cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5634901.v1
title: ELEMENTARY CHARACTERIZATION OF RICE HUSK AND THEIR ASHES BY MIP OES AFTER ACID DECOMPOSITION WITH REFLUX SYSTEM

description: This paper describes the optimization of a sample preparation method using response surface methodology for Al, Cd, Cu, Fe, Mg, Mn, Mo, Na, Ni and Ti determinations in samples of rice husk and rice husk ash by MIP OES. Sample preparation was performed using a reflux system adapted to the digestion tubes. This system allowed the decomposition of the samples without the necessity of replacement of the acids during this step without any loss of volatile elements. The decompositions were performed with 3.6 mL of HNO3 and 1.4 mL of H2SO4 for 205 min in a digester block at 225 ºC. The detection limit for determination of respective analytes in both samples were satisfactory. The RSDs for the analytes were less than 10%. Moreover, the accuracy of the method can be verified by recovery tests, whose values ranged from 82 to 115% for husk samples and 82 to 120% for ashes. The proposed method was presented as a simple, safe and low cost procedure being suitable for sample preparation and subsequent determination of metals by MIP OES.
DOI: 10.6084/m9.figshare.5634898
title: Economic profitability in conventional and irrigated coffee production systems in three municipalities in the Marilia region of São Paulo, Brazil

description: ABSTRACT: The objective of this study was to evaluate the economic benefit of coffee cultivation, with a focus on the distinction between conventional and irrigated coffee production systems. For the development of the study, the various productive systems were delineated from the data provided by a sample of producers to generate a matrix of average technical coefficients. The methodology used to estimate the operating cost of production is the one used by the Instituto de Economia Agrícola (IEA). Profitability indicators were also evaluated. Results indicated that the effective operational cost (EOC) incurred in the irrigated production system is higher than that in the conventional system. As regards the cost composition, in the conventional coffee production system, the largest cost incurred is on fertilizers among all inputs, whereas in the irrigated production system, the largest cost incurred is on machinery and equipment that are mainly used in harvesting, for the period 2013-2015. Profitability index of the conventional coffee production system in 2015 was 44.8%, and that of the drip irrigated production system was 49.7%. In 2014, profitability rates were negative for both the conventional (-13.9%) and irrigated coffee production systems (-8.6%). The most preferable choice was found to be the irrigated production system, as it allows reducing the risk of loss in production during prolonged periods of water shortage as well as greater yields due to a larger production of grains.
DOI: 10.6084/m9.figshare.5634898.v1
title: Economic profitability in conventional and irrigated coffee production systems in three municipalities in the Marilia region of São Paulo, Brazil

description: ABSTRACT: The objective of this study was to evaluate the economic benefit of coffee cultivation, with a focus on the distinction between conventional and irrigated coffee production systems. For the development of the study, the various productive systems were delineated from the data provided by a sample of producers to generate a matrix of average technical coefficients. The methodology used to estimate the operating cost of production is the one used by the Instituto de Economia Agrícola (IEA). Profitability indicators were also evaluated. Results indicated that the effective operational cost (EOC) incurred in the irrigated production system is higher than that in the conventional system. As regards the cost composition, in the conventional coffee production system, the largest cost incurred is on fertilizers among all inputs, whereas in the irrigated production system, the largest cost incurred is on machinery and equipment that are mainly used in harvesting, for the period 2013-2015. Profitability index of the conventional coffee production system in 2015 was 44.8%, and that of the drip irrigated production system was 49.7%. In 2014, profitability rates were negative for both the conventional (-13.9%) and irrigated coffee production systems (-8.6%). The most preferable choice was found to be the irrigated production system, as it allows reducing the risk of loss in production during prolonged periods of water shortage as well as greater yields due to a larger production of grains.
DOI: 10.6084/m9.figshare.5634895
title: COMPUTATIONAL STUDY OF THE INTERACTION N∙∙∙C ON MOLECULAR SYSTEMS (R)nN-CO2 (n=1,2,3)

