Neurodevelopmental Outcomes of Infants after Neonatal Surgical Intervention for Tetralogy of Fallot or Pulmonary Atresia

OBJECTIVE

To determine the 2-year neurodevelopmental outcomes for survivors of neonatal cardiac surgery for the most common right ventricular outflow tract obstructive lesions: tetralogy of Fallot and pulmonary atresia with a ventricular septal defect.

STUDY DESIGN

A single-center consecutive cohort of 77 children underwent neonatal surgery for tetralogy of Fallot or pulmonary atresia with a ventricular septal defect at ≤6 weeks of age between 2006 and 2017. The patients underwent a multidisciplinary neurodevelopmental assessment at 18-24 months of age. Survivor outcomes were compared by univariable and multivariable analyses.

RESULTS

The 2-year mortality was 7.8% (6/77) with a postoperative in-hospital mortality of 3.9% (3/77). Freedom from reintervention by cardiac catheterization or surgical intervention at 2 years was 36%. Functional and neurodevelopmental assessment for 69 of 71 survivors was completed at a mean age of 22.6 ± 4.0 months using the Bayley Scales of Infant and Toddler Development III. The mean neurodevelopmental outcome scores were 83.4 ± 16.5 for cognitive skills, 82.2 ± 18.7 for language skills, and 81.4 ± 18.1 for motor skills. Cognitive, language, and motor delay, defined as a score of <70, was identified in 25%, 25%, and 23% of patients, respectively. Multivariable analyses for factors associated with worse neurodevelopmental outcomes identified chromosomal anomalies (P < .001) and postoperative complications (P < .03).

CONCLUSIONS

Cyanotic tetralogy of Fallot and pulmonary atresia with ventricular septal defect requiring neonatal repair showed similar 2-year neurodevelopmental outcomes below normative values and a high prevalence of cognitive, language and motor delays.

A complicated Glenn procedure: risk factors and association with adverse long-term neurodevelopmental and functional outcomes

OBJECTIVES

To determine potentially modifiable risk factors for a complicated Glenn procedure (cGP) and whether a cGP predicted adverse neurodevelopmental and functional outcomes. A cGP was defined as post-operative death, heart transplant, extracorporeal life support, Glenn takedown, or prolonged ventilation.

METHODS

All 169 patients having a Glenn procedure from 2012 to 2017 were included. Neurodevelopmental assessments were performed at age 2 years in consenting survivors (n = 156/159 survivors). The Bayley Scales of Infant and Toddler Development-3rd Edition (Bayley-III) and the Adaptive Behavior Assessment System-2nd Edition (ABAS-II) were administered. Adaptive functional outcomes were determined by the General Adaptive Composite (GAC) score from the ABAS-II. Predictors of outcomes were determined using univariate and multiple variable linear or Cox regressions.

RESULTS

Of patients who had a Glenn procedure, 10/169 (6%) died by 2 years of age and 27/169 (16%) had a cGP. Variables statistically significantly associated with a cGP were the inotrope score on post-operative day 1 (HR 1.04, 95%CI 1.01, 1.06; p = 0.010) and use of inhaled nitric oxide post-operatively (HR 7.31, 95%CI 3.19, 16.76; p < 0.001). A cGP was independently statistically significantly associated with adverse Bayley-III Cognitive (ES -10.60, 95%CI -17.09, -4.11; p = 0.002) and Language (ES -11.43, 95%CI -19.25, -3.60; p = 0.004) scores and adverse GAC score (ES -14.89, 95%CI -22.86, -6.92; p < 0.001).

CONCLUSIONS

Higher inotrope score and inhaled nitric oxide used post-operatively were associated with a cGP. A cGP was independently associated with adverse 2-year neurodevelopmental and functional outcomes. Whether early recognition and intervention for risk of a cGP can prevent adverse outcomes warrants study.

Maternal co-exposure to mercury and perfluoroalkyl acid isomers and their associations with child neurodevelopment in a Canadian birth cohort

BACKGROUND

Perfluoroalkyl acids (PFAAs) within the broader class of per- and polyfluoroalkyl substances (PFAS) are present in human serum as isomer mixtures, but epidemiological studies have yet to address isomer-specific associations with child development and behavior.

OBJECTIVES

To examine associations between prenatal exposure to 25 PFAAs, including perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) isomers, and child neurodevelopment among 490 mother-child pairs in a prospective Canadian birth cohort, the Alberta Pregnancy Outcomes and Nutrition (APrON) study. To consider the influence of a classic neurotoxicant, total mercury (THg), based on its likelihood of co-exposure with PFAAs from common dietary sources.

METHODS

Maternal blood samples were collected in the second trimester and child neurodevelopment was assessed at 2 years of age using the Bayley Scales of Infant and Toddler Development, 3rd Edition (Bayley-III). Linear or curvilinear multiple regression models were used to examine associations between exposures and neurodevelopment outcomes.

RESULTS

Select PFAAs were associated with lower Cognitive composite scores, including perfluoroheptanoate (PFHpA) (β = -0.88, 95% confidence interval (CI): -1.7, -0.06) and perfluorododecanoate (PFDoA) (β = -2.0, 95% CI: -3.9, -0.01). Non-linear relationships revealed associations of total PFOS (β = -4.4, 95% CI: -8.3, -0.43), and linear-PFOS (β = -4.0, 95% CI: -7.5, -0.57) and 1m-PFOS (β = -1.8, 95% CI: -3.3, -0.24) isomers with lower Language composite scores. Although there was no effect modification, including THg interaction terms in PFAA models revealed negative associations between perfluorononanoate (PFNA) and Motor (β = -3.3, 95% CI: -6.2, -0.33) and Social-Emotional (β = -3.0, 95% CI: -5.6, -0.40) composite scores.

DISCUSSION

These findings reinforce previous reports of adverse effects of maternal PFAA exposure during pregnancy on child neurodevelopment. The unique hazards posed from isomers of PFOS justify isomer-specific analysis in future studies. To control for possible confounding, mercury co-exposure may be considered in studies of PFAAs.

Introducing novel key genes and transcription factors associated with rectal cancer response to chemoradiation through co-expression network analysis

Preoperative radiochemotherapy is a promising therapeutic method for locally advanced rectal cancer patients. However, the response of colorectal cancer (CRC) patients to preoperative radiotherapy varies widely. In this study, we aimed to identify novel biomarkers that could predict the response of colorectal tumors to treatment using a systems biology approach. We applied the Weighted Gene Co-Expression Network Analysis to construct co-expression networks and evaluated the correlation of these networks with radiation using the module-trait relationship. We then identified hub genes and related transcription factors in the selected co-expression module. Our analysis of seven constructed modules revealed that one module, which contained 113 nodes and 6066 edges, had the strongest correlation with radiation effects on CRC (correlation = 0.85; p-value = 6e-7). By analyzing the selected module with the CytoHubba plugin, we identified four hub genes, including ZEB2, JAM2, NDN, and PPAP2A. We also identified seven important transcription factors, including KLF4, SUZ12, TCF4, NANOG, POU5F1, SOX2, and SMARCA4, which may play essential roles in regulating the four hub genes. In summary, our findings suggest that ZEB2, JAM2, NDN, and PPAP2A, along with the seven transcription factors related to these hub genes, may be associated with the response of colorectal tumors to chemoradiotherapy.

Identification of Prognostic Biomarkers for Breast Cancer Metastasis Using Penalized Additive Hazards Regression Model

Background:

Breast cancer (BC) has been reported as one of the most common cancers diagnosed in females throughout the world. Survival rate of BC patients is affected by metastasis. So, exploring its underlying mechanisms and identifying related biomarkers to monitor BC relapse/recurrence using new statistical methods is essential. This study investigated the high-dimensional gene-expression profiles of BC patients using penalized additive hazards regression models.

Methods:

A publicly available dataset related to the time to metastasis in BC patients (GSE2034) was used. There was information of 22 283 genes expression profiles related to 286 BC patients. Penalized additive hazards regression models with different penalties, including LASSO, SCAD, SICA, MCP and Elastic net were used to identify metastasis related genes.

Results:

Five regression models with penalties were applied in the additive hazards model and jointly found 9 genes including SNU13, CLINT1, MAPK9, ABCC5, NKX3-1, NCOR2, COL2A1, and ZNF219. According the median of the prognostic index calculated using the regression coefficients of the penalized additive hazards model, the patients were labeled as high/low risk groups. A significant difference was detected in the survival curves of the identified groups. The selected genes were examined using validation data and were significantly associated with the hazard of metastasis.

Conclusion:

This study showed that MAPK9, NKX3-1, NCOR1, ABCC5, and CD44 are the potential recurrence and metastatic predictors in breast cancer and can be taken into account as candidates for further research in tumorigenesis, invasion, metastasis, and epithelial-mesenchymal transition of breast cancer.

