cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4531355
title: Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems

description: Toxin-antitoxin (TA) systems are gene modules that appear to be horizontally mobile across a wide range of prokaryotes. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons have been made. We searched for type I, II and III toxin families using iterative searches with profile hidden Markov models across phyla and replicons. The distribution of type I toxin families were comparatively narrow, but these patterns weakened with recently discovered families. We discuss how the function and phenotypes of TA systems as well as biases in our search methods may account for differences in their distribution.
DOI: 10.6084/m9.figshare.4531337
title: Comparative analysis of the complete mitochondrial genomes of three geographical topmouth culter (<i>Culter alburnus</i>) groups and implications for their phylogenetics

description: Topmouth culter (<i>C. alburnus</i>) is an important commercial fish in China. We compared the nucleotide variations in the mtDNA genomes among three geographical groups of <i>Culter alburnus</i>: Liangzi Lake, Hubei Province (referred to as LZH); Taihu Lake, Jiangsu Province (TH); and Poyang Lake, Jiangxi Province (PYH). The similarity of whole mtDNA genomes ranged from 0.992 to 0.999. The similarity among 13 protein-coding genes, 2 rRNA genes, and the D-loop sequences was found to range from 0.982 to 0.996. This is useful data for future designing work for making specific molecular marker for distinguishing individuals of <i>C. alburnus</i> from the three geographical groups. An extended termination-associated sequence (ETAS) and several conserved blocks (CSB-F, CSB-E, CSB-D, CSB1, CSB2, and CSB3) were identified in the mtDNA control regions. A phylogenetic analysis shows a monophyletic relationship of the LZF-female and the LZF-male. However, the analysis also showed paraphyletic relationships for the other two geological groups. This result will be useful for the future breeding work of <i>C. alburnus.</i> Circular representation of the complete mitochondrial genomes of <i>C. alburnus.</i>
DOI: 10.6084/m9.figshare.4531340
title: Supplementary Material for: Single Nucleotide Polymorphisms in Adiponectin Gene Are Not Directly Associated with Increased Risk of Obstructive Sleep Apnea Syndrome in a Chinese Han Population

description: <i>Purpose:</i> This study aims to test the possible correlation between single nucleotide polymorphisms (SNPs) in the adiponectin gene and increased risk of obstructive sleep apnea syndrome (OSAS) in a Chinese Han population. <i>Materials and Methods:</i> A total of 266 subjects were enrolled into the study to detect 9 SNPs in the adiponectin gene. Multivariate unconditional logistic regression analysis, adjusted for gender and age, was used to estimate the associations of these SNPs with OSAS risk. <i>Results:</i> No evidence of a direct association was observed between these SNPs and the risk of OSAS in the Chinese Han population. However, the stratified analysis also revealed a remarkable genotype difference for SNP rs6773957 between cases and controls in the overweight subgroup (<i>p </i>&lt; 0.05). In addition, the allele or genotype distributions of rs12495941, rs182052, and rs16861205 had significant differences with regard to the severity of OSAS (<i>p </i>&lt; 0.05). No differences were identified in the other subgroups. <i>Conclusion:</i> The current research demonstrated that the SNPs in the adiponectin gene did not represent susceptibility loci for OSAS in Chinese Han individuals overall. However, variants of rs6773957 have an association with OSAS in overweight individuals. In addition, polymorphisms of rs12495941, rs182052, and rs16861205 are associated with the severity of OSAS.
DOI: 10.6084/m9.figshare.4531355.v2
title: Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems

description: Toxin-antitoxin (TA) systems are gene modules that appear to be horizontally mobile across a wide range of prokaryotes. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons have been made. We searched for type I, II and III toxin families using iterative searches with profile hidden Markov models across phyla and replicons. The distribution of type I toxin families were comparatively narrow, but these patterns weakened with recently discovered families. We discuss how the function and phenotypes of TA systems as well as biases in our search methods may account for differences in their distribution.
DOI: 10.6084/m9.figshare.4531337.v1
title: Comparative analysis of the complete mitochondrial genomes of three geographical topmouth culter (<i>Culter alburnus</i>) groups and implications for their phylogenetics

