Development of a targeted amplicon sequencing method for genotyping Cyclospora cayetanensis from fresh produce and clinical samples with enhanced genomic resolution and sensitivity.

Outbreaks of cyclosporiasis, an enteric illness caused by the parasite Cyclospora cayetanensis, have been associated with consumption of various types of fresh produce. Although a method is in use for genotyping C. cayetanensis from clinical specimens, the very low abundance of C. cayetanensis in food and environmental samples presents a greater challenge. To complement epidemiological investigations, a molecular surveillance tool is needed for use in genetic linkage of food vehicles to cyclosporiasis illnesses, estimation of the scope of outbreaks or clusters of illness, and determination of geographical areas involved. We developed a targeted amplicon sequencing (TAS) assay that incorporates a further enrichment step to gain the requisite sensitivity for genotyping C. cayetanensis contaminating fresh produce samples. The TAS assay targets 52 loci, 49 of which are located in the nuclear genome, and encompasses 396 currently known SNP sites. The performance of the TAS assay was evaluated using lettuce, basil, cilantro, salad mix, and blackberries inoculated with C. cayetanensis oocysts. A minimum of 24 markers were haplotyped even at low contamination levels of 10 oocysts in 25 g leafy greens. The artificially contaminated fresh produce samples were included in a genetic distance analysis based on haplotype presence/absence with publicly available C. cayetanensis whole genome sequence assemblies. Oocysts from two different sources were used for inoculation, and samples receiving the same oocyst preparation clustered together, but separately from the other group, demonstrating the utility of the assay for genetically linking samples. Clinical fecal samples with low parasite loads were also successfully genotyped. This work represents a significant advance in the ability to genotype C. cayetanensis contaminating fresh produce along with greatly expanding the genomic diversity included for genetic clustering of clinical specimens.

Patterns of antiemetic medication use during pregnancy: A multi-country retrospective cohort study.

OBJECTIVE: To compare patterns in use of different antiemetics during pregnancy in Canada, the United Kingdom, and the United States, between 2002 and 2014. METHODS: We constructed population-based cohorts of pregnant women using administrative healthcare data from five Canadian provinces (Alberta, British Columbia, Manitoba, Ontario, and Saskatchewan), the Clinical Practice Research Datalink from the United Kingdom, and the IBM MarketScan Research Databases from the United States. We included pregnancies ending in live births, stillbirth, spontaneous abortion, or induced abortion. We determined maternal use of antiemetics from pharmacy claims in Canada and the United States and from prescriptions in the United Kingdom. RESULTS: The most common outcome of 3 848 734 included pregnancies (started 2002-2014) was live birth (66.7% of all pregnancies) followed by spontaneous abortion (20.2%). Use of antiemetics during pregnancy increased over time in all three countries. Canada had the highest prevalence of use of prescription antiemetics during pregnancy (17.7% of pregnancies overall, 13.2% of pregnancies in 2002, and 18.9% in 2014), followed by the United States (14.0% overall, 8.9% in 2007, and 18.1% in 2014), and the United Kingdom (5.0% overall, 4.2% in 2002, and 6.5% in 2014). Besides use of antiemetic drugs being considerably lower in the United Kingdom, the increase in its use over time was more modest. The most commonly used antiemetic was combination doxylamine/pyridoxine in Canada (95.2% of pregnancies treated with antiemetics), ondansetron in the United States (72.2%), and prochlorperazine in the United Kingdom (63.5%). CONCLUSIONS: In this large cohort study, we observed an overall increase in antiemetic use during pregnancy, and patterns of use varied across jurisdictions. Continued monitoring of antiemetic use and further research are warranted to better understand the reasons for differences in use of these medications and to assess their benefit-risk profile in this population.

DSIF modulates RNA polymerase II occupancy according to template G + C content.

