cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9121568.v1
title: Additional file 3: of Humanized yeast genetic interaction mapping predicts synthetic lethal interactions of FBXW7 in breast cancer

description: Table S2. HYGIN network table. This table contains the initial mapping data from the yeast network where SL interactions are represented in pairs by A and B (Yeast Gene ID A, Yeast Gene ID B, Yeast Gene Name A, Yeast Gene Name B, E-value, and P-value). Through the 3-stage mapping process used to generate HYGIN, it also contains columns corresponding to Yeast Protein Accession (A and B), Human Protein Accession (A and B), and Human Gene Name (A and B). Human gene names were used to generate the network in Cytoscape. Due to some reciprocal screens in the initial yeast screen, there were some duplicate (reciprocal) entries in this table. Once the network was loaded into Cytoscape, â Remove duplicate edgesâ was used to eliminate reciprocal hits. This resulted in the 1,009 genes and 10,419 edges in the final HYGIN network. (XLS 2700 kb)
DOI: 10.6084/m9.figshare.9121589.v1
title: Additional file 7: of Humanized yeast genetic interaction mapping predicts synthetic lethal interactions of FBXW7 in breast cancer

description: Table S6. Genetic interactions in the breast cancer subnetwork. The table contains a list of the SL gene pairs that make up the breast cancer specific subnetwork where column GeneA represents the genes that are down-regulated in breast cancer, and column GeneB are their SL gene pairs. (XLS 66 kb)
DOI: 10.6084/m9.figshare.9121625
title: Christian-tutorial-stamps2019

description: Christian-tutorial-stamps2019
DOI: 10.6084/m9.figshare.9121754
title: Multitask-oriented manufacturing service composition in an uncertain environment using a hyper-heuristic algorithm

description: This is the simulation data for the article "Multitask-oriented manufacturing service composition in an uncertain environment using a hyper-heuristic algorithm"
DOI: 10.6084/m9.figshare.9121877
title: data.zip

description: Matlab (.mat) files for figures in the paper
DOI: 10.25400/lincolnuninz.9122504
title: Appendix D Endophytic fungi from cabbage in New Zealand 2016

description: Table of fungal isolates recovered from cabbage (Brassica oleracea var capitata) in New Zealand on February 2016. Columns contain a recorded value for variables:<br><br>frag_no - arbitrary tissue fragment numbering <br>region - regions in New Zealand where cabbage plants were sampled (Canterbury – h, Nelson – m and Pukekohe – a).<br>plant - arbitrary numbering of plants in given region<br>part - cabbage tissue R- root, S -stem, L - leaf<br>medium - cultivation medium - Potato dextrose agar (p), 1/4 strength potato dextrose agar (1), Sabouraud dextrose agar (s) and Aspergillus minimal medium (a)<br>well - arbitrary numbering of wels on cultivation plate<br>for plant2, part2, medium2 similar to above<br>fragment - code for tissue fragment from which given isolate originated<br>isolate - code for isolate<br>description of morphotypes<br>mycelium_color - colour of mycelium <br>mycelium_color_under - colour of the bottom of cultivation dish<br>mycelium_texture - texture of mycelim <br>sclerotia - whether present or not<br>spores - colour and texture of spores concentric on petri dish (conc), <br>media_coloring - colouring of the cultivation media by growing isolate<br> colours white (w), grey(g), green(gn), brown(b), yellow(yel), black (bl), purple (pu), orange (o), pink (pi), beige (be), dark(dk), light(li), pinch (P)<br> texture - fluffy (fl), growing in agar (ia), yeast-like (yes), chunky (ch) scant (s), compact (comp), flat(ft)<br> other abbreviations - somewhat (sw), in mycelium (im), vis (visible), dry (d), oozing (ooze), fragmente (frg), at the edge of colony (oe)<br><br>sequence - ITS sequence <br>MatchUNITE - match with UNITE database<br>identityUNITE - BLAST identity result for the best match with UNITE database<br>lengthUNITE - BLAST length result for the best match with UNITE database<br>lineageUNITE - taxonomy extracted from the best match with UNITE database<br>speciesUNITE - species extracted from the best match with UNITE database<br>genusUNITE- genus extracted from the best match with UNITE database<br>identityNCBI - BLAST identity result for the best match with NCBI database<br>MatchNCBI - BLAST identity result for the best match with NCBI database<br>speciesNCBI - species extracted from the best match with NCBI database<br>genusNCBI - genus extracted from the best match with NCBI database<br>lengthNCBI - BLAST length result for the best match with NCBI database<br>species - species name <br>genus - genus name <br>identity - BLAST identity result for the best match<br>blastlength - BLAST length result for the best match<br>seqlength - length of sequence<br>family - family name<br>order - order name<br>class - class name<br>phylum - phylum name
DOI: 10.25400/lincolnuninz.9122507
title: Appendix E Fungal guilds and synonymy of endophytic fungi isolated from cabbage in New Zealand 2015 and 2016

description: <br>List of recovered isolates in this project with the most likely species name and current synonymy based on NZFUNGI2 by Manaaki Whenua Landcare research. Fungal guilds are provided according to an online tool FUNGuild<br>
DOI: 10.25400/lincolnuninz.9122513
title: Appendix C Endophytic fungi from cabbage in New Zealand 2015

description: <br>Table of fungal isolates recovered from cabbage (Brassica oleracea var capitata) in Canterbury region, New Zealand on February 2015.<br><br>practice - agricultural practice in sampled fields - 1 organic , 2 conventional <br>place - arbitrary numbering of fields for given practice <br>plant - arbitrary numbering of plants in given practice <br>part - cabbage tissue R- root, S -stem, L - leaf<br>isolate - code for isolate<br>morfotype - <br>dish - <br>sequence - ITS sequence <br>MatchUNITE - match with UNITE database<br>identityUNITE - BLAST identity result for the best match with UNITE database<br>lengthUNITE - BLAST length result for the best match with UNITE database<br>lineageUNITE - taxonomy extracted from the best match with UNITE database<br>speciesUNITE - species extracted from the best match with UNITE database<br>genusUNITE- genus extracted from the best match with UNITE database<br>identityNCBI - BLAST identity result for the best match with NCBI database<br>MatchNCBI - BLAST identity result for the best match with NCBI database<br>speciesNCBI - species extracted from the best match with NCBI database<br>genusNCBI - genus extracted from the best match with NCBI database<br>lengthNCBI - BLAST length result for the best match with NCBI database<br>species - species name <br>genus - genus name <br>identity - BLAST identity result for the best match<br>blastlength - BLAST length result for the best match<br>seqlength - length of sequence<br>family - family name<br>order - order name<br>class - class name<br>phylum - phylum name<br>fragment - code for tissue fragment from which given isolate originated<br>part2 - cabbage tissue R- root, S -stem, L - leaf<br>medium - cultivation medium - Potato dextrose agar (PDA), Sabouraud dextrose agar (SDA; Difco, BD, USA) and Aspergillus minimal medium<br>(AMM)<br>bengal - whether bengal rose was used for cultivation medium<br><br>
DOI: 10.6084/m9.figshare.9121625.v2
title: Christian-tutorial-stamps2019

description: Christian-tutorial-stamps2019
DOI: 10.6084/m9.figshare.9121877.v1
title: data.zip

description: Matlab (.mat) files for figures in the paper
DOI: 10.6084/m9.figshare.9122135
title: Understanding the intricacy of canid social systems: Structure and temporal stability of red fox (Vulpes vulpes) groups

description: Data used for the network analyses published in PLOS ONE paper ‘Understanding the intricacy of canid social systems: Structure and temporal stability of red fox (Vulpes vulpes) groups'.<br>associations_by_territory.zip: dataset for network construction and analysis of social differentiation, lagged association rate and lagged identification rates in SOCPROG. Comprises associations and animal attributes, arranged in dyadic format suitable for the construction of association matrices in SOCPROG. Self-associations are used for patch visits whern foxes were alone. Associations are separated by territory into tabs within the Excel document.<br>associations_by_season_and_year.zip: dataset of associations and attributes. Associations are split into tabs by season and year, and used to detect communities. <br><br>all_territories_pooled_for_spaceuse_network.zip: dataset of associations and attributes. Associations are based on shared space and not necessarily time. Associations from all territories and seasons are pooled into a single dataset that was used to construct space-use networks.<br>spatial_profiles.zip: patch utilisation by individual and patch within detected communities, used to construct spatial profile plots in the paper.<br>Distributions of N days observed.csv: sighting frequency distribution used for Fig A in S1 Appendix.
DOI: 10.6084/m9.figshare.9122135.v1
title: Data for network construction and analysis

description: Data used for the analyses published in PLOS ONE paper ‘Understanding the intricacy of canid social systems: Structure and temporal stability of red fox (Vulpes vulpes) groups'.<br>associations_by_territory.zip: dataset for network construction and analysis of social differentiation, lagged association rate and lagged identification rates in SOCPROG. Comprises associations and animal attributes, arranged in dyadic format suitable for the construction of association matrices in SOCPROG. Self-associations are used for patch visits whern foxes were alone. Associations are separated by territory into tabs within the Excel document.<br>associations_by_season_and_year.zip: dataset of associations and attributes. Associations are split into tabs by season and year, and used to detect communities. <br><br>Distributions of N days observed.csv: sighting frequency distribution used for Fig A in S1 Appendix.
DOI: 10.6084/m9.figshare.9122135.v2
title: Data for network construction and analysis

description: Data used for the analyses published in PLOS ONE paper ‘Understanding the intricacy of canid social systems: Structure and temporal stability of red fox (Vulpes vulpes) groups'.<br>associations_by_territory.zip: dataset for network construction and analysis of social differentiation, lagged association rate and lagged identification rates in SOCPROG. Comprises associations and animal attributes, arranged in dyadic format suitable for the construction of association matrices in SOCPROG. Self-associations are used for patch visits whern foxes were alone. Associations are separated by territory into tabs within the Excel document.<br>associations_by_season_and_year.zip: dataset of associations and attributes. Associations are split into tabs by season and year, and used to detect communities. <br><br>all_territories_pooled_for_spaceuse_network.zip: dataset of associations and attributes. Associations are based on shared space and not necessarily time. Associations from all territories and seasons are pooled into a single dataset that was used to construct space-use networks.<br>Distributions of N days observed.csv: sighting frequency distribution used for Fig A in S1 Appendix.
DOI: 10.6084/m9.figshare.9122135.v3
title: Data for network construction and analysis

description: Data used for the analyses published in PLOS ONE paper ‘Understanding the intricacy of canid social systems: Structure and temporal stability of red fox (Vulpes vulpes) groups'.<br>associations_by_territory.zip: dataset for network construction and analysis of social differentiation, lagged association rate and lagged identification rates in SOCPROG. Comprises associations and animal attributes, arranged in dyadic format suitable for the construction of association matrices in SOCPROG. Self-associations are used for patch visits whern foxes were alone. Associations are separated by territory into tabs within the Excel document.<br>associations_by_season_and_year.zip: dataset of associations and attributes. Associations are split into tabs by season and year, and used to detect communities. <br><br>all_territories_pooled_for_spaceuse_network.zip: dataset of associations and attributes. Associations are based on shared space and not necessarily time. Associations from all territories and seasons are pooled into a single dataset that was used to construct space-use networks.<br>spatial_profiles.zip: patch utilisation by individual and patch within detected communities, used to construct spatial profile plots in the paper.<br>Distributions of N days observed.csv: sighting frequency distribution used for Fig A in S1 Appendix.
DOI: 10.6084/m9.figshare.9122135.v4
title: Data for network construction and analysis

description: Data used for the analyses published in PLOS ONE paper ‘Understanding the intricacy of canid social systems: Structure and temporal stability of red fox (Vulpes vulpes) groups'.<br>associations_by_territory.zip: dataset for network construction and analysis of social differentiation, lagged association rate and lagged identification rates in SOCPROG. Comprises associations and animal attributes, arranged in dyadic format suitable for the construction of association matrices in SOCPROG. Self-associations are used for patch visits whern foxes were alone. Associations are separated by territory into tabs within the Excel document.<br>associations_by_season_and_year.zip: dataset of associations and attributes. Associations are split into tabs by season and year, and used to detect communities. <br><br>all_territories_pooled_for_spaceuse_network.zip: dataset of associations and attributes. Associations are based on shared space and not necessarily time. Associations from all territories and seasons are pooled into a single dataset that was used to construct space-use networks.<br>spatial_profiles.zip: patch utilisation by individual and patch within detected communities, used to construct spatial profile plots in the paper.<br>Distributions of N days observed.csv: sighting frequency distribution used for Fig A in S1 Appendix.
DOI: 10.6084/m9.figshare.9122591
title: Additional file 2: of Cardiac MRI improves cardiovascular risk stratification in hazardous occupations

