cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6448895
title: Additional file 4: of MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization

description: Final module list. This is the refined module list after removing irrelevant genes. (TXT 2736Â kb)
DOI: 10.6084/m9.figshare.6448895.v1
title: Additional file 4: of MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization

description: Final module list. This is the refined module list after removing irrelevant genes. (TXT 2736Â kb)
DOI: 10.6084/m9.figshare.6448892
title: MOESM4 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 4: Table S1. Genes in Group I-IV; List of genes with number of GATC fragments within the presumptive regulatory region (2.5 kb upstream to 1.5 kb downstream of the transcriptional start sites (TSS)) displaying transitions between Pc-binding states (gain, loss or no-change transition between enriched, intermediate and depleted HMM states) in scrib1 if compared to WT profiles, and changes in gene expression levels of the respective gene in scrib1 to whose TSS the taGATC fragments had been mapped to. Group I (RNA – up regulated; Pc binding – gain); group II (RNA – down regulated; Pc binding – gain); group III (RNA – up regulated; Pc binding – loss); group IV (RNA – down regulated; Pc binding – loss); m1 (RNA – down regulated; Pc binding – loss and gain); m2 (RNA – up regulated; Pc binding – loss and gain).
DOI: 10.6084/m9.figshare.6448892.v2
title: MOESM4 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 4: Table S1. Genes in Group I-IV; List of genes with number of GATC fragments within the presumptive regulatory region (2.5 kb upstream to 1.5 kb downstream of the transcriptional start sites (TSS)) displaying transitions between Pc-binding states (gain, loss or no-change transition between enriched, intermediate and depleted HMM states) in scrib1 if compared to WT profiles, and changes in gene expression levels of the respective gene in scrib1 to whose TSS the taGATC fragments had been mapped to. Group I (RNA – up regulated; Pc binding – gain); group II (RNA – down regulated; Pc binding – gain); group III (RNA – up regulated; Pc binding – loss); group IV (RNA – down regulated; Pc binding – loss); m1 (RNA – down regulated; Pc binding – loss and gain); m2 (RNA – up regulated; Pc binding – loss and gain).
DOI: 10.6084/m9.figshare.6448892.v1
title: MOESM4 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 4: Table S1. Genes in Group I-IV; List of genes with number of GATC fragments within the presumptive regulatory region (2.5 kb upstream to 1.5 kb downstream of the transcriptional start sites (TSS)) displaying transitions between Pc-binding states (gain, loss or no-change transition between enriched, intermediate and depleted HMM states) in scrib 1 if compared to WT profiles, and changes in gene expression levels of the respective gene in scrib 1 to whose TSS the taGATC fragments had been mapped to. Group I (RNA – up regulated; Pc binding – gain); group II (RNA – down regulated; Pc binding – gain); group III (RNA – up regulated; Pc binding – loss); group IV (RNA – down regulated; Pc binding – loss); m1 (RNA – down regulated; Pc binding – loss and gain); m2 (RNA – up regulated; Pc binding – loss and gain).
DOI: 10.6084/m9.figshare.6448886
title: Additional file 13: of Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

description: Table S10. NGS sequencing of patient #3.Â (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6448886.v1
title: Additional file 13: of Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

description: Table S10. NGS sequencing of patient #3.Â (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6448874
title: Additional file 3: of MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization

description: Breast-Cancer-Gene. This is the known breast cancer-related genes downloaded from SNP4Disease. (TXT 2Â kb)
DOI: 10.6084/m9.figshare.6448874.v1
title: Additional file 3: of MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization

description: Breast-Cancer-Gene. This is the known breast cancer-related genes downloaded from SNP4Disease. (TXT 2Â kb)
DOI: 10.6084/m9.figshare.6448868
title: MOESM3 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 3: SF3. WIG file containing the results of the three-state HMM analysis of scrib1 wing imaginal discs for all GATC fragment mapped on dm6 genome annotation. The following values were attributed to the three states: enriched = 1, intermediate = 0, depleted = â 1.
DOI: 10.6084/m9.figshare.6448868.v2
title: MOESM3 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 3: SF3. WIG file containing the results of the three-state HMM analysis of scrib1 wing imaginal discs for all GATC fragment mapped on dm6 genome annotation. The following values were attributed to the three states: enriched = 1, intermediate = 0, depleted = â 1.
DOI: 10.6084/m9.figshare.6448868.v1
title: MOESM3 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 3: SF3. WIG file containing the results of the three-state HMM analysis of scrib 1 wing imaginal discs for all GATC fragment mapped on dm6 genome annotation. The following values were attributed to the three states: enriched = 1, intermediate = 0, depleted = â 1.
DOI: 10.6084/m9.figshare.6448859
title: Additional file 2: of MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization

description: GSEA gene module. This file is all the gene modules downloaded from GSEA website. (TXT 2837Â kb)
DOI: 10.6084/m9.figshare.6448859.v1
title: Additional file 2: of MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization

description: GSEA gene module. This file is all the gene modules downloaded from GSEA website. (TXT 2837Â kb)
DOI: 10.6084/m9.figshare.6448841
title: MOESM2 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 2: SF2. Â WIG file containing the results of the three-state HMM analysis of wild type wing imaginal discs in late third instar stage for all GATC fragment mapped on dm6 genome annotation. The following values were attributed to the three states: enriched = 1, intermediate = 0, depleted = â 1.
DOI: 10.6084/m9.figshare.6448841.v2
title: MOESM2 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 2: SF2. Â WIG file containing the results of the three-state HMM analysis of wild type wing imaginal discs in late third instar stage for all GATC fragment mapped on dm6 genome annotation. The following values were attributed to the three states: enriched = 1, intermediate = 0, depleted = â 1.
DOI: 10.6084/m9.figshare.6448841.v1
title: MOESM2 of DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis

description: Additional file 2: SF2. Â WIG file containing the results of the three-state HMM analysis of wild type wing imaginal discs in late third instar stage for all GATC fragment mapped on dm6 genome annotation. The following values were attributed to the three states: enriched = 1, intermediate = 0, depleted = â 1.
DOI: 10.6084/m9.figshare.6448835
title: Additional file 11: of Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

description: Table S8. Weights of the 9 genes signature.Â (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6448835.v1
title: Additional file 11: of Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma

description: Table S8. Weights of the 9 genes signature.Â (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6448814
title: Additional file 10: of De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

description: SNPs_Japan_vs_Pmnk6_CPP27_China. High-confidence single nucleotide polymorphisms among kudzu accessions from Japan (reference: Ref) and reads from US kudzu (Pmnk6 and CPP27) and China (variants: Var). Abbreviations as described for Additional file 6. (XLSX 30817 kb)
DOI: 10.6084/m9.figshare.6448814.v1
title: Additional file 10: of De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

description: SNPs_Japan_vs_Pmnk6_CPP27_China. High-confidence single nucleotide polymorphisms among kudzu accessions from Japan (reference: Ref) and reads from US kudzu (Pmnk6 and CPP27) and China (variants: Var). Abbreviations as described for Additional file 6. (XLSX 30817 kb)
DOI: 10.6084/m9.figshare.6448631
title: Temperature data

description: Temperature of the sphere and ambient liquid water are contained within the files for each experimental trial. <br><b>Data from experiments using a rough sphere: </b>RO1-temperature.csv, RO2-temperature.csv, RO3-temperature.csv, and RO4-temperature.csv<br><br><b>Data from experiments using a smooth sphere: </b>SM2-temperature.csv, SM3-temperature.csv, SM4-temperature.csv, and SM5-temperature.csv<br><br><b>Data from experiments using a thermoprobe: </b>TP1-temperature.csv, TP2-temperature.csv, and TP3-temperature.csv
DOI: 10.6084/m9.figshare.6448568
title: Three-Dimensional Determination of Superposed Helical Wires Constraint Ability