description: The structures and molecular interactions of (R)nN-CO2 complexes of amines and CO2 in the gas phase were computationally studied by using ab-initio methods and quantum theory of atoms in molecules (QTAIM). The analysis of the electrostatic potential showed that the interaction N∙∙∙C present in this type of aggregates is favored by the potential difference between the N and C atoms. On the other hand, it was observed the interaction energy is being more exergonic in molecular aggregates having highly substituted amino groups and cyclic structure; in addition, the geometric deformation of CO2 and other additional molecular interactions facilitate the process of complexation of this gas. The QTAIM analysis showed that the interaction N∙∙∙C has an electrostatic character and its strength increases with the substitution of the amino group.
DOI: 10.6084/m9.figshare.5634895.v1
title: COMPUTATIONAL STUDY OF THE INTERACTION N∙∙∙C ON MOLECULAR SYSTEMS (R)nN-CO2 (n=1,2,3)

description: The structures and molecular interactions of (R)nN-CO2 complexes of amines and CO2 in the gas phase were computationally studied by using ab-initio methods and quantum theory of atoms in molecules (QTAIM). The analysis of the electrostatic potential showed that the interaction N∙∙∙C present in this type of aggregates is favored by the potential difference between the N and C atoms. On the other hand, it was observed the interaction energy is being more exergonic in molecular aggregates having highly substituted amino groups and cyclic structure; in addition, the geometric deformation of CO2 and other additional molecular interactions facilitate the process of complexation of this gas. The QTAIM analysis showed that the interaction N∙∙∙C has an electrostatic character and its strength increases with the substitution of the amino group.
DOI: 10.6084/m9.figshare.5634892
title: BIOPRODUCTION AND CHARACTERIZATION OF SODIUM, POTASSIUM, AND CALCIUM LACTOBIONATES

description: Lactobionic acid and its salts are substances that have several applications in the pharmaceutical area. These products were obtained by bioconversion through the enzymatic complex glucose-fructose-oxidoreductase (GFOR)/gluconolactonase (GL) present in calcium alginate immobilized cells of Zymomonas mobilis. In the reactions catalyzed by this enzyme system, the medium pH must be controlled at slightly acid values. For this purpose, NaOH, KOH, or Ca(OH)2 were used, and as a result, the respective salts were formed. The kinetic study on the formation of sodium, potassium and calcium lactobionates was followed by the steps of purification and characterization aiming the potential use of these compounds in the pharmaceutical area. In the assays for the bioproduction of sodium, potassium or calcium lactobionates, yields of 74, 77 and 84% were obtained, respectively. In the salts purification step, purity levels of approximately 95% were achieved. The structural identities of the lactobionate salts were determined by high resolution mass spectrometry, in addition to the 13C and 1H NMR analysis. The characterization demonstrates the selectivity of the enzymatic reaction of GFOR/GL of Z. mobilis, in the production of lactobionic acid and its salts.
DOI: 10.6084/m9.figshare.5634892.v1
title: BIOPRODUCTION AND CHARACTERIZATION OF SODIUM, POTASSIUM, AND CALCIUM LACTOBIONATES

description: Lactobionic acid and its salts are substances that have several applications in the pharmaceutical area. These products were obtained by bioconversion through the enzymatic complex glucose-fructose-oxidoreductase (GFOR)/gluconolactonase (GL) present in calcium alginate immobilized cells of Zymomonas mobilis. In the reactions catalyzed by this enzyme system, the medium pH must be controlled at slightly acid values. For this purpose, NaOH, KOH, or Ca(OH)2 were used, and as a result, the respective salts were formed. The kinetic study on the formation of sodium, potassium and calcium lactobionates was followed by the steps of purification and characterization aiming the potential use of these compounds in the pharmaceutical area. In the assays for the bioproduction of sodium, potassium or calcium lactobionates, yields of 74, 77 and 84% were obtained, respectively. In the salts purification step, purity levels of approximately 95% were achieved. The structural identities of the lactobionate salts were determined by high resolution mass spectrometry, in addition to the 13C and 1H NMR analysis. The characterization demonstrates the selectivity of the enzymatic reaction of GFOR/GL of Z. mobilis, in the production of lactobionic acid and its salts.
DOI: 10.6084/m9.figshare.5634889
title: Paula Coutinho’s outstanding contribution to the definition of Machado-Joseph disease