Geographically weighted linear combination test for gene-set analysis of a continuous spatial phenotype as applied to intratumor heterogeneity

Background: The impact of gene-sets on a spatial phenotype is not necessarily uniform across different locations of cancer tissue. This study introduces a computational platform, GWLCT, for combining gene set analysis with spatial data modeling to provide a new statistical test for location-specific association of phenotypes and molecular pathways in spatial single-cell RNA-seq data collected from an input tumor sample.

Methods: The main advantage of GWLCT consists of an analysis beyond global significance, allowing the association between the gene-set and the phenotype to vary across the tumor space. At each location, the most significant linear combination is found using a geographically weighted shrunken covariance matrix and kernel function. Whether a fixed or adaptive bandwidth is determined based on a cross-validation cross procedure. Our proposed method is compared to the global version of linear combination test (LCT), bulk and random-forest based gene-set enrichment analyses using data created by the Visium Spatial Gene Expression technique on an invasive breast cancer tissue sample, as well as 144 different simulation scenarios.

Results: In an illustrative example, the new geographically weighted linear combination test, GWLCT, identifies the cancer hallmark gene-sets that are significantly associated at each location with the five spatially continuous phenotypic contexts in the tumors defined by different well-known markers of cancer-associated fibroblasts. Scan statistics revealed clustering in the number of significant gene-sets. A spatial heatmap of combined significance over all selected gene-sets is also produced. Extensive simulation studies demonstrate that our proposed approach outperforms other methods in the considered scenarios, especially when the spatial association increases.

Conclusion: Our proposed approach considers the spatial covariance of gene expression to detect the most significant gene-sets affecting a continuous phenotype. It reveals spatially detailed information in tissue space and can thus play a key role in understanding the contextual heterogeneity of cancer cells.

Infants' gut microbiome data: A Bayesian Marginal Zero-inflated Negative Binomial regression model for multivariate analyses of count data

The infants' gut microbiome is dynamic in nature. Literature has shown high inter-individual variability of gut microbial composition in the early years of infancy compared to adulthood. Although next-generation sequencing technologies are rapidly evolving, several statistical analysis aspects need to be addressed to capture the variability and dynamic nature of the infants' gut microbiome. In this study, we proposed a Bayesian Marginal Zero-inflated Negative Binomial (BAMZINB) model, addressing complexities associated with zero-inflation and multivariate structure of the infants' gut microbiome data. Here, we simulated 32 scenarios to compare the performance of BAMZINB with glmFit and BhGLM as the two other widely similar methods in the literature in handling zero-inflation, over-dispersion, and multivariate structure of the infants' gut microbiome. Then, we showed the performance of the BAMZINB approach on a real dataset using SKOT cohort (I and II) studies. Our simulation results showed that the BAMZINB model performed as well as those two methods in estimating the average abundance difference and had a better fit for almost all scenarios when the signal and sample size were large. Applying BAMZINB on SKOT cohorts showed remarkable changes in the average absolute abundance of specific bacteria from 9 to 18 months for infants of healthy and obese mothers. In conclusion, we recommend using the BAMZINB approach for infants' gut microbiome data taking zero-inflation and over-dispersion properties into account in multivariate analysis when comparing the average abundance difference.

Evaluating the Prevalence and Factors Associated With an Optimal Neurodevelopmental Outcome in 4- to 6-Year-Old Children With Fontan Circulation

BACKGROUND

We sought to evaluate the prevalence and factors associated with "optimal" neurodevelopmental outcomes in 4- to 6-year-old children with Fontan circulation.

METHODS

Patients followed through the Western Canadian Complex Pediatric Therapies Follow-Up Program, and born between September 1996 and December 2015, were included. Optimal neurodevelopmental outcome was defined as full-scale intelligence quotient; visual-motor integration; adaptive behaviour assessment system-general adaptive composite scores of ≥ 80 each; and the absence of chronic motor disability, permanent hearing loss, visual impairment, and seizure disorder. Multivariable regression models and decision algorithms evaluated variables associated with optimal outcomes.

RESULTS

The Fontan procedure was completed on 225 children, with neurodevelopmental outcome data available for 205 (mean [standard deviation]) age at Fontan 3.4 (0.9) years, 37% female). Optimal neurodevelopmental outcome was identified in 55% (112 of 205). Factors independently associated with optimal neurodevelopmental outcome were female sex (odds ratio [OR], 2.1; 95% confidence interval [CI] 1.1-4.1), years of maternal schooling (OR, 1.2 [1.1-1.4]), age at Fontan (years) (OR, 0.97 [0.94-1.0]), need for concomitant atrioventricular valve (AVV) intervention (OR, 0.4 [0.2-1.0]), and time (hours) for lactate to be ≤ 2 mmol/L (OR, 0.9 [0.8-1.0]). Of those with Fontan completion < 3.25 years, without concomitant AVV intervention and lactate normalization within 8 hours post-Fontan, 87% (27 of 31) had optimal neurodevelopmental outcomes.

CONCLUSIONS

Optimal neurodevelopmental outcome was present in more than one-half of 4- to 6-year-old children with Fontan circulation in this cohort study, with important associated factors identified, including potentially modifiable factors such as younger age at Fontan surgery and lack of concomitant AVV intervention.

“50 shades of groin pain” in an unusual case of osteomyelitis pubis following surgery

Osteomyelitis pubis (OP) is a rare type of infection involving the pubic bones that often poses diagnostic and consecutive therapeutic problems. The infection can be mono or polymicrobial, bacterial, mycotic or bacillary with Staphylococcus aureus being the most common infectious agent involved. OP is generally seen in immune-suppressed patients of oncologic and diabetic population or in pediatric and geriatric subjects. The main symptom is represented by local pain with radiation to thighs which in later stages is accompanied by general non-specific symptoms such as malaise, fever and loss of appetite. The specificity-lacking initial presentation often leads to diagnostic delays which furthermore decrease the effectiveness of drug therapy, leading to higher chances of bone and joint destruction. Initial therapy consists of empirical antibiotherapy that should cover Staph. aureus; depending on culture results, the scheme should be changed accordingly. Moreover, symptomatic treatment of pain and inflammation consisting of NSAIDs, small dose glucocorticoids and minor opioids should be considered. Selected cases may benefit from surgical intervention when improvement or remission is considered improbable under drug therapy or when severe bony destructions are present.

COVID-19, a phantomatic trigger for relapsing polychondritis

Relapsing polychondritis (RP) is an auto-immune disease which affects the cartilaginous parts of sites like the ear, nose or upper respiratory tract. The condition can also involve other cartilage-containing structures such as the eyes, joints, the heart, kidneys and central nervous system. Early diagnosis of RPis essential for preventing significant damage to vital organs that can lead to increased morbi-mortality rates. First-line therapy in RP is systemic glucocorticoids, while in refractory cases monoclonal antibodies can be used despite scarcity of efficacy data available in published literature. The link between RP and neoplasia, especially hematological malignancy, should not be omitted when screening patients with suspicion of RP diagnosis. The onset of COVID-19 pandemic has generated a new source of immune mediated pathologies, such as small vessel vasculitis, immune thrombocytopenic purpura or Guillain-Barre syndrome and other auto-inflammatory syndromes triggered by COVID-19 seem to unveil. The present case depicts a female patient who presented with erythematous and painful areas of her right ear after priorly experiencing similar episodes in both ears and nose bridge shortly after having the COVID-19 vaccine booster dose.

Interaction of prenatal bisphenols, maternal nutrients, and toxic metal exposures on neurodevelopment of 2-year-olds in the APrON cohort

BACKGROUND

Epidemiological studies suggest that Bisphenol-A (BPA) is a developmental neurotoxicant, but the modifying effects of maternal nutrient status or neurotoxicant metal co-exposures have not been reported. Bisphenol-S (BPS) is being used as a BPA-alternative, but few epidemiological studies have evaluated its effects.

OBJECTIVES

To examine if prenatal maternal BPA or BPS exposure are associated with children's neurodevelopment at two years of age while adjusting for effect-measure modification by sex, maternal nutrients, and co-exposure to neurotoxic metals.

METHODS

Total BPA and BPS concentrations were analyzed in spot maternal urine from the second trimester; metals and maternal nutrient status were analyzed in blood. Child neurodevelopment was evaluated with the Bayley Scales of Infant Development-III (Bayley-III) at age 2 (394 maternal-child pairs) and linear regression was used to investigate associations.

