cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20011253.v1
title: Vigour in maize seeds: influence on seedling development under conditions of salt stress

description: ABSTRACT Using seeds of high vigour can be a strategy to reduce problems in the development of seedlings, and allow adequate stand establishment under different environmental conditions, especially under conditions of stress, such as salt stress. Accordingly, the aim of this work was to evaluate the influence of vigour in maize seeds on germination performance and seedling development when exposed to different levels of salt stress. Seeds from cultivars of two single hybrids were used, each in four batches; initially, water content and seedling emergence in the field were determined. To verify vigour behaviour, 200 seeds were planted on a roll of paper towelling moistened with different solutions of NaCl in five concentrations (0, 25, 50, 75 and 100 mol m-3). The variables being analysed were: germination percentage, length of shoot and root, root volume and seedling dry matter. At the concentrations under test, seed vigour had no effect on germination in the maize seeds exposed to salt stress; there was however a positive effect on seedling development up to the concentration of 50 mol NaCl m-3 (EC 5.11≤dS m-1). The variables of root volume and seedling dry weight are the most suitable for evaluating the effect of salt stress on development in maize seedlings.
DOI: 10.6084/m9.figshare.20011258
title: Non-hierarchical clustering of Manihot esculenta Crantz germplasm based on quantitative traits

description: ABSTRACT The knowledge of the phenotypic variation of cassava (Manihot esculenta Crantz) germplasm allows the estimative of the genetic variability to support the selection of contrasting genitors. Therefore, the aim of this work was to define homogeneous groups of cassava germplasm based on yield traits, disease resistance and root quality using K-means as a non-hierarchical method. Breeding values estimated by Best Linear Unbiased Predictor (BLUP) were used for the cluster analysis. The number of groups was defined according to the stabilization of the smallest within-group sum of squares. Seventeen clusters were defined to represent the diversity of the germplasm, whose number of accessions ranged from 7 (Group 15) to 69 (Group 9). In general, accessions belonging to Groups 1, 4, 7, 12, 15 and 16 showed good agronomic traits, such as high fresh root yield and starch yield (&gt; 60.7 t ha-1 and 18.6 t ha-1, respectively). In contrast, only Group 15 presented low bacterial blight severity. The groups obtained showed strong differences, as evidenced by the within-groups sums of squares values, which ranged from 215.1 (Group 15) to 2,338.3 (Group 8). The K-means algorithm allowed the formation of consistent groups based on yield traits, disease resistance and root quality. Therefore, the K-means algorithm was efficient in the formation of groups with low within genotypic variation, especially concerning large amounts of data, such as in cassava germplasm banks.
DOI: 10.6084/m9.figshare.20011258.v1
title: Non-hierarchical clustering of Manihot esculenta Crantz germplasm based on quantitative traits

description: ABSTRACT The knowledge of the phenotypic variation of cassava (Manihot esculenta Crantz) germplasm allows the estimative of the genetic variability to support the selection of contrasting genitors. Therefore, the aim of this work was to define homogeneous groups of cassava germplasm based on yield traits, disease resistance and root quality using K-means as a non-hierarchical method. Breeding values estimated by Best Linear Unbiased Predictor (BLUP) were used for the cluster analysis. The number of groups was defined according to the stabilization of the smallest within-group sum of squares. Seventeen clusters were defined to represent the diversity of the germplasm, whose number of accessions ranged from 7 (Group 15) to 69 (Group 9). In general, accessions belonging to Groups 1, 4, 7, 12, 15 and 16 showed good agronomic traits, such as high fresh root yield and starch yield (&gt; 60.7 t ha-1 and 18.6 t ha-1, respectively). In contrast, only Group 15 presented low bacterial blight severity. The groups obtained showed strong differences, as evidenced by the within-groups sums of squares values, which ranged from 215.1 (Group 15) to 2,338.3 (Group 8). The K-means algorithm allowed the formation of consistent groups based on yield traits, disease resistance and root quality. Therefore, the K-means algorithm was efficient in the formation of groups with low within genotypic variation, especially concerning large amounts of data, such as in cassava germplasm banks.
DOI: 10.25452/figshare.plus.19310870
title: Training Cohort Slide Images for "Intratumoral resolution of driver gene mutation heterogeneity in renal cancer using deep learning"

