cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3807006.v1
title: Photoluminescence data of (-)-platinahelicene thin film in OXD-7:PVK 1:1 matrix

description: PL and CP-PL data
DOI: 10.6084/m9.figshare.3806964
title: Different responses of Caco-2 and MCF-7 cells to silver nanoparticles are based on highly similar mechanisms of action

description: The mode of action of silver nanoparticles (AgNPs) is suggested to be exerted through both Ag<sup>+</sup> and AgNP dependent mechanisms. Ingestion is one of the major NP exposure routes, and potential effects are often studied using Caco-2 cells, a well-established model for the gut epithelium. MCF-7 cells are epithelial breast cancer cells with extensive well-characterized toxicogenomics profiles. In the present study, we aimed to gain a deeper understanding of the cellular molecular responses in Caco-2 and MCF-7 cells after AgNP exposure in order to evaluate whether epithelial cells derived from different tissues demonstrated similar responses. These insights could possibly reduce the size of cell panels for NP hazard identification screening purposes. AgNPs of 20, 30, 60, and 110 nm, and AgNO<sub>3</sub> were exposed for 6 h and 24 h. AgNPs were shown to be taken up and dissolve intracellularly. Compared with MCF-7 cells, Caco-2 cells showed a higher sensitivity to AgNPs, slower gene expression kinetics and absence of NP size-dependent responses. However, on a molecular level, no significant differences were observed between the two cell types. Transcriptomic analysis showed that Ag(NP) exposure caused (oxidative) stress responses, possibly leading to cell death in both cell lines. There was no indication for effects specifically induced by AgNPs. Responses to AgNPs appeared to be induced by silver ions released from the AgNPs. In conclusion, differences in mRNA responses to AgNPs between Caco-2 and MCF-7 cells were mainly related to timing and magnitude, but not to a different underlying mechanism.
DOI: 10.6084/m9.figshare.3806964.v1
title: Different responses of Caco-2 and MCF-7 cells to silver nanoparticles are based on highly similar mechanisms of action

description: The mode of action of silver nanoparticles (AgNPs) is suggested to be exerted through both Ag<sup>+</sup> and AgNP dependent mechanisms. Ingestion is one of the major NP exposure routes, and potential effects are often studied using Caco-2 cells, a well-established model for the gut epithelium. MCF-7 cells are epithelial breast cancer cells with extensive well-characterized toxicogenomics profiles. In the present study, we aimed to gain a deeper understanding of the cellular molecular responses in Caco-2 and MCF-7 cells after AgNP exposure in order to evaluate whether epithelial cells derived from different tissues demonstrated similar responses. These insights could possibly reduce the size of cell panels for NP hazard identification screening purposes. AgNPs of 20, 30, 60, and 110 nm, and AgNO<sub>3</sub> were exposed for 6 h and 24 h. AgNPs were shown to be taken up and dissolve intracellularly. Compared with MCF-7 cells, Caco-2 cells showed a higher sensitivity to AgNPs, slower gene expression kinetics and absence of NP size-dependent responses. However, on a molecular level, no significant differences were observed between the two cell types. Transcriptomic analysis showed that Ag(NP) exposure caused (oxidative) stress responses, possibly leading to cell death in both cell lines. There was no indication for effects specifically induced by AgNPs. Responses to AgNPs appeared to be induced by silver ions released from the AgNPs. In conclusion, differences in mRNA responses to AgNPs between Caco-2 and MCF-7 cells were mainly related to timing and magnitude, but not to a different underlying mechanism.
DOI: 10.6084/m9.figshare.3806904
title: Thin film optical microscopy images of platinahelicene in OXD-7:PVK 1:1 matrix

description: Thin film optical microscopy images of platinahelicene in OXD-7:PVK 1:1 matrix
DOI: 10.6084/m9.figshare.3806904.v1
title: Thin film optical microscopy images of platinahelicene in OXD-7:PVK 1:1 matrix