RESULTS

Among nutrients and neurotoxic metals, selenium (Se) and cadmium (Cd) were the most significant predictors of Bayley-III scale scores. Higher maternal Cd was significantly correlated with poorer motor performance (p < 0.01), and higher levels of maternal Se were significantly associated with poorer performance on the cognitive, motor, and adaptive behavior scales (p < 0.05). While maternal Cd did not modify relationships between bisphenol exposures and Bayley-III scores, both maternal Se and child sex were significant effect-measure modifiers. Associations between BPA exposure and social emotional scores were negative for boys (p = 0.056) but positive for girls (p = 0.046). Higher exposure to bisphenols was associated with lower motor scores among children with lower levels of maternal Se.

CONCLUSION

Higher maternal Cd was associated with poorer motor development, but it was not an effect-measure modifier of bisphenols' effects on motor development. Maternal Se may be protective against adverse effects of bisphenols, and additional nutrient-bisphenol interaction studies examining sex-specific effects of BPA and BPS on child development are warranted.

An updated reference for age-sex-specific birth weight percentiles stratified for ethnicity based on data from all live birth infants between 2005 and 2014 in Alberta, Canada

OBJECTIVE

This study aims to update the current reference for sex-specific birth weight percentiles by gestational age, overall and for specific ethnic groups, based on data from all singleton live-birth deliveries from 2005 to 2014 in Alberta, Canada.

METHODS

Infant and maternal information were captured in the Alberta Vital Statistics-Births Database for 473,115 singleton infants born to 311,800 women between January 1, 2005 and December 31, 2014. Within each sex, and each sex-ethnic group, birth weights were modelled by gestational age using generalized additive models and natural cubic splines. Crude and corrected estimates for birth weight percentiles including cut-off values for large for gestational age (LGA) and small for gestational age (SGA) were calculated by sex and sex-ethnic group, and gestational age for singleton live births.

RESULTS

LGA and SGA cut-offs were lower for females than for males for all gestational ages. The SGA and LGA percentiles were greater for both male and female very preterm infants in Alberta compared to previous national references. Ethnicity-specific LGA and SGA cut-offs for term Chinese and preterm and at-term South Asian infants were consistently lower than those for both the general population in Alberta and the previous national reference. South Asian infants had lower birth weights at almost all gestational ages compared with the other groups.

CONCLUSION

The updated birth weight percentiles presented in this study highlight the differences in SGA and LGA cut-offs among infants from South Asian, Chinese, and the general population, which may be important for clinical perinatal care.

Efficacy of metformin and fermentable fiber combination therapy in adolescents with severe obesity and insulin resistance: study protocol for a double-blind randomized controlled trial

Background

Accumulating evidence suggests that the metabolic effects of metformin and fermentable fibers are mediated, in part, through diverging or overlapping effects on the composition and metabolic functions of the gut microbiome. Pre-clinical animal models have established that the addition of fiber to metformin monotherapy improves glucose tolerance. However, possible synergistic effects of combination therapy (metformin plus fiber) have not been investigated in humans. Moreover, the underlying mechanisms of synergy have yet to be elucidated. The aim of this study is to compare in adolescents with obesity the metabolic effects of metformin and fermentable fibers in combination with those of metformin or fiber alone. We will also determine if therapeutic responses correlate with compositional and functional features of the gut microbiome.

Methods

This is a parallel three-armed, double-blinded, randomized controlled trial. Adolescents (aged 12–18 years) with obesity, insulin resistance (IR), and a family history of type 2 diabetes mellitus (T2DM) will receive either metformin (850 mg p.o. twice/day), fermentable fibers (35 g/day), or a combination of metformin plus fiber for 12 months. Participants will be seen at baseline, 3, 6, and 12 months, with a phone follow-up at 1 and 9 months. Primary and secondary outcomes will be assessed at baseline, 6, and 12 months. The primary outcome is change in IR estimated by homeostatic model assessment of IR; key secondary outcomes include changes in the Matsuda index, oral disposition index, body mass index z-score, and fat mass to fat-free mass ratio. To gain mechanistic insight, endpoints that reflect host-microbiota interactions will also be assessed: obesity-related immune, metabolic, and satiety markers; humoral metabolites; and fecal microbiota composition, short-chain fatty acids, and bile acids.

Discussion

This study will compare the potential metabolic benefits of fiber with those of metformin in adolescents with obesity, determine if metformin and fiber act synergistically to improve IR, and elucidate whether the metabolic benefits of metformin and fiber associate with changes in fecal microbiota composition and the output of health-related metabolites. This study will provide insight into the potential role of the gut microbiome as a target for enhancing the therapeutic efficacy of emerging treatments for T2DM prevention.

Trial registration

ClinicalTrials.gov NCT04578652. Registered on 8 October 2020.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13063-021-05060-8.

37 Growth and neurodevelopment in early childhood of preterm infants with complex congenital heart defects following open cardiac surgery

Background

Compared with those born at term gestation, infants with complex congenital heart defects (CCHD) who were delivered before 37 weeks of gestational age and received neonatal open cardiac surgery (OHS) have poorer neurodevelopmental outcomes in early childhood. Specific details related to the neurodevelopmental outcome of these infants remain unpublished.

Objectives

To describe the growth, disability, functional, and neurodevelopmental outcome in early childhood of preterm infants (born at &lt;37+0 weeks gestation) with CCHD and neonatal OHS.

Design/Methods

We studied all infants with CCHD who received OHS within 6 weeks of corrected age between 1996 and 2016. In the Western Canadian Complex Pediatric Therapies Follow-up Program, comprehensive neurodevelopmental assessments at a corrected age of 18-24 months were done by multidisciplinary teams at the original referral sites. In addition to demographic and clinical data, standardized age-appropriate outcome measures included physical growth with calculated Z-scores, disabilities including cerebral palsy, visual impairment, sensorineural hearing loss; adaptive function (Adaptive Behavioural Assessment System-II); and cognitive, language, and motor skills (Bayley Scales of Infant and Toddler Development-III).

Results

From 1996 to 2016, 115 preterm infants (34±2 weeks gestation, 2339±637g, 64% males) with CCHD had OHS with 11(10%) deaths before first discharge and 21 (18%) by 2 years. Prior to the first surgery, 7 (6%) neonates had cerebral injuries. Overall, 7 had necrotizing enterocolitis; none had retinopathy of prematurity. All 94 surviving infants received comprehensive evaluation at 2 years corrected age; Eighteen (19%) had congenital syndromes who had worse functional and neurodevelopmental outcomes compared to those (n=76) without syndromal abnormalities (SA) (Table).

Conclusion

For preterm neonates with CCHD and early OHS, the mortality was significant, but the short-term neonatal morbidity was not increased. Compared with published preterm outcomes, the early outcome suggests more cerebral palsy but not sensorineural hearing loss, and greater neurodevelopmental delay. This information is important for management care of the infants, parental counselling and the decision-making process.

Co-consumption of Vegetables and Fruit, Whole Grains, and Fiber Reduces the Cancer Risk of Red and Processed Meat in a Large Prospective Cohort of Adults from Alberta's Tomorrow Project

We examined whether co-consumption of red and processed meat with key foods items and food constituents recommended for cancer prevention (vegetables and fruit, whole grains, and fiber) mitigates cancer incidence. In a prospective cohort of 26,218 adults aged 35–69 years at baseline, dietary intake was collected through 124-item past-year food frequency questionnaire. Incidence of all-cause and 15 cancers previously linked to red and processed meat intake was obtained through data linkage with a cancer registry (average follow-up 13.5 years). Competing risk Cox Proportional Hazard models estimated cancer risk and Accelerated Failure Time models estimated time-to-cancer occurrence for different combinations of intake levels while considering mortality from vital statistics and established confounders. Co-consumption of low vegetables and fruit intake with high processed meat was associated with higher incidence of all-cause and 15 cancers (men: HR = 1.85, 1.91; women: HR = 1.44, 1.49) and accelerated time-to-cancer occurrence (men: 6.5 and 7.1 years and women: 5.6 and 6.3 years, respectively), compared to high vegetables and fruit with low processed meat intake. Less pronounced and less consistent associations were observed for whole grains and fiber and for red meat. The findings provide initial evidence toward refining existing cancer prevention recommendations to optimize the intake and combination of foods in the general adult population.

The relationship between personality traits and psychosomatic complaints in a sample of Iranian adults

BACKGROUND

It has been suggested that personality traits may be related to the psychological conditions of people. The current study aimed to explore the relationship between personality traits and psychosomatic complaints.

METHODS

This study was carried out on a sample of Iranian adults living in Isfahan province. The NEO Five- Factor Inventory questionnaire was used to assess personality traits. A 30-item comprehensive questionnaire was used to assess somatoform symptoms and factor analysis was performed to construct psychosomatic complaints profiles. Data was analyzed by Multiple Indicators Multiple Causes (MIMIC) model, using R software.

