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1.  Differences in Detection Rates of Adenomas and Serrated Polyps in Screening Versus Surveillance Colonoscopies, Based on the New Hampshire Colonoscopy Registry 
BACKGROUND & AIMS
The adenoma detection rate (ADR) is an important quality indicator originally developed for screening colonoscopies. However, it is unclear whether the ADR should be calculated using data from screening and surveillance examinations. The recommended benchmark ADR for screening examinations is 20% (15% for women and 25% for men ≥ 50 y). There are few data available to compare ADRs from surveillance vs screening colonoscopies. We used a population-based registry to compare ADRs from screening vs surveillance colonoscopies. The serrated polyp detection rate (SDR), a potential new quality indicator, also was examined.
METHODS
By using data from the statewide New Hampshire Colonoscopy Registry, we excluded incomplete and diagnostic colonoscopies, and those performed in patients with inflammatory bowel disease, familial syndromes, or poor bowel preparation. We calculated the ADR and SDR (number of colonoscopies with at least 1 adenoma or serrated polyp detected, respectively, divided by the number of colonoscopies) from 9100 colonoscopies. The ADR and SDR were compared by colonoscopy indication (screening, surveillance), age at colonoscopy (50–64 y, ≥65 y), and sex.
RESULTS
The ADR was significantly higher in surveillance colonoscopies (37%) than screening colonoscopies (25%; P < .001). This difference was observed for both sexes and age groups. There was a smaller difference in the SDR of screening (8%) vs surveillance colonoscopies (10%; P < .001).
CONCLUSIONS
In a population-based study, we found that addition of data from surveillance colonoscopies increased the ADR, but had a smaller effect on the SDR. These findings indicate that when calculating ADR as a quality measure, endoscopists should use screening, rather than surveillance colonoscopy, data.
doi:10.1016/j.cgh.2013.04.042
PMCID: PMC3841980  PMID: 23660415
Colon Cancer; Early Detection; Endoscopy; Tumor
2.  Serrated and Adenomatous Polyp Detection Increases with Longer Withdrawal Time: Results from the New Hampshire Colonoscopy Registry 
Background
Detection and removal of adenomas and clinically significant serrated polyps is critical to the effectiveness of colonoscopy in preventing colorectal cancer. While longer withdrawal time has been found to increase polyp detection, this association, and the use of withdrawal time as a quality indicator, remains controversial. Few studies have reported on withdrawal time and serrated polyp detection. Using data from the New Hampshire Colonoscopy Registry, we examined how an endoscopist’s withdrawal time in normal colonoscopies affects adenoma and serrated polyp detection.
Methods
We analyzed 7996 colonoscopies performed in 7972 patients between 2009 and 2011 by 42 endoscopists at 14 hospitals, ambulatory surgery centers, and community practices. Clinically significant serrated polyps (CSSPs) were defined as sessile serrated polyps and hyperplastic polyps proximal to the sigmoid. Adenoma and CSSP detection rates were calculated based on median endoscopist withdrawal time in normal exams. Regression models were used to estimate the association of increased normal withdrawal time and polyp, adenoma, and CSSP detection.
Results
Polyp and adenoma detection rates were highest among endoscopists with 9 minute median normal withdrawal time, while detection of CSSPs reached its highest levels at 8 to 9 minutes. Incident rate ratios for adenoma and CSSP detection increased with each minute of normal withdrawal time above 6 minutes, with maximum benefit at 9 minutes for adenomas (1.50, 95% CI (1.21,1.85)) and CSSPs (1.77, 95% CI (1.15, 2.72)). When modeling was used to set the minimum withdrawal time at 9 minutes, we predicted that adenomas and CSSPs would be detected in 302 (3.8%) and 191 (2.4%) more patients. The increase in detection was most striking for the CSSPs, with nearly a 30% relative increase.