The DSIF complex comprising the Supt4h and Supt5h transcription elongation proteins clamps RNA polymerase II (RNAPII) onto DNA templates, facilitating polymerase processivity. Lowering DSIF components can differentially decrease expression of alleles containing nucleotide repeat expansions, suggesting that RNAPII transit through repeat expansions is dependent on DSIF functions. To globally identify sequence features that affect dependence of the polymerase on DSIF in human cells, we used ultra-deep ChIP-seq analysis and RNA-seq to investigate and quantify the genome-wide effects of Supt4h loss on template occupancy and transcript production. Our results indicate that RNAPII dependence on Supt4h varies according to G + C content. Effects of DSIF knockdown were prominent during transcription of sequences high in G + C but minimal for sequences low in G + C and were particularly evident for G + C-rich segments of long genes. Reanalysis of previously published ChIP-seq data obtained from mouse cells showed similar effects of template G + C composition on Supt5h actions. Our evidence that DSIF dependency varies globally in different template regions according to template sequence composition suggests that G + C content may have a role in the selectivity of Supt4h knockdown and Supt5h knockdown during transcription of gene alleles containing expansions of G + C-rich repeats.

A comprehensive HPV-STI NGS assay for detection of 29 HPV types and 14 non-HPV sexually transmitted infections.

BACKGROUND: Sexually transmitted infections (STIs) are prevalent throughout the world and impose a significant burden on individual health and public health systems. Missed diagnosis and late treatment of STIs can lead to serious complications such as infertility and cervical cancer. Although sexually transmitted co-infections are common, most commercial assays target one or a few STIs. The HPV-STI ChapterDx Next Generation Sequencing (NGS) assay detects and quantifies 29 HPVs and 14 other STIs in a single-tube and single-step PCR reaction and can be applied to tens to thousands of samples in a single sequencing run. METHODS: A cohort of 274 samples, previously analyzed by conventional cytology/histology and Roche cobas HPV Test, were analyzed by ChapterDx HPV-STI NGS assay for detection of 43 HPV and STI. A set of 43 synthetic control DNA fragments for 43 HPV and STI were developed to evaluate the limit of detection, specificity, and sensitivity of ChapterDx HPV-STI NGS assay. RESULTS: The assay was evaluated in this study, and the limit of detection was 100% at 50 copies for all targets, and 100%, 96%, 88% at 20 copies for 34, 8, and 1 target, respectively. The performance of this assay has been compared to Roche cobas HPV test, showing an overall agreement of 97.5% for hr-HPV, and 98.5% for both, HPV16 and HPV18. The assay also detected all HPV-infected CIN2/3 with 100% agreement with Roche cobas HPV results. Moreover, several co-infections with non-HPV STIs, such as C. trachomatis, T. vaginalis, M. genitalium, and HSV2 were identified. CONCLUSIONS: The ChapterDx HPV-STI NGS assay is a user-friendly, easy to automate and cost-efficient assay, which provides accurate and comprehensive results for a wide spectrum of HPVs and STIs.

Comparison of Pregnancy Outcomes of Patients Treated With Ondansetron vs Alternative Antiemetic Medications in a Multinational, Population-Based Cohort.

Importance: Ondansetron is frequently used to treat nausea and vomiting during pregnancy. Although some studies reported important safety signals, few studies have been sufficiently large to assess rare pregnancy outcomes. Objective: To study the association between ondansetron exposure during pregnancy and the risks of spontaneous abortion, stillbirth, and major congenital malformations. Design, Setting, and Participants: This is a cohort study conducted in 3 countries, with a meta-analysis. Participants included women and girls aged 12 to 55 years who experienced spontaneous abortion, induced abortion, stillbirth, or live birth between April 2002 and March 2016, as recorded in administrative data from 5 Canadian provinces (British Columbia, Alberta, Saskatchewan, Manitoba, and Ontario), the US IBM MarketScan Research Databases, and the UK Clinical Practice Research Datalink. The statistical analysis was completed in October 2020. Exposures: Exposure to ondansetron during pregnancy was compared with exposure to other commonly used antiemetics to minimize confounding by indication. Main Outcomes and Measures: The primary outcome was fetal death, defined as either spontaneous abortion or stillbirth. Secondary outcomes were the 2 components of the primary outcome and major congenital malformations identified during the year after a live birth. Adjusted hazard ratios were estimated using Cox proportional hazards models with time-dependent drug exposures and were adjusted using high-dimensional propensity scores. For major congenital malformations, adjusted odds ratios were estimated from logistic models. Site-level results were pooled using random-effects meta-analysis. Sensitivity analyses considered second-line antiemetic exposure and exposure specifically during 4 to 10 weeks of gestation. Results: Data from 456 963 pregnancies were included in this study of fetal death (249 787 [54.7%] in Canada, 197 913 [43.3%] in the US, and 9263 [2.0%] in the UK; maternal age, ≤24 years, 93 201 patients [20.4%]; 25-29 years, 149 117 patients [32.6%]; 30-34 years, 142 442 patients [31.2%]; and ≥35 years, 72 203 patients [15.8%]). Fetal death occurred in 12 907 (7.9%) of 163 810 pregnancies exposed to ondansetron, and 17 476 (5.7%) of 306 766 pregnancies exposed to other antiemetics. The adjusted hazard ratios were 0.91 (95% CI, 0.67-1.23) for fetal death with time-dependent ondansetron exposure during pregnancy, 0.82 (95% CI, 0.64-1.04) for spontaneous abortion, and 0.97 (95% CI, 0.79-1.20) for stillbirth. For major congenital malformations, the estimated odds ratio was 1.06 (95% CI, 0.91-1.22). Results of sensitivity analyses were generally consistent with those of the primary analyses. Conclusions and Relevance: In this large, multicenter cohort study, there was no association between ondansetron exposure during pregnancy and increased risk of fetal death, spontaneous abortion, stillbirth, or major congenital malformations compared with exposure to other antiemetic drugs.