description: This item contains whole slide images (in SVS format) of all samples from the Training cohort analyzed in the paper "Intratumoral resolution of driver gene mutation heterogeneity in renal cancer using deep learning" by Acosta et al in Cancer Research (https://doi.org/10.1158/0008-5472.CAN-21-2318). This work demonstrates that deep learning (DL) models can predict the intratumor heterogeneity in driver mutation status purely from Hematoxylin and Eosin (H&E) stained slides. <br> Specifically, we trained and validated DL models that predict the status of three of the most frequently mutated driver genes (BAP1, PBRM1, and SETD2) in clear cell renal cell carcinoma. The DL models were trained on a large cohort of whole slide images (N=1282, referred to as WSI cohort in the paper/code) and tested on several independent cohorts including the TCGA KIRC (N=363 patients), two human tissue microarray (TMA) cohorts (referred to as TMA1 with 118 patients and TMA2 with 365 patients respectively) and a patient-derived xenograft TMA (referred to as PDX1). <br> The current dataset contains the H&E stained whole slide images for the WSI cohort. <br> See related materials in collection at: https://doi.org/10.25452/figshare.plus.c.5983795
DOI: 10.6084/m9.figshare.20011259
title: The morphological characterization of the dry seeds and reserve mobilization during germination in Morinda citrifolia L.

description: ABSTRACT Information about the morphology, chemical composition and reserve mobilization is important in understanding the establishment of native and exotic species. The purpose of this study was to describe the morphology, chemical composition, and mobilization of reserves during germination of noni (Morinda citrifolia L.). Biometric and morphological analyzes were performed with 100 randomly selected dried seeds. Other seeds were treated with sulfuric acid PA and soaked in Petri dishes. Collected seeds of five different times of germination were used for cytochemical and chemical analysis. For cytochemical analysis, the cuts of 5μm were submitted to dyes TB at pH 4.0; XP at pH 2.5, reaction of PAS and Sudan IV. The seeds were crushed for chemical analysis with lipids, proteins and soluble sugars extraction that were determined gravimetrically, by the Bradford method and the Antrona method, respectively. The fatty acid composition of the dry seed was determined by gas chromatography. Noni seeds are albuminous and have a thick seed coat, rich in lignin. Lipid and protein bodies were observed inside the endosperm cells, representing 43.50% and 9.15% respectively, while the reservoir of soluble sugars was less than 5%. Linoleic acid was the most prevalent with 68.1%. The lipids were mobilized during germination, suffering a reduction of up to 38% of its total. Proteins, as well as lipids decreased by 25.78% during the germination period observed. The main reserves of noni seeds are lipids and proteins that are mobilized during germination to provide energy and matter to the developing embryo and synthesis of more complex compounds.
DOI: 10.6084/m9.figshare.20011259.v1
title: The morphological characterization of the dry seeds and reserve mobilization during germination in Morinda citrifolia L.

description: ABSTRACT Information about the morphology, chemical composition and reserve mobilization is important in understanding the establishment of native and exotic species. The purpose of this study was to describe the morphology, chemical composition, and mobilization of reserves during germination of noni (Morinda citrifolia L.). Biometric and morphological analyzes were performed with 100 randomly selected dried seeds. Other seeds were treated with sulfuric acid PA and soaked in Petri dishes. Collected seeds of five different times of germination were used for cytochemical and chemical analysis. For cytochemical analysis, the cuts of 5μm were submitted to dyes TB at pH 4.0; XP at pH 2.5, reaction of PAS and Sudan IV. The seeds were crushed for chemical analysis with lipids, proteins and soluble sugars extraction that were determined gravimetrically, by the Bradford method and the Antrona method, respectively. The fatty acid composition of the dry seed was determined by gas chromatography. Noni seeds are albuminous and have a thick seed coat, rich in lignin. Lipid and protein bodies were observed inside the endosperm cells, representing 43.50% and 9.15% respectively, while the reservoir of soluble sugars was less than 5%. Linoleic acid was the most prevalent with 68.1%. The lipids were mobilized during germination, suffering a reduction of up to 38% of its total. Proteins, as well as lipids decreased by 25.78% during the germination period observed. The main reserves of noni seeds are lipids and proteins that are mobilized during germination to provide energy and matter to the developing embryo and synthesis of more complex compounds.
DOI: 10.6084/m9.figshare.20011261
title: Adjustment of growth parameters for the major body components of pullets

