cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4038060.v1
title: Supplementary Tables S3-S5 detailing reduced biological function GO terms from REVIGO of differentially expressed transcripts between Winter Skate Populations from Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish <i>Leucoraja ocellata</i> (Rajidae)

description: The relative importance of genetic versus epigenetic changes in adaptive evolution is a hotly debated topic, with studies showing that some species appear to be able to adapt rapidly without significant genetic change. Epigenetic mechanisms may be particularly important for the evolutionary potential of species with long maturation times and low reproductive potential ('K-strategists'), particularly when faced with rapidly changing environmental conditions. Here we study the transcriptome of two populations of the winter skate (<i>Leucoraja ocellata</i>), a typical 'K-strategist', in Atlantic Canada; an endemic population in southern Gulf of St. Lawrence and a large population on the Scotian Shelf. The endemic population has been able to adapt to a 10 degrees Celsius higher water temperatures over short evolutionary time (7000 years), dramatically reducing its body size (by 45%) significantly below the minimum maturation size of Scotian Shelf and other populations of winter skate, as well as exhibiting other adaptations in life history and physiology. We demonstrate that the adaptive response to selection has an epigenetic basis, cataloguing 3653 changes in gene expression that may have enabled this species to rapidly respond to the novel environment. We argue that the epigenetic augmentation of species evolutionary potential (its regulation though gene expression) can enable K-strategists to survive and adapt to different environments, and this mechanism may be particularly important for the persistence of sharks, skates and rays in the light of future climate change.
DOI: 10.7910/dvn/v1rjpf/oyxhlb
title: blc20170925_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/naffmw
title: blc20170215_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038054
title: The Drosophila chromosomal protein Mst77F is processed to generate an essential component of mature sperm chromatin Shuhei Kimura and Benjamin Loppin. DOI 10.1098/rsOb.1600207 from The <i>Drosophila</i> chromosomal protein Mst77F is processed to generate an essential component of mature sperm chromatin

description: Table S1
DOI: 10.6084/m9.figshare.4038054.v2
title: The Drosophila chromosomal protein Mst77F is processed to generate an essential component of mature sperm chromatin Shuhei Kimura and Benjamin Loppin. DOI 10.1098/rsOb.1600207 from The <i>Drosophila</i> chromosomal protein Mst77F is processed to generate an essential component of mature sperm chromatin

description: Table S1
DOI: 10.7910/dvn/v1rjpf/jbpick
title: blc20170617_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038048
title: Virtual Machine with Case Study workflow in Jupyter Notebook

description: A virtual machine with the case study workflow for SciLuigi, runnable from within a Jupyter Notebook. <br>Usage: <br>1. Import the .ova image into a Virtual Machine software such as Virtual box. <br>2. Start the virtual machine. <br>3. Log in with ubuntu and changethis...<br>4. Open a terminal and execute the passwd command, to immediately set a new password.<br>5. Click the "Open Jupyter Notebook" icon on the desktop.6. Inside Jupyter, click: Cell &gt; Run all cells<br>7. The workflow will now start.
DOI: 10.6084/m9.figshare.4038054.v1
title: The Drosophila chromosomal protein Mst77F is processed to generate an essential component of mature sperm chromatin Shuhei Kimura and Benjamin Loppin. DOI 10.1098/rsob.1600207 from The <i>Drosophila</i> chromosomal protein Mst77F is processed to generate an essential component of mature sperm chromatin

description: Table S1
DOI: 10.7910/dvn/v1rjpf/4xat1f
title: blc20171127_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038045
title: Supplementary Material for: Effects of Dendritic Cell Subset Manipulation on Airway Allergy in a Mouse Model