RESULTS

In total, 4763 participants were recruited 44.2% males and 55.8% females, with a mean age of 36.54 ± 8.04 years. The results of the MIMIC model showed that there is a significant association between the dimensions of personality (neuroticism, extroversion, openness, agreeableness and conscientiousness) and dimensions of psychosomatic complaints profiles (gastrointestinal, neuro-skeletal, pharyngeal-respiratory and psychological) (P < 0.05). In addition, we found that characteristics such as age, sex, marital status, education, physical activity, and body mass index are related to psychosomatic complaints (P < 0.05) and can affect the association between personality traits and psychosomatic complaints.

CONCLUSIONS

Given the relationship between personality traits and psychosomatic complaints, it is possible to provide preventive and therapeutic interventions for psychosomatic complaints based on personality traits specific to each individual.

Longitudinal linear combination test for gene set analysis

Background

Although microarray studies have greatly contributed to recent genetic advances, lack of replication has been a continuing concern in this area. Complex study designs have the potential to address this concern, though they remain undervalued by investigators due to the lack of proper analysis methods. The primary challenge in the analysis of complex microarray study data is handling the correlation structure within data while also dealing with the combination of large number of genetic measurements and small number of subjects that are ubiquitous even in standard microarray studies. Motivated by the lack of available methods for analysis of repeatedly measured phenotypic or transcriptomic data, herein we develop a longitudinal linear combination test (LLCT).

Results

LLCT is a two-step method to analyze multiple longitudinal phenotypes when there is high dimensionality in response and/or explanatory variables. Alternating between calculating within-subjects and between-subjects variations in two steps, LLCT examines if the maximum possible correlation between a linear combination of the time trends and a linear combination of the predictors given by the gene expressions is statistically significant. A generalization of this method can handle family-based study designs when the subjects are not independent. This method is also applicable to time-course microarray, with the ability to identify gene sets that exhibit significantly different expression patterns over time. Based on the results from a simulation study, LLCT outperformed its alternative: pathway analysis via regression. LLCT was shown to be very powerful in the analysis of large gene sets even when the sample size is small.

Conclusions

This self-contained pathway analysis method is applicable to a wide range of longitudinal genomics, proteomics, metabolomics (OMICS) data, allows adjusting for potentially time-dependent covariates and works well with unbalanced and incomplete data. An important potential application of this method could be time-course linkage of OMICS, an attractive possibility for future genetic researchers.

Availability: R package of LLCT is available at: https://github.com/its-likeli-jeff/LLCT

Gene set analysis and reduction for a continuous phenotype: Identifying markers of birth weight variation based on embryonic stem cells and immunologic signatures

BACKGROUND

Gene set analysis is a popular approach to examine the association between a predefined gene set and a phenotype. Few methods have been developed for a continuous phenotype. However, often not all the genes within a significant gene set contribute to its significance. There is no gene set reduction method developed for continuous phenotype. We developed a computationally efficient analytical tool, called linear combination test for gene set reduction (LCT-GSR) to identify core subsets of gene sets associated with a continuous phenotype. Identifying the core subset enhances our understanding of the biological mechanism and reduces costs of disease risk assessment, diagnosis and treatment.

RESULTS

We evaluated the performance of our analytical tool by applying it to two real microarray studies. In the first application, we analyzed pathway expression measurements in newborns' blood to discover core genes contributing to the variation in birth weight. On average, we were able to reduce the number of genes in the 33 significant gene sets of embryonic stem cell signatures by 84.3% resulting in 229 unique genes. Using immunologic signatures, on average we reduced the number of genes in the 210 significant gene sets by 89% leading to 1603 unique genes. There were 180 unique core genes overlapping across the two databases. In the second application, we analyzed pathway expression measurements in a cohort of lethal prostate cancer patients from Swedish Watchful Waiting cohort to identify main genes associated with tumor volume. On average, we were able to reduce the number of genes in the 17 gene sets by 90% resulting in 47 unique genes.

CONCLUSIONS

We conclude that LCT-GSR is a statistically sound analytical tool that can be used to extract core genes associated with a continuous phenotype. It can be applied to a wide range of studies in which dichotomizing the continuous phenotype is neither easy nor meaningful. Reduction to the most predictive genes is crucial in advancing our understanding of issues such as disease prevention, faster and more efficient diagnosis, intervention strategies and personalized medicine.

Longitudinal analysis reveals early-pregnancy associations between perfluoroalkyl sulfonates and thyroid hormone status in a Canadian prospective birth cohort

Serum perfluoroalkyl acids (PFAAs) have been linked to disruption of maternal thyroid hormone homeostasis, but results have varied between studies which we hypothesized was due to timing of the thyroid hormone measurements, variability in PFAA isomer patterns, or presence of other stressors. In a longitudinal study design, we investigated the time-dependency of associations between PFAA isomers and thyroid hormones during pregnancy and post-partum while considering thyroid peroxidase antibody (TPOAb) status and mercury (Hg) co-exposure. In participants of a prospective Canadian birth cohort (n = 494), free thyroxine (FT4), free triiodothyronine (FT3), thyroid stimulating hormone (TSH) and TPOAb were quantified in maternal plasma collected in each trimester and 3-months postpartum, and 25 PFAAs (15 linear and 10 branched) and Hg were quantified in samples collected during the second trimester. Perfluorohexane sulfonate (PFHxS) and total branched isomers of perfluorooctane sulfonate (PFOS) were positively associated with TSH in mixed-effect models, with strongest associations early in gestation. Throughout pregnancy and post-partum, PFHxS was inversely associated with FT4, consistent with elevated TSH, while Hg was inversely associated with FT3. In TPOAb-positive women, negative associations were found between PFUnA and FT4, and 1m-PFOS and TSH, supporting previous studies that thyroid disorder could increase susceptibility to PFAA-mediated hormone dysregulation. Hg did not confound associations but was a significant interaction term, revealing further positive associations between PFOS isomers (∑3m+4m-PFOS) and TSH. Higher perfluoroalkyl sulfonate exposures were associated with higher TSH and/or lower FT4, strongly suggestive that PFHxS and branched PFOS isomers are risk factors for subclinical maternal hypothyroidism. Isomer-specific analysis is important in future studies, as crude measures of 'total-PFOS' masked the associations of branched isomers. A concerning result was for PFHxS which had consistent negative associations with FT4 at all time points and a positive association with TSH in early pregnancy when fetal development is most sensitive to disruption.

LARGE CELL METASTATIC PANCREATIC NEUROENDOCRINE CARCINOMA TREATED WITH SOMATOSTATIN ANALOGUES - CASE REPORT AND LITERATURE REVIEW

We report the case of a 55-year-old-male with a large cell metastatic pancreatic neuroendocrine carcinoma treated for 14 months with lanreotide autogel having a stable disease (SD) and not responding to chemotherapy. The somatostatin analogues (SSA) were introduced after an episode of diarrhea and controlled the disease. Progression-free survival (PFS) as determined by Computerized Tomography (CT) scans was obtained for 14 months. After more than a year, the patient's health state deteriorated along with progressive disease. The capecitabine-temozolomide regimen was challenged, but after three cycles, a rapid clinical decline was noted.

Conclusion

This unexpected event (diarrhea) in the course of the disease could represent the beginning of carcinoid syndrome. While the lanreotide autogel helped the episode of diarrhea pass, it also helped gain control over the disease itself.

Exposure and dietary sources of bisphenol A (BPA) and BPA-alternatives among mothers in the APrON cohort study

Diet is regarded as the main source of bisphenol A (BPA) exposure, but comparatively little is known about dietary sources of BPA-alternatives. Here we measured exposure of BPA and BPA-alternatives among pregnant women in Canada, estimated their 24-h intakes and examined the importance of various dietary sources. Free and total BPA, bisphenol S (BPS) and bisphenol F (BPF) were measured in 467 second trimester maternal urine samples, and in 455 paired samples collected at three months postpartum. Linear regression was used to evaluate associations between urinary concentrations of bisphenols and 24-h dietary recall data. The geometric means of total BPA in second trimester and postpartum urine (1.2 and 0.95 ng/mL, respectively) were 5-7 times higher than corresponding total BPS (0.16 and 0.17 ng/mL). The detection frequency of BPF was only 9% (i.e. >1.0 ng/mL). However, at both time points 95th percentiles of total BPF (7.3 and 4.2 ng/mL, respectively) were similar to total BPA (8.2 and 5.0 ng/mL). Free BPS and BPF were detected in <2% of samples, but were detectable when total BPS or BPF concentrations were highest, always at <1% of the total concentration. The tolerable daily intake for total BPA (i.e. 18 nmol/kg BW/d) was not exceeded, but for BPS the estimated 24-h intake was as high as 14 nmol/kg BW/d (95th percentile: 0.12 nmol/kg BW/d), and for BPF was even higher among the highest centile of exposure (maximum and 95th percentile: 30, 0.81 nmol/kg BW/d). Canned food consumption was associated with higher total BPA, but was not associated with BPS. For BPF, mustard consumption may be an important exposure source, particularly among the highest exposed. Relatively high exposure to BPS and BPF in a minority of pregnant women highlights the need to better understand the associated health risks and exposure sources of BPA-alternatives.