description: Thin film optical microscopy images of platinahelicene in OXD-7:PVK 1:1 matrix
DOI: 10.6084/m9.figshare.3806898
title: Bilateral Breast Cancer

description: Bilateral Breast Cancer
DOI: 10.6084/m9.figshare.3806898.v2
title: Bilateral Breast Cancer

description: Bilateral Breast Cancer
DOI: 10.6084/m9.figshare.3806898.v1
title: Bilateral Breast Cancer

description: Bilateral Breast Cancer
DOI: 10.6084/m9.figshare.3806895
title: Dataset of pictures showing neoplastic growth on surface roots

description: The photos appended constitute a dataset that describes the phenomenon of neoplastic growth on surface roots in many trees around Singapore. Incidentally, tree species in Singapore seems to have (what looks to be peculiar to me) surface roots. I am not a plant biologist, but I thought the phenomenon to be interesting for plant biologists around the world to know. Thus, I am sharing this dataset now so as not to delay research, and I may pen my thoughts on the phenomenon in a preprint at a later date. Researchers who find the phenomenon interesting can work on the problem immediately. These photos were taken with a 5 megapixel smartphone camera.
DOI: 10.6084/m9.figshare.3806895.v1
title: Dataset of pictures showing neoplastic growth on surface roots

description: The photos appended constitute a dataset that describes the phenomenon of neoplastic growth on surface roots in many trees around Singapore. Incidentally, tree species in Singapore seems to have (what looks to be peculiar to me) surface roots. I am not a plant biologist, but I thought the phenomenon to be interesting for plant biologists around the world to know. Thus, I am sharing this dataset now so as not to delay research, and I may pen my thoughts on the phenomenon in a preprint at a later date. Researchers who find the phenomenon interesting can work on the problem immediately. These photos were taken with a 5 megapixel smartphone camera.
DOI: 10.6084/m9.figshare.3806892
title: Thin film AFM images of platinahelicene in OXD-7:PVK 1:1

description: Thin film AFM images of platinahelicene in OXD-7:PVK 1:1
DOI: 10.6084/m9.figshare.3806886
title: Thin film CD data of 15% platinahelicene in OXD-7:PVK 1:1

description: Thin film CD spectra of enantiopure 15 weight% platinahelicene in OXD-7:PVK 1:1 matrix.
DOI: 10.6084/m9.figshare.3806886.v1
title: Thin film CD data of 15% platinahelicene in OXD-7:PVK 1:1

description: Thin film CD spectra of enantiopure 15 weight% platinahelicene in OXD-7:PVK 1:1 matrix.
DOI: 10.6084/m9.figshare.3806880
title: 2-Methoxy-5-(pyridin-2-yl)benzaldehyde NMR data

description: H-NMR and C-NMR data of 2-Methoxy-5-(pyridin-2-yl)benzaldehyde
DOI: 10.6084/m9.figshare.3806880.v1
title: 2-Methoxy-5-(pyridin-2-yl)benzaldehyde NMR data

description: H-NMR and C-NMR data of 2-Methoxy-5-(pyridin-2-yl)benzaldehyde
DOI: 10.17028/rd.lboro.3806823
title: A study of computational methods for wake structure and base pressure prediction of a generic SUV model with fixed and rotating wheels - dataset

description: Dataset from the IMechE Special Edition Journal Paper 2016.<br>Comparison of wake flow field and base pressure predictions from several CFD codes for a Generic SUV geometry.<br>The files were created in Tecplot software. They can also be opened in other technical plotting software or text editors.<br>
DOI: 10.17028/rd.lboro.3806823.v1
title: A study of computational methods for wake structure and base pressure prediction of a generic SUV model with fixed and rotating wheels - dataset

description: Dataset from the IMechE Special Edition Journal Paper 2016.<br>Comparison of wake flow field and base pressure predictions from several CFD codes for a Generic SUV geometry.<br>The files were created in Tecplot software. They can also be opened in other technical plotting software or text editors.<br>
DOI: 10.6084/m9.figshare.3806787
title: Phylogenetic position of the extinct insect family Vetanthocoridae (Heteroptera) in Cimiciformes