description: ABSTRACT Machado-Joseph disease, also known as spinocerebellar ataxia type 3, is the most common form of autosomal dominant ataxia in the world. Paula Coutinho, a highly-regarded Portuguese neurologist worldwide, had a seminal participation in the definition of this disease, more than 40 years ago.
DOI: 10.6084/m9.figshare.5634889.v1
title: Paula Coutinho’s outstanding contribution to the definition of Machado-Joseph disease

description: ABSTRACT Machado-Joseph disease, also known as spinocerebellar ataxia type 3, is the most common form of autosomal dominant ataxia in the world. Paula Coutinho, a highly-regarded Portuguese neurologist worldwide, had a seminal participation in the definition of this disease, more than 40 years ago.
DOI: 10.6084/m9.figshare.5634886
title: DEVELOPMENT AND VALIDATION OF AN HPLC-DAD ANALYTICAL METHOD TO QUANTIFY 5-METHOXYFLAVONES IN METHANOLIC EXTRACTS OF Vochysia divergens POHL CULTURED UNDER STRESS CONDITIONS

description: Vochysia divergens Pohl, known as "Cambara" in Brazil, is an invasive species that is expanding throughout Pantanal in Brazil, to form mono-dominant communities. This expansion is affecting the agricultural areas that support the typical seasonal flood and drought conditions of this biome. This article describes the development and validation of an HPLC-DAD analytical method to quantify 5-methoxyflavones in methanolic extracts of greenhouse-grown V. divergens associated with one of two endophytic fungal species Zopfiella tetraspora (Zt) or Melanconiella elegans (Me) and later subjected to water stress. The developed method gave good validation parameters and was successfully applied to quantify the flavones 3',5-dimethoxy luteolin-7-O-β-glucopyranoside (1), 5-methoxy luteolin (2), and 3',5-dimethoxy luteolin (3) in the target extracts. Inoculation of the plant with Zt decreased the concentration of flavone 1 in the extract by 2.69-fold as compared to the control. Inoculation of the plant with Zt or Me did not significantly alter the contents of flavones 2 and 3 in the extracts as compared to the control. Therefore, the aerial parts of germinated V. divergens plants inoculated with either Zt or Me responded differently in terms of the production of flavones. These results can cast light on the symbiosis between fungal microorganisms and V. divergens, which most likely influences the response of V. divergens to changes in the availability of water in Pantanal.
DOI: 10.6084/m9.figshare.5634886.v1
title: DEVELOPMENT AND VALIDATION OF AN HPLC-DAD ANALYTICAL METHOD TO QUANTIFY 5-METHOXYFLAVONES IN METHANOLIC EXTRACTS OF Vochysia divergens POHL CULTURED UNDER STRESS CONDITIONS

description: Vochysia divergens Pohl, known as "Cambara" in Brazil, is an invasive species that is expanding throughout Pantanal in Brazil, to form mono-dominant communities. This expansion is affecting the agricultural areas that support the typical seasonal flood and drought conditions of this biome. This article describes the development and validation of an HPLC-DAD analytical method to quantify 5-methoxyflavones in methanolic extracts of greenhouse-grown V. divergens associated with one of two endophytic fungal species Zopfiella tetraspora (Zt) or Melanconiella elegans (Me) and later subjected to water stress. The developed method gave good validation parameters and was successfully applied to quantify the flavones 3',5-dimethoxy luteolin-7-O-β-glucopyranoside (1), 5-methoxy luteolin (2), and 3',5-dimethoxy luteolin (3) in the target extracts. Inoculation of the plant with Zt decreased the concentration of flavone 1 in the extract by 2.69-fold as compared to the control. Inoculation of the plant with Zt or Me did not significantly alter the contents of flavones 2 and 3 in the extracts as compared to the control. Therefore, the aerial parts of germinated V. divergens plants inoculated with either Zt or Me responded differently in terms of the production of flavones. These results can cast light on the symbiosis between fungal microorganisms and V. divergens, which most likely influences the response of V. divergens to changes in the availability of water in Pantanal.
DOI: 10.6084/m9.figshare.5634883
title: Optimization of conditions to achieve high content of gamma amino butyric acid in germinated black rice, and changes in bioactivities

