cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7822490
title: Changes in bird assemblages in an afforestation landscape in the Lower Delta of the Paraná River, Argentina

description: Global loss of wetlands has increased significantly in recent years. As a result, many wetlands have experienced changes in biotic communities, including birds. We compare the temporal variation in bird communities and the effects of land-use change on the structure and function of avian assemblages in the Lower Delta of the Paraná River (Argentina). We detected 28 families and 80 species of birds, with the highest richness, diversity and evenness in spring and summer because of the arrival of migratory species. Bird diversity, richness and evenness were significantly higher in secondary forests than in poplar plantations and cattle-grazing grasslands. Bird assemblages were related to structural differences of the habitat types and only generalist forest species were found in active plantations. Secondary forests exhibited species typical of the original riparian forest, practically extinct in the region. We speculate that abundance of guilds among habitat types is related to food supply and to plant composition. Our study shows for the first time how the conversion of wetlands into a Salicaceae plantation impacts on birds, particularly on wetland species. This demonstrates the need to implement management strategies to maintain a mosaic including secondary forests and freshwater marshes in order to conserve these species.
DOI: 10.6084/m9.figshare.7822490.v1
title: Changes in bird assemblages in an afforestation landscape in the Lower Delta of the Paraná River, Argentina

description: Global loss of wetlands has increased significantly in recent years. As a result, many wetlands have experienced changes in biotic communities, including birds. We compare the temporal variation in bird communities and the effects of land-use change on the structure and function of avian assemblages in the Lower Delta of the Paraná River (Argentina). We detected 28 families and 80 species of birds, with the highest richness, diversity and evenness in spring and summer because of the arrival of migratory species. Bird diversity, richness and evenness were significantly higher in secondary forests than in poplar plantations and cattle-grazing grasslands. Bird assemblages were related to structural differences of the habitat types and only generalist forest species were found in active plantations. Secondary forests exhibited species typical of the original riparian forest, practically extinct in the region. We speculate that abundance of guilds among habitat types is related to food supply and to plant composition. Our study shows for the first time how the conversion of wetlands into a Salicaceae plantation impacts on birds, particularly on wetland species. This demonstrates the need to implement management strategies to maintain a mosaic including secondary forests and freshwater marshes in order to conserve these species.
DOI: 10.6084/m9.figshare.7822451
title: Sociodemographic disparities in stage-specific incidences of endometrial cancer: a registry-based study in West Sweden, 1995–2016

description: <b>Background:</b> For a few types of cancer, lower socioeconomic status (SES) is associated with higher incidence, and for even more cancer types it is associated with having a less favorable tumor stage at diagnosis. For endometrial cancer (EC), however, there is no clear evidence of such associations with SES. There is a need for analysis of sociodemographic disparities in EC incidences according to stage at diagnosis, which may provide support for trying to improve early detection of EC. <b>Material and methods:</b> Stage-specific incidences of endometrioid and non-endometrioid endometrial carcinomas [EECs (∼90% of all EC cases) and NECs (∼10%)] were analyzed for the population of the Western Swedish Healthcare Region, taking into account year (1995–2016), age, educational level (low, intermediate and high), and immigrant status (Swedish-born, foreign-born). All EC cases were identified and data were obtained from population-based registries. <b>Results:</b> Stage distribution of diagnosed EECs differed significantly according to the educational level of patients who were aged between 50 and 74 years at diagnosis, but not in the case of younger or older patients. An analysis based on 3113 EEC cases aged 50–74 years at diagnosis revealed marked disparities in the stage-II to stage-IV EEC incidences but not in the stage-I EEC incidence. Compared to women with a high level of education, the incidence rate ratios of stage-I, stage-II and stage-III and -IV EEC in women with a low level of education were 1.00 (95% CI: 0.90–1.12), 1.65 (1.13–2.42), and 1.82 (1.33–2.49), respectively. For NEC, we found no such association. <b>Conclusions:</b> Elevated incidences of stage-II to stage-IV EEC in 50- to 74-year-old women with a low level of education suggest that there should be targeted health service trials aimed at improving awareness of EC. Well-targeted EC awareness programs might lead to considerable health benefits.
DOI: 10.6084/m9.figshare.7822451.v1
title: Sociodemographic disparities in stage-specific incidences of endometrial cancer: a registry-based study in West Sweden, 1995–2016

