Is the Bland-Altman plot method useful without inferences for accuracy, precision, and agreement?

ABSTRACT OBJECTIVE This study aims to propose a comprehensive alternative to the Bland-Altman plot method, addressing its limitations and providing a statistical framework for evaluating the equivalences of measurement techniques. This involves introducing an innovative three-step approach for assessing accuracy, precision, and agreement between techniques, which enhances objectivity in equivalence assessment. Additionally, the development of an R package that is easy to use enables researchers to efficiently analyze and interpret technique equivalences. METHODS Inferential statistics support for equivalence between measurement techniques was proposed in three nested tests. These were based on structural regressions with the goal to assess the equivalence of structural means (accuracy), the equivalence of structural variances (precision), and concordance with the structural bisector line (agreement in measurements obtained from the same subject), using analytical methods and robust approach by bootstrapping. To promote better understanding, graphical outputs following Bland and Altman's principles were also implemented. RESULTS The performance of this method was shown and confronted by five data sets from previously published articles that used Bland and Altman's method. One case demonstrated strict equivalence, three cases showed partial equivalence, and one showed poor equivalence. The developed R package containing open codes and data are available for free and with installation instructions at Harvard Dataverse at https://doi.org/10.7910/DVN/AGJPZH. CONCLUSION Although easy to communicate, the widely cited and applied Bland and Altman plot method is often misinterpreted, since it lacks suitable inferential statistical support. Common alternatives, such as Pearson's correlation or ordinal least-square linear regression, also fail to locate the weakness of each measurement technique. It may be possible to test whether two techniques have full equivalence by preserving graphical communication, in accordance with Bland and Altman's principles, but also adding robust and suitable inferential statistics. Decomposing equivalence into three features (accuracy, precision, and agreement) helps to locate the sources of the problem when fixing a new technique.

Association of ticagrelor with risk of infection：a two-sample Mendelian randomization study based on the GWAS database / 中国药房

OBJECTIVE To investigate the causal association between ticagrelor and risk of infection METHODS Two-sample Mendelian randomization was adopted. Genetic instrumental variables were selected based on the results of the largest genome-wide association analysis to in vivo exposure of ticagrelor and its major active metabolite AR-C124910XX. The causal associations of ticagrelor and its major active metabolite AR-C124910XX with drug indications （coronary artery disease， unstable angina pectoris， myocardial infarction， stroke and ischemic stroke）were analyzed by inverse variance weighted Mendelian randomization model as a positive control for genetic instrumental variables. The causal relationship between ticagrelor and bacterial infection， acute lower respiratory infection， bacterial pneumoniae， pneumoniae，acute upper respiratory infection and sepsis were furtheranalyzed by using this method， and the robustness of the results was assessed by using heterogeneity tests and horizontal 202002030415） pleiotropy tests. RESULTS The increase of area under the curve at steady state （AUCss） of the genetic surrogated ticagrelor significantly reduced the risk of coronary artery disease， myocardial infarction and unstable angina pectoris （P＜0.001）. AUCss genetic instrument variables of its main active metabolite AR-C124910XX failed to pass positive control. Further analysis showed that the increase of the genetic surrogated ticagrelor exposure suggestively reduced the risk of bacterial infection [OR（95%CI）＝0.80（0.65，0.99），P＝0.040] and sepsis [OR （95%CI）＝0.84（0.73， 0.98）， P＝0.023]. The results of the heterogeneity tests showed that there was no heterogeneity in the causal association of the genetic surrogated ticagrelor AUCss with bacterial infection and sepsis （P＞0.05）. The results of horizontal pleiotropy tests showed that the causal association of genetic surrogated ticagrelor AUCss with bacterial infection and sepsis had no effects on horizontal pleiotropy （P＞0.05）. CONCLUSIONS Ticagrelor has a potential role in reducing the risk of sepsis and bacterial infections.

Challenges and Perspectives in Target Identification and Mechanism Illustration for Chinese Medicine / 中国结合医学杂志

Chinese medicine (CM) is an important resource for human life understanding and discovery of drugs. However, due to the unclear pharmacological mechanism caused by unclear target, research and international promotion of many active components have made little progress in the past decades of years. CM is mainly composed of multi-ingredients with multi-targets. The identification of targets of multiple active components and the weight analysis of multiple targets in a specific pathological environment, that is, the determination of the most important target is the main obstacle to the mechanism clarification and thus hinders its internationalization. In this review, the main approach to target identification and network pharmacology were summarized. And BIBm (Bayesian inference modeling), a powerful method for drug target identification and key pathway determination was introduced. We aim to provide a new scientific basis and ideas for the development and international promotion of new drugs based on CM.

