cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5463499
title: Genetic variability of <i>CYP2D6</i>, <i>CYP2B6</i>, <i>CYP2C9</i> and <i>CYP2C19</i> genes across the Italian Peninsula

description: <b>Background:</b> Environmental conditions and past migratory events may have shaped genetic heterogeneity of clinically relevant enzymes involved in the phase I metabolism of the most common therapeutic drugs. <b>Aim:</b> To investigate the genetic variability of <i>CYP2D6</i>, <i>CYP2B6</i>, <i>CYP2C19</i> and <i>CYP2C9</i> across the Italian Peninsula, by sampling only ancestrally and geographically homogeneous individuals from northern, central and southern Italy. <b>Subjects and methods:</b> A total of 25 SNPs were genotyped in 174 unrelated Italian individuals by means of multiplex PCR and minisequencing reactions. <i>CYP2D6</i> genotypic data were used to predict phenotypes and the phylogenetic relationships among reconstructed haplotypes were represented by means of a Median Joining Network. <b>Results:</b> Pairwise Fisher Exact tests revealed significant differences between northern and southern Italy in the distribution of <i>CYP2C19</i> genotypes, with the <i>CYP2C19*2</i> allele appearing over-represented in northern Italy. Likewise, significant differences in the distribution of <i>CYP2D6</i> genotypes (*4/*3, *4/*4 and *6/*4) responsible for the poor metabolizer phenotype were observed in northern with respect to both central and southern Italy. <b>Conclusions:</b> The north–south structuring pattern showed by <i>CYP2D6</i> and <i>CYP2C19</i> underline how a deeper knowledge of the geographic distribution of alleles may improve clinical practice and help to avoid hypothetical bias in drug trials.
DOI: 10.6084/m9.figshare.5463484
title: BARM annotations

description: Functional and taxonomic annotations of the sequences published with the Baltic Sea reference Metagenome. Details of how the annotations are made are available in the publication.
DOI: 10.6084/m9.figshare.5463499.v1
title: Genetic variability of <i>CYP2D6</i>, <i>CYP2B6</i>, <i>CYP2C9</i> and <i>CYP2C19</i> genes across the Italian Peninsula

description: <b>Background:</b> Environmental conditions and past migratory events may have shaped genetic heterogeneity of clinically relevant enzymes involved in the phase I metabolism of the most common therapeutic drugs. <b>Aim:</b> To investigate the genetic variability of <i>CYP2D6</i>, <i>CYP2B6</i>, <i>CYP2C19</i> and <i>CYP2C9</i> across the Italian Peninsula, by sampling only ancestrally and geographically homogeneous individuals from northern, central and southern Italy. <b>Subjects and methods:</b> A total of 25 SNPs were genotyped in 174 unrelated Italian individuals by means of multiplex PCR and minisequencing reactions. <i>CYP2D6</i> genotypic data were used to predict phenotypes and the phylogenetic relationships among reconstructed haplotypes were represented by means of a Median Joining Network. <b>Results:</b> Pairwise Fisher Exact tests revealed significant differences between northern and southern Italy in the distribution of <i>CYP2C19</i> genotypes, with the <i>CYP2C19*2</i> allele appearing over-represented in northern Italy. Likewise, significant differences in the distribution of <i>CYP2D6</i> genotypes (*4/*3, *4/*4 and *6/*4) responsible for the poor metabolizer phenotype were observed in northern with respect to both central and southern Italy. <b>Conclusions:</b> The north–south structuring pattern showed by <i>CYP2D6</i> and <i>CYP2C19</i> underline how a deeper knowledge of the geographic distribution of alleles may improve clinical practice and help to avoid hypothetical bias in drug trials.
DOI: 10.6084/m9.figshare.5463448
title: Biostratigraphic results from Miocene-Pliocene sites in the Dardanelles area (Turkey).

