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author:("walleye, T")
1.  Macrophage gene expression in adipose tissue is associated with insulin sensitivity and serum lipid levels independent of obesity 
Obesity (Silver Spring, Md.)  2013;21(12):10.1002/oby.20443.
Objective
Obesity is linked to both increased metabolic disturbances and increased adipose tissue macrophage infiltration. However, whether macrophage infiltration directly influences human metabolism is unclear. The aim of this study was to investigate if there are obesity-independent links between adipose tissue macrophages and metabolic disturbances.
Design and Methods
Expression of macrophage markers in adipose tissue was analyzed by DNA microarrays in the SOS Sib Pair study and in patients with type 2 diabetes and a BMI-matched healthy control group.
Results
The expression of macrophage markers in adipose tissue was increased in obesity and associated with several metabolic and anthropometric measurements. After adjustment for BMI, the expression remained associated with insulin sensitivity, serum levels of insulin, C-peptide, high density lipoprotein cholesterol (HDL-cholesterol) and triglycerides. In addition, the expression of most macrophage markers was significantly increased in patients with type 2 diabetes compared to the control group.
Conclusion
Our study shows that infiltration of macrophages in human adipose tissue, estimated by the expression of macrophage markers, is increased in subjects with obesity and diabetes and associated with insulin sensitivity and serum lipid levels independent of BMI. This indicates that adipose tissue macrophages may contribute to the development of insulin resistance and dyslipidemia.
doi:10.1002/oby.20443
PMCID: PMC3763968  PMID: 23512687
2.  Aberrant DNA methylation at genes associated with a stem cell-like phenotype in cholangiocarcinoma tumours 
Cancer prevention research (Philadelphia, Pa.)  2013;6(12):10.1158/1940-6207.CAPR-13-0104.
Genetic abnormalities of cholangiocarcinoma have been widely studied; however, epigenomic changes related to cholangiocarcinogenesis have been less well characterised. We have profiled the DNA methylomes of 28 primary cholangiocarcinoma and six matched adjacent normal tissues using Infinium’s HumanMethylation27 BeadChips with the aim of identifying gene sets aberrantly epigenetically regulated in this tumour type.
Using a linear model for microarray data we identified 1610 differentially methylated autosomal CpG sites with 809 CpG sites (representing 603 genes) being hypermethylated and 801 CpG sites (representing 712 genes) being hypomethylated in cholangiocarcinoma versus adjacent normal tissues (false discovery rate ≤ 0.05). Gene ontology and gene set enrichment analyses identified gene sets significantly associated with hypermethylation at linked CpG sites in cholangiocarcinoma including homeobox genes and target genes of PRC2, EED, SUZ12 and histone H3 trimethylation at lysine 27. We confirmed frequent hypermethylation at the homeobox genes HOXA9 and HOXD9 by bisulfite pyrosequencing in a larger cohort of cholangiocarcinoma (n = 102).
Our findings indicate a key role for hypermethylation of multiple CpG sites at genes associated with a stem cell-like phenotype as a common molecular aberration in cholangiocarcinoma. These data have implications for cholangiocarcinogenesis, as well as possible novel treatment options using histone methyltransferase inhibitors.
doi:10.1158/1940-6207.CAPR-13-0104
PMCID: PMC3855864  PMID: 24089088
DNA methylation; cholangiocarcinoma; cancer; stem cells; HOX
3.  Introduction 
doi:10.1098/rsta.2013.0220
PMCID: PMC3982657  PMID: 24711497
Bertram Hopkinson; Hopkinson bar; blast; impact; high strain rate
4.  The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth 
The Encyclopedia of Life (EOL, http://eol.org) aims to provide unprecedented global access to a broad range of information about life on Earth. It currently contains 3.5 million distinct pages for taxa and provides content for 1.3 million of those pages. The content is primarily contributed by EOL content partners (providers) that have a more limited geographic, taxonomic or topical scope. EOL aggregates these data and automatically integrates them based on associated scientific names and other classification information. EOL also provides interfaces for curation and direct content addition. All materials in EOL are either in the public domain or licensed under a Creative Commons license. In addition to the web interface, EOL is also accessible through an Application Programming Interface.
In this paper, we review recent developments added for Version 2 of the web site and subsequent releases through Version 2.2, which have made EOL more engaging, personal, accessible and internationalizable. We outline the core features and technical architecture of the system. We summarize milestones achieved so far by EOL to present results of the current system implementation and establish benchmarks upon which to judge future improvements.
We have shown that it is possible to successfully integrate large amounts of descriptive biodiversity data from diverse sources into a robust, standards-based, dynamic, and scalable infrastructure. Increasing global participation and the emergence of EOL-powered applications demonstrate that EOL is becoming a significant resource for anyone interested in biological diversity.
doi:10.3897/BDJ.2.e1079
PMCID: PMC4031434  PMID: 24891832
5.  Overdose rescues by trained and untrained participants and change in opioid use among substance-using participants in overdose education and naloxone distribution programs: a retrospective cohort study 
BMC Public Health  2014;14:297.
Background
One approach to preventing opioid overdose, a leading cause of premature, preventable mortality, is to provide overdose education and naloxone distribution (OEND). Two outstanding issues for OEND implementation include 1) the dissemination of OEND training from trained to untrained community members; and 2) the concern that OEND provides active substance users with a false sense of security resulting in increased opioid use.