description: ABSTRACT The purpose of this research was analyze the fit of Gompertz function with or without fixing some of the parameters to describe body growth and major bodily chemical constituents of growing pullets. Weekly, data of body weight and chemical components of body free of feathers and feathers were collected from 1,200 chicks of four laying strains (Hisex Brown, Hisex White, Hy Line Brown and Hy Line White W36) until 18 weeks of age. The variables were subjected to two adjustments fixing, or not, some parameters of Gompertz function. The allometric model parameters were calculated for the chemical components. The lipid and protein composition of the body free of feathers were the components with the biggest change in the last weeks. Moreover, the chemical composition of the feather showed small variation. The parameters of the Gompertz function assumed values according to the employed adjustment, especially for protein and fat of the body free of feathers carcass. The adjustment of the Gompertz function by fixing the two parameters allowed coherence and biological significance. The allometric coefficients indicate that as the protein weight increased, the proportion of fat increased and the proportion of water and ashes in the body decreased. The fit of the model allows setting the parameters with consistency and biological significance without losing accuracy in the estimates.
DOI: 10.6084/m9.figshare.20011261.v1
title: Adjustment of growth parameters for the major body components of pullets

description: ABSTRACT The purpose of this research was analyze the fit of Gompertz function with or without fixing some of the parameters to describe body growth and major bodily chemical constituents of growing pullets. Weekly, data of body weight and chemical components of body free of feathers and feathers were collected from 1,200 chicks of four laying strains (Hisex Brown, Hisex White, Hy Line Brown and Hy Line White W36) until 18 weeks of age. The variables were subjected to two adjustments fixing, or not, some parameters of Gompertz function. The allometric model parameters were calculated for the chemical components. The lipid and protein composition of the body free of feathers were the components with the biggest change in the last weeks. Moreover, the chemical composition of the feather showed small variation. The parameters of the Gompertz function assumed values according to the employed adjustment, especially for protein and fat of the body free of feathers carcass. The adjustment of the Gompertz function by fixing the two parameters allowed coherence and biological significance. The allometric coefficients indicate that as the protein weight increased, the proportion of fat increased and the proportion of water and ashes in the body decreased. The fit of the model allows setting the parameters with consistency and biological significance without losing accuracy in the estimates.
DOI: 10.6084/m9.figshare.20011262.v1
title: Dynamic of dominance, growth and bromatology of Eragrostis plana Nees in secondary vegetation area

description: ABSTRACT The objective of this work was to evaluate the dominance, growth and bromatology of tough lovegrass or 'annoni' grass (Eragrostis plana) in secondary vegetation area. The evaluations were carried out at 23, 45, 64, 86, 111, 132, 153, and 174 days of growth after a mowing. The tough lovegrass was the dominant species on the area, accounting for 76 to 90% of biomass. There was a linear increase for leaf (9.8 kg DM ha-1 day-1) and total dry mass (16.9 kg DM ha-1 day-1) of the tough lovegrass. During the 111 days of the vegetative stage, the biomass was composed only of leaves, and the flowering started at 132 days. At 174 days, the tough lovegrass accumulated about 4,000 kg DM ha-1, 650 kg DM ha-1 of which was composed of inflorescences. The growth analysis revealed a specific leaf area of 72 cm2 g-1 and a maximum leaf area index of 2.1. The leaf area ratio decreased from 72.2 to 43.9 cm2 g-1 between the 23rd and 174th days. The bromatological analysis showed a high content of neutral detergent fiber (85.3-90.4%) and acid detergent fiber (39.4-42.8%), as well as low crude protein content (3.9-9.9%), indicating the low forage quality of the species.
DOI: 10.6084/m9.figshare.20011264.v1
title: Spectral regionalization of tropical soils in the estimation of soil attributes

