cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1029236.v2
title: Bridging and mirroring registrations for Drosophila neuroanatomy

description: The fly brain is a highly stereotyped 3D structure. A number of groups have now published 3D confocal image datasets where all images have been registered to a specific template brain. In order to co-visualise image data from different studies, data registered against different template brains must be brought into the same 3D coordinate space. This can be achieved by applying a <strong>bridging registration</strong> which maps one template brain onto another. For almost all purposes the fly brain should be considered symmetric about its mid-sagittal plane (i.e. the plane perpendicular to the medio-lateral axis – typically the x-axis in image data). However, while the platonic fly brain may be symmetric, individual fly brains that have been fixed, stained and imaged are often significantly asymmetric and not placed exactly in the centre of the image with respect to their mid-sagittal plane. While it is trivial to make template brains that are centred and possible to make symmetric template brains if one wishes, this has rarely been done in practice. It is therefore necessary to do more than simply mirror along the medio- lateral axis if one desires to map neurons/structures in the left brain hemisphere onto the right hemisphere. <strong>Mirroring registrations</strong> account for this asymmetry and allow for comparisons across brain hemispheres. This collection contains bridging and mirroring registrations for a number of common Drosophila template brains, including those used by the FlyLight GAL4 collection, FlyCircuit, the Vienna Tiles collection, and the new systematic nomenclature for the insect brain.
DOI: 10.6084/m9.figshare.1029169.v1
title: Web Table 4. Free energy activation barriers for the formation of iodotriazoles via Mono- and bis Cu-catalysed cycloaddition pathways

description: Two complementary catalytic systems are reported for the 1,3-dipolar cycloaddition of azides and iodoalkynes. These are based on two commercially available/readily available copper complexes, [CuCl(IPr)] or [CuI(PPh3)3], which are active at low metal loadings (PPh3 system) or in the absence of any other additive (IPr system). These systems were used for the first reported mechanistic studies on this particular reaction. An experimental/computational-DFT approach allowed to establish that 1) some iodoalkynes might be prone to dehalogenation under copper catalysis conditions and, more importantly, 2) that two distinct mechanistic pathways are likely to be competitive with these catalysts: either through a copper(III) metallacycle or via direct p-activation of the starting iodoalkyne.
DOI: 10.6084/m9.figshare.1029142
title: Horizontal Traceability for Just-In-Time Requirements

description: Agile projects typically employ just-in-time requirements engineering and record their requirements (socalled feature requests) in an issue tracker. In open source projects we observed large networks of feature requests that are linked to each other. Both when trying to understand the current state of the system and to understand how a new feature request should be implemented, it is important to know and understand all these (tightly) related feature requests. However, we still lack tool support to visualize and navigate these networks of feature requests. A first step in this direction is to see whether we can identify additional links that are not made explicit in the feature requests, by measuring the text-based similarity with a Vector Space Model (VSM) using Term Frequency - Inverse Document Frequency (TF-IDF) as a weighting factor. We show that a high text-based similarity score is a good indication for related feature requests. This means that with a TF-IDF VSM we can establish horizontal traceability links, thereby providing new insights for users or developers exploring the feature request space. The inpunt data XML files, the stop words list and the cosine similarity measures can be found online in this fileset.
DOI: 10.6084/m9.figshare.1029084
title: Model 2 Fileset

description: This fileset encompasses simulation data from Model 2 (postural control model with reciprocal inhibition). Biomechanical variables and surface EMGs are two-dimension arrays in the form [time value]. Spike trains are two-dimension arrays in the form [time_stamp neuron_index]. Numbers 1-3 represent three independent 30-s duration simulations.
DOI: 10.6084/m9.figshare.1029142.v2
title: Horizontal Traceability for Just-In-Time Requirements