Methods
To compare overdose rescue behaviors between trained and untrained rescuers among people reporting naloxone rescue kit use; and determine whether heroin use changed after OEND, we conducted a retrospective cohort study among substance users in the Massachusetts OEND program from 2006 to 2010. We used chi square and t-test statistics to compare the differences in overdose management characteristics among overdoses managed by trained versus untrained participants. We employed Wilcoxon signed rank test to compare median difference among two repeated measures of substance use among participants with drug use information collected more than once.
Results
Among 4,926 substance-using participants, 295 trained and 78 untrained participants reported one or more rescues, resulting in 599 rescue reports. We found no statistically significant differences in help-seeking (p = 0.41), rescue breathing (p = 0.54), staying with the victim (p = 0.84) or in the success of naloxone administration (p = 0.69) by trained versus untrained rescuers. We identified 325 OEND participants who had drug use information collected more than once. We found no significant overall change in the number of days using heroin in past 30 days (decreased 38%, increased 35%, did not change 27%, p = 0.52).
Conclusion
Among 4926 substance users who participated in OEND, 373(7.6%) reported administering naloxone during an overdose rescue. We found few differences in behavior between trained and untrained overdose rescuers. Prospective studies will be needed to determine the optimal level of training and whether naloxone rescue kits can meet an over-the-counter standard. With no clear evidence of increased heroin use, this concern should not impede expansion of OEND programs or policies that support them.
doi:10.1186/1471-2458-14-297
PMCID: PMC4004504  PMID: 24684801
Overdose; Opioids; Bystander naloxone; Rescue; People who use drugs
6.  China Tuberculosis Policy at Crucial Crossroads: Comparing the Practice of Different Hospital and Tuberculosis Control Collaboration Models Using Survey Data 
PLoS ONE  2014;9(3):e90596.
Background
Currently three hospital and tuberculosis (TB) collaboration models exist in China: the dispensary model where TB has to be diagnosed and treated in TB dispensaries, the specialist model where TB specialist hospital also treat TB patients, and the integrated model where TB diagnosis and treatment is integrated into a general hospital. The study compared effects of the three models through exploring patient experience in TB diagnosis and treatment.
Methods
We selected two sites in each model of TB service in four provinces of China. In each site, 50 patients were selected from TB patient registries for a structured questionnaire survey, with a total of 293 patients recruited. All participants were newly registered uncomplicated TB cases without any major complications or resistance to first-line anti-TB drugs, and having successfully completed treatment. Diagnostic and treatment procedures were reviewed from medical charts of the surveyed patients to compare with national guidelines.
Results
Specialist sites had the highest patient expenditure, hospitalization rates and mostly used second-line anti-TB drugs, while the integrated model reported the opposite. The median health expenditure was USD 1,499 for the specialist sites and USD 306 for the integrated sites, with 83% and 15% patients respectively having unnecessary hospitalization. 74% of the specialist sites and 19% of the integrated sites used second-line anti-TB drugs. Mixed results were identified in the two dispensary sites. One site had median health expenditure of USD 138 with 12% of patients hospitalized, while the other had USD 912 and 65% respectively.
Conclusion
The study observed prohibitive financial expenditure and a high level of deviation from national guidelines in all sites, which may be related to the profit-seeking behavior of public hospitals. The study supports the integrated model as the better policy option for future TB health reform in China.
doi:10.1371/journal.pone.0090596
PMCID: PMC3951218  PMID: 24621996
7.  Qualitative evaluation of care plans for Canadian breast and head-and-neck cancer survivors 
Current Oncology  2014;21(1):e18-e28.
Background
Survivorship care plans (scps) have been recommended as a way to ease the transition from active cancer treatment to follow-up care, to reduce uncertainty for survivors in the management of their ongoing health, and to improve continuity of care. The objective of the demonstration project reported here was to assess the value of scps for cancer survivors in western Canada.
Methods
The Alberta CancerBridges team developed, implemented, and evaluated scps for 36 breast and 21 head-and-neck cancer survivors. For the evaluation, we interviewed 12 of the survivors, 9 nurses who delivered the scps, and 3 family physicians who received the scps (n = 24 in total). We asked about satisfaction, usefulness, emotional impact, and communication value. We collected written feedback from the three groups about positive aspects of the scps and possible improvements (n = 85). We analyzed the combined data using qualitative thematic analysis.
Results
Survivors, nurses, and family physicians agreed that scps could ease the transition to survivorship partly by enhancing communication between survivors and care providers. Survivors appreciated the individualized attention and the comprehensiveness of the plans. They described positive emotional impacts, but wanted a way to ensure that their physicians received the scps. Nurses and physicians responded positively, but expressed concern about the time required to implement the plans. Suggestions for streamlining the process included providing survivors with scp templates in advance, auto-populating the templates for the nurses, and creating summary pages for physicians.
Conclusions
The results suggest ways in which scps could help to improve the transition to cancer survivorship and provide starting points for larger feasibility studies.
doi:10.3747/co.21.1698
PMCID: PMC3921045  PMID: 24523618
Care plans; survivorship; communication; breast cancer; head-and-neck cancer; qualitative analysis
8.  Definition of molecular determinants of prostate cancer cell bone extravasation 
Cancer research  2012;73(2):942-952.
