Changes in Gut Bacterial Translation Occur before Symptom Onset and Dysbiosis in Dextran Sodium Sulfate-Induced Murine Colitis.

Longitudinal studies on the gut microbiome that follow the effect of a perturbation are critical in understanding the microbiome's response and succession to disease. Here, we use a dextran sodium sulfate (DSS) mouse model of colitis as a tractable perturbation to study how gut bacteria change their physiology over the course of a perturbation. Using single-cell methods such as flow cytometry, bioorthogonal noncanonical amino acid tagging (BONCAT), and population-based cell sorting combined with 16S rRNA sequencing, we determine the diversity of physiologically distinct fractions of the gut microbiota and how they respond to a controlled perturbation. The physiological markers of bacterial activity studied here include relative nucleic acid content, membrane damage, and protein production. There is a distinct and reproducible succession in bacterial physiology, with an increase in bacteria with membrane damage and diversity changes in the translationally active fraction, both, critically, occurring before symptom onset. Large increases in the relative abundance of Akkermansia were seen in all physiological fractions, most notably in the translationally active bacteria. Performing these analyses within a detailed, longitudinal framework determines which bacteria change their physiology early on, focusing therapeutic efforts in the future to predict or even mitigate relapse in diseases like inflammatory bowel diseases. IMPORTANCE Most studies on the gut microbiome focus on the composition of this community and how it changes in disease. However, how the community transitions from a healthy state to one associated with disease is currently unknown. Additionally, common diversity metrics do not provide functional information on bacterial activity. We begin to address these two unknowns by following bacterial activity over the course of disease progression, using a tractable mouse model of colitis. We find reproducible changes in gut bacterial physiology that occur before symptom onset, with increases in the proportion of bacteria with membrane damage, and changes in community composition of the translationally active bacteria. Our data provide a framework to identify possible windows of intervention and which bacteria to target in microbiome-based therapeutics.

Parametric modelling of prevalent cohort data with uncertainty in the measurement of the initial onset date.

In prevalent cohort studies with follow-up, if disease duration is the focus, the date of onset must be obtained retrospectively. For some diseases, such as Alzheimer's disease, the very notion of a date of onset is unclear, and it can be assumed that the reported date of onset acts only as a proxy for the unknown true date of onset. When adjusting for onset dates reported with error, the features of left-truncation and potential right-censoring of the failure times must be modeled appropriately. Under the assumptions of a classical measurement error model for the onset times and an underlying parametric failure time model, we propose a maximum likelihood estimator for the failure time distribution parameters which requires only the observed backward recurrence times. Costly and time-consuming follow-up may therefore be avoided. We validate the maximum likelihood estimator on simulated datasets under varying parameter combinations and apply the proposed method to the Canadian Study of Health and Aging dataset.

Long-term effects of intermittent androgen suppression therapy on lean and fat mass: a 33-month prospective study.

BACKGROUND: To examine changes to whole body and regional lean mass (LM) and fat mass (FM) over 33 months of intermittent androgen suppression therapy (IAST). METHODS: Phase II cohort study of 72 prostate cancer patients without metastatic bone disease. Patients received flutamide 250 mg tid and leuprolide 22.5 mg three monthly depot for the 9-month initial treatment phase (iTREAT), at which point patients ceased therapy providing PSA <4 ng ml(-1) with continued monitoring for further 2 years (POST). AST was recommenced when PSA exceeded pretreatment level or ≥ 20 ng ml(-1). Body composition was assessed using dual energy X-ray absorptiometry at baseline, completion of treatment phase, and 1 and 2 years post treatment phase (months 21 and 33). RESULTS: LM decreased by 1.3 kg and FM increased by 2.3 kg (P<0.001) following iTREAT. During the POST period, there were no further adverse effects on LM or FM, but also no recovery to pretreatment levels. Patients who failed to recover testosterone by month 33 experienced a significant increase in FM compared with those who recovered eugonadal levels of testosterone (10 nmol ml(-1); P = 0.019). Change in testosterone was moderately correlated to changes in % FM (r = -0.314, P<0.028) and LM (r = 0.300, P<0.036) during POST phase. Waist circumference progressively increased over time and by 2 years, POST had not recovered to baseline levels. CONCLUSIONS: Loss of LM and gain in FM during the 9-month iTREAT was not reversed during 2-year POST, although further deterioration was not observed. Subgroup analysis identified those recovering testosterone showed some body composition improvements. These findings suggest potential benefits of IAST, where testosterone levels are able to recover, to reduce the ongoing adverse effects on body composition, such as the acceleration of sarcopenia and risks associated with metabolic disease.