Sports injuries in high-level aerobic gymnastics athletes / Lesões esportivas em atletas de ginástica aeróbica de alto nível / Lesiones deportivas en atletas de gimnasia aeróbica de alto nivel

ABSTRACT Introduction: With the rapid development of aerobic gymnastics worldwide, research is required to constantly increase. Objective: Analyze the main causes of sports injuries, proposing measures for prevention, treatment, and rehabilitation, as well as providing a theoretical basis for reducing the risk of sports injuries and actively seeking ways and measures to prevent and treat sports injuries in aerobic gymnastics athletes. Methods: Statistical-mathematical analysis was used, mainly including the coefficient of variation method, correlation matrix method, and factor analysis. The common variable of the trend of sports injuries was found. Results: The research shows that the scientific awareness, self-protection, and injury prevention of aerobic gymnastics training strengthen the ideological education and theoretical guidance of athletes, improve athletes' awareness of sports injuries, regulate technical specifications, strengthen fitness training and improve Chinese competitive aerobics. Conclusion: In the healthy period before injuries, we should take various measures to improve physical fitness and skills, enabling good health work in the acute period after injuries and understanding the working principle of early diagnosis and treatment to better use treatment time. Level of evidence II; Therapeutic studies - investigation of treatment outcomes.

RESUMO Introdução: Com o rápido desenvolvimento da ginástica aeróbica no mundo, é requisitado o aumento no nível das pesquisas constantemente. Objeto: Analisar as principais causas de lesões esportivas, propondo medidas de prevenção, tratamento e reabilitação, além de fornecer uma base teórica para reduzir o risco de lesões esportivas e buscar ativamente formas e medidas para prevenir e tratar lesões esportivas em atletas de ginástica aeróbica. Métodos: Foi utilizada uma análise estatística-matemática, principalmente incluindo o método de coeficiente de variação, método de matriz de correlação e análise de fatores. Encontrou-se a variável comum da tendência das lesões esportivas. Resultados: A pesquisa mostra que a consciência científica, autoproteção e prevenção de lesões dos métodos de treinamento de ginástica aeróbica fortalece a educação ideológica e a orientação teórica dos atletas, melhora a consciência dos atletas sobre lesões esportivas, regula especificações técnicas, fortalece o treinamento de aptidão física e melhora a aeróbica competitiva chinesa. Conclusão: No período saudável antes das lesões, devemos tomar várias medidas para aprimorar a aptidão física e as habilidades, permitindo um bom trabalho de saúde no período agudo após as lesões, compreendendo o princípio de trabalho de diagnóstico e tratamento precoces para aproveitar melhor o tempo de tratamento. Nível de evidência II; Estudos terapêuticos - investigação dos resultados do tratamento.

RESUMEN Introducción: Con el rápido desarrollo de la gimnasia aeróbica en el mundo, es necesario aumentar constantemente el nivel de investigación. Objetivo: Analizar las principales causas de las lesiones deportivas, proponiendo medidas de prevención, tratamiento y rehabilitación, así como proporcionar una base teórica para reducir el riesgo de lesiones deportivas y buscar activamente formas y medidas para prevenir y tratar las lesiones deportivas en los deportistas de gimnasia aeróbica. Métodos: Se utilizó el análisis estadístico-matemático, que incluye principalmente el método del coeficiente de variación, el método de la matriz de correlación y el análisis factorial. Se encontró la variable común de la tendencia de las lesiones deportivas. Resultados: La investigación muestra que la concienciación científica, la autoprotección y la prevención de lesiones de los métodos de entrenamiento de la gimnasia aeróbica refuerzan la educación ideológica y la orientación teórica de los atletas, mejoran la concienciación de los atletas sobre las lesiones deportivas, regulan las especificaciones técnicas, refuerzan el entrenamiento físico y mejoran el aeróbic de competición chino. Conclusión: En el período de salud antes de la lesión, debemos tomar varias medidas para mejorar la aptitud física y las habilidades, lo que permite un buen trabajo de salud en el período agudo después de la lesión, la comprensión del principio de trabajo de diagnóstico y tratamiento temprano para hacer un mejor uso del tiempo de tratamiento. Nivel de evidencia II; Estudios terapéuticos - investigación de los resultados del tratamiento.

Causal Relationship Between Acromegaly and Colon Cancer: A Two-sample Mendelian Randomization Study / 肿瘤防治研究

Objective To determine the causal relationship between acromegaly and colon cancer by using two-sample Mendelian randomization. Methods Genetic loci closely related to acromegaly in the whole genome-wide association study (GWAS) were selected as tool variables, and the genetic data of colon cancer from different GWASs were analyzed by two-sample Mendelian randomization (MR).The inverse variance weighting method (IVW) of the random effect model was used for analysis, and MR-weighted median and MR-Egger methods were used to supplement the analysis. Results were presented as OR values. Results Four SNPs closely related to acromegaly were obtained as tool variables, and the multiplicity test of tool variables showed that P=0.59.Three methods were used to estimate causal effects.The IVW analysis were OR=1.00(0.99-1.001) and P=0.42;the MR-Egger analysis results were OR=1.00(0.99-1.001) and P=0.42;and the Weighted median analysis results were OR=1.00(1.00-1.001) and P=0.03.The sensitivity test showed that the confidence interval of the tool variable SNP passed through 0, indicating the robustness of the MR results. Conclusion Acromegaly is not an independent risk factor for colon cancer.

