cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8190791
title: Additional file 2: of Repeated evolution of asymmetric genitalia and right-sided mating behavior in the Drosophila nannoptera species group

description: Length measurements at the left and right sides of the ventral aedeagus tip of D. acanthoptera, D. nannoptera, D. machalilla and D. bromeliae (CSV 9 kb)
DOI: 10.6084/m9.figshare.8190797
title: Additional file 4: of Repeated evolution of asymmetric genitalia and right-sided mating behavior in the Drosophila nannoptera species group

description: Multi-species analysis of courtship and copulation periods, shown in Additional file 1:: Figure S6. (CSV 69 kb)
DOI: 10.6084/m9.figshare.8190797.v1
title: Additional file 4: of Repeated evolution of asymmetric genitalia and right-sided mating behavior in the Drosophila nannoptera species group

description: Multi-species analysis of courtship and copulation periods, shown in Additional file 1:: Figure S6. (CSV 69 kb)
DOI: 10.6084/m9.figshare.8190818.v1
title: Additional file 7: of Repeated evolution of asymmetric genitalia and right-sided mating behavior in the Drosophila nannoptera species group

description: Copulation times of couples filmed for the position analysis of D. nannoptera from a frontal perspective, shown in Additional file 1: Figure S8. (CSV 15 kb)
DOI: 10.6084/m9.figshare.8190827
title: Additional file 8: of Repeated evolution of asymmetric genitalia and right-sided mating behavior in the Drosophila nannoptera species group

description: Angle measurements for the position analysis of D. nannoptera from a frontal perspective, shown in Fig. 3. (CSV 41 kb)
DOI: 10.6084/m9.figshare.8190830
title: Additional file 4: of DNA methylation screening after roux-en Y gastric bypass reveals the epigenetic signature stems from genes related to the surgery per se

description: Raw data. Datasets generated and/or analyzed during the current study. (XLSB 395235 kb)
DOI: 10.6084/m9.figshare.8190830.v1
title: Additional file 4: of DNA methylation screening after roux-en Y gastric bypass reveals the epigenetic signature stems from genes related to the surgery per se

description: Raw data. Datasets generated and/or analyzed during the current study. (XLSB 395235 kb)
DOI: 10.6084/m9.figshare.8190758
title: Additional file 7: of A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism

description: Table S5. Predicted SNP effects for the top 50 Internode DEGs. Genes correspond to those shown in Fig. 5. Columns 4â  31 are taken directly from the output of the program snpEff. Details can be found in the snpEff reference manual. Column 32 (GT.pvalue) is the significance of the Genotype x Time interaction term in the differential expression analysis. Columns 33â  37 are the Fold Changes at each developmental stage, calculated as Rio/PR22 (Sweet/Non-Sweet). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8190758.v1
title: Additional file 7: of A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism

description: Table S5. Predicted SNP effects for the top 50 Internode DEGs. Genes correspond to those shown in Fig. 5. Columns 4â  31 are taken directly from the output of the program snpEff. Details can be found in the snpEff reference manual. Column 32 (GT.pvalue) is the significance of the Genotype x Time interaction term in the differential expression analysis. Columns 33â  37 are the Fold Changes at each developmental stage, calculated as Rio/PR22 (Sweet/Non-Sweet). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8190767.v1
title: MOESM2 of Genomic measures of inbreeding in the Norwegian–Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits

description: Additional file 2: Table S2. Correlation matrix between FPED and all FROH estimates.
DOI: 10.6084/m9.figshare.8190773
title: MOESM3 of Genomic measures of inbreeding in the Norwegian–Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits

description: Additional file 3: Table S3. Results of the paired t-test (P-values) between FPED and all FROH estimates.
DOI: 10.6084/m9.figshare.8190776.v1
title: Additional file 9: of A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism

description: Table S7. Predicted SNP effects for the top 50 Meristem DEGs. Genes correspond to those shown in Fig. 5. Details about columns are the same as described for Additional file 7: Table S5. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8190785
title: MOESM6 of Genomic measures of inbreeding in the Norwegian–Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits

description: Additional file 6: Table S4. Homozygous regions of the genome that are shared by at least 95% of the sample of Norwegian-Swedish Coldblooded Trotters (n = 566).
DOI: 10.6084/m9.figshare.8190785.v1
title: MOESM6 of Genomic measures of inbreeding in the Norwegian–Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits

description: Additional file 6: Table S4. Homozygous regions of the genome that are shared by at least 95% of the sample of Norwegian-Swedish Coldblooded Trotters (n = 566).
DOI: 10.6084/m9.figshare.8190809.v1
title: Additional file 6: of Repeated evolution of asymmetric genitalia and right-sided mating behavior in the Drosophila nannoptera species group

description: Landmark position measurements, used to calculate angle values for the multi-species mating position analysis, shown in Fig. 3. (CSV 101 kb)
DOI: 10.6084/m9.figshare.8191316
title: Annotation results of Oryza granulata genome

description: The annotation results of protein-coding genes, non-coding genes, repeated sequences and functional prediction for the de novo assembled genome of <em>Oryza granulata</em>.
DOI: 10.6084/m9.figshare.8191169
title: Testing the efficacy of a thermal camera as a search tool for locating wild bumble bee nests

description: Research into how bumble bee colonies respond to the stressors affecting their populations are currently studied in the laboratory using commercially reared <i>Bombus terrestris</i> colonies. Understanding how these stressors affect wild bumble bee colonies in the field would be a crucial step forward for the conservation of bumble bee species. Currently, visual cues are used to locate bumble bee nests, using human searchers looking for the worker nest traffic, but the limitations of this method mean that low numbers of nests are found and so a new method that looks to tackle these limitations is needed. Thermal cameras have been considered as a potential nest searching tool because they reduce the visual complexity of the environment by displaying a homogenized thermal landscape to the searcher. In this study, we compare the use of a thermal camera to human searches using two trials: (<i>i</i>) using inexperienced volunteers to search along the transect for a known bumble bee nest and (<i>ii</i>) using an experienced individual to search across a number of novel locations. We found thermal cameras are not a better nest detection technique than human searches, having low success rates across both trials. We discuss the limitations of thermal cameras as a technique and propose how the technology could be improved for future studies.
DOI: 10.6084/m9.figshare.8191169.v1
title: Testing the efficacy of a thermal camera as a search tool for locating wild bumble bee nests

description: Research into how bumble bee colonies respond to the stressors affecting their populations are currently studied in the laboratory using commercially reared <i>Bombus terrestris</i> colonies. Understanding how these stressors affect wild bumble bee colonies in the field would be a crucial step forward for the conservation of bumble bee species. Currently, visual cues are used to locate bumble bee nests, using human searchers looking for the worker nest traffic, but the limitations of this method mean that low numbers of nests are found and so a new method that looks to tackle these limitations is needed. Thermal cameras have been considered as a potential nest searching tool because they reduce the visual complexity of the environment by displaying a homogenized thermal landscape to the searcher. In this study, we compare the use of a thermal camera to human searches using two trials: (<i>i</i>) using inexperienced volunteers to search along the transect for a known bumble bee nest and (<i>ii</i>) using an experienced individual to search across a number of novel locations. We found thermal cameras are not a better nest detection technique than human searches, having low success rates across both trials. We discuss the limitations of thermal cameras as a technique and propose how the technology could be improved for future studies.
DOI: 10.6084/m9.figshare.8191232
title: simulatedAfB1Data.csv

description: Simulated data for forecasting AFB1
DOI: 10.6084/m9.figshare.8191232.v1
title: simulatedAfB1Data.csv

description: Simulated data for forecasting AFB1
DOI: 10.6084/m9.figshare.8191826.v1
title: Bayesian Model Search for Nonstationary Periodic Time Series