description: Abstract A three-dimensional theoretical model for predicting the maximum force sustained by a flexible line wound around a rigid cylindrical body is developed based on Clebsch-Kirchhoff equilibrium equations, considering its bending rigidity, no sliding, modified non-linear frictional law in terms of stress and an external pressure exerted on the line. Likewise, this model is extended to solve the constraint problem of superposed counter wound helical wires. Results given by 4th order Runge-Kutta numerical algorithm show that, except for the line thickness, the constraint ability grows with an increase of other geometric parameters and external pressure. However, it cannot be significantly enhanced by applying external pressure for large initial forces, especially when there is an initial binormal force.
DOI: 10.6084/m9.figshare.6448568.v1
title: Three-Dimensional Determination of Superposed Helical Wires Constraint Ability

description: Abstract A three-dimensional theoretical model for predicting the maximum force sustained by a flexible line wound around a rigid cylindrical body is developed based on Clebsch-Kirchhoff equilibrium equations, considering its bending rigidity, no sliding, modified non-linear frictional law in terms of stress and an external pressure exerted on the line. Likewise, this model is extended to solve the constraint problem of superposed counter wound helical wires. Results given by 4th order Runge-Kutta numerical algorithm show that, except for the line thickness, the constraint ability grows with an increase of other geometric parameters and external pressure. However, it cannot be significantly enhanced by applying external pressure for large initial forces, especially when there is an initial binormal force.
DOI: 10.6084/m9.figshare.6448562
title: POLYSACCHARIDE-BASED NANOCOMPOSITE HYDROGELS WITH ZEOLITE: EVALUATION OF THE SORPTION PROCESS OF PESTICIDE PARAQUAT

description: In this work, nanocomposites formed from the natural polymer carboxymethylcellulose in combination with the polyacrylamide polymer and zeolite were obtained and characterized in relation to pesticide sorption capability. Hydrogels are three-dimensional network with large capacity of water or biological fluid adsorption. They have biocompatibility, biodegradability and non-toxicity properties, ensuring this class of polymers is widely used in different agriculture fields. Thus, the objective of the work was to investigate the process of paraquat sorption using a novel biodegradable nanocomposite. By mathematical modeling, it was possible to found that better models were the Freundlich-Langmuir isotherm and pseudosecond order kinetic, indicating that sorption is heterogeneous and similar to chemisorption process. Thus, such nanocomposites have great potential to be applied as an adsorbent material for removal of pesticides from contaminated water.
DOI: 10.6084/m9.figshare.6448562.v1
title: POLYSACCHARIDE-BASED NANOCOMPOSITE HYDROGELS WITH ZEOLITE: EVALUATION OF THE SORPTION PROCESS OF PESTICIDE PARAQUAT

description: In this work, nanocomposites formed from the natural polymer carboxymethylcellulose in combination with the polyacrylamide polymer and zeolite were obtained and characterized in relation to pesticide sorption capability. Hydrogels are three-dimensional network with large capacity of water or biological fluid adsorption. They have biocompatibility, biodegradability and non-toxicity properties, ensuring this class of polymers is widely used in different agriculture fields. Thus, the objective of the work was to investigate the process of paraquat sorption using a novel biodegradable nanocomposite. By mathematical modeling, it was possible to found that better models were the Freundlich-Langmuir isotherm and pseudosecond order kinetic, indicating that sorption is heterogeneous and similar to chemisorption process. Thus, such nanocomposites have great potential to be applied as an adsorbent material for removal of pesticides from contaminated water.
DOI: 10.6084/m9.figshare.6448559
title: Evaluation of meso-substituted cationic corroles as potential antibacterial agents