description: The extinct fossil family Vetanthocoridae, with the tribes Vetanthocorini and Crassicerini, was considered a member of the Cimicoidea. Because the tribe Vetanthocorini has been transferred to Nabidae, the systematic position of Vetanthocoridae is in doubt. <i>Punctivetanthocoris pubens</i> gen. et sp. nov. from the Early Cretaceous Yixian Formation of China is assigned to Vetanthocoridae. Based on the combination of fossil and extant taxa, two cladistic analyses were conducted to confirm the phylogenetic position of the fossil family Vetanthocoridae within Cimiciformes and Cimicoidea. The monophyly of Cimiciformes and Cimicoidea is supported. The fossil family Vetanthocoridae is included in Cimicoidea, and forms a monophyletic group with the extant flower bugs. http://zoobank.org/urn:lsid:zoobank.org:pub:404279F9-D9F7-4871-A7C7-9839E62139BD
DOI: 10.6084/m9.figshare.3806787.v1
title: Phylogenetic position of the extinct insect family Vetanthocoridae (Heteroptera) in Cimiciformes

description: The extinct fossil family Vetanthocoridae, with the tribes Vetanthocorini and Crassicerini, was considered a member of the Cimicoidea. Because the tribe Vetanthocorini has been transferred to Nabidae, the systematic position of Vetanthocoridae is in doubt. <i>Punctivetanthocoris pubens</i> gen. et sp. nov. from the Early Cretaceous Yixian Formation of China is assigned to Vetanthocoridae. Based on the combination of fossil and extant taxa, two cladistic analyses were conducted to confirm the phylogenetic position of the fossil family Vetanthocoridae within Cimiciformes and Cimicoidea. The monophyly of Cimiciformes and Cimicoidea is supported. The fossil family Vetanthocoridae is included in Cimicoidea, and forms a monophyletic group with the extant flower bugs. http://zoobank.org/urn:lsid:zoobank.org:pub:404279F9-D9F7-4871-A7C7-9839E62139BD
DOI: 10.6084/m9.figshare.3806781
title: New material of the Late Cretaceous marine turtle <i>Ctenochelys acris</i> Zangerl, 1953 and a phylogenetic reassessment of the ‘toxochelyid’-grade taxa

description: Late Cretaceous marine turtles formerly referred to the family Toxochelyidae represent perhaps the earliest members of the clade including extant marine species of cryptodire (Chelonioidea). Though more pelagically specialized marine taxa such as Protostegidae (i.e. <i>Archelon</i>, <i>Desmatochelys</i>) predate the first occurrence of any known ‘toxochelyid’ species, phylogenetic analyses of modern and fossil Testudines have shown that the protostegids may be a separate radiation of stem cryptodires only distantly related to modern marine turtles. This hypothesis has since been supported by ancillary evidence from the stratigraphic record and has been argued from a perspective of rampant homoplasy. This information brings into question our understanding of chelonioid evolution with regard to their previously assumed monophyly, and supports the placement of ‘toxochelyids’ as perhaps the earliest definitive members of total group Chelonioidea (Pan-Chelonioidea). However, many ‘toxochelyids’ are known from partial holotypes, preventing accurate species diagnosis and precluding these species from character-based phylogenetic analyses. A poorly known member of this clade, <i>Ctenochelys acris</i>, is herein redescribed based on several nearly complete specimens from the early Campanian Mooreville Chalk of Alabama. <i>Ctenochelys acris</i> is characterized by large, dorsolaterally oriented orbits, significant contributions of the palatines to the secondary palate, a broad maxillary triturating surface, and almost equilaterally pentagonal posterior peripherals. This redescription not only identifies previously unknown apomorphies of <i>Ctenochelys</i> spp. but also provides an opportunity to examine the ‘toxochelyids’ within a global phylogenetic context. A constraint tree reflecting the recognized molecular topology for extant Testudines is used as a backbone and the resulting phylogeny is then placed within a chronostratigraphic framework in an effort to present a scenario that reconciles anatomical, temporal and phylogenomic patterns for marine turtles. This analysis supports the placement of protostegids outside of Chelonioidea as marine eucryptodirans and establishes <i>Ctenochelys</i> spp. as perhaps some of the earliest representatives of Pan-Cheloniidae.
DOI: 10.6084/m9.figshare.3806781.v1
title: New material of the Late Cretaceous marine turtle <i>Ctenochelys acris</i> Zangerl, 1953 and a phylogenetic reassessment of the ‘toxochelyid’-grade taxa

