Background: Epigenetic modifications, such as DNA methylation, due to in utero exposures may play a critical role in early programming for childhood and adult illness. Maternal smoking is a major risk factor for multiple adverse health outcomes in children, but the underlying mechanisms are unclear.
Objective: We investigated epigenome-wide methylation in cord blood of newborns in relation to maternal smoking during pregnancy.
Methods: We examined maternal plasma cotinine (an objective biomarker of smoking) measured during pregnancy in relation to DNA methylation at 473,844 CpG sites (CpGs) in 1,062 newborn cord blood samples from the Norwegian Mother and Child Cohort Study (MoBa) using the Infinium HumanMethylation450 BeadChip (450K).
Results: We found differential DNA methylation at epigenome-wide statistical significance (p-value < 1.06 × 10–7) for 26 CpGs mapped to 10 genes. We replicated findings for CpGs in AHRR, CYP1A1, and GFI1 at strict Bonferroni-corrected statistical significance in a U.S. birth cohort. AHRR and CYP1A1 play a key role in the aryl hydrocarbon receptor signaling pathway, which mediates the detoxification of the components of tobacco smoke. GFI1 is involved in diverse developmental processes but has not previously been implicated in responses to tobacco smoke.
Conclusions: We identified a set of genes with methylation changes present at birth in children whose mothers smoked during pregnancy. This is the first study of differential methylation across the genome in relation to maternal smoking during pregnancy using the 450K platform. Our findings implicate epigenetic mechanisms in the pathogenesis of the adverse health outcomes associated with this important in utero exposure.
epigenetics; epigenome-wide; in utero; maternal smoking; methylation
The U.S. Centers for Medicare and Medicaid Services established the Electronic Health Record (EHR) Incentive Program in 2009 to stimulate the adoption of EHRs. One component of the program requires eligible providers to implement clinical decision support (CDS) interventions that can improve performance on one or more quality measures pre-selected for each specialty. Because the unique decision-making challenges and existing HIT capabilities vary widely across specialties, the development of meaningful objectives for CDS within such programs must be supported by deliberative analysis.
We developed a conceptual framework and protocol that combines evidence review with expert opinion to elicit clinically meaningful objectives for CDS directly from specialists. The framework links objectives for CDS to specialty-specific performance gaps while ensuring that a workable set of CDS opportunities are available to providers to address each performance gap. Performance gaps may include those with well-established quality measures but also priorities identified by specialists based on their clinical experience. Moreover, objectives are not constrained to performance gaps with existing CDS technologies, but rather may include those for which CDS tools might reasonably be expected to be developed in the near term, for example, by the beginning of Stage 3 of the EHR Incentive program. The protocol uses a modified Delphi expert panel process to elicit and prioritize CDS meaningful use objectives. Experts first rate the importance of performance gaps, beginning with a candidate list generated through an environmental scan and supplemented through nominations by panelists. For the highest priority performance gaps, panelists then rate the extent to which existing or future CDS interventions, characterized jointly as “CDS opportunities,” might impact each performance gap and the extent to which each CDS opportunity is compatible with specialists’ clinical workflows. The protocol was tested by expert panels representing four clinical specialties: oncology, orthopedic surgery, interventional cardiology, and pediatrics.
To evaluate the ability of the structure and code sets specified in the National Council for Prescription Drug Programs Structured and Codified Sig Format to represent ambulatory electronic prescriptions.
We parsed the Sig strings from a sample of 20 161 de-identified ambulatory e-prescriptions into variables representing the fields of the Structured and Codified Sig Format. A stratified random sample of these representations was then reviewed by a group of experts. For codified Sig fields, we attempted to map the actual words used by prescribers to the equivalent terms in the designated terminology.
Proportion of prescriptions that the Format could fully represent; proportion of terms used that could be mapped to the designated terminology.
The fields defined in the Format could fully represent 95% of Sigs (95% CI 93% to 97%), but ambiguities were identified, particularly in representing multiple-step instructions. The terms used by prescribers could be codified for only 60% of dose delivery methods, 84% of dose forms, 82% of vehicles, 95% of routes, 70% of sites, 33% of administration timings, and 93% of indications.
The findings are based on a retrospective sample of ambulatory prescriptions derived mostly from primary care physicians.
The fields defined in the Format could represent most of the patient instructions in a large prescription sample, but prior to its mandatory adoption, further work is needed to ensure that potential ambiguities are addressed and that a complete set of terms is available for the codified fields.
