cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1466911.v6
title: Passenger strand loading in overexpression experiments using microRNA mimics

description: MicroRNAs (miRNAs) are important regulators of gene function and manipulation of miRNAs is a central component of basic research. Modulation of gene expression by miRNA gain-of-function can be based on different approaches including transfection with miRNA mimics; artificial, chemically modified miRNA-like small RNAs. These molecules are intended to mimic the function of a miRNA guide strand while bypassing the maturation steps of endogenous miRNAs. Due to easy accessibility through commercial providers this approach has gained popularity, and accuracy is often assumed without prior independent testing. Our <i>in silico</i> analysis of over-represented sequence motifs in microarray expression data and sequencing of AGO-associated small RNAs indicate, however, that miRNA mimics may be associated with considerable side-effects due to the unwanted activity of the miRNA mimic complementary strand.
DOI: 10.6084/m9.figshare.1466911.v5
title: Passenger strand loading in overexpression experiments using microRNA mimics

description: MicroRNAs (miRNAs) are important regulators of gene function and manipulation of miRNAs is a central component of basic research. Modulation of gene expression by miRNA gain-of-function can be based on different approaches including transfection with miRNA mimics; artificial, chemically modified miRNA-like small RNAs. These molecules are intended to mimic the function of a miRNA guide strand while bypassing the maturation steps of endogenous miRNAs. Due to easy accessibility through commercial providers this approach has gained popularity, and accuracy is often assumed without prior independent testing. Our <i>in silico</i> analysis of over-represented sequence motifs in microarray expression data and sequencing of AGO-associated small RNAs indicate, however, that miRNA mimics may be associated with considerable side-effects due to the unwanted activity of the miRNA mimic complementary strand.
DOI: 10.6084/m9.figshare.1466899
title: SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

description: Scripts and configuration files to benchmark, validate and perform a small test-case study with SimPhy, a novel gene family evolution simulator tool.
DOI: 10.6084/m9.figshare.1466899.v1
title: SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

description: Scripts and configuration files to benchmark, validate and perform a small test-case study with SimPhy, a novel gene family evolution simulator tool.
DOI: 10.6084/m9.figshare.1466898
title: Geomorphometric analysis of a rocky coastline: an example from Hornsund, Svalbard

description: We describe a method to extract a number of quantitative morphometric characteristics of a rocky coastline. The algorithm, which is implemented in the free open-source software GNU Octave, takes as its input an ordered set of coordinate pairs defining the coastline. It finds vertices of specific angularity at two different levels, first approximating convex features (headlands) and then looking for local maxima (embayment edges) in their vicinity. It extracts numerical parameters for each embayment delimited by the former points, including basic geometric parameters (e.g. area, depth and width) and coefficients expressing shapes of embayments (e.g. form factor, coefficient of asymmetry and compactness). These we adapted from morphometric studies of other geomorphic features. Complex headlands and random sectors of the coastline which are delimited by embayment edges are automatically removed. The method was developed and tested on Hornsund in Svalbard, where 20 headlands, 28 embayment edges and 20 embayments were identified, but could be adapted to a wide range of coastal situations. We consider a range of possible applications of the methods, including to the classification of coastlines, change detection and identifying controls on their morphologies, and we discuss the choice of optimum parameters for the algorithm.
DOI: 10.6084/m9.figshare.1466892
title: Poster for #smbe15

description: my poster for the #smbe15 conference in Vienna.
DOI: 10.6084/m9.figshare.1466890
title: Nature Communications: Assessing the transition to full open access

description: <em>Nature Communications</em> is an open access journal that publishes high-quality research from all areas of the natural sciences. Launched in 2010, the journal published a mixture of both subscription and open access content until 20th October 2014 before becoming fully open access. The switch to fully open access did not come without risks: subscription content made up 70% of the journal’s content, but as a company, Nature Publishing Group (NPG) wanted to provide a flagship open access title for the natural sciences. This poster demonstrates how the transition has affected the journal six months on.
DOI: 10.6084/m9.figshare.1466892.v2
title: Poster for #smbe15

description: my poster for the #smbe15 conference in Vienna.
DOI: 10.6084/m9.figshare.1466898.v2
title: Geomorphometric analysis of a rocky coastline: an example from Hornsund, Svalbard

