cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4315730
title: Mobile-phone radiation-induced perturbation of gene-expression profiling, redox equilibrium and sporadic-apoptosis control in the ovary of <i>Drosophila melanogaster</i>

description: The daily use by people of wireless communication devices has increased exponentially in the last decade, begetting concerns regarding its potential health hazards. <i>Drosophila melanogaster</i> four days-old adult female flies were exposed for 30 min to radiation emitted by a commercial mobile phone at a SAR of 0.15 W/kg and a SAE of 270 J/kg. ROS levels and apoptotic follicles were assayed in parallel with a genome-wide microarrays analysis. ROS cellular contents were found to increase by 1.6-fold (x), immediately after the end of exposure, in follicles of pre-choriogenic stages (germarium - stage 10), while sporadically generated apoptotic follicles (germarium 2b and stages 7–9) presented with an averaged 2x upregulation in their sub-population mass, 4 h after fly's irradiation with mobile device. Microarray analysis revealed 168 genes being differentially expressed, 2 h post-exposure, in response to radiofrequency (RF) electromagnetic field-radiation exposure (≥1.25x, <i>P &lt; 0.05)</i> and associated with multiple and critical biological processes, such as basic metabolism and cellular subroutines related to stress response and apoptotic death. Exposure of adult flies to mobile-phone radiation for 30 min has an immediate impact on ROS production in animal's ovary, which seems to cause a global, systemic and non-targeted transcriptional reprogramming of gene expression, 2 h post-exposure, being finally followed by induction of apoptosis 4 h after the end of exposure. Conclusively, this unique type of pulsed radiation, mainly being derived from daily used mobile phones, seems capable of mobilizing critical cytopathic mechanisms, and altering fundamental genetic programs and networks in <i>D. melanogaster</i>.
DOI: 10.6084/m9.figshare.4315727
title: Date fruits inhibit hepatocyte apoptosis and modulate the expression of hepatocyte growth factor, cytochrome P450 2E1 and heme oxygenase-1 in carbon tetrachloride-induced liver fibrosis

description: <i>Context</i>: Date fruits have protective effects against liver fibrosis; however their anti-apoptotic effects have not been investigated. <i>Objective</i>: To investigate the modulating effects of date fruits on pro- and anti-apoptotic markers, cytochrome P450 2E1 (CYP2E1) and hepatocyte growth factor (HGF) in liver fibrosis. <i>Materials and methods</i>: Liver fibrosis was induced by injection of carbon tetrachloride (CCl<sub>4</sub>) for eight weeks. Date flesh extract (DFE) and pits extract (DPE) were taken daily concomitant with CCl<sub>4</sub>. Hepatocyte apoptosis was determined by measuring the expression of Fas, caspase-3, Bax, Bcl2 and hemeoxygenase-1 (HO-1). Hepatic levels of HGF and CYP2E1 were determined. <i>Results</i>: Treatment with DFE and DPE significantly attenuated the elevated levels of Fas, caspase 3, Bax and CYP2E1 induced by CCl<sub>4</sub>. In addition, they alleviated the reduction in Bcl2, HGF and HO-1, the cytoprotective and anti-apoptotic factors in liver. <i>Conclusions</i> DFE and DPE treatment can ameliorate liver fibrosis by inhibiting hepatocyte apoptosis.
DOI: 10.6084/m9.figshare.4315730.v2
title: Mobile-phone radiation-induced perturbation of gene-expression profiling, redox equilibrium and sporadic-apoptosis control in the ovary of <i>Drosophila melanogaster</i>

