cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4038168
title: Supplementary Table S2 from Physico-chemical properties that control protein aggregation also determine whether a protein is retained or released from necrotic cells

description: Complete list of enriched molecular functions in NCC-participating and NCC-resistant protein subsets.
DOI: 10.7910/dvn/v1rjpf/5dmwi3
title: blc20171114_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038168.v1
title: Supplementary Table S2 from Physico-chemical properties that control protein aggregation also determine whether a protein is retained or released from necrotic cells

description: Complete list of enriched molecular functions in NCC-participating and NCC-resistant protein subsets.
DOI: 10.6084/m9.figshare.4038171
title: Supplemental File 2 computed stress strain data from Hydration affects the physical and mechanical properties of baleen tissue

description: Baleen, an anisotropic oral filtering tissue found only in the mouth of mysticete whales and made solely of alpha-keratin, exhibits markedly differing physical and mechanical properties between dried or (as in life) hydrated states. On average baleen is 32.35% water by weight in North Atlantic right whales (<i>Eubalaena glacialis</i>) and 34.37% in bowhead whales (<i>Balaena mysticetus</i>). Baleen's wettability measured by water droplet contact angles shows that dried baleen is hydrophobic whereas hydrated baleen is highly hydrophilic. Three-point flexural bending tests of mechanical strength reveal that baleen is strong yet ductile. Dried baleen is brittle and shatters at about 20-30 N mm<sup>-2</sup> but hydrated baleen is less stiff; it bends with little force and absorbed water is squeezed out when force is applied. Maximum recorded stress was 4 times higher in dried (mean 14.29 N mm<sup>-2</sup>) versus hydrated (mean 3.69 N mm<sup>-2</sup>) baleen, and the flexural stiffness was &gt;10 times higher in dried (mean 633 N mm<sup>-2</sup>) versus hydrated (mean 58 N mm<sup>-2</sup>) baleen. In addition to documenting hydration's powerful effects on baleen, this study indicates that baleen is far more pliant and malleable than commonly supposed, with implications for studies of baleen's structure and function as well as its susceptibility to oil or other hydrophobic pollutants.
DOI: 10.7910/dvn/v1rjpf/acmrsu
title: blc20170218_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038150
title: Supplementary Material for: Proteomics of Secretory-Stage and Maturation-Stage Enamel of Genetically Distinct Mice

description: The mechanisms by which excessive ingestion of fluoride (F) during amelogenesis leads to dental fluorosis (DF) are still not precisely known. Inbred strains of mice vary in their susceptibility to develop DF, and therefore permit the investigation of underlying molecular events influencing DF severity. We employed a proteomic approach to characterize and evaluate changes in protein expression from secretory-stage and maturation-stage enamel in 2 strains of mice with different susceptibilities to DF (A/J, i.e. ‘susceptible' and 129P3/J, i.e. ‘resistant'). Weanling male and female susceptible and resistant mice fed a low-F diet were divided into 2 F-water treatment groups. They received water containing 0 (control) or 50 mg F/l for 6 weeks. Plasma and incisor enamel was analyzed for F content. For proteomic analysis, the enamel proteins extracted for each group were separated by 2-dimensional electrophoresis and subsequently characterized by liquid-chromatography electrospray-ionization quadrupole time-of-flight mass spectrometry. F data were analyzed by 2-way ANOVA and Bonferroni's test (p &lt; 0.05). Resistant mice had significantly higher plasma and enamel F concentrations when compared with susceptible mice in the F-treated groups. The proteomic results for mice treated with 0 mg F/l revealed that during the secretory stage, resistant mice had a higher abundance of proteins than their susceptible counterparts, but this was reversed during the maturation stage. Treatment with F greatly increased the number of protein spots detected in both stages. Many proteins not previously described in enamel (e.g. type 1 collagen) as well as some uncharacterized proteins were identified. Our findings reveal new insights regarding amelogenesis and how genetic background and F affect this process.
DOI: 10.6084/m9.figshare.4038141
title: Mouse V1 grating and natural movie response correlations

description: Figure S1d from Muir et al. Accepted at Plos Comp Biol.
DOI: 10.6084/m9.figshare.4038150.v1
title: Supplementary Material for: Proteomics of Secretory-Stage and Maturation-Stage Enamel of Genetically Distinct Mice