description: <b><i>Background:</i></b> Two major distinct subsets of dendritic cells (DCs) are arranged to regulate immune responses: DEC-205+ DCs drive Th1 polarization and 33D1+ DCs establish Th2 dominancy. Th1 polarization can be achieved either by depletion of 33D1+ DCs with a 33D1-specific monoclonal antibody (mAb) or by activation of DEC-205+ DCs via intraperitoneal injection of α-galactosylceramide (α-GalCer). We studied the effect of 33D1+ DC depletion or DEC-205+ DC activation in vivo using an established mouse model of allergic rhinitis (AR). <b><i>Methods:</i></b> Mice were injected intraperitoneally with OVA plus alum and challenged 4 times with daily intranasal administration of OVA. Immediately after the last challenge, allergic symptoms such as sneezing and nasal rubbing as well as the number of cells in the bronchoalveolar lavage fluid (BALF) and nasal lavage fluid (NALF) were counted. The levels of serum OVA-specific IgG1, IgG2a, and IgE were also determined by ELISA. <b><i>Results:</i></b> The allergic symptom scores were significantly decreased in 33D1+ DC-depleted or DEC-205+ DC-activated AR mice. The levels of OVA-specific IgG1, IgG2a, and IgE, and the number of NALF cells, but not BALF cells, were reduced in 33D1+ DC-depleted but not in DEC-205+ DC-activated AR mice. Moreover, the activated DEC-205+ DCs suppressed histamine release from IgE-sensitized mast cells, probably through IL-12 secretion. <b><i>Conclusions:</i></b> The manipulation of innate DC subsets may provide a new therapeutic strategy for controlling various allergic diseases by reducing histamine release from IgE-sensitized mast cells by driving the immune response towards Th1 dominancy via activation of DEC-205+ DCs in vivo.
DOI: 10.7910/dvn/v1rjpf/tzzqeu
title: blc20170905_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038048.v1
title: Virtual Machine with Case Study workflow in Jupyter Notebook

description: A virtual machine with the case study workflow for SciLuigi, runnable from within a Jupyter Notebook. <br>Usage: <br>1. Import the .ova image into a Virtual Machine software such as Virtual box. <br>2. Start the virtual machine. <br>3. Log in with ubuntu and changethis...<br>4. Open a terminal and execute the passwd command, to immediately set a new password.<br>5. Click the "Open Jupyter Notebook" icon on the desktop.6. Inside Jupyter, click: Cell &gt; Run all cells<br>7. The workflow will now start.
DOI: 10.7910/dvn/v1rjpf/qsihrd
title: blc20170921_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038048.v2
title: Virtual Machine with Case Study workflow in Jupyter Notebook

description: A virtual machine with the case study workflow for SciLuigi, runnable from within a Jupyter Notebook. <br>Usage: <br>1. Import the .ova image into a Virtual Machine software such as Virtual box. <br>2. Start the virtual machine. <br>3. Log in with ubuntu and changethis...<br>4. Open a terminal and execute the passwd command, to immediately set a new password.<br>5. Click the "Open Jupyter Notebook" icon on the desktop.6. Inside Jupyter, click: Cell &gt; Run all cells<br>7. The workflow will now start.
DOI: 10.7910/dvn/v1rjpf/tbbbrq
title: blc20170130_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038048.v3
title: Virtual Machine with Case Study workflow in Jupyter Notebook

description: A virtual machine with the case study workflow for SciLuigi, runnable from within a Jupyter Notebook. <br>Usage: <br>1. Import the .ova image into a Virtual Machine software such as Virtual box. <br>2. Start the virtual machine. <br>3. Log in with ubuntu and changethis...<br>4. Open a terminal and execute the passwd command, to immediately set a new password.<br>5. Click the "Open Jupyter Notebook" icon on the desktop.6. Inside Jupyter, click: Cell &gt; Run all cells<br>7. The workflow will now start.
DOI: 10.7910/dvn/v1rjpf/jz2iln
title: blc20170709_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fp12wm
title: blc20170803_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sltvot
title: blc20170627_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4037997
title: Datasets supporting this article from Queen reproductive tract secretions enhance sperm motility in ants

description: Full datasets from the experiments testing (i) measurement repeatability, (ii) the effect of queen reproductive tract secretions on sperm motility and (iii) the effects of additional queen body secretions on sperm motility.
DOI: 10.7910/dvn/v1rjpf/ystt9m
title: blc20171109_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4037997.v1
title: Datasets supporting this article from Queen reproductive tract secretions enhance sperm motility in ants

