Bayesian inference for discretely observed continuous time multi-state models.

Multi-state models are frequently applied to represent processes evolving through a discrete set of states. Important classes of multi-state models arise when transitions between states may depend on the time passed since entry into the current state or on the time elapsed from the start of the process. The former models are called semi-Markov while the latter are known as inhomogeneous Markov models. Inference for both the models presents computational difficulties when the process is only observed at discrete time points with no additional information about the state transitions. In fact, in both the cases, the likelihood function is not available in closed form. To obtain Bayesian inference under these two classes of models, we reconstruct the entire unobserved trajectories conditioned on the observed points via a Metropolis-Hastings algorithm. As proposal density we use that given by the nested Markov models whose conditioned trajectories can easily be drawn with the uniformization technique. The resulting inference is illustrated via simulation studies and the analysis of two benchmark datasets for multi-state models.

Bayesian analysis of one-inflated models for elusive population size estimation.

The identification and treatment of "one-inflation" in estimating the size of an elusive population has received increasing attention in capture-recapture literature in recent years. The phenomenon occurs when the number of units captured exactly once clearly exceeds the expectation under a baseline count distribution. Ignoring one-inflation has serious consequences for estimation of the population size, which can be drastically overestimated. In this paper we propose a Bayesian approach for Poisson, geometric, and negative binomial one-inflated count distributions. Posterior inference for population size will be obtained applying a Gibbs sampler approach. We also provide a Bayesian approach to model selection. We illustrate the proposed methodology with simulated and real data and propose a new application in official statistics to estimate the number of people implicated in the exploitation of prostitution in Italy.

Approximate Bayesian inference for discretely observed continuous-time multi-state models.

Inference for continuous time multi-state models presents considerable computational difficulties when the process is only observed at discrete time points with no additional information about the state transitions. In fact, for general multi-state Markov model, evaluation of the likelihood function is possible only via intensive numerical approximations. Moreover, in real applications, transitions between states may depend on the time since entry into the current state, and semi-Markov models, where the likelihood function is not available in closed form, should be fitted to the data. Approximate Bayesian Computation (ABC) methods, which make use only of comparisons between simulated and observed summary statistics, represent a solution to intractable likelihood problems and provide alternative algorithms when the likelihood calculation is computationally too costly. In this article we investigate the potentiality of ABC techniques for multi-state models both to obtain the posterior distributions of the model parameters and to compare Markov and semi-Markov models. In addition, we will also exploit ABC methods to estimate and compare hidden Markov and semi-Markov models when observed states are subject to classification errors. We illustrate the performance of the ABC methodology both with simulated data and with a real data example.

Efficient mitochondrial biogenesis drives incomplete penetrance in Leber's hereditary optic neuropathy.

Leber's hereditary optic neuropathy is a maternally inherited blinding disease caused as a result of homoplasmic point mutations in complex I subunit genes of mitochondrial DNA. It is characterized by incomplete penetrance, as only some mutation carriers become affected. Thus, the mitochondrial DNA mutation is necessary but not sufficient to cause optic neuropathy. Environmental triggers and genetic modifying factors have been considered to explain its variable penetrance. We measured the mitochondrial DNA copy number and mitochondrial mass indicators in blood cells from affected and carrier individuals, screening three large pedigrees and 39 independently collected smaller families with Leber's hereditary optic neuropathy, as well as muscle biopsies and cells isolated by laser capturing from post-mortem specimens of retina and optic nerves, the latter being the disease targets. We show that unaffected mutation carriers have a significantly higher mitochondrial DNA copy number and mitochondrial mass compared with their affected relatives and control individuals. Comparative studies of fibroblasts from affected, carriers and controls, under different paradigms of metabolic demand, show that carriers display the highest capacity for activating mitochondrial biogenesis. Therefore we postulate that the increased mitochondrial biogenesis in carriers may overcome some of the pathogenic effect of mitochondrial DNA mutations. Screening of a few selected genetic variants in candidate genes involved in mitochondrial biogenesis failed to reveal any significant association. Our study provides a valuable mechanism to explain variability of penetrance in Leber's hereditary optic neuropathy and clues for high throughput genetic screening to identify the nuclear modifying gene(s), opening an avenue to develop predictive genetic tests on disease risk and therapeutic strategies.

m6A modification inhibits miRNAs' intracellular function, favoring their extracellular export for intercellular communication.

