cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5961997
title: Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of <i>Pseudomonas aeruginosa</i> and <i>Candida albicans</i>

description: Experimental incapacity to track microbe–microbe interactions in structures like biofilms, and the complexity inherent to the mathematical modelling of those interactions, raises the need for feasible, alternative modelling approaches. This work proposes an agent-based representation of the diffusion of N-acyl homoserine lactones (AHL) in a multicellular environment formed by <i>Pseudomonas aeruginosa</i> and <i>Candida albicans</i>. Depending on the spatial location, <i>C. albicans</i> cells were variably exposed to AHLs, an observation that might help explain why phenotypic switching of individual cells in biofilms occurred at different time points. The simulation and algebraic results were similar for simpler scenarios, although some statistical differences could be observed (<i>p </i>&lt;<i> </i>0.05). The model was also successfully applied to a more complex scenario representing a small multicellular environment containing <i>C. albicans</i> and <i>P. aeruginosa</i> cells encased in a 3-D matrix. Further development of this model may help create a predictive tool to depict biofilm heterogeneity at the single-cell level.
DOI: 10.6084/m9.figshare.5961997.v1
title: Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of <i>Pseudomonas aeruginosa</i> and <i>Candida albicans</i>

description: Experimental incapacity to track microbe–microbe interactions in structures like biofilms, and the complexity inherent to the mathematical modelling of those interactions, raises the need for feasible, alternative modelling approaches. This work proposes an agent-based representation of the diffusion of N-acyl homoserine lactones (AHL) in a multicellular environment formed by <i>Pseudomonas aeruginosa</i> and <i>Candida albicans</i>. Depending on the spatial location, <i>C. albicans</i> cells were variably exposed to AHLs, an observation that might help explain why phenotypic switching of individual cells in biofilms occurred at different time points. The simulation and algebraic results were similar for simpler scenarios, although some statistical differences could be observed (<i>p </i>&lt;<i> </i>0.05). The model was also successfully applied to a more complex scenario representing a small multicellular environment containing <i>C. albicans</i> and <i>P. aeruginosa</i> cells encased in a 3-D matrix. Further development of this model may help create a predictive tool to depict biofilm heterogeneity at the single-cell level.
DOI: 10.6084/m9.figshare.5961031
title: nifH-based community metrics fail to predict benthic nitrogen fixation rates

description: data acompanying the article "nifH-based community metrics fail to predict benthic nitrogen fixation rates". <br>preprint here: https://peerj.com/manuscripts/17768/
DOI: 10.6084/m9.figshare.5960992
title: Supplementary Material for: Clinical and Biomarker Evaluations of Sunitinib in Patients with Grade 3 Digestive Neuroendocrine Neoplasms

description: <b><i>Background/Aims:</i></b> Angiogenesis is extensively developed in well-differentiated pancreatic neuroendocrine tumours (PanNET) where sunitinib was shown to prolong progression-free survival, leading to nationwide approval. However, clinical experience in patients with grade 3 gastroenteropancreatic neuroendocrine neoplasms (GEPNEN-G3) remains limited. This prospective phase II trial evaluated potential predictive biomarkers of sunitinib activity in patients with advanced GEPNEN-G3. <b><i>Methods:</i></b> Sunitinib was given at a dose of 37.5 mg/day as a continuous daily dosing until progression or unacceptable toxicity. Evaluation of activity was based on RECIST1.1. Safety was evaluated according to NCI-CTCAE v4. Pharmacokinetics of sunitinib and its main active metabolite SU12662 were evaluated. All tumour samples were reviewed histologically for tumour differentiation. PDGFRβ, carbonic anhydrase 9, Ki-67, VEGFR2, and p-AKT were quantified using immunohistochemistry and their expression correlated with response by RECIST1.1. <b><i>Results:</i></b> Thirty-one patients were included and 26 had available histological tissue. Six and 20 patients presented well-differentiated tumours (NET-G3) and neuroendocrine carcinoma (NEC), respectively. Eighteen patients responded to sunitinib (4 experienced partial responses and 14 tumour stabilization). A high p-AKT expression correlated with lower response to sunitinib (OR 0.94, 95% CI 0.89–0.99, <i>p</i> = 0.04). Safety and PK exposure to sunitinib and SU12662 in these patients were consistent with that reported in PanNET. <b><i>Conclusion:</i></b> Sunitinib showed evidence of activity in patients with GEPNEN-G3 with expected toxicity profile. In the NET-G3 and NEC groups, 4/6 and 11/20 patients were responders, respectively. High p-AKT expression predicted a lower response to sunitinib. Our study allowed the identification of a potential biomarker of resistance/sensitivity to sunitinib in aggressive GEPNEN-G3.
DOI: 10.6084/m9.figshare.5960992.v1
title: Supplementary Material for: Clinical and Biomarker Evaluations of Sunitinib in Patients with Grade 3 Digestive Neuroendocrine Neoplasms

description: <b><i>Background/Aims:</i></b> Angiogenesis is extensively developed in well-differentiated pancreatic neuroendocrine tumours (PanNET) where sunitinib was shown to prolong progression-free survival, leading to nationwide approval. However, clinical experience in patients with grade 3 gastroenteropancreatic neuroendocrine neoplasms (GEPNEN-G3) remains limited. This prospective phase II trial evaluated potential predictive biomarkers of sunitinib activity in patients with advanced GEPNEN-G3. <b><i>Methods:</i></b> Sunitinib was given at a dose of 37.5 mg/day as a continuous daily dosing until progression or unacceptable toxicity. Evaluation of activity was based on RECIST1.1. Safety was evaluated according to NCI-CTCAE v4. Pharmacokinetics of sunitinib and its main active metabolite SU12662 were evaluated. All tumour samples were reviewed histologically for tumour differentiation. PDGFRβ, carbonic anhydrase 9, Ki-67, VEGFR2, and p-AKT were quantified using immunohistochemistry and their expression correlated with response by RECIST1.1. <b><i>Results:</i></b> Thirty-one patients were included and 26 had available histological tissue. Six and 20 patients presented well-differentiated tumours (NET-G3) and neuroendocrine carcinoma (NEC), respectively. Eighteen patients responded to sunitinib (4 experienced partial responses and 14 tumour stabilization). A high p-AKT expression correlated with lower response to sunitinib (OR 0.94, 95% CI 0.89–0.99, <i>p</i> = 0.04). Safety and PK exposure to sunitinib and SU12662 in these patients were consistent with that reported in PanNET. <b><i>Conclusion:</i></b> Sunitinib showed evidence of activity in patients with GEPNEN-G3 with expected toxicity profile. In the NET-G3 and NEC groups, 4/6 and 11/20 patients were responders, respectively. High p-AKT expression predicted a lower response to sunitinib. Our study allowed the identification of a potential biomarker of resistance/sensitivity to sunitinib in aggressive GEPNEN-G3.
DOI: 10.6084/m9.figshare.5960929
title: Presentation on shortest path calculations for two data sets from Metabolights repository.

description: Presentation for the DeNBI WINTERSCHOOL 2018 on the shortest path analysis for two data sets on metabolites from the Metabolights repository, using Cytoscape and Neo4j.
DOI: 10.6084/m9.figshare.5960929.v1
title: Presentation on shortest path calculations for two data sets from Metabolights repository.

description: Presentation for the DeNBI WINTERSCHOOL 2018 on the shortest path analysis for two data sets on metabolites from the Metabolights repository, using Cytoscape and Neo4j.
DOI: 10.6084/m9.figshare.5960926
title: DNA barcoding evaluation and implications for phylogenetic relationships in ladybird beetles (Coleoptera: Coccinellidae)