description: Full datasets from the experiments testing (i) measurement repeatability, (ii) the effect of queen reproductive tract secretions on sperm motility and (iii) the effects of additional queen body secretions on sperm motility.
DOI: 10.7910/dvn/v1rjpf/ym7hnh
title: blc20170104_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xuxphe
title: blc20170725_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/tnet8k
title: blc20171107_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sf8782
title: blc20171113_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/wqd9ck
title: blc20170923_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7026ab
title: blc20170523_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/9xfi2p
title: blc20171025_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/yy6drj
title: blc20171218_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/x8bcd0
title: blc20170908_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4037871
title: Supplementary Material for: The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae

description: Repetitive DNA is the largest fraction of the eukaryote genome and comprises tandem and dispersed sequences. It presents variations in relation to its composition, number of copies, distribution, dynamics, and genome organization, and participates in the evolutionary diversification of different vertebrate species. Repetitive sequences are usually located in the heterochromatin of centromeric and telomeric regions of chromosomes, contributing to chromosomal structures. Therefore, the aim of this study was to physically map repetitive DNA sequences (5S rDNA, telomeric sequences, tropomyosin gene 1, and retroelements <i>Rex</i><i>1</i> and <i>SINE</i>) of mitotic chromosomes of Amazonian species of teiids <i>(Ameiva ameiva</i>, <i>Cnemidophorus </i>sp. 1, <i>Kentropyx calcarata</i>, <i>Kentropyx pelviceps,</i> and <i>Tupinambis teguixin)</i> to understand their genome organization and karyotype evolution. The mapping of repetitive sequences revealed a distinct pattern in <i>Cnemidophorus</i> sp. 1, whereas the other species showed all sequences interspersed in the heterochromatic region. Physical mapping of the tropomyosin 1 gene was performed for the first time in lizards and showed that in addition to being functional, this gene has a structural function similar to the mapped repetitive elements as it is located preferentially in centromeric regions and termini of chromosomes.
DOI: 10.7910/dvn/v1rjpf/dtnvj8
title: blc20170321_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4037868
title: F1 CTmax.csv

description: CTmax of adult F1 rainforest sunskinks from two populations: Hervey Range and Paluma.<br>
DOI: 10.6084/m9.figshare.4037871.v1
title: Supplementary Material for: The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae

description: Repetitive DNA is the largest fraction of the eukaryote genome and comprises tandem and dispersed sequences. It presents variations in relation to its composition, number of copies, distribution, dynamics, and genome organization, and participates in the evolutionary diversification of different vertebrate species. Repetitive sequences are usually located in the heterochromatin of centromeric and telomeric regions of chromosomes, contributing to chromosomal structures. Therefore, the aim of this study was to physically map repetitive DNA sequences (5S rDNA, telomeric sequences, tropomyosin gene 1, and retroelements <i>Rex</i><i>1</i> and <i>SINE</i>) of mitotic chromosomes of Amazonian species of teiids <i>(Ameiva ameiva</i>, <i>Cnemidophorus </i>sp. 1, <i>Kentropyx calcarata</i>, <i>Kentropyx pelviceps,</i> and <i>Tupinambis teguixin)</i> to understand their genome organization and karyotype evolution. The mapping of repetitive sequences revealed a distinct pattern in <i>Cnemidophorus</i> sp. 1, whereas the other species showed all sequences interspersed in the heterochromatic region. Physical mapping of the tropomyosin 1 gene was performed for the first time in lizards and showed that in addition to being functional, this gene has a structural function similar to the mapped repetitive elements as it is located preferentially in centromeric regions and termini of chromosomes.
DOI: 10.6084/m9.figshare.4037868.v1
title: F1 CTmax.csv

description: CTmax of adult F1 rainforest sunskinks from two populations: Hervey Range and Paluma.<br>
DOI: 10.7910/dvn/v1rjpf/sosotl
title: blc20170610_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ozzb03
title: blc20170609_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/cqz2pc
title: blc20170328_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gkxsy3
title: blc20171031_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/drhdjw
title: blc20170812_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xgsuun
title: blc20170705_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ulogbj
title: blc20171231_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/uo6t2y
title: blc20170914_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/cwdqmh
title: blc20170208_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/4dtzft
title: blc20170717_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7m9gtd
title: blc20170101_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4037748
title: Exposure to metal oxide nanoparticles administered at occupationally relevant doses induces pulmonary effects in mice