description: Biostratigraphic results from sites in the Dardanelles area (Turkey). <br>Data used in paper Karakaş et al., Crustal strain in the Marmara pull-apart region associated with the propagation process of the North Anatolian fault, published in Tectonics, 2018 - https://doi.org/10.1029/2017TC004636<br><br>
DOI: 10.6084/m9.figshare.5463448.v1
title: Biostratigraphic results from Miocene-Pliocene sites in the Dardanelles area (Turkey).

description: Biostratigraphic results from sites in the Dardanelles area (Turkey). <br>Data used in paper Karakaş et al., Crustal strain in the Marmara pull-apart region associated with the propagation process of the North Anatolian fault, published in Tectonics, 2018 - https://doi.org/10.1029/2017TC004636<br><br>
DOI: 10.6084/m9.figshare.5463460.v2
title: Poster IODP-ITALIA 2017

description: IODP-ITALIA
DOI: 10.6084/m9.figshare.5462500
title: Learning multilingual named entity recognition from Wikipedia

description: This is the data associated with Joel Nothman, Nicky Ringland, Will Radford, Tara Murphy and James R. Curran (2013), "Learning multilingual named entity recognition from Wikipedia", <i>Artificial Intelligence</i> 194 (DOI: 10.1016/j.artint.2012.03.006). A preprint is included here as wikiner-preprint.pdf<br>This data was originally available at http://schwa.org/resources (which linked to http://schwa.org/projects/resources/wiki/Wikiner).<br>The .bz2 files are NER training corpora produced as reported in the Artificial Intelligence paper. wp2 and wp3 are differentiated by wp3 using a higher level of link inference. They use a pipe-delimited format that can be converted to CoNLL 2003 format with system2conll.pl.<br>nothman08types.tsv is a manual classification of articles first used in Joel Nothman, James R. Curran and Tara Murphy (2008), "Transforming Wikipedia into Named Entity Training Data", In <i>Proceedings of the Australasian Language Technology Association Workshop 2008</i>. http://aclanthology.coli.uni-saarland.de/pdf/U/U08/U08-1016.pdf<br>popular.tsv and random.tsv are manual article classifications developed for the Artifiical Intelligence paper based on different strategies for sampling articles from Wikipedia in order to account for Wikipedia's biased distribution (see that paper). scheme.tsv maps these fine-grained labels to coarser annotations including CoNLL 2003-style.<br>wikigold.conll.txt is a manual NER annotation of some Wikipedia text as presented in Dominic Balasuriya and Nicky Ringland and Joel Nothman and Tara Murphy and James R. Curran (2009), in <i>Proceedings of the 2009 Workshop on The People's Web Meets NLP: Collaboratively Constructed Semantic Resources</i> (http://www.aclweb.org/anthology/W/W09/W09-3302).<br><br>See also corpora produced similarly in an enhanced version of this work work (Pan et al., "Cross-lingual Name Tagging and Linking for 282 Languages", ACL 2017) at http://nlp.cs.rpi.edu/wikiann/.
DOI: 10.6084/m9.figshare.5462272
title: Developmental Delay in the Amazon

description: Social determinants and child development evaluation
DOI: 10.6084/m9.figshare.5462272.v1
title: Developmental Delay in the Amazon

description: Social determinants and child development evaluation
DOI: 10.6084/m9.figshare.5462431.v2
title: Identifying knowledge gap workshop (5-6 Oct 2017)

description: The slides for Identifying knowledge gap workshop: <br>Aston Braga 5-6 Oct 2017.<br>
DOI: 10.6084/m9.figshare.5462431.v3
title: Identifying knowledge gap workshop (5-6 Oct 2017)

description: The slides for Identifying knowledge gap workshop: <br>Aston Braga 5-6 Oct 2017.<br>
DOI: 10.6084/m9.figshare.5462152
title: Infant rhesus monkey -- stool microbiome -- mapping file (16s V4)

