Developmental stages and sex differences of white matter and behavioral development through adolescence: a longitudinal diffusion tensor imaging (DTI) study

White matter (WM) continues to mature through adolescence in parallel with gains in cognitive ability. To date, developmental changes in human WM microstructure have been inferred using analyses of cross-sectional or two time-point follow-up studies, limiting our understanding of individual developmental trajectories. The aims of the present longitudinal study were to characterize the timing of WM growth and investigate how sex and behavior are associated with different developmental trajectories. We utilized diffusion tensor imaging (DTI) in 128 individuals aged 8-28, who received annual scans for up to 5 years and completed motor and cognitive tasks. Flexible nonlinear growth curves indicated a hierarchical pattern of WM development. By late childhood, posterior cortical-subcortical connections were similar to adults. During adolescence, WM microstructure reached adult levels, including frontocortical, frontosubcortical and cerebellar connections. Later to mature in adulthood were major corticolimbic association tracts and connections at terminal gray matter sites in cortical and basal ganglia regions. These patterns may reflect adolescent maturation of frontal connectivity supporting cognitive abilities, particularly the protracted refinement of corticolimbic connectivity underlying cognition-emotion interactions. Sex and behavior also played a large role. Males showed continuous WM growth from childhood through early adulthood, whereas females mainly showed growth during mid-adolescence. Further, earlier WM growth in adolescence was associated with faster and more efficient responding and better inhibitory control whereas later growth in adulthood was associated with poorer performance, suggesting that the timing of WM growth is important for cognitive development.

Overview of hepatitis B viral replication and genetic variability

Chronic infection with hepatitis B virus (HBV) greatly increases the risk for liver cirrhosis and hepatocellular carcinoma (HCC). HBV isolates worldwide can be divided into ten genotypes. Moreover, the immune clearance phase selects for mutations in different parts of the viral genome. The outcome of HBV infection is shaped by the complex interplay of the mode of transmission, host genetic factors, viral genotype and adaptive mutations, as well as environmental factors. Core promoter mutations and mutations abolishing hepatitis B e antigen (HBeAg) expression have been implicated in acute liver failure, while genotypes B, C, subgenotype A1, core promoter mutations, preS deletions, C-terminal truncation of envelope proteins, and spliced pregenomic RNA are associated with HCC development. Our efforts to treat and prevent HBV infection are hampered by the emergence of drug resistant mutants and vaccine escape mutants. This paper provides an overview of the HBV life cycle, followed by review of HBV genotypes and mutants in terms of their biological properties and clinical significance.

It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR

RNA sequencing (RNA-seq) is widely used to profile transcriptional activity in biological systems. Here we present an analysis pipeline for differential expression analysis of RNA-seq experiments using the Rsubread and edgeR software packages. The basic pipeline includes read alignment and counting, filtering and normalization, modelling of biological variability and hypothesis testing. For hypothesis testing, we describe particularly the quasi-likelihood features of edgeR. Some more advanced downstream analysis steps are also covered, including complex comparisons, gene ontology enrichment analyses and gene set testing. The code required to run each step is described, along with an outline of the underlying theory. The chapter includes a case study in which the pipeline is used to study the expression profiles of mammary gland cells in virgin, pregnant and lactating mice.

Beyond the mean: A systematic review on the correlates of daily intraindividual variability of sleep/wake patterns

Features of an individual's sleep/wake patterns across multiple days are governed by two dimensions, the mean and the intraindividual variability (IIV). The existing literature focuses on the means, while the nature and correlates of sleep/wake IIV are not well understood. A systematic search of records in five major databases from inception to November 2014 identified 53 peer-reviewed empirical publications that examined correlates of sleep/wake IIV in adults. Overall, this literature appeared unsystematic and post hoc, with under-developed theoretical frameworks and inconsistent methodologies. Correlates most consistently associated with greater IIV in one or more aspects of sleep/wake patterns were: younger age, non-White race/ethnicity, living alone, physical health conditions, higher body mass index, weight gain, bipolar and unipolar depression symptomatology, stress, and evening chronotype; symptoms of insomnia and poor sleep were associated with higher sleep/wake IIV, which was reduced following sleep interventions. The effects of experimentally reduced sleep/wake IIV on daytime functioning were inconclusive. In extending current understanding of sleep/wake patterns beyond the mean values, IIV should be incorporated as an additional dimension when sleep is examined across multiple days. Theoretical and methodological shortcomings in the existing literature, and opportunities for future research are discussed.