Advanced prostate cancer (PCa) commonly metastasizes to bone, but transit of malignant cells across the bone marrow endothelium (BMEC) remains a poorly understood step in metastasis. PCa cells roll on E-selectin+ BMEC through E-selectin ligand-binding interactions under shear flow, and PCa cells exhibit firm adhesion to BMEC via β1, β4 and αVβ3 integrins in static assays. However, whether these discrete PCa cell-BMEC adhesive contacts culminate in cooperative, step-wise transendothelial migration into bone is not known. Herein, we describe how metastatic PCa cells breach BMEC monolayers in a step-wise fashion under physiologic hemodynamic flow. PCa cells tethered and rolled on BMEC and then firmly adhered to and traversed BMEC via sequential dependence on E-selectin ligands and β1 and αVβ3 integrins. Expression analysis in human metastatic PCa tissue revealed that β1 was markedly upregulated compared with expression of other β subunits. PCa cell breaching was regulated by Rac1 and Rap1 GTPases and, notably, did not require exogenous chemokines as β1, αVβ3, Rac1 and Rap1 were constitutively active. In homing studies, PCa cell trafficking to murine femurs was dependent on E-selectin ligand, β1 integrin and Rac1. Moreover, eliminating E-selectin ligand-synthesizing α1,3 fucosyltransferases (α1,3 FT) in transgenic adenoma of mouse prostate (TRAMP) mice dramatically reduced PCa incidence. These results unify the requirement for E-selectin ligands, α1,3 fucosyltransferases, β1 and αVβ3 integrins and Rac/Rap1 GTPases in mediating PCa cell homing and entry into bone and offer new insight on the role of α1,3 fucosylation in PCa development.
doi:10.1158/0008-5472.CAN-12-3264
PMCID: PMC3548951  PMID: 23149920
fucosyltransferases; integrins; prostate cancer; E-selectin; homing
9.  Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China 
Background
This paper reports findings from the prevalence survey conducted in Shandong China in 2010, a province with a population of 94 million. This study aimed to estimate TB prevalence of the province in 2010 in comparison with the 2000 survey; and to compare yields of TB cases from different case finding approaches.
Methods
A population based, cross-sectional survey was conducted using multi-stage random cluster sampling. 54,279 adults participated in the survey with a response rate of 96%. Doctors interviewed and classified participants as suspected TB cases if they presented with persistent cough, abnormal chest X-ray (CXRAY), or both. Three sputum specimens of all suspected cases were collected and sent for smear microscopy and culture.
Results
Adjusted prevalence rate of bacteriologically confirmed cases was 34 per 100,000 for adults in Shandong in 2010. Compared to the 2000 survey, TB prevalence has declined by 80%. 53% of bacteriologically confirmed cases did not present persistent cough. The yield of bacteriologically confirmed cases was 47% by symptom screening and 95% by CXRAY. Over 50% of TB cases were among over 65’s.
Conclusions
The prevalence rate of bacteriologically confirmed cases was significantly reduced compared with 2000. The survey raised challenges to identify TB cases without clear symptoms.
doi:10.1186/1471-2334-14-21
PMCID: PMC3890533  PMID: 24410932
Tuberculosis; Population based prevalence survey; Case finding; China
10.  Nondisclosure of HIV Infection to Sex Partners and Alcohol’s Role: A Russian Experience 
AIDS and behavior  2013;17(1):390-398.
Nondisclosure of one’s HIV infection to sexual partners obviates safer sex negotiations and thus jeopardizes HIV transmission prevention. The role of alcohol use in the disclosure decision process is largely unexplored. This study assessed the association between alcohol use and recent nondisclosure of HIV serostatus to sex partners by HIV-infected risky drinkers in St. Petersburg, Russia. Approximately half (317/605; 52.4 %) reported not having disclosed their HIV serostatus to all partners since awareness of infection. Using three separate GEE logistic regression models, we found no significant association between alcohol dependence, risky alcohol use (past 30 days), or alcohol use at time of sex (past 30 days) with recent (past 3 months) nondisclosure (AOR [95 %CI] 0.81 [0.55, 1.20], 1.31 [0.79, 2.17], 0.75 [0.54, 1.05], respectively). Alcohol use at time of sex was associated with decreased odds of recent nondisclosure among seroconcordant partners and among casual partners. Factors associated with nondisclosure were relationship with a casual partner, a serodiscordant partner, multiple sex partners, awareness of HIV diagnosis less than 1 year, and a lifetime history of sexually transmitted disease. Nondisclosure of HIV status to sex partners is common among HIV-infected Russians, however alcohol does not appear to be a predictor of recent disclosure.
doi:10.1007/s10461-012-0216-z
PMCID: PMC3634358  PMID: 22677972
Nondisclosure; Disclosure; HIV; Russia; Alcohol
11.  Cytokines and Signaling Molecules Predict Clinical Outcomes in Sepsis 
PLoS ONE  2013;8(11):e79207.
Introduction
Inflammatory response during sepsis is incompletely understood due to small sample sizes and variable timing of measurements following the onset of symptoms. The vasopressin in septic shock trial (VASST) compared the addition of vasopressin to norepinephrine alone in patients with septic shock. During this study plasma was collected and 39 cytokines measured in a 363 patients at both baseline (before treatment) and 24 hours. Clinical features relating to both underlying health and the acute organ dysfunction induced by the severe infection were collected during the first 28 days of admission.