CTLA-4 expression by B-1a B cells is essential for immune tolerance.

CTLA-4 is an important regulator of T-cell function. Here, we report that expression of this immune-regulator in mouse B-1a cells has a critical function in maintaining self-tolerance by regulating these early-developing B cells that express a repertoire enriched for auto-reactivity. Selective deletion of CTLA-4 from B cells results in mice that spontaneously develop autoantibodies, T follicular helper (Tfh) cells and germinal centers (GCs) in the spleen, and autoimmune pathology later in life. This impaired immune homeostasis results from B-1a cell dysfunction upon loss of CTLA-4. Therefore, CTLA-4-deficient B-1a cells up-regulate epigenetic and transcriptional activation programs and show increased self-replenishment. These activated cells further internalize surface IgM, differentiate into antigen-presenting cells and, when reconstituted in normal IgH-allotype congenic recipient mice, induce GCs and Tfh cells expressing a highly selected repertoire. These findings show that CTLA-4 regulation of B-1a cells is a crucial immune-regulatory mechanism.

Estimated GFR and Incidence of Major Surgery: A Population-Based Cohort Study.

RATIONALE & OBJECTIVE: Kidney disease is associated with an increased risk for postoperative morbidity and mortality. However, the incidence of major surgery on a population level is unknown. We aimed to determine the incidence of major surgery by level of kidney function. STUDY DESIGN: Retrospective cohort study with entry from January 1, 2008, through December 31, 2009, and outcome surveillance from January 1, 2010, through December 31, 2016. SETTING & PARTICIPANTS: Population-based study using administrative health data from Alberta, Canada; adults with an outpatient serum creatinine measurement or receiving maintenance dialysis formed the study cohort. EXPOSURE: Participants were categorized into 6 estimated glomerular filtration rate (eGFR) categories: ≥60 (G1-G2), 45 to 59 (G3a), 30 to 44 (G3b), 15 to 29 (G4), and<15mL/min/1.73m2 with (G5D) and without (G5) dialysis. eGFR was examined as a time-varying exposure based on means of measurements within 3-month ascertainment periods throughout the study period. OUTCOME: Major surgery defined as surgery requiring admission to the hospital for at least 24 hours. ANALYTICAL APPROACH: Incidence rates (IRs) for overall major surgery were estimated using quasi-Poisson regression and adjusted for age, sex, income, location of residence, albuminuria, and Charlson comorbid conditions. Age- and sex-stratified IRs of 13 surgery subtypes were also estimated. RESULTS: 1,455,512 cohort participants were followed up for a median of 7.0 (IQR, 5.3) years, during which time 241,989 (16.6%) underwent a major surgery. Age and sex modified the relationship between eGFR and incidence of surgery. Men younger than 65 years receiving maintenance dialysis experienced the highest rates of major surgery, with an adjusted IR of 243.8 (95% CI, 179.8-330.6) per 1,000 person-years. There was a consistent trend of increasing surgery rates at lower eGFRs for most subtypes of surgery. LIMITATIONS: Outpatient preoperative serum creatinine measurement was necessary for inclusion and outpatient surgical procedures were not included. CONCLUSIONS: People with reduced eGFR have a significantly higher incidence of major surgery compared with those with normal eGFR, and age and sex modify this increased risk. This study informs our understanding of how surgical burden changes with differing levels of kidney function.

Association between change in physician remuneration and use of peritoneal dialysis: a population-based cohort analysis.

BACKGROUND: Health care payers are interested in policy-level interventions to increase peritoneal dialysis use in end-stage renal disease. We examined whether increases in physician remuneration for peritoneal dialysis were associated with greater peritoneal dialysis use. METHODS: We studied a cohort of patients in Alberta who started long-term dialysis with at least 90 days of preceding nephrologist care between Jan. 1, 2001, and Dec. 31, 2014. We compared peritoneal dialysis use 90 days after dialysis initiation in patients cared for by fee-for-service nephrologists and those cared for by salaried nephrologists before and after weekly peritoneal dialysis remuneration increased from $0 to $32 (fee change 1, Apr. 1, 2002), $49 to $71 (fee change 2, Apr. 1, 2007), and $71 to $135 (fee change 3, Apr. 1, 2009). Remuneration for peritoneal dialysis remained less than hemodialysis until fee change 3. We performed a patient-level differences-in-differences logistic regression, adjusted for demographic characteristics and comorbidities, as well as an unadjusted interrupted time-series analysis of monthly outcome data. RESULTS: Our cohort included 4262 patients. There was no statistical evidence of a difference in the adjusted differences-indifferences estimator following fee change 1 (0.89, 95% confidence interval [CI] 0.44-1.81), 2 (1.15, 95% CI 0.73-1.83), or 3 (1.52, 95% CI 0.96-2.40). There was no significant difference in the immediate change or the trend over time in peritoneal dialysis use between fee-for-service and salaried groups following any of the fee changes in the interrupted time-series analysis. INTERPRETATION: We identified no statistical evidence of an increase in peritoneal dialysis use following increased fee-for-service remuneration for peritoneal dialysis. It remains unclear what role, if any, physician payment plays in selection of dialysis modality.

Association of Specialist Physician Payment Model With Visit Frequency, Quality, and Costs of Care for People With Chronic Disease.

Importance: Specialist physicians are key members of chronic care management teams; to date, however, little is known about the association between specialist payment models and outcomes for patients with chronic diseases. Objective: To examine the association of payment model with visit frequency, quality of care, and costs for patients with chronic diseases seen by specialists. Design, Setting, and Participants: A retrospective cohort study using propensity-score matching in patients seen by a specialist physician was conducted between April 1, 2011, and September 31, 2014. The study was completed on March 31, 2015, and data analysis was conducted from June 2017 to February 2018 and finalized in August 2019. In a population-based design, 109 839 adults with diabetes or chronic kidney disease newly referred to specialists were included. Because patients seen by independent salary-based and fee-for-service (FFS) specialists were significantly different in observed baseline characteristics, patients were matched 1:1 on demographic, illness, and physician characteristics. Exposures: Specialist physician payment model (salary-based or FFS). Main Outcomes and Measures: Follow-up outpatient visits, guideline-recommended care delivery, adverse events, and costs. Results: A total of 90 605 patients received care from FFS physicians and 19 234 received care from salary-based physicians. Before matching, the patients seen by salary-based physicians had more advanced chronic kidney disease (2630 of 14 414 [18.2%] vs 6627 of 54 489 [12.2%]), and a higher proportion had 5 or more comorbidities (5989 of 19 234 [31.3%] vs 23 326 of 90 605 [25.7%]). Propensity-score matching resulted in a cohort of 31 898 patients (15 949 FFS, 15 949 salary-based) seeing 489 specialists. In the matched cohort, patients were similar (mean [SD] age, 61.3 [18.2] years; 17 632 women [55.3%]; 29 251 residing in urban settings [91.7%]). Patients seen by salary-based specialists had a higher follow-up visit rate compared with those seen by FFS specialists (1.74 visits; 95% CI, 1.58-1.92 visits vs 1.54 visits; 95% CI, 1.41-1.68 visits), but the difference was not significant (rate ratio, 1.13; 95% CI, 0.99-1.28; P = .06). There was no statistical difference in guideline-recommended care delivery, hospital or emergency department visits for ambulatory care-sensitive conditions, or costs between patients seeing FFS and salary-based specialists. The median association of physician clustering with health care use and quality outcomes was consistently greater than the association with the physician payment, suggesting variation between physicians (eg, median rate ratio for follow-up outpatient visit rate was 1.74, which is greater than the rate ratio of 1.13). Conclusions and Relevance: Specialist physician payment does not appear to be associated with variation in visits, quality, and costs for outpatients with chronic diseases; however, there is variation in outcomes between physicians. This finding suggests the need to consider other strategies to reduce physician variation to improve the value of care and outcomes for people with chronic diseases.