description: Ladybird beetles (Coleoptera: Coccinellidae), with broad morphological diversity, wide geographic distribution and substantial agricultural significance, are a challenging group for taxonomists and phylogenetics. As a promising tool to identify and discover new species, DNA barcoding might offer significant potential for identification, taxonomy and phylogeny of ladybird beetles. In the present study, a total of 1364 COI (cytochrome C oxidase subunit I) sequences representing 128 species from 52 genera of ladybird beetles were screened for barcoding evaluation and phylogenetic analysis. Our results from the barcoding analysis revealed that COI displays a similar level of species identification efficiency (nearly 90%) either based on Kimura two-parameter (K2P) distances calculation or on simplified neighbour-joining (NJ) tree construction. The phylogenetic relationships within the family Coccinellidae was analyzed by Bayesian-inference (BI) method. The phylogenetic results confirmed the monophyly of the subfamilies Microweisinae and Coccinellinae <i>sensu</i> Ślipiński (2007), and suggested that the subfamilies Coccidulinae, Chilocorinae and Scymninae are paraphyletic. However, the phylogenetic relationships among different subfamilies are not clearly defined and thus remain to be thoroughly studied. Overall, our study confirmed the usefulness of DNA barcoding for coccinellid species identification and phylogenetic inference.
DOI: 10.6084/m9.figshare.5960926.v1
title: DNA barcoding evaluation and implications for phylogenetic relationships in ladybird beetles (Coleoptera: Coccinellidae)

description: Ladybird beetles (Coleoptera: Coccinellidae), with broad morphological diversity, wide geographic distribution and substantial agricultural significance, are a challenging group for taxonomists and phylogenetics. As a promising tool to identify and discover new species, DNA barcoding might offer significant potential for identification, taxonomy and phylogeny of ladybird beetles. In the present study, a total of 1364 COI (cytochrome C oxidase subunit I) sequences representing 128 species from 52 genera of ladybird beetles were screened for barcoding evaluation and phylogenetic analysis. Our results from the barcoding analysis revealed that COI displays a similar level of species identification efficiency (nearly 90%) either based on Kimura two-parameter (K2P) distances calculation or on simplified neighbour-joining (NJ) tree construction. The phylogenetic relationships within the family Coccinellidae was analyzed by Bayesian-inference (BI) method. The phylogenetic results confirmed the monophyly of the subfamilies Microweisinae and Coccinellinae <i>sensu</i> Ślipiński (2007), and suggested that the subfamilies Coccidulinae, Chilocorinae and Scymninae are paraphyletic. However, the phylogenetic relationships among different subfamilies are not clearly defined and thus remain to be thoroughly studied. Overall, our study confirmed the usefulness of DNA barcoding for coccinellid species identification and phylogenetic inference.
DOI: 10.6084/m9.figshare.5960923
title: Neither barriers nor refugia explain genetic structure in a major biogeographic break: phylogeography of praying mantises in the Brazilian Atlantic Forest

description: The Atlantic Forest is one of the world’s top biodiversity hotspots, but the diversification processes of its biota are still poorly known, with competing models attributing dominant roles to either Quaternary climatic changes or geographic barriers. Many studies identify the Doce river as a major phylogeographic break, but the reasons for this phenomenon are highly debated. Here we test the predictions of the refugial and barrier models for a common species of praying mantis, <i>Miobantia fuscata</i>, focusing in the areas immediately south and north of the Doce river. Our analyses show high intraspecific genetic diversity, deep coalescence times and no evidence for recent population expansion. Phylogeographic structure is inconsistent with a refugial hypothesis. Significant gene flow between northern and southern populations also conflicts with a strong role for geographic barriers. This study highlights the need for considering invertebrate taxa to infer recent landscape changes, and points towards a more complex picture of genetic diversification in the Atlantic Forest.
DOI: 10.6084/m9.figshare.5960923.v2
title: Neither barriers nor refugia explain genetic structure in a major biogeographic break: phylogeography of praying mantises in the Brazilian Atlantic Forest

description: The Atlantic Forest is one of the world’s top biodiversity hotspots, but the diversification processes of its biota are still poorly known, with competing models attributing dominant roles to either Quaternary climatic changes or geographic barriers. Many studies identify the Doce river as a major phylogeographic break, but the reasons for this phenomenon are highly debated. Here we test the predictions of the refugial and barrier models for a common species of praying mantis, <i>Miobantia fuscata</i>, focusing in the areas immediately south and north of the Doce river. Our analyses show high intraspecific genetic diversity, deep coalescence times and no evidence for recent population expansion. Phylogeographic structure is inconsistent with a refugial hypothesis. Significant gene flow between northern and southern populations also conflicts with a strong role for geographic barriers. This study highlights the need for considering invertebrate taxa to infer recent landscape changes, and points towards a more complex picture of genetic diversification in the Atlantic Forest.
DOI: 10.6084/m9.figshare.5960923.v1
title: Neither barriers nor refugia explain genetic structure in a major biogeographic break: phylogeography of praying mantises in the Brazilian Atlantic Forest

