cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1456232.v2
title: The combined benefits of motorcycle antilock braking systems (ABS) in preventing crashes and reducing crash severity

description: <b>Objective</b>: Several studies have reported the benefits of motorcycle antilock braking systems (ABS) in reducing injury crashes, due to improved stability and braking performance. Both aspects may prevent crashes but may also reduce the crash severity when a collision occurs. However, it is still unknown to what extent the reductions in injury crashes with ABS may be due to a combination of these mechanisms. <b>Methods</b>: Swedish hospital and police reports (2003–2012) were used. The risk for permanent medical impairment (RPMI) was calculated, showing the risk of at least 1 or 10% permanent medical impairment. In total, 165 crashes involving ABS-equipped motorcycles were compared with 500 crashes with similar motorcycles without ABS. The analysis was performed in 3 steps. First, the reduction in emergency care visits with ABS was calculated using an induced exposure approach. Secondly, the injury mitigating effects of ABS were investigated. The mean RPMI 1+ and RPMI 10+ were analyzed for different crash types. The distributions of impairing injuries (PMI 1+) and severely impairing injuries (PMI 10+) were also analyzed. In the third step, the total reduction of PMI 1+ and PMI 10+ injured motorcyclists was calculated by combining the reductions found in the previous steps. An additional analysis of combined braking systems (CBS) together with ABS was also performed. <b>Results</b>: The results showed that emergency care visits were reduced by 47% with ABS. In the second step, it was found that the mean RPMI 1+ and RPMI 10+ with ABS were 15 and 37% lower, respectively. Finally, the third step showed that the total reductions in terms of crash avoidance and mitigation of PMI 1+ and PMI 10+ injured motorcyclists with ABS were 67 and 55%, respectively. However, PMI 1+ and PMI 10+ leg injuries were not reduced by ABS to the same extent. Indications were found suggesting that the benefits of ABS together with CBS may be greater than ABS alone. <b>Conclusions</b>: This article indicated that motorcycle ABS reduced impairing injuries, mostly due to fewer emergency care visits but also due to a reduction in crash severity. This may seem reasonable as the improved stability and braking performance provided by ABS could prevent some crashes but would also decrease crash severity if a collision still occurs. As suggested by previous studies, however, the lower extremities would be more exposed in a crash with ABS. It is recommended that future research should follow up these results with additional data.
DOI: 10.6084/m9.figshare.1456233.v1
title: DNA hypomethylation-mediated activation of <i>Cancer/Testis Antigen 45</i> (<i>CT45</i>) genes is associated with disease progression and reduced survival in epithelial ovarian cancer

description: ABSTRACTEpithelial ovarian cancer (EOC) is a highly lethal malignancy due to a lack of early detection approaches coupled with poor outcomes for patients with clinically advanced disease. Cancer-testis (CT) or cancer-germline genes encode antigens known to generate spontaneous anti-tumor immunity in cancer patients. CT45 genes are a recently discovered six-member family of X-linked CT genes with oncogenic function. Here, we determined CT45 expression in EOC and fully defined its epigenetic regulation by DNA methylation. <i>CT45</i> was silent and hypermethylated in normal control tissues, but a large subset of EOC samples showed increased <i>CT45</i> expression in conjunction with promoter DNA hypomethylation. In contrast, copy number status did not correlate with <i>CT45</i> expression in the TCGA database for EOC. <i>CT45</i> promoter methylation inversely correlated with both CT45 mRNA and protein expression, the latter determined using IHC staining of an EOC TMA. <i>CT45</i> expression was increased and <i>CT45</i> promoter methylation was decreased in late-stage and high-grade EOC, and both measures were associated with poor survival. <i>CT45</i> hypomethylation was directly associated with <i>LINE-1</i> hypomethylation, and <i>CT45</i> was frequently co-expressed with other CT antigen genes in EOC. Decitabine treatment induced CT45 mRNA and protein expression in EOC cells, and promoter transgene analyses indicated that DNA methylation directly represses <i>CT45</i> promoter activity. These data verify CT45 expression and promoter hypomethylation as possible prognostic biomarkers, and suggest CT45 as an immunological or therapeutic target in EOC. Treatment with decitabine or other epigenetic modulators could provide a means for more effective immunological targeting of CT45.
DOI: 10.6084/m9.figshare.1456362.v12
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456232.v1
title: The Combined Benefits of Motorcycle Antilock Braking Systems (Abs) in Preventing Crashes and Reducing Crash Severity