description: Agile projects typically employ just-in-time requirements engineering and record their requirements (socalled feature requests) in an issue tracker. In open source projects we observed large networks of feature requests that are linked to each other. Both when trying to understand the current state of the system and to understand how a new feature request should be implemented, it is important to know and understand all these (tightly) related feature requests. However, we still lack tool support to visualize and navigate these networks of feature requests. A first step in this direction is to see whether we can identify additional links that are not made explicit in the feature requests, by measuring the text-based similarity with a Vector Space Model (VSM) using Term Frequency - Inverse Document Frequency (TF-IDF) as a weighting factor. We show that a high text-based similarity score is a good indication for related feature requests. This means that with a TF-IDF VSM we can establish horizontal traceability links, thereby providing new insights for users or developers exploring the feature request space. The inpunt data XML files, the stop words list and the cosine similarity measures can be found online in this fileset.
DOI: 10.6084/m9.figshare.1027609
title: Model 1 Fileset

description: This fileset encompasses simulation data from Model 1 (postural control model without reciprocal inhibition). Biomechanical variables and surface EMGs are two-dimension arrays in the form [time value]. Spike trains are two-dimension arrays in the form [time_stamp neuron_index]. Numbers 1-3 represent three independent 30-s duration simulations.
DOI: 10.6084/m9.figshare.1029084.v1
title: Model 2 Fileset

description: This fileset encompasses simulation data from Model 2 (postural control model with reciprocal inhibition). Biomechanical variables and surface EMGs are two-dimension arrays in the form [time value]. Spike trains are two-dimension arrays in the form [time_stamp neuron_index]. Numbers 1-3 represent three independent 30-s duration simulations.
DOI: 10.6084/m9.figshare.1029142.v1
title: Horizontal Traceability for Just-In-Time Requirements

description: Agile projects typically employ just-in-time requirements engineering and record their requirements (socalled feature requests) in an issue tracker. In open source projects we observed large networks of feature requests that are linked to each other. Both when trying to understand the current state of the system and to understand how a new feature request should be implemented, it is important to know and understand all these (tightly) related feature requests. However, we still lack tool support to visualize and navigate these networks of feature requests. A first step in this direction is to see whether we can identify additional links that are not made explicit in the feature requests, by measuring the text-based similarity with a Vector Space Model (VSM) using Term Frequency - Inverse Document Frequency (TF-IDF) as a weighting factor. We show that a high text-based similarity score is a good indication for related feature requests. This means that with a TF-IDF VSM we can establish horizontal traceability links, thereby providing new insights for users or developers exploring the feature request space. The inpunt data XML files, the stop words list and the cosine similarity measures can be found online in this fileset.
DOI: 10.6084/m9.figshare.1027609.v1
title: Model 1 Fileset

description: This fileset encompasses simulation data from Model 1 (postural control model without reciprocal inhibition). Biomechanical variables and surface EMGs are two-dimension arrays in the form [time value]. Spike trains are two-dimension arrays in the form [time_stamp neuron_index]. Numbers 1-3 represent three independent 30-s duration simulations.
DOI: 10.6084/m9.figshare.1027503
title: Data for article "Selective Control of Attention Supports the Positivity Effect in Aging"

description: Data for article "Selective Control of Attention Supports the Positivity Effect in Aging" in PLOS ONE (under review). In this study, 25 younger and 25 older adults’ eye movements were tracked while they viewed 40 triads of one positive, one negative and one neutral social scenario. The 3 scenarios were either all own-age relevant or other-age relevant (e.g. wedding versus playing with grandchildren). The data revealed a significant positivity effect (PE): Older adults devoted significantly more fixations to positive over negative stimuli than younger adults and this was enhanced for own-age stimuli. Moreover, the PE was correlated with the elderlies' specific ability to adaptively control attention over salient visual distraction, measured in a visual search (singleton) task. On the following day, recognition memory was assessed for all stimuli. The results indicated that again, a positivity preference (positive&gt;neutral) was significantly more affected by own-age relevance in older than in young age. The data includes the relative amount of the number of fixations (fixN) as well as the relative durations of fixations (fixD) to positive, negative and neutral own-age and other-age stimuli. In addition, the file contains a column for the singleton score measuring visual top-down control (higher values indicate lower performance). The singleton_filter variable indentifies the subject who's score is missing due to technical recording problems. Finally, the file includes the corrected hitrates from the recognition memory test (hitrate-false alarms; corHit). The group variable is coded as 1 for the young and 2 for the older participants.
DOI: 10.6084/m9.figshare.1027482
title: Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis

description: Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.
DOI: 10.6084/m9.figshare.1027482.v1
title: Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis

description: Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.
DOI: 10.6084/m9.figshare.1027360
title: Videos showing reprogramming of preiPSCs into iPSCs

description: Videos showing the kinetics of the emergence of Nanog-GFP+ colonies from Nanog+EV or Nanog+Mbd3 transgenic preiPSCs during a 12-day culture in 2i/LIF condition. For more videos and information, please follow the links below.
DOI: 10.6084/m9.figshare.1027482.v2
title: Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis

description: Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.
DOI: 10.6084/m9.figshare.1027360.v1
title: Videos showing reprogramming of preiPSCs into iPSCs

description: Videos showing the kinetics of the emergence of Nanog-GFP+ colonies from Nanog+EV or Nanog+Mbd3 transgenic preiPSCs during a 12-day culture in 2i/LIF condition. For more videos and information, please follow the links below.
DOI: 10.6084/m9.figshare.1027482.v3
title: Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis

description: Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.
DOI: 10.6084/m9.figshare.1027482.v4
title: Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis

description: Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.
DOI: 10.6084/m9.figshare.1027356
title: A unique, Late Oligocene shrew-like marsupial from western Argentina and the evolution of dental morphology

description: We describe a new metatherian mammal, <i>Fieratherium sorex</i> gen. et sp. nov., found in western Argentina (Quebrada Fiera locality, southern Mendoza Province), in Late Oligocene deposits (Agua de la Piedra Formation, Deseadan age). The only known specimen is a juvenile with fragments of both dentaries, the right maxilla and a fragment of the left premaxilla with dentition. The loci and the number teeth preserved suggest a dental formula of I?3/i3, C1/c1, P3/p3, M?3/m?3. <i>Fieratherium sorex</i> has a convergent shrew-like appearance and a unique combination of features among metatherians and other South American mammals of Palaeogene age, including the well-known faunas of Patagonia. An analysis of its phylogenetic affinities suggests that <i>Fieratherium</i> is the sister-group of the Paucituberculata. As already described by other authors for several mammalian taxa, the mainly Patagonian South American Palaeogene fossil record offers little information to understanding the evolution of northern lineages. <i>Fieratherium</i> may represent a taxon belonging to a lineage that had its origin in Neotropical regions, so far unrecorded in the southern region of South America.http://zoobank.org/urn:lsid:zoobank.org:pub:5F6D3A50-6345-4E66-BE3E-7FEF6CC66A9B
DOI: 10.6084/m9.figshare.1027357
title: A new durophagous phocid (Mammalia: Carnivora) from the late Neogene of Peru and considerations on monachine seals phylogeny

description: Here we describe a new phocid, <i>Hadrokirus martini</i> gen. et sp. nov., from the Pisco Formation, in the locality of Sud-Sacaco (Late Miocene to Early Pliocene of Peru). This taxon is the third true seal described from this locality. It is characterized by strong dentition paired with a powerful masticatory musculature and a peculiar atlas. No precise diet is inferred here, but a propensity for durophagy and predation on large prey (such as the extant leopard seal, <i>Hydrurga leptonyx</i>) can be considered. A cladistic analysis including characters from the literature as well as original ones places <i>Hadrokirus</i> among lobodontines in a clade with <i>Piscophoca pacifica</i>, another phocid from the Pisco Formation. In addition, this analysis supports the monophyly of both Phocinae and Monachinae and recognizes a clade consisting of the four extant species of lobodontines, with <i>Acrophoca longirostris</i> (the third phocid from the Pisco Formation) as sister-group of this clade. All clades are supported by unambiguous non-homoplastic synapomorphies. Following the optimization, our analysis recognizes aquatic innovations as phocine reversions at the scale of Carnivora, or as convergences of monachines with non-phocid pinnipeds.http://zoobank.org/urn:lsid:zoobank.org:pub:A9884A4D-99C2-4CB0-BEE9-E2D2830481DD
DOI: 10.6084/m9.figshare.1027482.v5
title: Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis

description: Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.
DOI: 10.6084/m9.figshare.1027482.v7
title: Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis

description: Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.
DOI: 10.6084/m9.figshare.1027482.v6
title: Sources of variation in small rodent trophic niche: new insights from DNA metabarcoding and stable isotope analysis

description: Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales.