cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6850691.v1
title: Mis-splicing and breast cancer: systematic analysis of splicing variants of BRCA2 exons 2-9 by minigene assays

description: Paper minigene BRCA2 exons 2-9"Mis-splicing in breast cancer: identification of pathogenic BRCA2 variants by systematic minigene assays"<b>Abstract </b><br>Splicing disruption is a common mechanism of gene inactivation associated with germline variants of susceptibility genes. To study the role of BRCA2 mis-splicing in hereditary breast/ovarian cancer (HBOC), we performed a comprehensive analysis of variants from BRCA2 exons 2 to 9, as well as the initial characterization of the regulatory mechanisms of such exons. A pSAD-based minigene with exons 2-9 was constructed and validated in MCF-7 cells, producing the expected transcript (1,016-nt/V1-BRCA2_exons_2-9-V2). DNA variants from mutational databases were analyzed by NNSplice and Human Splicing Finder softwares. To refine ESE-variant prediction, we mapped the regulatory regions through a functional strategy whereby 26 exonic microdeletions were introduced into the minigene and tested in MCF-7 cells. Thus, we identified nine spliceogenic ESE-rich intervals where ESE-variants may be located. Combining bioinformatics and microdeletion assays, 83 variants were selected and genetically engineered in the minigene. Fifty-three changes impaired splicing: 28 variants disrupted the canonical sites, four created new ones, 10 abrogated enhancers, eight created silencers and three caused a double-effect. Notably, nine spliceogenic-ESE variants were located within ESE-containing intervals. Capillary electrophoresis and sequencing revealed more than 23 aberrant transcripts, where exon skipping was the most common event. Interestingly, variant c.67G&gt;A triggered the usage of a non-canonical GC-donor 4-nt upstream. Thirty-six variants that induced severe anomalies (&gt;60% aberrant transcripts) were analyzed according to the ACMG guidelines. Thus, 28 variants were classified as pathogenic, five as likely pathogenic and three as variants of uncertain significance. Interestingly, 13 VUS were reclassified as pathogenic or likely pathogenic variants.<br>In conclusion, a large fraction of BRCA2 variants (~64%) provoked splicing anomalies lending further support to the high prevalence of this disease-mechanism. The low accuracy of ESE-prediction algorithms may be circumvented by functional ESE-mapping that represents an optimal strategy to identify spliceogenic ESE-variants. Finally, systematic functional assays by minigenes depict a valuable tool for the initial characterization of splicing anomalies and the clinical interpretation of variants.<br><br>
DOI: 10.6084/m9.figshare.6850676
title: Low-cost agricultural waste accelerates tropical forest regeneration - Costa Rica 2014

description: This .zip file provides all the data and an R Markdown document (written to .html but the original .Rmd is also included) that recreates all of the analyses that went into our 2018 Restoration Ecology Paper entitled <i>Low-cost agricultural waste accelerates tropical forest regeneration</i>. The methods describing how data were collected are available within the paper itself. The data was collected in Guanacaste Province, Costa Rica, in the summer of 2014.
DOI: 10.6084/m9.figshare.6850664
title: Data analysis intermediate results files

description: Intermediate analysis results files for analyses of neural populations in PfC: see GitHub repository link
DOI: 10.6084/m9.figshare.6850664.v1
title: Data analysis intermediate results files

description: Intermediate analysis results files for analyses of neural populations in PfC: see GitHub repository link
DOI: 10.6084/m9.figshare.6850676.v1
title: LowCostAgriculturalWasteAcceleratesTropicalForestRegeneration_CostaRica2014

description: This .zip file provides all the data and an R Markdown document (written to .html but the original .Rmd is also included) that recreates all of the analyses that went into our 2018 Restoration Ecology Paper entitled <i>Low-cost agricultural waste accelerates tropical forest regeneration</i>. The methods describing how data were collected are available within the paper itself.
DOI: 10.6084/m9.figshare.6850676.v2
title: LowCostAgriculturalWasteAcceleratesTropicalForestRegeneration_CostaRica2014

description: This .zip file provides all the data and an R Markdown document (written to .html but the original .Rmd is also included) that recreates all of the analyses that went into our 2018 Restoration Ecology Paper entitled <i>Low-cost agricultural waste accelerates tropical forest regeneration</i>. The methods describing how data were collected are available within the paper itself.
DOI: 10.6084/m9.figshare.6850676.v4
title: Low-cost agricultural waste accelerates tropical forest regeneration - Costa Rica 2014