description: ABSTRACT<b>Objective</b> Several studies have reported the benefits of Motorcycle ABS in reducing injury crashes, due to improved stability and braking performance. Both aspects may prevent crashes but may also reduce the crash severity when a collision occurs. However, it is still unknown at what extent the reductions of injury crashes with ABS may be to due to a combination of these mechanisms. <b>Methods</b> Swedish hospital and police reports (2003–2012) were used. The Risk for Permanent Medical Impairment (RPMI) was calculated, showing the risk of at least 1% or 10% permanent medical impairment. In total, 165 crashes involving ABS-motorcycles were compared with 500 crashes with similar motorcycles without ABS. The analysis was performed in three steps. First, the reduction of emergency care visits with ABS was calculated using an induced exposure approach. Secondly, the injury mitigating effects of ABS were investigated. The mean RPMI 1+ and RPMI 10+ were analyzed for different crash types. The distributions of impairing injuries (PMI 1+) and severely impairing injuries (PMI 10+) were also analyzed. In the third step, the total reduction of PMI 1+ and PMI 10+ injured motorcyclists was calculated by combining the reductions found in the previous steps. An additional analysis of CBS (Combined Braking Systems) together with ABS was also performed. <b>Results</b> The results showed that emergency care visits were reduced by 47% with ABS. In the second step, it was found that the mean RPMI 1+ and RPMI 10+ with ABS were 15% and 37% lower, respectively. Finally, the third step showed that the total reductions in terms of crash avoidance and mitigation of PMI 1+ and PMI 10+ injured motorcyclists with ABS were 67% and 55%, respectively. However, PMI 1+ and PMI 10+ leg injuries were not reduced by ABS to the same extent. Indications were found suggesting that the benefits of ABS together with CBS may be greater than ABS alone. <b>Conclusions</b> This paper indicated that Motorcycle ABS reduced impairing injuries, mostly due to fewer emergency care visits but also due to a reduction of the crash severity. This may seem reasonable as the improved stability and braking performance provided by ABS could prevent some crashes but would also decrease crash severity if a collision still occurs. As suggested by previous studies, however, the lower extremities would be more exposed in a crash with ABS. It is recommended that future research should follow up these results with additional data.
DOI: 10.6084/m9.figshare.1456233.v3
title: DNA hypomethylation-mediated activation of <i>Cancer/Testis Antigen 45</i> (<i>CT45</i>) genes is associated with disease progression and reduced survival in epithelial ovarian cancer

description: Epithelial ovarian cancer (EOC) is a highly lethal malignancy due to a lack of early detection approaches coupled with poor outcomes for patients with clinically advanced disease. Cancer-testis (CT) or cancer-germline genes encode antigens known to generate spontaneous anti-tumor immunity in cancer patients. CT45 genes are a recently discovered 6-member family of X-linked CT genes with oncogenic function. Here, we determined CT45 expression in EOC and fully defined its epigenetic regulation by DNA methylation. <i>CT45</i> was silent and hypermethylated in normal control tissues, but a large subset of EOC samples showed increased <i>CT45</i> expression in conjunction with promoter DNA hypomethylation. In contrast, copy number status did not correlate with <i>CT45</i> expression in the TCGA database for EOC. <i>CT45</i> promoter methylation inversely correlated with both CT45 mRNA and protein expression, the latter determined using IHC staining of an EOC TMA. <i>CT45</i> expression was increased and <i>CT45</i> promoter methylation was decreased in late-stage and high-grade EOC, and both measures were associated with poor survival. <i>CT45</i> hypomethylation was directly associated with <i>LINE-1</i> hypomethylation, and <i>CT45</i> was frequently co-expressed with other CT antigen genes in EOC. Decitabine treatment induced CT45 mRNA and protein expression in EOC cells, and promoter transgene analyses indicated that DNA methylation directly represses <i>CT45</i> promoter activity. These data verify CT45 expression and promoter hypomethylation as possible prognostic biomarkers, and suggest CT45 as an immunological or therapeutic target in EOC. Treatment with decitabine or other epigenetic modulators could provide a means for more effective immunological targeting of CT45.
DOI: 10.6084/m9.figshare.1456234.v1
title: <i>Ganguroo robustiter</i>, sp. nov. (Macropodoidea, Marsupialia), a middle to early late Miocene basal macropodid from Riversleigh World Heritage Area, Australia

