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1.
JAMA Netw Open ; 7(4): e241429, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38598241

ABSTRACT

Importance: Equity-driven citywide park redesign and renovation, such as the Community Parks Initiative (CPI), has the potential to increase park use and opportunities for physical activity in underserved communities. Objective: To evaluate changes in patterns of park use following park redesign and renovation in low-income New York City (NYC) neighborhoods. Design, Setting, and Participants: The Physical Activity and Redesigned Community Spaces study was a prospective quality improvement preintervention-postintervention study design with matched control parks. Thirty-three intervention and 21 control neighborhood parks were selected based on specific criteria related to poverty rates, population growth, and population density in park neighborhoods and not having received more than $250 000 in investment in the past 2 decades. Data were collected at baseline (prerenovation) and 2 follow-up points (3 months and 1 year post renovation) between June 5 and December 4 from 2016 to 2022. Participants were individuals observed as users of study parks. Intervention: The CPI, which involved the redesign and renovation of neighborhood parks by the municipal government of New York City. Main Outcomes and Measures: Main outcomes encompassed park use and physical activity levels assessed using the well-validated System for Observing Play and Recreation in Communities. Park use was quantified by total number of park users, categorized by age group (≤20 years vs ≥21 years), sex, and physical activity level (sitting or standing vs walking or vigorous activity). Changes in outcomes between groups were compared via the generalized estimation equation. Results: A total of 28 322 park users were observed across 1458 scans. At baseline, 6343 of 10 633 users (59.7%) were 20 years or younger, 4927 of 10 632 (46.3%) were female and 5705 (53.7%) were male, and 4641 of 10 605 (43.8%) were sitting or standing. Intervention parks showed more net park users compared with control parks from baseline to the final follow-up (difference-in-difference relative rate ratio, 1.69 [95% CI, 1.22-2.35] users/scan; P = .002). The association was driven by a significant increase in adult users at intervention parks and overall decrease in all users at control parks. Park users engaging in sitting or standing at intervention parks increased (difference, 4.68 [95% CI, 1.71-7.62] users/scan; P = .002) and park users engaging in walking or vigorous physical activity at control parks decreased (difference, -7.30 [95% CI, -10.80 to -4.26] users/scan; P < .001) over time. Conclusions and Relevance: In this quality improvement study, park redesign and renovation were positively associated with park use in low-income neighborhoods. However, park renovations may need to be accompanied by other programmatic strategies to increase physical activity.


Subject(s)
Exercise , Investments , Adult , Humans , Female , Male , Young Adult , New York City , Prospective Studies , Local Government
2.
J Arthroplasty ; 39(3): 819-824.e1, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37757982

ABSTRACT

BACKGROUND: The COVID-19 pandemic has been associated with increased risks of venous thromboembolism (VTE), including deep vein thrombosis (DVT) and pulmonary embolism (PE). However, there is limited literature investigating prothrombotic states and complications after total hip arthroplasty (THA) and total knee arthroplasty (TKA). We investigated (1) trends in VTE, PE, and DVT rates post-THA and TKA from 2016 to 2019 compared to 2020 to 2021 and (2) associations between prior COVID-19 diagnosis and VTE, PE, and DVT. METHODS: A national dataset was queried for elective THA and TKA cases from 2016 to 2021. We first assessed trends in 90-day VTE prevalence between 2016 to 2019 and 2020 to 2021. Second, we investigated associations between previous COVID-19 and 90-day VTE with regression models. RESULTS: From 2016 to 2021, a total of 2,422,051 cases had an annual decreasing VTE prevalence from 2.2 to 1.9% (THA) and 2.5 to 2.2% (TKA). This was evident for both PE and DVT (all trend tests P < .001). After adjusting for covariates (including vaccination status), prior COVID-19 was associated with significantly increased odds of developing VTE in TKA patients (odds ratio 1.2, 95% confidence interval 1.1 to 1.4, P = .007), but not DVT or PE (P > .05). There were no significant associations between prior COVID-19 and VTE, DVT, or PE after THA (P > .05). CONCLUSIONS: Our study suggests that a previous diagnosis of COVID-19 is associated with increased odds of VTE, but not DVT or PE, in TKA patients. Ongoing data monitoring is needed given our effect estimates, emerging COVID-19 variants, and evolving vaccination rates.


