Repeatability for Gaussian and non‐Gaussian data: a practical guide for biologists

Repeatability (more precisely the common measure of repeatability, the intra‐class correlation coefficient, ICC) is an important index for quantifying the accuracy of measurements and the constancy of phenotypes. It is the proportion of phenotypic variation that can be attributed to between‐subject (or between‐group) variation. As a consequence, the non‐repeatable fraction of phenotypic variation is the sum of measurement error and phenotypic flexibility. There are several ways to estimate repeatability for Gaussian data, but there are no formal agreements on how repeatability should be calculated for non‐Gaussian data (e.g. binary, proportion and count data). In addition to point estimates, appropriate uncertainty estimates (standard errors and confidence intervals) and statistical significance for repeatability estimates are required regardless of the types of data. We review the methods for calculating repeatability and the associated statistics for Gaussian and non‐Gaussian data. For Gaussian data, we present three common approaches for estimating repeatability: correlation‐based, analysis of variance (ANOVA)‐based and linear mixed‐effects model (LMM)‐based methods, while for non‐Gaussian data, we focus on generalised linear mixed‐effects models (GLMM) that allow the estimation of repeatability on the original and on the underlying latent scale. We also address a number of methods for calculating standard errors, confidence intervals and statistical significance; the most accurate and recommended methods are parametric bootstrapping, randomisation tests and Bayesian approaches. We advocate the use of LMM‐ and GLMM‐based approaches mainly because of the ease with which confounding variables can be controlled for. Furthermore, we compare two types of repeatability (ordinary repeatability and extrapolated repeatability) in relation to narrow‐sense heritability. This review serves as a collection of guidelines and recommendations for biologists to calculate repeatability and heritability from both Gaussian and non‐Gaussian data.     

A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.)

Cicer arietinum L. (chickpea) is the third most important food legume crop. We have generated the draft sequence of a desi‐type chickpea genome using next‐generation sequencing platforms, bacterial artificial chromosome end sequences and a genetic map. The 520‐Mb assembly covers 70% of the predicted 740‐Mb genome length, and more than 80% of the gene space. Genome analysis predicts the presence of 27 571 genes and 210 Mb as repeat elements. The gene expression analysis performed using 274 million RNA‐Seq reads identified several tissue‐specific and stress‐responsive genes. Although segmental duplicated blocks are observed, the chickpea genome does not exhibit any indication of recent whole‐genome duplication. Nucleotide diversity analysis provides an assessment of a narrow genetic base within the chickpea cultivars. We have developed a resource for genetic markers by comparing the genome sequences of one wild and three cultivated chickpea genotypes. The draft genome sequence is expected to facilitate genetic enhancement and breeding to develop improved chickpea varieties.     

Comparison between the cultures of human induced pluripotent stem cells (hiPSCs) on feeder-and serum-free system (Matrigel matrix), MEF and HDF feeder cell lines

Human induced pluripotent stem cells (hiPSCs) are a type of pluripotent stem cells artificially derived from an adult somatic cell (typically human fibroblast) by forced expression of specific genes. In recent years, different feeders like inactivated mouse embryonic fibroblasts (MEFs), human dermal fibroblasts (HDFs), and feeder free system have commonly been used for supporting the culture of stem cells in undifferentiated state. In the present work, the culture of hiPSCs and their characterizations on BD Matrigel (feeder-and serum-free system), MEF and HDF feeders using cell culture methods and molecular techniques were evaluated and compared. The isolated HDFs from foreskin samples were reprogrammed to hiPSCs using gene delivery system. Then, the pluripotency ability of hiPSCs cultured on each layer was determined by teratoma formation and immunohistochemical staining. After EBs generation the expression level of three germ layers genes were evaluated by Q-real-time PCR. Also, the cytogenetic stability of hiPSCs cultured on each condition was analyzed by karyotyping and comet assay. Then, the presence of pluripotency antigens were confirmed by Immunocytochemistry (ICC) test and alkaline phosphatase staining. This study were showed culturing of hiPSCs on BD Matrigel, MEF and HDF feeders had normal morphology and could maintain in undifferentiated state for prolonged expansion. The hiPSCs cultured in each system had normal karyotype without any chromosomal abnormalities and the DNA lesions were not observed by comet assay. Moreover, up-regulation in three germ layers genes in cultured hiPSCs on each layer (same to ESCs) compare to normal HDFs were observed (p < 0.05). The findings of the present work were showed in stem cells culturing especially hiPSCs both MEF and HDF feeders as well as feeder free system like Matrigel are proper despite benefits and disadvantages. Although, MEFs is suitable for supporting of stem cell culturing but it can animal pathogens transferring and inducing immune response. Furthermore, HDFs have homologous source with hiPSCs and can be used as feeder instead of MEF but in therapeutic approaches the cells contamination is a problem. So, this study were suggested feeder free culturing of hiPSCs on Matrigel in supplemented media (without using MEF conditioned medium) resolves these problems and could prepare easy applications of hiPSCs in therapeutic approaches of regenerative medicine such as stem-cell therapy and somatic cell nuclear in further researches.     