Understanding the impact of symptoms on the burden of COPD

Chronic obstructive pulmonary disease (COPD) imposes a substantial burden on individuals with the disease, which can include a range of symptoms (breathlessness, cough, sputum production, wheeze, chest tightness) of varying severities. We present an overview of the biomedical literature describing reported relationships between COPD symptoms and disease burden in terms of quality of life, health status, daily activities, physical activity, sleep, comorbid anxiety, and depression, as well as risk of exacerbations and disease prognosis. In addition, the substantial variability of COPD symptoms encountered (morning, daytime, and nighttime) is addressed and their implications for disease burden considered. The findings from this narrative review, which mainly focuses on real-world and observational studies, demonstrate the impact of COPD symptoms on the burden of disease and that improved recognition and understanding of their impact is central to alleviating this burden.

Technical performance of a novel, fully automated electrochemiluminescence immunoassay for the quantitation of β-amyloid (1-42) in human cerebrospinal fluid

INTRODUCTION

Available assays for quantitation of the Alzheimer's disease (AD) biomarker amyloid-beta 1-42 (Aβ [1-42]) in cerebrospinal fluid demonstrate significant variability and lack of standardization to reference measurement procedures (RMPs). We report analytical performance data for the novel Elecsys β-amyloid (1-42) assay (Roche Diagnostics).

METHODS

Lot-to-lot comparability was tested using method comparison. Performance parameters were measured according to Clinical & Laboratory Standards Institute (CLSI) guidelines. The assay was standardized to a Joint Committee for Traceability in Laboratory Medicine (JCTLM) approved RMP.

RESULTS

Limit of quantitation was <11.28 pg/mL, and the assay was linear throughout the measuring range (200-1700 pg/mL). Excellent lot-to-lot comparability was observed (correlation coefficients [Pearson's r] >0.995; bias in medical decision area <2%). Repeatability coefficients of variation (CVs) were 1.0%-1.6%, intermediate CVs were 1.9%-4.0%, and intermodule CVs were 1.1%-3.9%. Estimated total reproducibility was 2.0%-5.1%. Correlation with the RMP was good (Pearson's r, 0.93).

DISCUSSION

The Elecsys β-amyloid (1-42) assay has high analytical performance that may improve biomarker-based AD diagnosis.

Identification of reproducible individualized targets for treatment of depression with TMS based on intrinsic connectivity

Transcranial magnetic stimulation (TMS) to the left dorsolateral prefrontal cortex (DLPFC) is used clinically for the treatment of depression however outcomes vary greatly between patients. We have shown that average clinical efficacy of different left DLPFC TMS sites is related to intrinsic functional connectivity with remote regions including the subgenual cingulate and suggested that functional connectivity with these remote regions might be used to identify optimized left DLPFC targets for TMS. However it remains unclear if and how this connectivity-based targeting approach should be applied at the single-subject level to potentially individualize therapy to specific patients. In this article we show that individual differences in DLPFC connectivity are large, reproducible across sessions, and can be used to generate individualized DLPFC TMS targets that may prove clinically superior to those selected on the basis of group-average connectivity. Factors likely to improve individualized targeting including the use of seed maps and the focality of stimulation are investigated and discussed. The techniques presented here may be applicable to individualized targeting of focal brain stimulation across a range of diseases and stimulation modalities and can be experimentally tested in clinical trials.