Hypothesis
Cluster analysis of cytokines identifies subgroups of patients at differing risk of death and organ failure.
Methods
Circulating cytokines and other signaling molecules were measured using a Luminex multi-bead analyte detection system. Hierarchical clustering was performed on plasma values to create patient subgroups. Enrichment analysis identified clinical outcomes significantly different according to these chemically defined patient subgroups. Logistic regression was performed to assess the importance of cytokines for predicting patient subgroups.
Results
Plasma levels at baseline produced three subgroups of patients, while 24 hour levels produced two subgroups. Using baseline cytokine data, one subgroup of 47 patients showed a high level of enrichment for severe septic shock, coagulopathy, renal failure, and risk of death. Using data at 24 hours, a larger subgroup of 81 patients that largely encompassed the 47 baseline subgroup patients had a similar enrichment profile. Measurement of two cytokines, IL2 and CSF2 and their product were sufficient to classify patients into these subgroups that defined clinical risks.
Conclusions
A distinct pattern of cytokine levels measured early in the course of sepsis predicts disease outcome. Subpopulations of patients have differing clinical outcomes that can be predicted accurately from small numbers of cytokines. Design of clinical trials and interventions may benefit from consideration of cytokine levels.
doi:10.1371/journal.pone.0079207
PMCID: PMC3828333  PMID: 24244449
13.  Cardiovascular disease risk reduction in rural China: a clustered randomized controlled trial in Zhejiang 
Trials  2013;14:354.
Background
Cardiovascular disease (CVD) is a major cause of death in China. Despite government efforts, the majority of hypertensive and diabetic patients in China do not receive proper treatment. Reducing CVD events requires long-term care that is proactive, patient-centred, community-based, and sustainable. We have designed a package of interventions for patients at high risk of CVD to be implemented by family doctors based in township hospitals (providers of primary care) in rural Zhejiang, China. This trial aims to determine whether the systematic CVD risk reduction package results in reduced CVD events among patients at risk of CVD compared with usual care, and whether the package is cost-effective and suitable for routine implementation and scale-up.
Methods/Design
This is a prospective, open-label, cluster randomized controlled trial (RCT) with blinded data analysis. The trial will randomize 67 township hospitals with 31,708 participants in three counties in Zhejiang Province. Participants will be identified from existing health records and will comprise adults aged 50 to 74 years, with a calculated 10-year CVD risk of 20% or higher, or diabetes. In the intervention arm, participants will receive a package of interventions including: 1) healthy lifestyle counseling (smoking cessation, and salt, oil, and alcohol reduction); 2) prescription of a combination of drugs (antihypertensives, aspirin, and statin); and 3) adherence support for drug compliance and healthy lifestyle change. In the control arm, participants will receive usual care for hypertension and diabetes management at individual clinicians’ discretion. The primary outcome is the incidence of severe CVD events over 24 months of follow-up. All CVD events will be defined according to the World Health Organization (WHO) monitoring of trends and determinants in cardiovascular disease (MONICA) definitions, diagnosed at the county hospital or higher level, and reported by the Zhejiang surveillance system. Secondary outcomes include: mean systolic and diastolic blood pressure, blood glucose, serum total cholesterol (TC), and adherence to appointments, and drugs and lifestyle changes.
Discussion
This trial focuses on risk reduction of CVD rather than specific diseases. It is not designed to compare therapeutic and healthy lifestyle interventions, but rather their combined effects in primary care settings. Through the trial, we intend to understand the effectiveness of the comprehensive CVD reduction package in routine practice. We also intend to understand the barriers and facilitators to implementing the package, and thus to advise on policy and practice change.
Trial registration
Current Controlled Trials: ISRCTN58988083
doi:10.1186/1745-6215-14-354
PMCID: PMC4015636  PMID: 24160442
Cardiovascular disease; Risk; Events; Randomized controlled trial; Primary care
14.  Delivering enhanced cardiovascular (Hypertension) disease care through private health facilities in Pakistan 
Background
Cardiovascular diseases (CVDs) are one of the leading causes of death and disability in the world. Over 80% of CVD deaths take place in low-and middle-income countries. One-third of the population aged above 40 years suffers from Hypertension (HTN) and this is largely unreported as there is no registry for CVDs. No guidelines are available for use in health care facilities, especially private health facilities where practice among GPs varies considerably. We aim to conduct a Cluster Randomized Controlled trial delivering a quality HTN-CVD care package at strengthened private health facilities as compared to current practice at private health facilities.
Methods/Design
A pragmatic cluster randomized trial, with qualitative and economic studies, will be conducted in Sargodha district of Punjab, Pakistan, from January 2012 to December 2016. At least 912 hypertensives will be registered in the two arms, six clusters per arm. The proposed cluster randomized controlled trial will evaluate the effects of delivering quality HTN-CVD care, through enabled private health care facilities, to achieve better case registration, adherence and hypertension control also blood glucose and serum cholesterol control. The trial will be conducted through the doctors and paramedics at private health facilities. Main outcomes are mean difference in Systolic blood pressure among the two arms. Secondary outcomes are mean change in total serum cholesterol levels and mean change in glycaemic control achieved in the adult hypertensive patients. Individual and Cluster level analysis will be done according to intention-to-treat.