Conclusions
A withdrawal time of 9 minutes resulted in a statistically significant increase in adenoma and serrated polyp detection. Colonoscopy quality may improve with a median normal withdrawal time benchmark of 9 minutes.
doi:10.1038/ajg.2013.442
PMCID: PMC4082336  PMID: 24394752
Colon cancer; cancer early detection; quality indicators; cancer prevention
3.  Parental Efficacy and Child Behavior in a Community Sample of Children with and without Attention-Deficit Hyperactivity Disorder (ADHD) 
Purpose
Most studies of ADHD youth have obtained data from the perspective of either children or parents, but not both simultaneously. The purpose of this study was to examine child and parent perspectives on parenting in a large community-based sample of children with and without ADHD.
Methods
We identified children in grades 4-6 and their parents through surveys administered to a random sample of public schools. We used multivariable logistic regression to determine independent associations between child and parent characteristics and presence of ADHD while controlling for covariates and clustering by school.
Results
Sufficient data were achieved for 2509 child/parent dyads. Ten percent of youths (n=240) had been diagnosed with ADHD. Compared with those without ADHD, those with ADHD were more commonly male (67.9% vs. 48.0%, P<.001) and age 12 or over (16.3% vs. 10.3%). After adjusting for covariates and clustering, compared to children without ADHD, children with ADHD were significantly more likely to report lower self-regulation (OR= 0.68, 95% CI=0.53, 0.88) and higher levels of rebelliousness (OR= 2.00, 95% CI=1.52, 2.69). Compared with parents whose children did not have ADHD, parents of children with ADHD rated their overall parental efficacy substantially lower (OR=0.23, 95% CI=0.15, 0.33). However, child assessment of parenting style was similar by ADHD.
Conclusions
Despite the internal challenges community-based youth with ADHD face, many parents of ADHD youth exhibit valuable parental skills from the perspective of their children. Feedback of this information to parents may improve parental self-efficacy, which is known to be positively associated with improved ADHD outcomes.
doi:10.1007/s12402-012-0089-z
PMCID: PMC3562484  PMID: 22886756
ADHD; child behavior; parental efficacy; school performance
4.  Screening mammography intervals among postmenopausal hormone therapy users and nonusers 
Cancer causes & control : CCC  2009;21(1):147-152.
Background
The recent decline in US breast cancer incidence rates has been attributed to the marked reduction in use of postmenopausal hormone therapy (HT). An alternative explanation is that women who are not routinely seeking medical care to renew HT prescriptions may be less adherent to recommendations for mammographic screening. To investigate the latter possibility, we compared mammographic intervals according to HT use.
Methods
Using data (1995–2007) from the New Hampshire Mammography Network (NHMN), a state-based mammography registry, we assessed mammographic intervals corresponding to HT use or nonuse among postmenopausal women. We used linear mixed effects models to assess whether the length of screening mammogram intervals differed according to HT use.
Results
A total of 310,185 mammograms, representing 76,192 postmenopausal women and 319,353 person-years of screening, were included in the analysis. The median screening interval corresponding to HT use overall was 13.0 months (interquartile range: 12.4–15.1) and for nonuse was 13.1 (interquartile range: 12.4–15.8). Virtually, all screening mammograms occurred within a 2-year interval regardless of HT use or nonuse (98.5 and 98.1%, respectively).
Conclusions
Our findings indicate that screening mammography intervals are similar whether or not women are using HT. Thus, reduced utilization of screening mammography is unlikely to account for the decrease in breast cancer incidence seen soon after the WHI report.
doi:10.1007/s10552-009-9444-6
PMCID: PMC3786216  PMID: 19844798
Mammography; Screening; Hormone therapy; Breast cancer
5.  Development of a Configurable Growth Chamber with a Computer Vision System to Study Circadian Rhythm in Plants 
Sensors (Basel, Switzerland)  2012;12(11):15356-15375.