description: ABSTRACT——Cranial and dental remains of the middle to early late Miocene macropodid kangaroo, <i>Ganguroo robustiter</i>, sp. nov., are described. Postcranial remains of <i>G. robustiter</i> were previously described as referable to <i>G. bilamina</i>. <i>Ganguroo robustiter</i> is more robust (approximately 20% larger) and more derived than <i>G. bilamina</i> and <i>G. bites</i>, in having a larger m4, a well-developed posterolingual ridge and lingual cingulum on P3, a longer P3/p3, and no stylar cusp C on M3–M4. We used previously published data matrices to analyze the phylogenetic relationship of <i>G. robustiter</i>. Both phylogenetic analyses, using craniodental and postcranial characters, place <i>G. robustiter</i> within Macropodidae, as the sister taxon to sthenurines and macropodines. Species of <i>Ganguroo</i> are not found to be monophyletic despite their extreme similarity in character scores. This may be due to the large amount of missing data for <i>G. bilamina</i> and <i>G. bites</i> for which no postcranial remains have been identified. Phylogenetic results are ambiguous, recovering unresolved trees with low bootstrap values, but the generic assignment of these taxa is maintained because they are remarkably similar. Species of <i>Ganguroo</i> may represent a phyletic lineage, with species increasing in size and losing cusp/cuspids on their premolars through time, which appears to coincide with a broader record of changing vegetation and climates through the middle Miocene.http://zoobank.org/urn:lsid:zoobank.org:pub:D0B542BE-C673-4260-8381-8B163A35AC36SUPPLEMENTAL DATA——Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1456362.v13
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456233.v2
title: DNA hypomethylation-mediated activation of <i>Cancer/Testis Antigen 45</i> (<i>CT45</i>) genes is associated with disease progression and reduced survival in epithelial ovarian cancer

description: Epithelial ovarian cancer (EOC) is a highly lethal malignancy due to a lack of early detection approaches coupled with poor outcomes for patients with clinically advanced disease. Cancer-testis (CT) or cancer-germline genes encode antigens known to generate spontaneous anti-tumor immunity in cancer patients. CT45 genes are a recently discovered 6-member family of X-linked CT genes with oncogenic function. Here, we determined CT45 expression in EOC and fully defined its epigenetic regulation by DNA methylation. <i>CT45</i> was silent and hypermethylated in normal control tissues, but a large subset of EOC samples showed increased <i>CT45</i> expression in conjunction with promoter DNA hypomethylation. In contrast, copy number status did not correlate with <i>CT45</i> expression in the TCGA database for EOC. <i>CT45</i> promoter methylation inversely correlated with both CT45 mRNA and protein expression, the latter determined using IHC staining of an EOC TMA. <i>CT45</i> expression was increased and <i>CT45</i> promoter methylation was decreased in late-stage and high-grade EOC, and both measures were associated with poor survival. <i>CT45</i> hypomethylation was directly associated with <i>LINE-1</i> hypomethylation, and <i>CT45</i> was frequently co-expressed with other CT antigen genes in EOC. Decitabine treatment induced CT45 mRNA and protein expression in EOC cells, and promoter transgene analyses indicated that DNA methylation directly represses <i>CT45</i> promoter activity. These data verify CT45 expression and promoter hypomethylation as possible prognostic biomarkers, and suggest CT45 as an immunological or therapeutic target in EOC. Treatment with decitabine or other epigenetic modulators could provide a means for more effective immunological targeting of CT45.
DOI: 10.6084/m9.figshare.1456362.v14
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456226
title: Compilation of DNA Methylation Genome Feature Tracks (Crassostrea gigas)

description: Genome feature tracks and accompanying IGV session file to visualize DNA methyation data for the Pacific oyster (Crassostrea gigas).
DOI: 10.6084/m9.figshare.1456227.v1
title: Agricultural production and bird conservation in complex landscapes of the dry Chaco