description: We describe a method to extract a number of quantitative morphometric characteristics of a rocky coastline. The algorithm, which is implemented in the free open-source software GNU Octave, takes as its input an ordered set of coordinate pairs defining the coastline. It finds vertices of specific angularity at two different levels, first approximating convex features (headlands) and then looking for local maxima (embayment edges) in their vicinity. It extracts numerical parameters for each embayment delimited by the former points, including basic geometric parameters (e.g. area, depth and width) and coefficients expressing shapes of embayments (e.g. form factor, coefficient of asymmetry and compactness). These we adapted from morphometric studies of other geomorphic features. Complex headlands and random sectors of the coastline which are delimited by embayment edges are automatically removed. The method was developed and tested on Hornsund in Svalbard, where 20 headlands, 28 embayment edges and 20 embayments were identified, but could be adapted to a wide range of coastal situations. We consider a range of possible applications of the methods, including to the classification of coastlines, change detection and identifying controls on their morphologies, and we discuss the choice of optimum parameters for the algorithm.
DOI: 10.6084/m9.figshare.1466890.v1
title: Nature Communications: Assessing the transition to full open access

description: <em>Nature Communications</em> is an open access journal that publishes high-quality research from all areas of the natural sciences. Launched in 2010, the journal published a mixture of both subscription and open access content until 20th October 2014 before becoming fully open access. The switch to fully open access did not come without risks: subscription content made up 70% of the journal’s content, but as a company, Nature Publishing Group (NPG) wanted to provide a flagship open access title for the natural sciences. This poster demonstrates how the transition has affected the journal six months on.
DOI: 10.6084/m9.figshare.1466892.v1
title: Poster for #smbe15

description: my poster for the #smbe15 conference in Vienna.
DOI: 10.6084/m9.figshare.1466898.v1
title: Geomorphometric analysis of a rocky coastline: an example from Hornsund, Svalbard

description: We describe a method to extract a number of quantitative morphometric characteristics of a rocky coastline. The algorithm, which is implemented in the free open-source software GNU Octave, takes as its input an ordered set of coordinate pairs defining the coastline. It finds vertices of specific angularity at two different levels, first approximating convex features (headlands) and then looking for local maxima (embayment edges) in their vicinity. It extracts numerical parameters for each embayment delimited by the former points, including basic geometric parameters (e.g. area, depth and width) and coefficients expressing shapes of embayments (e.g. form factor, coefficient of asymmetry and compactness). These we adapted from morphometric studies of other geomorphic features. Complex headlands and random sectors of the coastline which are delimited by embayment edges are automatically removed. The method was developed and tested on Hornsund in Svalbard, where 20 headlands, 28 embayment edges and 20 embayments were identified, but could be adapted to a wide range of coastal situations. We consider a range of possible applications of the methods, including to the classification of coastlines, change detection and identifying controls on their morphologies, and we discuss the choice of optimum parameters for the algorithm.
DOI: 10.6084/m9.figshare.1466884
title: Intermittency as a Transition State in Combustor Dynamics: An Explanation for Flame Dynamics Near Lean Blowout

description: The dynamic transitions preceding lean blowout were investigated experimentally in a laboratory scale turbulent combustor by systematically varying the flow Reynolds number . Previous studies on combustor dynamics have shown that the onset of large-amplitude, combustion-driven oscillations is, at times, presaged by intermittent bursts of high-amplitude periodic pressure pulsations. These intermittent bursts appear in a near random fashion amidst regions of aperiodic low-amplitude fluctuations, provided the underlying flow-field is turbulent. In the present study, we show that intermittent burst oscillations are also observed in combustors close to the lean blowout limit. We show that such intermittent oscillations emerge through the establishment of homoclinic orbits in the phase space of pressure oscillations. The formation of such orbits points to the complex nature of the interaction between the hydrodynamics and acoustic subsystems, which operate over a range of different time scales. High-speed flame images reveal that the intermittent states observed prior to lean blowout correspond to aperiodic detachment of the flame from the bluff-body lip. These findings are consistent with other reports of possibly intermittent states in the literature.
DOI: 10.5517/ccdc.csd.cc20fsx5
title: CCDC 1860307: Experimental Crystal Structure Determination

description: Related Article: Sunny Goon, Chinky Shiu Chen Liu, Uddipta Ghosh Dastidar, Barnali Paul, Suravi Mukherjee, Himadri Sekhar Sarkar, Milie Desai, Rituparna Jana, Sourav Pal, Namala Venkata Sreedevi, Dipyaman Ganguly, Arindam Talukdar|2024|J.Med.Chem.|67|8225|doi:10.1021/acs.jmedchem.4c00322
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2grb2n
title: CCDC 2286531: Experimental Crystal Structure Determination