description: In spite of the great promises that the development of nanotechnologies can offer, concerns regarding potential adverse health effects of occupational exposure to nanoparticle (NP) is raised. We recently identified metal oxide NP in lung tissue sections of welders, located inside macrophages infiltrated in fibrous regions. This suggests a role of these NP in the lung alterations observed in welders. We therefore designed a study aimed to investigate the pulmonary effects, in mice, of repeated exposure to NP administered at occupationally relevant doses. We therefore chose four metal oxide NPs representative of those found in the welder’s lungs: Fe<sub>2</sub>O<sub>3</sub>, Fe<sub>3</sub>O<sub>4</sub>, MnFe<sub>2</sub>O<sub>4</sub> and CrOOH. These NPs were administered weekly for up to 3 months at two different doses: 5 μg, chosen as occupationally relevant to welding activity, and 50 μg, chosen as occupationally relevant to the context of an NP-manufacturing facility. Our results show that 3 month-repeated exposures to 5 μg NP induced limited pulmonary effects, characterized by the development of a mild peribronchiolar fibrosis observed for MnFe<sub>2</sub>O<sub>4</sub> and CrOOH NP only. This fibrotic event was further extended in terms of intensity and localization after the repeated administration of 50 μg NP: all but Fe<sub>2</sub>O<sub>3</sub> NP induced the development of peribronchiolar, perivascular and alveolar fibrosis, together with an interstitial inflammation. Our data demonstrate for the first time a potential risk for respiratory health posed by repeated exposure to NP at occupationally relevant doses. Given these results, the development of occupational exposure limits (OELs) specifically dedicated to NP exposure might therefore be an important issue to address.
DOI: 10.6084/m9.figshare.4037739
title: Survivability and storage stability of <i>Trichoderma atroviride</i> TRS40 preserved by fluidised bed drying on various agriculture by-products

description: Agriculture by-products were applied to proliferate biomass of <i>Trichoderma atroviride</i> TRS40 in solid state fermentation (SSF) cultures. The culture media overgrown with mycelium together with conidia were preserved by fluidised bed drying at various temperatures (50°C, 60°C and 70°C) and the received biopreparations were stored for 12 months. In order to determine the suitability of TRS40 in the production of biopreparations, the influence of preservation process and storage time on their survivability was examined. The three-component mixture proved more effective in the SSF cultures, ensuring TRS40 count at 6.07 × 10<sup>9 </sup>CFU/g dm, which was ca. 6 times higher than in the mono-component medium. TRS40 survivability after preservation at various temperatures ranged from 40.4% to 100%, regardless of carrier type. In turn, after 12-month storage of the biopreparations produced on the three-component medium, regardless of drying temperature, the number of viable cells ranged from 2.43 × 10<sup>8</sup> to 2.49 × 10<sup>8 </sup>CFU/g dm. Furthermore, selected parameters of growth kinetics in the Bioscreen C system were determined. The storage time of biopreparations had various effects on growth kinetic parameters. In addition, the preserved preparations based on the TRS40 retained their capability for biosynthesis of hydrolases, even after 12 months of storage.
DOI: 10.6084/m9.figshare.4037739.v1
title: Survivability and storage stability of <i>Trichoderma atroviride</i> TRS40 preserved by fluidised bed drying on various agriculture by-products

description: Agriculture by-products were applied to proliferate biomass of <i>Trichoderma atroviride</i> TRS40 in solid state fermentation (SSF) cultures. The culture media overgrown with mycelium together with conidia were preserved by fluidised bed drying at various temperatures (50°C, 60°C and 70°C) and the received biopreparations were stored for 12 months. In order to determine the suitability of TRS40 in the production of biopreparations, the influence of preservation process and storage time on their survivability was examined. The three-component mixture proved more effective in the SSF cultures, ensuring TRS40 count at 6.07 × 10<sup>9 </sup>CFU/g dm, which was ca. 6 times higher than in the mono-component medium. TRS40 survivability after preservation at various temperatures ranged from 40.4% to 100%, regardless of carrier type. In turn, after 12-month storage of the biopreparations produced on the three-component medium, regardless of drying temperature, the number of viable cells ranged from 2.43 × 10<sup>8</sup> to 2.49 × 10<sup>8 </sup>CFU/g dm. Furthermore, selected parameters of growth kinetics in the Bioscreen C system were determined. The storage time of biopreparations had various effects on growth kinetic parameters. In addition, the preserved preparations based on the TRS40 retained their capability for biosynthesis of hydrolases, even after 12 months of storage.
DOI: 10.6084/m9.figshare.4037748.v1
title: Exposure to metal oxide nanoparticles administered at occupationally relevant doses induces pulmonary effects in mice