Genome-wide effects of social status on DNA methylation in the brain of a cichlid fish, Astatotilapia burtoni.

BACKGROUND: Successful social behavior requires real-time integration of information about the environment, internal physiology, and past experience. The molecular substrates of this integration are poorly understood, but likely modulate neural plasticity and gene regulation. In the cichlid fish species Astatotilapia burtoni, male social status can shift rapidly depending on the environment, causing fast behavioral modifications and a cascade of changes in gene transcription, the brain, and the reproductive system. These changes can be permanent but are also reversible, implying the involvement of a robust but flexible mechanism that regulates plasticity based on internal and external conditions. One candidate mechanism is DNA methylation, which has been linked to social behavior in many species, including A. burtoni. But, the extent of its effects after A. burtoni social change were previously unknown. RESULTS: We performed the first genome-wide search for DNA methylation patterns associated with social status in the brains of male A. burtoni, identifying hundreds of Differentially Methylated genomic Regions (DMRs) in dominant versus non-dominant fish. Most DMRs were inside genes supporting neural development, synapse function, and other processes relevant to neural plasticity, and DMRs could affect gene expression in multiple ways. DMR genes were more likely to be transcription factors, have a duplicate elsewhere in the genome, have an anti-sense lncRNA, and have more splice variants than other genes. Dozens of genes had multiple DMRs that were often seemingly positioned to regulate specific splice variants. CONCLUSIONS: Our results revealed genome-wide effects of A. burtoni social status on DNA methylation in the brain and strongly suggest a role for methylation in modulating plasticity across multiple biological levels. They also suggest many novel hypotheses to address in mechanistic follow-up studies, and will be a rich resource for identifying the relationships between behavioral, neural, and transcriptional plasticity in the context of social status.

Association of Mental Health Disorders With Health Care Utilization and Costs Among Adults With Chronic Disease.

Importance: A population-based study using validated algorithms to estimate the costs of treating people with chronic disease with and without mental health disorders is needed. Objective: To determine the association of mental health disorders with health care costs among people with chronic diseases. Design, Setting, and Participants: This population-based cohort study in the Canadian province of Alberta collected data from April 1, 2012, to March 31, 2015, among 991 445 adults 18 years and older with a chronic disease (ie, asthma, congestive heart failure, myocardial infarction, diabetes, epilepsy, hypertension, chronic pulmonary disease, or chronic kidney disease). Data analysis was conducted from October 2017 to August 2018. Exposures: Mental health disorder (ie, depression, schizophrenia, alcohol use disorder, or drug use disorder). Main Outcomes and Measures: Resource use, mean total unadjusted and adjusted 3-year health care costs, and mean total unadjusted 3-year costs for hospitalization and emergency department visits for ambulatory care-sensitive conditions. Results: Among 991 445 participants, 156 296 (15.8%) had a mental health disorder. Those with no mental health disorder were older (mean [SD] age, 58.1 [17.6] years vs 55.4 [17.0] years; P < .001) and less likely to be women (50.4% [95% CI, 50.3%-50.5%] vs 57.7% [95% CI, 57.4%-58.0%]; P < .001) than those with mental health disorders. For those with a mental health disorder, mean total 3-year adjusted costs were $38 250 (95% CI, $36 476-$39 935), and for those without a mental health disorder, mean total 3-year adjusted costs were $22 280 (95% CI, $21 780-$22 760). Having a mental health disorder was associated with significantly higher resource use, including hospitalization and emergency department visit rates, length of stay, and hospitalization for ambulatory care-sensitive conditions. Higher resource use by patients with mental health disorders was not associated with health care presentations owing to chronic diseases compared with patients without a mental health disorder (chronic disease hospitalization rate per 1000 patient days, 0.11 [95% CI, 0.11-0.12] vs 0.06 [95% CI, 0.06-0.06]; P < .001; overall hospitalization rate per 1000 patient days, 0.88 [95% CI, 0.87-0.88] vs 0.43 [95% CI, 0.43-0.43]; P < .001). Conclusions and Relevance: This study suggests that mental health disorders are associated with substantially higher resource utilization and health care costs among patients with chronic diseases. These findings have clinical and health policy implications.