description: The Atlantic Forest is one of the world’s top biodiversity hotspots, but the diversification processes of its biota are still poorly known, with competing models attributing dominant roles to either Quaternary climatic changes or geographic barriers. Many studies identify the Doce river as a major phylogeographic break, but the reasons for this phenomenon are highly debated. Here we test the predictions of the refugial and barrier models for a common species of praying mantis, <i>Miobantia fuscata</i>, focusing in the areas immediately south and north of the Doce river. Our analyses show high intraspecific genetic diversity, deep coalescence times and no evidence for recent population expansion. Phylogeographic structure is inconsistent with a refugial hypothesis. Significant gene flow between northern and southern populations also conflicts with a strong role for geographic barriers. This study highlights the need for considering invertebrate taxa to infer recent landscape changes, and points towards a more complex picture of genetic diversification in the Atlantic Forest.
DOI: 10.6084/m9.figshare.5960920
title: Supplementary Material for: The International Caries Detection and Assessment System – ICDAS: A Systematic Review

description: The aims of this study were: (1) to evaluate the overall reproducibility and accuracy of the International Caries Detection and Assessment System (ICDAS) for assessing coronal caries lesions, and (2) to investigate the use of systems associated with the ICDAS for activity assessment of coronal caries lesions. Specific search strategies were adopted to identify studies published up to 2016. For the<sup></sup> first objective, we selected studies that assessed primary coronal caries lesions using the ICDAS as a reference standard. A total of 54 studies were included. Meta-analyses summarized the results concerning reproducibility and accuracy (correlation with histology, summary ROC curves [SROC], and diagnostic odds ratio [DOR]). The latter 2 were expressed at D1/D3 levels. The heterogeneity of the studies was also assessed. Reproducibility values (pooled) were &gt; 0.65. The ICDAS mostly presented a good overall performance as most areas under SROC were &gt; 0.75 at D1 and &gt; 0.90 at D3; DOR ≥6. For the<sup></sup> second objective, we selected studies investigating activity assessment associated with the ICDAS. The meta-analyses pooled results based on the same methodology and parameters as above. Longitudinal findings regarding caries progression were described to estimate the validity of these systems. On average, the systems for activity assessment of caries lesions showed moderate values concerning reproducibility and overall performance. Active caries lesions were more prone to progress than inactive ones after 2 years. In conclusion, the ICDAS presented a substantial level of reproducibility and accuracy for assessing primary coronal caries lesions. Additional systems associated with the ICDAS that classify caries lesion activity can be useful as they are moderately reproducible and accurate.
DOI: 10.6084/m9.figshare.5960920.v1
title: Supplementary Material for: The International Caries Detection and Assessment System – ICDAS: A Systematic Review

description: The aims of this study were: (1) to evaluate the overall reproducibility and accuracy of the International Caries Detection and Assessment System (ICDAS) for assessing coronal caries lesions, and (2) to investigate the use of systems associated with the ICDAS for activity assessment of coronal caries lesions. Specific search strategies were adopted to identify studies published up to 2016. For the<sup></sup> first objective, we selected studies that assessed primary coronal caries lesions using the ICDAS as a reference standard. A total of 54 studies were included. Meta-analyses summarized the results concerning reproducibility and accuracy (correlation with histology, summary ROC curves [SROC], and diagnostic odds ratio [DOR]). The latter 2 were expressed at D1/D3 levels. The heterogeneity of the studies was also assessed. Reproducibility values (pooled) were &gt; 0.65. The ICDAS mostly presented a good overall performance as most areas under SROC were &gt; 0.75 at D1 and &gt; 0.90 at D3; DOR ≥6. For the<sup></sup> second objective, we selected studies investigating activity assessment associated with the ICDAS. The meta-analyses pooled results based on the same methodology and parameters as above. Longitudinal findings regarding caries progression were described to estimate the validity of these systems. On average, the systems for activity assessment of caries lesions showed moderate values concerning reproducibility and overall performance. Active caries lesions were more prone to progress than inactive ones after 2 years. In conclusion, the ICDAS presented a substantial level of reproducibility and accuracy for assessing primary coronal caries lesions. Additional systems associated with the ICDAS that classify caries lesion activity can be useful as they are moderately reproducible and accurate.
DOI: 10.6084/m9.figshare.5960917
title: Data_Automatic Classification of Children with Autism Spectrum Disorder by Using a Computerized Visual Orienting Task