description: <b>Background:</b> For a few types of cancer, lower socioeconomic status (SES) is associated with higher incidence, and for even more cancer types it is associated with having a less favorable tumor stage at diagnosis. For endometrial cancer (EC), however, there is no clear evidence of such associations with SES. There is a need for analysis of sociodemographic disparities in EC incidences according to stage at diagnosis, which may provide support for trying to improve early detection of EC. <b>Material and methods:</b> Stage-specific incidences of endometrioid and non-endometrioid endometrial carcinomas [EECs (∼90% of all EC cases) and NECs (∼10%)] were analyzed for the population of the Western Swedish Healthcare Region, taking into account year (1995–2016), age, educational level (low, intermediate and high), and immigrant status (Swedish-born, foreign-born). All EC cases were identified and data were obtained from population-based registries. <b>Results:</b> Stage distribution of diagnosed EECs differed significantly according to the educational level of patients who were aged between 50 and 74 years at diagnosis, but not in the case of younger or older patients. An analysis based on 3113 EEC cases aged 50–74 years at diagnosis revealed marked disparities in the stage-II to stage-IV EEC incidences but not in the stage-I EEC incidence. Compared to women with a high level of education, the incidence rate ratios of stage-I, stage-II and stage-III and -IV EEC in women with a low level of education were 1.00 (95% CI: 0.90–1.12), 1.65 (1.13–2.42), and 1.82 (1.33–2.49), respectively. For NEC, we found no such association. <b>Conclusions:</b> Elevated incidences of stage-II to stage-IV EEC in 50- to 74-year-old women with a low level of education suggest that there should be targeted health service trials aimed at improving awareness of EC. Well-targeted EC awareness programs might lead to considerable health benefits.
DOI: 10.6084/m9.figshare.7822454
title: Cry me a river: building trust and maintaining legitimacy in environmental flows

description: Water reforms in Australia over a decade ago have seen large-scale recovery of water for the environment. While the recovery programme commenced with bilateral political support, there has remained ongoing debate in the media around the recovery volume, method of recovery and delivering of this water through the river system. In November 2017, a group of academics and practitioners met to discuss the need for <i>legitimacy</i> as a core component of environmental water programmes. We discuss legitimacy in terms of both the process and outcome of an environmental water programme. This article, along with the others in the special issue, makes the case for investing in community support for, and demonstrating outcomes from, environmental water programmes.
DOI: 10.6084/m9.figshare.7822454.v1
title: Cry me a river: building trust and maintaining legitimacy in environmental flows

description: Water reforms in Australia over a decade ago have seen large-scale recovery of water for the environment. While the recovery programme commenced with bilateral political support, there has remained ongoing debate in the media around the recovery volume, method of recovery and delivering of this water through the river system. In November 2017, a group of academics and practitioners met to discuss the need for <i>legitimacy</i> as a core component of environmental water programmes. We discuss legitimacy in terms of both the process and outcome of an environmental water programme. This article, along with the others in the special issue, makes the case for investing in community support for, and demonstrating outcomes from, environmental water programmes.
DOI: 10.6084/m9.figshare.7822403
title: gVCF_NA07051

description: 1000 Genomes gVCF mapped to hs37d5 for NA07051.
DOI: 10.6084/m9.figshare.7822403.v1
title: gVCF_NA07051

description: 1000 Genomes gVCF mapped to hs37d5 for NA07051.
DOI: 10.6084/m9.figshare.7822340
title: Small variations in nanoparticle structure dictate differential cellular stress responses and mode of cell death

description: For optimal exploitation of nanoparticles (NPs) in biomedicine, and to predict nanotoxicity, detailed knowledge of the cellular responses to cell-bound or internalized NPs is imperative. The final outcome of NP-cell interaction is dictated by the type and magnitude of the NP insult and the cellular response. Here, this has been systematically studied by using poly(alkylcyanoacrylate) (PACA) particles differing only in their alkyl side chains; butyl (PBCA), ethylbutyl (PEBCA), or octyl (POCA), respectively. Surprisingly, these highly similar NPs induced different stress responses and modes of cell death in human cell lines. The POCA particles generally induced endoplasmic reticulum stress and apoptosis. In contrast, PBCA and PEBCA particles induced oxidative stress and lipid peroxidation depending on the level of the glutathione precursor cystine and transcription of the cystine transporter <i>SLC7A11</i>. The latter was induced as a protective response by the transcription factors ATF4 and Nrf2. PBCA particles strongly activated ATF4 downstream of the eIF2α kinase HRI, whereas PEBCA particles more potently induced Nrf2 antioxidant responses. Intriguingly, PBCA particles activated the cell death mechanism ferroptosis; a promising option for targeting multidrug-resistant cancers. Our findings highlight that even minor differences in NP composition can severely impact the cellular response to NPs. This may have important implications in therapeutic settings.
DOI: 10.6084/m9.figshare.7822232
title: A first genetic portrait of synaptonemal complex variation