Plant development is the result of an endogenous morphogenetic program that integrates environmental signals. The so-called circadian clock is a set of genes that integrates environmental inputs into an internal pacing system that gates growth and other outputs. Study of circadian growth responses requires high sampling rates to detect changes in growth and avoid aliasing. We have developed a flexible configurable growth chamber comprising a computer vision system that allows sampling rates ranging between one image per 30 s to hours/days. The vision system has a controlled illumination system, which allows the user to set up different configurations. The illumination system used emits a combination of wavelengths ensuring the optimal growth of species under analysis. In order to obtain high contrast of captured images, the capture system is composed of two CCD cameras, for day and night periods. Depending on the sample type, a flexible image processing software calculates different parameters based on geometric calculations. As a proof of concept we tested the system in three different plant tissues, growth of petunia- and snapdragon (Antirrhinum majus) flowers and of cladodes from the cactus Opuntia ficus-indica. We found that petunia flowers grow at a steady pace and display a strong growth increase in the early morning, whereas Opuntia cladode growth turned out not to follow a circadian growth pattern under the growth conditions imposed. Furthermore we were able to identify a decoupling of increase in area and length indicating that two independent growth processes are responsible for the final size and shape of the cladode.
doi:10.3390/s121115356
PMCID: PMC3522967  PMID: 23202214
circadian clock; floral size; diel growth; Petunia opuntia; Antirrhinum majus; computer vision
6.  pcrEfficiency: a Web tool for PCR amplification efficiency prediction 
BMC Bioinformatics  2011;12:404.
Background
Relative calculation of differential gene expression in quantitative PCR reactions requires comparison between amplification experiments that include reference genes and genes under study. Ignoring the differences between their efficiencies may lead to miscalculation of gene expression even with the same starting amount of template. Although there are several tools performing PCR primer design, there is no tool available that predicts PCR efficiency for a given amplicon and primer pair.
Results
We have used a statistical approach based on 90 primer pair combinations amplifying templates from bacteria, yeast, plants and humans, ranging in size between 74 and 907 bp to identify the parameters that affect PCR efficiency. We developed a generalized additive model fitting the data and constructed an open source Web interface that allows the obtention of oligonucleotides optimized for PCR with predicted amplification efficiencies starting from a given sequence.
Conclusions
pcrEfficiency provides an easy-to-use web interface allowing the prediction of PCR efficiencies prior to web lab experiments thus easing quantitative real-time PCR set-up. A web-based service as well the source code are provided freely at http://srvgen.upct.es/efficiency.html under the GPL v2 license.
doi:10.1186/1471-2105-12-404
PMCID: PMC3234296  PMID: 22014212
7.  Quantitative Shotgun Proteomics Using a Uniform 15N-Labeled Standard to Monitor Proteome Dynamics in Time Course Experiments Reveals New Insights into the Heat Stress Response of Chlamydomonas reinhardtii* 
Molecular & Cellular Proteomics : MCP  2011;10(9):M110.004739.
Crop-plant-yield safety is jeopardized by temperature stress caused by the global climate change. To take countermeasures by breeding and/or transgenic approaches it is essential to understand the mechanisms underlying plant acclimation to heat stress. To this end proteomics approaches are most promising, as acclimation is largely mediated by proteins. Accordingly, several proteomics studies, mainly based on two-dimensional gel-tandem MS approaches, were conducted in the past. However, results often were inconsistent, presumably attributable to artifacts inherent to the display of complex proteomes via two-dimensional-gels. We describe here a new approach to monitor proteome dynamics in time course experiments. This approach involves full 15N metabolic labeling and mass spectrometry based quantitative shotgun proteomics using a uniform 15N standard over all time points. It comprises a software framework, IOMIQS, that features batch job mediated automated peptide identification by four parallelized search engines, peptide quantification and data assembly for the processing of large numbers of samples. We have applied this approach to monitor proteome dynamics in a heat stress time course using the unicellular green alga Chlamydomonas reinhardtii as model system. We were able to identify 3433 Chlamydomonas proteins, of which 1116 were quantified in at least three of five time points of the time course. Statistical analyses revealed that levels of 38 proteins significantly increased, whereas levels of 206 proteins significantly decreased during heat stress. The increasing proteins comprise 25 (co-)chaperones and 13 proteins involved in chromatin remodeling, signal transduction, apoptosis, photosynthetic light reactions, and yet unknown functions. Proteins decreasing during heat stress were significantly enriched in functional categories that mediate carbon flux from CO2 and external acetate into protein biosynthesis, which also correlated with a rapid, but fully reversible cell cycle arrest after onset of stress. Our approach opens up new perspectives for plant systems biology and provides novel insights into plant stress acclimation.