description: Data for paper Automatic Classification of Children with Autism Spectrum Disorder by Using a Computerized Visual Orienting Task<br> <br>
DOI: 10.6084/m9.figshare.5960896
title: Functional annotations

description: Functional annotations (InterProScan 5) of the dinoflagellates protein coding domains predicted with TransDecoder
DOI: 10.6084/m9.figshare.5960896.v1
title: Functional annotations

description: Functional annotations (InterProScan 5) of the dinoflagellates protein coding domains predicted with TransDecoder
DOI: 10.6084/m9.figshare.5960890
title: Protein coding domains

description: Protein coding domains from de novo assembled (Trinity) dinoflagellates Transcriptomes
DOI: 10.6084/m9.figshare.5960890.v1
title: Protein coding domains

description: Protein coding domains from de novo assembled (Trinity) dinoflagellates Transcriptomes
DOI: 10.6084/m9.figshare.5960881
title: Self-amplifying feedbacks accelerate greening and warming of the Arctic

description: These data sets are supported for the paper submitted to the journal Geophysical Research Letters.
DOI: 10.6084/m9.figshare.5960881.v1
title: Self-amplifying feedbacks accelerate greening and warming of the Arctic

description: These data sets are supported for the paper submitted to the journal Geophysical Research Letters.
DOI: 10.6084/m9.figshare.5960878
title: QSAR classification and regression models for β-secretase inhibitors using relative distance matrices

description: The development of robust QSAR models to predict the activity of molecules of β-secretase inhibitors is an area of interest due to the increase of Alzheimer’s disease in patients in the global population. In this paper, we present a proposal based on the use of relative distance matrices as input data to the QSAR algorithms. These matrices store measurements of distances between the structural characteristics of pairs of molecules and between the molecules and a structural pattern extracted from the whole data set, thus efficiently representing a correlation between structural changes and activity. For the building of the classification and regression models support vector machine, tree complex and Gaussian process algorithms have been used; and for the validation of the models cross-validation, bootstrapping and <i>y</i>-randomizing techniques have been applied. The results obtained are close to 100% in accuracy and area under receiver operating characteristic values in classification, and close to 1.0 for <i>r</i> <sup>2</sup> and 0.1 for root mean square error in regression in training and in external validation, proving the ‘goodness’ of the proposal.
DOI: 10.6084/m9.figshare.5960737
title: Additional file 5: of Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

description: Hepatic expression of ACACA, C19H17orf78, DUSP14, AATF and SYNRG for female layers (n = 40). RNAseq data are normalized by the classical rpkm method (Chickstress Project – ANR-13-ADAP). (XLSX 54 kb)
DOI: 10.6084/m9.figshare.5960737.v1
title: Additional file 5: of Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

description: Hepatic expression of ACACA, C19H17orf78, DUSP14, AATF and SYNRG for female layers (n = 40). RNAseq data are normalized by the classical rpkm method (Chickstress Project – ANR-13-ADAP). (XLSX 54 kb)
DOI: 10.6084/m9.figshare.5960719
title: Additional file 4 of Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

description: DEG in liver between the two diets and some features. Array_FC and Array_Pvalue provide the HF/LF expression ratio and the p-value adjusted for the multiple test obtained with the microarray technology. qPCR_FC and qPCR_Pvalue provide the HF/LF expression ratio and the p-value obtained with the RT-qPCR technology. (XLSX 70Â kb)
DOI: 10.6084/m9.figshare.5960719.v1
title: Additional file 4 of Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

description: DEG in liver between the two diets and some features. Array_FC and Array_Pvalue provide the HF/LF expression ratio and the p-value adjusted for the multiple test obtained with the microarray technology. qPCR_FC and qPCR_Pvalue provide the HF/LF expression ratio and the p-value obtained with the RT-qPCR technology. (XLSX 70Â kb)