Epitranscriptomics represents a further layer of gene expression regulation. Specifically, N6-methyladenosine (m6A) regulates RNA maturation, stability, degradation, and translation. Regarding microRNAs (miRNAs), while it has been reported that m6A impacts their biogenesis, the functional effects on mature miRNAs remain unclear. Here, we show that m6A modification on specific miRNAs weakens their coupling to AGO2, impairs their function on target mRNAs, determines their delivery into extracellular vesicles (EVs), and provides functional information to receiving cells. Mechanistically, the intracellular functional impairment is caused by m6A-mediated inhibition of AGO2/miRNA interaction, the EV loading is favored by m6A-mediated recognition by the RNA-binding protein (RBP) hnRNPA2B1, and the EV-miRNA function in the receiving cell requires their FTO-mediated demethylation. Consequently, cells express specific miRNAs that do not impact endogenous transcripts but provide regulatory information for cell-to-cell communication. This highlights that a further level of complexity should be considered when relating cellular dynamics to specific miRNAs.

From diverticulosis to complicated diverticular disease: Progression of myogenic alterations and oxidative imbalance.

BACKGROUND: The natural history and pathophysiology of diverticular disease (DD) are still uncertain. An ex-vivo human complicated DD (cDD) model has recently shown a predominant transmural oxidative imbalance. The present study aims to evaluate whether the previously described alterations may precede the symptomatic form of the disease. METHODS: Colonic surgical samples obtained from patients with asymptomatic diverticulosis (DIV), complicated DD, and controls were systematically and detailed morphologically and molecularly analyzed. Therefore, histologic, histomorphometric, immunohistochemical evaluation, and gene and protein expression analysis were performed to characterize colonic muscle changes and evaluate chronic inflammation, oxidative imbalance, and hypoxia. Functional muscle activity was tested on strips and isolated cells in response to contractile and relaxant agents. KEY RESULTS: Compared with controls, DD showed a marketed increase in muscle layer thickness, smooth muscle cell syncytium disarray, and increased interstitial fibrosis; moreover, the observed features were more evident in the cDD group. These changes mainly affected longitudinal muscle and were associated with altered contraction-relaxation dynamics and fibrogenic switch of smooth muscle cells. Chronic lymphoplasmacytic inflammation was primarily evident in the mucosa and spared the muscle. A transmural increase in carbonylated and nitrated proteins, with loss of antioxidant molecules, characterized both stages of DD, suggesting early oxidative stress probably triggered by recurrent ischemic events, more pronounced in cDD, where HIF-1 was detected in both muscle and mucosa. CONCLUSION & INFERENCES: The different DD clinical scenarios are part of a progressive process, with oxidative imbalance representing a new target in the management of DD.

A new double immunohistochemistry method to detect mucosal anti-transglutaminase IgA deposits in coeliac children.

BACKGROUND: Intestinal transglutaminase (TG2) IgA deposits represent early marker of coeliac disease (CeD) and can predict the evolution towards intestinal atrophy. AIMS: To validate a double immunohistochemistry method for the determination of intestinal TG2 IgA deposits on formalin-fixed paraffin-embedded biopsies. METHODS: Immunohistochemistry was tested on: 1) children with overt CeD [persistently positive serum IgA anti-tissue transglutaminase type 2 (TGA-IgA) with moderate or low titer, and histological findings of CeD]; 2) potential CeD (persistently positive serum TGA-IgA and normal intestinal mucosa) and 3) controls (negative serum TGA-IgA and normal intestinal mucosa). RESULTS: Samples from 61 children were analyzed (32 overt CeD, 14 potential CeD, and 15 controls). Deposits appeared as focal, multifocal, or confluent extracellular foci of red and brown staining colocalization in the sub-epithelium and around mucosal vessels. Deposits were present in all 32 children with overt CeD and in 9/14 potential CeD. Deposits were never observed in the 15 controls. Patients with higher serum level of TGA-IgA and with mucosal atrophy showed mostly a multifocal/diffuse pattern of deposits distribution. The bulb appeared most severely involved. In potential CeD deposits showed mainly a focal distribution. CONCLUSION: Our results indicate double immunohistochemistry as promising diagnostic tool to improve diagnosis of CeD.