Discussion
Due to the high burden of disease where 1 in 3 individuals aged above 45 suffers from hypertension, topped with the fact that there is a dearth of a set of available, standardised guidelines for management, the disease is constantly on a hike in Pakistan. The government has made no effort to issue a set of guidelines adapted specifically for our population and this becomes more of a problem when managing CVD in urban population through private practitioners whose practices vary widely.If our set of context sensitive guidelines show an effectiveness in the proposed intervention districts it will be replicated in other such settings.
Trial registration
Current Controlled Trials ISRCTN34381594
doi:10.1186/1471-2261-13-76
PMCID: PMC3848995  PMID: 24066730
Cardiovascular disease; Public private mix; Urban health
15.  Association of Sirtuin 1 (SIRT1) Gene SNPs and Transcript Expression Levels With Severe Obesity 
Obesity (Silver Spring, Md.)  2011;20(1):178-185.
Recent studies have reported associations of sirtuin 1 (SIRT1) single nucleotide polymorphisms (SNPs) to both obesity and BMI. This study was designed to investigate association between SIRT1 SNPs, SIRT1 gene expression and obesity. Case-control analyses were performed using 1,533 obese subjects (896 adults, BMI >40 kg/m2 and 637 children, BMI >97th percentile for age and sex) and 1,237 nonobese controls, all French Caucasians. Two SNPs (in high linkage disequilibrium (LD), r2 = 0.96) were significantly associated with adult obesity, rs33957861 (P value = 0.003, odds ratio (OR) = 0.75, confidence interval (CI) = 0.61–0.92) and rs11599176 (P value: 0.006, OR = 0.74, CI = 0.61–0.90). Expression of SIRT1 mRNA was measured in BMI-discordant siblings from 154 Swedish families. Transcript expression was significantly correlated to BMI in the lean siblings (r2 = 0.13, P value = 3.36 × 10−7) and lower SIRT1 expression was associated with obesity (P value = 1.56 × 10−35). There was also an association between four SNPs (rs11599176, rs12413112, rs33957861, and rs35689145) and BMI (P values: 4 × 10−4, 6 × 10−4, 4 × 10−4, and 2 × 10−3) with the rare allele associated with a lower BMI. However, no SNP was associated with SIRT1 transcript expression level. In summary, both SNPs and SIRT1 gene expression are associated with severe obesity.
doi:10.1038/oby.2011.200
PMCID: PMC3760128  PMID: 21760635
16.  Methadone Dose, Take Home Status and Hospital Admission among Methadone Maintenance Patients 
Journal of addiction medicine  2012;6(3):186-190.
Objectives
Among patients receiving methadone maintenance treatment (MMT) for opioid dependence, receipt of unobserved dosing privileges (take homes) and adequate doses (i.e. ≥ 80mg) are each associated with improved addiction treatment outcomes, but the association with acute care hospitalization is unknown. We studied whether take-home dosing and adequate doses (i.e. ≥ 80 mg) were associated with decreased hospital admission among patients in a MMT program.
Methods
We reviewed daily electronic medical records of patients enrolled in one MMT program to determine receipt of take home doses, methadone dose ≥ 80mg and hospital admission date. Non-linear mixed effects logistic regression models were used to evaluate whether take home doses or dose ≥ 80mg on a given day were associated with hospital admission on the subsequent day. Covariates in adjusted models included age, gender, race/ethnicity, HIV status, medical illness, mental illness, and polysubstance use at program admission.
Results
Subjects (n=138) had the following characteristics: mean age 43 years; 52% female; 17% HIV-infected; 32% medical illness; 40% mental illness; and 52% polysubstance use. During a mean follow-up of 20 months, 42 patients (30%) accounted for 80 hospitalizations. Receipt of take homes was associated with significantly lower odds of a hospital admission (AOR 0.26; 95%CI: 0.11-0.62), whereas methadone dose ≥ 80mg was not (AOR 1.01; 95% CI: 0.56-1.83).
Conclusions
Among MMT patients, receipt of take homes, but not dose of methadone, was associated with decreased hospital admission. Take home status may reflect not only patients’ improved addiction outcomes, but also reduced healthcare utilization.
doi:10.1097/ADM.0b013e3182584772
PMCID: PMC3416958  PMID: 22694929
Methadone maintenance treatment; dose; take home status; hospital admission
17.  Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity 
Human Molecular Genetics  2012;21(16):3727-3738.
Variable number tandem repeats (VNTRs) constitute a relatively under-examined class of genomic variants in the context of complex disease because of their sequence complexity and the challenges in assaying them. Recent large-scale genome-wide copy number variant mapping and association efforts have highlighted the need for improved methodology for association studies using these complex polymorphisms. Here we describe the in-depth investigation of a complex region on chromosome 8p21.2 encompassing the dedicator of cytokinesis 5 (DOCK5) gene. The region includes two VNTRs of complex sequence composition which flank a common 3975 bp deletion, all three of which were genotyped by polymerase chain reaction and fragment analysis in a total of 2744 subjects. We have developed a novel VNTR association method named VNTRtest, suitable for association analysis of multi-allelic loci with binary and quantitative outcomes, and have used this approach to show significant association of the DOCK5 VNTRs with childhood and adult severe obesity (Pempirical= 8.9 × 10−8 and P= 3.1 × 10−3, respectively) which we estimate explains ∼0.8% of the phenotypic variance. We also identified an independent association between the 3975 base pair (bp) deletion and obesity, explaining a further 0.46% of the variance (Pcombined= 1.6 × 10−3). Evidence for association between DOCK5 transcript levels and the 3975 bp deletion (P= 0.027) and both VNTRs (Pempirical= 0.015) was also identified in adipose tissue from a Swedish family sample, providing support for a functional effect of the DOCK5 deletion and VNTRs. These findings highlight the potential role of DOCK5 in human obesity and illustrate a novel approach for analysis of the contribution of VNTRs to disease susceptibility through association studies.