Urinary metabolites of organophosphate flame retardants and their variability in pregnant women

Organophosphate flame retardants (OPFRs) are commonly added to consumer products to reduce their flammability. Based on levels of OPFRs in indoor environments, human exposure is likely chronic and ubiquitous. Animal studies suggest that exposure to some OPFRs may result in adverse health impacts, particularly for Tris (1,3-dichloropropyl) phosphate (TDCPP); however, human data on the impacts of exposure to OPFRs are lacking. To design human studies, more information is needed on the stability of measured OPFRs in human samples over time. In this study, we sought to assess the degree of temporal variability of urinary TDCPP and triphenyl phosphate (TPP) metabolites throughout pregnancy in a cohort of women from central North Carolina. Eight pregnant women provided multiple urine samples: 3 during the 18th week of pregnancy, 1 during the 28th week, and 1 shortly after the child's birth. Bis (1,3-dichloropropyl) phosphate (BDCPP) and diphenyl phosphate (DPP), the respective metabolites of TDCPP and TPP, were measured in urine samples using liquid chromatography-tandem mass spectrometry. BDCPP and DPP were each detected in 38 of 39 urine samples and were not normally distributed. Geometric mean BDCPP and DPP concentrations were 1.3ng/mL (interquartile range (IQR): 0.8, 2.7ng/mL) and 1.9ng/mL (IQR: 0.9, 3.5ng/mL), respectively. BDCPP and DPP were moderately to strongly reliable over one week (intraclass correlation coefficient (ICC)=0.5; 95% confidence interval (CI): 0.4, 0.7 and ICC=0.7; 95% CI: 0.5, 0.8, respectively), and over the entire pregnancy (ICC=0.5 95% CI: 0.3, 0.7 and ICC=0.6; 95% CI: 0.4, 0.7, respectively). These data suggest that exposures to TDCPP and TPP are widespread and variable for pregnant women, and that a single measure of BDCPP or DPP, taken in the second trimester, likely captures information on the rank order of exposure throughout pregnancy.

Cholesterol variability and the risk of mortality, myocardial infarction, and stroke: a nationwide population-based study

Aims

A high visit-to-visit variability in cholesterol levels has been suggested to be an independent predictor of major adverse cardiovascular events in patients with coronary artery disease (CAD). Because whether this notion applies to general population is not known, we aimed to investigate the associations between total cholesterol (TC) variability and the risk of all-cause mortality, myocardial infarction (MI), and stroke.

Methods and results

We identified 3 656 648 subjects without a history of MI and stroke who underwent ≥3 health examinations from 2002 to 2007 in the Korean National Health Insurance System cohort. Total cholesterol variability was measured using the coefficient of variation (CV), standard deviation (SD), and variability independent of the mean (VIM). There were 84 625 deaths (2.3%), 40 991 cases of MI (1.1%), and 42 861 cases of stroke (1.2%) during the median follow-up of 8.3 years. There was a linear association between higher TC variability and outcome measures. In the multivariable adjusted model, the hazard ratios and 95% confidence intervals comparing the highest vs. lowest quartiles of CV of TC were 1.26 (1.24-1.28) for all-cause mortality, 1.08 (1.05-1.11) for MI, and 1.11 (1.08-1.14) for stroke, which was independent of mean TC levels and the use of lipid-lowering agents. The results were consistent when modelling variability of TC using SD and VIM, and in various sensitivity analyses.

Conclusion

High variability in lipid levels is associated with adverse health-related outcomes. These findings suggest that lipid variability is an important risk factor in the general population.

Intraindividual variability of sleep/wake patterns in relation to child and adolescent functioning: A systematic review

Substantial research attention has been devoted to understanding the importance and impact of sleep in children and adolescents. Traditionally, this has focused on mean sleep variables (e.g., a child's "typical" or average sleep duration), yet research increasingly suggests that intraindividual variability (IIV) of sleep/wake patterns (sometimes referred to as sleep variability or night-to-night variability) regularly occurs and may have implications for adjustment. A systematic search of five electronic databases identified 52 empirical studies published between 2000 and 2015 that examined correlates of sleep IIV in children and adolescents, with a recent increase in the publication rate of such studies. Identified studies were often atheoretical and included post hoc analyses, though IIV in select aspects of sleep does appear to be associated with increasing age/pubertal status, non-White race, physical and neurodevelopmental conditions (e.g., attention-deficit/hyperactivity disorder; autism), psychopathology symptoms (e.g., anxiety, depression, inattention), body weight, stress, aspects of cognitive functioning, and poorer sleep functioning/habits. The limited intervention work examining sleep IIV in adolescents is promising, though studies are needed using more rigorous intervention designs. Clinical sleep recommendations may not only need to address overall sleep duration and sleep habits but also the stability of sleep duration and timing. It will be important for future research examining sleep IIV in children and adolescents to use a developmental framework in advancing theory pertaining to the causes, mechanisms, moderators, and outcomes of sleep IIV in youth, and a conceptual model is proposed to help guide such efforts.