description: <b><i>Infant monkey_processing_info.txt</i></b>: contains processing information, prepared using Qiita's guidline.<b><br></b><b><i>Infant_monkey_sample_info.txt</i></b>: contains sample information, prepared using Qiita's guideline.<br><b><i>mapping_forward_rhesus_monkey_fecal.txt</i></b>: a simplified Qiime mapping file including most useful sample info. <br>Annotation on treatment groups: FF = exclusive formula-fed; FF-probiotics = exclusive fed with probiotics supplemented formula; BF = exclusive breast-fed.
DOI: 10.6084/m9.figshare.5462431.v5
title: Identifying knowledge gap workshop (5-6 Oct 2017)

description: The slides for Identifying knowledge gap workshop: <br>Aston Braga 5-6 Oct 2017.<br>
DOI: 10.6084/m9.figshare.5462152.v1
title: Infant rhesus monkey -- stool microbiome -- mapping file (16s V4)

description: <b><i>Infant monkey_processing_info.txt</i></b>: contains processing information, prepared using Qiita's guidline.<b><br></b><b><i>Infant_monkey_sample_info.txt</i></b>: contains sample information, prepared using Qiita's guideline.<br><b><i>mapping_forward_rhesus_monkey_fecal.txt</i></b>: a simplified Qiime mapping file including most useful sample info. <br>Annotation on treatment groups: FF = exclusive formula-fed; FF-probiotics = exclusive fed with probiotics supplemented formula; BF = exclusive breast-fed.
DOI: 10.6084/m9.figshare.5461891
title: Infant rhesus monkey -- stool microbiome -- forward sequence (16s V4)

description: This forward primer starts with an 8 bp barcodes, then a linker sequence (<b>GT</b>), then the PCR forward primer. The forward primer is <b>GTGCCAGCMGCCGCGGTAA.</b>This forward read sequence contains data from other studies. Please use the mapping file for demultiplexing. <b><br></b>
DOI: 10.6084/m9.figshare.5462044
title: Infant rhesus monkey -- stool microbiome -- sequence after demultiplexing (16s V4)

description: <b>seqs.fna</b> is the output from Qiime script (v 1.8.0) split_libraries_fastq.pyParameter used:--barcode_type hamming_8 --max_barcode_errors 0 <br><br><b>seqs_8_bases_removed.fna</b> is generated from seqs.fna after removing the 8 bp barcode at the beginning of the sequence. <br><b>Note</b>: Linker sequence (GT) and PCR forward primers are still at the beginning of this sequence. The forward primer is GTGCCAGCMGCCGCGGTAA<br>
DOI: 10.6084/m9.figshare.5462065
title: Hindlimb Loading by Experimental Group

description: Boxplot of the average amount of load (as a percentage of body mass), experienced by the hindlimbs over a 60 minute exercise period in each experimental group, over a twelve week experiment. All comparisons are significantly different (p&lt;0.001).
DOI: 10.6084/m9.figshare.5462044.v1
title: Infant rhesus monkey -- stool microbiome -- sequence after demultiplexing (16s V4)

description: <b>seqs.fna</b> is the output from Qiime script (v 1.8.0) split_libraries_fastq.pyParameter used:--barcode_type hamming_8 --max_barcode_errors 0 <br><br><b>seqs_8_bases_removed.fna</b> is generated from seqs.fna after removing the 8 bp barcode at the beginning of the sequence. <br><b>Note</b>: Linker sequence (GT) and PCR forward primers are still at the beginning of this sequence. That is GTGCCAGCMGCCGCGGTAA<br>
DOI: 10.6084/m9.figshare.5462431.v4
title: Identifying knowledge gap workshop (5-6 Oct 2017)

description: The slides for Identifying knowledge gap workshop: <br>Aston Braga 5-6 Oct 2017.<br>
DOI: 10.6084/m9.figshare.5461891.v1
title: Infant rhesus monkey -- stool microbiome -- forward sequence (16s V4)