Gastrointestinal dysmotility in mitochondrial neurogastrointestinal encephalomyopathy is caused by mitochondrial DNA depletion.

Chronic intestinal pseudo-obstruction is a life-threatening condition of unknown pathogenic mechanisms. Chronic intestinal pseudo-obstruction can be a feature of mitochondrial disorders, such as mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), a rare autosomal-recessive syndrome, resulting from mutations in the thymidine phosphorylase gene. MNGIE patients show elevated circulating levels of thymidine and deoxyuridine, and accumulate somatic mitochondrial DNA (mtDNA) defects. The present study aimed to clarify the molecular basis of chronic intestinal pseudo-obstruction in MNGIE. Using laser capture microdissection, we correlated the histopathological features with mtDNA defects in different tissues from the gastrointestinal wall of five MNGIE and ten control patients. We found mtDNA depletion, mitochondrial proliferation, and smooth cell atrophy in the external layer of the muscularis propria, in the stomach and in the small intestine of MNGIE patients. In controls, the lowest amounts of mtDNA were present at the same sites, as compared with other layers of the gastrointestinal wall. We also observed mitochondrial proliferation and mtDNA depletion in small vessel endothelial and smooth muscle cells. Thus, visceral mitochondrial myopathy likely causes gastrointestinal dysmotility in MNGIE patients. The low baseline abundance of mtDNA molecules may predispose smooth muscle cells of the muscularis propria external layer to the toxic effects of thymidine and deoxyuridine, and exposure to high circulating levels of nucleosides may account for the mtDNA depletion observed in the small vessel wall.

The effect of recombinant PTH(1-34) and PTH(1-84) on serum ionized calcium, 1,25-dihydroxyvitamin D, and urinary calcium excretion: a pilot study.

We investigated the frequency of hypercalcemia and/or hypercalciuria following parathyroid hormone (PTH) 1-34 and 1-84 administration in a crossover trial. Ten postmenopausal osteoporotic women previously treated with bisphosphonates were subdivided into two groups of five patients each. A 24-h urine collection to determine baseline calcium (Ca) and creatinine (Cr) the day before administration of PTH was followed by determination of serum ionized Ca (Ca(2+)), Cr, 25(OH)D, and 1,25(OH)(2)D at baseline. Thereafter, 100 mcg of PTH(1-84) or 20 mcg of PTH(1-34) was administered. A 24-h urinary collection and blood samples 2, 4, and 24-h after each PTH administration were again taken. One week after the first PTH administration patients were rechallenged with the second PTH. The PTH peptides did not differ with respect to changes in Ca(2+) at 2, 4, and 24 h postinjection; at the last time point the values were virtually identical to the initial values. There was no difference in urinary Ca on the day following PTH injection compared to baseline, in terms both of Ca/Cr and of Ca excretion. The two PTH peptides did not differ with respect to changes in 1,25(OH)(2)D at 2, 4, and 24 h considering both the absolute values and the percent changes with respect to baseline (24-h 1-84 = 125.6 + or - 58.6 pg/ml, 153% increase; 1-34 = 124.1 + or - 64.7, 130%). Our results indicate no difference in postinjection serum Ca(2+), 1,25(OH)(2)D, or urinary Ca excretion after a single dose of either PTH(1-84) or PTH(1-34) in patients previously treated with bisphosphonates.