Early human motor development: From variation to the ability to vary and adapt

This review summarizes early human motor development. From early fetal age motor behavior is based on spontaneous neural activity: activity of networks in the brainstem and spinal cord that is modulated by supraspinal activity. The supraspinal activity, first primarily brought about by the cortical subplate, later by the cortical plate, induces movement variation. Initially, movement variation especially serves exploration; its associated afferent information is primarily used to sculpt the developing nervous system, and less to adapt motor behavior. In the next phase, beginning at function-specific ages, movement variation starts to serve adaptation. In sucking and swallowing, this phase emerges shortly before term age. In speech, gross and fine motor development, it emerges from 3 to 4 months post-term onwards, i.e., when developmental focus in the primary sensory and motor cortices has shifted to the permanent cortical circuitries. With increasing age and increasing trial-and-error exploration, the infant improves its ability to use adaptive and efficicient forms of upright gross motor behavior, manual activities and vocalizations belonging to the native language.

Gait variability in people with neurological disorders: A systematic review and meta-analysis

There has been growing evidence showing gait variability provides unique information about gait characteristics in neurological disorders. This study systemically reviewed and quantitatively synthesized (via meta-analysis) existing evidence on gait variability in various neurological diseases, including Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), cerebellar ataxia (CA), Huntington's disease (HD), multiple sclerosis (MS), and Parkinson's disease (PD). Keyword search were conducted in PubMed, Web of science, Cumulative Index to Nursing and Allied Health Literature, and Cochrane Library. Meta-analysis was performed to estimate the pooled effect size for gait variability for each neurological group. Meta-regression was performed to compare gait variability across multiple groups with neurological diseases. Gait variability of 777 patients with AD, ALS, CA, HD, MS, or PD participating in 25 studies was included in meta-analysis. All pathological groups had increased amount of gait variability and loss of fractal structure of gait dynamics compared to healthy controls, and gait variability differentiated distinctive neurological conditions. The HD groups had the highest alterations in gait variability among all pathological groups, whereas the PD, AD and MS groups had the lowest. Interventions that aim to improve gait function in patients with neurological disorders should consider the heterogeneous relationship between gait variability and neurological conditions.

Sham tDCS: A hidden source of variability? Reflections for further blinded, controlled trials

Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique increasingly used to modulate neural activity in the living brain. In order to establish the neurophysiological, cognitive or clinical effects of tDCS, most studies compare the effects of active tDCS to those observed with a sham tDCS intervention. In most cases, sham tDCS consists in delivering an active stimulation for a few seconds to mimic the sensations observed with active tDCS and keep participants blind to the intervention. However, to date, sham-controlled tDCS studies yield inconsistent results, which might arise in part from sham inconsistencies. Indeed, a multiplicity of sham stimulation protocols is being used in the tDCS research field and might have different biological effects beyond the intended transient sensations. Here, we seek to enlighten the scientific community to this possible confounding factor in order to increase reproducibility of neurophysiological, cognitive and clinical tDCS studies.

Inter-individual variability in cortical excitability and motor network connectivity following multiple blocks of rTMS

The responsiveness to non-invasive neuromodulation protocols shows high inter-individual variability, the reasons of which remain poorly understood. We here tested whether the response to intermittent theta-burst stimulation (iTBS) - an effective repetitive transcranial magnetic stimulation (rTMS) protocol for increasing cortical excitability - depends on network properties of the cortical motor system. We furthermore investigated whether the responsiveness to iTBS is dose-dependent. To this end, we used a sham-stimulation controlled, single-blinded within-subject design testing for the relationship between iTBS aftereffects and (i) motor-evoked potentials (MEPs) as well as (ii) resting-state functional connectivity (rsFC) in 16 healthy subjects. In each session, three blocks of iTBS were applied, separated by 15min. We found that non-responders (subjects not showing an MEP increase of ≥10% after one iTBS block) featured stronger rsFC between the stimulated primary motor cortex (M1) and premotor areas before stimulation compared to responders. However, only the group of responders showed increases in rsFC and MEPs, while most non-responders remained close to baseline levels after all three blocks of iTBS. Importantly, there was still a large amount of variability in both groups. Our data suggest that responsiveness to iTBS at the local level (i.e., M1 excitability) depends upon the pre-interventional network connectivity of the stimulated region. Of note, increasing iTBS dose did not turn non-responders into responders. The finding that higher levels of pre-interventional connectivity precluded a response to iTBS could reflect a ceiling effect underlying non-responsiveness to iTBS at the systems level.