Greater use of computerized decision support (DS) systems could address continuing safety and quality problems in healthcare, but the healthcare field has struggled to implement DS technology. This study surveys DS experience across multiple non-healthcare disciplines for new insights that are generalizable to healthcare provider decisions. In particular, it sought design principles and lessons learned from the other disciplines that could inform efforts to accelerate the adoption of clinical decision support (CDS).
Our systematic review drew broadly from non-healthcare databases in the basic sciences, social sciences, humanities, engineering, business, and defense: PsychINFO, BusinessSource Premier, Social Sciences Abstracts, Web of Science, and Defense Technical Information Center. Because our interest was in DS that could apply to clinical decisions, we selected articles that (1) provided a review, overview, discussion of lessons learned, or an evaluation of design or implementation aspects of DS within a non-healthcare discipline and (2) involved an element of human judgment at the individual level, as opposed to decisions that can be fully automated or that are made at the organizational level.
Clinical decisions share some similarities with decisions made by military commanders, business managers, and other leaders: they involve assessing new situations and choosing courses of action with major consequences, under time pressure, and with incomplete information. We identified seven high-level DS system design features from the non-healthcare literature that could be applied to CDS: providing broad, system-level perspectives; customizing interfaces to specific users and roles; making the DS reasoning transparent; presenting data effectively; generating multiple scenarios covering disparate outcomes (e.g., effective; effective with side effects; ineffective); allowing for contingent adaptations; and facilitating collaboration. The article provides examples of each feature. The DS literature also emphasizes the importance of organizational culture and training in implementation success. The literature contrasts “rational-analytic” vs. “naturalistic-intuitive” decision-making styles, but the best approach is often a balanced approach that combines both styles. It is also important for DS systems to enable exploration of multiple assumptions, and incorporation of new information in response to changing circumstances.
Complex, high-level decision-making has common features across disciplines as seemingly disparate as defense, business, and healthcare. National efforts to advance the health information technology agenda through broader CDS adoption could benefit by applying the DS principles identified in this review.
We studied the influence of glacial oscillations on the genetic structure of seven species of white-headed gull that breed at high latitudes (Larus argentatus, L. canus, L. glaucescens, L. glaucoides, L. hyperboreus, L. schistisagus, and L. thayeri). We evaluated localities hypothesized as ice-free areas or glacial refugia in other Arctic vertebrates using molecular data from 11 microsatellite loci, mitochondrial DNA (mtDNA) control region, and six nuclear introns for 32 populations across the Holarctic. Moderate levels of genetic structure were observed for microsatellites (FST= 0.129), introns (ΦST= 0.185), and mtDNA control region (ΦST= 0.461), with among-group variation maximized when populations were grouped based on subspecific classification. Two haplotype and at least two allele groups were observed across all loci. However, no haplotype/allele group was composed solely of individuals of a single species, a pattern consistent with recent divergence. Furthermore, northernmost populations were not well differentiated and among-group variation was maximized when L. argentatus and L. hyberboreus populations were grouped by locality rather than species, indicating recent hybridization. Four populations are located in putative Pleistocene glacial refugia and had larger τ estimates than the other 28 populations. However, we were unable to substantiate these putative refugia using coalescent theory, as all populations had genetic signatures of stability based on mtDNA. The extent of haplotype and allele sharing among Arctic white-headed gull species is noteworthy. Studies of other Arctic taxa have generally revealed species-specific clusters as well as genetic structure within species, usually correlated with geography. Aspects of white-headed gull behavioral biology, such as colonization ability and propensity to hybridize, as well as their recent evolutionary history, have likely played a large role in the limited genetic structure observed.
Genetic structure; hybridization; Larus; Pleistocene glacial refugia; white-headed gulls
Cellular oxidative and electrophilic stress triggers a protective response in mammals regulated by NRF2 (nuclear factor (erythroid-derived) 2-like; NFE2L2) binding to deoxyribonucleic acid-regulatory sequences near stress-responsive genes. Studies using Nrf2-deficient mice suggest that hundreds of genes may be regulated by NRF2. To identify human NRF2-regulated genes, we conducted chromatin immunoprecipitation (ChIP)-sequencing experiments in lymphoid cells treated with the dietary isothiocyanate, sulforaphane (SFN) and carried out follow-up biological experiments on candidates. We found 242 high confidence, NRF2-bound genomic regions and 96% of these regions contained NRF2-regulatory sequence motifs. The majority of binding sites were near potential novel members of the NRF2 pathway. Validation of selected candidate genes using parallel ChIP techniques and in NRF2-silenced cell lines indicated that the expression of about two-thirds of the candidates are likely to be directly NRF2-dependent including retinoid X receptor alpha (RXRA). NRF2 regulation of RXRA has implications for response to retinoid treatments and adipogenesis. In mouse, 3T3-L1 cells’ SFN treatment affected Rxra expression early in adipogenesis, and knockdown of Nrf2-delayed Rxra expression, both leading to impaired adipogenesis.
