cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5373160
title: OpenCitations Corpus provenance data of all the responsible agents, archived on 2017-08-25

description: This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) provenance data about responsible agents, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.
DOI: 10.6084/m9.figshare.5373163.v1
title: Supporting Online Material - Genetic interactions between the chromosome axis-associated protein Hop1 and homologous recombination determinants in Schizosaccharomyces pombe

description: Raw data and plasmid sequences accompanying Brown SD, Jarosinska OD, Lorenz A (2017) Genetic interactions between the chromosome axis-associated protein Hop1 and homologous recombination determinants in Schizosaccharomyces pombe.
DOI: 10.6084/m9.figshare.5373166.v1
title: Supplementary material 7

description: BayesTraits MultiState ML and MCMC ancestral state reconstruction output for colour character 2 on ML phylogram and ultrametric trees. The grey panel lists internal node IDs and subtending terminal taxa. The blue panel are results from ML ancestral state reconstruction. The yellow panel are results from MCMC ancestral state reconstruction. Abbreviations: Ultra 0, ultrametric tree generated with penalty = 0; Ultra 10, ultrametric tree generated with penalty = 10; Ultra 10000, ultrametric tree generated with penalty = 10000.
DOI: 10.6084/m9.figshare.5373160.v1
title: OpenCitations Corpus provenance data of all the responsible agents, archived on 2017-08-25

description: This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) provenance data about responsible agents, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.
DOI: 10.6084/m9.figshare.5373100
title: Postembryonic development of <i>Sejus togatus</i> CL Koch, 1836 (Parasitiformes: Mesostigmata: Sejida) with notes on moulting behaviour

description: <i>Sejus togatus</i> CL Koch, 1836 was studied using video recording of living individuals reared on nematodes in the laboratory at 20–21°C. We report the duration of juvenile stages and intra-stage changes in body length and width in juveniles and male and female adults. We describe the moulting behaviour and three-dimensional arrangement of selected setae in living larvae and protonymphs. In both males and females, the larva was the shortest (♀: 5.7 days, ♂: 6.6 days), and duration of the deutonymph was the longest (♀: 13.3 days, ♂: 11.6 days). Most juveniles increased their size significantly from the first day of life to the last day before moulting. There was no change in size from the final size of one instar to the initial size of the next instar. During the first 15 days after the last moult, males increased significantly in width, and females in length. Eventually, females were significantly longer and slightly wider than males.
DOI: 10.6084/m9.figshare.5373097
title: Prevalence of <i>Mycoplasma genitalium</i> and other sexually transmitted infections causing urethritis among high-risk heterosexual male patients in Estonia

description: <b>Background:</b> We aimed to evaluate the prevalence of sexually transmitted infections (STI, including <i>Mycoplasma genitalium</i>, <i>Chlamydia trachomatis</i>, <i>Neisseria gonorrhoeae</i>, <i>Trichomonas vaginalis</i>) among high-risk heterosexual male patients and to clarify their potency to cause complaints and inflammation. <b>Methods:</b> The study group included 825 men (18.0–49.5 y) consulting andrologist at Tartu University Hospital (Estonia) due to subjectively perceived risk of STI. Patients completed STI risk behaviour questionnaire. First voided urine was analysed for white blood cells and STIs. <b>Results:</b> In total 193 (23.4%) patients were positive for one or multiple STI. The prevalence of <i>C. trachomatis</i>, <i>M. genitalium</i>, <i>N. gonorrhoeae</i>, <i>T. vaginalis</i> and combined STI was 14.3%, 4.4%, 2.7%, 0.7% and 1.3%, respectively. <i>N. gonorrhoeae</i> had the highest potency to generate inflammatory reaction in first voided urine (100%) followed by <i>C. trachomatis</i> (72.0%), <i>M. genitalium</i> (63.9%) and <i>T. vaginalis</i> (33.3%). <i>N. gonorrhoeae</i> and <i>T. vaginalis</i> caused the highest mean number of complaints while half of <i>T. vaginalis</i> cases and nearly fifth of <i>M. genitalium</i> and <i>C. trachomatis</i> cases were asymptomatic. <b>Conclusions:</b><i>C. trachomatis</i> has the highest prevalence among Estonian high-risk men but <i>M. genitalium</i> holds an important second place. Prevalence of combined STIs is low. <i>N. gonorrhoeae</i> has the highest potency to generate urethral inflammation followed by <i>C. trachomatis</i> and <i>M. genitalium</i>. The highest number of complaints is also associated with <i>N. gonorrhoeae</i> while half of <i>T. vaginalis</i> cases and nearly a fifth of <i>M. genitalium</i> and <i>C. trachomatis</i> cases are asymptomatic.
DOI: 10.6084/m9.figshare.5373100.v1
title: Postembryonic development of <i>Sejus togatus</i> CL Koch, 1836 (Parasitiformes: Mesostigmata: Sejida) with notes on moulting behaviour

