Long-Term PEG-J Tube Safety in Patients With Advanced Parkinson's Disease

OBJECTIVES:

The objectives of this study were to present procedure- and device-associated adverse events (AEs) identified with long-term drug delivery via percutaneous endoscopic gastrojejunostomy (PEG-J). Levodopa-carbidopa intestinal gel (LCIG, also known in US as carbidopa-levodopa enteral suspension, CLES) is continuously infused directly to the proximal small intestine via PEG-J in patients with advanced Parkinson's disease (PD) to overcome slow and erratic gastric emptying and treat motor fluctuations that are not adequately controlled by oral or other pharmacological therapy.

METHODS:

An independent adjudication committee of three experienced (>25 years each) gastroenterologists reviewed gastrointestinal procedure- and device-associated AEs reported for PD patients (total n=395) enrolled in phase 3 LCIG studies. The rate, clinical significance, and causality of the procedure/device events were determined.

RESULTS:

The patient median exposure to PEG-J at the data cutoff was 480 days. Procedure- and device-associated serious AEs (SAEs) occurred in 67 (17%) patients. A total of 42% of SAEs occurred during the first 4 weeks following PEG-J placement. SAEs of major clinical significance with the highest procedural incidence were peritonitis (1.5%), pneumonia (1.5%), and abdominal pain (1.3%). The most common non-serious procedure- and device-associated AEs were abdominal pain (31%), post-operative wound infection (20%), and procedural pain (23%). In all, 17 (4.3%) patients discontinued treatment owing to an AE.

CONCLUSIONS:

In conclusion, incidences of PEG-J AEs with the LCIG delivery system and PEG-J longevity were compared favorably with ranges described in the PEG/PEG-J literature. A low discontinuation rate in this study suggests acceptable procedural outcomes and AE rates in PD patients treated with this PEG-J drug delivery system.

Capturing needles in haystacks: a comparison of B-cell receptor sequencing methods

Background

Deep-sequencing methods are rapidly developing in the field of B-cell receptor (BCR) and T-cell receptor (TCR) diversity. These promise to revolutionise our understanding of adaptive immune dynamics, identify novel antibodies, and allow monitoring of minimal residual disease. However, different methods for BCR and TCR enrichment and amplification have been proposed. Here we perform the first systematic comparison between different methods of enrichment, amplification and sequencing for generating BCR and TCR repertoires using large sample numbers.

Results

Resampling from the same RNA or cDNA pool results in highly correlated and reproducible repertoires, but resampling low frequency clones leads to stochastic variance. Repertoires generated by different sequencing methods (454 Roche and Illumina MiSeq) and amplification methods (multiplex PCR, 5’ Rapid amplification of cDNA ends (5’RACE), and RNA-capture) are highly correlated, and resulting IgHV gene frequencies between the different methods were not significantly different. Read length has an impact on captured repertoire structure, and ultimately full-length BCR sequences are most informative for repertoire analysis as diversity outside of the CDR is very useful for phylogenetic analysis. Additionally, we show RNA-based BCR repertoires are more informative than using DNA.

Conclusions

Repertoires generated by different sequencing and amplification methods are consistent, but we show that read lengths, depths and error profiles should be considered in experimental design, and multiple sampling approaches could be employed to minimise stochastic sampling variation. This detailed investigation of immune repertoire sequencing methods is essential for informing basic and clinical research.

Electronic supplementary material

The online version of this article (doi:10.1186/s12865-014-0029-0) contains supplementary material, which is available to authorized users.

The cost-effectiveness of New York City's Safe Routes to School Program

OBJECTIVE

We evaluated the cost-effectiveness of a package of roadway modifications in New York City funded under the Safe Routes to School (SRTS) program.

METHODS

We used a Markov model to estimate long-term impacts of SRTS on injury reduction and the associated savings in medical costs, lifelong disability, and death. Model inputs included societal costs (in 2013 US dollars) and observed spatiotemporal changes in injury rates associated with New York City's implementation of SRTS relative to control intersections. Structural changes to roadways were assumed to last 50 years before further investment is required. Therefore, costs were discounted over 50 consecutive cohorts of modified roadway users under SRTS.