description: ABSTRACT Conventional soil analysis produces large amount of residues and demand resources and time consuming. The construction of soil spectral database for estimating soil attributes is the newest alternative on soil mapping. The objective in this study was to build spectral libraries and study the quality of the generated prediction models for soil attributes. It was obtained 7185 soil spectral (400-2500 nm) in laboratory with respective soil analysis. The spectral libraries "general", "regional", and "local" were generated from these spectral readings. The general spectral library contained the full range of data and several states, the regional libraries contained data from geographically close municipalities, and the local libraries contained soil data from a single municipality. In general we observed the sequence of R2 for General (0.85), Regional (0.67 to 0.77) and Local (0.55 to 0.77). In conclusion, the best database was the general one. On the other hand, independent of the size of the database, predictive models based on physical attributes such as sand, clay, and organic matter generate good predictions until an R2 of 0.7. The determination of spectral libraries including highly variable soils formed from different parent materials create worse results for the estimation of chemical attributes and better results for the estimation of the physical ones. The low range of variation in a given attribute was a limiting factor in the generation of effective predictive models. A great spectral library can certainly improve soil quantitative evaluation.
DOI: 10.6084/m9.figshare.20011262
title: Dynamic of dominance, growth and bromatology of Eragrostis plana Nees in secondary vegetation area

description: ABSTRACT The objective of this work was to evaluate the dominance, growth and bromatology of tough lovegrass or 'annoni' grass (Eragrostis plana) in secondary vegetation area. The evaluations were carried out at 23, 45, 64, 86, 111, 132, 153, and 174 days of growth after a mowing. The tough lovegrass was the dominant species on the area, accounting for 76 to 90% of biomass. There was a linear increase for leaf (9.8 kg DM ha-1 day-1) and total dry mass (16.9 kg DM ha-1 day-1) of the tough lovegrass. During the 111 days of the vegetative stage, the biomass was composed only of leaves, and the flowering started at 132 days. At 174 days, the tough lovegrass accumulated about 4,000 kg DM ha-1, 650 kg DM ha-1 of which was composed of inflorescences. The growth analysis revealed a specific leaf area of 72 cm2 g-1 and a maximum leaf area index of 2.1. The leaf area ratio decreased from 72.2 to 43.9 cm2 g-1 between the 23rd and 174th days. The bromatological analysis showed a high content of neutral detergent fiber (85.3-90.4%) and acid detergent fiber (39.4-42.8%), as well as low crude protein content (3.9-9.9%), indicating the low forage quality of the species.
DOI: 10.6084/m9.figshare.20011264
title: Spectral regionalization of tropical soils in the estimation of soil attributes

description: ABSTRACT Conventional soil analysis produces large amount of residues and demand resources and time consuming. The construction of soil spectral database for estimating soil attributes is the newest alternative on soil mapping. The objective in this study was to build spectral libraries and study the quality of the generated prediction models for soil attributes. It was obtained 7185 soil spectral (400-2500 nm) in laboratory with respective soil analysis. The spectral libraries "general", "regional", and "local" were generated from these spectral readings. The general spectral library contained the full range of data and several states, the regional libraries contained data from geographically close municipalities, and the local libraries contained soil data from a single municipality. In general we observed the sequence of R2 for General (0.85), Regional (0.67 to 0.77) and Local (0.55 to 0.77). In conclusion, the best database was the general one. On the other hand, independent of the size of the database, predictive models based on physical attributes such as sand, clay, and organic matter generate good predictions until an R2 of 0.7. The determination of spectral libraries including highly variable soils formed from different parent materials create worse results for the estimation of chemical attributes and better results for the estimation of the physical ones. The low range of variation in a given attribute was a limiting factor in the generation of effective predictive models. A great spectral library can certainly improve soil quantitative evaluation.
DOI: 10.6084/m9.figshare.20011270
title: Drying of Mentha piperita leaves on a fixed bed at different temperatures and air velocities