A Bayesian model averaging approach for cost-effectiveness analyses.

We consider the problem of assessing new and existing technologies for their cost-effectiveness in the case where data on both costs and effects are available from a clinical trial, and we address it by means of the cost-effectiveness acceptability curve. The main difficulty in these analyses is that cost data usually exhibit highly skew and heavy-tailed distributions so that it can be extremely difficult to produce realistic probabilistic models for the underlying population distribution, and in particular to model accurately the tail of the distribution, which is highly influential in estimating the population mean. Here, in order to integrate the uncertainty about the model into the analysis of cost data and into cost-effectiveness analyses, we consider an approach based on Bayesian model averaging: instead of choosing a single parametric model, we specify a set of plausible models for costs and estimate the mean cost with a weighted mean of its posterior expectations under each model, with weights given by the posterior model probabilities. The results are compared with those obtained with a semi-parametric approach that does not require any assumption about the distribution of costs.

Muscle strength and bone in healthy women: effect of age and gonadal status.

OBJECTIVE: The aim of this work was to examine the effects of age and menopause on muscle strength and on the muscle-bone interaction. DESIGN: One hundred ninety-four healthy women (mean age 49.8 ± 12.6 SD years) were assessed. Maximal Voluntary Contraction (MVC, Newton, N) by Hand Grip Dynamometer, bone mineral density at one third of the radius (R-BMD) by dual-energy X-ray absorptiometry (DXA) and phalangeal ultrasound by the DBM Sonic 1200 device were evaluated at the upper dominant limb. Ultrasonometric parameters considered were Amplitude-Dependent Speed of Sound (ADSoS) and Ultrasound Bone Profile Index (UBPI). RESULTS: MVC significantly decreased with age (r²=-0.12, p<0.005). For each level of age, fertile women had a greater MVC compared to postmenopausal women (r²=0.015, p<0.005).In the whole sample, a statistically significant correlation between MVC and R-BMD (r=0.354, p<0.001) and between MVC and ADSoS (r=0.294) and UBPI (r=0.311)(p<0.001 for both) were observed. CONCLUSIONS: We conclude that age and menopausal status significantly contributed to the reduction of muscle strength. The decline of muscular strength significantly correlated with quantitative and qualitative bone features.

Mitochondrial neurogastrointestinal encephalomyopathy: evidence of mitochondrial DNA depletion in the small intestine.

BACKGROUND & AIMS: Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an autosomal recessive disease clinically defined by gastrointestinal dysmotility, cachexia, ptosis, ophthalmoparesis, peripheral neuropathy, white-matter changes in brain magnetic resonance imaging, and mitochondrial abnormalities. Loss-of-function mutations in thymidine phosphorylase gene induce pathologic accumulations of thymidine and deoxyuridine that in turn cause mitochondrial DNA (mtDNA) defects (depletion, multiple deletions, and point mutations). Our study is aimed to define the molecular basis of gastrointestinal dysmotility in a case of MNGIE. METHODS: By using laser capture microdissection techniques, we correlated histologic features with mtDNA abnormalities in different tissue components of the gastrointestinal wall in a MNGIE patient and ten controls. RESULTS: The patient's small intestine showed marked atrophy and mitochondrial proliferation of the external layer of muscularis propria. Genetic analysis revealed selective depletion of mtDNA in the small intestine compared with esophagus, stomach, and colon, and microdissection analysis revealed that mtDNA depletion was confined to the external layer of muscularis propria. Multiple deletions were detected in the upper esophagus and skeletal muscle. Site-specific somatic point mutations were detected only at low abundance both in the muscle and nervous tissue of the gastrointestinal tract. Analysis of the gastrointestinal tract from 10 controls revealed a non-homogeneous distribution of mtDNA content; the small intestine had the lowest levels of mtDNA. CONCLUSION: Atrophy, mitochondrial proliferation, and mtDNA depletion in the external layer of muscularis propria of small intestine indicate that visceral myopathy is responsible for gastrointestinal dysmotility in this MNGIE patient.