Marginal Structural Models: unbiased estimation for longitudinal studies.

INTRODUCTION: In this article, we introduce Marginal Structural Models, which yield unbiased estimates of causal effects of exposures in the presence of time-varying confounding variables that also act as mediators. OBJECTIVES: We describe estimation via inverse probability weighting; estimation may also be accomplished by g-computation (Robins in Latent Variable Modeling and Applications to Causality, Springer, New York, pp 69-117, 1997; van der Wal et al. in Stat Med 28:2325-2337, 2009) or targeted maximum likelihood (Rosenblum and van der Laan in Int J Biostat 6, 2010). CONCLUSIONS: When both time-varying confounding and mediation are present in a longitudinal setting data, Marginal Structural Models are a useful tool that provides unbiased estimates.

Using Directed Acyclic Graphs to detect limitations of traditional regression in longitudinal studies.

INTRODUCTION: Longitudinal data are increasingly available to health researchers; these present challenges not encountered in cross-sectional data, not the least of which is the presence of time-varying confounding variables and intermediate effects. OBJECTIVES: We review confounding and mediation in a longitudinal setting and introduce causal graphs to explain the bias that arises from conventional analyses. CONCLUSIONS: When both time-varying confounding and mediation are present in the data, traditional regression models result in estimates of effect coefficients that are systematically incorrect, or biased. In a companion paper (Moodie and Stephens in Int J Publ Health, 2010b, this issue), we describe a class of models that yield unbiased estimates in a longitudinal setting.

Effect of a proton pump inhibitor on postprandial gastric volume, emptying and symptoms in healthy human subjects: a pilot study.

BACKGROUND: In consensus guidelines, proton pump inhibitors (PPIs) are recommended for the treatment of functional dyspepsia. It is unclear whether PPIs change gastric volume or emptying. AIM: To assess the effect of a PPI, rabeprazole, on gastric volume and emptying and postprandial symptoms. METHODS: In a double-blind, parallel-group placebo-controlled trial, 13 healthy participants were randomized to rabeprazole, 20 mg b.d., or placebo. On day 3, fasting gastric volume was measured using intravenous (99m)Tc-pertechnate and single photon emission computed tomography (SPECT). After the last dose of study medication, an (111)In-chloride egg meal (300 kcal) was ingested, and postprandial gastric volume and emptying were measured by SPECT. Symptom ratings using a visual analogue scale (fullness, nausea, bloating, abdominal pain, aggregate score) were obtained at baseline and 15, 30, 45, 60 and 75 min postprandially. Group comparisons were performed using Mann-Whitney rank sum test. RESULTS: There were no statistically significant differences in gastric volume or emptying in the two groups. However, there was a borderline increase in gastric volume with rabeprazole compared with placebo. Rabeprazole treatment reduced aggregate postprandial symptoms, particularly fullness, 30 min after the meal (P = 0.01). CONCLUSIONS: In healthy participants, rabeprazole, 20 mg b.d., did not significantly change gastric emptying, but reduced symptoms and had a borderline effect on gastric volume postprandially. The mechanism of reduced postprandial symptoms with a PPI requires further study.

Effect of female sex hormone supplementation and withdrawal on gastrointestinal and colonic transit in postmenopausal women.