doi:10.1074/mcp.M110.004739
PMCID: PMC3186191  PMID: 21610104
8.  Influence of Movie Smoking Exposure and Team Sports Participation on Established Smoking 
Objective
To examine the joint effects of movie smoking exposure and team sports participation on established smoking.
Design
Longitudinal study.
Setting
School- and telephone-based surveys in New Hampshire and Vermont between September 1999 through November 1999 and February 2006 through February 2007.
Participants
A total of 2048 youths aged 16 to 21 years at follow-up.
Main Exposures
Baseline movie smoking exposure categorized in quartiles assessed when respondents were aged 9 to 14 years and team sports participation assessed when respondents were aged 16 to 21 years.
Main Outcome Measure
Established smoking (having smoked ≥100 cigarettes in one’s lifetime) at follow-up.
Results
At follow-up, 353 respondents (17.2%) were established smokers. Exposure to the highest quartile of movie smoking compared with the lowest increased the likelihood of established smoking (odds ratio=1.63; 95% confidence interval, 1.03–2.57), and team sports nonparticipants compared with participants were twice as likely to be established smokers (odds ratio=2.01; 95% confidence interval, 1.47–2.74). The joint effects of movie smoking exposure and team sports participation revealed that at each quartile of movie smoking exposure, the odds of established smoking were greater for team sports nonparticipants than for participants. We saw a dose-response relationship of movie smoking exposure for established smoking only among team sports participants.
Conclusions
Team sports participation clearly plays a protective role against established smoking, even in the face of exposure to movie smoking. However, movie smoking exposure increases the risk of established smoking among both team sports participants and nonparticipants. Parents, teachers, coaches, and clinicians should be aware that encouraging team sports participation in tandem with minimizing early exposure to movie smoking may offer the greatest likelihood of preventing youth smoking.
doi:10.1001/archpediatrics.2009.59
PMCID: PMC3006430  PMID: 19581547
9.  A molecular recombination map of Antirrhinum majus 
BMC Plant Biology  2010;10:275.
Background
Genetic recombination maps provide important frameworks for comparative genomics, identifying gene functions, assembling genome sequences and for breeding. The molecular recombination map currently available for the model eudicot Antirrhinum majus is the result of a cross with Antirrhinum molle, limiting its usefulness within A. majus.
Results
We created a molecular linkage map of A. majus based on segregation of markers in the F2 population of two inbred lab strains of A. majus. The resulting map consisted of over 300 markers in eight linkage groups, which could be aligned with a classical recombination map and the A. majus karyotype. The distribution of recombination frequencies and distorted transmission of parental alleles differed from those of a previous inter-species hybrid. The differences varied in magnitude and direction between chromosomes, suggesting that they had multiple causes. The map, which covered an estimated of 95% of the genome with an average interval of 2 cM, was used to analyze the distribution of a newly discovered family of MITE transposons and tested for its utility in positioning seven mutations that affect aspects of plant size.