doi:10.1093/hmg/dds187
PMCID: PMC3406755  PMID: 22595969
18.  Genetic Determinants of Variable Metabolism Have Little Impact on the Clinical Use of Leading Antipsychotics in the CATIE study 
Purpose
To evaluate systematically in real clinical settings whether functional genetic variations in drug metabolizing enzymes influence optimized doses, efficacy, and safety of antipsychotic medications.
Methods
DNA was collected from 750 patients with chronic schizophrenia treated with five antipsychotic drugs (olanzapine, quetiapine, risperidone, ziprasidone and perphenazine) as part of the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) study. Doses for each of the medicines were optimized to 1, 2, 3, or 4x units in identically-appearing capsules in a double blind design. We analyzed 25 known functional genetic variants in the major and minor metabolizing enzymes for each medication. These variants were tested for association with optimized dose and other relevant clinical outcomes.
Results
None of the tested variants showed a nominally significant main effect in association with any of the tested phenotypes in European-Americans, African-Americans or all patients. Even after accounting for potential covariates no genetic variant was found to be associated with dosing, efficacy, overall tolerability, or tardive dyskinesia.
Conclusion
There are no strong associations between common functional genetic variants in drug metabolizing enzymes and dosing, safety or efficacy of leading antipsychotics, strongly suggesting merely modest effects on the use of these medicines in most patients in typical clinical settings.
doi:10.1097/GIM.0b013e3181863239
PMCID: PMC3697113  PMID: 18813134
Pharmacogenetics; CYP 450; Drug Metabolizing Enzymes; Antipsychotics; Personalized Medicine
19.  One size does not fit all in severe infection: obesity alters outcome, susceptibility, treatment, and inflammatory response 
Critical Care  2013;17(3):R122.
Introduction
Obesity is an increasingly common comorbidity in critically ill patients. Whether obesity alters sepsis outcome, susceptibility, treatment, and response is not completely understood.
Methods
We conducted a retrospective analysis comparing three group of septic shock patients based on the intervals of actual body mass index (BMI) in patients enrolled in the VASST (Vasopressin and Septic Shock Trial) cohort. Primary outcome measurement was 28-day mortality. We tested for differences in patterns of infection by comparing the primary site of infection and organism. We also compared the treatments (fluids and vasopressors) and inflammatory response, measuring adipose tissue-related cytokine concentrations (interleukin [IL]-6, monocyte chemotactic protein [MCP]-1, tumor necrosis factor [TNF]-α, and resistin) in plasma in a subset of 382 patients. Of the 778 patients in VASST, 730 patients who had body weight and height measurements were analyzed. Patients with BMI <25 kg/m2 (n = 276) were grouped as a reference and compared to 'overweight' (25< BMI <30 kg/m2, n = 209) and 'obese' (BMI >30 kg/m2, n = 245) patients.
Results
Obese patients had the lowest 28-day mortality followed by overweight patients while patients with BMI <25 kg/m2 had the highest mortality (p = 0.02). Compared to the patients with BMI <25 kg/m2, obese and overweight patients also had a different pattern of infection with less lung (obese 35%, overweight 45%, BMI<25 kg/m2 50%, p = 0.003) and fungal infection (obese 8.2%, overweight 11%, and BMI<25 kg/m2 15.6%, p = 0.03). Per kilogram, obese and overweight patients received less fluid during the first four days (p<0.05) and received less norepinephrine (obese 0.14, overweight 0.21, BMI <25 kg/m2 0.26 µg/kg/min, p<0.0001) and vasopressin (obese 0.28, overweight 0.36, BMI <25 kg/m2 0.43 µU/kg/min, p<0.0001) on day 1 compared to patients with BMI <25 kg/m2. Obese and overweight patients also had a lower plasma IL-6 concentration at baseline (obese 106 [IQR 34-686], overweight 190 [IQR 44-2339], BMI <25 kg/m2 235 [IQR 44-1793] pg/mL, p = 0.046).
Conclusions
Overall obesity was associated with improved survival in septic shock and differences in pattern of infection, fluids, and vasopressors. Importantly, the magnitude of inflammatory IL-6 response is muted in the obese.
doi:10.1186/cc12794
PMCID: PMC4057102  PMID: 23786836
20.  Cardiac ischemia in patients with septic shock randomized to vasopressin or norepinephrine 
Critical Care  2013;17(3):R117.
Introduction
Cardiac troponins are sensitive and specific biomarkers of myocardial necrosis. We evaluated troponin, CK, and ECG abnormalities in patients with septic shock and compared the effect of vasopressin (VP) versus norepinephrine (NE) on troponin, CK, and ECGs.