description: <i>Sejus togatus</i> CL Koch, 1836 was studied using video recording of living individuals reared on nematodes in the laboratory at 20–21°C. We report the duration of juvenile stages and intra-stage changes in body length and width in juveniles and male and female adults. We describe the moulting behaviour and three-dimensional arrangement of selected setae in living larvae and protonymphs. In both males and females, the larva was the shortest (♀: 5.7 days, ♂: 6.6 days), and duration of the deutonymph was the longest (♀: 13.3 days, ♂: 11.6 days). Most juveniles increased their size significantly from the first day of life to the last day before moulting. There was no change in size from the final size of one instar to the initial size of the next instar. During the first 15 days after the last moult, males increased significantly in width, and females in length. Eventually, females were significantly longer and slightly wider than males.
DOI: 10.6084/m9.figshare.12901511
title: 200816_Evaluación_NTS_18-19.xlsx

description: Datos asociados al artículo "Educación en los vínculos entre naturaleza y sociedad: una experiencia didáctica con estudiantes universitarios"<b></b>
DOI: 10.6084/m9.figshare.5373085
title: Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography

description: Leveraging structural biology tools, we report the results of experiments seeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from ‘electrostatic’ or ‘base stacking’ influences without considering the larger context of altered helical geometry. Circular dichroism spectra of inosine-substituted oligonucleotides and longer base-substituted DNAs in solution indicated non-canonical helical conformations, with the degree of deviation from a standard B-form geometry depending on the number of I⋅C pairs. X-ray diffraction of a highly inosine-substituted DNA decamer crystal (eight I⋅C and two A⋅T pairs) revealed an A-tract-like conformation with a uniformly narrow minor groove, reduced helical rise, and the majority of sugars adopting a C1′-<i>exo</i> (southeastern) conformation. This contrasts with the standard B-DNA geometry with C2′-<i>endo</i> sugar puckers (south conformation). In contrast, the crystal structure of a decamer with only four I⋅C pairs has a geometry similar to that of the reference duplex with eight G⋅C and two A⋅T pairs. The unique crystal geometry of the inosine-rich duplex is noteworthy given its unusual CD signature in solution and the altered mechanical properties of some inosine-containing DNAs.
DOI: 10.6084/m9.figshare.5373097.v1
title: Prevalence of <i>Mycoplasma genitalium</i> and other sexually transmitted infections causing urethritis among high-risk heterosexual male patients in Estonia