Conclusions
The current map has an estimated interval of 1.28 Mb between markers. It shows a lower level of transmission ratio distortion and a longer length than the previous inter-species map, making it potentially more useful. The molecular recombination map further indicates that the IDLE MITE transposons are distributed throughout the genome and are relatively stable. The map proved effective in mapping classical morphological mutations of A. majus.
doi:10.1186/1471-2229-10-275
PMCID: PMC3017841  PMID: 21159166
10.  Floral organ size control 
Plant Signaling & Behavior  2009;4(9):814-817.
Growth of lateral organs is a complex mechanism that starts with formation of lateral primordia.Basal developmental programs like polarity, organ identity and environmental cues influence the final organ size achieved via coordinated cell division and expansion. recent evidence shows that the precise balance between these two processes, known as compensation mechanisms, seems to be influenced by the identity of the organ. Furthermore, studies of mutants affected in floral organ size suggest the existence of developmental compartments within different floral whorls that show distinct compensation behaviors.
PMCID: PMC2802805  PMID: 19847102
Antirrhinum majus; cell division; cell expansion; COMPACTA ÄHNLICH; compensation; floral size; FORMOSA; NITIDA; organ identity
11.  Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida 
BMC Plant Biology  2010;10:4.
Background
Identification of genes with invariant levels of gene expression is a prerequisite for validating transcriptomic changes accompanying development. Ideally expression of these genes should be independent of the morphogenetic process or environmental condition tested as well as the methods used for RNA purification and analysis.
Results
In an effort to identify endogenous genes meeting these criteria nine reference genes (RG) were tested in two Petunia lines (Mitchell and V30). Growth conditions differed in Mitchell and V30, and different methods were used for RNA isolation and analysis. Four different software tools were employed to analyze the data. We merged the four outputs by means of a non-weighted unsupervised rank aggregation method. The genes identified as optimal for transcriptomic analysis of Mitchell and V30 were EF1α in Mitchell and CYP in V30, whereas the least suitable gene was GAPDH in both lines.
Conclusions
The least adequate gene turned out to be GAPDH indicating that it should be rejected as reference gene in Petunia. The absence of correspondence of the best-suited genes suggests that assessing reference gene stability is needed when performing normalization of data from transcriptomic analysis of flower and leaf development.
doi:10.1186/1471-2229-10-4
PMCID: PMC2827423  PMID: 20056000
12.  Breast cancer risk factors in relation to breast density (United States) 
Cancer Causes & Control   2006;17(10):1281-1290.
Objectives
Evaluate known breast cancer risk factors in relation to breast density.
Methods
We examined factors in relation to breast density in 144,018 New Hampshire (NH) women with at least one mammogram recorded in a statewide mammography registry. Mammographic breast density was measured by radiologists using the BI-RADS classification; risk factors of interest were obtained from patient intake forms and questionnaires.
Results
Initial analyses showed a strong inverse influence of age and body mass index (BMI) on breast density. In addition, women with late age at menarche, late age at first birth, premenopausal women, and those currently using hormone therapy (HT) tended to have higher breast density, while those with greater parity tended to have less dense breasts. Analyses stratified on age and BMI suggested interactions, which were formally assessed in a multivariable model. The impact of current HT use, relative to nonuse, differed across age groups, with an inverse association in younger women, and a positive association in older women (p < 0.0001 for the interaction). The positive effects of age at menarche and age at first birth, and the inverse influence of parity were less apparent in women with low BMI than in those with high BMI (p = 0.04, p < 0.0001 and p = 0.01, respectively, for the interactions). We also noted stronger positive effects for age at first birth in postmenopausal women (p = 0.004 for the interaction). The multivariable model indicated a slight positive influence of family history of breast cancer.
Conclusions
The influence of age at menarche and reproductive factors on breast density is less evident in women with high BMI. Density is reduced in young women using HT, but increased in HT users of age 50 or more.
doi:10.1007/s10552-006-0071-1
PMCID: PMC1705538  PMID: 17111260
Hormone replacement therapy; Reproductive history; Mammographic breast density

Results 1-12 (12)