Differences in rates of diabetes-related lower extremity amputations represent one of the largest and most persistent health disparities found for African-Americans and Hispanics compared to whites in the United States. Since many minority patients receive care in under-resourced settings, quality improvement (QI) initiatives in these settings may offer a targeted approach to improve diabetes outcomes in these patient populations. Health information technology (health IT) is widely viewed as an essential component of health care QI and may be useful in decreasing diabetes disparities in under-resourced settings. This article reviews the effectiveness of health care interventions utilizing health IT to improve diabetes process of care and intermediate diabetes outcomes in African-American and Hispanic patients. Health IT interventions have addressed patient, provider, and system challenges in the provision of diabetes care but require further testing in minority patient populations to evaluate their effectiveness in improving diabetes outcomes and reducing diabetes-related complications.
diabetes; health information technology; health disparities; quality improvement; under resourced settings
Rationale: The NF-E2 related factor 2 (Nrf2)–antioxidant response element (ARE) pathway is essential for protection against oxidative injury and inflammation including hyperoxia-induced acute lung injury. Microarray expression profiling revealed that lung peroxisome proliferator activated receptor γ (PPARγ) induction is suppressed in hyperoxia-susceptible Nrf2-deficient (Nrf2−/−) mice compared with wild-type (Nrf2+/+) mice. PPARγ has pleiotropic beneficial effects including antiinflammation in multiple tissues.
Objectives: We tested the hypothesis that PPARγ is an important determinant of pulmonary responsivity to hyperoxia regulated by Nrf2.
Methods: A computational bioinformatic method was applied to screen potential AREs in the Pparg promoter for Nrf2 binding. The functional role of a potential ARE was investigated by in vitro promoter analysis. A role for PPARγ in hyperoxia-induced acute lung injury was determined by temporal silencing of PPARγ via intranasal delivery of PPARγ-specific interference RNA and by administration of a PPARγ ligand 15-deoxy-Δ12,14-prostaglandin J2 in mice.
Measurements and Main Results: Deletion or site-directed mutagenesis of a potential ARE spanning -784/-764 sequence significantly attenuated hyperoxia-increased Pparg promoter activity in airway epithelial cells overexpressing Nrf2, indicating that the -784/-764 ARE is critical for Nrf2-regulated PPARγ expression. Mice with decreased lung PPARγ by specific interference RNA treatment had significantly augmented hyperoxia-induced pulmonary inflammation and injury. 15 Deoxy-Δ12,14-prostaglandin J2 administration significantly reduced hyperoxia-induced lung inflammation and edema in Nrf2+/+, but not in Nrf2−/− mice.
Conclusions: Results indicate for the first time that Nrf2-driven PPARγ induction has an essential protective role in pulmonary oxidant injury. Our observations provide new insights into the therapeutic potential of PPARγ in airway oxidative inflammatory disorders.
antioxidant response element; hyperoxia; inflammation; siRNA; 15d-PGJ2
Poor communication between primary care and specialists often leads to delays, inefficiencies and suboptimal patient outcomes. This study examined implementation of an electronic referral system (eReferral) that creates direct communication between primary care providers and specialist reviewers. Semi-structured interviews were conducted to assess factors affecting the success of eReferral implementation; transcripts were analyzed using qualitative methods. Primary and specialty care providers were enthusiastic about the system. Primary care providers had favorable attitudes despite a number of challenges including increased workload due to a shift in tasks from specialists and administrative personnel, poor connectivity, and insufficient hardware. System acceptance was driven by perceptions of improved access to specialty care, better appointment tracking, and improved communication between primary and specialty care providers. Synergy among development processes, implementation practices, and technical factors, including human-centered design, iterative development, a phased rollout, and an intuitive user interface, also fostered uptake of the system.