The association between payment model and specialist physicians' selection of patients with diabetes: a descriptive study.

BACKGROUND: As the number of people with chronic diseases increases, understanding the impact of payment model on the types of patients seen by specialists has implications for improving the quality and value of care. We sought to determine if there is an association between specialist physician payment model and the types of patients seen. METHODS: In this descriptive study, we used administrative data to compare demographic characteristics, illness severity and visit indication of patients with diabetes seen by fee-for-service and salary-based internal medicine and diabetes specialists in Calgary and Edmonton between April 2011 and September 2014. The study cohort included all newly referred adults with diabetes (no appointment with a specialist in prior 4 yr). Diabetes was identified using a validated algorithm that excludes gestational diabetes. RESULTS: Patients managed by salary-based physicians (n = 2736) were sicker than those managed by fee-for-service physicians (n = 21 218). Patients managed by salary-based specialists were more likely to have 5 or more comorbidities (23.0% [n = 628] v. 18.1% [n = 3843]) and to have been admitted to hospital or seen in an emergency department for an ambulatory care sensitive condition in the year before their index visit, probably reflecting poorer disease control or barriers to optimal outpatient care. A higher proportion of visits to salary-based physicians were for appropriate indications (65.2% [n = 744] v. 55.6% [n = 5553]; risk ratio 1.17, 95% confidence interval 1.09-1.27). INTERPRETATION: Salary-based specialists were more likely to see patients with a clear indication for a specialist visit, while fee-for-service specialists were more likely to see healthier patients. Future research is needed to determine if the differences in types of patients are attributable to payment model or other provider- or system-level factors.

Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression.

The senescence of mammalian cells is characterized by a proliferative arrest in response to stress and the expression of an inflammatory phenotype. Here we show that histone H2A.J, a poorly studied H2A variant found only in mammals, accumulates in human fibroblasts in senescence with persistent DNA damage. H2A.J also accumulates in mice with aging in a tissue-specific manner and in human skin. Knock-down of H2A.J inhibits the expression of inflammatory genes that contribute to the senescent-associated secretory phenotype (SASP), and over expression of H2A.J increases the expression of some of these genes in proliferating cells. H2A.J accumulation may thus promote the signalling of senescent cells to the immune system, and it may contribute to chronic inflammation and the development of aging-associated diseases.

Warfarin Initiation, Atrial Fibrillation, and Kidney Function: Comparative Effectiveness and Safety of Warfarin in Older Adults With Newly Diagnosed Atrial Fibrillation.

BACKGROUND: The effectiveness and safety of warfarin use among patients with atrial fibrillation (AF) and reduced kidney function are uncertain. STUDY DESIGN: Community-based retrospective cohort study (May 1, 2003, to March 31, 2012) using province-wide laboratory and administrative data in Alberta, Canada. SETTING & PARTICIPANTS: 14,892 adults 66 years or older with new AF and a measurement of kidney function. Long-term dialysis patients or kidney transplant recipients were excluded. PREDICTOR: Propensity scores were used to construct a matched-pairs cohort of patients with AF who did and did not have a warfarin prescription within a 60-day period surrounding their AF diagnosis. OUTCOMES: Within 1 year of initiating warfarin therapy (or the matched date for nonusers): (1) the composite of all-cause death, ischemic stroke, or transient ischemic attack (also assessed as separate end points) and (2) first hospitalization or emergency department visit for a major bleeding episode defined as an intracranial, upper or lower gastrointestinal, or other bleeding. MEASUREMENTS: Baseline glomerular filtration rate (GFR) was estimated using the CKD-EPI creatinine equation. Patients were matched within estimated GFR (eGFR) categories: ≥90, 60 to 89, 45 to 59, 30 to 44, and <30mL/min/1.73m2. Information for baseline characteristics (sociodemographics, comorbid conditions, and prescription drug use) was obtained. RESULTS: Across eGFR categories, warfarin therapy initiation was associated with lower risk for the composite outcome compared to nonuse (adjusted HRs [95% CI] for eGFR categories ≥ 90, 60-89, 45-59, 30-44, and <30mL/min/1.73m2: 0.59 [0.35-1.01], 0.61 [0.54-0.70], 0.55 [0.47-0.65], 0.54 [0.44-0.67], and 0.64 [0.47-0.87] mL/min/1.73m2, respectively). Compared to nonuse, warfarin therapy was not associated with higher risk for major bleeding except for those with eGFRs of 60 to 89mL/min/1.73m2 (HR, 1.36; 95% CI, 1.13-1.64). LIMITATIONS: Selection bias. CONCLUSIONS: Among older adults with AF, warfarin therapy initiation was associated with a significantly lower 1-year risk for the composite outcome across all strata of kidney function. The risk for major bleeding associated with warfarin use was increased only among those with eGFRs of 60 to 89mL/min/1.73m2.