A mendelian randomization study of the causal association between gastroesophageal reflux and atrial fibrillation / 公共卫生与预防医学

Objective In this study，we performed two sampie Mendelian Randomization to infer a causal association between Gastroesophageal reflux(GERD) and Atrial fibrillation(AF)，it can effectively avoid the problems such as reverse causation and confounds in traditional epidemiology. Methods We used the Summary data of GERD and AF from published Genome wide association study(GWAS) of European Individuals. Single Nucleotide Polymorphisms (SNPs) were extracted as Instrumental Variables (IVs).The main MR methods include Inverse Variance [] Weighted(IVW)，Weighted Median(WME)，MR-Egger，Simple Mode，and Weighted Mode.In addition，we used the sensitivity analysis such as MR-PRESSO，Cochran's Q test etc. Results The IVW shows a causal association between GERD and AF(P<0.0001，OR=1.16，95%CI:1.10-1.23).The WME shows P＜0.0001，OR=1.20，95%CI:1.11-1.30；Simple Mode shows P=0.01，OR=1.34，95%CI:1.07-1.69；Weighted Mode shows P=0.02，OR=1.33，95%CI:1.06-1.66. Conclusion This study based on genetic data supports the causal association between GERD and AF. The occurrence of GERD could increase the risk of AF.

Significancia Estadística en Ciencias de la Salud: Limitaciones y Alternativas / Statistical significance in the field of health sciences: limitations and alternatives

Introducción. La prueba de significancia de la hipótesis nula (PSHN) constituye la herramienta más usada para evaluar hipótesis científicas y tomar decisiones al respecto, en especial en ciencias de la salud. Sin embargo, por décadas ha estado en el centro del debate, ya que se han identificado varios problemas conceptuales y de interpretación. Se realizó una revisión de artículos científicos que ilustran las críticas de esta controversia y su relevancia en el ámbito de la investigación en salud. Algunas alternativas para la PSHN son una adecuada interpretación del valor p, uso de intervalos de confianza, incluir el tamaño del efecto y adoptar un marco de inferencia bayesiana. En todos los casos en que se utilice PSHN, su uso debe ser claramente justificado.

Background. Null hypothesis significance testing (NSHT) constitutes the most widely applied tool for the evaluation of scientific hypotheses and decision making in health sciences. However, the method has been the centre of a heated debate where various criticisms related to conceptual and interpretational problems. A review of scientific articles that illustrate the criticisms of this controversy and its relevance in the field of health research was carried out. Some alternatives for the NSHT are an adequate interpretation of the p-value, use of confidence intervals, including the effect size and adopting a Bayesian inference framework. In all cases where NSHT is used, its use should be clearly justified.

El Enfoque Bayesiano en las Ciencias de la Salud / The Bayesian Approach in the Health Sciences

En estadística existen dos enfoques básicos, la estadística frecuentista que es la corriente principal y la estadística bayesiana. La mayoría de los principales métodos estadísticos son frecuentistas siendo el enfoque bayesiano más desconocido entre los investigadores. En el presente artículo se exponen los fundamentos lógicos del enfoque bayesiano y su uso mediante un ejemplo de aplicación. En este contexto, más que presentar un debate entre la lógica clásica y la bayesiana, se pretende mostrar de manera introductoria las enormes posibilidades que el enfoque bayesiano puede aportar a la investigación en las Ciencias de la Salud.

In the stadistic field there are two basic approaches, the Frequentist Statistics which is the primary one, and the Bayesian Statistics. The most used statistical methods are the Frequentist methods, being the Bayesian approach the most popular among researchers. In this article, the logical basis of the Bayendian approach and its use are exposed through an application example. In this context, rather than presenting a debate between the classic and the Bayensian logic, it is intended to demonstrate in an introductory method the considerable possibilities how Bayesian approach can contribute to Health and Sciences research.

Optimization and Developmental Validation of 38-plex InDel Panel for Ancestry Inference / 法医学杂志

OBJECTIVES@#The previously established 38-plex InDel system was optimized and its performance was validated according to the Scientific Working Group on DNA Analysis Method (SWGDAM) application guidelines. The ancestry inference accuracy of individuals from East Asian, European, African and mixed populations was verified.@*METHODS@#DNA standard sample 9947A was used as the template to establish the optimal amplification conditions by adjusting primer balance, Mg2+ final concentration and optimizing PCR thermal cycle parameters and amplification volume. The allelic dropout, nonspecific amplification and whether the origin of the inferred samples matched the known information were compared to evaluate the performance of this system.@*RESULTS@#The optimal dosage of this system was 0.125-2 ng DNA template. The results of InDel typing were accurate, the amplification equilibrium was good, and the species specificity was good. This system showed certain tolerance to DNA samples including the inhibitor such as hemoglobin (≤80 μmol/L), indigo (≤40 mmol/L), calcium ion (≤1.0 mmol/L), and humic acid (≤90 ng/μL). The system enabled the direct amplification of DNA from saliva and blood on filter paper, and the results of ethnic inference were accurate. The system successfully detected the mixed DNA sample from two individuals. The test results of the system for common biological materials in practical cases were accurate.@*CONCLUSIONS@#The results of the 38-plex InDel system are accurate and reliable, and the performance of the system meets the requirement of the SWGDAM guidelines. This system can accurately differentiate the ancestry origins of individuals from African, European, East Asian, and Eurasian populations and can be implemented in forensic practice.