Females are disproportionately affected by constipation, which is often aggravated during pregnancy. Bowel function also changes during the luteal phase of the menstrual cycle. The aim was to compare the effects of acute administration of female sex steroids on gastric emptying, small bowel transit and colonic transit in healthy postmenopausal subjects. A second aim was to determine whether withdrawal of the hormones was associated with a change in transit. Forty-nine postmenopausal females were randomized to receive for 7 days 400 mg day(-1) micronized progesterone, 0.2 mg day(-1) oestradiol, combination of the two, or placebo. Treatment groups were balanced on age. Participants underwent whole gut transit measurement by scintigraphy using a 99m-labeled technetium-egg meal and 111-labeled indium-charcoal via a delayed-release capsule. Transit measurement was repeated after withdrawal of the study medications. The primary endpoints were ascending colon (AC) emptying half-life time (t1/2) and colonic geometric centre (GC) at 24 h. Secondary analysis variables were GC at 4 and 48 h, gastric emptying t1/2 and colonic filling at 6 h. There was a significant overall effect of progesterone on colonic transit with shorter AC emptying t1/2 and significantly greater colonic GC at 48 h. No transit endpoints were altered by oestradiol or combined hormonal treatment relative to placebo. Oestradiol and progesterone resulted in looser stool consistency. Withdrawal of the hormone supplement was not associated with significant alteration in transit. Micronized progesterone does not retard colonic transit in postmenopausal females.

Effect of cyclooxygenase-2 inhibitors on gastric emptying and small intestinal transit in humans.

Endogenous prostaglandins regulate smooth muscle activity; prostaglandins and cyclooxygenase (COX) inhibitors influence gastrointestinal motility in inflammatory states such as postoperative ileus in animal models. The objective of this study was to evaluate the effects of two COX-2 inhibitors on gastric emptying and intestinal transit in healthy humans. In a double-blind, placebo-controlled, parallel-group study, 66 healthy volunteers were randomized to one of two commercially available oral COX-2 inhibitors (celecoxib and rofecoxib), cisapride (positive control), or placebo. Following 7 days on therapy, study participants underwent a test of gastric emptying and small bowel transit of liquids and solids using scintigraphy. Data were analysed using Kruskal-Wallis (ANOVA on ranks)and Mann-Whitney rank sum tests. There were significant group effects on transit of solids: gastric emptying (ANOVA, P = 0.005) and small bowel transit (ANOVA, P = 0.056). However, neither COX-2 inhibitor significantly accelerated the liquid or solid gastric emptying or small bowel transit compared with placebo. The positive control, cisapride, accelerated gastric emptying of solids (post-lag slope of gastric emptying, P < 0.05), and small bowel transit of solids (t10%, P = 0.016). At maximum clinically approved dosages, celecoxib and rofecoxib have no significant effects on gastric emptying or small intestinal transit in healthy humans. Cisapride accelerates gastric emptying and small bowel transit in healthy humans.

Refractive adaptation in amblyopia: quantification of effect and implications for practice.

AIM: To describe the visual response to spectacle correction ("refractive adaptation") for children with unilateral amblyopia as a function of age, type of amblyopia, and category of refractive error. METHOD: Measurement of corrected amblyopic and fellow eye logMAR visual acuity in newly diagnosed children. Measurements repeated at 6 weekly intervals for a total 18 weeks. RESULTS: Data were collected from 65 children of mean (SD) age 5.1 (1.4) years with previously untreated amblyopia and significant refractive error. Amblyopia was associated with anisometropia in 18 (5.5 (1.4) years), strabismus in 16 (4.2 (0.98) years), and mixed in 31 (5.2 (1.5) years) of the study participants. Mean (SD) corrected visual acuity of amblyopic eyes improved significantly (p<0.001) from 0.67 (0.38) to 0.43 (0.37) logMAR: a mean improvement of 0.24 (0.18), range 0.0-0.6 log units. Change in logMAR visual acuity did not significantly differ as a function of amblyopia type (p = 0.29) (anisometropia 0.22 (0.13); mixed 0.18 (0.14); strabismic 0.30 (0.24)) or for age (p = 0.38) ("under 4 years" 0.23 (0.18); "4-6 years" 0.24 (0.20); "over 6 years" 0.16 (0.23)). CONCLUSION: Refractive adaptation is a distinct component of amblyopia treatment. To appropriately evaluate mainstream therapies such as occlusion and penalisation, the beneficial effects of refractive adaptation need to be fully differentiated. A consequence for clinical practice is that children may start occlusion with improved visual acuity, possibly enhancing compliance, and in some cases unnecessary patching will be avoided.