RESULTS

SRTS was associated with an overall net societal benefit of $230 million and 2055 quality-adjusted life years gained in New York City.

CONCLUSIONS

SRTS reduces injuries and saves money over the long run.

General and substance-specific predictors of young adult nicotine dependence, alcohol use disorder, and problem behavior: replication in two samples

BACKGROUND

This paper presents two replications of a heuristic model for measuring environment in studies of gene-environment interplay in the etiology of young adult problem behaviors.

METHODS

Data were drawn from two longitudinal, U.S. studies of the etiology of substance use and related behaviors: the Raising Healthy Children study (RHC; N=1040, 47% female) and the Minnesota Twin Family Study (MTFS; N=1512, 50% female). RHC included a Pacific Northwest, school-based, community sample. MTFS included twins identified from state birth records in Minnesota. Both studies included commensurate measures of general family environment and family substance-specific environments in adolescence (RHC ages 10-18; MTFS age 18), as well as young adult nicotine dependence, alcohol and illicit drug use disorders, HIV sexual risk behavior, and antisocial behavior (RHC ages 24, 25; MTFS age 25).

RESULTS

Results from the two samples were highly consistent and largely supported the heuristic model proposed by Bailey et al. (2011). Adolescent general family environment, family smoking environment, and family drinking environment predicted shared variance in problem behaviors in young adulthood. Family smoking environment predicted unique variance in young adult nicotine dependence. Family drinking environment did not appear to predict unique variance in young adult alcohol use disorder.

CONCLUSIONS

Organizing environmental predictors and outcomes into general and substance-specific measures provides a useful way forward in modeling complex environments and phenotypes. Results suggest that programs aimed at preventing young adult problem behaviors should target general family environment and family smoking and drinking environments in adolescence.

Revealing individual signatures of human T cell CDR3 sequence repertoires with Kidera Factors

The recent development of High Throughput Sequencing technologies has enabled an individual's TCR repertoire to be efficiently analysed at the nucleotide level. However, with unique clonotypes ranging in the tens of millions per individual, this approach gives a surfeit of information that is difficult to analyse and interpret in a biological context and gives little information about TCR structural diversity. Using publicly available TCR CDR3 sequence data, we analysed TCR repertoires by converting the encoded CDR3 amino acid sequences into Kidera Factors, a set of orthogonal physico-chemical properties that reflect protein structure. This approach enabled the TCR repertoire from different individuals to be distinguished and demonstrated the close similarity of the repertoire in different samples from the same individual.

Bayesian approaches for mechanistic ion channel modeling

We consider the Bayesian analysis of mechanistic models describing the dynamic behavior of ligand-gated ion channels. The opening of the transmembrane pore in an ion channel is brought about by conformational changes in the protein, which results in a flow of ions through the pore. Remarkably, given the diameter of the pore, the flow of ions from a small number of channels or indeed from a single ion channel molecule can be recorded experimentally. This produces a large time-series of high-resolution experimental data, which can be used to investigate the gating process of these channels. We give a brief overview of the achievements and limitations of alternative maximum-likelihood approaches to this type of modeling, before investigating the statistical issues associated with analyzing stochastic model reaction mechanisms from a Bayesian perspective. Finally, we compare a number of Markov chain Monte Carlo algorithms that may be used to tackle this challenging inference problem.

Research utilization and evidence-based practice among Saskatchewan massage therapists

While massage therapy (MT) is an increasingly used health care service with a growing evidence base, there is insufficient information about the extent to which MT practice is evidence-based. The purpose of this study was to provide a comprehensive view of Saskatchewan MT's research utilization to inform the development of evidence-based massage therapy practice. The main objectives of the study were to describe MT's perceptions of research, their appraised self-efficacy in research literacy and to identify the characteristic of practitioners who use research. Using a survey design all 815 registered members of the Massage Therapist Association of Saskatchewan were invited to complete a mail-out questionnaire. A total of 333 questionnaires were completed and returned for a 41% response rate. Univariate and logistic regression analysis was conducted using SPSS 17.0. While overall perceptions of research were positive, self-efficacy in research literacy was low and research utilization was limited. Characteristics associated with research use included referring to online research databases and peer-reviewed journals, belief that practice should be based on research, and 20 or greater hours per week of practice. Provincial regulatory status may be the first step to quality service delivery and research literacy training and support is needed for practitioners.