description: Topmouth culter (<i>C. alburnus</i>) is an important commercial fish in China. We compared the nucleotide variations in the mtDNA genomes among three geographical groups of <i>Culter alburnus</i>: Liangzi Lake, Hubei Province (referred to as LZH); Taihu Lake, Jiangsu Province (TH); and Poyang Lake, Jiangxi Province (PYH). The similarity of whole mtDNA genomes ranged from 0.992 to 0.999. The similarity among 13 protein-coding genes, 2 rRNA genes, and the D-loop sequences was found to range from 0.982 to 0.996. This is useful data for future designing work for making specific molecular marker for distinguishing individuals of <i>C. alburnus</i> from the three geographical groups. An extended termination-associated sequence (ETAS) and several conserved blocks (CSB-F, CSB-E, CSB-D, CSB1, CSB2, and CSB3) were identified in the mtDNA control regions. A phylogenetic analysis shows a monophyletic relationship of the LZF-female and the LZF-male. However, the analysis also showed paraphyletic relationships for the other two geological groups. This result will be useful for the future breeding work of <i>C. alburnus.</i> Circular representation of the complete mitochondrial genomes of <i>C. alburnus.</i>
DOI: 10.6084/m9.figshare.4531340.v1
title: Supplementary Material for: Single Nucleotide Polymorphisms in Adiponectin Gene Are Not Directly Associated with Increased Risk of Obstructive Sleep Apnea Syndrome in a Chinese Han Population

description: <i>Purpose:</i> This study aims to test the possible correlation between single nucleotide polymorphisms (SNPs) in the adiponectin gene and increased risk of obstructive sleep apnea syndrome (OSAS) in a Chinese Han population. <i>Materials and Methods:</i> A total of 266 subjects were enrolled into the study to detect 9 SNPs in the adiponectin gene. Multivariate unconditional logistic regression analysis, adjusted for gender and age, was used to estimate the associations of these SNPs with OSAS risk. <i>Results:</i> No evidence of a direct association was observed between these SNPs and the risk of OSAS in the Chinese Han population. However, the stratified analysis also revealed a remarkable genotype difference for SNP rs6773957 between cases and controls in the overweight subgroup (<i>p </i>&lt; 0.05). In addition, the allele or genotype distributions of rs12495941, rs182052, and rs16861205 had significant differences with regard to the severity of OSAS (<i>p </i>&lt; 0.05). No differences were identified in the other subgroups. <i>Conclusion:</i> The current research demonstrated that the SNPs in the adiponectin gene did not represent susceptibility loci for OSAS in Chinese Han individuals overall. However, variants of rs6773957 have an association with OSAS in overweight individuals. In addition, polymorphisms of rs12495941, rs182052, and rs16861205 are associated with the severity of OSAS.
DOI: 10.6084/m9.figshare.4531355.v1
title: Why so narrow: distribution of anti-sense regulated, type I toxin-antitoxin systems compared to type II and type III systems

description: Toxin-antitoxin (TA) systems are gene modules that appear to be horizontally mobile across a wide range of prokaryotes. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons have been made. We searched for type I, II and III toxin families using iterative searches with profile hidden Markov models across phyla and replicons. The distribution of type I toxin families were comparatively narrow, but these patterns weakened with recently discovered families. We discuss how the function and phenotypes of TA systems as well as biases in our search methods may account for differences in their distribution.
DOI: 10.6084/m9.figshare.4531265
title: 5_20_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4531184
title: 5_17_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions. Data taken on 5/17/2016 using HTI 96-MIN hydrophones with zoom H1 digital recorders.<br>
DOI: 10.6084/m9.figshare.4531265.v1
title: 5_20_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4531184.v1
title: 5_17_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions. Data taken on 5/17/2016 using HTI 96-MIN hydrophones with zoom H1 digital recorders.<br>
DOI: 10.6084/m9.figshare.4531037
title: Jacome-Flores_etal_Data.xlsx

description: data set that includes:Individual plants geographic coordinates Individual larvae occurenceIndividual synchronyIndividual nomber of flowers
DOI: 10.6084/m9.figshare.4531037.v1
title: Jacome-Flores_etal_Data.xlsx