Design of the Monitored Occlusion Treatment of Amblyopia Study (MOTAS).

BACKGROUND/AIMS: The effectiveness of occlusion therapy for the treatment of amblyopia is a research priority. The authors describe the design of the Monitored Occlusion Treatment for Amblyopia Study (MOTAS) and its methodology. MOTAS will determine the dose-response relation for occlusion therapy as a function of age and category of amblyopia. METHODS: Subjects progress through up to three study phases: (1) Assessment and baseline phase: On confirmation of eligibility, and after parental consent, baseline visual functions are determined, and spectacles prescribed as necessary; (2) Refractive adaptation phase: Subjects wear spectacles full time and return to clinic at 6 weekly intervals until 18 weeks, by which time all improvement due to refractive correction is complete; (3) Occlusion phase: All subjects are prescribed 6 hours of occlusion per day. Daily occlusion is objectively monitored using an occlusion dose monitor (ODM). OUTCOME VARIABLES: visual acuity (logMAR charts), log contrast sensitivity (Pelli-Robson chart), and stereoacuity (Frisby) are assessed at 2 weekly intervals until gains in visual acuity cease to be statistically verifiable. CONCLUSION: Four methodological issues have been addressed; firstly, baseline stability of visual function; secondly, differentiation of refractive adaptation from occlusion; thirdly, objective measurement of occlusion dose and concordance; fourthly, use of validated outcome measures.

Is there a role for gastric accommodation and satiety in asymptomatic obese people?

OBJECTIVE: The relationships of gastric accommodation and satiety in moderately obese individuals are unclear. We hypothesized that obese people had increased gastric accommodation and reduced postprandial satiety. The objective of this study was to compare gastric accommodation and satiety between obese and non-obese asymptomatic subjects. RESEARCH METHODS AND PROCEDURES: In 13 obese (body mass index [BMI] > or = 30 kg/m(2); mean BMI, 37.0 +/- 4.9 kg/m(2)) and 19 non-obese control subjects (BMI < 30 kg/m(2); mean BMI, 26.2 +/- 2.9 kg/m(2)), we used single photon emission computed tomography to measure fasting and postprandial gastric volumes and expressed the accommodation response as the ratio of postprandial/fasting volumes. The satiety test measured maximum tolerable volume of ingestion of liquid nutrient meal (Ensure) and symptoms 30 minutes after cessation of ingestion. RESULTS: Total fasting and postprandial gastric volumes and the ratio of postprandial/fasting gastric volume were not different between asymptomatic obese and control subjects. However, the fasting volume of the distal stomach was greater in obese than in control subjects. Maximum tolerable volume of ingested Ensure and aggregate symptom score 30 minutes later were also not different between obese and control subjects. DISCUSSION: Asymptomatic obese individuals (within the BMI range of 32.6 to 48 kg/m(2)) did not show either increased postprandial gastric accommodation or reduced satiety. These data suggest that gastric accommodation is unlikely to provide an important contribution to development of moderate obesity.

Noninvasive measurement of gastric accommodation in patients with idiopathic nonulcer dyspepsia.