description: ABSTRACT Cationic derivatives of 5,10,15-tris[4-(pyridin-4-ylsulphanyl)-2,3,5,6-tetrafluorophenyl]-corrolategallium(III)pyridine and 5,10,15-tris[4-(pyridin-2-ylsulfanyl)-2,3,5,6-tetrafluorophenyl]-correlategallium(III)pyridine were synthesized and their photosensitizing properties against the naturally bioluminescent Gram-negative bacterium Allivibrio fischeri were evaluated. The cationic corrole derivatives exhibited antibacterial activity at micromolar concentrations against this Gram-negative bacterium strain.
DOI: 10.6084/m9.figshare.6448559.v1
title: Evaluation of meso-substituted cationic corroles as potential antibacterial agents

description: ABSTRACT Cationic derivatives of 5,10,15-tris[4-(pyridin-4-ylsulphanyl)-2,3,5,6-tetrafluorophenyl]-corrolategallium(III)pyridine and 5,10,15-tris[4-(pyridin-2-ylsulfanyl)-2,3,5,6-tetrafluorophenyl]-correlategallium(III)pyridine were synthesized and their photosensitizing properties against the naturally bioluminescent Gram-negative bacterium Allivibrio fischeri were evaluated. The cationic corrole derivatives exhibited antibacterial activity at micromolar concentrations against this Gram-negative bacterium strain.
DOI: 10.6084/m9.figshare.6448553
title: Prospective scenarios for regional development in Bolivar, Colombia: Great Vision study 2014-2064

description: Abstract Under the premise on how public policy can contribute to decision-making on the consolidation of the urban-regional system, physical-productive integration, connectivity and social mobility in the Department of Bolivar, Colombia, from its planning with a horizon of 50 years, the study determines strategic recommendations necessary for its competitive positioning before more developed regions in the country. The study intends to visualize territorial planning based on integrating elements such as the culture, geographic characteristics, economic vocation and infrastructure of the Bolivarian territory, based on its great wealth, but a great affectation for the violence of the Colombian conflict, and the forget about centralized development. Based on an integral vision of the department, a long-term perspective means an opportunistic vision supported on transversal and inclusive elements of the territory, leading the discussion towards the feasible application of adjusted prospective planning methodology, and even continental scales of vision in which the region registers but whose processes are very questionable.
DOI: 10.6084/m9.figshare.6448553.v1
title: Prospective scenarios for regional development in Bolivar, Colombia: Great Vision study 2014-2064

description: Abstract Under the premise on how public policy can contribute to decision-making on the consolidation of the urban-regional system, physical-productive integration, connectivity and social mobility in the Department of Bolivar, Colombia, from its planning with a horizon of 50 years, the study determines strategic recommendations necessary for its competitive positioning before more developed regions in the country. The study intends to visualize territorial planning based on integrating elements such as the culture, geographic characteristics, economic vocation and infrastructure of the Bolivarian territory, based on its great wealth, but a great affectation for the violence of the Colombian conflict, and the forget about centralized development. Based on an integral vision of the department, a long-term perspective means an opportunistic vision supported on transversal and inclusive elements of the territory, leading the discussion towards the feasible application of adjusted prospective planning methodology, and even continental scales of vision in which the region registers but whose processes are very questionable.
DOI: 10.6084/m9.figshare.6448550
title: Flexible urban planning in the contemporary city: contributions from the analysis of 22@ Barcelona Plan

description: Abstract This article aims to analyse the 22@ Barcelona Plan, considering that this example can contribute with reflections to processes of transformation of urban areas in a similar situation. This plan proposes to promote the conversion of an industrial sector into an innovation sector. We hypothesize that the traditional rational and finalist planning has not been able to grasp the urban object, leaving a gap in the reading and understanding of the city. The discussion and analysis are based on issues identified as possible contributions to experiences of similar urban transformation, including Brazilian ones. The results show that the 22@ Barcelona Plan contributes to urban management by exemplifying the territorial transformation based on an instrument that considers progressive implantation, morphological diversity, the performance of several agents and mechanisms that are articulated in different scales, in a flexible planning system. However, we highlight still present issues in the usual practices of urban transformation; especially regarding the incorporation of social aspects to the process. Thus, we suggest incorporating the design dimension into proposals of this nature, considering, more appropriately, the territorial physical results, and aiming at transformations that guarantee the full right to the city.
DOI: 10.6084/m9.figshare.6448550.v1
title: Flexible urban planning in the contemporary city: contributions from the analysis of 22@ Barcelona Plan