description: Table S1 â Indication for CMR by frequency of referral. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9122528
title: Gallant et al. datasets for study "Disentangling the relative influences of global drivers of change in biodiversity: a study of the twentieth-century red fox expansion into the Canadian Arctic"

description: Gallant et al. datasets for study "Disentangling the relative influences of global drivers of change in biodiversity: a study of the twentieth-century red fox expansion into the Canadian Arctic"
DOI: 10.6084/m9.figshare.9122579
title: Limits to load-lifting performance in a passerine bird: the effects of intraspecific variation in morphological and kinematic parameters

description: Raw data for article ： “Limits to load-lifting performance in a passerine bird: the effects of intraspecific variation in morphological and kinematic parameters”.
DOI: 10.6084/m9.figshare.9122591.v1
title: Additional file 2: of Cardiac MRI improves cardiovascular risk stratification in hazardous occupations

description: Table S1 â Indication for CMR by frequency of referral. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9122597
title: Additional file 3: of Cardiac MRI improves cardiovascular risk stratification in hazardous occupations

description: Table S2 â Age and gender of referral groups. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9122597.v1
title: Additional file 3: of Cardiac MRI improves cardiovascular risk stratification in hazardous occupations

description: Table S2 â Age and gender of referral groups. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9122606
title: Additional file 5: of Cardiac MRI improves cardiovascular risk stratification in hazardous occupations

description: Table S5 â CMR chamber dimensions for military aircrew cohort. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9122606.v1
title: Additional file 5: of Cardiac MRI improves cardiovascular risk stratification in hazardous occupations

description: Table S5 â CMR chamber dimensions for military aircrew cohort. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9125294
title: Chapitre 2 Supplementary

description: Chapitre 2 Supplementary
DOI: 10.6084/m9.figshare.9125303
title: Reducing INS-IGF1 signaling protects against non-cell autonomous vesicle rupture caused by SNCA spreading

description: Aging is associated with a gradual decline of cellular proteostasis, giving rise to devastating protein misfolding diseases, such as Alzheimer disease (AD) or Parkinson disease (PD). These diseases often exhibit a complex pathology involving non-cell autonomous proteotoxic effects, which are still poorly understood. Using <i>Caenorhabditis elegans</i> we investigated how local protein misfolding is affecting neighboring cells and tissues showing that misfolded PD-associated SNCA/α-synuclein is accumulating in highly dynamic endo-lysosomal vesicles. Irrespective of whether being expressed in muscle cells or dopaminergic neurons, accumulated proteins were transmitted into the hypodermis with increasing age, indicating that epithelial cells might play a role in remote degradation when the local endo-lysosomal degradation capacity is overloaded. Cell biological and genetic approaches revealed that inter-tissue dissemination of SNCA was regulated by endo- and exocytosis (neuron/muscle to hypodermis) and basement membrane remodeling (muscle to hypodermis). Transferred SNCA conformers were, however, inefficiently cleared and induced endo-lysosomal membrane permeabilization. Remarkably, reducing INS (insulin)-IGF1 (insulin-like growth factor 1) signaling provided protection by maintaining endo-lysosomal integrity. This study suggests that the degradation of lysosomal substrates is coordinated across different tissues in metazoan organisms. Because the chronic dissemination of poorly degradable disease proteins into neighboring tissues exerts a non-cell autonomous toxicity, this implies that restoring endo-lysosomal function not only in cells with pathological inclusions, but also in apparently unaffected cell types might help to halt disease progression. <b>Abbreviations</b>: AD: Alzheimer disease; BM: basement membrane; BWM: body wall muscle; CEP: cephalic sensilla; CLEM: correlative light and electron microscopy; CTNS-1: cystinosin (lysosomal protein) homolog; DA: dopaminergic; DAF-2: abnormal dauer formation; ECM: extracellular matrix; FLIM: fluorescence lifetime imaging microscopy; fps: frames per second; GFP: green fluorescent protein; HPF: high pressure freezing; IGF1: insulin-like growth factor 1; INS: insulin; KD: knockdown; LMP: lysosomal membrane permeabilization; MVB: multivesicular body; NOC: nocodazole; PD: Parkinson disease; RFP: red fluorescent protein; RNAi: RNA interference; sfGFP: superfolder GFP; SNCA: synuclein alpha; TEM: transmission electron microscopy; TNTs: tunneling nanotubes; TCSPC: time correlated single photon counting; YFP: yellow fluorescent protein.
DOI: 10.6084/m9.figshare.9125303.v1
title: Reducing INS-IGF1 signaling protects against non-cell autonomous vesicle rupture caused by SNCA spreading