Lifetime risk of diabetes among First Nations and non-First Nations people.

BACKGROUND: Lifetime risk is a relatively straightforward measure used to communicate disease burden, representing the cumulative risk of an outcome during the remainder of an individual's life starting from a disease-free index age. We estimated the lifetime risk of diabetes among men and women in both First Nations and non-First Nations populations using a cohort of adults in a single Canadian province. METHODS: We used a population-based cohort consisting of Alberta residents from 1997 to 2008 who were free of diabetes at cohort entry to estimate the lifetime risk of diabetes among First Nations and non-First Nations people. We calculated age-specific incidence rates with the person-year method in 5-year bands. We estimated the sex- and index-age-specific lifetime risk of incident diabetes, after adjusting for the competing risk of death. RESULTS: The cohort included 70 631 First Nations and 2 732 214 non-First Nations people aged 18 years or older. The lifetime risk of diabetes at 20 years of age was 75.6% among men and 87.3% among women in the First Nations group, as compared with 55.6% among men and 46.5% among women in the non-First Nations group. The risk was higher among First Nations people than among non-First Nations people for all index ages and for both sexes. Among non-First Nations people, men had a higher lifetime risk of diabetes than women across all index ages. In contrast, among First Nations people, women had a higher lifetime risk than men across all index ages. INTERPRETATION: About 8 in 10 First Nations people and about 5 in 10 non-First Nations people of young age will develop diabetes in their remaining lifetime. These population-based estimates may help health care planners and decision-makers set priorities and increase public awareness and interest in the prevention of diabetes.

The association between kidney function and major bleeding in older adults with atrial fibrillation starting warfarin treatment: population based observational study.

OBJECTIVE: To determine rates of major bleeding by level of kidney function for older adults with atrial fibrillation starting warfarin. DESIGN: Retrospective cohort study. SETTING: Community based, using province wide laboratory and administrative data in Alberta, Canada. PARTICIPANTS: 12,403 adults aged 66 years or more, with atrial fibrillation who started warfarin treatment between 1 May 2003 and 31 March 2010 and had a measure of kidney function at baseline. Kidney function was estimated using the Chronic Kidney Disease Epidemiology Collaboration equation and participants were categorised based on estimated glomerular filtration rate (eGFR): ≥ 90, 60-89, 45-59, 30-44, 15-29, <15 mL/min/1.73 m(2). We excluded participants with end stage renal disease (dialysis or renal transplant) at baseline. MAIN OUTCOME MEASURES: Admission to hospital or visit to an emergency department for major bleeding (intracranial, upper and lower gastrointestinal, or other). RESULTS: Of 12,403 participants, 45% had an eGFR <60 mL/min/1.73 m(2). Overall, 1443 (11.6%) experienced a major bleeding episode over a median follow-up of 2.1 (interquartile range: 1.0-3.8) years. During the first 30 days of warfarin treatment, unadjusted and adjusted rates of major bleeding were higher at lower eGFR (P for trend <0.001 and 0.001, respectively). Adjusted bleeding rates per 100 person years were 63.4 (95% confidence interval 24.9 to 161.6) in participants with eGFR <15 mL/min/1.73 m(2) compared with 6.1 (1.9 to 19.4) among those with eGFR >90 mL/min/1.73 m(2) (adjusted incidence rate ratio 10.3, 95% confidence interval 2.3 to 45.5). Similar associations were observed at more than 30 days after starting warfarin, although the magnitude of the increase in rates across eGFR categories was attenuated. Across all eGFR categories, adjusted rates of major bleeding were consistently higher during the first 30 days of warfarin treatment compared with the remainder of follow-up. Increases in major bleeding rates were largely due to gastrointestinal bleeding (3.5-fold greater in eGFR <15 mL/min/1.73 m(2) compared with ≥ 90 mL/min/1.73 m(2)). Intracranial bleeding was not increased with worsening kidney function. CONCLUSIONS: Reduced kidney function was associated with an increased risk of major bleeding among older adults with atrial fibrillation starting warfarin; excess risks from reduced eGFR were most pronounced during the first 30 days of treatment. Our results support the need for careful consideration of the bleeding risk relative to kidney function when assessing the risk-benefit ratio of warfarin treatment in people with chronic kidney disease and atrial fibrillation, particularly in the first 30 days of treatment.

Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders.

The prevalence of autism spectrum disorders (ASDs) is rapidly growing, yet its molecular basis is poorly understood. We used a systems approach in which ASD candidate genes were mapped onto the ubiquitous human protein complexes and the resulting complexes were characterized. The studies revealed the role of histone deacetylases (HDAC1/2) in regulating the expression of ASD orthologs in the embryonic mouse brain. Proteome-wide screens for the co-complexed subunits with HDAC1 and six other key ASD proteins in neuronal cells revealed a protein interaction network, which displayed preferential expression in fetal brain development, exhibited increased deleterious mutations in ASD cases, and were strongly regulated by FMRP and MECP2 causal for Fragile X and Rett syndromes, respectively. Overall, our study reveals molecular components in ASD, suggests a shared mechanism between the syndromic and idiopathic forms of ASDs, and provides a systems framework for analyzing complex human diseases.

A comparative encyclopedia of DNA elements in the mouse genome.

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.

Principles of regulatory information conservation between mouse and human.

To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human-mouse erythroid progenitor, lymphoblast and embryonic stem-cell lines. By combining the genome-wide transcription factor occupancy repertoires, associated epigenetic signals, and co-association patterns, here we deduce several evolutionary principles of gene regulatory features operating since the mouse and human lineages diverged. The genomic distribution profiles, primary binding motifs, chromatin states, and DNA methylation preferences are well conserved for TF-occupied sequences. However, the extent to which orthologous DNA segments are bound by orthologous TFs varies both among TFs and with genomic location: binding at promoters is more highly conserved than binding at distal elements. Notably, occupancy-conserved TF-occupied sequences tend to be pleiotropic; they function in several tissues and also co-associate with many TFs. Single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences.

Insect-induced tree mortality of boreal forests in eastern Canada under a changing climate.

Forest insects are major disturbances that induce tree mortality in eastern coniferous (or fir-spruce) forests in eastern North America. The spruce budworm (SBW) (Choristoneura fumiferana [Clemens]) is the most devastating insect causing tree mortality. However, the relative importance of insect-caused mortality versus tree mortality caused by other agents and how this relationship will change with climate change is not known. Based on permanent sample plots across eastern Canada, we combined a logistic model with a negative model to estimate tree mortality. The results showed that tree mortality increased mainly due to forest insects. The mean difference in annual tree mortality between plots disturbed by insects and those without insect disturbance was 0.0680 per year (P < 0.0001, T-test), and the carbon sink loss was about 2.87t C ha(-1) year(-1) larger than in natural forests. We also found that annual tree mortality increased significantly with the annual climate moisture index (CMI) and decreased significantly with annual minimum temperature (T min), annual mean temperature (T mean) and the number of degree days below 0°C (DD0), which was inconsistent with previous studies (Adams et al. 2009; van Mantgem et al. 2009; Allen et al. 2010). Furthermore, the results for the trends in the magnitude of forest insect outbreaks were consistent with those of climate factors for annual tree mortality. Our results demonstrate that forest insects are the dominant cause of the tree mortality in eastern Canada but that tree mortality induced by insect outbreaks will decrease in eastern Canada under warming climate.