Roles of interstitial cells of Cajal in regulating gastrointestinal motility: in vitro versus in vivo studies

The aim of this article is to provide a better understanding of the roles of interstitial cells of Cajal (ICC) in regulating gastrointestinal motility by reviewing in vitro and in vivo physiological motility studies. Based on the in vitro studies, ICC are proposed to have the following functions: to generate slow waves, to mediate neurotransmission between the enteric nerves and the gastrointestinal muscles and to act as mechanoreceptors. However, there is limited evidence available for these hypotheses from the in vivo motility studies. In this review, we first introduce the major subtypes of ICC and their established functions. Three Kit mutant mouse and rodent models are presented and the loss of ICC subtypes in these mutants is reviewed. The physiological motility findings from various in vitroand in vivo experiments are discussed to give a critical review on the roles of ICC in generating slow waves, regulating gastrointestinal motility, mediating neural transmission and serving as mechanoreceptors. It is concluded that the role of ICC as pacemakers may be well established, but other cells may also be involved in the generation of slow waves; the theory that ICC are mediators of neurotransmission is challenged by the majority of the in vivo motility studies; the hypothesis that ICC are mechanoreceptors has not found supportive evidence from the in vivo studies yet. More studies are needed to explain discrepancies in motility findings between the in vitro and in vivo experiments.     

Repeatability of maximal voluntary force and of surface EMG variables during voluntary isometric contraction of quadriceps muscles in healthy subjects

The repeatability of initial values and rate of change of EMG signal mean spectral frequency (MNF), average rectified values (ARV), muscle fiber conduction velocity (CV) and maximal voluntary contraction (MVC) was investigated in the vastus medialis obliquus (VMO) and vastus lateralis (VL) muscles of both legs of nine healthy male subjects during voluntary, isometric contractions sustained for 50 s at 50% MVC. The values of MVC were recorded for both legs three times on each day and for three subsequent days, while the EMG signals have been recorded twice a day for three subsequent days. The degree of repeatability was investigated using the Fisher test based upon the ANalysis Of VAriance (ANOVA), the Standard Error of the Mean (SEM) and the Intraclass Correlation Coefficient (ICC).

Data collected showed a high level of repeatability of MVC measurement (normalized SEM from 1.1% to 6.4% of the mean). MNF and ARV initial values also showed a high level of repeatability (ICC>70% for all muscles and legs except right VMO). At 50% MVC level no relevant pattern of fatigue was observed for the VMO and VL muscles, suggesting that other portions of the quadriceps might have contributed to the generated effort. These observations seem to suggest that in the investigation of muscles belonging to a multi-muscular group at submaximal level, the more selective electrically elicited contractions should be preferred to voluntary contractions.     

Maintaining viability and characteristics of cholangiocarcinoma tissue by vitrification-based cryopreservation

Tumor tissue has great clinical and scientific value which relies highly on the proper preservation of primary materials. Conventional tumor tissue cryopreservation using slow-freezing method has yielded limited success, leading to significant cell loss and morphological damage. Here we report a standardized vitrification-based cryopreservation method, by which we have successfully vitrified and warmed 35 intrahepatic cholangiocarcinoma (ICC) tissues with up to 80% viability of the fresh tumor tissues. Cryopreserved ICC tissue could generate patient-derived xenografts (PDXs) with take rates of 68.2% compared to 72.7% using fresh tumor tissues. Histological and genetic analyses showed that no significant alterations in morphology and gene expression were introduced by this cryopreservation method. Our procedure may facilitate collection, long-time storage and propagation of cholangiocarcinoma or other tumor specimens for (pre)clinical studies of novel therapies or for basic research.     