description: Late Cretaceous marine turtles formerly referred to the family Toxochelyidae represent perhaps the earliest members of the clade including extant marine species of cryptodire (Chelonioidea). Though more pelagically specialized marine taxa such as Protostegidae (i.e. <i>Archelon</i>, <i>Desmatochelys</i>) predate the first occurrence of any known ‘toxochelyid’ species, phylogenetic analyses of modern and fossil Testudines have shown that the protostegids may be a separate radiation of stem cryptodires only distantly related to modern marine turtles. This hypothesis has since been supported by ancillary evidence from the stratigraphic record and has been argued from a perspective of rampant homoplasy. This information brings into question our understanding of chelonioid evolution with regard to their previously assumed monophyly, and supports the placement of ‘toxochelyids’ as perhaps the earliest definitive members of total group Chelonioidea (Pan-Chelonioidea). However, many ‘toxochelyids’ are known from partial holotypes, preventing accurate species diagnosis and precluding these species from character-based phylogenetic analyses. A poorly known member of this clade, <i>Ctenochelys acris</i>, is herein redescribed based on several nearly complete specimens from the early Campanian Mooreville Chalk of Alabama. <i>Ctenochelys acris</i> is characterized by large, dorsolaterally oriented orbits, significant contributions of the palatines to the secondary palate, a broad maxillary triturating surface, and almost equilaterally pentagonal posterior peripherals. This redescription not only identifies previously unknown apomorphies of <i>Ctenochelys</i> spp. but also provides an opportunity to examine the ‘toxochelyids’ within a global phylogenetic context. A constraint tree reflecting the recognized molecular topology for extant Testudines is used as a backbone and the resulting phylogeny is then placed within a chronostratigraphic framework in an effort to present a scenario that reconciles anatomical, temporal and phylogenomic patterns for marine turtles. This analysis supports the placement of protostegids outside of Chelonioidea as marine eucryptodirans and establishes <i>Ctenochelys</i> spp. as perhaps some of the earliest representatives of Pan-Cheloniidae.
DOI: 10.6084/m9.figshare.3806778
title: budding yeast RNA-seq data for prp45(1-169) and wild type (read_1 in FASTQ)