The p53 protein is crucial for adapting programs of gene expression in response to stress. Recently, we revealed that this occurs partly through the formation of stress-specific p53 binding patterns. However, the mechanisms that generate these binding patterns remain largely unknown. It is not established whether the selective binding of p53 is achieved through modulation of its binding affinity to certain response elements (REs) or via a chromatin-dependent mechanism. To shed light on this issue, we used a microsphere assay for protein–DNA binding to measure p53 binding patterns on naked DNA. In parallel, we measured p53 binding patterns within chromatin using chromatin immunoprecipitation and DNase I coupled to ligation-mediated polymerase chain reaction footprinting. Through this experimental approach, we revealed that UVB and Nutlin-3 doses, which lead to different cellular outcomes, induce similar p53 binding patterns on naked DNA. Conversely, the same treatments lead to stress-specific p53 binding patterns on chromatin. We show further that altering chromatin remodeling using an histone acetyltransferase inhibitor reduces p53 binding to REs. Altogether, our results reveal that the formation of p53 binding patterns is not due to the modulation of sequence-specific p53 binding affinity. Rather, we propose that chromatin and chromatin remodeling are required in this process.
p53 coordinates the expression of an intricate network of genes in response to stress signals. Sequence-specific DNA binding is essential for p53-mediated tumor suppression. We evaluated the impact of single-nucleotide polymorphisms (SNPs) in p53 response elements (p53RE) on DNA binding and gene expression in response to DNA damage. Using a bioinformatics approach based on incorporating p53 binding strength into a position weight matrix, we selected 32 SNPs in putative and validated p53REs. The microsphere assay for protein–DNA binding (MAPD) and allele-specific expression analysis was employed to assess the impact of SNPs on p53-DNA binding and gene expression, respectively. Comparing activated p53 binding in nuclear extracts from doxorubicin- or ionizing radiation (IR)-treated human cells, we observed little difference in binding profiles. Significant p53 binding was observed for most polymorphic REs and several displayed binding comparable to the p21 RE. SNP alleles predicted to lower p53 binding indeed reduced binding in 25 of the 32 sequences. Chromatin immunoprecipitation-sequencing in lymphoblastoid cells confirmed p53 binding to seven polymorphic p53 REs in response to doxorubicin. In addition, five polymorphisms were associated with altered gene expression following doxorubicin treatment. Our findings demonstrate an effective strategy to identify and evaluate SNPs that may alter p53-mediated stress responses.
Prior microarray studies of smokers at high risk for lung cancer have demonstrated that heterogeneity in bronchial airway epithelial cell gene expression response to smoking can serve as an early diagnostic biomarker for lung cancer. As a first step in applying functional genomic analysis to population studies, we have examined the relationship between gene expression variation and genetic variation in a central molecular pathway (NRF2-mediated antioxidant response) associated with smoking exposure and lung cancer. We assessed global gene expression in histologically normal airway epithelial cells obtained at bronchoscopy from smokers who developed lung cancer (SC, n = 20), smokers without lung cancer (SNC, n = 24), and never smokers (NS, n = 8). Functional enrichment analysis showed that the NRF2-mediated, antioxidant response element (ARE)-regulated genes, were significantly lower in SC, when compared with expression levels in SNC. Importantly, we found that the expression of MAFG (a binding partner of NRF2) was correlated with the expression of ARE genes, suggesting MAFG levels may limit target gene induction. Bioinformatically we identified single nucleotide polymorphisms (SNPs) in putative ARE genes and to test the impact of genetic variation, we genotyped these putative regulatory SNPs and other tag SNPs in selected NRF2 pathway genes. Sequencing MAFG locus, we identified 30 novel SNPs and two were associated with either gene expression or lung cancer status among smokers. This work demonstrates an analysis approach that integrates bioinformatics pathway and transcription factor binding site analysis with genotype, gene expression and disease status to identify SNPs that may be associated with individual differences in gene expression and/or cancer status in smokers. These polymorphisms might ultimately contribute to lung cancer risk via their effect on the airway gene expression response to tobacco-smoke exposure.
US hospitals have had voluntary incident reporting systems for many years, but the effectiveness of these systems is unknown. To facilitate substantial improvements in patient safety, the systems should capture incidents reflecting the spectrum of adverse events that are known to occur in hospitals.
To characterise the incidents from established voluntary hospital reporting systems.
Observational study examining about 1000 reports of hospitalised patients at each of two hospitals.
Patients and setting
16 575 randomly selected patients from an academic and a community hospital in the US in 2001.
Main outcome measures
Rates of incidents reported per hospitalised patient and characteristics of reported incidents.
9% of patients had at least one reported incident; 17 incidents were reported per 1000 patient‐days in hospital. Nurses filed 89% of reports, physicians 1.9% and other providers 8.9%. The most common types were medication incidents (29%), falls (14%), operative incidents (15%) and miscellaneous incidents (16%); 59% seemed preventable and preventability was not clear for 32%. Among the potentially preventable incidents, 43% involved nurses, 16% physicians and 19% other types of providers. Qualitative examination of reports indicated that very few involved prescribing errors or high‐risk procedures.