description: <b>Background:</b> We aimed to evaluate the prevalence of sexually transmitted infections (STI, including <i>Mycoplasma genitalium</i>, <i>Chlamydia trachomatis</i>, <i>Neisseria gonorrhoeae</i>, <i>Trichomonas vaginalis</i>) among high-risk heterosexual male patients and to clarify their potency to cause complaints and inflammation. <b>Methods:</b> The study group included 825 men (18.0–49.5 y) consulting andrologist at Tartu University Hospital (Estonia) due to subjectively perceived risk of STI. Patients completed STI risk behaviour questionnaire. First voided urine was analysed for white blood cells and STIs. <b>Results:</b> In total 193 (23.4%) patients were positive for one or multiple STI. The prevalence of <i>C. trachomatis</i>, <i>M. genitalium</i>, <i>N. gonorrhoeae</i>, <i>T. vaginalis</i> and combined STI was 14.3%, 4.4%, 2.7%, 0.7% and 1.3%, respectively. <i>N. gonorrhoeae</i> had the highest potency to generate inflammatory reaction in first voided urine (100%) followed by <i>C. trachomatis</i> (72.0%), <i>M. genitalium</i> (63.9%) and <i>T. vaginalis</i> (33.3%). <i>N. gonorrhoeae</i> and <i>T. vaginalis</i> caused the highest mean number of complaints while half of <i>T. vaginalis</i> cases and nearly fifth of <i>M. genitalium</i> and <i>C. trachomatis</i> cases were asymptomatic. <b>Conclusions:</b><i>C. trachomatis</i> has the highest prevalence among Estonian high-risk men but <i>M. genitalium</i> holds an important second place. Prevalence of combined STIs is low. <i>N. gonorrhoeae</i> has the highest potency to generate urethral inflammation followed by <i>C. trachomatis</i> and <i>M. genitalium</i>. The highest number of complaints is also associated with <i>N. gonorrhoeae</i> while half of <i>T. vaginalis</i> cases and nearly a fifth of <i>M. genitalium</i> and <i>C. trachomatis</i> cases are asymptomatic.
DOI: 10.6084/m9.figshare.12901511.v1
title: 200816_Evaluación_NTS_18-19.xlsx

description: Datos asociados al artículo "Educación en los vínculos entre naturaleza y sociedad: una experiencia didáctica con estudiantes universitarios"<b></b>
DOI: 10.6084/m9.figshare.5372980
title: Monte Carlo studies on photon interactions in radiobiological experiments

description: X-ray or γ-ray photons are widely used to study radiobiological effects of ionizing radiations. Photons are indirectly ionizing radiations so they need to set in motion electrons to perform the ionizations. When the photon dose decreases to below a certain limit, the number of electrons set in motion will become so small that not all cells in the “exposed” cell population will get at least one electron hit. When some cells in the cell population are not irradiated, there will be rescue effect between the irradiated and non-irradiated cells, and the overall radiobiological effect observed for the cell population will be different. In the present paper, the mechanisms underlying photon interactions in radiobiological experiments were studied using our developed NRUphoton computer code, which was benchmarked against the MCNP5 code by comparing the photon dose delivered to the cell layer underneath the water medium. The following results were obtained: (1) Interaction fractions decreased in the order: <sup>16</sup>O &gt; <sup>12</sup>C &gt; <sup>14</sup>N &gt; <sup>1</sup>H. Bulges in the interaction fractions (versus water medium thickness) were observed, which reflected the changes in the energies of the propagating photons as a result of the water medium thickness as well as the energy-dependent photon interaction cross-sections. (2) Photoelectric interaction and incoherent scattering dominated for lower-energy (10 keV) and higher-energy (100 keV and 1 MeV) incident photons. (3) The fractions of electron ejection from different nuclei were mainly governed by the photoelectric effect cross-sections, and the fractions from the 1s subshell were the largest. (4) The penetration fractions in general decreased with increasing medium thickness, and increased with increasing incident photon energy, the latter being explained by the corresponding reduction in interaction cross-sections. (5) The area under the angular distributions of photons exiting medium layer and then interacting with cell layer decreased with increasing incident photon energy. (6) The number of cells suffering at least one electron hit increased with the administrated dose. For larger incident photon energies, the numbers of cells suffering at least one electron hit became smaller, which was attributed to the reduction in the photon interaction cross-section. These results highlighted the importance of the administered dose in radiobiological experiments. In particular, the threshold administrated doses at which all cells in the array suffered at least one electron hit might provide thoughts on the intriguing observation that radiation-induced cancers can be statistically detected only above the threshold value of ~100 mSv, and thus on controversies over the linear no-threshold model.
DOI: 10.6084/m9.figshare.5372980.v1
title: Monte Carlo studies on photon interactions in radiobiological experiments