description: This .zip file provides all the data and an R Markdown document (written to .html but the original .Rmd is also included) that recreates all of the analyses that went into our 2018 Restoration Ecology Paper entitled <i>Low-cost agricultural waste accelerates tropical forest regeneration</i>. The methods describing how data were collected are available within the paper itself. The data was collected in Guanacaste Province, Costa Rica, in the summer of 2014.
DOI: 10.6084/m9.figshare.6850646
title: Jittered data results files

description: Intermediate analysis results files for control analyses using <b>jittered </b>versions of neural population activity in PfC <br>See GitHub repository link
DOI: 10.6084/m9.figshare.6850676.v3
title: Low-cost agricultural waste accelerates tropical forest regeneration

description: This .zip file provides all the data and an R Markdown document (written to .html but the original .Rmd is also included) that recreates all of the analyses that went into our 2018 Restoration Ecology Paper entitled <i>Low-cost agricultural waste accelerates tropical forest regeneration</i>. The methods describing how data were collected are available within the paper itself.
DOI: 10.6084/m9.figshare.6850643
title: Data from: Ecosystem type shapes trophic position and omnivory in fish

description: This file includes global data for fishes compliled from (http://www.fishbase.org). The database included 5,726 species distributed in 53 orders based on three common feeding strategies (herbivory, filter-feeding and predatory).
DOI: 10.6084/m9.figshare.6850646.v1
title: Jittered data results files

description: Intermediate analysis results files for control analyses using <b>jittered </b>versions of neural population activity in PfC <br>See GitHub repository link
DOI: 10.6084/m9.figshare.6850640
title: Diadema antillarum survey data - Panama 2014

description: Data collected by Joshua Hamilton, Jonathan Choi, and Nicole Zenes while affiliated with Princeton University in February 2014. For additional information, contact Jonathan Choi at jonathan.j.choi[at]duke.edu. This document was created on 12 July 2018.We conducted our surveys in February 2014 at three reef sites near Bocas del Toro, Panama (9.33° N, 82.25° W): Coco Key, a backreef site dominated by scleractinian corals and sponges; Coral Key, a backreef site primarily dominated by gorgonian corals and <i>Millepora</i>, and Salt Creek, a forereef site characterized by scleractinian coral dominance including large stands of Acropora. The two backreef sites were characterized by lower wave-action relative to Salt Creek. <i>D. antillarum</i> individuals were present at all sites, despite not sampling <i>D. antillarum</i> in our quadrats at all sites.We placed 30 m line transects on to the reef at random by determining a clock-face direction with the aid of a wristwatch and then placing the transect in the direction using our boat as a reference point. We placed 1 m<sup>2</sup> quadrats every 4 m on alternating sides of the transect line. We counted all <i>Echinometra viridis, E. lucunter</i> (binned as <i>Echinometra spp.</i> for analysis), and <i>D. antillarum</i> individuals within the quadrat. We estimated percent coral, algal, and bare substrate cover by partitioning the quadrat into 100 equal-sized squares with twine and recording the dominant form of substrate within each square. We stratified algal cover into broad functional groups: fleshy macroalgae (e.g. <i>Dictyota spp., Cladophora spp.,</i> etc.), calcareous algae (e.g. <i>Halimeda spp. & Galaxaura spp</i>.), and encrusting coralline algae (e.g. <i>Porolithon spp</i>.). We took the average of percent coral and algal cover estimates of two independent observers in order to minimize personal bias.
DOI: 10.6084/m9.figshare.6850640.v2
title: Diadema antillarum survey data - Panama 2014

description: Data collected by Joshua Hamilton, Jonathan Choi, and Nicole Zenes while affiliated with Princeton University in February 2014. For additional information, contact Jonathan Choi at jonathan.j.choi[at]duke.edu. This document was created on 12 July 2018.We conducted our surveys in February 2014 at three reef sites near Bocas del Toro, Panama (9.33° N, 82.25° W): Coco Key, a backreef site dominated by scleractinian corals and sponges; Coral Key, a backreef site primarily dominated by gorgonian corals and <i>Millepora</i>, and Salt Creek, a forereef site characterized by scleractinian coral dominance including large stands of Acropora. The two backreef sites were characterized by lower wave-action relative to Salt Creek. <i>D. antillarum</i> individuals were present at all sites, despite not sampling <i>D. antillarum</i> in our quadrats at all sites.We placed 30 m line transects on to the reef at random by determining a clock-face direction with the aid of a wristwatch and then placing the transect in the direction using our boat as a reference point. We placed 1 m<sup>2</sup> quadrats every 4 m on alternating sides of the transect line. We counted all <i>Echinometra viridis, E. lucunter</i> (binned as <i>Echinometra spp.</i> for analysis), and <i>D. antillarum</i> individuals within the quadrat. We estimated percent coral, algal, and bare substrate cover by partitioning the quadrat into 100 equal-sized squares with twine and recording the dominant form of substrate within each square. We stratified algal cover into broad functional groups: fleshy macroalgae (e.g. <i>Dictyota spp., Cladophora spp.,</i> etc.), calcareous algae (e.g. <i>Halimeda spp. & Galaxaura spp</i>.), and encrusting coralline algae (e.g. <i>Porolithon spp</i>.). We took the average of percent coral and algal cover estimates of two independent observers in order to minimize personal bias.
DOI: 10.6084/m9.figshare.6850640.v1
title: Diademaantillarum_SurveyData_Panama2014