description: Abstract The present study estimated the optimum germination conditions to achieve high content of Gamma-amino butyric acid (GABA) and other phytochemicals in Thai black rice cultivar Kum Payao (BR). The Box–Behnken design of response surface methodology was employed to optimize the germination conditions. The changes in the GABA, phytochemical content, impact of salt, and temperature stress variation on phytochemical content, and stability of GABA were studied. The results showed that 12 h of soaking at pH 7, followed by 36 h of germination was the optimum condition to achieve maximum GABA content (0.2029 mg/g of germinated BR (GBR)). The temperature (8 and 30 °C), and salt (50-200 mM NaCl) content affected the phytochemicals of GBR, especially GABA, and anthocyanins. Obviously, the antioxidant capability, and enzyme (α-amylase and α-glucosidase) inhibiting nature of BR was significantly (P &lt; 0.001) increased after germination. The storage of GBR at 4 °C significantly, preserved the GABA content (∼80%) for 45 days. Primarily, the current study revealed the changes in phytochemical content, and bioactivity of Thai black rice cr. Kum Payao during germination. More studies should be carried out on pharmacological benefits of GABA-rich GBR.
DOI: 10.6084/m9.figshare.5634883.v1
title: Optimization of conditions to achieve high content of gamma amino butyric acid in germinated black rice, and changes in bioactivities

description: Abstract The present study estimated the optimum germination conditions to achieve high content of Gamma-amino butyric acid (GABA) and other phytochemicals in Thai black rice cultivar Kum Payao (BR). The Box–Behnken design of response surface methodology was employed to optimize the germination conditions. The changes in the GABA, phytochemical content, impact of salt, and temperature stress variation on phytochemical content, and stability of GABA were studied. The results showed that 12 h of soaking at pH 7, followed by 36 h of germination was the optimum condition to achieve maximum GABA content (0.2029 mg/g of germinated BR (GBR)). The temperature (8 and 30 °C), and salt (50-200 mM NaCl) content affected the phytochemicals of GBR, especially GABA, and anthocyanins. Obviously, the antioxidant capability, and enzyme (α-amylase and α-glucosidase) inhibiting nature of BR was significantly (P &lt; 0.001) increased after germination. The storage of GBR at 4 °C significantly, preserved the GABA content (∼80%) for 45 days. Primarily, the current study revealed the changes in phytochemical content, and bioactivity of Thai black rice cr. Kum Payao during germination. More studies should be carried out on pharmacological benefits of GABA-rich GBR.
DOI: 10.6084/m9.figshare.5634877
title: Simulation of soil water balance and partitioning of evapotranspiration of maize grown in two growing seasons in Southern Brazil

description: ABSTRACT: The objective of this study was to simulate the variation of the available soil water during maize crop growth, in two different sowing times (first and second growing season), using a drip irrigation system. The treatments consisted of different irrigation strategies (full to deficit). The SIMDualKc simulation model was used to determine the daily soil water balance and crop evapotranspiration using the dual crop coefficient approach. Soil, climate, crop and irrigation parameters were used as input data. Two experiments were carried out in a rainout shelter composed of two metallic structures (16x10m) in the city of Santa Maria, Rio Grande do Sul, Brazil, during 2010/11 (second crop, season 1) and 2011/12 (first crop, season 2) growing seasons, under no-tillage system. The simulations showed that all the irrigation management strategies used in season 2 resulted in soil water deficit, while only two strategies showed deficit in season 1. Results showed good agreement between observed and simulated soil water data, with an R2 ranging from 0.86 to 0.99 and the root mean square error ranging from 2.7 to 5.6% of the total available water for seasons 1 and 2, respectively. The observed results of water balance showed that maize grown in season 2 presented higher water consumption compared to season 1, due to the higher atmospheric demand of season 2. The SIMDualKc model allowed the partitioning of crop evapotranspiration into soil evaporation and crop transpiration, demonstrating that the vegetative growth subperiod presented the greatest differences between the two seasons compared to the others growth phases.
DOI: 10.6084/m9.figshare.5634877.v1
title: Simulation of soil water balance and partitioning of evapotranspiration of maize grown in two growing seasons in Southern Brazil