Hospital reporting systems receive many reports, but capture a spectrum of incidents that differs from the adverse events known to occur in hospitals, thereby substantially underdetecting physician incidents, particularly those involving operations, high‐risk procedures and prescribing errors. Increasing the reporting of physician incidents will be essential to enhance the effectiveness of hospital reporting systems; therefore, barriers to reporting such incidents must be minimised.
Poor communication between referring clinicians and specialists may lead to inefficient use of specialist services. San Francisco General Hospital implemented an electronic referral system (eReferral) that facilitates iterative pre-visit communication between referring and specialty clinicians to improve the referral process.
The purpose of the study was to determine the impact of eReferral (compared with paper-based referrals) on specialty referrals.
The study was based on a visit-based questionnaire appended to new patient charts at randomly selected specialist clinic sessions before and after the implementation of eReferral.
The questionnaire focused on the self-reported difficulty in identifying referral question, referral appropriateness, need for and avoidability of follow-up visits.
We collected 505 questionnaires from speciality clinicians. It was difficult to identify the reason for referral in 19.8% of medical and 38.0% of surgical visits using paper-based methods vs. 11.0% and 9.5% of those using eReferral (p-value 0.03 and <0.001). Of those using eReferral, 6.4% and 9.8% of medical and surgical referrals using paper methods vs. 2.6% and 2.1% were deemed not completely appropriate (p-value 0.21 and 0.03). Follow-up was requested for 82.4% and 76.2% of medical and surgical patients with paper-based referrals vs. 90.1% and 58.1% of eReferrals (p-value 0.06 and 0.01). Follow-up was considered avoidable for 32.4% and 44.7% of medical and surgical follow-ups with paper-based methods vs. 27.5% and 13.5% with eReferral (0.41 and <0.001).
Use of technology to promote standardized referral processes and iterative communication between referring clinicians and specialists has the potential to improve communication between primary care providers and specialists and to increase the effectiveness of specialty referrals.
access to care; communication; specialty care
Single nucleotide polymorphisms (SNPs) in transcription factor binding sites (TFBSs) may affect the binding of transcription factors, lead to differences in gene expression and phenotypes, and therefore affect susceptibility to environmental exposure. We developed an integrated computational system for discovering functional SNPs in TFBSs in the human genome and predicting their impact on the expression of target genes. In this system we: (1) construct a position weight matrix (PWM) from a collection of experimentally discovered TFBSs; (2) predict TFBSs in SNP sequences using the PWM and map SNPs to the upstream regions of genes; (3) examine the evolutionary conservation of putative TFBSs by phylogenetic footprinting; (4) prioritize candidate SNPs based on microarray expression profiles from tissues in which the transcription factor of interest is either deleted or over-expressed; and (5) finally, analyze association of SNP genotypes with gene expression phenotypes. The application of our system has been tested to identify functional polymorphisms in the antioxidant response element (ARE), a cis-acting enhancer sequence found in the promoter region of many genes that encode antioxidant and Phase II detoxification enzymes/proteins. In response to oxidative stress, the transcription factor NRF2 (nuclear factor erythroid-derived 2-like 2) binds to AREs, mediating transcriptional activation of its responsive genes and modulating in vivo defense mechanisms against oxidative damage. Using our novel computational tools, we have identified a set of polymorphic AREs with functional evidence, showing the utility of our system to direct further experimental validation of genomic sequence variations that could be useful for identifying high-risk individuals.
To compare the experiences of e-prescribing users and nonusers regarding prescription safety and workload and to assess the use of information from two e-prescribing standards (for medication history and formulary and benefit information), as they are implemented.
Cross-sectional survey of physicians who either had installed or were awaiting installation of one of two commercial e-prescribing systems.
Perceptions about medication history and formulary and benefit information among all respondents, and among e-prescribing users, experiences with system usability, job performance impact, and amount of e-prescribing.
Of 395 eligible physicians, 228 (58%) completed the survey. E-prescribers (n = 139) were more likely than non-e-prescribers (n = 89) to perceive that they could identify clinically important drug–drug interactions (83 versus 67%, p = 0.004) but not that they could identify prescriptions from other providers (65 versus 60%, p = 0.49). They also perceived no significant difference in calls about drug coverage problems (76 versus 71% reported getting 10 or fewer such calls per week; p = 0.43). Most e-prescribers reported high satisfaction with their systems, but 17% had stopped using the system and another 46% said they sometimes reverted to handwriting for prescriptions that they could write electronically. The volume of e-prescribing was correlated with perceptions that it enhanced job performance, whereas quitting was associated with perceptions of poor usability.
E-prescribing users reported patient safety benefits but they did not perceive the enhanced benefits expected from using standardized medication history or formulary and benefit information. Additional work is needed for these standards to have the desired effects.