description: The mechanisms by which excessive ingestion of fluoride (F) during amelogenesis leads to dental fluorosis (DF) are still not precisely known. Inbred strains of mice vary in their susceptibility to develop DF, and therefore permit the investigation of underlying molecular events influencing DF severity. We employed a proteomic approach to characterize and evaluate changes in protein expression from secretory-stage and maturation-stage enamel in 2 strains of mice with different susceptibilities to DF (A/J, i.e. ‘susceptible' and 129P3/J, i.e. ‘resistant'). Weanling male and female susceptible and resistant mice fed a low-F diet were divided into 2 F-water treatment groups. They received water containing 0 (control) or 50 mg F/l for 6 weeks. Plasma and incisor enamel was analyzed for F content. For proteomic analysis, the enamel proteins extracted for each group were separated by 2-dimensional electrophoresis and subsequently characterized by liquid-chromatography electrospray-ionization quadrupole time-of-flight mass spectrometry. F data were analyzed by 2-way ANOVA and Bonferroni's test (p &lt; 0.05). Resistant mice had significantly higher plasma and enamel F concentrations when compared with susceptible mice in the F-treated groups. The proteomic results for mice treated with 0 mg F/l revealed that during the secretory stage, resistant mice had a higher abundance of proteins than their susceptible counterparts, but this was reversed during the maturation stage. Treatment with F greatly increased the number of protein spots detected in both stages. Many proteins not previously described in enamel (e.g. type 1 collagen) as well as some uncharacterized proteins were identified. Our findings reveal new insights regarding amelogenesis and how genetic background and F affect this process.
DOI: 10.7910/dvn/v1rjpf/ttvobq
title: blc20170919_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/frj3zt
title: blc20170109_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038129
title: Supplementary Material for: Altered Expression of Cytoskeletal and Axonal Proteins in Oxaliplatin-Induced Neuropathy

description: <b><i>Background:</i></b> Oxaliplatin is a platinum compound widely used in the treatment of some solid tumors. Despite its usefulness, oxaliplatin-associated neurotoxicity represents the main dose-limiting factor of this drug. This study examined the structural neuronal effects of oxaliplatin treatment in spinal and supraspinal levels. <b><i>Methods:</i></b> Protein expression was investigated in the mouse cortex, thalamus, periaqueductal grey (PAG) matter and spinal cord (SC) by Western blotting. Thermal nociception was assessed by the hot plate test. <b><i>Results:</i></b> Results indicate a reduction in the levels of growth associated protein-43 (GAP43) in the cortex and SC areas at the end of thermal hyperalgesic response, while a decrease in neurofilament-H (NfH) phosphorylation was observed in the SC on day 21 when the pain-related manifestation reaches the neurotoxic peak. Counteracting phosphorylated NfH content increases in the SC and cortex regions at day 28 as a result of the beginning of neuro-regeneration process. We also revealed that the levels of HuD, a neuronal-specific RNA-binding protein, decreased, demonstrating the same temporal and regional expression pattern of GAP43. Oxaliplatin chronic treatment induced a region-specific upregulation of γ isoform of protein kinase C (PKC) within thalamus and PAG, and the administration of a PKC inhibitor suggests that PKC activity in these brain regions must be required to maintain the thermal hyperalgesic state. <b><i>Conclusions:</i></b> These results suggest that changes in the protein levels of the regulatory and structural proteins are due to oxaliplatin-induced neurotoxicity and imply that there is a direct link between structural changes in the central nervous system and chemotherapy-induced neurotoxicity.
DOI: 10.6084/m9.figshare.4038141.v1
title: Mouse V1 grating and natural movie response correlations

description: Figure S1d from Muir et al. Accepted at Plos Comp Biol.
DOI: 10.7910/dvn/v1rjpf/pucaew
title: blc20170106_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038129.v1
title: Supplementary Material for: Altered Expression of Cytoskeletal and Axonal Proteins in Oxaliplatin-Induced Neuropathy