Worldwide use of intrauterine contraception: a review

BACKGROUND

Globally, 14.3% of women of reproductive age use intrauterine contraception (IUC), but the distribution of IUC users is strikingly nonuniform. In some countries, the percentage of women using IUC is <2%, whereas in other countries, it is >40%. Reasons for this large variation are not well documented. The aims of this review are to describe the worldwide variation in IUC utilization and to explore factors that impact utilization rates among women of reproductive age in different continents and countries.

STUDY DESIGN

Published literature from 1982 to 2012 was reviewed, using Medline and Embase, to identify publications reporting diverse practices of IUC provision, including variation in the types of IUC available. Local experts who are active members of international advisory groups or congresses were also consulted to document variations in practice regulations, published guidelines and cost of IUC in different countries.

RESULTS

Multiple factors appear to contribute to global variability in IUC use, including government policy on family planning, the types of health care providers (HCPs) who are authorized to place and remove IUC, the medicolegal environment, the availability of practical training for HCPs, cost differences and the geographical spread of clinics providing IUC services.

CONCLUSIONS

Our review shows that the use of IUC is influenced more by factors such as geographic differences, government policy and the HCP's educational level than by medical eligibility criteria. These factors can be influenced through education of HCPs and greater understanding among policy makers of the effectiveness and cost-effectiveness of IUC methods.

IMPLICATIONS

Globally, 14.3% of women of reproductive age use IUC, but the percentage of women using IUC is in some countries <2%, whereas in other countries, it is >40%. This paper reviews the reasons for this diverse and highlights possible starting points to improve the inclusion of IUC in contraceptive counseling.

Comparing dynamical systems concepts and techniques for biomechanical analysis

Traditional biomechanical analyses of human movement are generally derived from linear mathematics. While these methods can be useful in many situations, they do not describe behaviors in human systems that are predominately nonlinear. For this reason, nonlinear analysis methods based on a dynamical systems approach have become more prevalent in recent literature. These analysis techniques have provided new insights into how systems (1) maintain pattern stability, (2) transition into new states, and (3) are governed by short- and long-term (fractal) correlational processes at different spatio-temporal scales. These different aspects of system dynamics are typically investigated using concepts related to variability, stability, complexity, and adaptability. The purpose of this paper is to compare and contrast these different concepts and demonstrate that, although related, these terms represent fundamentally different aspects of system dynamics. In particular, we argue that variability should not uniformly be equated with stability or complexity of movement. In addition, current dynamic stability measures based on nonlinear analysis methods (such as the finite maximal Lyapunov exponent) can reveal local instabilities in movement dynamics, but the degree to which these local instabilities relate to global postural and gait stability and the ability to resist external perturbations remains to be explored. Finally, systematic studies are needed to relate observed reductions in complexity with aging and disease to the adaptive capabilities of the movement system and how complexity changes as a function of different task constraints.

A review of rhythm and responsiveness of cortisol in individuals with autism spectrum disorders

Examination of the hypothalamic-pituitary-adrenal (HPA) axis via cortisol among individuals with autism spectrum disorder (ASD) has been a growing area of research interest. The following review includes investigations of cortisol conducted with cohorts of individuals with ASD across the lifespan over the past four decades. In general, studies find dysregulation when examining the diurnal rhythm as a whole in lower functioning children with ASD; however, limited evidence exists for alterations in higher functioning individuals and in specific aspects of the diurnal cycle (cortisol awakening response, daily decline, variability) relative to typically developing individuals. Studies examining the responsiveness of cortisol in ASD suggest an overall sluggishness of the HPA axis in responding to physiological or physical manipulation. Hypo-responsiveness was observed in stressors that involve social evaluative threat, however, hyper-responsiveness of the HPA axis was observed in situations involving unpleasant stimuli or relatively benign social situations. A number of important considerations when conducting studies of cortisol in ASD cohorts are discussed.