The epilepsy phenome/genome project

BACKGROUND

Epilepsy is a common neurological disorder that affects approximately 50 million people worldwide. Both risk of epilepsy and response to treatment partly depend on genetic factors, and gene identification is a promising approach to target new prediction, treatment, and prevention strategies. However, despite significant progress in the identification of genes causing epilepsy in families with a Mendelian inheritance pattern, there is relatively little known about the genetic factors responsible for common forms of epilepsy and so-called epileptic encephalopathies. Study design The Epilepsy Phenome/Genome Project (EPGP) is a multi-institutional, retrospective phenotype-genotype study designed to gather and analyze detailed phenotypic information and DNA samples on 5250 participants, including probands with specific forms of epilepsy and, in a subset, parents of probands who do not have epilepsy.

RESULTS

EPGP is being executed in four phases: study initiation, pilot, study expansion/establishment, and close-out. This article discusses a number of key challenges and solutions encountered during the first three phases of the project, including those related to (1) study initiation and management, (2) recruitment and phenotyping, and (3) data validation. The study has now enrolled 4223 participants.

CONCLUSIONS

EPGP has demonstrated the value of organizing a large network into cores with specific roles, managed by a strong Administrative Core that utilizes frequent communication and a collaborative model with tools such as study timelines and performance-payment models. The study also highlights the critical importance of an effective informatics system, highly structured recruitment methods, and expert data review.

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

Motivation: Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to control for the variability at the capture and sequencing steps. However, technical variability between samples complicates the analysis and can create spurious CNV calls.

Results: Here, we introduce ExomeDepth, a new CNV calling algorithm designed to control for this technical variability. ExomeDepth uses a robust model for the read count data and uses this model to build an optimized reference set in order to maximize the power to detect CNVs. As a result, ExomeDepth is effective across a wider range of exome datasets than the previously existing tools, even for small (e.g. one to two exons) and heterozygous deletions. We used this new approach to analyse exome data from 24 patients with primary immunodeficiencies. Depending on data quality and the exact target region, we find between 170 and 250 exonic CNV calls per sample. Our analysis identified two novel causative deletions in the genes GATA2 and DOCK8.

Availability: The code used in this analysis has been implemented into an R package called ExomeDepth and is available at the Comprehensive R Archive Network (CRAN).

Contact: v.plagnol@ucl.ac.uk

Supplementary Information:Supplementary data are available at Bioinformatics online.

Binaural loudness summation for speech presented via earphones and loudspeaker with and without visual cues

Preliminary data [M. Epstein and M. Florentine, Ear. Hear. 30, 234-237 (2009)] obtained using speech stimuli from a visually present talker heard via loudspeakers in a sound-attenuating chamber indicate little difference in loudness when listening with one or two ears (i.e., significantly reduced binaural loudness summation, BLS), which is known as "binaural loudness constancy." These data challenge current understanding drawn from laboratory measurements that indicate a tone presented binaurally is louder than the same tone presented monaurally. Twelve normal listeners were presented recorded spondees, monaurally and binaurally across a wide range of levels via earphones and a loudspeaker with and without visual cues. Statistical analyses of binaural-to-monaural ratios of magnitude estimates indicate that the amount of BLS is significantly less for speech presented via a loudspeaker with visual cues than for stimuli with any other combination of test parameters (i.e., speech presented via earphones or a loudspeaker without visual cues, and speech presented via earphones with visual cues). These results indicate that the loudness of a visually present talker in daily environments is little affected by switching between binaural and monaural listening. This supports the phenomenon of binaural loudness constancy and underscores the importance of ecological validity in loudness research.