description: This forward primer starts with an 8 bp barcodes, then a linker sequence (<b>GT</b>), then the PCR forward primer. The forward primer is <b>GTGCCAGCMGCCGCGGTAA.</b>This forward read sequence contains data from other studies. Please use the mapping file for demultiplexing. <b><br></b>
DOI: 10.6084/m9.figshare.5459878
title: Infant rhesus monkey -- stool microbiome -- barcode sequence (16s V4)

description: This 8 bp Hamming error-correcting barcode sequence is not generated via direct sequencing, instead, it was extracted from the forward reads. This barcode sequence also contains data from other studies. Please use the mapping file for demultiplexing. <br>
DOI: 10.6084/m9.figshare.5459680
title: The 3D OrbiSIMS – Label-Free Metabolic Imaging with Sub-cellular Lateral Resolution and High Mass Resolving Power

description: We have developed the 3D OrbiSIMS for label-free biomedical imaging. It has an unparalleled simultaneous combination of spatial resolution (under 200 nm for inorganics and under 1.5 µm for biomolecules) and mass resolving power of &gt; 240,000 at <i>m/z</i> 200. This allows the distribution of exogenous and endogenous metabolites to be visualized in 3D with sub-cellular resolution. We image the distribution of neurotransmitters—gamma-aminobutyric acid (GABA), dopamine and serotonin with high spectroscopic confidence in the CA3 and CA1 regions of the hippocampus (murine). GABA is most abundant in the <i>stratum oriens</i>. We identify and map the sub-cellular localisation of 53 glycosphingolipid sulfatide species and demonstrate the ability of tandem mass spectrometry to confirm lipid identity. Single cell metabolomic profiling is demonstrated using rat alveolar macrophage cells incubated with different concentrations of the drug amiodarone. The up-regulation of phospholipid species and cholesterol is correlated with the accumulation of amiodarone.
DOI: 10.6084/m9.figshare.5459878.v2
title: Infant rhesus monkey -- stool microbiome -- barcode sequence (16s V4)

description: This 8 bp Hamming error-correcting barcode sequence is not generated via direct sequencing, instead, it was extracted from the forward reads. This barcode sequence also contains data from other studies. Please use the mapping file for demultiplexing. <br>
DOI: 10.6084/m9.figshare.5459878.v1
title: Infant rhesus monkey -- stool microbiome -- Barcode sequence (16s V4)

description: This 8 bp Hamming error-correcting barcode sequence is not generated via direct sequencing, instead, it was extracted from the forward reads
DOI: 10.6084/m9.figshare.5459662
title: The role of self-incompatibility systems in the prevention of bi-parental inbreeding

description: Inbreeding in hermaphroditic plants can occur through two different mechanisms: biparental inbreeding, when a plant mates with a related individual, and self-fertilization, a more extreme form of inbreeding. To avoid inbreeding, many hermaphroditic plants have evolved self-incompatibility (SI) systems which prevent or limit self-fertilization. One particular SI system -- homomorphic SI -- can also reduce biparental inbreeding. Homomorphic SI is found in many angiosperm species, and it is often assumed that the additional benefit of reduced biparental inbreeding may be a factor in the success of this SI system. To test this assumption, we developed a spatially-explicit, individual-based simulation of plant populations that displayed three different types of homomorphic SI. We measured the total level of inbreeding avoidance by comparing each population to a self-compatible population (NSI), and we measured biparental inbreeding avoidance by comparing to a population of self-incompatible plants that were free to mate with any other individual (PSI). Because biparental inbreeding is more common when offspring dispersal is limited, we examined the levels of biparental inbreeding over a range of dispersal distances. We also tested whether the introduction of inbreeding depression affected the level of biparental inbreeding avoidance. We found that there was a statistically significant decrease in autozygosity in each of the homomorphic SI populations compared to the PSI population and, as expected, this was more pronounced when seed and pollen dispersal was limited. However, levels of homozygosity and inbreeding depression were not reduced. At low dispersal, homomorphic SI populations also suffered reduced female fecundity and had smaller census population sizes. Overall, our simulations showed that the homomorphic SI systems had little impact on the amount of biparental inbreeding in the population especially when compared to the overall reduction in inbreeding compared to the NSI population. With further study, this observation may have important consequences for research into the origin and evolution of homomorphic self-incompatibility systems.
DOI: 10.6084/m9.figshare.5462065.v4
title: Hindlimb Loading by Experimental Group

