Discriminating the effects of phylogenetic hypothesis,tree resolution and clade age estimates on phylogenetic signal measurements

Understanding how species traits evolved over time is the central question to comprehend assembly rules that govern the phylogenetic structure of communities. The measurement of phylogenetic signal (PS) in ecologically relevant traits is a first step to understand phylogenetically structured community patterns. The different methods available to estimate PS make it difficult to choose which is most appropriate. Furthermore, alternative phylogenetic tree hypotheses, node resolution and clade age estimates might influence PS measurements. In this study, we evaluated to what extent these parameters affect different methods of PS analysis, and discuss advantages and disadvantages when selecting which method to use. We measured fruit/seed traits and flowering/fruiting phenology of endozoochoric species occurring in Southern Brazilian Araucaria forests and evaluated their PS using Mantel regressions, phylogenetic eigenvector regressions (PVR) and K statistic. Mantel regressions always gave less significant results compared to PVR and K statistic in all combinations of phylogenetic trees constructed. Moreover, a better phylogenetic resolution affected PS, independently of the method used to estimate it. Morphological seed traits tended to show higher PS than diaspores traits, while PS in flowering/fruiting phenology depended mostly on the method used to estimate it. This study demonstrates that different PS estimates are obtained depending on the chosen method and the phylogenetic tree resolution. This finding has implications for inferences on phylogenetic niche conservatism or ecological processes determining phylogenetic community structure.     

Caloric restriction augments radiation efficacy in breast cancer

Dietary modification such as caloric restriction (CR) has been shown to decrease tumor initiation and progression. We sought to determine if nutrient restriction could be used as a novel therapeutic intervention to enhance cytotoxic therapies such as radiation (IR) and alter the molecular profile of triple-negative breast cancer (TNBC), which displays a poor prognosis. In two murine models of TNBC, significant tumor regression is noted with IR or diet modification, and a greater regression is observed combining diet modification with IR. Two methods of diet modification were compared, and it was found that a daily 30% reduction in total calories provided more significant tumor regression than alternate day feeding. At the molecular level, tumors treated with CR and IR showed less proliferation and more apoptosis. cDNA array analysis demonstrated the IGF-1R pathway plays a key role in achieving this physiologic response, and multiple members of the IGF-1R pathway including IGF-1R, IRS, PIK3ca and mTOR were found to be downregulated. The innovative use of CR as a novel therapeutic option has the potential to change the biology of tumors and enhance the opportunity for clinical benefit in the treatment of patients with TNBC.     

小儿喘息性疾病喘息反复发作的病原学及危险因素分析

摘要目的：分析小儿喘息性疾病病原学及与喘息发作有关的因素。方法：227例患儿来我院儿科住院的患儿,在有喘息发作及无喘息发作时均取分泌物进行细菌和病毒检测,并对可能与喘息发作有关的因素做统计分析。结果：喘息发作时细菌感染91例（40．1％）,病毒感染110例（48．5％）,无喘息时72例（31．7％）检出细菌感染,59例（26％）检出病毒感染,喘息发作时细菌和病毒感染检出率均显著高于无喘息时（P〈0．05）。单因素分析过敏史、细菌感染、病毒感染、被动吸烟史、家族史和季节等暴露因素在喘息次数超过和低于4次患儿之间存在差异（P〈O．05）。多因素非条件Logistic回归分析显示病毒感染（OR=2．839）、细菌感染（OR=2．434）、过敏史（OR=4．412）和家族史（OR=2．158）为喘息性疾病患儿喘息发作次数增多的主要危险因素。结论：病毒和细菌感染为小儿喘息性疾病的主要致病原,病毒和细菌感染、有过敏史与家族史是喘息反复发作的危险因素。     

Cubic regression-based degree of correction predicts the performance of whole bisulfitome amplified DNA methylation analysis

Epigenetic mechanisms, including DNA methylation, are important determinants in development and disease. There is a need for technologies capable of detecting small variations in methylation levels in an accurate and reproducible manner, even if only limited amounts of DNA are available (which is the case in many studies in humans). Quantitative methylation analysis of minute DNA amounts after whole bisulfitome amplification (qMAMBA) has been proposed as an alternative, but this technique has not been adequately standardized and no comparative study against conventional methods has been performed, that includes a wide range of methylation percentages and different target assays. We designed an experiment to compare the performance of qMAMBA and bisulfite-treated genomic (non-amplified) DNA pyrosequencing. Reactions were performed in duplicate for each technique in eight different target genes, using nine artificially constructed DNA samples with methylation levels ranging between 0% and 100% with intervals of 12.5%. Cubic polynomial curves were plotted from the experimental results and the real methylation values and the resulting equation was used to estimate new corrected data points. The use of the cubic regression-based correction benefits the accuracy and the power of discrimination in methylation studies. Additionally, dispersion of the new estimated data around a y = x line (R²) served to fix a cutoff that can discriminate, with a single 9-point curve experiment, whether whole bisulfitome amplification and subsequent qMAMBA can produce accurate methylation results. Finally, even with an optimized reagent kit, DNA samples subjected to whole bisulfitome amplification enhance the preferential amplification of unmethylated alleles, and subtle changes in methylation levels cannot be detected confidently.     