KINDERGARTEN-AGE QUALITY OF LIFE OUTCOMES AFTER LIVER TRANSPLANTATION AT <6 YEARS

BACKGROUND

Given the improved mortality after paediatric liver transplantation, health related quality of life (HRQL) is an important outcome measure and provides valuable information for families.

OBJECTIVES

To determine the HRQL of kindergarten-age children who have undergone liver transplantation at age <6 years old.

DESIGN/METHODS

Between 1999–2014, all paediatric liver transplant recipients at our center were enrolled in this ethics board approved, longitudinal inception-cohort study. Following informed consent, HRQL was measured using the parent completed Pediatric Quality of Life Inventory, version 4.0 (PedsQL). The association between pre-transplant, transplant, and post-transplant variables and HRQL was examined using multiple regression analyses. Scores were compared to normative scores for HRQL in 8700 children [total PedsQL 82.2 (15.5), psychosocial summary 81.2 (15.3), and physical summary 84.0 (19.7)] and to scores for 130 children with surgical congenital heart disease from early infancy [81.1 (13.9), 77.5 (16.4), and 86.4 (15.3) respectively].

RESULTS

78 liver transplants for children <6 years of age were performed; 69 patients (88.5%) survived, and all (100%) were assessed at 55.4 (7.2) months of age: 38 with biliary atresia, 11 with acute liver failure, 11 with cholestasis, and 9 with metabolic disease. The mean total PedsQL was 75.6 (SD=15.6), psychosocial summary 72 (15.9) [a composite of emotional functioning 73.8 (16.4), social functioning 74.6 (19.2), and school functioning 70.6 (19.1)], and physical summary 78.2 (20.9). These composite scores were all statistically significantly different from population norms (p<0.001, <0.001, 0.026 respectively) and surgical congenital heart disease patients (p=0.015, 0.029, 0.005). The proportion having a score >1 (expected 15.9%) and >2 (expected 2.27%) SD below population norms were: total PedsQL 20.6% and 11.8%, psychosocial summary 32.3% and 11.3%, and physical summary 19.1% and 7.4%. Having a wait-list status 1 on the Canadian System of Classification was associated with higher total PedsQL (Effect size 9, 95%CI 2, 16; p=0.018) and physical summary (Effect size 15, 95%CI 16, 79; p=.004). None of the perioperative variables were predictive for psychosocial summary. Variables not associated with PedsQL included metabolic disease, PELD score, growth failure, any post-operative severe complication, age at transplant, weight at transplant, socioeconomic status, and year of transplant.

CONCLUSION

HRQL after liver transplantation is lower than population norms and congenital heart disease patients. More research is needed to determine why HRQL is low in order to improve the lives of these children.

KINDERGARTEN-AGE NEUROCOGNITIVE AND FUNCTIONAL OUTCOMES AFTER LIVER TRANSPLANTATION DONE AT AGE <6 YEARS

BACKGROUND

Mortality after liver transplant has improved, making long-term outcomes increasingly important.

OBJECTIVES

To describe neurocognitive and functional outcomes after liver transplant done in young children, and determine potentially modifiable risk factors for adverse outcomes.

DESIGN/METHODS

Between 1999–2014, all <6 years old liver transplant recipients at our center were enrolled in this ethics board approved, longitudinal inception-cohort. Demographic, pre-transplant, transplant, and post-transplant data were prospectively collected. Following informed consent, outcomes were determined by experienced paediatric psychologists using Wechsler Preschool and Primary Scale of Intelligence III, Beery-Buktenica Developmental Test of Visual-Motor Integration-V (VMI), and Adaptive Behavior Assessment System-II. Associations with outcomes (Full-Scale intelligence quotient [FSIQ], Performance IQ [PIQ], Verbal IQ [VIQ], VMI and General Adaptive Composite [GAC]) were determined using multiple linear regression. Population norms for each score are mean 100 (SD15).

RESULTS

78 liver transplants were performed; 69 patients survived, and all completed follow-up. Outcomes for the 60 patients without metabolic disease are reported. FSIQ, PIQ, and VIQ were 94.5 (17.0), 95.4 (17.8), and 93.7 (17.6). VMI and GAC were 91.6 (16.2) and 89.7 (18.0). Outcomes were shifted to the left of population norms, with the proportion having IQ scores >1 SD (score <85, expected 15.9%) and >2 SD (score <70, expected 2.27%) below population norms being: 23.3% and 8.3%, 25% and 8.3%, and 21.7% and 11.7% respectively. For VMI and GAC these proportions were 25% and 8.3%, and 35% and 13.3%. There were few predictors of outcomes: for FSIQ, grade-IV encephalopathy [effect size -15, 95%CI -29,-1; p=0.03]; PIQ, grade-IV encephalopathy [effect size -16, 95%CI -31, -1; p=0.04], VIQ, grade-IV encephalopathy [effect size -17, 95%CI -31, -4; p=0.01], living-related donor [effect size 10, 95%CI 2, 18; p=0.02], and rejection in first 30d [effect size 9, 95%CI 0.5, 17; p=0.04]; and VMI, grade-IV encephalopathy [effect size -20, 95%CI -33, -7; p=0.002], and PELD at activation [effect size 0.5, 95%CI 0.2, 0.9; p=0.006]. Variables not associated with neurocognitive outcomes included: age at transplant, year of transplant, having any severe complication post-operatively, growth failure, and socioeconomic status.

CONCLUSION

Neurocognitive and functional outcomes after liver transplant at age <6 years are shifted to the left of population norms. Severe encephalopathy at transplant predicted a poorer outcome. More research is needed to determine risk factors for the over 3X higher prevalence of scores <70 compared to population norms.

Gene-Set Reduction for Analysis of Major and Minor Gleason Scores Based on Differential Gene-Set Expressions and Biological Pathways in Prostate Cancer

The Gleason score (GS) plays an important role in prostate cancer detection and treatment. It is calculated based on a sum between its major and minor components, each ranging from 1 to 5, assigned after examination of sample cells taken from each side of the prostate gland during biopsy. A total GS of at least 7 is associated with more aggressive prostate cancer. However, it is still unclear how prostate cancer outcomes differ for various distributions of GS between its major and minor components. This article applies Significance Analysis of Microarray for Gene-Set Reduction to a real microarray study of patients with prostate cancer and identifies 13 core genes differentially expressed between patients with a major GS of 3 and a minor GS of 4, or (3,4), vs patients with a combination of (4,3), starting from a less aggressive GS combination of (3,3), and moving toward a more aggressive one of (4,4) via gray areas of (3,4) and (4,3). The resulting core genes may improve understanding of prostate cancer in patients with a total GS of 7, the most common grade and most challenging with respect to prognosis.

Bisphenol A Metabolites and Bisphenol S in Paired Maternal and Cord Serum

Human studies show associations between maternal bisphenol A (BPA) exposure and developmental effects in children, yet biomonitoring of BPA metabolites in maternal and fetal serum remains limited, and less is known for BPA alternatives. BPA-glucuronide, BPA-sulfate, and bisphenol S (BPS) were quantified in 61 pairs of maternal and cord sera from Chinese participants. Total BPS was only detectable in four maternal (<0.03-0.07 ng/mL) and seven cord sera (<0.03-0.12 ng/mL), indicating low exposure but providing the first evidence that BPS crosses the human placenta. Total BPA metabolites in cord serum were significantly higher than in maternal serum (p < 0.05), suggesting that these may be formed in the fetus or cleared more slowly from the fetoplacental compartment. Unlike the pharmacokinetic results from controlled oral exposure studies in which BPA-glucuronide is the major BPA metabolite, here, BPA-sulfate was the dominant metabolite (GM: 0.06 and 0.08 ng/mL), significantly higher than BPA-glucuronide (GM: 0.02 and 0.04 ng/mL) (p < 0.01) in both maternal and cord sera. Moreover, the proportion of BPA-sulfate increased with total BPA. These are the first human data for BPA metabolites in paired maternal and cord serum, and results suggest that the human fetus and pregnant mother have unique exposure to BPA metabolites. Direct analysis of BPA metabolites in serum provides complementary information for evaluating early life-stage exposure and risks of BPA.