Characterizing the morbid genome of ciliopathies

Background

Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; however, our knowledge of their morbid genome, pleiotropy, and variable expressivity remains incomplete.

Results

We applied genomic approaches on a large patient cohort of 371 affected individuals from 265 families, with phenotypes that span the entire ciliopathy spectrum. Likely causal mutations in previously described ciliopathy genes were identified in 85% (225/265) of the families, adding 32 novel alleles. Consistent with a fully penetrant model for these genes, we found no significant difference in their “mutation load” beyond the causal variants between our ciliopathy cohort and a control non-ciliopathy cohort. Genomic analysis of our cohort further identified mutations in a novel morbid gene TXNDC15, encoding a thiol isomerase, based on independent loss of function mutations in individuals with a consistent ciliopathy phenotype (Meckel-Gruber syndrome) and a functional effect of its deficiency on ciliary signaling. Our study also highlighted seven novel candidate genes (TRAPPC3, EXOC3L2, FAM98C, C17orf61, LRRCC1, NEK4, and CELSR2) some of which have established links to ciliogenesis. Finally, we show that the morbid genome of ciliopathies encompasses many founder mutations, the combined carrier frequency of which accounts for a high disease burden in the study population.

Conclusions

Our study increases our understanding of the morbid genome of ciliopathies. We also provide the strongest evidence, to date, in support of the classical Mendelian inheritance of Bardet-Biedl syndrome and other ciliopathies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1099-5) contains supplementary material, which is available to authorized users.

Measurement of foot placement and its variability with inertial sensors

Gait parameters such as stride length, width, and period, as well as their respective variabilities, are widely used as indicators of mobility and walking function. Foot placement and its variability have thus been applied in areas such as aging, fall risk, spinal cord injury, diabetic neuropathy, and neurological conditions. But a drawback is that these measures are presently best obtained with specialized laboratory equipment such as motion capture systems and instrumented walkways, which may not be available in many clinics and certainly not during daily activities. One alternative is to fix inertial measurement units (IMUs) to the feet or body to gather motion data. However, few existing methods measure foot placement directly, due to drift associated with inertial data. We developed a method to measure stride-to-stride foot placement in unconstrained environments, and tested whether it can accurately quantify gait parameters over long walking distances. The method uses ground contact conditions to correct for drift, and state estimation algorithms to improve estimation of angular orientation. We tested the method with healthy adults walking over-ground, averaging 93 steps per trial, using a mobile motion capture system to provide reference data. We found IMU estimates of mean stride length and duration within 1% of motion capture, and standard deviations of length and width within 4% of motion capture. Step width cannot be directly estimated by IMUs, although lateral stride variability can. Inertial sensors measure walks over arbitrary distances, yielding estimates with good statistical confidence. Gait can thus be measured in a variety of environments, and even applied to long-term monitoring of everyday walking.

Response of bone turnover markers to three oral bisphosphonate therapies in postmenopausal osteoporosis: the TRIO study

We used bone turnover markers to identify women who responded to bisphosphonate treatment for osteoporosis. Response was more likely with alendronate and ibandronate than risedronate. There was a greater decrease in bone markers if baseline bone turnover markers were higher and if the patient took more than 80 % of her medication.

INTRODUCTION

Biochemical response to bisphosphonate therapy can be assessed using either a decrease in bone turnover marker beyond the least significant change (LSC) or a reduction to within a reference interval (RI). We compared the performance of these target responses and determined whether response was related to the type of bisphosphonate, compliance and baseline bone turnover markers.

METHODS

Biochemical responses to three oral bisphosphonates were assessed in an open, controlled trial comprising 172 postmenopausal osteoporotic women (age 53-84 years), randomised to alendronate, ibandronate or risedronate, plus calcium and vitamin D supplementation for 2 years. The LSC for each marker was derived within the study population, whereas RIs were obtained from a control group of healthy premenopausal women (age 35-40 years).