description: <b>Samples (read_1 from PE sequencing)</b><b>WT sample:</b> 13-BY4741-_1.fq.gz <b>prp45(1-169) sample:</b> 14-prp45-_1.fq.gz<br><b><i>Saccharomyces cerevisiae</i> strain genotypes</b><b>WT BY4741:</b> <i>MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0</i><b>prp45(1-169):</b> <i>MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 prp45(1-169)-3HA::NatMX6</i><br><b>Growth protocol</b>Thirty milliliters of yeast cultures were grown at 30 °C in the YPAD medium (1% yeast extract, 2% peptone, 0.01% adenine, 2% glucose). Cells (8 ml of culture) were harvested by centrifugation (1000 g, 3 min, room temperature) at the exponentional growth phase (OD600 ~1.8). Cell pellets were stored at -80 °C.<br><b>Nucleic acid extraction protocol</b>Thaw cell pellets on ice (~5 min). Add 400 ul of extraction buffer (1 mM EDTA, 0.1 M LiCl, 0.1 M Tris-HCl pH 7.5, 1% SDS), 400 ul of glass beads and 400 ul of acidic phenol (pH 4.3):chloroform:isoamylalcohol (25:24:1) solution. Disrupt the cells in FastPrep-24 (MP Biomedicals) (speed 6, duration 25 s) using 3 shaking cycles with 5 minutes incubations on ice in between. Pellet the debris by centrifugation (20 000 g, 10 min, 4 °C). Transfer the supernatant to a new microcentrifuge tube. Add 30 ul of 40% KAc (pH 5.5) and 400 ul of phenol (pH 4.3):chloroform:isoamylalcohol (25:24:1) solution. Mix vigorously by vortexing for 30 s and repeat the centrifugation step. Transfer the upper phase to a new microcentrifuge tube, add 1 ml of 96% EtOH, mix by inverting the tube and let RNA precipitate for at least 1 h at -20 °C. Pellet the RNA by centrifugation (20 000 g, 15 min, 4 °C). Remove the supernatant and rinse the pellet with 70% EtOH. Let the RNA pellet dry. Dissolve the RNA pellet in 150 ul of DEPC-treated water and measure RNA concentration on Nanodrop 2000 (Thermo Scientific). Take the volume corresponding to 150 ug of RNA. Add DEPC-treated water to the final volume of 175 ul, add 20 ul of DNase buffer and 5 ul of DNase from the MasterPure Yeast RNA purification kit (Epicentre). Finish the RNA preparation with this kit according to the manufacturer’s protocol, starting with step 4 in section B of the protocol. After the last rinse with 70% EtOH (step 12), add 500 ul of 70% EtOH to the RNA pellet and store the samples at -20 °C.<br><b>Nucleic acid library construction protocol</b>Strand-specific paired-end RNA-seq libraries were constructed from poly(A)-enriched RNA samples by BGI Genomics using their standard procedure.<br><b>Nucleic acid sequencing protocol</b>RNA-seq libraries were sequenced (100 nt, paired-end) by BGI Genomics using the Illumina HiSeq platform. Raw reads were filtered after sequencing, including removal of adapter sequences, contamination and low-quality reads.
DOI: 10.6084/m9.figshare.3806778.v1
title: budding yeast RNA-seq data for prp45(1-169) and wild type (read_1 in FASTQ)

description: <b>Samples (read_1 from PE sequencing)</b><b>WT sample:</b> 13-BY4741-_1.fq.gz <b>prp45(1-169) sample:</b> 14-prp45-_1.fq.gz<br><b><i>Saccharomyces cerevisiae</i> strain genotypes</b><b>WT BY4741:</b> <i>MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0</i><b>prp45(1-169):</b> <i>MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 prp45(1-169)-3HA::NatMX6</i><br><b>Growth protocol</b>Thirty milliliters of yeast cultures were grown at 30 °C in the YPAD medium (1% yeast extract, 2% peptone, 0.01% adenine, 2% glucose). Cells (8 ml of culture) were harvested by centrifugation (1000 g, 3 min, room temperature) at the exponentional growth phase (OD600 ~1.8). Cell pellets were stored at -80 °C.<br><b>Nucleic acid extraction protocol</b>Thaw cell pellets on ice (~5 min). Add 400 ul of extraction buffer (1 mM EDTA, 0.1 M LiCl, 0.1 M Tris-HCl pH 7.5, 1% SDS), 400 ul of glass beads and 400 ul of acidic phenol (pH 4.3):chloroform:isoamylalcohol (25:24:1) solution. Disrupt the cells in FastPrep-24 (MP Biomedicals) (speed 6, duration 25 s) using 3 shaking cycles with 5 minutes incubations on ice in between. Pellet the debris by centrifugation (20 000 g, 10 min, 4 °C). Transfer the supernatant to a new microcentrifuge tube. Add 30 ul of 40% KAc (pH 5.5) and 400 ul of phenol (pH 4.3):chloroform:isoamylalcohol (25:24:1) solution. Mix vigorously by vortexing for 30 s and repeat the centrifugation step. Transfer the upper phase to a new microcentrifuge tube, add 1 ml of 96% EtOH, mix by inverting the tube and let RNA precipitate for at least 1 h at -20 °C. Pellet the RNA by centrifugation (20 000 g, 15 min, 4 °C). Remove the supernatant and rinse the pellet with 70% EtOH. Let the RNA pellet dry. Dissolve the RNA pellet in 150 ul of DEPC-treated water and measure RNA concentration on Nanodrop 2000 (Thermo Scientific). Take the volume corresponding to 150 ug of RNA. Add DEPC-treated water to the final volume of 175 ul, add 20 ul of DNase buffer and 5 ul of DNase from the MasterPure Yeast RNA purification kit (Epicentre). Finish the RNA preparation with this kit according to the manufacturer’s protocol, starting with step 4 in section B of the protocol. After the last rinse with 70% EtOH (step 12), add 500 ul of 70% EtOH to the RNA pellet and store the samples at -20 °C.<br><b>Nucleic acid library construction protocol</b>Strand-specific paired-end RNA-seq libraries were constructed from poly(A)-enriched RNA samples by BGI Genomics using their standard procedure.<br><b>Nucleic acid sequencing protocol</b>RNA-seq libraries were sequenced (100 nt, paired-end) by BGI Genomics using the Illumina HiSeq platform. Raw reads were filtered after sequencing, including removal of adapter sequences, contamination and low-quality reads.
DOI: 10.6084/m9.figshare.3806766
title: Codes