description: The daily use by people of wireless communication devices has increased exponentially in the last decade, begetting concerns regarding its potential health hazards. <i>Drosophila melanogaster</i> four days-old adult female flies were exposed for 30 min to radiation emitted by a commercial mobile phone at a SAR of 0.15 W/kg and a SAE of 270 J/kg. ROS levels and apoptotic follicles were assayed in parallel with a genome-wide microarrays analysis. ROS cellular contents were found to increase by 1.6-fold (x), immediately after the end of exposure, in follicles of pre-choriogenic stages (germarium - stage 10), while sporadically generated apoptotic follicles (germarium 2b and stages 7–9) presented with an averaged 2x upregulation in their sub-population mass, 4 h after fly's irradiation with mobile device. Microarray analysis revealed 168 genes being differentially expressed, 2 h post-exposure, in response to radiofrequency (RF) electromagnetic field-radiation exposure (≥1.25x, <i>P &lt; 0.05)</i> and associated with multiple and critical biological processes, such as basic metabolism and cellular subroutines related to stress response and apoptotic death. Exposure of adult flies to mobile-phone radiation for 30 min has an immediate impact on ROS production in animal's ovary, which seems to cause a global, systemic and non-targeted transcriptional reprogramming of gene expression, 2 h post-exposure, being finally followed by induction of apoptosis 4 h after the end of exposure. Conclusively, this unique type of pulsed radiation, mainly being derived from daily used mobile phones, seems capable of mobilizing critical cytopathic mechanisms, and altering fundamental genetic programs and networks in <i>D. melanogaster</i>.
DOI: 10.6084/m9.figshare.4315727.v1
title: Date fruits inhibit hepatocyte apoptosis and modulate the expression of hepatocyte growth factor, cytochrome P450 2E1 and heme oxygenase-1 in carbon tetrachloride-induced liver fibrosis

description: <i>Context</i>: Date fruits have protective effects against liver fibrosis; however their anti-apoptotic effects have not been investigated. <i>Objective</i>: To investigate the modulating effects of date fruits on pro- and anti-apoptotic markers, cytochrome P450 2E1 (CYP2E1) and hepatocyte growth factor (HGF) in liver fibrosis. <i>Materials and methods</i>: Liver fibrosis was induced by injection of carbon tetrachloride (CCl<sub>4</sub>) for eight weeks. Date flesh extract (DFE) and pits extract (DPE) were taken daily concomitant with CCl<sub>4</sub>. Hepatocyte apoptosis was determined by measuring the expression of Fas, caspase-3, Bax, Bcl2 and hemeoxygenase-1 (HO-1). Hepatic levels of HGF and CYP2E1 were determined. <i>Results</i>: Treatment with DFE and DPE significantly attenuated the elevated levels of Fas, caspase 3, Bax and CYP2E1 induced by CCl<sub>4</sub>. In addition, they alleviated the reduction in Bcl2, HGF and HO-1, the cytoprotective and anti-apoptotic factors in liver. <i>Conclusions</i> DFE and DPE treatment can ameliorate liver fibrosis by inhibiting hepatocyte apoptosis.
DOI: 10.6084/m9.figshare.4315730.v1
title: Mobile-phone Radiation-induced Perturbation of Gene-expression Profiling, Redox Equilibrium and Sporadic-apoptosis Control in the Ovary of <i>Drosophila melanogaster</i>

description: <b>Background</b>: The daily use by people of wireless communication devices has increased exponentially in the last decade, begetting concerns regarding its potential health hazards. <b>Methods</b>: <i>Drosophila melanogaster</i> four days-old adult female flies were exposed for 30 min to radiation emitted by a commercial mobile phone at a SAR of 0.15 W/kg and a SAE of 270 J/kg. ROS levels and apoptotic follicles were assayed in parallel with a genome-wide microarrays analysis. <b>Results</b>: ROS cellular contents were found to increase by 1.6 fold (x), immediately after the end of exposure, in follicles of pre-choriogenic stages (germarium - stage 10), while sporadically generated apoptotic follicles (germarium 2b and stages 7–9) presented with an averaged 2x upregulation in their sub-population mass, 4 h after fly's irradiation with mobile device. Microarray analysis revealed 168 genes being differentially expressed, 2 h post-exposure, in response to radiofrequency (RF) electromagnetic field-radiation exposure (≥1.25x, <i>P</i>&lt;0.05) and associated with multiple and critical biological processes, such as basic metabolism and cellular subroutines related to stress response and apoptotic death. <b>Conclusion</b>: Exposure of adult flies to mobile-phone radiation for 30 min has an immediate impact on ROS production in animal's ovary, which seems to cause a global, systemic and non-targeted transcriptional reprogramming of gene expression, 2 h post-exposure, being finally followed by induction of apoptosis 4 h after the end of exposure. Conclusively, this unique type of pulsed radiation, mainly being derived from daily used mobile phones, seems capable of mobilizing critical cytopathic mechanisms, and altering fundamental genetic programs and networks in <i>D. melanogaster</i>.
DOI: 10.6084/m9.figshare.4315715
title: Non-invasive pre-implantation aneuploidy screening and diagnosis of beta thalassemia IVSII654 mutation using spent embryo culture medium