description: data set that includes:Individual plants geographic coordinates Individual larvae occurenceIndividual synchronyIndividual nomber of flowers
DOI: 10.6084/m9.figshare.4530965
title: S1-dataset-tweetIDS.txt.zip

description: Tweet IDs for all tweets studied in The Lexicocalorimeter: Gauging public health through caloric input and output on social media.<br>Best version of the paper is on the aXiv at https://arxiv.org/abs/1507.05098<br>Paper also published by PLoS ONE.<br><br>
DOI: 10.6084/m9.figshare.4530959
title: A comparison of fate and toxicity of selenite, biogenically, and chemically synthesized selenium nanoparticles to zebrafish (<i>Danio rerio</i>) embryogenesis

description: Microbial reduction of selenium (Se) oxyanions to elemental Se is a promising technology for bioremediation and treatment of Se wastewaters. But a fraction of biogenic nano-Selenium (nano-Se<sup>b</sup>) formed in bioreactors remains suspended in the treated waters, thus entering the aquatic environment. The present study investigated the toxicity of nano-Se<sup>b</sup> formed by anaerobic granular sludge biofilms on zebrafish embryos in comparison with selenite and chemogenic nano-Se (nano-Se<sup>c</sup>). The nano-Se<sup>b</sup> formed by granular sludge biofilms showed a LC<sub>50</sub> value of 1.77 mg/L, which was 3.2-fold less toxic to zebrafish embryos than selenite (LC<sub>50 </sub>=<sub> </sub>0.55 mg/L) and 10-fold less toxic than bovine serum albumin stabilized nano-Se<sup>c</sup> (LC<sub>50 </sub>=<sub> </sub>0.16 mg/L). Smaller (nano-Se<sup>cs</sup>; particle diameter range: 25–80 nm) and larger (nano-Se<sup>cl</sup>; particle diameter range: 50–250 nm) sized chemically synthesized nano-Se<sup>c</sup> particles showed comparable toxicity on zebrafish embryos. The lower toxicity of nano-Se<sup>b</sup> in comparison with nano-Se<sup>c</sup> was analyzed in terms of the stabilizing organic layer. The results confirmed that the organic layer extracted from the nano-Se<sup>b</sup> consisted of components of the extracellular polymeric substances (EPS) matrix, which govern the physiochemical stability and surface properties like ζ-potential of nano-Se<sup>b</sup>. Based on the data, it is contented that the presence of humic acid like substances of EPS on the surface of nano-Se<sup>b</sup> plays a major role in lowering the bioavailability (uptake) and toxicity of nano-Se<sup>b</sup> by decreasing the interactions between nanoparticles and embryos.
DOI: 10.6084/m9.figshare.4530959.v1
title: A comparison of fate and toxicity of selenite, biogenically, and chemically synthesized selenium nanoparticles to zebrafish (<i>Danio rerio</i>) embryogenesis

description: Microbial reduction of selenium (Se) oxyanions to elemental Se is a promising technology for bioremediation and treatment of Se wastewaters. But a fraction of biogenic nano-Selenium (nano-Se<sup>b</sup>) formed in bioreactors remains suspended in the treated waters, thus entering the aquatic environment. The present study investigated the toxicity of nano-Se<sup>b</sup> formed by anaerobic granular sludge biofilms on zebrafish embryos in comparison with selenite and chemogenic nano-Se (nano-Se<sup>c</sup>). The nano-Se<sup>b</sup> formed by granular sludge biofilms showed a LC<sub>50</sub> value of 1.77 mg/L, which was 3.2-fold less toxic to zebrafish embryos than selenite (LC<sub>50 </sub>=<sub> </sub>0.55 mg/L) and 10-fold less toxic than bovine serum albumin stabilized nano-Se<sup>c</sup> (LC<sub>50 </sub>=<sub> </sub>0.16 mg/L). Smaller (nano-Se<sup>cs</sup>; particle diameter range: 25–80 nm) and larger (nano-Se<sup>cl</sup>; particle diameter range: 50–250 nm) sized chemically synthesized nano-Se<sup>c</sup> particles showed comparable toxicity on zebrafish embryos. The lower toxicity of nano-Se<sup>b</sup> in comparison with nano-Se<sup>c</sup> was analyzed in terms of the stabilizing organic layer. The results confirmed that the organic layer extracted from the nano-Se<sup>b</sup> consisted of components of the extracellular polymeric substances (EPS) matrix, which govern the physiochemical stability and surface properties like ζ-potential of nano-Se<sup>b</sup>. Based on the data, it is contented that the presence of humic acid like substances of EPS on the surface of nano-Se<sup>b</sup> plays a major role in lowering the bioavailability (uptake) and toxicity of nano-Se<sup>b</sup> by decreasing the interactions between nanoparticles and embryos.
DOI: 10.6084/m9.figshare.4530938
title: Occupational exposure limits for manufactured nanomaterials, a systematic review