description: This is codes of a distance-weighted string kernel SVM that can be used for prediction of A-to-I RNA editing events
DOI: 10.6084/m9.figshare.3806766.v2
title: Codes

description: This is codes of a distance-weighted string kernel SVM that can be used for prediction of A-to-I RNA editing events
DOI: 10.6084/m9.figshare.3806766.v1
title: Codes

description: This is codes of a distance-weighted string kernel SVM that can be used for prediction of A-to-I RNA editing events
DOI: 10.6084/m9.figshare.3806751
title: Development of NODA-SSRW

description: This files is datasets to develop new questionnaire "NODA-SSRW". The NODA-SSRW is to abridge "the Natural and Other Disaster Association Stress Scales for Rescue Workers" and able to measure stressor, stress-coping, and social-support for firefighters and Emergency Medical Technicians.
DOI: 10.6084/m9.figshare.3806751.v1
title: Development of NODA-SSRW

description: This files is datasets to develop new questionnaire "NODA-SSRW". The NODA-SSRW is to abridge "the Natural and Other Disaster Association Stress Scales for Rescue Workers" and able to measure stressor, stress-coping, and social-support for firefighters and Emergency Medical Technicians.
DOI: 10.6084/m9.figshare.3806649
title: Dutch translation and validation of the readiness for interprofessional learning scale (RIPLS) in a primary healthcare context

description: <b>Background:</b> Interprofessional education and collaborative practice are gradually gaining importance in the context of growing healthcare complexity. The readiness for interprofessional learning scale (RIPLS) is a well-known scale that can identify attitudinal barriers and variance across professions, which may affect educational interventions. <b>Objectives:</b> This study aims to translate the English RIPLS into Dutch and to test its reliability and validity. <b>Methods:</b> The scale was translated and back-translated by two pairs of people independently and tested for feasibility and comprehensibility. The translated scale was used with 219 general practitioners, 238 community nurses, and 53 palliative home-care nurses. Exploratory factor analysis was used to assess construct validity. Confirmatory factor analysis was done to generate a fit model. Cronbach’s alpha was computed to evaluate internal consistency. Regression analysis was used to evaluate the effect of the RIPLS score on the level of learning through collaboration and to gauge the influence of the participants’ gender, age, previous palliative care education, type of practice and years in practice. <b>Results:</b> Confirmatory and exploratory factor analysis confirms the factor structure of the original version. The Dutch version shows good reliability (overall Cronbach’s alpha: 0.88; intraclass correlation coefficient after test-retest: 0.718 (95%CI: 0.499–0.852). The RIPLS score correlates with the amount of workplace learning during collaboration (discriminant validity: <i>P</i> <b>Conclusion:</b> The Dutch translation of the RIPLS is now ready for comparative studies.