Methods
This was a prospective substudy of a randomized trial. Adults with septic shock randomly received, blinded, a low-dose infusion of VP (0.01 to 0.03 U/min) or NE (5 to 15 μg/min) in addition to open-label vasopressors, titrated to maintain a mean blood pressure of 65 to 75 mm Hg. Troponin I/T, CK, and CK-MB were measured, and 12-lead ECGs were recorded before study drug, and 6 hours, 2 days, and 4 days after study-drug initiation. Two physician readers, blinded to patient data and drug, independently interpreted ECGs.
Results
We enrolled 121 patients (median age, 63.9 years (interquartile range (IQR), 51.1 to 75.3), mean APACHE II 28.6 (SD 7.7)): 65 in the VP group and 56 in the NE group. At the four time points, 26%, 36%, 32%, and 21% of patients had troponin elevations, respectively. Baseline characteristics and outcomes were similar between patients with positive versus negative troponin levels. Troponin and CK levels and rates of ischemic ECG changes were similar in the VP and the NE groups. In multivariable analysis, only APACHE II was associated with 28-day mortality (OR, 1.07; 95% CI, 1.01 to 1.14; P = 0.033).
Conclusions
Troponin elevation is common in adults with septic shock. We observed no significant differences in troponin, CK, and ECGs in patients treated with vasopressin and norepinephrine. Troponin elevation was not an independent predictor of mortality.
Trial registration
Controlled-trials.com ISRCTN94845869
doi:10.1186/cc12789
PMCID: PMC4057204  PMID: 23786655
Septic shock; myocardial ischemia; vasopressin; norepinephrine; troponin; electrocardiogram
21.  Using no-cost mobile phone reminders to improve attendance for HIV test results: a pilot study in rural Swaziland 
Background
Mobile technology has great potential to improve adherence and treatment outcomes in healthcare settings. However, text messaging and phone calls are unaffordable in many resource-limited areas. This study investigates the use of a no-cost alternative mobile phone technology using missed calls (‘buzzing’) to act as a patient reminder. The use of missed calls as a patient reminder was evaluated for feasibility and effectiveness as an appointment reminder in the follow-up of newly-diagnosed human immunodeficiency virus (HIV) positive patients in an HIV testing and counselling department in rural Swaziland.
Methods
This pilot study uses a before-and-after operational research study design, with all patients with mobile phones being offered the intervention. The primary outcome was the rate of attendance at the HIV testing and counselling department for collection of results in those with mobile phones before and after the introduction of the intervention.
Results
Over two-thirds, 71.8% (459/639), of patients had a mobile phone. All patients with a mobile phone consented to being buzzed. There was no difference in attendance for follow-up at the clinic before and after the intervention was implemented (80.1% versus 83.3%, p = 0.401), or after adjusting for confounding factors (OR 1.13, p = 0.662).
Conclusion
This pilot study illustrates that mobile technology may be feasible in rural, resource-poor settings as there are high rates of mobile phone ownership and the intervention had a 100% uptake rate, with positive feedback from staff and patients. In this particular setting, the intervention did not improve attendance rates. However, further research is planned to investigate the impact on adherence to appointments and medications in other settings, such as HIV chronic care follow-up and as part of an enhanced package to improve adherence.
doi:10.1186/2049-9957-2-12
PMCID: PMC3710074  PMID: 23849508
HIV infections; Mobile phone; Africa; Rural health; Text messaging; Buzzing; MHealth
23.  A Preliminary Investigation of Corpus Callosum and Anterior Commissure Aberrations in Aggressive Youth with Bipolar Disorders 
Abstract
Objective
Although behavioral deficits in bipolar disorder (BPD) are well described, the specific brain white matter (WM) disruptions have not been completely characterized, and neural mechanisms underlying dysfunction in BPD are not well established, particularly for youth with BPD and aggression. This preliminary study utilized diffusion tensor imaging (DTI) to investigate commissural tracts (corpus callosum [CC] and anterior commissure [AC]) in youth with BPD, because disruption of interhemispheric communication may contribute to the emotional deficits that are characteristic of the illness.
Method
DTI was used to investigate WM in 10 youth (7–17 years of age) with BPD and 10 typically developing age-matched controls. Tract-based spatial statistics voxel-wise analysis was used to compare fractional anisotropy (FA) of the two groups. We specifically focused on five subdivisions of the midsagittal CC as well as on the decussation of AC, which connects the temporal lobes. Exploratory correlations between FA values and life history of aggression scores were calculated for the BPD group.
Results
Youth with BPD had significantly lower FA values in the callosal genu and AC. FA values in the AC were negatively correlated with a life history of aggression in the BPD group.
Conclusions
These results contribute to a growing literature implicating a role for the genu of the CC in BPD and are the first to report WM variations in the AC of children with BPD. Taken together with the correlational data for aggression and the role of the AC in emotional processing, our data provide preliminary evidence for a possible association between the structural integrity of the WM of the AC and aggression in pediatric BPD.
doi:10.1089/cap.2011.0063
PMCID: PMC3362324  PMID: 22375854
24.  Integration of clinical data with a genome-scale metabolic model of the human adipocyte 
Combining large-scale immunohistochemical analysis and proteomics data, 7340 gene products are identified in human adipocytes. Based on this data, a genome-scale metabolic model is reconstructed and used to integrate clinical and transcriptome data from lean and obese subjects.