description: Data and code used in the manuscript, "A first genetic portrait of synaptonemal complex variation".<br>Phenotype and genotype data as well as genetic maps for both the <i>musc</i><sub>PWD</sub> × <i>cast</i><sub>CAST</sub> and the<i> dom</i><sub>GI</sub> × <i>dom</i><sub>WSB</sub> cross are included.<br><br>Two tables of candidate genes from the <i>musc</i><sub>PWD</sub> × <i>cast</i><sub>CAST</sub> cross are in tab-delimited (.tsv) format. The first, (AllCandidateGenes.tsv) includes all 301 candidates from chromosomes 5 and X. The second, (GOCandidates.tsv) includes only candidates associated with terms that include "recomb", "synapton", or "meio" within the name.<br><br>Also includes python code (skeletonize_script.py) used to measure SC length from spermatocyte spreads.<br>
DOI: 10.6084/m9.figshare.7822100
title: Data from - Can behaviour explain invasion success? A comparison between sympatric invasive and native lizards

description: Dataset from a study that investigated differences in behavioural traits between two sympatric congeneric species, being one invasive (Podarcis sicula) and the other native (Podarcis virescens).
DOI: 10.6084/m9.figshare.7822232.v1
title: A first genetic portrait of synaptonemal complex evolution

description: Data and code used in the manuscript, "A first genetic portrait of synaptonemal complex evolution".<br>Includes phenotype and genotype data as well as genetic maps for both the <i>musc</i><sub>PWD</sub> × <i>cast</i><sub>CAST</sub> and the<i> dom</i><sub>GI</sub> × <i>dom</i><sub>WSB</sub> cross.<br>Also includes python code used to measure SC length from spermatocyte spreads.<br>
DOI: 10.6084/m9.figshare.7822232.v3
title: A first genetic portrait of synaptonemal complex variation

description: Data and code used in the manuscript, "A first genetic portrait of synaptonemal complex variation".<br>Phenotype and genotype data as well as genetic maps for both the <i>musc</i><sub>PWD</sub> × <i>cast</i><sub>CAST</sub> and the<i> dom</i><sub>GI</sub> × <i>dom</i><sub>WSB</sub> cross are included.<br><br>Two tables of candidate genes from the <i>musc</i><sub>PWD</sub> × <i>cast</i><sub>CAST</sub> cross are in tab-delimited (.tsv) format. The first, (AllCandidateGenes.tsv) includes all 301 candidates from chromosomes 5 and X. The second, (GOCandidates.tsv) includes only candidates associated with terms that include "recomb", "synapton", or "meio" within the name.<br><br>Also includes python code (skeletonize_script.py) used to measure SC length from spermatocyte spreads.<br>
DOI: 10.6084/m9.figshare.7822232.v2
title: A first genetic portrait of synaptonemal complex evolution

description: Data and code used in the manuscript, "A first genetic portrait of synaptonemal complex evolution".<br>Includes phenotype and genotype data as well as genetic maps for both the <i>musc</i><sub>PWD</sub> × <i>cast</i><sub>CAST</sub> and the<i> dom</i><sub>GI</sub> × <i>dom</i><sub>WSB</sub> cross.<br>Also includes python code used to measure SC length from spermatocyte spreads.<br>
DOI: 10.6084/m9.figshare.7820381
title: Differentially expressed genes between CD34+ and CD34- melanocyte stem cells (McSCs) using RNA-Seq analysis

description: <b>Raw counts for all genes for CD34+ and CD34- McSCs that were generated by HTSeq-count. </b>The file comprises of two separate datasets: (a) with all gene counts and (b) without genes with zero counts for all six samples (3 CD34+ McSC samples and 3 CD34- McSC samples).
DOI: 10.6084/m9.figshare.7820354
title: Pheno data