RESULTS

Over 70 % of women achieved a target response for serum CTX and PINP, irrespective of the approach used. The percentage decrease at 12 weeks was greater for women with baseline PINP above the RI -63 % (difference 13 %, 95 % CI 0 to 27.1, P = 0.049) and good compliance -67 % (difference 15.9 %, 95 % CI 6.3 to 25.5, P = 0.001). Responders had a greater increase in spine bone density compared to nonresponders; for example 6.2 vs. 2.3 % (difference 3.9 %, 95 % CI 1.6 to 6.3, P = 0.0011) for PINP LSC. The magnitude of change in bone markers was greater with ibandronate and alendronate than risedronate.

CONCLUSIONS

Both approaches to response identified similar proportions of women as responders. Nonresponders had smaller increases in BMD, and we suggest that biochemical assessment of response is a useful tool for the management of women with postmenopausal osteoporosis.

Variability and predictors of urinary phthalate metabolites in Spanish pregnant women

Developmental exposure to phthalates may be associated with adverse health outcomes but information on the variability and predictors of urinary phthalate metabolite concentrations during pregnancy is limited. We evaluated in Spanish pregnant women (n=391) the reproducibility of urinary phthalate metabolite concentrations and predictors of exposure. We measured mono-(4-methyl-7-hydroxyoctyl) phthalate (7-OHMMeOP), mono-(2-ethylhexyl) phthalate (MEHP), mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP), mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP), mono-(2-ethyl-5-carboxypentyl) phthalate (MECPP), mono-(2-carboxyhexyl) phthalate (MCMHP), mono-benzyl phthalate (MBzP), mono-ethyl phthalate (MEP), mono-iso-butyl phthalate (MiBP) and mono-n-butyl phthalate (MnBP) in two spot urine samples collected in the first and third pregnancy trimesters. Questionnaires on predictors and food-frequency questionnaires were administered in the first and/or third pregnancy trimesters. Using creatinine-adjusted phthalate metabolite concentrations (log10-trasformed) we calculated intraclass correlation coefficients (ICCs). Linear mixed and regression models assessed the associations between predictors and phthalate metabolites. The ICCs ranged from 0.24 to 0.07 and were higher for MBzP, MEP, MiBP, and lower for MEOHP and MEHHP. Overweight, lower education and social class, and less frequent consumption of organic food were associated with higher levels of some phthalate metabolites. The use of household cleaning products (bleach, ammonia, glass cleaners, oven cleaning sprays and degreasing products) at least once per week during pregnancy was associated with 10-44% higher urinary phthalate metabolites. Bottled-water consumption, consumption of food groups usually stored in plastic containers or cans, use of plastic containers for heating food and cosmetic use were not associated with increased concentrations of phthalate metabolites. This large study with repeated phthalate measurements suggests that, in this Spanish setting, sociodemographic and lifestyle factors and household cleaning product use are better predictors of phthalate exposure levels in pregnant women than average water and food consumption and use of plastic containers and cosmetics.

Urinary levels of bisphenol A, F and S and markers of oxidative stress among healthy adult men: Variability and association analysis

BACKGROUND

Bisphenol F (BPF) and bisphenol S (BPS) are increasingly used as alternatives to endocrine disrupting chemical bisphenol A (BPA). Evidence from in vitro and animal studies demonstrates that BPA, BPF and BPS induce oxidative stress, a proposed mechanism that is relevant to various adverse health effects. Evaluation in humans is hampered by the potentially high within-subject variability of urinary measurements.

OBJECTIVE

To evaluate the variability and associations of levels of BPA, BPS, BPF and 3 oxidative stress markers [i.e., 8-hydroxy-2-deoxyguanosine (8-OHdG), 8-iso-prostaglandin F_2α (8-isoPGF_2α) and 4-hydroxy-2-nonenal-mercapturic acid (HNE-MA)] in urine collected on multiple occasions over 3 months.

METHOD

A total of 529 spot urine samples, including 88 first morning voids (FMVs) and 24-h specimens, were gathered from 11 adult men on days 0, 1, 2, 3, 4, 30, 60 and 90 and analyzed for BPA, BPF, BPS, 8-OHdG, 8-isoPGF_2α and HNE-MA. Intraclass correlation coefficients (ICCs) were estimated to characterize the reproducibility of urinary bisphenols and oxidative stress markers, and linear mixed models were applied to assess the associations between markers of exposure and response.