Local dynamic stability of treadmill walking: Intrasession and week-to-week repeatability

Repetitive falls degrade the quality of life of elderly people and of patients suffering of various neurological disorders. In order to prevent falls while walking, one should rely on relevant early indicators of impaired dynamic balance. The local dynamic stability (LDS) represents the sensitivity of gait to small perturbations: divergence exponents (maximal Lyapunov exponents) assess how fast a dynamical system diverges from neighbor points. Although numerous findings attest the validity of LDS as a fall risk index, reliability results are still sparse. The present study explores the intrasession and intersession repeatability of gait LDS using intraclass correlation coefficients (ICC) and standard error of measurement (SEM). Ninety-five healthy individuals performed 5 min treadmill walking in two sessions separated by 9 days. Trunk acceleration was measured with a 3D accelerometer. Three time scales were used to estimate LDS: over 4–10 strides (λ_4–10), over one stride (λ₁) and over one step (λ_0.5). The intrasession repeatability was assessed from three repetitions of either 35 strides or 70 strides taken within the 5 min tests. The intersession repeatability compared the two sessions, which totalized 210 strides. The intrasession ICCs (70-strides estimates/35-strides estimates) were 0.52/0.18 for λ_4–10 and 0.84/0.77 for λ₁ and λ_0.5. The intersession ICCs were around 0.60. The SEM results revealed that λ_0.5 measured in medio-lateral direction exhibited the best reliability, sufficient to detect moderate changes at individual level (20%). However, due to the low intersession repeatability, one should average several measurements taken on different days in order to better approximate the true LDS.     

Ultrastructure of interstitial cells of Cajal in myenteric plexus of human colon

The role of the interstitial cells of Cajal (ICC) associated with the myenteric plexus (ICC-MP) as regulators of the motility of the colonic external muscle remains unclear. Ultrastructural studies of myenteric interstitial cells are lacking in human colon. We therefore characterized the distinctive ultrastructure of these cells in the myenteric region of the colon by transmission electron microscopy of the region between the main muscle layers in all parts of the colon in unaffected areas of resected specimens from nine adult human patients. ICC-MP were similar in various colonic regions and had myoid features such as scattered caveolae, prominent intermediate filaments, and cytoplasmic dense bodies. We found characteristic dense membrane-associated bands with a patchy basal lamina, invaginating cellular protrusions (peg and socket junctions) between ICC and between ICC and muscle cells, and close contacts (<100 nm) between ICC and nerves. No gap junctions were observed. Fibroblast-like cells (FLC) were abundant showing well-developed secretory organelles, including coated vesicles, but lacked prominent intermediate filaments and caveolae. FLC had a patchy basal lamina, and peg and socket junctions were observed between them. Macrophage-like cells frequently occurred in close apposition with FLC and, more seldomly, with ICC-MP. The ultrastructure of ICC and FLC in the myenteric region of the human colon thus differs characteristically, but significant overlaps in the ultrastructure between ICC and FLC might complicate any interpretation in pathological ultrastructural studies of the human colonic muscle layer. An erratum to this article can be found at     

Quantifying intraclass correlations for count and time‐to‐event data

The intraclass correlation is commonly used with clustered data. It is often estimated based on fitting a model to hierarchical data and it leads, in turn, to several concepts such as reliability, heritability, inter‐rater agreement, etc. For data where linear models can be used, such measures can be defined as ratios of variance components. Matters are more difficult for non‐Gaussian outcomes. The focus here is on count and time‐to‐event outcomes where so‐called combined models are used, extending generalized linear mixed models, to describe the data. These models combine normal and gamma random effects to allow for both correlation due to data hierarchies as well as for overdispersion. Furthermore, because the models admit closed‐form expressions for the means, variances, higher moments, and even the joint marginal distribution, it is demonstrated that closed forms of intraclass correlations exist. The proposed methodology is illustrated using data from agricultural and livestock studies.