description: ABSTRACT The species Mentha piperita, popularly known as peppermint, is not only a medicinal plant but is also used in the pharmaceutical, food and cosmetic industries. Consequently, the drying process is necessary to increase shelf and product life, facilitating transport, handling and storage. For mint derivatives of quality, work into pre- and post-harvest is necessary. The aim of this study was to evaluate drying. To obtain the curves, temperatures in the range of 30 ºC to 70 ºC were used, with drying air velocity varying between 0.3 and 0.5 m.s-1. For drying the leaves, a laboratory-scale, fixed bed dryer was used, having a fan to move the air and a heating system. The results showed that the Midili model best fit the experimental data. The relationship of the diffusion coefficient to the drying temperature can be described by the Arrhenius equation, giving an activation energy of 68.42 KJ mol-1for a velocity of 0.3 m.s-1, and 78.27 KJ mol-1 for a velocity of 0.5 m.s-1.
DOI: 10.6084/m9.figshare.20011270.v1
title: Drying of Mentha piperita leaves on a fixed bed at different temperatures and air velocities

description: ABSTRACT The species Mentha piperita, popularly known as peppermint, is not only a medicinal plant but is also used in the pharmaceutical, food and cosmetic industries. Consequently, the drying process is necessary to increase shelf and product life, facilitating transport, handling and storage. For mint derivatives of quality, work into pre- and post-harvest is necessary. The aim of this study was to evaluate drying. To obtain the curves, temperatures in the range of 30 ºC to 70 ºC were used, with drying air velocity varying between 0.3 and 0.5 m.s-1. For drying the leaves, a laboratory-scale, fixed bed dryer was used, having a fan to move the air and a heating system. The results showed that the Midili model best fit the experimental data. The relationship of the diffusion coefficient to the drying temperature can be described by the Arrhenius equation, giving an activation energy of 68.42 KJ mol-1for a velocity of 0.3 m.s-1, and 78.27 KJ mol-1 for a velocity of 0.5 m.s-1.
DOI: 10.6084/m9.figshare.20011273
title: Brazilian organic sugarcane spirits: Physicochemical and chromatographic profile

description: ABSTRACT There has been a growing demand for products from organic agriculture for the food market. Brazil leads the production of sugarcane spirits and produces about 1.6 billion liters/year. New technologies have been sought throughout the supply chain to improve production, and organic raw material has been used in the production of sugar cane for the production of beverages. This study aimed to define the physicochemical and chromatographic profiles of eleven organic sugarcane spirits samples from various Brazilian states. The secondary components and contaminants were identified and quantified through physicochemical analyses, HPLC and gas chromatography (GC). A significant percentage of the organic sugarcane spirits samples contained concentrations of components that were above the limits required by the Ministry of Agriculture, Livestock and Provisioning (MAPA), specifically the esters (18.20%), copper and dry extract (9.10%). This contamination is caused by bad conditions employed during the production process, which are not in compliance with the good manufacturing practices determined and legislated by Brazilian law.
DOI: 10.6084/m9.figshare.20011273.v1
title: Brazilian organic sugarcane spirits: Physicochemical and chromatographic profile

description: ABSTRACT There has been a growing demand for products from organic agriculture for the food market. Brazil leads the production of sugarcane spirits and produces about 1.6 billion liters/year. New technologies have been sought throughout the supply chain to improve production, and organic raw material has been used in the production of sugar cane for the production of beverages. This study aimed to define the physicochemical and chromatographic profiles of eleven organic sugarcane spirits samples from various Brazilian states. The secondary components and contaminants were identified and quantified through physicochemical analyses, HPLC and gas chromatography (GC). A significant percentage of the organic sugarcane spirits samples contained concentrations of components that were above the limits required by the Ministry of Agriculture, Livestock and Provisioning (MAPA), specifically the esters (18.20%), copper and dry extract (9.10%). This contamination is caused by bad conditions employed during the production process, which are not in compliance with the good manufacturing practices determined and legislated by Brazilian law.