description: Boxplot of the average amount of load (as a percentage of body mass), experienced by the hindlimbs over a 60 minute exercise period in each experimental group, over a twelve week experiment. All comparisons are significantly different (p&lt;0.001).
DOI: 10.6084/m9.figshare.5459662.v2
title: The role of self-incompatibility systems in the prevention of bi-parental inbreeding

description: Inbreeding in hermaphroditic plants can occur through two different mechanisms: biparental inbreeding, when a plant mates with a related individual, and self-fertilization, a more extreme form of inbreeding. To avoid inbreeding, many hermaphroditic plants have evolved self-incompatibility (SI) systems which prevent or limit self-fertilization. One particular SI system -- homomorphic SI -- can also reduce biparental inbreeding. Homomorphic SI is found in many angiosperm species, and it is often assumed that the additional benefit of reduced biparental inbreeding may be a factor in the success of this SI system. To test this assumption, we developed a spatially-explicit, individual-based simulation of plant populations that displayed three different types of homomorphic SI. We measured the total level of inbreeding avoidance by comparing each population to a self-compatible population (NSI), and we measured biparental inbreeding avoidance by comparing to a population of self-incompatible plants that were free to mate with any other individual (PSI). Because biparental inbreeding is more common when offspring dispersal is limited, we examined the levels of biparental inbreeding over a range of dispersal distances. We also tested whether the introduction of inbreeding depression affected the level of biparental inbreeding avoidance. We found that there was a statistically significant decrease in autozygosity in each of the homomorphic SI populations compared to the PSI population and, as expected, this was more pronounced when seed and pollen dispersal was limited. However, levels of homozygosity and inbreeding depression were not reduced. At low dispersal, homomorphic SI populations also suffered reduced female fecundity and had smaller census population sizes. Overall, our simulations showed that the homomorphic SI systems had little impact on the amount of biparental inbreeding in the population especially when compared to the overall reduction in inbreeding compared to the NSI population. With further study, this observation may have important consequences for research into the origin and evolution of homomorphic self-incompatibility systems.
DOI: 10.6084/m9.figshare.5459662.v1
title: The role of self-incompatibility systems in the prevention of bi-parental inbreeding

description: Inbreeding in hermaphroditic plants can occur through two different mechanisms: biparental inbreeding, when a plant mates with a related individual, and self-fertilization, a more extreme form of inbreeding. To avoid inbreeding, many hermaphroditic plants have evolved self-incompatibility (SI) systems which prevent or limit self-fertilization. One particular SI system -- homomorphic SI -- can also reduce biparental inbreeding. Homomorphic SI is found in many angiosperm species, and it is often assumed that the additional benefit of reduced biparental inbreeding may be a factor in the success of this SI system. To test this assumption, we developed a spatially-explicit, individual-based simulation of plant populations that displayed three different types of homomorphic SI. We measured the total level of inbreeding avoidance by comparing each population to a self-compatible population (NSI), and we measured biparental inbreeding avoidance by comparing to a population of self-incompatible plants that were free to mate with any other individual (PSI). Because biparental inbreeding is more common when offspring dispersal is limited, we examined the levels of biparental inbreeding over a range of dispersal distances. We also tested whether the introduction of inbreeding depression affected the level of biparental inbreeding avoidance. We found that there was a statistically significant decrease in autozygosity in each of the homomorphic SI populations compared to the PSI population and, as expected, this was more pronounced when seed and pollen dispersal was limited. However, levels of homozygosity and inbreeding depression were not reduced. At low dispersal, homomorphic SI populations also suffered reduced female fecundity and had smaller census population sizes. Overall, our simulations showed that the homomorphic SI systems had little impact on the amount of biparental inbreeding in the population especially when compared to the overall reduction in inbreeding compared to the NSI population. With further study, this observation may have important consequences for research into the origin and evolution of homomorphic self-incompatibility systems.
DOI: 10.6084/m9.figshare.5459572
title: morph JBMS evaluation files