description: <b>Background:</b> Cell-free nuclear DNA has been isolated from spent embryo culture medium. Whether this small amount of DNA can be amplified at the whole genome level and the concordance rate of karyotypes and specific alleles between biopsied cells and media has not been evaluated. <b>Methods:</b> Seven couples were recruited, 88 donated embryos and their corresponding media were collected for whole genome amplification (WGA). The efficiency of WGA, the concordance of chromosome status, and the HBB gene IVSII654 allele between biopsied cells and media were investigated. <b>Results:</b> After WGA, the DNA detection rate was 90.90% with a mean concentration of 26.15 ng/μl. The full chromosome concordance rate between biopsied cells and medium was 64.52%, and it increased to 90.00% for diploid blastocyst samples. Analysis of the mutated IVSII654 locus and SNP linkage verified that the DNA present in the medium originated from embryonic cells. <b>Conclusion:</b> We confirmed that nuclear DNA is present in spent culture medium and that the majority of this DNA can be amplified for subsequent analysis. Our results showed that non-invasive embryo genetic testing at the chromosomal-level using medium can concordant to the biopsied cells, but it needs further optimized before use in clinical applications.KEY MESSAGESThe aggressive biopsy step during PGD/PGS procedure would have a negative effect on the future development of the embryo.Cell-free nuclear DNA has been observed in spent embryo culture medium, which holds promise for the development of non-invasive PGD/PGS approaches. The presence of DNA in medium, its efficiency for WGA, and the concordance between chromosome status and the HBB gene IVSII654 allele as diagnosed from biopsied cells or medium were investigated.Non-invasive embryo genetic testing at the chromosomal-level and allele site using medium can concordant to the biopsied cells, but it needs further optimized before use in clinical applications. The aggressive biopsy step during PGD/PGS procedure would have a negative effect on the future development of the embryo. Cell-free nuclear DNA has been observed in spent embryo culture medium, which holds promise for the development of non-invasive PGD/PGS approaches. The presence of DNA in medium, its efficiency for WGA, and the concordance between chromosome status and the HBB gene IVSII654 allele as diagnosed from biopsied cells or medium were investigated. Non-invasive embryo genetic testing at the chromosomal-level and allele site using medium can concordant to the biopsied cells, but it needs further optimized before use in clinical applications.
DOI: 10.6084/m9.figshare.4315715.v1
title: Non-invasive pre-implantation aneuploidy screening and diagnosis of beta thalassemia IVSII654 mutation using spent embryo culture medium