OBJECTIVES: Postprandial symptoms are associated with impaired postprandial gastric accommodation. The aims of this study were to apply a noninvasive method to measure accommodation of the entire stomach in healthy subjects and in patients with idiopathic dyspeptic symptoms, and to assess the frequency of abnormal gastric accommodation and emptying of solids in these patients. METHODS: In 20 healthy volunteers and 32 tertiary referral patients, we used i.v. 99mTc-single photon emission computed tomography (SPECT) to measure fasting and postprandial gastric volumes; we expressed the volume response to feeding ("accommodation") as the change in gastric volume and the ratio of postprandial/fasting volumes. The stomach was identified in transaxial SPECT tomographic images using a semiautomated, intensity-based extraction algorithm. Whole gastric volumes were measured using AnalyzeAVW software. Gastric emptying in patients was measured by scintigraphy. We also assessed dyspeptic symptoms and the association with normal or reduced accommodation. RESULTS: SPECT imaging detects the postprandial change in gastric volume ("accommodation") in health and disease. Among healthy subjects (eight men, 12 women), the postprandial/fasting gastric volume ratio was 4.9+/-1.7 (mean +/- SD; fifth through 95th percentiles 3-8, median 4.6). Thirteen (41%) patients with idiopathic nonulcer dyspepsia had reduced postprandial "accommodation." Gastric emptying was fast in four (13%), normal in 25 (78%), and slow in three (9%) patients. Both tests were normal in 50% of patients. Weight loss of >10 pounds tended to be more frequently observed in those with reduced "accommodation" (62% vs 32%, p = 0.09). CONCLUSIONS: SPECT imaging noninvasively measures fasting and postprandial gastric volumes in humans. Half the patients with idiopathic nonulcer dyspepsia had impaired gastric accommodation or emptying. Reduced gastric "accommodation" was observed in 41% of a group with idiopathic nonulcer dyspepsia. Abnormal gastric emptying is less frequent (22%).

Identification of a yellow impurity in aged samples of aqueous butamben suspension: evidence for the oxidative degradation of poly(ethylene glycol).

Butamben (butyl p-aminobenzoate) has been formulated to provide long-acting treatment for chronic pain. The suspension, which contains poly(ethylene glycol) and polysorbate 80, was found to yellow under ambient conditions if not adequately protected from oxygen. The impurity responsible for the color was isolated and identified on the basis of nuclear magnetic resonance spectroscopy and mass spectrometry. The compound is an oxalamidine, which is formally the condensation product of oxalic acid with four equivalents of butamben, and may be formed by the reaction of butamben with an oxidation product of poly(ethylene glycol).

The Bayesian analysis of a pivotal pharmacokinetic study.

The aim of this paper is to carry out a detailed Bayesian population pharmacokinetic analysis of a three-period cross-over study of the drug fluticasone propionate carried out in 12 healthy male volunteers. The study was carried out to characterize the pharmacokinetics of the drug, in particular to investigate dose proportionality. We examine the appropriateness of modelling assumptions via a variety of diagnostic techniques. We also examine the effect of deleting time points at which the concentration was recorded as below the limit of quantification, as opposed to including these points as censored observations. We assess dose proportionality before carrying out a final combined analysis of data from all three doses.

Estimating linkage heterogeneity.

The admixture model for linkage heterogeneity is modified to take account of the difference in recombination fractions in the two sexes. The data used may concern a single (marker) locus on one chromosome, which is suspected of being sometimes near a (disease) locus for a particular condition of interest, or there may be data on more than one locus on this chromosome. There may be data on a locus or loci on a second chromosome, which is also suspected of sometimes carrying an allele for the condition in question. The general principle for the analysis is the same in all such cases, though details may differ. The object is to estimate the relevant recombination fractions, and the proportions of cases in which the allele for the condition falls on each chromosome.

Estimating multipoint recombination fractions.

The likelihood in linkage investigations can be expressed as a polynomial in the relevant recombination fractions. With polymorphic characters, this can be reduced to a product of separate factors for female and male recombinations, with only mild loss of information. With three generation data the polynomials take a specially simple form. Algorithms are given for finding maximum likelihood estimates and their standard errors.

Uretero-fallopian fistula: an unusual complication of open ureterolithotomy.

We report a case of uretero-fallopian fistula, manifesting as complete urinary incontinence, following open ureterolithotomy for a lower ureteral calculus.

Bayesian inference in multipoint gene mapping.

The problem of ordering and mapping genes on the basis of recombinant data and radiation hybrid data is formulated as a problem of Bayesian inference for an unknown permutation. The challenging computational problems posed by this approach are shown to be resolvable using Markov chain Monte Carlo methods.