description: Data collected by Joshua Hamilton, Jonathan Choi, and Nicole Zenes while affiliated with Princeton University in February 2014. For additional information, contact Jonathan Choi at jonathan.j.choi[at]duke.edu. This document was created on 12 July 2018.We conducted our surveys in February 2014 at three reef sites near Bocas del Toro, Panama (9.33° N, 82.25° W): Coco Key, a backreef site dominated by scleractinian corals and sponges; Coral Key, a backreef site primarily dominated by gorgonian corals and <i>Millepora</i>, and Salt Creek, a forereef site characterized by scleractinian coral dominance including large stands of Acropora. The two backreef sites were characterized by lower wave-action relative to Salt Creek. <i>D. antillarum</i> individuals were present at all sites, despite not sampling <i>D. antillarum</i> in our quadrats at all sites.We placed 30 m line transects on to the reef at random by determining a clock-face direction with the aid of a wristwatch and then placing the transect in the direction using our boat as a reference point. We placed 1 m<sup>2</sup> quadrats every 4 m on alternating sides of the transect line. We counted all <i>Echinometra viridis, E. lucunter</i> (binned as <i>Echinometra spp.</i> for analysis), and <i>D. antillarum</i> individuals within the quadrat. We estimated percent coral, algal, and bare substrate cover by partitioning the quadrat into 100 equal-sized squares with twine and recording the dominant form of substrate within each square. We stratified algal cover into broad functional groups: fleshy macroalgae (e.g. <i>Dictyota spp., Cladophora spp.,</i> etc.), calcareous algae (e.g. <i>Halimeda spp. & Galaxaura spp</i>.), and encrusting coralline algae (e.g. <i>Porolithon spp</i>.). We took the average of percent coral and algal cover estimates of two independent observers in order to minimize personal bias.
DOI: 10.6084/m9.figshare.6850643.v1
title: Dataset of the entitled article "Ecosystem type shapes trophic position and omnivory in fish" published in Fish and Fisheries (DOI: 10.1111/faf.12308)

description: This file includes global data for fishes compliled from (http://www.fishbase.org). The database included 5,726 species distributed in 53 orders based on three common feeding strategies (herbivory, filter-feeding and predatory).
DOI: 10.6084/m9.figshare.6850625
title: Dataset for: Elena Butaitė, Jos Kramer, Stefan Wyder and Rolf Kümmerli: Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities. Environmental Microbiology [doi:10.11111462-2920.14355].

description: Data used for statistical analyses and to generate graphs for the paper. A more detailed description is provided in the file.
DOI: 10.6084/m9.figshare.6850625.v1
title: Dataset for: Elena Butaitė, Jos Kramer, Stefan Wyder and Rolf Kümmerli: Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities. Environmental Microbiology [doi:10.11111462-2920.14355].

description: Data used for statistical analyses and to generate graphs for the paper. A more detailed description is provided in the file.
DOI: 10.6084/m9.figshare.6850577
title: Mosaicism in autoinflammatory diseases: Cryopyrin-associated periodic syndromes (CAPS) and beyond. A systematic review