Review and Prospect of Diagnosis of Drowning Deaths in Water / 法医学杂志

Drowning is the death caused by asphyxiation due to fluid blocking the airway. In the practice of forensic medicine, it is the key to determine whether the corpse was drowned or entered the water after death. At the same time, the drowning site inference and postmortem submersion interval (PMSI) play an important role in the investigating the identity of the deceased, narrowing the investigation scope, and solving the case. Based on diatoms testing, molecular biology, imaging and artificial intelligence and other technologies, domestic and foreign forensic scientists have done relative research in the identification of the cause of death, drowning site inference and PMSI, and achieved certain results in forensic medicine application. In order to provide a reference for future study of bodies in the water, this paper summarizes the above research contents.

Drug target inference by mining transcriptional data using a novel graph convolutional network framework

A fundamental challenge that arises in biomedicine is the need to characterize compounds in a relevant cellular context in order to reveal potential on-target or off-target effects. Recently, the fast accumulation of gene transcriptional profiling data provides us an unprecedented opportunity to explore the protein targets of chemical compounds from the perspective of cell transcriptomics and RNA biology. Here, we propose a novel Siamese spectral-based graph convolutional network (SSGCN) model for inferring the protein targets of chemical compounds from gene transcriptional profiles. Although the gene signature of a compound perturbation only provides indirect clues of the interacting targets, and the biological networks under different experiment conditions further complicate the situation, the SSGCN model was successfully trained to learn from known compound-target pairs by uncovering the hidden correlations between compound perturbation profiles and gene knockdown profiles. On a benchmark set and a large time-split validation dataset, the model achieved higher target inference accuracy as compared to previous methods such as Connectivity Map. Further experimental validations of prediction results highlight the practical usefulness of SSGCN in either inferring the interacting targets of compound, or reversely, in finding novel inhibitors of a given target of interest.

Association of C-reactive Protein with Cardiovascular Outcomes: A Mendelian Randomization Study in the Japanese Population / 生物医学与环境科学（英文）

OBJECTIVE@#Traditional epidemiological studies have shown that C-reactive protein (CRP) is associated with the risk of cardiovascular diseases (CVDs). However, whether this association is causal remains unclear. Therefore, Mendelian randomization (MR) was used to explore the causal relationship of CRP with cardiovascular outcomes including ischemic stroke, atrial fibrillation, arrhythmia and congestive heart failure.@*METHODS@#We performed two-sample MR by using summary-level data obtained from Japanese Encyclopedia of Genetic association by Riken (JENGER), and we selected four single-nucleotide polymorphisms associated with CRP level as instrumental variables. MR estimates were calculated with the inverse-variance weighted (IVW), penalized weighted median and weighted median. MR-Egger regression was used to explore pleiotropy.@*RESULTS@#No significant causal association of genetically determined CRP level with ischemic stroke, atrial fibrillation or arrhythmia was found with all four MR methods (all Ps > 0.05). The IVW method indicated suggestive evidence of a causal association between CRP and congestive heart failure ( OR: 1.337, 95% CI: 1.005-1.780, P = 0.046), whereas the other three methods did not. No clear pleiotropy or heterogeneity were observed.@*CONCLUSIONS@#Suggestive evidence was found only in analysis of congestive heart failure; therefore, further studies are necessary. Furthermore, no causal association was found between CRP and the other three cardiovascular outcomes.

Phylogenetic relationships of the supercontig of sodium channel subunit I (NaV) in 17 species of Anopheles (Diptera: Culicidae)

ABSTRACT Background: Malaria is a global health problem and is transmitted by the Anopheles species. Due to the epidemiological importance of the genus, studies on biological, phylogenetic, and evolutionary aspects have contributed to the understanding of adaptation, vector capacity, and resistance to insecticides. The latter may result from different causes such as mutations in the gene that encodes the sodium channel (NaV). Methods: In this study, the NaV subunit I scaffold of 17 anopheline species was used to infer phylogenetic relationships of the genus Anopheles using Bayesian inference. The evolutionary phylogenetic tree of the NaV gene was aligned in the AliView program and analyzed utilizing Bayesian inference, using the software MrBayes. Results: The anophelines were grouped into five well-supported clusters: 1 - Anopheles darlingi and Anopheles albimanus; 2 - Anopheles sinensis and Anopheles atroparvus; 3 - Anopheles dirus; 4 - Anopheles minimus, Anopheles culicifacies, Anopheles funestus, Anopheles maculatus, and Anopheles stephensi; and 5 - Anopheles christyi, Anopheles epiroticus, Anopheles merus, Anopheles melas, Anopheles gambiae, Anopheles coluzzii, and Anopheles arabiensis. Conclusions: The topology confirms the phylogenetic relationships proposed in studies based on the genome of some anophelines and reflects the current taxonomy of the genus, which suggests that NaV undergoes selection pressure during the evolution of the species. These data are useful tools for inferring their ability to resist insecticides and also help in better understanding the evolutionary processes of the genus Anopheles.