We simulated the metabolic differences between the individuals with different body mass indexes (BMIs) using transcriptome and fluxome data.An increase in the metabolic activity around androsterone, ganglioside GM2 and degradation products of heparan sulfate and keratan sulfate, and a decrease in mitochondrial metabolic activities are found in obese subjects compared with lean subjects.We simulated the change in lipid droplet (LD) size and found that lean subjects have large dynamic changes in LD formation compared with obese subjects.Besides enabling patient stratification, our study allows the identification of novel therapeutic targets for obesity.
We evaluated the presence/absence of proteins encoded by 14 077 genes in adipocytes obtained from different tissue samples using immunohistochemistry. By combining this with previously published adipocyte-specific proteome data, we identified proteins associated with 7340 genes in human adipocytes. This information was used to reconstruct a comprehensive and functional genome-scale metabolic model of adipocyte metabolism. The resulting metabolic model, iAdipocytes1809, enables mechanistic insights into adipocyte metabolism on a genome-wide level, and can serve as a scaffold for integration of omics data to understand the genotype–phenotype relationship in obese subjects. By integrating human transcriptome and fluxome data, we found an increase in the metabolic activity around androsterone, ganglioside GM2 and degradation products of heparan sulfate and keratan sulfate, and a decrease in mitochondrial metabolic activities in obese subjects compared with lean subjects. Our study hereby shows a path to identify new therapeutic targets for treating obesity through combination of high throughput patient data and metabolic modeling.
doi:10.1038/msb.2013.5
PMCID: PMC3619940  PMID: 23511207
adipocyte; flux balance analysis; genome-scale metabolic model; obesity; proteome
25.  De novo mutations in ATP1A3 cause alternating hemiplegia of childhood 
Heinzen, Erin L. | Swoboda, Kathryn J. | Hitomi, Yuki | Gurrieri, Fiorella | Nicole, Sophie | de Vries, Boukje | Tiziano, F. Danilo | Fontaine, Bertrand | Walley, Nicole M. | Heavin, Sinéad | Panagiotakaki, Eleni | Fiori, Stefania | Abiusi, Emanuela | Di Pietro, Lorena | Sweney, Matthew T. | Newcomb, Tara M. | Viollet, Louis | Huff, Chad | Jorde, Lynn B. | Reyna, Sandra P. | Murphy, Kelley J. | Shianna, Kevin V. | Gumbs, Curtis E. | Little, Latasha | Silver, Kenneth | Ptác̆ek, Louis J. | Haan, Joost | Ferrari, Michel D. | Bye, Ann M. | Herkes, Geoffrey K. | Whitelaw, Charlotte M. | Webb, David | Lynch, Bryan J. | Uldall, Peter | King, Mary D. | Scheffer, Ingrid E. | Neri, Giovanni | Arzimanoglou, Alexis | van den Maagdenberg, Arn M.J.M. | Sisodiya, Sanjay M. | Mikati, Mohamad A. | Goldstein, David B. | Nicole, Sophie | Gurrieri, Fiorella | Neri, Giovanni | de Vries, Boukje | Koelewijn, Stephany | Kamphorst, Jessica | Geilenkirchen, Marije | Pelzer, Nadine | Laan, Laura | Haan, Joost | Ferrari, Michel | van den Maagdenberg, Arn | Zucca, Claudio | Bassi, Maria Teresa | Franchini, Filippo | Vavassori, Rosaria | Giannotta, Melania | Gobbi, Giuseppe | Granata, Tiziana | Nardocci, Nardo | De Grandis, Elisa | Veneselli, Edvige | Stagnaro, Michela | Gurrieri, Fiorella | Neri, Giovanni | Vigevano, Federico | Panagiotakaki, Eleni | Oechsler, Claudia | Arzimanoglou, Alexis | Nicole, Sophie | Giannotta, Melania | Gobbi, Giuseppe | Ninan, Miriam | Neville, Brian | Ebinger, Friedrich | Fons, Carmen | Campistol, Jaume | Kemlink, David | Nevsimalova, Sona | Laan, Laura | Peeters-Scholte, Cacha | van den Maagdenberg, Arn | Casaer, Paul | Casari, Giorgio | Sange, Guenter | Spiel, Georg | Boneschi, Filippo Martinelli | Zucca, Claudio | Bassi, Maria Teresa | Schyns, Tsveta | Crawley, Francis | Poncelin, Dominique | Vavassori, Rosaria
Nature genetics  2012;44(9):1030-1034.
Alternating hemiplegia of childhood (AHC) is a rare, severe neurodevelopmental syndrome characterized by recurrent hemiplegic episodes and distinct neurologic manifestations. AHC is usually a sporadic disorder with unknown etiology. Using exome sequencing of seven patients with AHC, and their unaffected parents, we identified de novo nonsynonymous mutations in ATP1A3 in all seven AHC patients. Subsequent sequence analysis of ATP1A3 in 98 additional patients revealed that 78% of AHC cases have a likely causal ATP1A3 mutation, including one inherited mutation in a familial case of AHC. Remarkably, six ATP1A3 mutations explain the majority of patients, including one observed in 36 patients. Unlike ATP1A3 mutations that cause rapid-onset-dystonia-parkinsonism, AHC-causing mutations revealed consistent reductions in ATPase activity without effects on protein expression. This work identifies de novo ATP1A3 mutations as the primary cause of AHC, and offers insight into disease pathophysiology by expanding the spectrum of phenotypes associated with mutations in this gene.
doi:10.1038/ng.2358
PMCID: PMC3442240  PMID: 22842232

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