description: Related Article: Woonkee S. Jo, Brian J. Curtis, Mohammad Rehan, Maria L. Adrover-Castellano, David H. Sherman, Alan R. Healy|2024|JACS Au|4|2058|doi:10.1021/jacsau.4c00257
description: Related Article: Yao He|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2grb3p
title: CCDC 2286532: Experimental Crystal Structure Determination

description: Related Article: Woonkee S. Jo, Brian J. Curtis, Mohammad Rehan, Maria L. Adrover-Castellano, David H. Sherman, Alan R. Healy|2024|JACS Au|4|2058|doi:10.1021/jacsau.4c00257
description: Related Article: Yao He|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2grb9w
title: CCDC 2286538: Experimental Crystal Structure Determination

description: Related Article: Woonkee S. Jo, Brian J. Curtis, Mohammad Rehan, Maria L. Adrover-Castellano, David H. Sherman, Alan R. Healy|2024|JACS Au|4|2058|doi:10.1021/jacsau.4c00257
description: Related Article: Yao He|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2grbbx
title: CCDC 2286539: Experimental Crystal Structure Determination

description: Related Article: Woonkee S. Jo, Brian J. Curtis, Mohammad Rehan, Maria L. Adrover-Castellano, David H. Sherman, Alan R. Healy|2024|JACS Au|4|2058|doi:10.1021/jacsau.4c00257
description: Related Article: Yao He|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hchr4
title: CCDC 2304966: Experimental Crystal Structure Determination

description: Related Article: Léo Boivin, Adrien Schlachter, Daniel Fortin, Christophe Lescop, Pierre D. Harvey|2023|Molecules|28|7781|doi:10.3390/molecules28237781
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hcht6
title: CCDC 2304968: Experimental Crystal Structure Determination

description: Related Article: Léo Boivin, Adrien Schlachter, Daniel Fortin, Christophe Lescop, Pierre D. Harvey|2023|Molecules|28|7781|doi:10.3390/molecules28237781
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hchs5
title: CCDC 2304967: Experimental Crystal Structure Determination

description: Related Article: Léo Boivin, Adrien Schlachter, Daniel Fortin, Christophe Lescop, Pierre D. Harvey|2023|Molecules|28|7781|doi:10.3390/molecules28237781
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hchv7
title: CCDC 2304969: Experimental Crystal Structure Determination

description: Related Article: Léo Boivin, Adrien Schlachter, Daniel Fortin, Christophe Lescop, Pierre D. Harvey|2023|Molecules|28|7781|doi:10.3390/molecules28237781
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.mdpne7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Thanatus aridorum Šilhavý, 1940",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094877-240626123714530/datasets/export for details.
DOI: 10.5517/ccdc.csd.cc20fsw4
title: CCDC 1860306: Experimental Crystal Structure Determination

description: Related Article: Sunny Goon, Chinky Shiu Chen Liu, Uddipta Ghosh Dastidar, Barnali Paul, Suravi Mukherjee, Himadri Sekhar Sarkar, Milie Desai, Rituparna Jana, Sourav Pal, Namala Venkata Sreedevi, Dipyaman Ganguly, Arindam Talukdar|2024|J.Med.Chem.|67|8225|doi:10.1021/acs.jmedchem.4c00322
description: Related Article: Sunny Goon, Uddipta Ghosh Dastidar, Barnali Paul, Himadri Sekhar Sarkar, N.V. Sreedevi|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.rsevtg
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((9.85872 45.584,9.91122 45.584,9.91122 45.6127,9.85872 45.6127,9.85872 45.584))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 123 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094878-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fwsh9s
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Carabus odoratus Motschulsky, 1844",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 14 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094880-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5tapk8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Caridina masapi Woltereck, 1937)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094879-240626123714530/datasets/export for details.
DOI: 10.15468/dl.p2tm4u
title: Occurrence Download

description: A dataset containing 6642 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Evarcha falcata (Clerck, 1757)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 6642 records from 221 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094881-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8qd94z
title: Occurrence Download

description: A dataset containing 93119 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lacerta bilineata Daudin, 1802",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 93119 records from 2246 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094875-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh160162.07fu
title: SH160162.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh160163.07fu
title: SH160163.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.