Theoretical and Practical Foundations of Mokken Scale Analysis in Psychology / Fundamentos Teóricos e Práticos da Análise de Escala de Mokken em Psicologia / Fundamentos Teóricos y Prácticos del Análisis de la Escala de Mokken en Psicología

Abstract Item Response Theory represents one of the major advances in the field of developing valid and reliable measures in psychology. Among the main models used in this perspective are the Rasch model and the logistic models. These parametric models, however, are not suitable for all applications in psychology, since a substantial number of databases in psychology do not satisfy the assumptions of these models: unidimensionality; latent monotonicity; local independence; and, for some models, non-intersecting functions. Given this framework, the objective of this study was to present the theoretical and practical foundations of Mokken Scale Analysis (MSA). We present some historical issues involving the development of MSA, in addition to the main characteristics and assumptions of the two models used in this perspective. After exemplifying a MSA application, limitations and final considerations are presented, supporting the decision-making process for researchers who come to use MSA.

Resumo A Teoria de Resposta ao Item representa um dos principais avanços para a construção de medidas válidas e confiáveis em psicologia. Entre os principais modelos utilizados nessa perspectiva estão o modelo de Rasch e os modelos logísticos. Esses modelos paramétricos, no entanto, não podem ser utilizados em todas as aplicações em psicologia, uma vez que um número substancial dos bancos de dados em psicologia não satisfaz os pressupostos desses modelos: unidimensionalidade; monotonicidade latente; independência local; e, para alguns modelos, não-interseção de funções. Dessa forma, o objetivo deste estudo foi apresentar os fundamentos teóricos e práticos da Análise de Escala de Mokken (AEM). São apresentadas questões históricas envolvendo o desenvolvimento da AEM, além das principais características e pressupostos dos dois modelos usados nessa perspectiva. Após exemplificação de uma AEM, limitações e considerações finais são apresentadas, apoiando o processo de tomada decisão para pesquisadores que venham a usar a AEM.

Resumen La Teoría de Respuesta al Ítem representa uno de los mayores avances en el campo del desarrollo de medidas válidas en psicología. Entre los principales modelos utilizados en esta perspectiva se encuentran los modelos logísticos. Estos modelos no son adecuados para todas las aplicaciones en psicología, ya que algunas bases de datos en psicología no satisfacen las suposiciones de estos modelos: unidimensionalidad; monotonicidad latente; e independencia local; y, para algunos modelos, funciones que no se interceptan. Teniendo en cuenta este marco, el objetivo de este estudio fue presentar los fundamentos teóricos y prácticos del Análisis de la Escala de Mokken (AEM). Presentamos algunas cuestiones históricas relacionadas con el desarrollo de AEM, además de las principales características y suposiciones de los dos modelos utilizados en esta perspectiva. Después de ejemplificar un AEM, se presentan las limitaciones y consideraciones finales, apoyando o procesando la tomada de decisión para investigadores que van a usar el AEM.

The reading comprehension and inferential process of an elderly student / A compreensão da leitura e o processo inferencial de um estudante idoso / La comprensión lectora y el proceso inferencial de un estudiante anciano

This article is part of a master's dissertation that investigated the reading comprehension and the inferential process of elderly students from a youth and adults class. Only data from one of the participants will be considered, which were constructed through semi-structured interviews and reading sessions. The interviews aimed to identify the participant's life and reading stories. The reading sessions consisted of answering inferential questions about two texts - a cordel and a poem - divided into parts previously established by the researcher. The results showed that: the participant's reading comprehension and inferential processes were based mainly on the textual material; there was a connection between the participant's life and reading histories and his comprehension of the texts, and, moreover, it was demonstrated that there was a greater difficulty for the participant in reading the poetic genre than in reading the cordel genre.

Este artigo é parte de uma dissertação de mestrado que investigou a compreensão da leitura e o processo inferencial de estudantes idosos de uma turma de jovens e adultos. Foram considerados apenas os dados de um dos participantes, construídos por meio de entrevistas semiestruturadas e sessões de leitura. As entrevistas objetivaram identificar as histórias de vida e de leitura do participante. As sessões de leitura consistiram em responder a perguntas inferenciais sobre dois textos - um cordel e um poema -, que foram divididos em partes previamente estabelecidas pelos pesquisadores. Os resultados evidenciaram que a compreensão da leitura e o processo inferencial do participante basearam-se principalmente no material textual; que houve relação entre as histórias de vida e de leitura do participante e sua compreensão dos textos; e, ainda, que existiram maiores dificuldades do participante na leitura do gênero poético do que na leitura do gênero cordel.

Este artículo es parte de una tesis de maestría que investigó la comprensión lectora y el proceso inferencial de estudiantes ancianos de un grupo de jóvenes y adultos. Solo se considerarán los datos de uno de los participantes, construidos a través de entrevistas semiestructuradas y sesiones de lectura. Las entrevistas tuvieron como objetivo identificar las historias de vida y lectura del participante. Las sesiones de lectura consistieron en responder preguntas inferenciales sobre dos textos, un cordel y un poema, que se dividieron en partes previamente establecidas por el investigador. Los resultados mostraron que la comprensión de lectura y el proceso de inferencia del participante se basaron principalmente en el material textual, que existía una relación entre las historias de vida y lectura del participante y su comprensión de los textos, y que también era evidente que el participante tenía mayores dificultades para leer el género poético que para leer el género cordel.