description: In spite of the great promises that the development of nanotechnologies can offer, concerns regarding potential adverse health effects of occupational exposure to nanoparticle (NP) is raised. We recently identified metal oxide NP in lung tissue sections of welders, located inside macrophages infiltrated in fibrous regions. This suggests a role of these NP in the lung alterations observed in welders. We therefore designed a study aimed to investigate the pulmonary effects, in mice, of repeated exposure to NP administered at occupationally relevant doses. We therefore chose four metal oxide NPs representative of those found in the welder’s lungs: Fe<sub>2</sub>O<sub>3</sub>, Fe<sub>3</sub>O<sub>4</sub>, MnFe<sub>2</sub>O<sub>4</sub> and CrOOH. These NPs were administered weekly for up to 3 months at two different doses: 5 μg, chosen as occupationally relevant to welding activity, and 50 μg, chosen as occupationally relevant to the context of an NP-manufacturing facility. Our results show that 3 month-repeated exposures to 5 μg NP induced limited pulmonary effects, characterized by the development of a mild peribronchiolar fibrosis observed for MnFe<sub>2</sub>O<sub>4</sub> and CrOOH NP only. This fibrotic event was further extended in terms of intensity and localization after the repeated administration of 50 μg NP: all but Fe<sub>2</sub>O<sub>3</sub> NP induced the development of peribronchiolar, perivascular and alveolar fibrosis, together with an interstitial inflammation. Our data demonstrate for the first time a potential risk for respiratory health posed by repeated exposure to NP at occupationally relevant doses. Given these results, the development of occupational exposure limits (OELs) specifically dedicated to NP exposure might therefore be an important issue to address.
DOI: 10.7910/dvn/v1rjpf/vpvlaa
title: blc20171222_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4037733
title: Appendix 2: (A).High resolution (1Hz) GPS track and associated movement data of Himalayan Vulture. (B). Wing area and weight data of Himalayan Vulture from Behavioural adaptations to flight into thin air

description: (A). Data from Sherub et al., 2016. The start point of each identified thermalling circle is provided with annotated air density and ground elevation, and ground speed during the circle (provided by the GPS), and wind and air speed (estimated using the Sherub et al approach). Circle radius and change of elevation with the circle are included as well. Mean vertical soaring speed was calculated from the change of elevation. Circles are considered continuous thermalling movement for 30 seconds. X component refers to horizontal latitudinal movement and Y to horizontal longitudinal. (B). Legend: Data from Sherub et al., 2016. Wing area and wing loading measurements for individual Himalayan Griffon Vultures. Individuals whose name is "Griffon" were measured, but were not fitted with a GPS tag and did not participate in movement study. Wing area was measured following Pennycuick's method: the wing area was traced on a gridded paper chart. A photograph of the wing-trace was taken, and the number of occupied pixel was determined using Adobe Photoshop, and converted from pixels to m^2 using the dimensions of the gridded chart.
DOI: 10.6084/m9.figshare.4037736
title: Data table from Living on the edge of a shrinking habitat: the ivory gull, <i>Pagophila eburnea</i>, an endangered sea-ice specialist

description: Living on the edge of a shrinking habitat: the ivory gull, Pagophila eburnea, an endangered sea-ice specialist
DOI: 10.7910/dvn/v1rjpf/ajudcx
title: blc20170224_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4037736.v1
title: Data table from Living on the edge of a shrinking habitat: the ivory gull, <i>Pagophila eburnea</i>, an endangered sea-ice specialist

description: Living on the edge of a shrinking habitat: the ivory gull, Pagophila eburnea, an endangered sea-ice specialist