description: X-ray or γ-ray photons are widely used to study radiobiological effects of ionizing radiations. Photons are indirectly ionizing radiations so they need to set in motion electrons to perform the ionizations. When the photon dose decreases to below a certain limit, the number of electrons set in motion will become so small that not all cells in the “exposed” cell population will get at least one electron hit. When some cells in the cell population are not irradiated, there will be rescue effect between the irradiated and non-irradiated cells, and the overall radiobiological effect observed for the cell population will be different. In the present paper, the mechanisms underlying photon interactions in radiobiological experiments were studied using our developed NRUphoton computer code, which was benchmarked against the MCNP5 code by comparing the photon dose delivered to the cell layer underneath the water medium. The following results were obtained: (1) Interaction fractions decreased in the order: <sup>16</sup>O &gt; <sup>12</sup>C &gt; <sup>14</sup>N &gt; <sup>1</sup>H. Bulges in the interaction fractions (versus water medium thickness) were observed, which reflected the changes in the energies of the propagating photons as a result of the water medium thickness as well as the energy-dependent photon interaction cross-sections. (2) Photoelectric interaction and incoherent scattering dominated for lower-energy (10 keV) and higher-energy (100 keV and 1 MeV) incident photons. (3) The fractions of electron ejection from different nuclei were mainly governed by the photoelectric effect cross-sections, and the fractions from the 1s subshell were the largest. (4) The penetration fractions in general decreased with increasing medium thickness, and increased with increasing incident photon energy, the latter being explained by the corresponding reduction in interaction cross-sections. (5) The area under the angular distributions of photons exiting medium layer and then interacting with cell layer decreased with increasing incident photon energy. (6) The number of cells suffering at least one electron hit increased with the administrated dose. For larger incident photon energies, the numbers of cells suffering at least one electron hit became smaller, which was attributed to the reduction in the photon interaction cross-section. These results highlighted the importance of the administered dose in radiobiological experiments. In particular, the threshold administrated doses at which all cells in the array suffered at least one electron hit might provide thoughts on the intriguing observation that radiation-induced cancers can be statistically detected only above the threshold value of ~100 mSv, and thus on controversies over the linear no-threshold model.
DOI: 10.6084/m9.figshare.5372914
title: Mind over Matter data-package Study 1

description: The dataset called biomarkersdataset.dta is a dataset containing information on the class and class identity of respondents from 2004/2005 (wave_2_core_data_v4.dta) and their health outcomes in 2012/2013 (wave_6_elsa_nurse_data_v2.dta). Additionally, this data-package includes the wave_6_elsa_nurse_data_v2.dta, that is used in a robustness check.<br>The included syntax is the syntax needed to run the analyses used in our study by employing the biomarkerdataset.dta-file. It is also possible to first merge this dataset by using the first part of the syntax through the other included files. These files are the original files as freely obtainable from the ELSA-website.
DOI: 10.6084/m9.figshare.5372914.v1
title: Mind over Matter data-package Study 1

description: The dataset called biomarkersdataset.dta is a dataset containing information on the class and class identity of respondents from 2004/2005 (wave_2_core_data_v4.dta) and their health outcomes in 2012/2013 (wave_6_elsa_nurse_data_v2.dta). Additionally, this data-package includes the wave_6_elsa_nurse_data_v2.dta, that is used in a robustness check.<br>The included syntax is the syntax needed to run the analyses used in our study by employing the biomarkerdataset.dta-file. It is also possible to first merge this dataset by using the first part of the syntax through the other included files. These files are the original files as freely obtainable from the ELSA-website.
DOI: 10.6084/m9.figshare.5372881
title: Cytokine profile in gingival crevicular fluid and plasma of patients with aggressive periodontitis