Cesarean Section, Formula Feeding, and Infant Antibiotic Exposure: Separate and Combined Impacts on Gut Microbial Changes in Later Infancy

Established during infancy, our complex gut microbial community is shaped by medical interventions and societal preferences, such as cesarean section, formula feeding, and antibiotic use. We undertook this study to apply the significance analysis of microarrays (SAM) method to quantify changes in gut microbial composition during later infancy following the most common birth and postnatal exposures affecting infant gut microbial composition. Gut microbiota of 166 full-term infants in the Canadian Healthy Infant Longitudinal Development birth cohort were profiled using 16S high-throughput gene sequencing. Infants were placed into groups according to mutually exclusive combinations of birth mode (vaginal/cesarean birth), breastfeeding status (yes/no), and antibiotic use (yes/no) by 3 months of age. Based on repeated permutations of data and adjustment for the false discovery rate, the SAM statistic identified statistically significant changes in gut microbial abundance between 3 months and 1 year of age within each infant group. We observed well-known patterns of microbial phyla succession in later infancy (declining Proteobacteria; increasing Firmicutes and Bacteroidetes) following vaginal birth, breastfeeding, and no antibiotic exposure. Genus Lactobacillus, Roseburia, and Faecalibacterium species appeared in the top 10 increases to microbial abundance in these infants. Deviations from this pattern were evident among infants with other perinatal co-exposures; notably, the largest number of microbial species with unchanged abundance was seen in gut microbiota following early cessation of breastfeeding in infants. With and without antibiotic exposure, the absence of a breast milk diet by 3 months of age following vaginal birth yielded a higher proportion of unchanged abundance of Bacteroidaceae and Enterobacteriaceae in later infancy, and a higher ratio of unchanged Enterobacteriaceae to Alcaligenaceae microbiota. Gut microbiota of infants born vaginally and exclusively formula fed became less enriched with family Veillonellaceae and Clostridiaceae, showed unchanging levels of Ruminococcaceae, and exhibited a greater decline in the Rikenellaceae/Bacteroidaceae ratio compared to their breastfed, vaginally delivered counterparts. These changes were also evident in cesarean-delivered infants to a lesser extent. The clinical relevance of these trajectories of microbial change is that they culminate in taxon-specific abundances in the gut microbiota of later infancy, which we and others have observed to be associated with food sensitization.

Can Public Health Risk Assessment Using Risk Matrices Be Misleading?

The risk assessment matrix is a widely accepted, semi-quantitative tool for assessing risks, and setting priorities in risk management. Although the method can be useful to promote discussion to distinguish high risks from low risks, a published critique described a problem when the frequency and severity of risks are negatively correlated. A theoretical analysis showed that risk predictions could be misleading. We evaluated a practical public health example because it provided experiential risk data that allowed us to assess the practical implications of the published concern that risk matrices would make predictions that are worse than random. We explored this predicted problem by constructing a risk assessment matrix using a public health risk scenario-Tainted blood transfusion infection risk-That provides negative correlation between harm frequency and severity. We estimated the risk from the experiential data and compared these estimates with those provided by the risk assessment matrix. Although we validated the theoretical concern, for these authentic experiential data, the practical scope of the problem was limited. The risk matrix has been widely used in risk assessment. This method should not be abandoned wholesale, but users must address the source of the problem, apply the risk matrix with a full understanding of this problem and use matrix predictions to inform, but not drive decision-making.

Sepsis After Cardiac Surgery Early in Infancy and Adverse 4.5-Year Neurocognitive Outcomes

Background

We aimed to determine whether sepsis is associated with neurocognitive outcomes 4.5 years after congenital heart disease surgery in early infancy.

Methods and Results

A secondary analysis from a prospective inception cohort included all children having congenital heart disease surgery done at ≤6 weeks of age with cardiopulmonary bypass at the Western Canadian referral center from 1996 to 2009. Follow-up at the referral center determined the primary outcomes at 4.5 years with full-scale, performance, and verbal intelligence quotients on the Wechsler Preschool and Primary Scale of Intelligence. Perioperative variables were collected prospectively, and confirmation of blood culture–positive sepsis was done retrospectively. Multiple linear regression models for neurocognitive outcomes and multiple Cox proportional hazards regression for mortality were determined. Sepsis occurred in 97 of 502 patients (19%) overall and in 76 of 396 survivors (19%) with 4.5-year follow-up. By 4.5 years, there were 91 (18%) deaths, and 396 of 411 survivors (96%) had follow-up completed. Extracorporeal membrane oxygenation was associated with worse scores on all neurocognitive outcomes on multivariable regression; the association between extracorporeal membrane oxygenation and full-scale intelligence quotient had a regression coefficient of −13.6 (95% CI −21.3 to −5.9; P =0.001). Sepsis perioperatively was associated with performance and verbal intelligence quotients, with a trend for full-scale intelligence quotient (P =0.058) on multivariable regression. The regression coefficient for sepsis was strongest for performance intelligence quotient (−5.31; 95% CI −9.84 to −0.78; P =0.022). Sepsis was not but extracorporeal membrane oxygenation was associated with mortality by 4.5 years.

Conclusions

Perioperative sepsis and extracorporeal membrane oxygenation were associated with adverse neurocognitive outcomes on multivariable regression. Quality improvement to prevent sepsis has the potential to improve long-term neurocognitive outcomes in infants after surgery for congenital heart disease.

Biomaterials for orbital fractures repair

The unique and complex anatomy of the orbit requires significant contouring of the implants to restore the proper anatomy. Fractures of the orbital region have an incidence of 10-25% from the total facial fractures and the most common age group was the third decade of life. The majority of cases required reconstruction of the orbital floor to support the globe position and restore the shape of the orbit. The reason for this was that the bony walls were comminuted and/ or bone fragments were missing. Therefore, the reconstruction of the missing bone was important rather than reducing the bone fragments. This could be accomplished by using various materials. There is hardly any anatomic region in the human body that is so controversial in terms of appropriate material used for fracture repair: non resorbable versus resorbable, autogenous/ allogeneic/ xenogenous versus alloplastic material, non-prebent versus preformed (anatomical) plates, standard versus custom-made plates, nonporous versus porous material, non-coated versus coated plates. Thus, the importance of the material used for reconstruction becomes more challenging for the ophthalmologist and the oral and maxillofacial surgeon.

Gene set enrichment analysis for multiple continuous phenotypes

Background

Gene set analysis (GSA) methods test the association of sets of genes with phenotypes in gene expression microarray studies. While GSA methods on a single binary or categorical phenotype abounds, little attention has been paid to the case of a continuous phenotype, and there is no method to accommodate correlated multiple continuous phenotypes.

Result

We propose here an extension of the linear combination test (LCT) to its new version for multiple continuous phenotypes, incorporating correlations among gene expressions of functionally related gene sets, as well as correlations among multiple phenotypes. Further, we extend our new method to its nonlinear version, referred as nonlinear combination test (NLCT), to test potential nonlinear association of gene sets with multiple phenotypes. Simulation study and a real microarray example demonstrate the practical aspects of the proposed methods.

Conclusion

The proposed approaches are effective in controlling type I errors and powerful in testing associations between gene-sets and multiple continuous phenotypes. They are both computationally effective. Naively (univariately) analyzing a group of multiple correlated phenotypes could be dangerous. R-codes to perform LCT and NLCT for multiple continuous phenotypes are available at http://www.ualberta.ca/~yyasui/homepage.html.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-260) contains supplementary material, which is available to authorized users.

Biomaterials for orbital fractures repair

The unique and complex anatomy of the orbit requires significant contouring of the implants to restore the proper anatomy. Fractures of the orbital region have an incidence of 10-25% from total facial fractures and the most common age group was the third decade of life. The majority of cases require reconstruction of the orbital floor to support the globe position and restore the shape of the orbit. The reason for this is that the bony walls are comminuted and/or bone fragments are missing. Therefore, the reconstruction of missing bone is important rather than reducing bone fragments. This can be accomplished using various materials. There is hardly any anatomic region in the human body that is so controversial in terms of appropriate material used for fracture repair: nonresorbable versus resorbable, autogenous/allogenous/xenogenous versus alloplastic material, non-prebent versus preformed (anatomical) plates, standard versus custom-made plates, nonporous versus porous material, non-coated versus coated plates. Thus, the importance of material used for reconstruction becomes more challenging for the ophthalmologist and the oral and maxillofacial surgeon.