description: We propose a novel Bayesian methodology for analyzing nonstationary time series that exhibit oscillatory behaviour. We approximate the time series using a piecewise oscillatory model with unknown periodicities, where our goal is to estimate the change-points while simultaneously identifying the potentially changing periodicities in the data. Our proposed methodology is based on a trans-dimensional Markov chain Monte Carlo (MCMC) algorithm that simultaneously updates the change-points and the periodicities relevant to any segment between them. We show that the proposed methodology successfully identifies time changing oscillatory behaviour in two applications which are relevant to e-Health and sleep research, namely the occurrence of ultradian oscillations in human skin temperature during the time of night rest, and the detection of instances of sleep apnea in plethysmographic respiratory traces.
DOI: 10.6084/m9.figshare.8191871.v1
title: Spatial and seasonal patterns of flood change across Brazil

description: Brazil has some of the largest rivers in the world and has the second greatest flood loss potential among the emergent countries. Despite that, flood studies in this area are still scarce. In this paper, we used flood seasonality and trend analysis at the annual and seasonal scales in order to describe flood regimes and changes across the whole of Brazil in the period 1976–2015. We identified a strong seasonality of floods and a well-defined spatio-temporal pattern for flood occurrence. There are positive trends in the frequency and magnitude of floods in the North, South and parts of Southeast Brazil; and negative trends in the North-east and the remainder of Southeast Brazil. Trends in the magnitude (frequency) were predominant in the winter (summer). Overall, floods are becoming more frequent and intense in Brazilian regions characterized by wet conditions, and less frequent and intense in drier regions.
DOI: 10.25387/g3.7706717
title: Supplemental Material for Mosca et al., 2019

description: The document
included all supplementary materials for the <i>Abies alba</i> genome assembly. The following data are listed in the
supplementary tables: the estimation of DNA concentration (Table S1), the Gene Ontology
(GO) term categories used to count the GO terms (Table S2), the genome
annotation statistics (Table S3), the intron and exon statistics (Table S4),
and the count and percentage of the GO terms (Table S5). The supplementary
figures are also inclueded: <i>Abies alba</i>
distribution map (Figure S1), the location of the sampled tree AA_WSL01 (Figure S2), plot
for the comparison between <i>Abies</i> cloroplast
(Figure S3), boxplots of the gene distribution lengths in <i>A. alba</i> (Figure S4) and in other conifers (Figure S5), distribution
of the most abundant GO terms.
DOI: 10.25387/g3.7706717.v3
title: Supplemental Material for Mosca et al., 2019

description: The document
included all supplementary materials for the <i>Abies alba</i> genome assembly. The following data are listed in the
supplementary tables: the estimation of DNA concentration (Table S1), the Gene Ontology
(GO) term categories used to count the GO terms (Table S2), the genome
annotation statistics (Table S3), the intron and exon statistics (Table S4),
and the count and percentage of the GO terms (Table S5). The supplementary
figures are also inclueded: <i>Abies alba</i>
distribution map (Figure S1), the location of the sampled tree AA_WSL01 (Figure S2), plot
for the comparison between <i>Abies</i> cloroplast
(Figure S3), boxplots of the gene distribution lengths in <i>A. alba</i> (Figure S4) and in other conifers (Figure S5), distribution
of the most abundant GO terms.
DOI: 10.6084/m9.figshare.8191850.v1
title: Main effects and interactions in mixed and incomplete data frames

description: A mixed data frame (MDF) is a table collecting categorical, numerical and count observations. The use of MDF is widespread in statistics and the applications are numerous from abundance data in ecology to recommender systems. In many cases, an MDF exhibits simultaneously <i>main effects</i>, such as row, column or group effects and <i>interactions</i>, for which a low-rank model has often been suggested. Although the literature on low-rank approximations is very substantial, with few exceptions, existing methods do not allow to incorporate main effects and interactions while providing statistical guarantees. The present work fills this gap. We propose an estimation method which allows to recover simultaneously the main effects and the interactions. We show that our method is near optimal under conditions which are met in our targeted applications. We also propose an optimization algorithm which provably converges to an optimal solution. Numerical experiments reveal that our method, mimi, performs well when the main effects are sparse and the interaction matrix has low-rank. We also show that mimi compares favorably to existing methods, in particular when the main effects are significantly large compared to the interactions, and when the proportion of missing entries is large. The method is available as an R package on the Comprehensive R Archive Network.
DOI: 10.6084/m9.figshare.8191871
title: Spatial and seasonal patterns of flood change across Brazil