description: ABSTRACT: The objective of this study was to simulate the variation of the available soil water during maize crop growth, in two different sowing times (first and second growing season), using a drip irrigation system. The treatments consisted of different irrigation strategies (full to deficit). The SIMDualKc simulation model was used to determine the daily soil water balance and crop evapotranspiration using the dual crop coefficient approach. Soil, climate, crop and irrigation parameters were used as input data. Two experiments were carried out in a rainout shelter composed of two metallic structures (16x10m) in the city of Santa Maria, Rio Grande do Sul, Brazil, during 2010/11 (second crop, season 1) and 2011/12 (first crop, season 2) growing seasons, under no-tillage system. The simulations showed that all the irrigation management strategies used in season 2 resulted in soil water deficit, while only two strategies showed deficit in season 1. Results showed good agreement between observed and simulated soil water data, with an R2 ranging from 0.86 to 0.99 and the root mean square error ranging from 2.7 to 5.6% of the total available water for seasons 1 and 2, respectively. The observed results of water balance showed that maize grown in season 2 presented higher water consumption compared to season 1, due to the higher atmospheric demand of season 2. The SIMDualKc model allowed the partitioning of crop evapotranspiration into soil evaporation and crop transpiration, demonstrating that the vegetative growth subperiod presented the greatest differences between the two seasons compared to the others growth phases.
DOI: 10.6084/m9.figshare.5634874.v2
title: Analysis of Distributional Variation Through Graphical Multi-Scale Beta-Binomial Models

description: Many scientific studies involve comparing multiple datasets collected under different conditions to identify the difference in the underlying distributions. A common challenge in these multi-sample comparison problems is the presence of overdispersion, or extraneous causes other than the conditions of interest that also contribute to the cross-sample difference, which frequently results in false findings—identified “differences” not replicable in follow-up studies. When proper replicate samples are available under the conditions, one can in principle identify the interesting distributional variation from overdispersion through what we call the “analysis of distributional variation” (ANDOVA). We introduce a fully probabilistic framework for ANDOVA that achieves high computational efficiency. We take a divide-and-conquer multi-scale inference strategy: (i) first transform a general nonparametric ANDOVA task into a collection of ANDOVA tasks on Binomial experiments—each characterizing variations in the distributions at a particular location and scale, (ii) address each Binomial ANDOVA using a Beta-Binomial (BB) model, and (iii) use hierarchical graphical modeling to combine the inference from the BB models. We derive efficient MCMC-free Bayesian inference recipe under this framework through a combination of Laplace approximation-based numerical integration and message passing, and evaluate the performance of our method through extensive simulation. We apply the framework to analyzing DNase-seq data for identifying differences in transcriptional factor binding. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5634874.v1
title: Analysis of distributional variation through graphical multi-scale Beta-Binomial models

description: Many scientific studies involve comparing multiple data sets collected under different conditions to identify the difference in the underlying distributions. A common challenge in these multi-sample comparison problems is the presence of overdispersion, or extraneous causes other than the conditions of interest that also contribute to the cross-sample difference, which frequently results in false findings—identified “differences” not replicable in follow-up studies. When proper replicate samples are available under the conditions, one can in principle identify the interesting distributional variation from overdispersion through what we call the “analysis of distributional variation” (ANDOVA). We introduce a fully probabilistic framework for ANDOVA that achieves high computational efficiency. We take a divide-and-conquer multi-scale inference strategy: (i) first transform a general nonparametric ANDOVA task into a collection of ANDOVA tasks on Binomial experiments—each characterizing variations in the distributions at a particular location and scale, (ii) address each Binomial ANDOVA using a Beta-Binomial (BB) model, and (iii) use hierarchical graphical modeling to combine the inference from the BB models. We derive efficient MCMC-free Bayesian inference recipe under this framework through a combination of integrated nested Laplace approximation based numerical integration and message passing, and evaluate the performance of our method through extensive simulation. We apply the framework to analyzing DNase-seq data for identifying differences in transcriptional factor binding.