description: <b>Objective:</b> This study aimed to determine the content of cytokines in gingival crevicular fluid (GCF) as well as in plasma of Sudanese patients with aggressive periodontitis (AgP) and healthy controls (HC). <b>Materials and methods:</b> Nineteen AgP patients and 19 HC were included. The mean probing pocket depth and clinical attachment level of the GCF sampled sites in patients were both ≥5 mm. The GCF and plasma levels of 27 cytokines were determined using 27-multiplex fluorescent bead-based immunoassays. Ratios were calculated among cytokines of the T-helper cell subsets Th1 and Th2. Descriptive statistics, the Mann–Whitney U-test and Spearman’s <i>rho</i> rank correlation coefficient analysis were used. <b>Results:</b> Interferon-γ was the only cytokine found in significantly lower levels in GCF of patients compared with HC. Levels of interleukin (IL)-10, IL-13, IL-1Ra, monocyte chemoattractant protein-1 (MCP-1), regulated on activation normal T-cell expressed and secreted (RANTES), granulocyte-colony-stimulating factor (G-CSF), and granulocyte-macrophage-CSF (GM-CSF) were significantly lower in plasma of AgP compared with HC. The ratios of Th1:Th2 in GCF and Treg:Th17 in plasma were significantly lower in AgP. <b>Conclusions:</b> The lower levels of cytokines detected systemically in plasma of AgP patients may have an impact on the immune response. The lower ratio of Th1:Th2 cytokines in GCF samples of AgP patients suggests a role for Th2 at the local site of disease.
DOI: 10.6084/m9.figshare.5372884
title: Dataset Summary

description: Summary of the dataset with information on human subjects involved and indication of relevant file locations
DOI: 10.6084/m9.figshare.5372881.v1
title: Cytokine profile in gingival crevicular fluid and plasma of patients with aggressive periodontitis

description: <b>Objective:</b> This study aimed to determine the content of cytokines in gingival crevicular fluid (GCF) as well as in plasma of Sudanese patients with aggressive periodontitis (AgP) and healthy controls (HC). <b>Materials and methods:</b> Nineteen AgP patients and 19 HC were included. The mean probing pocket depth and clinical attachment level of the GCF sampled sites in patients were both ≥5 mm. The GCF and plasma levels of 27 cytokines were determined using 27-multiplex fluorescent bead-based immunoassays. Ratios were calculated among cytokines of the T-helper cell subsets Th1 and Th2. Descriptive statistics, the Mann–Whitney U-test and Spearman’s <i>rho</i> rank correlation coefficient analysis were used. <b>Results:</b> Interferon-γ was the only cytokine found in significantly lower levels in GCF of patients compared with HC. Levels of interleukin (IL)-10, IL-13, IL-1Ra, monocyte chemoattractant protein-1 (MCP-1), regulated on activation normal T-cell expressed and secreted (RANTES), granulocyte-colony-stimulating factor (G-CSF), and granulocyte-macrophage-CSF (GM-CSF) were significantly lower in plasma of AgP compared with HC. The ratios of Th1:Th2 in GCF and Treg:Th17 in plasma were significantly lower in AgP. <b>Conclusions:</b> The lower levels of cytokines detected systemically in plasma of AgP patients may have an impact on the immune response. The lower ratio of Th1:Th2 cytokines in GCF samples of AgP patients suggests a role for Th2 at the local site of disease.
DOI: 10.6084/m9.figshare.5372851
title: Foliar and soil N and <i>δ</i><sup>15</sup>N as restoration metrics at Pūtaringamotu Riccarton Bush, Christchurch city

description: Delta<sup>15</sup>N values and associated N concentrations may be useful nutrient cycling metrics for assessing restoration progress, and complement biodiversity assessment. We tested this hypothesis at Pūtaringamotu Riccarton Bush (‘Pūtaringamotu’), a low-rainfall urban forest fragment under restoration since 1974. Foliar and soil measurements came from four indigenous forests (Pūtaringamotu; Saltwater, high rainfall, logged until 2002; Ōkārito, high rainfall, never logged; Scotchman’s Creek, high rainfall, burrowing seabirds present). Despite different disturbance histories, Pūtaringamotu, Ōkārito and Saltwater results all fitted global <i>δ</i><sup>15</sup>N regressions between rainfall and foliar N concentration. Enhanced foliar N concentrations accompanying low rainfall at Pūtaringamotu were similar to seabird-affected Scotchman’s Creek. Although Pūtaringamotu foliar <i>δ</i><sup>15</sup>N values showed differences between taxa, they were less pronounced than for Ōkārito; Saltwater showed no effect. Further investigation of nutrient cycling restoration metrics at Pūtaringamotu should therefore emphasise progressive development of differences in foliar <i>δ</i><sup>15</sup>N between plant taxa, pooled values being insufficiently sensitive.