description: Autoinflammatory diseases (AIDs) are conditions related to defective regulation of the innate immune system. Sanger sequencing of the causative genes has long been the reference for confirming the diagnosis. However, for many patients with a typical AID phenotype, the genetic cause remains unknown. A pioneering study in 2005 demonstrated mosaicism in patients with cryopyrin-associated periodic syndromes (CAPS); the authors found somatic mosaicism in 69% of their cohort of Sanger-negative CAPS patients. We aim to address the extent to which mosaicism contributes to the etiology of AIDs and its impact on phenotype. We retrieved English-language publications reporting mosaicism in AIDs by querying PubMed with no restriction on date and we surveyed French reference centers. We provide a comprehensive clinical and genetic picture of mosaicism in AIDs. We estimate that the proportion of CAPS-like patients presenting mosaicism ranges from 0.5% to 19%. We also discuss the possible links between the proportion of mutated alleles and various clinical features. This review reevaluates the contribution of mosaic DNA variants in CAPS. Mosaicism may be more common than anticipated in other AIDs. No significant difference was demonstrated between variant allele frequency and clinical phenotype. Such knowledge has implications for the development of guidelines for genetic diagnosis, genetic counseling of affected families and effective patient care.
DOI: 10.6084/m9.figshare.6850577.v1
title: Mosaicism in autoinflammatory diseases: Cryopyrin-associated periodic syndromes (CAPS) and beyond. A systematic review

description: Autoinflammatory diseases (AIDs) are conditions related to defective regulation of the innate immune system. Sanger sequencing of the causative genes has long been the reference for confirming the diagnosis. However, for many patients with a typical AID phenotype, the genetic cause remains unknown. A pioneering study in 2005 demonstrated mosaicism in patients with cryopyrin-associated periodic syndromes (CAPS); the authors found somatic mosaicism in 69% of their cohort of Sanger-negative CAPS patients. We aim to address the extent to which mosaicism contributes to the etiology of AIDs and its impact on phenotype. We retrieved English-language publications reporting mosaicism in AIDs by querying PubMed with no restriction on date and we surveyed French reference centers. We provide a comprehensive clinical and genetic picture of mosaicism in AIDs. We estimate that the proportion of CAPS-like patients presenting mosaicism ranges from 0.5% to 19%. We also discuss the possible links between the proportion of mutated alleles and various clinical features. This review reevaluates the contribution of mosaic DNA variants in CAPS. Mosaicism may be more common than anticipated in other AIDs. No significant difference was demonstrated between variant allele frequency and clinical phenotype. Such knowledge has implications for the development of guidelines for genetic diagnosis, genetic counseling of affected families and effective patient care.
DOI: 10.6084/m9.figshare.6850571
title: Data.sav

description: This data studies the difference between cardiogenic shock and non cardiogenic shock patients. The patients are divided into these two groups.
DOI: 10.6084/m9.figshare.6850565
title: Shuffled data intermediate results files

description: Intermediate analysis results files for control analyses using <b>shuffled </b>versions of neural population activity in PfC <br>See GitHub repository link
DOI: 10.6084/m9.figshare.6850571.v1
title: Data.sav

description: This data studies the difference between cardiogenic shock and non cardiogenic shock patients. The patients are divided into these two groups.
DOI: 10.6084/m9.figshare.6850565.v1
title: Shuffled data intermediate results files

description: Intermediate analysis results files for control analyses using <b>shuffled </b>versions of neural population activity in PfC <br>See GitHub repository link
DOI: 10.21942/uva.6850535.v1
title: Impersonal reference in Russian Sign Language

description: This is a data set and an Rmd file containing the R script of statistical analysis of the data set which resulted from an acceptability judgment experiment where signers of Russian Sign Language were asked to judge impersonal sentences of different types in three different types of contexts. The results of this experiment are published in the following paper: <br>Kimmelman, V. (2018) Impersonal reference in Russian Sign Language. <i>Sign Language & Linguistics, </i>21(2)<i>. </i>
DOI: 10.6084/m9.figshare.6850448
title: COMMSBIO-18-0374B Fig. 7 slo-1, slo-2, slo-1; slo-2

description: COMMSBIO-18-0374B Fig. 7
DOI: 10.6084/m9.figshare.6850448.v1
title: COMMSBIO-18-0374B Fig. 7 slo-1, slo-2, slo-1; slo-2

description: COMMSBIO-18-0374B Fig. 7
DOI: 10.21942/uva.6850298.v1
title: Iconicity Patterns in Sign Languages

description: This is a database containing 1542 signs from 19 signs languages in 7 semantic fields annotated according to several iconicity features. Please see the website link below for all the details, or read the following paper describing the database: <br>Kimmelman, V., Klezovich, A., & Moroz, G. (2018). IPSL: A Database of Iconicity Patterns in Sign Languages. Creation and Use. In Proceedings of the Eleventh International Conference on Language Resources and Evaluation (LREC 2018) (pp. 4230-4234). ELRA. URL: http://www.lrec-conf.org/proceedings/lrec2018/summaries/102.html <br>
DOI: 10.6084/m9.figshare.6850271.v1
title: lherm_basilisk_stretching