description: The South American dry Chaco is a mosaic of woody vegetation and grasslands with high deforestation rates in recent decades. Considering forests and grasslands as the main natural habitats, we assessed the trade-offs between bird populations and agricultural production to compare the potential consequences of different land use strategies (‘sharing’, ‘sparing’, and intermediate) for populations of bird species sensitive to agriculture, while attaining a regional production target. We evaluated how populations responded to scenarios with different proportions of forest and grasslands, considering three reference states (100% forest, 80:20% and 50:50% forest and grasslands, respectively); and scenarios capable of meeting three after-farming scenarios, with land destined to reach a regional production target with three variations of forest:grasslands within spared land. We fitted curves to relate bird abundance to agricultural yield along a gradient of meat production intensity; and we classified bird species as ‘losers’ (if their populations were lower than the baseline population in the reference state, at any level of production) and ‘winners’ (if their current populations were higher than the baseline population). At the ‘current’ (c. 2010) level of regional agricultural production, we found a similar number of loser species maximized by land-sparing and land-sharing strategies; while intermediate strategies were the least favourable to balance production and bird populations. Under the most probable scenarios of increases in regional meat production, most loser bird species populations were maximized by a land-sparing strategy, suggesting that if meat production targets are going to increase in the region, this can be more efficiently achieved by combining well-protected forests and grasslands, and high-yielding mechanized agriculture (e.g. soybean). Our results highlight the importance of assessing all the important natural habitats (e.g. forests and grasslands) of a region to explore conservation strategies at a regional scale.
DOI: 10.6084/m9.figshare.1456177
title: Methods and results of Whelan et al 2015 reanalysis

description: Reanalysis of data from : Whelan, Nathan V., Kevin M. Kocot, Leonid L. Moroz, and Kenneth M. Halanych. "Error, signal, and the placement of Ctenophora sister to all other animals." Proceedings of the National Academy of Sciences 112, no. 18 (2015): 5773-5778.
DOI: 10.6084/m9.figshare.1456226.v2
title: Compilation of DNA Methylation Genome Feature Tracks (Crassostrea gigas)

description: Genome feature tracks and accompanying IGV session file to visualize DNA methyation data for the Pacific oyster (Crassostrea gigas).
DOI: 10.6084/m9.figshare.1456176
title: Methods and results of reanalysis of Philippe et al. 2009

description: Reanalysis of data from Philippe, Hervé, Romain Derelle, Philippe Lopez, Kerstin Pick, Carole Borchiellini, Nicole Boury-Esnault, Jean Vacelet et al. "Phylogenomics revives traditional views on deep animal relationships." Current Biology 19, no. 8 (2009): 706-712.
DOI: 10.6084/m9.figshare.1456176.v1
title: Methods and results of reanalysis of Philippe et al. 2009

description: Reanalysis of data from Philippe, Hervé, Romain Derelle, Philippe Lopez, Kerstin Pick, Carole Borchiellini, Nicole Boury-Esnault, Jean Vacelet et al. "Phylogenomics revives traditional views on deep animal relationships." Current Biology 19, no. 8 (2009): 706-712.
DOI: 10.6084/m9.figshare.1456226.v1
title: Compilation of DNA Methylation Genome Feature Tracks (Crassostrea gigas)

description: Genome feature tracks and accompanying IGV session file to visualize DNA methyation data for the Pacific oyster (Crassostrea gigas).
DOI: 10.6084/m9.figshare.1456175
title: Reanalyses done for the blog post "Modest reproducibility success"

description: These reanalyses accompany the blog post "Modest reproducibility success" The figures in the following locations: <strong>Fig1</strong>: github-importDojj9C.zip/figures/sort_by_entropy.png <strong>Fig2:</strong> github-importDojj9C.zip/figures/802761433193085.89_entropy_2.44_1.83_loci_0_to_49.png <strong>Fig3</strong>: github-importjalDCs.zip/figures/148851433838626.65_entropy_0.73_0.00_loci_100_to_149.png <strong>Fig4</strong>: github-importjalDCs.zip/figures/752761434054805.63_no_rp_low_entropy_concat_ent_0.99_0.15.png <strong>The notebook for the Philippe reanalysis:</strong> http://nbviewer.ipython.org/github/szitenberg/philippe2009/blob/master/Philippe2009.ipynb <strong>The notebook for the Whelan reanalysis:</strong> http://nbviewer.ipython.org/github/szitenberg/Whelan2015/blob/master/Whelan2015_Dataset12.ipynb
DOI: 10.6084/m9.figshare.1456166
title: TEN-GALLON ECONOMY: SIZING UP GROWTH IN TEXAS (Online appendix)