Subject(s)
Arthroplasty, Replacement, Hip , Arthroplasty, Replacement, Knee , COVID-19 , Pulmonary Embolism , Venous Thromboembolism , Humans , Venous Thromboembolism/epidemiology , Venous Thromboembolism/etiology , COVID-19 Testing , Pandemics , COVID-19/complications , COVID-19/epidemiology , SARS-CoV-2 , Pulmonary Embolism/epidemiology , Pulmonary Embolism/etiology , Arthroplasty, Replacement, Knee/adverse effects , Arthroplasty, Replacement, Hip/adverse effects , Anticoagulants , Risk Factors
3.
BMC Public Health ; 23(1): 2472, 2023 12 11.
Article in English | MEDLINE | ID: mdl-38082378

ABSTRACT

BACKGROUND: Evidence of the effects of the built environment on children has mainly focused on disease outcomes; however, quality of life (QoL) has gained increasing attention as an important health and policy endpoint itself. Research on built environment effects on children's QoL could inform public health programs and urban planning and design. OBJECTIVE: We aimed to review and synthesize the evidence of the relationship between built environment features and children's QoL. METHODS: Five research databases were searched for quantitative peer-reviewed studies on children between 2 and 18 years, published in English or German between January 2010 and August 2023. Only primary research was considered. Included studies (n = 17) were coded and methodologically assessed with the Joanna Briggs Critical Appraisal Checklists, and relevant data were extracted, analyzed, and synthesized, using the following built environment framework: (1) neighborhood green and blue space, (2) neighborhood infrastructure, and (3) neighborhood perception. RESULTS: Green space was positively associated with children's QoL. Infrastructure yielded inconclusive results across all measured aspects. Overall neighborhood satisfaction was positively correlated with higher QoL but results on perceived environmental safety were mixed. CONCLUSIONS: Most studies are correlational, making it difficult to infer causality. While the positive findings of green space on QoL are consistent, specific features of the built environment show inconsistent results. Overall perception of the built environment, such as neighborhood satisfaction, also shows more robust results compared to perceptions of specific features of the built environment. Due to the heterogeneity of both built environment and QoL measures, consistent measures of both concepts will help advance this area of research.


Subject(s)
Environment Design , Quality of Life , Child , Humans , Built Environment , Residence Characteristics , Policy
4.
J Am Acad Orthop Surg ; 31(24): 1228-1235, 2023 Dec 15.
Article in English | MEDLINE | ID: mdl-37831947

ABSTRACT

INTRODUCTION: Despite a rapid increase in utilization of reverse total shoulder arthroplasty (rTSA), volume-outcome studies focusing on surgeon volume are lacking. Surgeon-specific volume-outcome studies may inform policymakers and provide insight into learning curves and measures of efficiency with greater case volume. METHODS: This retrospective cohort study with longitudinal data included all rTSA cases as recorded in the Centers for Medicare & Medicaid Services Limited Data Set (2016 to 2018). The main effect was surgeon volume; this was categorized using two measures of surgeon volume: (1) rTSA case volume and (2) rTSA + TSA case volume. Volume cutoff values were calculated by applying a stratum-specific likelihood ratio analysis. RESULTS: Among 90,318 rTSA cases performed by 7,097 surgeons, we found a mean annual rTSA surgeon volume of 6 ± 10 and a mean rTSA + TSA volume of 9 ± 14. Regression models using surgeon-specific rTSA volume revealed that surgery from low (<29 cases) compared with medium (29 to 96 cases) rTSA-volume surgeons was associated with a significantly higher 90-day all-cause readmission (odds ratio [OR], 1.17; confidence interval [CI], 1.10 to 1.25; P < 0.0001), higher 90-day readmission rates because of an infection (OR, 1.46; CI, 1.16 to 1.83; P = 0.0013) or dislocation (OR, 1.43; CI, 1.19 to 1.72; P = 0.0001), increased 90-day postoperative cost (+11.3% CI, 4.2% to 19.0%; P = 0.0016), and a higher transfusion rate (OR, 2.06; CI, 1.70 to 2.50; P < 0.0001). Similar patterns existed when using categorizations based on rTSA + TSA case volume. CONCLUSION: Surgeon-specific volume-outcome relationships exist in this rTSA cohort, and we were able to identify thresholds that may identify low and medium/high volume surgeons. Observed volume-outcome relationships were independent of the definition of surgeon volume applied: either by focusing on the number of rTSAs performed per surgeon or anatomic TSAs performed. LEVEL OF EVIDENCE: III.