description: MALDI
DOI: 10.6084/m9.figshare.7820381.v1
title: Differentially expressed genes between CD34+ and CD34- melanocyte stem cells (McSCs) using RNA-Seq analysis

description: <b>Raw counts for all genes for CD34+ and CD34- McSCs that were generated by HTSeq-count. </b>The file comprises of two separate datasets: (a) with all gene counts and (b) without genes with zero counts for all six samples (3 CD34+ McSC samples and 3 CD34- McSC samples).
DOI: 10.6084/m9.figshare.7820342.v1
title: Mapping gene markers for apple fruit ring rot disease resistance using a multi-omics approach

description: <b>all the datasets for 'Mapping gene markers for apple fruit ring rot disease resistance using a multi-omics approach'</b><b><br></b>'Readme' contains all the descriptions of the datasets
DOI: 10.6084/m9.figshare.7820354.v1
title: MALDI Raw Data

description: MALDI
DOI: 10.6084/m9.figshare.7820300
title: Moon effect Dupont´s lark

description: Raw data<br>
DOI: 10.6084/m9.figshare.7820324
title: Cohort Data

description: Behavioral dataset for both cohorts performing discriminations on temporally patterned odour stimuli
DOI: 10.6084/m9.figshare.7820354.v2
title: Raw

description: MALDI
DOI: 10.6084/m9.figshare.7820324.v1
title: Cohort Data

description: Behavioral dataset for both cohorts performing discriminations on temporally patterned odour stimuli
DOI: 10.6084/m9.figshare.7820354.v4
title: Pheno data

description: MALDI
DOI: 10.6084/m9.figshare.7820126
title: Nomogram connecting source radius, stress drop, corner frequency, and seismic moment/magnitude

description: A nomogram similar to that published by M. Mahdyiar (1987) connecting source radius, stress drop, corner frequency, and seismic moment/magnitude assuming the Brune (1970, 1971) source model and a shear-wave velocity at the source of 3.5km/s (the results would be similar for the normal range of shear-wave velocity, about 3 to 4km/s).<br>Connect up two axes and where the line crosses the third axis is the result. An example line is shown for a stress drop (delta sigma) of 10bars and a moment magnitude (M) of 6, which gives a corner frequency (f0) of about 0.15Hz and a source radius (r) of 8km.<br><br>Created using pynomo using a type 1 nomogram with type 8 nomograms for each of the principal axes
DOI: 10.6084/m9.figshare.7820354.v3
title: Raw

description: MALDI
DOI: 10.6084/m9.figshare.7820126.v3
title: Nomogram connecting source radius, stress drop, corner frequency, and seismic moment/magnitude

description: A nomogram similar to that published by M. Mahdyiar (1987) connecting source radius, stress drop, corner frequency, and seismic moment/magnitude assuming the Brune (1970, 1971) source model and a shear-wave velocity at the source of 3.5km/s (the results would be similar for the normal range of shear-wave velocity, about 3 to 4km/s).<br>Connect up two axes and where the line crosses the third axis is the result. An example line is shown for a stress drop (delta sigma) of 10bars and a moment magnitude (M) of 6, which gives a corner frequency (f0) of about 0.15Hz and a source radius (r) of 8km.<br><br>Created using pynomo using a type 1 nomogram with type 8 nomograms for each of the principal axes
DOI: 10.6084/m9.figshare.7820060
title: Assemblies of Diplonemid-like SAG

description: <b>9G_35B_original_assembly.fasta</b><br>- original prep and assembly<br><b>9G_35B_from_2515_scaffolds.fasta</b><br>- resequencing of original prep and assembly<b>9G_35B_new_prep_scaffolds.fasta<br></b>- new prep and assemblye<b>9G_35B_coassembly_scaffolds.fasta</b><br>- combination of all read libraries assembled
DOI: 10.6084/m9.figshare.7820126.v2
title: Nomogram connecting source radius, stress drop, corner frequency, and seismic moment/magnitude

description: A nomogram similar to that published by M. Mahdyiar (1987) connecting source radius, stress drop, corner frequency, and seismic moment/magnitude assuming the Brune (1970, 1971) source model and a shear-wave velocity at the source of 3.5km/s (the results would be similar for the normal range of shear-wave velocity, about 3 to 4km/s).<br>Connect up two axes and where the line crosses the third axis is the result. An example line is shown for a stress drop (delta sigma) of 10bars and a moment magnitude (M) of 6, which gives a corner frequency (f0) of about 0.15Hz and a source radius (r) of 8km.<br><br>Created using pynomo using a type 1 nomogram with type 8 nomograms for each of the principal axes
DOI: 10.6084/m9.figshare.7820060.v1
title: Assemblies of Diplonemid-like SAG