Métodos para avaliação da efetividade de vacinas para COVID-19 com ênfase em abordagens quase-experimentais / Methods to evaluate COVID-19 vaccine effectiveness, with an emphasis on quasi-experimental approaches

Resumo A avalição da efetividade de vacinas é feita com dados do mundo real e é essencial para monitorar o desempenho dos programas de vacinação ao longo do tempo bem como frente a novas variantes. Até o momento, a avaliação da efetividade das vacinas para COVID-19 tem sido baseada em métodos clássicos como estudos de coorte e caso controle teste-negativo, que muitas vezes podem não permitir o adequado controle dos vieses intrínsecos da alocação das campanhas de vacinação. O objetivo dessa revisão foi discutir os desenhos de estudo disponíveis para avaliação de efetividade das vacinas, enfatizando os estudos quase-experimentais, que buscam mimetizar os estudos aleatorizados ao introduzir um componente exógeno para atribuição ao tratamento, bem como suas vantagens, limitações e aplicabilidade no contexto dos dados brasileiros. O emprego de métodos quase-experimentais, incluindo as séries temporais interrompidas, o método de diferença em diferenças, escore de propensão, variáveis instrumentais e regressão descontínua, são relevantes pela possibilidade de gerar estimativas mais acuradas da efetividade de vacinas para COVID-19 em cenários como o brasileiro, que se caracteriza pelo uso de várias vacinas, com respectivos número e intervalos entre doses, aplicadas em diferentes faixas etárias e em diferentes momentos da pandemia.

Abstract The evaluation of vaccine effectiveness is conducted with real-world data. They are essential to monitor the performance of vaccination programmes over time, and in the context of the emergence of new variants. Until now, the effectiveness of COVID-19 vaccines has been assessed based on classic methods, such as cohort and test-negative case-control studies, which may often not allow for adequate control of inherent biases in the assignment of vaccination campaigns. The aim of this review was to discuss the study designs available to evaluate vaccine effectiveness, highlighting quasi-experimental studies, which seek to mimic randomized trials, by introducing an exogenous component to allocate to treatment, in addition to the advantages, limitations, and applicability in the context of Brazilian data. The use of quasi-experimental approaches, such as interrupted time series, difference-in-differences, propensity scores, instrumental variables, and regression discontinuity design, are relevant due to the possibility of providing more accurate estimates of COVID-19 vaccine effectiveness. This is especially important in scenarios such as the Brazilian, which characterized by the use of various vaccines, with the respective numbers and intervals between doses, applied to different age groups, and introduced at different times during the pandemic.

Genotype by environment interactions for body weight in Mediterranean buffaloes using reaction norm models / Interacción genotipo × ambiente para peso corporal de búfalos Mediterráneos utilizando modelos de norma de reacción / Interação genótipo × ambiente para peso corporal de búfalos Mediterrâneos utilizando modelos de norma de reação

Abstract Background: Buffalo breeding has significantly increased in Brazil over recent years. However, few genetic evaluations have been conducted. Objective: To assess Genotype x Environment Interactions in the Mediterranean Water Buffalo in Brazil, for weight at 205 days of age, using reaction norm models via random regression. Methods: Data for buffaloes born between 1990 and 2014 were collected from five farms ascribed to the Brazilian Buffaloe Improvement Program, located in the North (1), Northeast (1), South (2) and Southeast (1) regions of Brazil. The initial database consisted of 5,280 observations at 205 days of age (W205). We assessed fit using two hierarchical reaction norm models: a two-step (HRNM2s) and a one-step (HRNM1s). Model fit was estimated using the Deviance Information Criterion, Deviance Based on Bayes Factors and Deviance based on Conditional Predictive Ordinate. The environmental descriptors were created to group individuals into common production environments based on year, season, herd and sex. Results: The best fit was obtained for the hierarchical reaction norm model with one-step (HRNM1s). Direct heritability estimates for this model ranged from 0.17 to 0.67 and the maternal heritability from 0.02 to 0.11 with increasing environmental gradient. Lower correlations among the sire classifications were obtained in comparison with HRNM1s in environments with low and high management, confirming the presence of genotype x environment interactions. Conclusion: We recommend a wider application of genetic evaluation in buffalo aimed at identifying optimal genotypes within specific environments.

Resumen Antecedentes: La cría de búfalos ha aumentado significativamente en Brasil en los últimos años. Sin embargo, se han realizado escasas evaluaciones genéticas. Objetivo: Evaluar las interacciones genotipo x ambiente en búfalos de agua Mediterráneos criados en Brasil, para peso a los 205 días de edad, utilizando modelos de reacción mediante regresión aleatoria. Métodos: Los datos de búfalos nacidos entre 1990 y 2014 se obtuvieron de cinco granjas situadas en el Norte (1), Nordeste (1), Sur (2) y del Sureste (1) de Brasil. Todas estas haciendas participan en el Programa Brasileño de Mejoramiento de Búfalos. Nuestra base de datos inicial consistió de 5.280 observaciones a los 205 días de edad (P205). Evaluamos el ajuste utilizando dos modelos de norma de reacción jerárquica: de dos pasos (HRNM2s) y un paso (HRNM1s). El ajuste del modelo se estimó usando el Criterio de información de la desviación, desviación basado en los factores de bayes y desviación basado en la ordenación predictiva condicional. Los descriptores ambientales fueron creados para agrupar individuos en ambientes de producción comunes basados en año, estación, rebaño y sexo. Resultados: El mejor ajuste se obtuvo para el modelo de norma de reacción jerárquica con un paso (HRNM1s). Las estimaciones de heredabilidad directa para este modelo variaron de 0,17 a 0,67 y la heredabilidad materna de 0,02 a 0,11 con gradiente ambiental creciente. Las correlaciones más bajas entre las clasificaciones de los reproductores se obtuvieron en comparación con las HRNM1s, en ambientes con bajo y alto manejo, confirmando la presencia de interacciones genotipo x ambiente. Conclusiones: Recomendamos la aplicación amplia de la evaluación genética en búfalos para identificar genotipos óptimos en ambientes específicos.

