lcc: an R package to estimate the concordance correlation, Pearson correlation and accuracy over time

Background and Objective: Observational studies and experiments in medicine, pharmacology and agronomy are often concerned with assessing whether different methods/raters produce similar values over the time when measuring a quantitative variable. This article aims to describe the statistical package lcc, for are, that can be used to estimate the extent of agreement between two (or more) methods over the time, and illustrate the developed methodology using three real examples. Methods: The longitudinal concordance correlation, longitudinal Pearson correlation, and longitudinal accuracy functions can be estimated based on fixed effects and variance components of the mixed-effects regression model. Inference is made through bootstrap confidence intervals and diagnostic can be done via plots, and statistical tests. Results: The main features of the package are estimation and inference about the extent of agreement using numerical and graphical summaries. Moreover, our approach accommodates both balanced and unbalanced experimental designs or observational studies, and allows for different within-group error structures, while allowing for the inclusion of covariates in the linear predictor to control systematic variations in the response. All examples show that our methodology is flexible and can be applied to many different data types. Conclusions: The lcc package, available on the CRAN repository, proved to be a useful tool to describe the agreement between two or more methods over time, allowing the detection of changes in the extent of agreement. The inclusion of different structures for the variance-covariance matrices of random effects and residuals makes the package flexible for working with different types of databases

Key factors influencing the sale of bulls in livestock auctions

This research determines which factors most influence the purchase price of bulls in livestock auctions in the State of Rio Grande do Sul, Southern Brazil. Hence, 760 beef bulls sold in eleven different auctions between August and November 2013 were analysed. The data consists of: breed, muscularity (MUSC), frame (FRAME), body condition score (BCS), scrotal circumference (SC) and body weight (BW). Other data such as the animal entry order and the purchase price of the bulls was collected during the auction. A linear generalized model was used to evaluate the interaction of each variable with the purchase price of the bulls. An ANOVA with Tukey post-hoc was used to compare the differences between the categories that influenced the purchase price of bulls and were realized in the software SPSS 20.0. All breeds presented declining pricesfrom the first to the second entry order and increasing purchase prices from the order third to forth. Bulls with large frame received higher purchase prices independent of the auction order, except for the second order of entry, in which medium and small animals were more valued. Angus bulls obtained the highest prices in relation to the breeds Brangus and Hereford. The frame and breed constituted the main phenotypic characteristics that influence in price. In addition, the order of entry of bulls in the ring influence the purchase price

Correlation of mixed lymphocyte culture with chronic graft-versus-host disease following allogeneic stem cell transplantation

The purpose of the present study was to evaluate the mixed lymphocyte culture as a predictive assay of acute and chronic graft-versus-host disease (GVHD). We studied 153 patients who received a first bone marrow transplantation from human leukocyte antigen-identical siblings. Acute GVHD was observed in 26 of 128 (20.3%) patients evaluated and chronic GVHD occurred in 60 of 114 (52.6%). One-way mixed lymphocyte culture (MLC) assays were performed by the standard method. MLC results are reported as the relative response (RR) from donor against patient cells. The responses ranged from -47.0 to 40.7%, with a median of 0.5%. The Kaplan-Meier probability of developing GVHD was determined for patients with positive and negative MLC. There was no significant difference in incidence of acute GVHD between the groups studied. However, the incidence of chronic GVHD was higher in recipients with RR >4.5% than in those with RR 4.5%), 2.9 for those who received peripheral blood progenitor cells as a graft, and 2.2 for patients who developed previous acute GVHD. MLC was not useful for predicting acute GVHD, but MLC with RR >4.5% associated with other risk factors could predict the development of chronic GVHD, being of help for the prevention and/or treatment of this late complication.56757

The availability of full match sibling donors and feasibility of allogeneic bone marrow transplantation in Brazil

The feasibility of allogeneic bone marrow transplantation (alloBMT) in a developing country has not yet been demonstrated. Many adverse factors including social and economic limitations may reduce the overall results of this complex and expensive procedure. Our objective was to characterize the most important clinical, social and economic features of candidates for transplantation and their potential donors as well as the influence of these factors on overall survival in a retrospective and exploratory analysis at a university hospital. From July 1993 to July 2001, candidates for BMT were referred to the Bone Marrow Transplantation Unit by Hematology and Oncology Centers from several regions of Brazil. A total of 1138 patients were referred to us as candidates for alloBMT. Median age was 25 years (range: 2 months-60 years), 684 (60.1%) were males and 454 (39.9%) were females. The clinical indications were severe aplastic anemia and hematological malignancies. From the total of 1138 patients, 923 had HLA-typing; 497/923 (53.8%) candidates had full match donors; 352/1138 (30.8%) were eligible for alloBMT. Only 235 of 352 (66.7%) were transplanted. Schooling was 1st to 8th grade for 123/235 (52.3%); monthly family income ranged from US$60 (7$400 (36%). Overall survival for patients with chronic myeloid leukemia, severe aplastic anemia and acute myeloid leukemia was 58, 60 and 30%, respectively. Thus, overall survival rates for the most frequent hematological diseases were similar to those reported in the International Registry, except for acute myeloid leukemia. This descriptive and exploratory analysis suggests the feasibility of alloBMT in a developing country like Brazil.31532

Multifaceted roles of nitric oxide in tomato fruit ripening: NO-induced metabolic rewiring and consequences for fruit quality traits