description: The appendix has figures, tables as well as documentation
DOI: 10.6084/m9.figshare.1456130
title: Tilburg University | PhD records without on-line PhD thesis publications | @ 7/6/2015

description: Via The Tilburg University Research Portal.
DOI: 10.6084/m9.figshare.1456166.v1
title: TEN-GALLON ECONOMY: SIZING UP GROWTH IN TEXAS (Online appendix)

description: The appendix has figures, tables as well as documentation
DOI: 10.6084/m9.figshare.1456175.v1
title: Reanalysis done for the blog post "Modest reproducibility success"

description: These reanalysis accompany the blog post "Modest reproducibility success"
DOI: 10.6084/m9.figshare.1456119
title: Plant regeneration through direct somatic embryogenesis, antioxidant properties, and metabolite profiles of <i>Swertia corymbosa</i> (Griseb.) Wight <i>ex</i> C.B. Clarke

description: A protocol for induction of direct somatic embryogenesis and subsequent plant regeneration for the medicinally important and endangered plant of <i>Swertia corymbosa</i> has been developed for the first time. In the present study, <i>in vitro</i> derived leaf explants were cultured on Murashige and Skoog (MS) medium supplemented with 2,4-dichlorophenoxyacetic acid (2,4-D) individually and in combination with cytokinins for its effectiveness to induce the differentiation of somatic embryos. The antioxidant activities of methanolic extracts from non-embryonic callus (NEC), pre-embryoid masses (PEM), somatic embryos at globular stage (SEG), somatic embryos at heart-shaped stage (SEHS), and cotyledonary embryos (SEC) of <i>S. corymbosa</i> were evaluated using three <i>in vitro</i> assays: scavenging of free radicals (DPPH and ABTS) and ferric reducing antioxidant test. In all cases, the methanolic extract from SEG demonstrated better antioxidant activity than those taken from other tested samples. Higher amounts of swertianin (<b>1</b>), methylswertianin (<b>2</b>), and 1,2- dihydroxy-6-methoxyxanthone-8-O-β-D-xylopyranosyl (<b>3</b>) were found in SEG stage followed by SEHS and PEM when compared to NEC and SEC.
DOI: 10.6084/m9.figshare.1456175.v2
title: Reanalyses done for the blog post "Modest reproducibility success"

description: These reanalysis accompany the blog post "Modest reproducibility success"
DOI: 10.6084/m9.figshare.1456119.v2
title: Plant regeneration through direct somatic embryogenesis, antioxidant properties, and metabolite profiles of <i>Swertia corymbosa</i> (Griseb.) Wight <i>ex</i> C.B. Clarke

description: A protocol for induction of direct somatic embryogenesis and subsequent plant regeneration for the medicinally important and endangered plant of <i>Swertia corymbosa</i> has been developed for the first time. In the present study, <i>in vitro</i> derived leaf explants were cultured on Murashige and Skoog (MS) medium supplemented with 2,4-dichlorophenoxyacetic acid (2,4-D) individually and in combination with cytokinins for its effectiveness to induce the differentiation of somatic embryos. The antioxidant activities of methanolic extracts from non-embryonic callus (NEC), pre-embryoid masses (PEM), somatic embryos at globular stage (SEG), somatic embryos at heart-shaped stage (SEHS), and cotyledonary embryos (SEC) of <i>S. corymbosa</i> were evaluated using three <i>in vitro</i> assays: scavenging of free radicals (DPPH and ABTS) and ferric reducing antioxidant test. In all cases, the methanolic extract from SEG demonstrated better antioxidant activity than those taken from other tested samples. Higher amounts of swertianin (<b>1</b>), methylswertianin (<b>2</b>), and 1,2- dihydroxy-6-methoxyxanthone-8-O-β-D-xylopyranosyl (<b>3</b>) were found in SEG stage followed by SEHS and PEM when compared to NEC and SEC.