Resumo Antecedentes: A criação de búfalos aumentou significativamente no Brasil nos últimos anos. No entanto, eles raramente foram objeto de avaliações genéticas. Objetivo: Avaliar as interações genótipo x ambiente em búfalo Mediterrâneo criados no Brasil, para peso aos 205 dias de idade, utilizando modelos de reação por meio de regressão aleatória. Métodos: Os dados para búfalos de água do Mediterrâneo nascidos entre 1990 e 2014 foram coletados de cinco fazendas localizadas nas regiões Norte (1), Nordeste (1), Sul (2) e Sudeste (1) do Brasil. Todas essas fazendas participam do Programa Brasileiro de Melhoramento dos Búfalos. Nosso banco de dados inicial consistiu de 5.280 observações aos 205 dias de idade (P205). Nós avaliamos o ajuste usando dois modelos de norma de reação hierárquica: um de dois passos (HRNM2s) e um passo (HRNM1s). O ajuste do modelo foi estimado usando o Critério de informações do desvio, desvio baseado nos fatores de bayes e desvio baseado na ordenação preditiva condicional. Os descritores ambientais foram criados para agrupar indivíduos em ambientes de produção comuns baseados em ano, estação, rebanho e sexo. Resultados: O melhor ajuste foi obtido para o modelo de norma de reação hierárquica com um passo (HRNM1s). As estimativas de herdabilidade direta para este modelo variaram de 0,17 a 0,67 e a herdabilidade materna de 0,02 a 0,11 com gradiente ambiental crescente. As correlações mais baixas entre as classificações dos reprodutores foram obtidas em comparação com as HRNM1s, em ambientes com baixo e alto manejo, confirmando a presença de interações genótipo x ambiente. Conclusões: Recomendamos a aplicação mais ampla da avaliação genética em búfalos visando identificar genótipos ótimos em ambientes específicos.

Genetic parameters for ultrasound-evaluated carcass and body traits in Anglo-Nubian goats / Parámetros genéticos para las características de la canal y del cuerpo evaluadas por ultrasonido en cabras Anglo-Nubianas / Parâmetros genéticos para características da carcaça avaliadas por ultrassom e corporais em caprinos Anglo-Nubianos

Abstract Background: Meat goat breeding programs should prioritize the identification and selection of genetically superior animals for traits related to meat quality and carcass yield in order to increase the value of the final product. Objective: To estimate (co)variance components and genetic parameters for ultrasound-measured carcass traits, body size and body weight in Anglo- Nubian breed goats raised in the Mid-North region of Brazil. Methods: (Co)variance components and genetic parameters were estimated using the single and two-trait animal model analyses via Bayesian inference for loin eye dimensions (area, length, and depth), sternal fat thickness, rump height, chest circumference and depth, leg perimeter, and body weight. Results: Heritability estimates were higher when two-trait analyses were used. This finding implies that it is possible to recover part of the additive genetic variance included in the residual variance due to the correlation between traits. Genetic correlations between carcass and body size traits showed different magnitudes. On the other hand, genetic correlations between the traits related to muscularity showed high magnitudes. Conclusions: Body weight was not a good indicator of muscularity; therefore, it is not recommended as a criterion for indirect selection to improve carcass traits of Anglo-Nubian goats. Leg perimeter and chest circumference may be important to construct selection indexes in meat goat breeding programs.

Resumen Antecedentes: los programas de mejoramiento de caprinos de carne deben priorizar la identificación y selección de animales genéticamente superiores para características relacionadas con la calidad de la carne y rendimiento de la canal, con el fin de agregar valor al producto final. Objetivo: estimar los componentes de (co)varianza y parámetros genéticos para características de canal obtenidas por ultrasonografía, características de tamaño y peso corporal en caprinos de la raza Anglonubiana, criados en la región medio-norte de Brasil. Métodos: los componentes de (co)varianza y parámetros genéticos fueron estimados mediante un modelo animal usando análisis uni y bi-carácter vía metodología Bayesiana para las dimensiones del ojo de lomo (área, profundidad y longitud), grosor de la grasa esternal, altura de la grupa, circunferencia y profundidad torácica, perímetro de la pierna y peso corporal. Resultados: las estimativas de heredabilidad obtenidas a partir del análisis bi-carácteristico fueron mayores que las obtenidas a partir del análisis uni-carácteristico. Este supuesto implica que es posible recuperar parte de la variancia genética aditiva incluida en la variancia residual, debido a la correlación entre las características. Las correlaciones genéticas entre las características de canal y las medidas corporales presentaron diferentes magnitudes. Por otro lado, las correlaciones genéticas entre las características relacionadas con musculatura presentaron alta magnitud. Conclusiones: el peso corporal no fue un buen indicador de musculatura; por eso no es recomendado como criterio de selección indirecta para mejorar la canal de caprinos Anglonubianos. El perímetro de la pierna y la circunferencia del pecho pueden ser importantes para la construcción de índices de selección en programas de mejoramiento de carne caprina.