Comparison of random-effects meta-analysis models for the relative risk in the case of rare events: A simulation study

Pooling the relative risk (RR) across studies investigating rare events, for example, adverse events, via meta-analytical methods still presents a challenge to researchers. The main reason for this is the high probability of observing no events in treatment or control group or both, resulting in an undefined log RR (the basis of standard meta-analysis). Other technical challenges ensue, for example, the violation of normality assumptions, or bias due to exclusion of studies and application of continuity corrections, leading to poor performance of standard approaches. In the present simulation study, we compared three recently proposed alternative models (random-effects [RE] Poisson regression, RE zero-inflated Poisson [ZIP] regression, binomial regression) to the standard methods in conjunction with different continuity corrections and to different versions of beta-binomial regression. Based on our investigation of the models' performance in 162 different simulation settings informed by meta-analyses from the Cochrane database and distinguished by different underlying true effects, degrees of between-study heterogeneity, numbers of primary studies, group size ratios, and baseline risks, we recommend the use of the RE Poisson regression model. The beta-binomial model recommended by Kuss (2015) also performed well. Decent performance was also exhibited by the ZIP models, but they also had considerable convergence issues. We stress that these recommendations are only valid for meta-analyses with larger numbers of primary studies. All models are applied to data from two Cochrane reviews to illustrate differences between and issues of the models. Limitations as well as practical implications and recommendations are discussed; a flowchart summarizing recommendations is provided.     

Identification of novel prognostic alternative splicing signature in papillary renal cell carcinoma

Papillary renal cell carcinoma (pRCC) is a heterogeneous disease containing multifocal or solitary tumors with an aggressive phenotype. Increasing evidence has indicated the involvement of aberrant splicing variants in renal cell cancer, while systematic profiling of aberrant alternative splicing (AS) in pRCC was lacking and largely unknown. In the current study, comprehensive profiling of AS events were performed based on the integration of pRCC cohort from the Cancer Genome Atlas database and SpliceSeq software. With rigorous screening and univariate Cox analysis, a total of 2077 prognoses AS events from 1642 parent genes were identified. Then, stepwise least absolute shrinkage and selection operator method-penalized Cox regression analyses with 10-fold cross-validation followed by multivariate Cox regression were used to construct the prognostic AS signatures within each AS type. And a final 21 AS event-based signature was proposed which showed potent prognostic capability in stratifying patients into low- and high-risk subgroups (P < .0001). Furthermore, time-dependent receiver operating characteristics curves confirmed that the final AS signature was effective and robust in predicting overall survival for pRCC patients with the area under the curve above 0.9 from 1 to 5 years. In addition, splicing correlation network was built to uncover the potential regulatory pattern among prognostic splicing factors and candidate AS events. Besides, gene set enrichment analysis revealed the involvement of these candidates AS events in tumor-related pathways including extracellular matrix organization, oxidative phosphorylation, and P53 signaling pathways. Taken together, our results could contribute to elucidating the underlying mechanism of AS in the oncogenesis process and broaden the novel field of prognostic and clinical application of molecule-targeted approaches in pRCC.     

Physical maturity in common bottlenose dolphins (Tursiops truncatus) from Sarasota Bay,Florida

Cetacean physical maturity is defined by growth cessation and complete fusion of epiphyses to vertebral bodies indicated by invisible sutures. Many studies have shown epiphyseal fusion is highly variable among individuals. In-depth examinations into fusion variability are lacking. We analyzed vertebrae of 37 (n = 21 female, n = 16 male) stranded common bottlenose dolphins (Tursiops truncatus) from the well-studied Gulf of Mexico, Sarasota Bay community. For each specimen, vertebrae were examined by vertebral region for degree of fusion anteriorly and posteriorly of each centrum and categorized from unfused to fused in five degrees. An ordinal logistic regression was used to estimate degree of fusion probability for each epiphysis. The model had fixed effects for age, number of offspring, sex, sexual maturity, and a random effect for epiphysis. Results show that age/reproductive status significantly explains an individual's degree of fusion. Adult females with fewer calves had more fusion than those with more reproductive experience across multiple ages. Access to long-term observational and sample data on the dolphins residing in the area served by Mote Marine Laboratory's Stranding Investigations Program offers a unique opportunity to examine the relationship between energetic demands of reproduction (calcium production/reproductive output) versus preconceived definitions of physical maturity (skeletal fusion) more closely.     

A design criterion for symmetric model discrimination based on flexible nominal sets

Experimental design applications for discriminating between models have been hampered by the assumption to know beforehand which model is the true one, which is counter to the very aim of the experiment. Previous approaches to alleviate this requirement were either symmetrizations of asymmetric techniques, or Bayesian, minimax, and sequential approaches. Here we present a genuinely symmetric criterion based on a linearized distance between mean-value surfaces and the newly introduced tool of flexible nominal sets. We demonstrate the computational efficiency of the approach using the proposed criterion and provide a Monte-Carlo evaluation of its discrimination performance on the basis of the likelihood ratio. An application for a pair of competing models in enzyme kinetics is given.     

Comparison of complex modeling strategies for prediction of a binary outcome based on a few,highly correlated predictors

Motivated by a clinical prediction problem, a simulation study was performed to compare different approaches for building risk prediction models. Robust prediction models for hospital survival in patients with acute heart failure were to be derived from three highly correlated blood parameters measured up to four times, with predictive ability having explicit priority over interpretability. Methods that relied only on the original predictors were compared with methods using an expanded predictor space including transformations and interactions. Predictors were simulated as transformations and combinations of multivariate normal variables which were fitted to the partly skewed and bimodally distributed original data in such a way that the simulated data mimicked the original covariate structure. Different penalized versions of logistic regression as well as random forests and generalized additive models were investigated using classical logistic regression as a benchmark. Their performance was assessed based on measures of predictive accuracy, model discrimination, and model calibration. Three different scenarios using different subsets of the original data with different numbers of observations and events per variable were investigated. In the investigated setting, where a risk prediction model should be based on a small set of highly correlated and interconnected predictors, Elastic Net and also Ridge logistic regression showed good performance compared to their competitors, while other methods did not lead to substantial improvements or even performed worse than standard logistic regression. Our work demonstrates how simulation studies that mimic relevant features of a specific data set can support the choice of a good modeling strategy.