description: Abstract This article aims to analyse the 22@ Barcelona Plan, considering that this example can contribute with reflections to processes of transformation of urban areas in a similar situation. This plan proposes to promote the conversion of an industrial sector into an innovation sector. We hypothesize that the traditional rational and finalist planning has not been able to grasp the urban object, leaving a gap in the reading and understanding of the city. The discussion and analysis are based on issues identified as possible contributions to experiences of similar urban transformation, including Brazilian ones. The results show that the 22@ Barcelona Plan contributes to urban management by exemplifying the territorial transformation based on an instrument that considers progressive implantation, morphological diversity, the performance of several agents and mechanisms that are articulated in different scales, in a flexible planning system. However, we highlight still present issues in the usual practices of urban transformation; especially regarding the incorporation of social aspects to the process. Thus, we suggest incorporating the design dimension into proposals of this nature, considering, more appropriately, the territorial physical results, and aiming at transformations that guarantee the full right to the city.
DOI: 10.6084/m9.figshare.6448547
title: The case of the Paraisópolis Complex management: conceptual differences of the slums intervention programs in São Paulo

description: Abstract The paper presents and analyzes the urban interventions led by the government in Paraisópolis Complex, São Paulo, in the period between 2001-2016, during the administrations of Marta Suplicy (2001-2004), José Serra (2005-2006), Gilberto Kassab (2006-2012) and Fernando Haddad (2013-2016). Paraisópolis Complex is the second largest slum in São Paulo, with approximately 60,000 people and about 18,000 households. The area was an old farmhouse, which in 1921 was split in 2,200 lots. The road structure, unsuited to topography, resulted in slope greater than 40%, imparing the occupation of lots, invaded since 1970. We present the urban interventions carried out in Paraisópolis during four municipal administrations, qualitatively analyze the differences and similarities between them, to understand and characterize the recent practices of the government. Our results, especially the specializations of the interventions, made it possible to perceive the difficulties and fragility involved in the intervention dynamics in precarious settlements, since many projects represent, in practice, forced evictions because they constitute incomplete actions. Thus, through the analysis of Paraisópolis, this paper discusses the major impasses, limits and social implications that limit restrict the effectiveness of intervention programs in slums, which are still extraterritorial issues, mostly political.
DOI: 10.6084/m9.figshare.6448547.v1
title: The case of the Paraisópolis Complex management: conceptual differences of the slums intervention programs in São Paulo

description: Abstract The paper presents and analyzes the urban interventions led by the government in Paraisópolis Complex, São Paulo, in the period between 2001-2016, during the administrations of Marta Suplicy (2001-2004), José Serra (2005-2006), Gilberto Kassab (2006-2012) and Fernando Haddad (2013-2016). Paraisópolis Complex is the second largest slum in São Paulo, with approximately 60,000 people and about 18,000 households. The area was an old farmhouse, which in 1921 was split in 2,200 lots. The road structure, unsuited to topography, resulted in slope greater than 40%, imparing the occupation of lots, invaded since 1970. We present the urban interventions carried out in Paraisópolis during four municipal administrations, qualitatively analyze the differences and similarities between them, to understand and characterize the recent practices of the government. Our results, especially the specializations of the interventions, made it possible to perceive the difficulties and fragility involved in the intervention dynamics in precarious settlements, since many projects represent, in practice, forced evictions because they constitute incomplete actions. Thus, through the analysis of Paraisópolis, this paper discusses the major impasses, limits and social implications that limit restrict the effectiveness of intervention programs in slums, which are still extraterritorial issues, mostly political.