Comparison between the efficacy and side effects of intravitreal versus anterior chamber Bevacizumab injection in neovascular glaucoma patients

Rationale. Neovascular glaucoma is the type of glaucoma most refractory to treatment. The most frequent causes are those associated with retinal hypoxia, which promotes the upregulation of the VEGF synthesis and produces fibrovascular membranes over the anterior chamber angle. Because the administration of anti VEGF products is still off label for neovascular glaucoma, there is not a single accepted way of treatment. There are differences between the site of administration (vitreal or anterior chamber or both at the same time), the dose or the setting of the procedure. Objective. The objective of our study was to asses the difference of efficacy and complications of bevacizumab injection for vitreal administration versus anterior chamber administration. Methods and results. Prospective study with 18 eyes from 18 patients with neovascular glaucoma associated with proliferative diabetic retinopathy or retinal vein occlusion. Group A (10 patients) received intravitreal injection with 0.05 ml Bevacizumab. Group B (8 patients) received anterior chamber injection with 0.03 ml Bevacizumab. There was a significant decrease of intraocular pressure (p<0.01 for group A, p<0.05 for group B) for both groups. Group A also had a statistically significant decrease of the macular edema (p<0.05). The side effects were reduced for both groups. Discussion. Our conclusion was that for the neovascular glaucoma, which associates significant macular edema, the intravitreal procedure should be performed, while for neovascular glaucoma patients without retinal edema, the anterior chamber procedure should be preferred because of reduced potential side effects.

Early childhood outcomes of infants born with gastroschisis

PURPOSE

To describe neonatal and childhood outcomes of a contemporary cohort of infants with gastroschisis.

METHODS

Observational, single center, inception cohort of children born with gastroschisis from January 2005 to December 2008.

RESULTS

Of 63 infants, 61 survived to hospital discharge and 39 were seen for follow-up. Complications included sepsis (37%), necrotizing enterocolitis (10%), parenteral nutrition related cholestasis (25%), and short bowel syndrome (13%). Of survivors, 5% had visual impairment and 10% had hearing loss. No child tested had mental delay or cerebral palsy. Early gestational age predicted death or disability (OR 0.60, 95% CI 0.38, 0.96; p=0.033). There was a high incidence of prescription medications for presumed gastroesophageal reflux (90%). Some infants continued to require tube feeds (15%). There were improvements in longitudinal growth reflected in increasing z-scores.

CONCLUSIONS

Although children with gastroschisis are at risk for disability, childhood outcomes are encouraging.

Linear combination test for gene set analysis of a continuous phenotype

BACKGROUND

Gene set analysis (GSA) methods test the association of sets of genes with a phenotype in gene expression microarray studies. Many GSA methods have been proposed, especially methods for use with a binary phenotype. Equally, if not more importantly however, is the ability to test the enrichment of a gene signature or pathway against the continuous phenotypes which are routinely and commonly observed in, for example, clinicopathological measurements. It is not always easy or meaningful to dichotomize continuous phenotypes into two classes, and attempting to do this may lead to the inaccurate classification of samples, which would affect the downstream enrichment analysis. In the present study, we have build on recent efforts to incorporate correlation structure within gene sets and pathways into the GSA test statistic. To address the issue of continuous phenotypes directly without the need for artificial discrete classification and thus increase the power of the test while ensuring computational efficiency and rigor, new GSA methods that can incorporate a covariance matrix estimator for a continuous phenotype may present an effective approach.

RESULTS

We have designed a new method by extending the GSA approach called Linear Combination Test (LCT) from a binary to a continuous phenotype. Simulation studies and a real microarray dataset were used to compare the proposed LCT for a continuous phenotype, a modification of LCT (referred to as LCT2), and two publicly available GSA methods for continuous phenotypes.

CONCLUSIONS

We found that the LCT methods performed better than the other two GSA methods; however, this finding should be understood in the context of our specific simulation studies and the real microarray dataset that were used to compare the methods. Free R-codes to perform LCT for binary and continuous phenotypes are available at http://www.ualberta.ca/~yyasui/homepage.html. The R-code to perform LCT for a continuous phenotype is available as Additional file 1.

Surgical treatment of advanced ovarian cancer

BACKGROUND

The classical treatment for advanced ovarian cancer (OC) consists of a optimal cytoreductive surgery (when the postoperative residual tumor is under 1 cm.), followed by adjuvant chemotherapy based on platinum or paclitaxel derivatives. The 5-year survival rate in case of advanced OC with secondary peritoneal carcinomatosis (PC) is below 25%. The treatment of PC (interpreted as a local-regional disease and not as a systemic disease) is based on an aggressive surgical act (a full or maximal cytoreduction without residual tumor), followed by local chemotherapy or hypertermic intraperitoneal chemotherapy. This is a retrospective study which reassesses the surgical treatment of advanced OC within the period January 2004 - December 2010 in the Center of General Surgery and Liver Transplantation within Fundeni Institute.

METHODS

In the period January 2004 - December 2010 in the Center of General Surgery and Liver Transplantation within Fundeni Institute were operated 405 patients with advanced ovarian cancer. In 105 patients (25.9%) intraperitoneal chemotherapy with Cisplatin was performed.

RESULTS

Overal survival was calculated for a subsample of 297 patients, for whom it was possible to properly ensure the follow-up, being of 43 months in the patients with intraperitoneal chemotherapy (p = 0.02) and 37 months in the patients without intraperitoneal chemotherapy.

CONCLUSIONS

The maximal cytoreduction associating IPCH is an aggressive multidisciplinary therapeutic approach in advanced OC, reserved for difficult cases, considered in the past without solution. In properly selected cases, this shows a clear increase in survival rate.

Teaching child development to medical students

PURPOSE

Several published strategies on teaching the screening of normal child development were integrated into a small group learning experience for second-year medical students to address practical and logistical problems of approaches used individually. This study examines the effectiveness of this integrated approach using student evaluations.

METHOD

A total of 191 second-year university medical and dental students were invited to participate. Well-described learning objectives, the Ages and Stages Questionnaire (ASQ), live parent-child dyads and video backup were used. Students rotated through three small group stations. Feedback was provided using a Likert scale (from 1, low, to 5, high) and written comments. Consent was obtained. Live parent-child dyads versus video clip groups were analysed by averaging overall scores. Generalised estimating equation (GEE) analysis in stata (Stata Corporation, College Station, Texas) was used for comparing the two groups.

RESULTS

A total of 178 students (93%) agreed to participate and filled out the evaluation forms. The overall score on the Likert scale was 4.6 (range 4-5). On two occasions video clips were substituted for live parent-child dyad presentations in one of the three stations. These students (n=43, rating 4.61/5) rated their experience as comparable with those who had three live family stations (n=135, rating 4.56/5). Student comments were grouped into broad themes, with most being positive about their learning experience.

CONCLUSIONS

This integrated approach is highly acceptable. Video clip usage, live dyads, clear written objectives and use of a standardised screening tool preserved the interaction and immediacy of a clinical encounter, while maintaining consistency in content.

Interrater reliability and convergent validity of the American Academy for Cerebral Palsy and Developmental Medicine methodology for conducting systematic reviews

AIM

The aim of this study was to evaluate the interrater reliability and convergent validity of the American Academy for Cerebral Palsy and Developmental Medicine's (AACPDM) methodology for conducting systematic reviews (group design studies).

METHOD

Four clinicians independently rated 24 articles for the level of evidence and conduct using AACPDM methodology. Study conduct was also assessed using the Effective Public Health Practice Project scale. Raters were randomly assigned to one of two pairs to resolve discrepancies. The level of agreement between individual raters and pairs was calculated using kappa (α=0.05) and intraclass correlations (ICCs; α=0.05). Spearman's rank correlation coefficient was calculated to evaluate the relationship between raters' categorization of quality categories using the two tools.

RESULTS

There was acceptable agreement between raters (κ=0.77; p<0.001; ICC=0.90) and between assigned pairs (κ=0.83; p<0.001; ICC=0.96) for the level of evidence ratings. There was acceptable agreement between pairs for four of the seven conduct questions (κ=0.53-0.87). ICCs (all raters) for conduct category ratings (weak, moderate, and strong) also indicated good agreement (ICC=0.76). Spearman's rho indicated a significant positive correlation for the overall quality category comparisons of the two tools (0.52; p<0.001).

CONCLUSIONS

The AACPDM rating system has acceptable interrater reliability. Evaluation of its study quality ratings demonstrated reasonable agreement when compared with a similar tool.