description: <b>9G_35B_original_assembly.fasta</b><br>- original prep and assembly<br><b>9G_35B_from_2515_scaffolds.fasta</b><br>- resequencing of original prep and assembly<b>9G_35B_new_prep_scaffolds.fasta<br></b>- new prep and assemblye<b>9G_35B_coassembly_scaffolds.fasta</b><br>- combination of all read libraries assembled
DOI: 10.25376/hra.7819997
title: Finnell et al LC-NE neuroinflammation BBI Supplement.docx

description: Supplemental Section of our accepted Manuscript: Exposure to psychosocial stress is known to precipitate the emergence of stress related psychiatric disorders such as depression and anxiety. While mechanisms by which this occurs remain largely unclear, recent evidence points towards a causative role for inflammation. Neurotransmitters, such as norepinephrine (NE) are capable of regulating expression of proinflammatory cytokines and thus may contribute to the emergence of stress-related disorders. The locus coeruleus (LC) is the major source of norepinephrine (NE) to the brain and therefore the current study utilized N-(2-chloroethyl)-N-ethyl-2-bromobenzylamine (DSP-4), an LC selective noradrenergic neurotoxin, to determine the discrete involvement of the LC-NE system in social defeat-induced inflammation in LC projection regions including the central amygdala (CeA), dorsal raphe (DR) and plasma. In the current study, rats were exposed to brief social defeat or control manipulations on 5 consecutive days. To determine whether a history of social defeat enhanced or “primed” the inflammatory response to a subsequent defeat exposure, all rats regardless of stress history were exposed to an acute social defeat challenge immediately prior to tissue collection. As anticipated, prior history of social defeat primed inflammatory responses in the plasma and CeA while neuroinflammation in the DR was markedly reduced. Notably, DSP-4 treatment suppressed stress-induced circulating inflammatory cytokines independent of prior stress history. In contrast, neuroinflammation in the CeA and DR were greatly augmented selectively in DSP-4 treated rats with a history of social defeat. Together these data highlight the dichotomous nature of NE in stress-induced inflammatory priming in the periphery and the brain and directly implicate the LC-NE system in these processes.
DOI: 10.25376/hra.7819997.v1
title: Finnell et al LC-NE neuroinflammation BBI Supplement.docx

description: Supplemental Section of our accepted Manuscript: Exposure to psychosocial stress is known to precipitate the emergence of stress related psychiatric disorders such as depression and anxiety. While mechanisms by which this occurs remain largely unclear, recent evidence points towards a causative role for inflammation. Neurotransmitters, such as norepinephrine (NE) are capable of regulating expression of proinflammatory cytokines and thus may contribute to the emergence of stress-related disorders. The locus coeruleus (LC) is the major source of norepinephrine (NE) to the brain and therefore the current study utilized N-(2-chloroethyl)-N-ethyl-2-bromobenzylamine (DSP-4), an LC selective noradrenergic neurotoxin, to determine the discrete involvement of the LC-NE system in social defeat-induced inflammation in LC projection regions including the central amygdala (CeA), dorsal raphe (DR) and plasma. In the current study, rats were exposed to brief social defeat or control manipulations on 5 consecutive days. To determine whether a history of social defeat enhanced or “primed” the inflammatory response to a subsequent defeat exposure, all rats regardless of stress history were exposed to an acute social defeat challenge immediately prior to tissue collection. As anticipated, prior history of social defeat primed inflammatory responses in the plasma and CeA while neuroinflammation in the DR was markedly reduced. Notably, DSP-4 treatment suppressed stress-induced circulating inflammatory cytokines independent of prior stress history. In contrast, neuroinflammation in the CeA and DR were greatly augmented selectively in DSP-4 treated rats with a history of social defeat. Together these data highlight the dichotomous nature of NE in stress-induced inflammatory priming in the periphery and the brain and directly implicate the LC-NE system in these processes.
DOI: 10.6084/m9.figshare.7820072
title: Histologies

description: Histologies of H&E staining image
DOI: 10.6084/m9.figshare.7820072.v4
title: Histologies

description: Histologies of H&E staining image