We evaluated the RxNorm standardized drug nomenclature for representing ambulatory e-prescriptions.
Using a sample of 19743 primary care e-prescriptions, we estimated the coverage rate of RxNorm for representing clinical drugs, measured the 6-month replacement rate for RxNorm concepts, assessed the consistency of two independent concept mappings, and investigated inconsistent mappings.
RxNorm contained concepts for nearly all prescriptions in the sample (99.995%). Of 1419 concepts used, 8.1% were replaced between April and October 2009. Independent mappings produced different concepts for 676 e-prescriptions (3.4%), but most differences would have low clinical significance. Most mismatches were related to the use of extended-release form concepts with no duration specified, inhalers vs. their contents, and clinically inert salts.
RxNorm provides concepts covering nearly all ambulatory e-prescriptions in this setting. Independent mappings were relatively consistent. Improvements could be made by enabling selection of the most-specific concepts when broader prescribable concepts exist.
In vitro, human isoenzymes encoded by genes homozygous for the ADH1C*1 or ADH1B*2 alleles metabolize ethanol to acetaldehyde at a faster rate than those homozygous for the ADH1C*2 or ADH1B*1 allele. Because alcohol is a known risk factor for breast cancer, we evaluated the joint association of genetic variants in ADH and alcohol consumption in relation to breast cancer.
A nested case-control study of 321 cases and matched controls was conducted. Five single nucleotide polymorphisms (SNPs) of the ADH1C and ADH1B genes were genotyped. Conditional logistic regression was used to assess odds ratios (OR) and 95% confidence intervals (CI) for each SNP. Haplotype analysis of all 5 SNPs was also undertaken.
Among drinkers, the median intake of total alcohol was 13 grams per week (10th to 90th percentiles; 4.5 – 135.9) in cases and 18 grams per week (10th to 90th percentiles; 4.5–104.1) in controls. Women who drank alcohol tended to be at an increased risk of developing breast cancer compared to those who did not drink (O.R. =1.40, 95% CI 0.97, 2.03), particularly those who were pre-menopausal at the time of breast cancer diagnosis (OR = 2.69, 95% CI: 1.00, 7.26). Of the known functional alleles, breast cancer risk was not significantly increased among carriers of at least one ADH1C*1 or ADH1B*2 allele, when compared to those heterozygous or homozygous for either the ADH1C*2 or ADH1B*1 allele. However, breast cancer risk tended to be lower among women who inherited the ADH1B*896G allele (O.R. = 0.62, 95%CI 0.37,_ 1.04). Haplotype frequencies were not significantly different between cases and controls.
Low levels of alcohol are associated with a modest increase in breast cancer risk that is not altered by known functional allelic variants of the ADH1B and 1C gene. The protective association conferred by the ADH1B*896G allele needs further evaluation.
Alcohol dehydrogenase; genotypes; breast cancer
Genetically determined factors that alter the metabolism of tobacco carcinogens can influence an individual’s susceptibility to bladder cancer. The associations between the genotypes of glutathione S-transferase (GST) M1, GSTP1, GSTT1 and N-acetyltransferase (NAT) 1 and the phenotypes of NAT2 and cytochrome P450 (CYP) 1A2 and bladder cancer risk were examined in a case-control study involving 731 bladder cancer patients and 740 control subjects in Los Angeles County, California. Individual null/low-activity genotypes of GSTM1, GSTT1 and GSTP1 were associated with a 19–48% increase in odds ratio (OR) of bladder cancer. The strongest association was noted for GSTM1 [OR for the null genotype = 1.48, 95% confidence interval (CI) = 1.19–1.83]. When the three GST genes were examined together, there was a monotonic, statistically significant association between increasing number of null/low-activity genotypes and risk (P for trend = 0.002). OR (95% CI) for one and two or more null/low-activity GST genotypes was 1.42 (1.12–1.81) and 1.71 (1.25–2.34), respectively, relative to the absence of null/low-activity GST genotype. NAT2 slow acetylation was associated with doubled risk of bladder cancer among individuals with known high exposures to carcinogenic arylamines (OR = 2.03, 95% CI = 1.12–3.69, P = 0.02). The effect of NAT2 slow acetylation was even stronger in the presence of two or more null/low-activity GST genotypes. There were no associations between bladder cancer risk and NAT1 genotype or CYP1A2 phenotype.
The time course of physicians’ knowledge retention after learning activities has not been well characterized. Understanding the time course of retention is critical to optimizing the reinforcement of knowledge.
Educational follow-up experiment with knowledge retention measured at 1 of 6 randomly assigned time intervals (0–55 days) after an online tutorial covering 2 American Diabetes Association guidelines.