Resumo Antecedentes: programas de melhoramento de caprinos de corte devem priorizar a identificação e seleção de animais geneticamente superiores para características relacionadas à qualidade da carne e rendimento de carcaça, para aumentar o valor ao produto final. Objetivo: estimar componentes de (co)variância e parâmetros genéticos para características de carcaça obtidas por ultrassonografia, características de tamanho e peso corporal em caprinos da raça Anglo-Nubiana criados na região Meio-Norte do Brasil. Métodos: os componentes de (co)variância e parâmetros genéticos foram estimados usando análises uni e bicaracterísticas de um modelo animal via metodologia Bayesiana para área, profundidade e comprimento de olho de lombo, espessura da gordura esternal, altura da garupa, circunferência e profundidade torácica, perímetro da perna e peso corporal. Resultados: as estimativas de herdabilidade obtidas a partir das análises bicaracterísticas foram maiores que as obtidas a partir das análises unicaracterísticas. Esse resultado implica que é possível recuperar parte da variância genética aditiva incluída na variância residual devido à correlação entre as características. As correlações genéticas entre as características de carcaça e as medidas corporais apresentaram magnitudes variáveis. Por outro lado, as correlações genéticas entre as características relacionadas à musculosidade apresentaram altas magnitudes. Conclusões: o peso corporal não se mostrou um bom indicador de muscularidade, de modo que não é recomendado como critério de seleção indireta para melhorar a carcaça de caprinos Anglo-Nubiano. O perímetro de perna e a circunferência torácica podem ser importantes para a construção de índices de seleção em programas de melhoramento de carne caprina.

SNP Panel Analysis of Ancestry Inference in East Asian Populations / 法医学杂志

Objective To develop an SNP Panel for East Asian population, which has a high individual identification rate and the capability of ancestry analysis. Methods The 55 SNP Panel by Professor KIDD of Yale University and the 128 SNP Panel by Professor SELDIN of Davis School of California University, 170 SNP Panel in total was used as the basis and its test data in the East Asian population was collected. The genetic parameters of SNP loci were calculated and combined with the results of heatmap analysis to screen SNP loci suitable for East Asian population. Some Tibetan and Han samples were tested. The possibility of using the SNP loci in ancestry inference was analyzed by means of STRUCTURE analysis, principal component analysis and heatmap analysis. Results A Panel with 45 SNPs （45 SNP Panel） was screened out, and the average genetic parameters of each SNP were better than 170 SNP Panel, with the same ancestry analysis and inference ability. Conclusion In terms of ancestry inference information, the 45 SNP Panel can completely replace the 170 SNP Panel and achieve the same ancestry analysis and inference ability. In genetic parameters, 45 SNP Panel is better than 170 SNP Panel in the East Asian population, which shows its important potential forensic application value.

Geolocation Inference of Forensic Individual Origin by Soil Metagenomic Analysis / 法医学杂志

Objective To preliminarily discuss the feasibility of geolocation inference of forensic individual origin by soil metagenomic analysis. Methods The 33 soil samples from Heilongjiang, Qinghai and Tibet were collected, total bacterial DNA in the samples were extracted, and universal primers were used to amplify the V3 and V4 hypervariable region of bacterial 16S rDNA. The region was sequenced by high-throughput sequencing （HTS） with the MiSeq sequencer. Bioinformatics analysis such as species composition and sample comparison was performed on sequencing data. The richness index and diversity index were calculated based on operational taxonomic unit （OTU） results. Results A total of 2 720 149 sequences were generated by sequencing. Those sequences were clustered into 114 848 OTUs. The Chao1 indexes of soil microorganisms in Heilongjiang, Qinghai, and Tibet were 797.45, 745.11 and 535.98, respectively, and Shannon indexes were 6.46, 6.36 and 6.25, respectively. The number of bacterial species and the community diversity in the soil from high to low were Heilongjiang > Qinghai > Tibet. The composition of soil bacteria in three provinces at various classification levels were obtained, the dominant genuses in Heilongjiang were Chthoniobacteraceae DA101 and an unannotated genus of Thermogemmatisporaceae; the dominant genuses in Qinghai were an unannotated genus of Cytophagaceae and an unannotated genus of Nocardioidaceae; the dominant genuses in Tibet were an unannotated genus of Comamonadaceae and Verrucomicrobiaceae Luteolibacter. The results of principal co-ordinates analysis demonstrated that, according to the weighted UniFrac analysis, the three principle components represented 56.36% of the total variable, and according to the unweighted UniFrac analysis, the three principle components represented 34.81% of the total variable. The samples from the same province could be clustered together, and the species and content of soil microorganisms from different provinces were significantly different. Conclusion Based on the metagenomic analysis method, soil samples from different regions can be effectively distinguished, which has potential application value in geolocation inference of forensic individual origin in the future.