difference. Results are demonstrated both analytically and with computer simulations. An example with calculations is provided in the article. Supplementary materials for this article are avalilable online.