description: <b>Background:</b> The toxicological properties of manufactured nanomaterials (MNMs) can be different from their bulk-material and uncertainty remains about the adverse health effects they may have on humans. Proposals for OELs have been put forward which can be useful for risk management and workers’ protection. We performed a systematic review of proposals for OELs for MNMs to better understand the extent of such proposals, as well as their derivation methods. <b>Methods:</b> We searched PubMed and Embase with an extensive search string and also assessed the references in the included studies. Two authors extracted the data independently. <b>Results:</b> We identified 20 studies that proposed in total 56 OEL values. Of these, two proposed a generic level for all MNMs, 14 proposed a generic OEL for a category of MNMs and 40 proposed an OEL for a specific nanomaterial. For specific fibers, four studies proposed a similar value but for carbon nanotubes (CNTs) the values differed with a factor ranging from 30 to 50 and for metals with a factor from 100 to 300. The studies did not provide explanations for this variation. We found that exposure to MNMs measured at selected workplaces may exceed even the highest proposed OEL. This indicates that the application and use of OELs may be useful for exposure reduction. <b>Conclusion:</b> OELs can provide a valuable reference point for exposure reduction measures in workplaces. There is a need for more and better supported OELs based on a more systematic approach to OEL derivation.
DOI: 10.6084/m9.figshare.4530938.v1
title: Occupational exposure limits for manufactured nanomaterials, a systematic review

description: <b>Background:</b> The toxicological properties of manufactured nanomaterials (MNMs) can be different from their bulk-material and uncertainty remains about the adverse health effects they may have on humans. Proposals for OELs have been put forward which can be useful for risk management and workers’ protection. We performed a systematic review of proposals for OELs for MNMs to better understand the extent of such proposals, as well as their derivation methods. <b>Methods:</b> We searched PubMed and Embase with an extensive search string and also assessed the references in the included studies. Two authors extracted the data independently. <b>Results:</b> We identified 20 studies that proposed in total 56 OEL values. Of these, two proposed a generic level for all MNMs, 14 proposed a generic OEL for a category of MNMs and 40 proposed an OEL for a specific nanomaterial. For specific fibers, four studies proposed a similar value but for carbon nanotubes (CNTs) the values differed with a factor ranging from 30 to 50 and for metals with a factor from 100 to 300. The studies did not provide explanations for this variation. We found that exposure to MNMs measured at selected workplaces may exceed even the highest proposed OEL. This indicates that the application and use of OELs may be useful for exposure reduction. <b>Conclusion:</b> OELs can provide a valuable reference point for exposure reduction measures in workplaces. There is a need for more and better supported OELs based on a more systematic approach to OEL derivation.
DOI: 10.6084/m9.figshare.4530899
title: Differential response of normal and transformed mammary epithelial cells to combined treatment of anti-miR-21 and radiation