description: <b><i>Background:</i></b> Oxaliplatin is a platinum compound widely used in the treatment of some solid tumors. Despite its usefulness, oxaliplatin-associated neurotoxicity represents the main dose-limiting factor of this drug. This study examined the structural neuronal effects of oxaliplatin treatment in spinal and supraspinal levels. <b><i>Methods:</i></b> Protein expression was investigated in the mouse cortex, thalamus, periaqueductal grey (PAG) matter and spinal cord (SC) by Western blotting. Thermal nociception was assessed by the hot plate test. <b><i>Results:</i></b> Results indicate a reduction in the levels of growth associated protein-43 (GAP43) in the cortex and SC areas at the end of thermal hyperalgesic response, while a decrease in neurofilament-H (NfH) phosphorylation was observed in the SC on day 21 when the pain-related manifestation reaches the neurotoxic peak. Counteracting phosphorylated NfH content increases in the SC and cortex regions at day 28 as a result of the beginning of neuro-regeneration process. We also revealed that the levels of HuD, a neuronal-specific RNA-binding protein, decreased, demonstrating the same temporal and regional expression pattern of GAP43. Oxaliplatin chronic treatment induced a region-specific upregulation of γ isoform of protein kinase C (PKC) within thalamus and PAG, and the administration of a PKC inhibitor suggests that PKC activity in these brain regions must be required to maintain the thermal hyperalgesic state. <b><i>Conclusions:</i></b> These results suggest that changes in the protein levels of the regulatory and structural proteins are due to oxaliplatin-induced neurotoxicity and imply that there is a direct link between structural changes in the central nervous system and chemotherapy-induced neurotoxicity.
DOI: 10.7910/dvn/v1rjpf/ugtfy1
title: blc20170713_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038117
title: Mouse V1 plaid responses - selectivity

description: Figure 2j from Muir et al. Accepted at Plos Comp Biol.
DOI: 10.7910/dvn/v1rjpf/ohfvlv
title: blc20170602_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038117.v1
title: Mouse V1 plaid responses - selectivity

description: Figure 2j from Muir et al. Accepted at Plos Comp Biol.
DOI: 10.7910/dvn/v1rjpf/3x1iro
title: blc20170220_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038096
title: Supplementary Material for: Genetic Burden Analyses of Phenotypes Relevant to Aging in the Berlin Aging Study II (BASE-II)

description: <b><i>Background:</i></b> Body mass index (BMI), bone mineral density (BMD), and telomere length are phenotypes that modulate the course of aging. Over 40% of their phenotypic variance is determined by genetics. Genome-wide association studies (GWAS) have recently uncovered &gt;100 independent single-nucleotide polymorphisms (SNPs) showing genome-wide significant (p &lt; 5 × 10<sup>-8</sup>) association with these traits. <b><i>Objective:</i></b> To test the individual and combined impact of previously reported GWAS SNPs on BMI, BMD, and relative leukocyte telomere length (rLTL) in ∼1,750 participants of the Berlin Aging Study II (BASE-II), a cohort consisting predominantly of individuals &gt;60 years of age. <b><i>Methods:</i></b> Linear regression analyses were performed on a total of 101 SNPs and BMI, BMD measurements of the femoral neck (FN) and lumbar spine (LS), and rLTL. The combined effect of all trait-specific SNPs was evaluated by generating a weighted genomic profile score (wGPS) used in the association analyses. The predictive capability of the wGPS was estimated by determining the area under the receiver operating curve (AUC) for osteoporosis status (determined by BMD) with and without the wGPS. <b><i>Results:</i></b> Five loci showed experiment-wide significant association with BMI (<i>FTO</i> rs1558902, p = 1.80 × 10<sup>-5</sup>) or BMD (<i>MEPE</i> rs6532023, p<sub>FN</sub> = 5.40 × 10<sup>-4</sup>, p<sub>LS</sub> = 1.09 × 10<sup>-4</sup>; <i>TNFRSF11B</i> rs2062377, p<sub>LS</sub> = 8.70 × 10<sup>-4</sup>; <i>AKAP11 </i>rs9533090, p<sub>LS</sub> = 1.05 × 10<sup>-3</sup>; <i>SMG6 </i>rs4790881, p<sub>FN</sub> = 3.41 × 10<sup>-4</sup>) after correction for multiple testing. Several additional loci showed nominally significant (p &lt; 0.05) association with BMI and BMD. The trait-specific wGPS was highly significantly associated with BMD (p &lt; 2 × 10<sup>-16</sup>) and BMI (p = 1.10 × 10<sup>-6</sup>). No significant association was detected for rLTL in either single-SNP or wGPS-based analyses. The AUC for osteoporosis improved modestly from 0.762 (95% CI 0.733-0.800) to 0.786 (95% CI 0.756-0.823) and 0.785 (95% CI 0.757-0.824) upon inclusion of the FN- and LS-BMD wGPS, respectively. <b><i>Conclusion:</i></b> Our study provides an independent validation of previously reported genetic association signals for BMI and BMD in the BASE-II cohort. Additional studies are needed to pinpoint the factors underlying the proportion of phenotypic variance that remains unexplained by the current models.
DOI: 10.7910/dvn/v1rjpf/wsoq8b
title: blc20170125_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038084
title: Mouse V1 plaid responses - facilitation

description: Figure 2i from Muir et al. Accepted at Plos Comp Biol.
DOI: 10.6084/m9.figshare.4038096.v1
title: Supplementary Material for: Genetic Burden Analyses of Phenotypes Relevant to Aging in the Berlin Aging Study II (BASE-II)

description: <b><i>Background:</i></b> Body mass index (BMI), bone mineral density (BMD), and telomere length are phenotypes that modulate the course of aging. Over 40% of their phenotypic variance is determined by genetics. Genome-wide association studies (GWAS) have recently uncovered &gt;100 independent single-nucleotide polymorphisms (SNPs) showing genome-wide significant (p &lt; 5 × 10<sup>-8</sup>) association with these traits. <b><i>Objective:</i></b> To test the individual and combined impact of previously reported GWAS SNPs on BMI, BMD, and relative leukocyte telomere length (rLTL) in ∼1,750 participants of the Berlin Aging Study II (BASE-II), a cohort consisting predominantly of individuals &gt;60 years of age. <b><i>Methods:</i></b> Linear regression analyses were performed on a total of 101 SNPs and BMI, BMD measurements of the femoral neck (FN) and lumbar spine (LS), and rLTL. The combined effect of all trait-specific SNPs was evaluated by generating a weighted genomic profile score (wGPS) used in the association analyses. The predictive capability of the wGPS was estimated by determining the area under the receiver operating curve (AUC) for osteoporosis status (determined by BMD) with and without the wGPS. <b><i>Results:</i></b> Five loci showed experiment-wide significant association with BMI (<i>FTO</i> rs1558902, p = 1.80 × 10<sup>-5</sup>) or BMD (<i>MEPE</i> rs6532023, p<sub>FN</sub> = 5.40 × 10<sup>-4</sup>, p<sub>LS</sub> = 1.09 × 10<sup>-4</sup>; <i>TNFRSF11B</i> rs2062377, p<sub>LS</sub> = 8.70 × 10<sup>-4</sup>; <i>AKAP11 </i>rs9533090, p<sub>LS</sub> = 1.05 × 10<sup>-3</sup>; <i>SMG6 </i>rs4790881, p<sub>FN</sub> = 3.41 × 10<sup>-4</sup>) after correction for multiple testing. Several additional loci showed nominally significant (p &lt; 0.05) association with BMI and BMD. The trait-specific wGPS was highly significantly associated with BMD (p &lt; 2 × 10<sup>-16</sup>) and BMI (p = 1.10 × 10<sup>-6</sup>). No significant association was detected for rLTL in either single-SNP or wGPS-based analyses. The AUC for osteoporosis improved modestly from 0.762 (95% CI 0.733-0.800) to 0.786 (95% CI 0.756-0.823) and 0.785 (95% CI 0.757-0.824) upon inclusion of the FN- and LS-BMD wGPS, respectively. <b><i>Conclusion:</i></b> Our study provides an independent validation of previously reported genetic association signals for BMI and BMD in the BASE-II cohort. Additional studies are needed to pinpoint the factors underlying the proportion of phenotypic variance that remains unexplained by the current models.
DOI: 10.6084/m9.figshare.4038084.v1
title: Mouse V1 plaid responses - facilitation

description: Figure 2i from Muir et al. Accepted at Plos Comp Biol.
DOI: 10.7910/dvn/v1rjpf/qvnkok
title: blc20171129_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038078
title: Supplementary Tables S2 detailing differential expression of 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: 10.6084/m9.figshare.4038078.v1
title: Supplementary Tables S2 detailing differential expression of 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/fnwakh
title: blc20170112_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038075
title: Scattering data from Guided wave tomography with an improved scattering model

description: Scattering data from FE across the tested defects at 50kHz
DOI: 10.6084/m9.figshare.4038075.v1
title: Scattering data from Guided wave tomography with an improved scattering model

description: Scattering data from FE across the tested defects at 50kHz
DOI: 10.7910/dvn/v1rjpf/5uieqg
title: blc20170614_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038066
title: Data and loss function tool from On the use of Bayesian decision theory for issuing natural hazard warnings

description: This contains all the data used in the paper as well as R code to implement the parametric loss function model for eliciting loss functions
DOI: 10.7910/dvn/v1rjpf/kjhob2
title: blc20171012_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4038060
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/714nln
title: blc20170417_03.txt.gz

description: :unav