Internal and family medicine residents.
Multiple-choice knowledge tests, subject characteristics including critical appraisal skills, and learner satisfaction.
Of 197 residents invited, 91 (46%) completed the tutorial and were randomized; of these, 87 (96%) provided complete follow-up data. Ninety-two percent of the subjects rated the tutorial as “very good” or “excellent.” Mean knowledge scores increased from 50% before the tutorial to 76% among those tested immediately afterward. Score gains were only half as great at 3–8 days and no significant retention was measurable at 55 days. The shape of the retention curve corresponded with a 1/4-power transformation of the delay interval. In multivariate analyses, critical appraisal skills and participant age were associated with greater initial learning, but no participant characteristic significantly modified the rate of decline in retention.
Education that appears successful from immediate posttests and learner evaluations can result in knowledge that is mostly lost to recall over the ensuing days and weeks. To achieve longer-term retention, physicians should review or otherwise reinforce new learning after as little as 1 week.
Electronic supplementary material
The online version of this article (doi:10.1007/s11606-008-0604-2) contains supplementary material, which is available to authorized users.
knowledge retention; online tutorial; randomized educational experiment; resident physicians; educational technology; learning theory
The most common form of genetic variation, single nucleotide polymorphisms or SNPs, can affect the way an individual responds to the environment and modify disease risk. Although most of the millions of SNPs have little or no effect on gene regulation and protein activity, there are many circumstances where base changes can have deleterious effects. Non-synonymous SNPs that result in amino acid changes in proteins have been studied because of their obvious impact on protein activity. It is well known that SNPs within regulatory regions of the genome can result in disregulation of gene transcription. However, the impact of SNPs located in putative regulatory regions, or rSNPs, is harder to predict for two primary reasons. First, the mechanistic roles of non-coding genomic sequence remain poorly defined. Second, experimental validation of the functional consequences of rSNPs is often slow and laborious. In this review, we summarize traditional and novel methodologies for candidate rSNPs selection, in particular in silico techniques that aid in candidate rSNP selection. Additionally we will discuss molecular biological techniques that assess the impact of rSNPs on binding of regulatory machinery, as well as functional consequences on transcription. Standard techniques such as EMSA and luciferase reporter constructs are still widely used to assess effects of rSNPs on binding and gene transcription; however, these protocols are often bottlenecks in the discovery process. Therefore, we highlight novel and developing high-throughput protocols that promise to aid in shortening the process of rSNP validation. Given the large amount of genomic information generated from a multitude of re-sequencing and genome-wide SNP array efforts, future focus should be to develop validation techniques that will allow greater understanding of the impact these polymorphisms have on human health and disease.
polymorphism; SNPs; gene regulation; functional genomics; microsphere assay
Genetically determined factors that alter the metabolism of tobacco carcinogens can influence an individual’s susceptibility to bladder cancer. The associations between the genotypes of glutathione S-transferase (GST) M1, GSTP1, GSTT1 and N-acetyltransferase (NAT) 1 and the phenotypes of NAT2 and cytochrome P450 (CYP) 1A2 and bladder cancer risk were examined in a case–control study involving 731 bladder cancer patients and 740 control subjects in Los Angeles County, California. Individual null/low-activity genotypes of GSTM1, GSTT1 and GSTP1 were associated with a 19–48% increase in odds ratio (OR) of bladder cancer. The strongest association was noted for GSTM1 [OR for the null genotype = 1.48, 95% confidence interval (CI) = 1.19–1.83]. When the three GST genes were examined together, there was a monotonic, statistically significant association between increasing number of null/low-activity genotypes and risk (P for trend = 0.002). OR (95% CI) for one and two or more null/low-activity GST genotypes was 1.42 (1.12–1.81) and 1.71 (1.25–2.34), respectively, relative to the absence of null/low-activity GST genotype. NAT2 slow acetylation was associated with doubled risk of bladder cancer among individuals with known high exposures to carcinogenic arylamines (OR = 2.03, 95% CI = 1.12–3.69, P = 0.02). The effect of NAT2 slow acetylation was even stronger in the presence of two or more null/low-activity GST genotypes. There were no associations between bladder cancer risk and NAT1 genotype or CYP1A2 phenotype.
This study seeks to examine the correlates of complementary and alternative medicine (CAM) use in depressed underserved minority populations receiving medical care in primary care settings.
A prospective study using interviewer-administered surveys and medical record reviews was conducted at 2 large outpatient primary care clinics providing care primarily to underserved African American and Hispanic individuals located in Los Angeles, California. A total of 2321 patients were screened for depression. Of these, 315 met the Patient Health Questionnaire-9 criteria for mild to severe depression.