description: Basilisk code investigating chemical/thermal equilibration and separation between metal and silicates during core formation.We focus on stretched sheets, stretched ligaments, and falling drops.We solve the incompressible Navier-Stokes equations in a 2D two-phase flow on an adaptative Cartesian mesh. The two-phase flow is implemented using a level-set method. The interface is computed with a VOF scheme and we compute surface tension with the curvature of the interface.<br>Main solver is available at basilisk.fr. Information on compilation are available at the same adress.
DOI: 10.5281/zenodo.4006485
title: SGB.Jan20

description: PhyloPhlAn metagenomic database "SGB.Jan20"
DOI: 10.5281/zenodo.4006484
title: SGB.Jan20

description: PhyloPhlAn metagenomic database "SGB.Jan20"
DOI: 10.6084/m9.figshare.6850145
title: Management and outcomes of 27 pregnancies in women with myeloproliferative neoplasms

description: <b>Introduction:</b> Philadelphia-negative myeloproliferative neoplasms (MPNs) greatly increase the risk of maternal and fetal complications during pregnancy. Currently, international agreements regarding the management of these women are lacking. <b>Patients and methods:</b> Our study aimed to assess the current management and outcomes of MPN pregnancies in a French cohort. We retrospectively analyzed 27 pregnancies in women with MPNs that were associated with a specific mutation. Nineteen pregnancies in nine women with essential thrombocythemia and eight pregnancies in five women with polycythemia vera were identified. <b>Results:</b> Our study showed 70% live births, but only 30% uneventful pregnancies. Fetal complications were mainly early spontaneous abortions (22%), fetal growth restriction (15%), and premature delivery (15%). Maternal issues were divided between thrombosis (15%) and hemorrhages (11%). High rates of preeclampsia and hemolysis, elevated liver enzymes, and low platelet count syndrome (15%) were reported. Uterine artery Doppler was performed in 70% pregnancies. Abnormal Doppler results were found in 43% pregnancies. Pregnancies with high platelet counts and packed cell volume remaining static or increasing ended with fetal death and utero-placental dysfunction. According to expert consensus, most of the pregnancies (67%) could be stratified in the high risk group and had a bad obstetrical outcome, with 50% standard-risk pregnancies versus 22% high-risk pregnancies that were uneventful. Higher risk pregnancies were prescribed heparin and/or interferon α in 72%. <b>Conclusions:</b> The prognosis of these pregnancies remains very bad and may be improved by a more effective collaboration between specialists as well as a therapeutic intensification including heparin and interferon α.
DOI: 10.6084/m9.figshare.6850145.v1
title: Management and outcomes of 27 pregnancies in women with myeloproliferative neoplasms

description: <b>Introduction:</b> Philadelphia-negative myeloproliferative neoplasms (MPNs) greatly increase the risk of maternal and fetal complications during pregnancy. Currently, international agreements regarding the management of these women are lacking. <b>Patients and methods:</b> Our study aimed to assess the current management and outcomes of MPN pregnancies in a French cohort. We retrospectively analyzed 27 pregnancies in women with MPNs that were associated with a specific mutation. Nineteen pregnancies in nine women with essential thrombocythemia and eight pregnancies in five women with polycythemia vera were identified. <b>Results:</b> Our study showed 70% live births, but only 30% uneventful pregnancies. Fetal complications were mainly early spontaneous abortions (22%), fetal growth restriction (15%), and premature delivery (15%). Maternal issues were divided between thrombosis (15%) and hemorrhages (11%). High rates of preeclampsia and hemolysis, elevated liver enzymes, and low platelet count syndrome (15%) were reported. Uterine artery Doppler was performed in 70% pregnancies. Abnormal Doppler results were found in 43% pregnancies. Pregnancies with high platelet counts and packed cell volume remaining static or increasing ended with fetal death and utero-placental dysfunction. According to expert consensus, most of the pregnancies (67%) could be stratified in the high risk group and had a bad obstetrical outcome, with 50% standard-risk pregnancies versus 22% high-risk pregnancies that were uneventful. Higher risk pregnancies were prescribed heparin and/or interferon α in 72%. <b>Conclusions:</b> The prognosis of these pregnancies remains very bad and may be improved by a more effective collaboration between specialists as well as a therapeutic intensification including heparin and interferon α.