description: Aging is associated with a gradual decline of cellular proteostasis, giving rise to devastating protein misfolding diseases, such as Alzheimer disease (AD) or Parkinson disease (PD). These diseases often exhibit a complex pathology involving non-cell autonomous proteotoxic effects, which are still poorly understood. Using <i>Caenorhabditis elegans</i> we investigated how local protein misfolding is affecting neighboring cells and tissues showing that misfolded PD-associated SNCA/α-synuclein is accumulating in highly dynamic endo-lysosomal vesicles. Irrespective of whether being expressed in muscle cells or dopaminergic neurons, accumulated proteins were transmitted into the hypodermis with increasing age, indicating that epithelial cells might play a role in remote degradation when the local endo-lysosomal degradation capacity is overloaded. Cell biological and genetic approaches revealed that inter-tissue dissemination of SNCA was regulated by endo- and exocytosis (neuron/muscle to hypodermis) and basement membrane remodeling (muscle to hypodermis). Transferred SNCA conformers were, however, inefficiently cleared and induced endo-lysosomal membrane permeabilization. Remarkably, reducing INS (insulin)-IGF1 (insulin-like growth factor 1) signaling provided protection by maintaining endo-lysosomal integrity. This study suggests that the degradation of lysosomal substrates is coordinated across different tissues in metazoan organisms. Because the chronic dissemination of poorly degradable disease proteins into neighboring tissues exerts a non-cell autonomous toxicity, this implies that restoring endo-lysosomal function not only in cells with pathological inclusions, but also in apparently unaffected cell types might help to halt disease progression. <b>Abbreviations</b>: AD: Alzheimer disease; BM: basement membrane; BWM: body wall muscle; CEP: cephalic sensilla; CLEM: correlative light and electron microscopy; CTNS-1: cystinosin (lysosomal protein) homolog; DA: dopaminergic; DAF-2: abnormal dauer formation; ECM: extracellular matrix; FLIM: fluorescence lifetime imaging microscopy; fps: frames per second; GFP: green fluorescent protein; HPF: high pressure freezing; IGF1: insulin-like growth factor 1; INS: insulin; KD: knockdown; LMP: lysosomal membrane permeabilization; MVB: multivesicular body; NOC: nocodazole; PD: Parkinson disease; RFP: red fluorescent protein; RNAi: RNA interference; sfGFP: superfolder GFP; SNCA: synuclein alpha; TEM: transmission electron microscopy; TNTs: tunneling nanotubes; TCSPC: time correlated single photon counting; YFP: yellow fluorescent protein.
DOI: 10.6084/m9.figshare.9125351.v1
title: Chapitre 1 Supplementary

description: Chapitre 1 Supplementary
DOI: 10.6084/m9.figshare.9125390
title: Prevalence of Atrial Fibrillation in Patients with Retinal Vessel Occlusion and Its Association: A Systematic Review and Meta-Analysis

description: <b>Objective</b>: Recent studies have shown that atrial fibrillation (AF) is more prevalent in patients with retinal vessel occlusion and may be associated with both central retinal artery occlusion (CRAO) and central retinal vein occlusion (CRVO). However, there is no systematic review and meta-analysis to confirm this finding. <b>Methods</b>: We searched the databases of MEDLINE and EMBASE from inception to January 2019. Included studies were published cohort, case-control or cross-sectional studies, and randomized control trials reporting the prevalence of AF in patients with CRAO or CRVO. Data from each study were combined using the random-effects model. <b>Results</b>: Eleven studies were included in our meta-analysis, involving a total population of 12,305 subjects with retinal vessel occlusion. The prevalence of AF ranged from 4.1% to 21.4% (pooled prevalence = 11.5%, 95% CI: 7.0–16.1, I<sup>2</sup> = 96.3%). Five studies reported a control group of patients without retinal vessel occlusion. We found that AF is significantly associated with retinal vessel occlusion (pooled OR = 2.24, 95% CI:2.07–2.43, I<sup>2</sup> = 0.0%). <b>Conclusion</b>: Our study showed that AF is significantly associated with retinal vessel occlusion. Further studies are needed to fully elucidate the exact mechanism linking AF with CRAO and CRVO.