Nitric oxide (NO) has been implicated as part of the ripening regulatory network in fleshy fruits. However, very little is known about the simultaneous action of NO on the network of regulatory events and metabolic reactions behind ripening-related changes in fruit color, taste, aroma and nutritional value. Here, we performed an in-depth characterization of the concomitant changes in tomato (Solanum lycopersicum) fruit transcriptome and metabolome associated with the delayed-ripening phenotype caused by NO supplementation at the pre-climacteric stage. Approximately one-third of the fruit transcriptome was altered in response to NO, including a multilevel down-regulation of ripening regulatory genes, which in turn restricted the production and tissue sensitivity to ethylene. NO also repressed hydrogen peroxide-scavenging enzymes, intensifying nitro-oxidative stress and S-nitrosation and nitration events throughout ripening. Carotenoid, tocopherol, flavonoid and ascorbate biosynthesis were differentially affected by NO, resulting in overaccumulation of ascorbate (25%) and flavonoids (60%), and impaired lycopene production. In contrast, the biosynthesis of compounds related to tomato taste (sugars, organic acids, amino acids) and aroma (volatiles) was slightly affected by NO. Our findings indicate that NO triggers extensive transcriptional and metabolic rewiring at the early ripening stage, modifying tomato antioxidant composition with minimal impact on fruit taste and aroma.This work was supported by the São Paulo Research Foundation (FAPESP) (grants 2018/16389-8, 2016/04924-0, 2017/17935-3 and 2016/01128-9), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (grants 422287/2018-0, 305012/2018-5, 303332/2019-0 and 300986/2018-1), and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001. The research work of FJC and JMP is supported by a European Regional Development Fund cofinanced grant from the Ministry of Economy and Competitiveness (AGL2015-65104-P and PID2019-103924GB-I00), Spain

Genetic diversity and population structure of early-maturing tropical maize inbred lines using SNP markers

Open Access Journal; Published online: 9 April 2019Information on genetic diversity and population structure are very important in any breeding programme for the improvement of traits of interest and the development of outstanding products for commercialization. In the present study, we assessed the genetic diversity of 94 early-maturing white and yellow tropical maize inbred lines using single nucleotide polymorphism (SNP) markers. The larger number of SNP markers used in this study allowed a clearer inference of the population structure of the 94 inbred lines. Cluster analysis resolved the inbred lines into different clusters based on their pedigree, selection history and endosperm colour. However, three heterotic groups were revealed by population structure analysis, but additional field evaluation could be more informative to confirm the heterotic groups identified. Nevertheless, wide genetic variability existed among the inbred lines making them unique with the potential to contribute new beneficial alleles to maize breeding programmes in the tropics, especially in the West and Central Africa (WCA) sub-region

Caracterização e ocorrência do distúrbio do amolecimento precoce em mamões 'Golden'

The occurrence of green skin and soft pulp in 'Golden' papaya fruit during certain seasons has been reported by farmers in the northern of the state of Espirito Santo, Brazil. The objective of this study was to characterize and determine the occurrence of this disorder, which was referred as "early softening disorder". Fruits were harvested weekly for 11 months (from September to July). The fruits were stored at 10°C, and then fruit flesh firmness and skin color were analyzed. The results of the firmness test were submitted to regression analysis assuming a linear trendline. The slope of the curve was called the 'softening index' (SI). Fruits with early softening are characterized by a loss of firmness in less than 10 days, even when stored under refrigeration. Although softened, the skin of the fruit remains partially green. Fruits with the disorder occurred more frequently from mid-summer to mid-autumn (February to May). It is not possible to distinguish early softening disorder fruits from those without the disorder by skin color and flesh firmness analysis at the time of the harvest.Tem sido relatado por produtores da região norte do Espírito Santo a ocorrência de mamões 'Golden' com casca verde e polpa mole, em determinadas épocas do ano. O objetivo deste trabalho foi caracterizar e determinar a ocorrência deste distúrbio denominado de amolecimento precoce. Foram realizadas coletas semanais durante 11 meses (período de setembro a julho). Os frutos foram armazenados a 10°C e analisados quanto à firmeza da polpa e à cor da casca. Os resultados de firmeza da polpa foram submetidos à análise de regressão, assumindo-se que a equação é do tipo linear, e o ângulo de inclinação da curva foi chamado Índice de Amolecimento (IA). Frutos com o distúrbio caracterizaram-se pela perda da firmeza em menos de 10 dias, mesmo quando armazenados sob refrigeração. Embora amolecidos, a coloração da casca manteve-se parcialmente verde. A maior frequência de frutos com o distúrbio ocorreu de meados de verão a meados de outono (fevereiro a maio). Não é possível distinguir frutos com o distúrbio do amolecimento precoce daqueles normais pela análise da cor da casca e da firmeza da polpa, no momento da colheita

Chitosan/TPP microparticles obtained by microemulsion method applied in controlled release of heparin

AbstractThis work deals with the preparation of chitosan/tripolyphosphate microparticles (CHT/TPP) using microemulsion system based on water/benzyl alcohol. The morphology of the microparticles was evaluated by scanning electron microscopy (SEM). The microparticles were also characterized through infrared spectroscopy (FTIR) and wide-angle X-ray scattering (WAXS). The morphology and crystallinity of microparticles depended mainly on CHT/TPP ratio. Studies of controlled release of HP were evaluated in distilled water and in simulated gastric fluid. Besides, the profile of HP releasing could be tailored by tuning the CHT/TPP molar ratio. Finally, these prospective results allow the particles to be employed as site-specific HP controlled release system