Over 57% of the sample reported using CAM sometimes or often (24%) and frequently (33%) for treatment of their depressive symptoms. Controlling for demographic characteristics, lack of health care coverage remained one of the strongest predictors of CAM use. Additionally, being moderately depressed, using psychotherapeutic prescription medications, and poorer self-reported health status were all associated with increased frequency of CAM utilization for treating depression.
The underserved African American and Hispanic individuals meeting the diagnostic criteria for depression or subsyndromal depression use CAM extensively for symptoms of depression. CAM is used as a substitute for conventional care when access to care is not available or limited. Since CAM is used so extensively for depression, understanding domains, types, and correlates of such use is imperative. This knowledge could be used to design interventions aimed at improving care for depression.
The p53 tumor suppressor regulates its target genes through sequence-specific binding to DNA response elements (REs). Although numerous p53 REs are established, the thousands more identified by bioinformatics are not easily subjected to comparative functional evaluation. To examine the relationship between RE sequence variation—including polymorphisms—and p53 binding, we have developed a multiplex format microsphere assay of protein-DNA binding (MAPD) for p53 in nuclear extracts. Using MAPD we measured sequence-specific p53 binding of doxorubicin-activated or transiently expressed p53 to REs from established p53 target genes and p53 consensus REs. To assess the sensitivity and scalability of the assay, we tested 16 variants of the p21 target sequence and a 62-multiplex set of single nucleotide (nt) variants of the p53 consensus sequence and found many changes in p53 binding that are not captured by current computational binding models. A group of eight single nucleotide polymorphisms (SNPs) was examined and binding profiles closely matched transactivation capability tested in luciferase constructs. The in vitro binding characteristics of p53 in nuclear extracts recapitulated the cellular in vivo transactivation capabilities for eight well-established human REs measured by luciferase assay. Using a set of 26 bona fide REs, we observed distinct binding patterns characteristic of transiently expressed wild type and mutant p53s. This microsphere assay system utilizes biologically meaningful cell extracts in a multiplexed, quantitative, in vitro format that provides a powerful experimental tool for elucidating the functional impact of sequence polymorphism and protein variation on protein/DNA binding in transcriptional networks.
Characterizing the functional roles of gene regulatory sequences and the impact of genetic polymorphism on protein-DNA binding are rapidly growing areas of genomics. The p53 tumor suppressor regulates its target genes through sequence-specific binding to DNA response elements, and we have developed a multiplex format microsphere assay (MAPD) to probe how sequence variation alters p53 binding. Testing pools of multiplexed oligonucleotides that contain numerous p53 binding targets or different sequence variants, we demonstrate that subtle changes in target sequence can impact p53 binding, and these effects are not captured by commonly used computational binding models. A group of single nucleotide polymorphisms was examined and binding profiles closely matched gene expression measured in a parallel system. We also observed distinct binding patterns that were characteristic of transiently expressed wild type and mutant p53s, suggesting that this method may be useful for probing the impact of protein structural variation on DNA binding. MAPD utilizes biologically meaningful cell extracts in a multiplexed, quantitative format that provides a powerful experimental tool for elucidating the functional impact of sequence polymorphism and protein variation on protein/DNA binding in transcriptional networks.
Electronic prescribing has been advocated as an important tool for improving the safety and quality of medication use in ambulatory settings. However, widespread adoption of e-prescribing in ambulatory settings has yet to be realized. The determinants of successful implementation and use in these settings are not well understood.
To describe the practice characteristics associated with implementation and use of e-prescribing in ambulatory settings.
Multi-method qualitative case study of ambulatory practices before and after e-prescribing implementation.
Sixteen physicians and 31 staff members working in 12 practices scheduled for implementation of an e-prescribing program and purposively sampled to ensure a mix of practice size and physician specialty.
Field researchers used observational and interview techniques to collect data on prescription-related clinical workflow, information technology experience, and expectations.
Five practices fully implemented e-prescribing, 3 installed but with only some prescribers or staff members using the program, 2 installed and then discontinued use, 2 failed to install. Compared to practice members in other groups, members of successful practices exhibited greater familiarity with the capabilities of health information technologies and had more modest expectations about the benefits likely to accrue from e-prescribing. Members of unsuccessful practices reported limited understanding of e-prescribing capabilities, expected that the program would increase the speed of clinical care and reported difficulties with technical aspects of the implementation and insufficient technical support.
Practice leaders should plan implementation carefully, ensuring that practice members prepare for the effective integration of this technology into clinical workflow.
electronic prescribing; medical informatics; qualitative research; health services research