description: <b>Purpose:</b> MicroRNA miR-21 has emerged as a therapeutic target in the treatment of breast cancer. This study was designed to compare the responses of breast cancer cells and non-transformed breast epithelial cells to a combined regimen of miR-21 inhibition and radiation. <b>Materials and methods:</b> The MDA-MB-361 (breast cancer) and MCF-10A (non-transformed mammary epithelial) cell lines were used for the comparison in this in vitro study. The stable knockdown of miR-21 was performed by using lentiviral approach. The response of the cells was monitored 4, 24 and 48 h after the irradiation with 0.25 and 2.5 Gy, using sham-irradiated cells as controls. The response of the cells was established by performing various functional assays – cell viability and cell attachment, clonogenic survival, cell cycle analysis and 3D microtissue formation. <b>Results:</b> The knockdown of miR-21 induced significant increase in apoptosis and growth delay in MDA-MB-361 cancer cells compared to non-transformed MCF-10A cells. After combined radiation and anti-miR-21 treatment, MDA-MB-361 cells show reduced cell growth and viability what is presented in their inability to form colonies. MCF-10A cells were not as sensitive to the combined treatment and that has also been confirmed with colony forming assay. <b>Conclusions:</b> Cellular response to a combined treatment of anti-miR-21 and radiation is different between cancer and non-cancer cells which highly support the idea of linking miR-21 inhibitor and radiation treatment in the future therapeutic approaches for breast cancer.
DOI: 10.6084/m9.figshare.4530899.v1
title: Differential response of normal and transformed mammary epithelial cells to combined treatment of anti-miR-21 and radiation

description: <b>Purpose:</b> MicroRNA miR-21 has emerged as a therapeutic target in the treatment of breast cancer. This study was designed to compare the responses of breast cancer cells and non-transformed breast epithelial cells to a combined regimen of miR-21 inhibition and radiation. <b>Materials and methods:</b> The MDA-MB-361 (breast cancer) and MCF-10A (non-transformed mammary epithelial) cell lines were used for the comparison in this in vitro study. The stable knockdown of miR-21 was performed by using lentiviral approach. The response of the cells was monitored 4, 24 and 48 h after the irradiation with 0.25 and 2.5 Gy, using sham-irradiated cells as controls. The response of the cells was established by performing various functional assays – cell viability and cell attachment, clonogenic survival, cell cycle analysis and 3D microtissue formation. <b>Results:</b> The knockdown of miR-21 induced significant increase in apoptosis and growth delay in MDA-MB-361 cancer cells compared to non-transformed MCF-10A cells. After combined radiation and anti-miR-21 treatment, MDA-MB-361 cells show reduced cell growth and viability what is presented in their inability to form colonies. MCF-10A cells were not as sensitive to the combined treatment and that has also been confirmed with colony forming assay. <b>Conclusions:</b> Cellular response to a combined treatment of anti-miR-21 and radiation is different between cancer and non-cancer cells which highly support the idea of linking miR-21 inhibitor and radiation treatment in the future therapeutic approaches for breast cancer.
DOI: 10.6084/m9.figshare.4530866
title: Chloroplast DNA variation in <i>Epipactis atrorubens</i> populations from northern Greece

description: <i>Epipactis</i> Zinn. is a highly diverse genus, with numerous taxa naturally occurring throughout Europe. While their morphological variability has resulted in contradictory opinions about their taxonomy, the knowledge of the genetic variation of many of its species is limited. Such an example is <i>E. atrorubens</i> in the Balkan Peninsula. In this work, the cpDNA variation of seven <i>E. atrorubens</i> populations from northern Greece and of one population from Germany has been investigated by means of PCR-RFLP markers. Two regions of the cpDNA were studied (<i>trn</i>H-<i>psb</i>A, <i>trn</i>L intron) and four PCR-RFLP markers were employed (<i>trn</i>H-<i>psb</i>A/<i>Hae</i>III, <i>trn</i>H-<i>psb</i>A/<i>Hinf</i>I, <i>trn</i>H-<i>psb</i>A/<i>Vsp</i>I, <i>trn</i>L/<i>Mbo</i>I), which have revealed variation in other <i>Epipactis</i> species. The results demonstrate limited genetic variability in the studied populations, as only one haplotype was present in all the populations (both Greek and German), with the exception of Mt. Menikion (Greece) where a second haplotype was also recorded. This limited variation may be attributed to the properties of the genetic markers involved, to the conserved status of the two cpDNA regions in this species or to factors related to the biology and evolutionary history of <i>E. atrorubens</i>. The presence of a second haplotype only in Mt. Menikion could be attributed to a hybridisation event in the past and/or to the potential existence of a glacial refugium on this mountain.