Regular Multivitamin Supplement Use, Single Nucleotide Polymorphisms in ATIC, SHMT2, and SLC46A1, and Risk of Ovarian Carcinoma

ATIC, SHMT2, and SLC46A1 have essential roles in one-carbon (1-C) transfer. The authors examined whether associations between ovarian carcinoma and 15 variants in these genes are modified by regular multivitamin use, a source of 1-C donors, among Caucasian participants from two US case–control studies. Using a phased study design, variant-by-multivitamin interactions were tested, and associations between variants and ovarian carcinoma were reported stratified by multivitamin supplement use. Per-allele risk associations were modified by multivitamin use at six variants among 655 cases and 920 controls (Phase 1). In a larger sample of 968 cases and 1,265 controls (Phases 1 and 2), interactions were significant (P ≤ 0.03) for two variants, particularly among regular multivitamin users: ATIC rs7586969 [odds ratio (OR) = 0.7, 95% confidence interval (CI) = 0.6–0.9] and ATIC rs16853834 (OR = 1.5, 95% CI = 1.1–2.0). The two ATIC single nucleotide polymorphisms (SNPs) did not share the same haplotype; however, the haplotypes they comprised mirrored their SNP risk associations among regular multivitamin supplement users. A multi-variant analysis was also performed by comparing the observed likelihood ratio test statistic from adjusted models with and without the two ATIC variant-by-multivitamin interaction terms with a null distribution of test statistics generated by permuting case status 10,000 times. The corresponding observed P value of 0.001 was more extreme than the permutation-derived P value of 0.009, suggesting rejection of the null hypothesis of no association. In summary, there is little statistical evidence that the 15 variants are independently associated with risk of ovarian carcinoma. However, the statistical interaction of ATIC variants with regular multivitamin intake, when evaluated at both the SNP and gene level, may support these findings as relevant to ovarian health and disease processes.

Abstract A38: Thrombospondin 2 CpG methylation is a marker of clear cell ovarian carcinomas: Evaluation of a DNA methylation assay in archival tissue

Introduction: Epigenomic markers can be used to identify subsets of patients or tumors in order to determine differences in risk of disease, to account for unexplained molecular heterogeneity, to improve our ability to subtype cancers and to refine our classification of cancers at a given organ site. Carcinomas classified as ovarian are the fourth most common among female cancers, and one of the most heterogeneous of all human malignancies. Few epigenomic platforms exist that accommodate archival formalin-fixed paraffin-embedded (FFPE) tumor tissue which, when incorporated into epidemiologic studies, offers the ability to investigate somatic alterations with both etiology and prognosis.

Methods: We tested different volumes (250ng and 400ng) of bisulfite-converted (bs) DNA from each of six FFPE primary ovarian carcinomas of serous, endometrioid and clear cell histologies and two constitutional genomes from Caucasians (CEPH) from the HapMap Project using the GoldenGate™ Cancer Panel I methylation assay protocol. The methylation status at each 1,505 CpG site was determined by calculating β, which is the ratio of the fluorescent signal from the methylated allele to the sum of the fluorescent signals of both methylated and unmethylated alleles (0=completely unmethylated, 1=completely methylated). To evaluate reproducibility of the assay, Spearman correlation coefficients were used to compare β-values at 250ng vs 400ng input bsDNA for (i) each sample separately and (ii) group data. We also compared reproducibility between replicate samples of the CEPH controls at 250ng. To evaluate validity, we examined gender-specific CpG sites among CEPH male and female controls at 250ng input bsDNA in housekeeping genes from the X chromosome represented on the assay. Methylation of these genes is expected to show gene dosage between males and females owing to gene silencing on one of the two X chromosomes in female somatic cells that compensates for the single X chromosome among males. Using the 400ng input bsDNA, we used Significance Analysis of Microarrays (SAM) to find overall differences in methylation across the three carcinoma types. Results: Spearman r2 comparing 400ng vs 250ng bsDNA ranged from 0.41 − 0.90 for subject data and r2=0.90 for group data, indicating that the findings with a lower volume of DNA did not always correlate well with the higher volume of DNA. Average methylation across 1,505 CpG loci among the six samples was higher at 250ng (average β-value=0.45, SD=0.29) than at 400ng (average β-value=0.36, SD=0.32), suggesting insufficient bsDNA leads to over-estimation of methylation. Reproducibility between duplicate HapMap samples at 250ng ranged from r2=0.76 for the CEPH male to r2=0.92 for the CEPH female. Further, methylation at X-chromosome loci was close to zero for one replicate sample of the CEPH male, as expected, but higher for the other CEPH male replicate. β-values were closer to one than to hemimethylation for the female replicate samples. SAM identified two genes, ERG and THBS2, that were differentially methylated across all three carcinoma types at FDR&lt;0.1%: both genes showed higher methylation at CpG sites among clear cell carcinomas. Conclusions: The manufacturer-recommended lower volume of 250ng bsDNA can bias methylation results even with non-FFPE sources of DNA. Using 400ng bsDNA, we identified histologic-specific methylation markers, including the confirmation from a previous report of higher methylation of thrombospondin 2 in ovarian clear cell carcinomas.

Citation Information: Cancer Prev Res 2011;4(10 Suppl):A38.

The effects of modified spaced-retrieval training on learning and retention of face-name associations by individuals with dementia

The purpose of this project was to assess the effects of spaced-retrieval training (SRT) on learning of new and previously known associations by individuals with dementia in two treatment conditions: one in which the recall intervals were filled with activities unrelated to the information being learned (unrelated condition) and one in which the intervals were filled with related activities (related condition). Thirty-two individuals with mild to moderate dementia (30 with a diagnosis of Alzheimer's disease; two with vascular dementia) participated in the study. On average, participants learned the associations in fewer than four sessions and retained the information for variable amounts of time, up to 6 weeks. Previously known associations were learned significantly faster than new associations. The modified SRT format, in which the within-session recall intervals were filled with information related to the target association, did not result in faster learning or longer retention of learned associations. Participants learned previously known associations in the standard SRT format (with unrelated information in the recall intervals) significantly faster than new associations taught in the modified SRT condition. Cognitive impairment, as measured by the Mini-Mental State Examination, was significantly correlated with time to learn new associations, but did not explain a large proportion of the variance in new learning. Theoretical and clinical implications are discussed.

A prospective outcome study on the effects of facet joint radiofrequency denervation on pain, analgesic intake, disability, satisfaction, cost, and employment

OBJECTIVE

To assess the effect of radiofrequency denervation (RFD) on patients with chronic low back pain (LBP) of facet joint origin.

DESIGN

Prospective cohort study.

SETTING

Interventional pain management program.

PARTICIPANTS

Consecutive subjects (N=44; 101 facet joints) over 2 years with chronic refractory mechanical LBP of facet origin established by 2 local anesthetic blocks (medial branch +/- intra-articular) resulting in more than 50% pain relief.

INTERVENTION

RFD of the symptomatic lumbar facet joints.

MAIN OUTCOME MEASURES

Self-reported pain intensity, frequency, bothersomeness, analgesic intake, satisfaction, disability, back pain-related costs, and employment twice prior to and at 1, 3, 6, 9, and 12 months post-RFD.

RESULTS

Post-RFD, significant improvements in pain, analgesic requirement, satisfaction, disability, and direct costs occurred. They peaked at 3 to 6 months and gradually diminished thereafter. Satisfaction with medical care and living with current symptoms improved similarly. Overall, satisfaction with the RFD procedure was high, and no complications were reported.

CONCLUSIONS

RFD provides safe and significant short-term improvement in pain, analgesic requirements, function, satisfaction, and direct costs in patients with chronic LBP of facet origin.

Gene-set analysis and reduction

Gene-set analysis aims to identify differentially expressed gene sets (pathways) by a phenotype in DNA microarray studies. We review here important methodological aspects of gene-set analysis and illustrate them with varying performance of several methods proposed in the literature. We emphasize the importance of distinguishing between 'self-contained' versus 'competitive' methods, following Goeman and Bühlmann. We also discuss reducing a gene set to its subset, consisting of 'core members' that chiefly contribute to the statistical significance of the differential expression of the initial gene set by phenotype. Significance analysis of microarray for gene-set reduction (SAM-GSR) can be used for an analytical reduction of gene sets to their core subsets. We apply SAM-GSR on a microarray dataset for identifying biological gene sets (pathways) whose gene expressions are associated with p53 mutation in cancer cell lines. Codes to implement SAM-GSR in the statistical package R can be downloaded from http://www.ualberta.ca/~yyasui/homepage.html.

Pathway analysis of microarray data via regression

Pathway analysis of microarray data evaluates gene expression profiles of a priori defined biological pathways in association with a phenotype of interest. We propose a unified pathway-analysis method that can be used for diverse phenotypes including binary, multiclass, continuous, count, rate, and censored survival phenotypes. The proposed method also allows covariate adjustments and correlation in the phenotype variable that is encountered in longitudinal, cluster-sampled, and paired designs. These are accomplished by combining the regression-based test statistic for each individual gene in a pathway of interest into a pathway-level test statistic. Applications of the proposed method are illustrated with two real pathway-analysis examples: one evaluating relapse-associated gene expression involving a matched-pair binary phenotype in children with acute lymphoblastic leukemia; and the other investigating gene expression in breast cancer tissues in relation to patients' survival (a censored survival phenotype). Implementations for various phenotypes are available in R. Additionally, an Excel Add-in for a user-friendly interface is currently being developed.