description: evaluation files of morph JBMS article
DOI: 10.6084/m9.figshare.5459572.v1
title: morph JBMS evaluation files

description: evaluation files of morph JBMS article
DOI: 10.6084/m9.figshare.5459359
title: Tables3_24hourpHmonitoring.csv from Fluctuating seawater pH/<i>p</i>CO<sub>2</sub> regimes are more energetically expensive than static pH/<i>p</i>CO<sub>2</sub> levels in the mussel <i>Mytilus edulis</i>

description: Seawater pH over 24 hours of exposure for the four treatments.
DOI: 10.6084/m9.figshare.5459359.v1
title: Tables3_24hourpHmonitoring.csv from Fluctuating seawater pH/<i>p</i>CO<sub>2</sub> regimes are more energetically expensive than static pH/<i>p</i>CO<sub>2</sub> levels in the mussel <i>Mytilus edulis</i>

description: Seawater pH over 24 hours of exposure for the four treatments.
DOI: 10.6084/m9.figshare.5459536
title: On the Dark World of Richard Dawkins

description: In The Selfish Gene, The Blind Watchmaker and The God Delusion, Richard Dawkins expresses what is undoubtedly the mainstream view of the origin of the species. An outgrowth of atomism, materialism, and the "scientific" revolution, the epistemological and ethical implications of the story of origins he champions ("Once upon a time there was a dark land in which might was the only right and in which no one lived happily after.") has given the world Nietzsche, Adolf Hitler and the Nazis, the Holocaust, the moral bankruptcy of modern America and their representative -the man most likely to start World War III - Donald Trump. And of course it has given us Dawkins himself. Here we focus on a pair of necessary conditions of the reality of Dawkins' brutal, mindless, pitiless, world and show that these conditions cannot be met.
DOI: 10.6084/m9.figshare.5459329
title: Variable sites in a 658-bp sequence of mitochondrial COI region from Maternally transmitted non-bacterial male killer in <i>Drosophila biauraria</i>

description: Variable sites of all-female line, normal line, and four injected lines are shown.
DOI: 10.6084/m9.figshare.5459329.v1
title: Variable sites in a 658-bp sequence of mitochondrial COI region from Maternally transmitted non-bacterial male killer in <i>Drosophila biauraria</i>

description: Variable sites of all-female line, normal line, and four injected lines are shown.
DOI: 10.6084/m9.figshare.5459266
title: Eye images do not promote prosocial behaviour or norm compliance in an online Dictator Game : data and code to reproduce analyses

description: Dataset and code to accompany: the paper: "Eye images do not promote prosocial behaviour or norm compliance in an online Dictator Game"
DOI: 10.6084/m9.figshare.5459266.v2
title: Eye images do not promote prosocial behaviour or norm compliance in an online Dictator Game : data and code to reproduce analyses

description: Dataset and code to accompany: the paper: "Eye images do not promote prosocial behaviour or norm compliance in an online Dictator Game"
DOI: 10.6084/m9.figshare.5459266.v1
title: Eye images do not promote prosocial behaviour or norm compliance in an online Dictator Game : data and code to reproduce analyses

description: Dataset and code to accompany: the paper: "Eye images do not promote prosocial behaviour or norm compliance in an online Dictator Game"