description: Brazil has some of the largest rivers in the world and has the second greatest flood loss potential among the emergent countries. Despite that, flood studies in this area are still scarce. In this paper, we used flood seasonality and trend analysis at the annual and seasonal scales in order to describe flood regimes and changes across the whole of Brazil in the period 1976–2015. We identified a strong seasonality of floods and a well-defined spatio-temporal pattern for flood occurrence. There are positive trends in the frequency and magnitude of floods in the North, South and parts of Southeast Brazil; and negative trends in the North-east and the remainder of Southeast Brazil. Trends in the magnitude (frequency) were predominant in the winter (summer). Overall, floods are becoming more frequent and intense in Brazilian regions characterized by wet conditions, and less frequent and intense in drier regions.
DOI: 10.6084/m9.figshare.8191916
title: Trends in incidence, treatment and survival of borderline ovarian tumors in the Netherlands: a nationwide analysis

description: <b>Background:</b> Population-based data on borderline ovarian tumors (BOTs) are scarce and information regarding recent trends in incidence, treatment and survival is lacking. The purpose of this study was to analyze these trends in the Netherlands and to assess the risk of developing a subsequent invasive ovarian tumor. <b>Material and methods:</b> All consecutive patients diagnosed with BOTs between 1993 and 2016 (<i>n</i> = 7113) were identified from the Netherlands Cancer Registry (NCR). Annual age-adjusted incidence rates were calculated. Relative survival (RS) analyses and multivariable analyses estimating excess mortality were conducted. Patients with a subsequent invasive ovarian tumor were identified by the NCR. <b>Results:</b> Age-adjusted incidence increased from 2.1/100,000 person-years in 1993 to 4.2/100,000 in 2011, after 2011 the incidence declined. The proportion of bilateral tumors decreased over time from 16% in 1993–1998 to 11% in 2005–2010 and remained stable onwards. Survival improved over time (excess mortality ratio<sub>adjusted</sub> 2011–2016 <i>versus</i> 1993–1998: 0.25; 95%CI: 0.13–0.47). Five-year RS increased from 91% in 1993–1998 to 98% in 2011–2016 and 10-year RS from 88% in 1993–1998 to 96% in 2005–2010. Fewer patients were treated with chemotherapy (4.4% in 1993–1998 <i>versus</i> 0.7% in 2011–2016). During a median follow-up time of 8 years, 0.9% developed a subsequent invasive ovarian carcinoma. <b>Conclusions:</b> The incidence of BOTs increased over time from 1993 until 2010 but declined since 2011. This decline may be partly due to changes in the classification of gynecological tumors, as serous BOTs are now more often diagnosed as low grade serous ovarian cancers. Survival is high and has improved since 1993. The risk of a subsequent invasive ovarian carcinoma seems low.
DOI: 10.6084/m9.figshare.8191916.v1
title: Trends in incidence, treatment and survival of borderline ovarian tumors in the Netherlands: a nationwide analysis