RESULTS

BPA and BPF were detected in ≥85% of the spot samples, while BPS in 13% of the samples. High degrees of within-subject variability were found for BPA, BPF, 8-OHdG, 8-isoPGF_2α and HNE-MA in spot samples, FMVs and 24-h specimens (creatinine-corrected ICCs ≤ 0.37). The sensitivities were low-to-moderate (0.30-0.63) when using single spot samples or FMVs to predict high (>27th, or 36th percentile) 3-month average urinary levels of BPA, BPF, 8-OHdG, 8-isoPGF_2α and HNE-MA. Collecting repeated specimens at different time points improved the accuracy of classification for markers of exposure and response. Elevated urinary BPA and BPF were associated with significantly higher levels of oxidative stress markers.

CONCLUSIONS

Repeated urinary specimens are required to characterize bisphenol exposure levels and the oxidative stress status of individuals. Exposure to BPA and BPF may partly contribute to the elevated urinary levels of oxidative stress makers in adult men.

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

BACKGROUND

Epigenetic change is a hallmark of ageing but its link to ageing mechanisms in humans remains poorly understood. While DNA methylation at many CpG sites closely tracks chronological age, DNA methylation changes relevant to biological age are expected to gradually dissociate from chronological age, mirroring the increased heterogeneity in health status at older ages.

RESULTS

Here, we report on the large-scale identification of 6366 age-related variably methylated positions (aVMPs) identified in 3295 whole blood DNA methylation profiles, 2044 of which have a matching RNA-seq gene expression profile. aVMPs are enriched at polycomb repressed regions and, accordingly, methylation at those positions is associated with the expression of genes encoding components of polycomb repressive complex 2 (PRC2) in trans. Further analysis revealed trans-associations for 1816 aVMPs with an additional 854 genes. These trans-associated aVMPs are characterized by either an age-related gain of methylation at CpG islands marked by PRC2 or a loss of methylation at enhancers. This distinct pattern extends to other tissues and multiple cancer types. Finally, genes associated with aVMPs in trans whose expression is variably upregulated with age (733 genes) play a key role in DNA repair and apoptosis, whereas downregulated aVMP-associated genes (121 genes) are mapped to defined pathways in cellular metabolism.

CONCLUSIONS

Our results link age-related changes in DNA methylation to fundamental mechanisms that are thought to drive human ageing.

Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR

Background

Plasmids are widely used for molecular cloning or production of proteins in laboratory and industrial settings. Constant modification has brought forth countless plasmid vectors whose characteristics in terms of average plasmid copy number (PCN) and stability are rarely known. The crucial factor determining the PCN is the replication system; most replication systems in use today belong to a small number of different classes and are available through repositories like the Standard European Vector Architecture (SEVA).

Results

In this study, the PCN was determined in a set of seven SEVA-based expression plasmids only differing in the replication system. The average PCN for all constructs was determined by Droplet Digital PCR and ranged between 2 and 40 per chromosome in the host organism Escherichia coli. Furthermore, a plasmid-encoded EGFP reporter protein served as a means to assess variability in reporter gene expression on the single cell level. Only cells with one type of plasmid (RSF1010 replication system) showed a high degree of heterogeneity with a clear bimodal distribution of EGFP intensity while the others showed a normal distribution. The heterogeneous RSF1010-carrying cell population and one normally distributed population (ColE1 replication system) were further analyzed by sorting cells of sub-populations selected according to EGFP intensity. For both plasmids, low and highly fluorescent sub-populations showed a remarkable difference in PCN, ranging from 9.2 to 123.4 for ColE1 and from 0.5 to 11.8 for RSF1010, respectively.

Conclusions

The average PCN determined here for a set of standardized plasmids was generally at the lower end of previously reported ranges and not related to the degree of heterogeneity. Further characterization of a heterogeneous and a homogeneous population demonstrated considerable differences in the PCN of sub-populations. We therefore present direct molecular evidence that the average PCN does not represent the true number of plasmid molecules in individual cells.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0610-8) contains supplementary material, which is available to authorized users.