description: <b>Background:</b> Cell-free nuclear DNA has been isolated from spent embryo culture medium. Whether this small amount of DNA can be amplified at the whole genome level and the concordance rate of karyotypes and specific alleles between biopsied cells and media has not been evaluated. <b>Methods:</b> Seven couples were recruited, 88 donated embryos and their corresponding media were collected for whole genome amplification (WGA). The efficiency of WGA, the concordance of chromosome status, and the HBB gene IVSII654 allele between biopsied cells and media were investigated. <b>Results:</b> After WGA, the DNA detection rate was 90.90% with a mean concentration of 26.15 ng/μl. The full chromosome concordance rate between biopsied cells and medium was 64.52%, and it increased to 90.00% for diploid blastocyst samples. Analysis of the mutated IVSII654 locus and SNP linkage verified that the DNA present in the medium originated from embryonic cells. <b>Conclusion:</b> We confirmed that nuclear DNA is present in spent culture medium and that the majority of this DNA can be amplified for subsequent analysis. Our results showed that non-invasive embryo genetic testing at the chromosomal-level using medium can concordant to the biopsied cells, but it needs further optimized before use in clinical applications.KEY MESSAGESThe aggressive biopsy step during PGD/PGS procedure would have a negative effect on the future development of the embryo.Cell-free nuclear DNA has been observed in spent embryo culture medium, which holds promise for the development of non-invasive PGD/PGS approaches. The presence of DNA in medium, its efficiency for WGA, and the concordance between chromosome status and the HBB gene IVSII654 allele as diagnosed from biopsied cells or medium were investigated.Non-invasive embryo genetic testing at the chromosomal-level and allele site using medium can concordant to the biopsied cells, but it needs further optimized before use in clinical applications. The aggressive biopsy step during PGD/PGS procedure would have a negative effect on the future development of the embryo. Cell-free nuclear DNA has been observed in spent embryo culture medium, which holds promise for the development of non-invasive PGD/PGS approaches. The presence of DNA in medium, its efficiency for WGA, and the concordance between chromosome status and the HBB gene IVSII654 allele as diagnosed from biopsied cells or medium were investigated. Non-invasive embryo genetic testing at the chromosomal-level and allele site using medium can concordant to the biopsied cells, but it needs further optimized before use in clinical applications.
DOI: 10.6084/m9.figshare.4315703
title: Interannual variability in the onset of the South China Sea summer monsoon from 1997 to 2014

description: Using observed and reanalysis datasets, the South China Sea summer monsoon (SCSSM) onset process is analyzed in each year from 1997 to 2014. Regional mean (5–20°N, 110–120°E) 850 hPa zonal wind, precipitation, and SST are used as indices to describe SCSSM onset. Three distinct onset types are identified: among the 18 years studied, nine are normal onset years, which are characterized by a well-established westerly wind and associated precipitation over the South China Sea (SCS); eight are intermittent onset years, in which monsoon precipitation does not occur continuously following the establishment of the westerly wind over the SCS; and one year, 2014, is a delayed onset year, in which the western Pacific subtropical high dominates over the SCS after the seasonal transition and prevents the monsoon onset. A comparison of the first two types suggests that a positive SST gradient in the northern Indian Ocean and local SST warming in the SCS are two key factors in the normal SCSSM onset type. With regard to the influence of the El Niño–Southern Oscillation background, there are four late onset years (1997, 1998, 2007, and 2010) that coincide with El Niño events, but only two early-onset years (1999 and 2012) out of the six years featuring La Niña events. Further analysis suggests that the zonal thermal contrast across the Indian and western Pacific oceans modulates monsoon onset in La Niña years.
DOI: 10.6084/m9.figshare.4315703.v1
title: Interannual variability in the onset of the South China Sea summer monsoon from 1997 to 2014

description: Using observed and reanalysis datasets, the South China Sea summer monsoon (SCSSM) onset process is analyzed in each year from 1997 to 2014. Regional mean (5–20°N, 110–120°E) 850 hPa zonal wind, precipitation, and SST are used as indices to describe SCSSM onset. Three distinct onset types are identified: among the 18 years studied, nine are normal onset years, which are characterized by a well-established westerly wind and associated precipitation over the South China Sea (SCS); eight are intermittent onset years, in which monsoon precipitation does not occur continuously following the establishment of the westerly wind over the SCS; and one year, 2014, is a delayed onset year, in which the western Pacific subtropical high dominates over the SCS after the seasonal transition and prevents the monsoon onset. A comparison of the first two types suggests that a positive SST gradient in the northern Indian Ocean and local SST warming in the SCS are two key factors in the normal SCSSM onset type. With regard to the influence of the El Niño–Southern Oscillation background, there are four late onset years (1997, 1998, 2007, and 2010) that coincide with El Niño events, but only two early-onset years (1999 and 2012) out of the six years featuring La Niña events. Further analysis suggests that the zonal thermal contrast across the Indian and western Pacific oceans modulates monsoon onset in La Niña years.
DOI: 10.6084/m9.figshare.4315652
title: Data from Evolutionary interplay between structure, energy and epistasis in the coat protein of the <i>ϕX</i>174 phage family