Subject(s)
Arthroplasty, Replacement, Shoulder , Shoulder Joint , Surgeons , Aged , Humans , United States , Retrospective Studies , Treatment Outcome , Medicare , Shoulder Joint/surgery , Range of Motion, Articular
5.
J Arthroplasty ; 38(12): 2634-2637, 2023 12.
Article in English | MEDLINE | ID: mdl-37315633

ABSTRACT

BACKGROUND: Osteonecrosis of the femoral head is a common indication for total hip arthroplasty (THA). It is unclear to what extent the COVID-19 pandemic has impacted its incidence. Theoretically, the combination of microvascular thromboses and corticosteroid use in patients who have COVID-19 may increase the risk of osteonecrosis. We aimed to (1) assess recent osteonecrosis trends and (2) investigate if a history of COVID-19 diagnosis is associated with osteonecrosis. METHODS: This retrospective cohort study utilized a large national database between 2016 and 2021. Osteonecrosis incidence in 2016 to 2019 was compared to 2020 to 2021. Secondly, utilizing a cohort from April 2020 through December 2021, we investigated whether a prior COVID-19 diagnosis was associated with osteonecrosis. For both comparisons, Chi-square tests were applied. RESULTS: Among 1,127,796 THAs performed between 2016 and 2021, we found an osteonecrosis incidence of 1.6% (n = 5,812) in 2020 to 2021 compared to 1.4% (n = 10,974) in 2016 to 2019; P < .0001. Furthermore, using April 2020 to December 2021 data from 248,183 THAs, we found that osteonecrosis was more common among those who had a history of COVID-19 (3.9%; 130 of 3,313) compared to patients who had no COVID-19 history (3.0%; 7,266 of 244,870); P = .001). CONCLUSION: Osteonecrosis incidence was higher in 2020 to 2021 compared to previous years and a previous COVID-19 diagnosis was associated with a greater likelihood of osteonecrosis. These findings suggest a role of the COVID-19 pandemic on an increased osteonecrosis incidence. Continued monitoring is necessary to fully understand the impact of the COVID-19 pandemic on THA care and outcomes.


Subject(s)
Arthroplasty, Replacement, Hip , COVID-19 , Femur Head Necrosis , Osteonecrosis , Humans , Aged , Arthroplasty, Replacement, Hip/adverse effects , Retrospective Studies , COVID-19 Testing , Pandemics , COVID-19/epidemiology , Osteonecrosis/epidemiology , Osteonecrosis/etiology , Treatment Outcome , Femur Head Necrosis/epidemiology , Femur Head Necrosis/etiology , Femur Head Necrosis/surgery
6.
Res Sq ; 2023 Apr 25.
Article in English | MEDLINE | ID: mdl-37163113

ABSTRACT

Background: Evidence of the effects of the built environment on children has mainly focused on disease outcomes; however, quality of life (QoL) has gained increasing attention as an important health and policy endpoint itself. Research on built environment effects on children's QoL could inform public health programs and urban planning and design. Objective: We aimed to review and synthesize the evidence of the relationship between built environment features and children's QoL. Methods: Five research databases were searched for quantitative peer-reviewed studies on children between 2-18 years, published in English or German between 2010-2021. Only primary research was considered. Included studies (n=17) were coded and methodologically assessed with the Joanna Briggs Critical Appraisal Checklists, and relevant data were extracted, analyzed, and synthesized, using the following built environment thematic framework: 1) neighborhood natural environment, 2) neighborhood infrastructure, and 3) neighborhood perception. Results: Green space was positively associated with children's QoL. Infrastructure yielded inconclusive results across all measured aspects. Overall neighborhood satisfaction was positively correlated with higher QoL but results on perceived environmental safety were mixed. Conclusions: Most studies are correlational, making it difficult to infer causality. While the positive findings of green space on QoL are consistent, specific features of the built environment show inconsistent results. Overall perception of the built environment, such as neighborhood satisfaction, also shows more robust results compared to perceptions of specific features of the built environment. Due to the heterogeneity of both built environment and QoL measures, consistent definitions of both concepts will help advance this area of research.

7.
Front Public Health ; 11: 1038288, 2023.
Article in English | MEDLINE | ID: mdl-36761118

ABSTRACT

Introduction: The literature is limited on the impact of neighborhood parks on quality of life (QoL) and the mechanism linking them. