cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1568311.v1
title: An RNA-based approach to sequence the mitogenome of <i>Hypoptopoma incognitum</i> (Siluriformes: Loricariidae)

description: <i>Hypoptopoma incognitum</i> is a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon. Only two species of Loricariidae fish have their complete mitogenomes sequence deposited in the Genbank. An innovative RNA-based approach was used to assemble the complete mitogenome of <i>H. incognitum</i> with an average coverage depth of 5292×. The typical vertebrate mitochondrial features were found; 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a non-coding control region. Moreover, the use of this approach allowed the measurement of mtRNA expression levels, the punctuation pattern of editing, and the detection of heteroplasmies.
DOI: 10.6084/m9.figshare.1568313.v1
title: DNA barcoding of Jamaican bats: implications to Neotropical biodiversity

description: We report on the first comprehensive DNA barcoding survey of bats from Jamaica and compare the genetic variation to similar species on South America and Central America. Bats comprise the majority of mammalian diversity in typical lowland forest in the Neotropics, but the Caribbean is one noticeable geographic gap in the International Barcode of Life reference database. Of the 20 known species reported from Jamaica, half were DNA barcoded and were genetically distinct with interspecific variation ranging from 17 to 33%. By contrast, intraspecific variation ranged from 0 to 0.5% indicating that the barcode gap was sufficient in differentiating bat species diversity in Jamaica. The low levels of intraspecific divergence indicate that the populations within each species are relatively homogeneous across the island. There were, however, several cases of high sequence divergence for widely distributed species that occur on both the Caribbean islands and the continental mainland, which warrant further taxonomic study.
DOI: 10.6084/m9.figshare.1568310.v2
title: The accuracy of self-reported adherence to an activity advice

description: <i>Objective</i>. The aim of this cross-sectional observational study was to investigate whether patients referred for non-specific low back pain accurately report whether they follow home-based activity advice. Research suggests that inadequate adherence to home-based activity advice during an intervention period might diminish the effectiveness of an intervention. Insight into patient adherence to home-based activity advice is hindered by a lack of objective data. Most data consist of self-reporting and interviews. <i>Methods</i>. Participants were advised to complete a home-based activity for 1 week. We validated self-reporting of home-based activity with data obtained from an activity monitor worn by 51 patients who reported non-specific low back pain. The proportion of accurate self-reporting and kappa values were calculated to determine the level of accuracy of self-reporting. <i>Results</i>. An analysis of 357 (51 × 7) walking days found accurate participant reports on 233 days; only 22% of the participants reported accurately on all 7 consecutive days. Low kappa scores between the barrier list and the activity monitor show the poor reliability of participants’ self-reporting. <i>Conclusion</i>. Self-reporting about the performance of advised home-based activity for the management of non-specific low back pain in a physiotherapy practice setting is rather inaccurate.
DOI: 10.6084/m9.figshare.1568310.v1
title: The accuracy of self-reported adherence to an activity advice

description: <i>Objective</i>. The aim of this cross-sectional observational study was to investigate whether patients referred for non-specific low back pain accurately report whether they follow home-based activity advice. Research suggests that inadequate adherence to home-based activity advice during an intervention period might diminish the effectiveness of an intervention. Insight into patient adherence to home-based activity advice is hindered by a lack of objective data. Most data consist of self-reporting and interviews. <i>Methods</i>. Participants were advised to complete a home-based activity for 1 week. We validated self-reporting of home-based activity with data obtained from an activity monitor worn by 51 patients who reported non-specific low back pain. The proportion of accurate self-reporting and kappa values were calculated to determine the level of accuracy of self-reporting. <i>Results</i>. An analysis of 357 (51 × 7) walking days found accurate participant reports on 233 days; only 22% of the participants reported accurately on all 7 consecutive days. Low kappa scores between the barrier list and the activity monitor show the poor reliability of participants’ self-reporting. <i>Conclusion</i>. Self-reporting about the performance of advised home-based activity for the management of non-specific low back pain in a physiotherapy practice setting is rather inaccurate.
DOI: 10.6084/m9.figshare.1568303
title: Antlerogenic stem cells: molecular features and potential in rabbit bone regeneration

description: <i>Aim</i>: (i) To assess the expression profiles of stem cell-associated markers including <i>Oct4, Sox2, Klf4, Nanog, C-myc, Stat3</i> and <i>Cd9</i>, (ii) analyze the nanotopography of the MIC-1 stem cells and (iii) evaluate the efficiency of live stem cell implants and stem cell culture derivatives on the regeneration of bone deficiencies in rabbit mandibles.<i>Materials and methods</i>: The expression profiles of stem cell-associated genes, including <i>Oct4, Sox2, Klf4, Nanog, C-myc, Stat3</i> and <i>CD9 </i>were assessed using reverse transcription polymerase chain reaction and flow cytometry. Nanotopography of the antlerogenic MIC-1 cell lineage was analyzed using atomic force microscopy. The effect of MIC-1 stem cells, their homogenate and supernatant on the regeneration of bone deficiencies in rabbit mandibles was evaluated using histological analysis. The effect of MIC-1 stem cells and stem cell-based derivatives on the immune responses of the animals was assessed by analyses of acute phase protein levels (haptoglobin and fibrinogen).<i>Results</i>: We found that the MIC-1 cells isolated from the apical regions of growing antlers exhibited molecular features that were characteristics of pluripotent stem cells. Using atomic force microscopy, we determined the details of the cell surface morphologies with a particular emphasis on the patterns of formation of plasma extensions for interlinking adjacent cells. We also demonstrated that not only implanted stem cells but also cell homogenates and cell post-culture supernatants have potential in the regeneration of bone deficiencies in the rabbit mandible.<i>Conclusions</i>: Our findings indicate that the use of both antlerogenic stem cell implants and the preparations derived from the cells offer alternative approaches to those based on autologous stem cells in the biological stimulation of osteogenesis and in bone regeneration.
DOI: 10.6084/m9.figshare.1568303.v1
title: Antlerogenic stem cells: molecular features and potential in rabbit bone regeneration

description: <i>Aim</i>: (i) To assess the expression profiles of stem cell-associated markers including <i>Oct4, Sox2, Klf4, Nanog, C-myc, Stat3</i> and <i>Cd9</i>, (ii) analyze the nanotopography of the MIC-1 stem cells and (iii) evaluate the efficiency of live stem cell implants and stem cell culture derivatives on the regeneration of bone deficiencies in rabbit mandibles.<i>Materials and methods</i>: The expression profiles of stem cell-associated genes, including <i>Oct4, Sox2, Klf4, Nanog, C-myc, Stat3</i> and <i>CD9 </i>were assessed using reverse transcription polymerase chain reaction and flow cytometry. Nanotopography of the antlerogenic MIC-1 cell lineage was analyzed using atomic force microscopy. The effect of MIC-1 stem cells, their homogenate and supernatant on the regeneration of bone deficiencies in rabbit mandibles was evaluated using histological analysis. The effect of MIC-1 stem cells and stem cell-based derivatives on the immune responses of the animals was assessed by analyses of acute phase protein levels (haptoglobin and fibrinogen).<i>Results</i>: We found that the MIC-1 cells isolated from the apical regions of growing antlers exhibited molecular features that were characteristics of pluripotent stem cells. Using atomic force microscopy, we determined the details of the cell surface morphologies with a particular emphasis on the patterns of formation of plasma extensions for interlinking adjacent cells. We also demonstrated that not only implanted stem cells but also cell homogenates and cell post-culture supernatants have potential in the regeneration of bone deficiencies in the rabbit mandible.<i>Conclusions</i>: Our findings indicate that the use of both antlerogenic stem cell implants and the preparations derived from the cells offer alternative approaches to those based on autologous stem cells in the biological stimulation of osteogenesis and in bone regeneration.
DOI: 10.6084/m9.figshare.1568294
title: Anti-amyloid compounds protect from silica nanoparticle-induced neurotoxicity in the nematode <i>C. elegans</i>

description: Identifying nanomaterial-bio-interactions are imperative due to the broad introduction of nanoparticle (NP) applications and their distribution. Here, we demonstrate that silica NPs effect widespread protein aggregation in the soil nematode <i>Caenorhabditis elegans</i> ranging from induction of amyloid in nucleoli of intestinal cells to facilitation of protein aggregation in body wall muscles and axons of neural cells. Proteomic screening revealed that exposure of adult <i>C. elegans</i> with silica NPs promotes segregation of proteins belonging to the gene ontology (GO) group of “protein folding, proteolysis and stress response” to an SDS-resistant aggregome network. Candidate proteins in this group include chaperones, heat shock proteins and subunits of the 26S proteasome which are all decisively involved in protein homeostasis. The pathway of protein homeostasis was validated as a major target of silica NPs by behavioral phenotyping, as inhibitors of amyloid formation rescued NP-induced defects of locomotory patterns and egg laying. The analysis of a reporter worm for serotonergic neural cells revealed that silica NP-induced protein aggregation likewise occurs in axons of HSN neurons, where presynaptic accumulation of serotonin, e.g. disturbed axonal transport reduces the capacity for neurotransmission and egg laying. The results suggest that in <i>C. elegans</i> silica NPs promote a cascade of events including disturbance of protein homeostasis, widespread protein aggregation and inhibition of serotonergic neurotransmission which can be interrupted by compounds preventing amyloid fibrillation.
DOI: 10.6084/m9.figshare.1568294.v2
title: Anti-amyloid compounds protect from silica nanoparticle-induced neurotoxicity in the nematode <i>C. elegans</i>

description: Identifying nanomaterial-bio-interactions are imperative due to the broad introduction of nanoparticle (NP) applications and their distribution. Here, we demonstrate that silica NPs effect widespread protein aggregation in the soil nematode <i>Caenorhabditis elegans</i> ranging from induction of amyloid in nucleoli of intestinal cells to facilitation of protein aggregation in body wall muscles and axons of neural cells. Proteomic screening revealed that exposure of adult <i>C. elegans</i> with silica NPs promotes segregation of proteins belonging to the gene ontology (GO) group of “protein folding, proteolysis and stress response” to an SDS-resistant aggregome network. Candidate proteins in this group include chaperones, heat shock proteins and subunits of the 26S proteasome which are all decisively involved in protein homeostasis. The pathway of protein homeostasis was validated as a major target of silica NPs by behavioral phenotyping, as inhibitors of amyloid formation rescued NP-induced defects of locomotory patterns and egg laying. The analysis of a reporter worm for serotonergic neural cells revealed that silica NP-induced protein aggregation likewise occurs in axons of HSN neurons, where presynaptic accumulation of serotonin, e.g. disturbed axonal transport reduces the capacity for neurotransmission and egg laying. The results suggest that in <i>C. elegans</i> silica NPs promote a cascade of events including disturbance of protein homeostasis, widespread protein aggregation and inhibition of serotonergic neurotransmission which can be interrupted by compounds preventing amyloid fibrillation.
DOI: 10.6084/m9.figshare.1568294.v1
title: Anti-amyloid compounds protect from silica nanoparticle-induced neurotoxicity in the nematode <i>C. elegans</i>

description: Identifying nanomaterial-bio-interactions are imperative due to the broad introduction of nanoparticle (NP) applications and their distribution. Here, we demonstrate that silica NPs effect widespread protein aggregation in the soil nematode <i>Caenorhabditis elegans</i> ranging from induction of amyloid in nucleoli of intestinal cells to facilitation of protein aggregation in body wall muscles and axons of neural cells. Proteomic screening revealed that exposure of adult <i>C. elegans</i> with silica NPs promotes segregation of proteins belonging to the gene ontology (GO) group of “protein folding, proteolysis and stress response” to an SDS-resistant aggregome network. Candidate proteins in this group include chaperones, heat shock proteins and subunits of the 26S proteasome which are all decisively involved in protein homeostasis. The pathway of protein homeostasis was validated as a major target of silica NPs by behavioral phenotyping, as inhibitors of amyloid formation rescued NP-induced defects of locomotory patterns and egg laying. The analysis of a reporter worm for serotonergic neural cells revealed that silica NP-induced protein aggregation likewise occurs in axons of HSN neurons, where presynaptic accumulation of serotonin, e.g. disturbed axonal transport reduces the capacity for neurotransmission and egg laying. The results suggest that in <i>C. elegans</i> silica NPs promote a cascade of events including disturbance of protein homeostasis, widespread protein aggregation and inhibition of serotonergic neurotransmission which can be interrupted by compounds preventing amyloid fibrillation.
DOI: 10.6084/m9.figshare.1568285.v2
title: Arabidopsis phosphatase under-producer mutants <i>pup1</i> and <i>pup3</i> contain mutations in the <i>AtPAP10</i> and <i>AtPAP26</i> genes

description: Production and secretion of acid phosphatases (APases) is a hallmark adaptive response of plants to phosphate (Pi) deprivation. Researchers have long hypothesized that Pi starvation-induced APases are involved in internal Pi recycling and remobilization as well as in external Pi utilization. Two phosphatase under-producer (<i>pup</i>) mutants, <i>pup1</i> and <i>pup3</i>, were previously isolated in <i>Arabidopsis</i>. Characterization of these 2 <i>pup</i> mutants provided the first genetic evidence for the above hypothesis. To date, however, the molecular lesions in these 2 <i>pup</i> mutants remain unknown. In this work, we demonstrate that <i>pup1</i> and <i>pup3</i> contain point mutations in the <i>Arabidopsis</i> purple acid phosphatase gene <i>AtPAP10</i> and <i>AtPAP26</i>, respectively. Our results answer a long-standing question about the molecular identity of the <i>PUP1</i> and <i>PUP3</i> genes and corroborate the conclusions from previous studies regarding the function of AtPAP10 and AtPAP26 in plant acclimation to Pi deprivation.
DOI: 10.6084/m9.figshare.1568281
title: Chum Salmon Genetic Diversity in the Northeastern Pacific Ocean Assessed with Single Nucleotide Polymorphisms (SNPs): Applications to Fishery Management

description: We examined genetic diversity patterns among 55 collections of Chum Salmon from the northeastern Pacific Ocean using 89 single nucleotide polymorphisms (SNPs). The distribution of Chum Salmon samples extended from the Nass River along the coast of British Columbia and along the coast of Washington as far south as the Columbia River. Chum Salmon represented three previously defined run-groups: fall (primarily), summer, and winter. Genetic variation at SNP loci, as measured by <i>F</i><sub>ST</sub>, ranged from 0.002 to 0.279 over all collections and averaged 0.062 over all loci. Similar to the genetic patterns detected with microsatellites and allozymes, genetic variation followed a regional structure along geographic distance, with genetic diversity being highest in the north and decreasing southward, then increasing in and near the Columbia River. Within Puget Sound, Washington, genetic variation was structured further according to run timing (fall, summer, and winter) and shared ancestry. Simulations indicated that this suite of SNPs is powerful for identifying regional components in a Chum Salmon mixed fishery. Because of the transferability of SNP data, the growing SNP baseline for Chum Salmon will be useful for multiple agencies managing Chum Salmon around the Pacific Rim.Received December 19, 2014; accepted May 20, 2015
DOI: 10.6084/m9.figshare.1568285.v1
title: Arabidopsis phosphatase under-producer mutants <i>pup1</i> and <i>pup3</i> contain mutations in the <i>AtPAP10</i> and <i>AtPAP26</i> genes

description: Production and secretion of acid phosphatases (APases) is a hallmark adaptive response of plants to phosphate (Pi) deprivation. Researchers have long hypothesized that Pi starvation-induced APases are involved in internal Pi recycling and remobilization as well as in external Pi utilization. Two phosphatase under-producer (<i>pup</i>) mutants, <i>pup1</i> and <i>pup3</i>, were previously isolated in <i>Arabidopsis</i>. Characterization of these 2 <i>pup</i> mutants provided the first genetic evidence for the above hypothesis. To date, however, the molecular lesions in these 2 <i>pup</i> mutants remain unknown. In this work, we demonstrate that <i>pup1</i> and <i>pup3</i> contain point mutations in the <i>Arabidopsis</i> purple acid phosphatase gene <i>AtPAP10</i> and <i>AtPAP26</i>, respectively. Our results answer a long-standing question about the molecular identity of the <i>PUP1</i> and <i>PUP3</i> genes and corroborate the conclusions from previous studies regarding the function of AtPAP10 and AtPAP26 in plant acclimation to Pi deprivation.
DOI: 10.6084/m9.figshare.1568281.v2
title: Chum Salmon Genetic Diversity in the Northeastern Pacific Ocean Assessed with Single Nucleotide Polymorphisms (SNPs): Applications to Fishery Management

description: We examined genetic diversity patterns among 55 collections of Chum Salmon from the northeastern Pacific Ocean using 89 single nucleotide polymorphisms (SNPs). The distribution of Chum Salmon samples extended from the Nass River along the coast of British Columbia and along the coast of Washington as far south as the Columbia River. Chum Salmon represented three previously defined run-groups: fall (primarily), summer, and winter. Genetic variation at SNP loci, as measured by <i>F</i><sub>ST</sub>, ranged from 0.002 to 0.279 over all collections and averaged 0.062 over all loci. Similar to the genetic patterns detected with microsatellites and allozymes, genetic variation followed a regional structure along geographic distance, with genetic diversity being highest in the north and decreasing southward, then increasing in and near the Columbia River. Within Puget Sound, Washington, genetic variation was structured further according to run timing (fall, summer, and winter) and shared ancestry. Simulations indicated that this suite of SNPs is powerful for identifying regional components in a Chum Salmon mixed fishery. Because of the transferability of SNP data, the growing SNP baseline for Chum Salmon will be useful for multiple agencies managing Chum Salmon around the Pacific Rim.Received December 19, 2014; accepted May 20, 2015
DOI: 10.6084/m9.figshare.1568281.v1
title: Chum Salmon Genetic Diversity in the Northeastern Pacific Ocean Assessed with Single Nucleotide Polymorphisms (SNPs): Applications to Fishery Management

description: We examined genetic diversity patterns among 55 collections of Chum Salmon from the northeastern Pacific Ocean using 89 single nucleotide polymorphisms (SNPs). The distribution of Chum Salmon samples extended from the Nass River along the coast of British Columbia and along the coast of Washington as far south as the Columbia River. Chum Salmon represented three previously defined run-groups: fall (primarily), summer, and winter. Genetic variation at SNP loci, as measured by <i>F</i><sub>ST</sub>, ranged from 0.002 to 0.279 over all collections and averaged 0.062 over all loci. Similar to the genetic patterns detected with microsatellites and allozymes, genetic variation followed a regional structure along geographic distance, with genetic diversity being highest in the north and decreasing southward, then increasing in and near the Columbia River. Within Puget Sound, Washington, genetic variation was structured further according to run timing (fall, summer, and winter) and shared ancestry. Simulations indicated that this suite of SNPs is powerful for identifying regional components in a Chum Salmon mixed fishery. Because of the transferability of SNP data, the growing SNP baseline for Chum Salmon will be useful for multiple agencies managing Chum Salmon around the Pacific Rim.Received December 19, 2014; accepted May 20, 2015
DOI: 10.6084/m9.figshare.1568257
title: Chronic Responses of <i>Daphnia magna</i> Under Dietary Exposure to Leaves of a Transgenic (Event MON810) Bt–Maize Hybrid and its Conventional Near-Isoline

description: Insect resistance is the second most common trait globally in cultivated genetically modified (GM) plants. Resistance is usually obtained by introducing into the plant’s genome genes from the bacterium <i>Bacillus thuringiensis</i> (Bt) coding for insecticidal proteins (Cry proteins or toxins) that target insect pests. The aim of this study was to examine the hypothesis that a chronic, high-dose dietary exposure to leaves of a Bt–maize hybrid (GM event MON810, expressing a transgenic or recombinant Cry1Ab toxin), exerted no adverse effects on fitness parameters of the aquatic nontarget organism <i>Daphnia magna</i> (water flea) when compared to an identical control diet based on leaves of the non-GM near-isoline. Cry1Ab was immunologically detected and quantified in GM maize leaf material used for <i>Daphnia</i> feed. A 69-kD protein near Bt’s active core-toxin size and a 34-kD protein were identified. The <i>D. magna</i> bioassay showed a resource allocation to production of resting eggs and early fecundity in <i>D. magna</i> fed GM maize, with adverse effects for body size and fecundity later in life. This is the first study to examine GM-plant leaf material in the <i>D. magna</i> model, and provides of negative fitness effects of a MON810 maize hybrid in a nontarget model organism under chronic, high dietary exposure. Based upon these results, it is postulated that the observed transgenic proteins exert a nontarget effect in <i>D. magna</i> and/or unintended changes were produced in the maize genome/metabolome by the transformation process, producing a nutritional difference between GM-maize and non-GM near-isoline.