description: <b>Background:</b> Population-based data on borderline ovarian tumors (BOTs) are scarce and information regarding recent trends in incidence, treatment and survival is lacking. The purpose of this study was to analyze these trends in the Netherlands and to assess the risk of developing a subsequent invasive ovarian tumor. <b>Material and methods:</b> All consecutive patients diagnosed with BOTs between 1993 and 2016 (<i>n</i> = 7113) were identified from the Netherlands Cancer Registry (NCR). Annual age-adjusted incidence rates were calculated. Relative survival (RS) analyses and multivariable analyses estimating excess mortality were conducted. Patients with a subsequent invasive ovarian tumor were identified by the NCR. <b>Results:</b> Age-adjusted incidence increased from 2.1/100,000 person-years in 1993 to 4.2/100,000 in 2011, after 2011 the incidence declined. The proportion of bilateral tumors decreased over time from 16% in 1993–1998 to 11% in 2005–2010 and remained stable onwards. Survival improved over time (excess mortality ratio<sub>adjusted</sub> 2011–2016 <i>versus</i> 1993–1998: 0.25; 95%CI: 0.13–0.47). Five-year RS increased from 91% in 1993–1998 to 98% in 2011–2016 and 10-year RS from 88% in 1993–1998 to 96% in 2005–2010. Fewer patients were treated with chemotherapy (4.4% in 1993–1998 <i>versus</i> 0.7% in 2011–2016). During a median follow-up time of 8 years, 0.9% developed a subsequent invasive ovarian carcinoma. <b>Conclusions:</b> The incidence of BOTs increased over time from 1993 until 2010 but declined since 2011. This decline may be partly due to changes in the classification of gynecological tumors, as serous BOTs are now more often diagnosed as low grade serous ovarian cancers. Survival is high and has improved since 1993. The risk of a subsequent invasive ovarian carcinoma seems low.
DOI: 10.6084/m9.figshare.8192111
title: A novel antisense RNA ASPACT confers multi-level suppression of PACT and associated signalling

description: The innate immune system is the frontline host protection against pathogens. Effective antiviral immunity is elicited upon recognition of viral RNAs by the host pattern recognition receptors. One of the major viral RNA sensors is retinoic acid inducible gene-1, which triggers the production of interferons (IFNs). In turn, this protective response requires another viral sensor and immunity factor interferon-inducible protein kinase RNA activator (PACT/PRKRA). Here, we report the identification and characterization of a novel antisense <i>PACT</i> gene that expresses a non-coding RNA in a convergent and interferon-inducible manner. Publicly available gene structure and expression data revealed that this gene, that we termed <i>ASPACT</i>, overlaps with the 3′ -end of the <i>PACT</i> locus and is highly expressed during viral infection. Our results confirm the IFN-β-inducibility of <i>ASPACT</i>, which is dependent on STAT-1/2. We further discovered that downregulation of ASPACT impacts both the expression and localization of the PACT transcript. At the transcription level, ChIP and ChIRP assays demonstrated that the ASPACT non-coding RNA occupies distinct chromatin regions of <i>PACT</i> gene and is important for promoter recruitment of the epigenetic silencer HDAC1. In parallel, ASPACT was also found to mediate nuclear retention of the PACT mRNA via direct RNA–RNA interaction, as revealed by RNA antisense purification assay. In summary, our results support the model that the non-coding RNA ASPACT acts as a negative regulator of PACT at multiple levels, and reveal a novel regulator of the viral counteractive response.
DOI: 10.6084/m9.figshare.8192162
title: SWAP70 is a universal GEF-like adaptor for tethering actin to phagosomes

description: We recently identified a key role for SWAP70 as the tethering factor stabilizing F-actin filaments on the surface of phagosomes in human dendritic cells by interacting both with Rho-family GTPases and the lipid phosphatidylinositol (3,4)-bisphosphate. In this study, we aimed to investigate whether this role of SWAP70 was general among immune phagocytes. Our data reveal that SWAP70 is recruited to early phagosomes of macrophages and dendritic cells from both human and mouse. The putative inhibitor of SWAP70 sanguinarine blocked phagocytosis and F-actin polymerization, supporting a key role for SWAP70 in phagocytosis as demonstrated previously with knock-down. Moreover, SWAP70 was recently shown to sequester the F-actin severing protein cofilin and we investigated this relationship in phagocytosis. Our data show an increased activation of cellular cofilin upon siRNA knockdown of SWAP70. Finally, we explored whether SWAP70 would be recruited to the immune synapse between dendritic cells and T cells required for antigen presentation, as the formation of such synapses depends on F-actin. However, we observed that SWAP70 was depleted at immune synapses and specifically was recruited to phagosomes. Our data support an essential and specific role for SWAP70 in tethering and stabilizing F-actin to the phagosomal surface in a wide range of phagocytes.