description: Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the <i>ϕ</i>X174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, <i>in silico</i>, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The d<i>N</i>/d<i>S</i> ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.
DOI: 10.6084/m9.figshare.4315652.v1
title: Data from Evolutionary interplay between structure, energy and epistasis in the coat protein of the <i>ϕX</i>174 phage family

description: Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the <i>ϕ</i>X174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, <i>in silico</i>, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The d<i>N</i>/d<i>S</i> ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.
DOI: 10.1285/i24212113v6i2-1p1
title: Enablers and inhibitors associated with the willingness to participate in child safety initiatives

description: Safety is a priority in South Africa, a country with amongst the highest recorded rates of violence and injury, with children a vulnerable group. The greatest opportunities for reducing the burden of violence and injury amongst children lies in the prevention of harmful environments and situations. Information on the psychosocial inhibitors and enablers of child safety promotion interventions are required to enhance and assure the efficacy of interventions. The determination of context-specific information is expected to be of considerable benefit to community uptake and impact of safety interventions. The primary aim of this study is to determine the factors that enable or inhibit the willingness to participate in child safety interventions. This qualitative study is located in a historically marginalised and under-resourced community consisting of low-cost government housing and backyard dwellings and situated 4km outside of Strand in the Western Cape, South Africa. Eleven interviews were conducted with long standing community members who had either attended, had knowledge on, or experience of child safety initiatives conducted in their community. The study utilised a thematic analysis within a Person-Process-Context-Time theoretical framework. The findings indicate that willingness to participate is influenced by multiple and interconnected enablers and inhibitors. The personal, relational and environmental factors included: muted individual agency (comprised of hopelessness and struggling alone, scepticism, and experiences of daily living struggles); community care provision (limited community connectedness, care and concern for children, and neighbourliness); and structural, physical and social constraints (competing priorities, unequal power relations, and physical community impediments)
DOI: 10.1285/i24212113v6i2-1p20
title: An experience of action research in Arab-Israeli schools

description: The hypotheses discussed herein are based on both Lewin's theory and, in view of their mutual affinity, Gramsci's ideas: in particular the role of school in the struggle for cultural hegemony. The research and results obtained support the validity of the theories forming the reference framework. What emerge are both the contradictions arising in a conflictual situation, and the possibility for school to be not only a place of conflict but, above all, of collaboration.
DOI: 10.4225/03/5850985e8371c
title: The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus

description: The effects of Wolbachia on the Aedes aegypti microbiome as determined by 16s sequencing. Also the effect of microbiome manipulation via antibiotic treatment on Wolbachia-mediated blocking of dengue virus.<br>There are three files containing raw data:1. OTU_table_normalised_annotated contains the relative abundances of OTUs detected in samples. 2. OTU-table_counts_annotated contains the same data as in file 1 but in sequence count form. 3. Genome copies of DENV-positive mosquitoes contains dengue virus loads from q-RT-PCR for all mosquitoes that were positive for viral infection.
DOI: 10.6084/m9.figshare.4315058
title: R code used for Toxicity Assays

description: This set of data includes my R scripts and the output data files that were used in the Toxicity Assay portion of the study
DOI: 10.6084/m9.figshare.4315058.v1
title: R code used for Toxicity Assays

description: This set of data includes my R scripts and the output data files that were used in the Toxicity Assay portion of the study