Daily variability in mineral metabolites in CKD and effects of dietary calcium and calcitriol

BACKGROUND AND OBJECTIVES

Primary prevention of disordered mineral metabolism in CKD necessitates knowledge of its early pathophysiology. This study evaluated daily fluctuations in mineral metabolites in patients with CKD stages 3 and 4 before and after short-term calcitriol treatment and tested the effects of dietary calcium and calcitriol supplementation on these parameters in the dynamic postprandial setting.

DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS

Twelve CKD patients received calcitriol (0.25 μg daily for 1 week) with hourly assessments of mineral metabolites made throughout the day and in the context of standardized meals before and after treatment. Calcium content (250 versus 500 mg) in the breakfasts constituted the dietary calcium intervention. Twelve healthy volunteers were used as controls.

RESULTS

At baseline, compared with controls, fasting CKD subjects had higher parathyroid hormone and fibroblast growth factor 23 levels and greater fractional excretion of phosphate. After breakfast, urinary calcium excretion increased and parathyroid hormone levels dipped transiently in both groups, but they rose soon thereafter, reaching higher peaks in CKD. Calcitriol decreased fasting parathyroid hormone levels, and when combined with dietary calcium load, it normalized the postprandial parathyroid and calcemic responses. Daily variability in mineral metabolites was preserved in CKD before and after calcitriol. Fibroblast growth factor 23 levels increased after calcitriol, although the response was heterogeneous.

CONCLUSIONS

Short-term treatment with calcitriol and dietary calcium supplementation normalizes the parathyroid and calcemic postprandial responses in patients with CKD, in whom the diurnal rhythms of mineral metabolites are preserved. Future studies should investigate the variable fibroblast growth factor 23 response to calcitriol in CKD.

Selection against small males in utero: a test of the Wells hypothesis

BACKGROUND

The argument that women in stressful environments spontaneously abort their least fit fetuses enjoys wide dissemination despite the fact that several of its most intuitive predictions remain untested. The literature includes no tests, for example, of the hypothesis that these mechanisms select against small for gestational age (SGA) males.

METHODS

We apply time-series modeling to 4.9 million California male term births to test the hypothesis that the rate of SGA infants in 1096 weekly birth cohorts varies inversely with labor market contraction, a known stressor of contemporary populations.

RESULTS

We find support for the hypothesis that small size becomes less frequent among term male infants when the labor market contracts.

CONCLUSIONS

Our findings contribute to the evidence supporting selection in utero. They also suggest that research into the association between maternal stress and adverse birth outcomes should acknowledge the possibility that fetal loss may affect findings and their interpretation. Strengths of our analyses include the large number and size of our birth cohorts and our control for autocorrelation. Weaknesses include that we, like nearly all researchers in the field, have no direct measure of fetal loss.

Objective estimation of loudness growth in hearing-impaired listeners

A methodology for the estimation of individual loudness growth functions using tone-burst otoacoustic emissions (TBOAEs) and tone-burst auditory brainstem responses (TBABRs) was proposed by Silva and Epstein [J. Acoust. Soc. Am. 127, 3629-3642 (2010)]. This work attempted to investigate the application of such technique to the more challenging cases of hearing-impaired listeners. The specific aims of this study were to (1) verify the accuracy of this technique with eight hearing-impaired listeners for 1- and 4-kHz tone-burst stimuli, (2) investigate the effect of residual noise levels from the TBABRs on the quality of the loudness growth estimation, and (3) provide a public dataset of physiological and psychoacoustical responses to a wide range of stimuli intensity. The results show that some of the physiological loudness growth estimates were within the mean-square-error range for standard psychoacoustical procedures, with closer agreement at 1 kHz. The median residual noise in the TBABRs was found to be related to the performance of the estimation, with some listeners showing strong improvements in the estimated loudness growth function when controlling for noise levels. This suggests that future studies using evoked potentials to estimate loudness growth should control for the estimated averaged residual noise levels of the TBABRs.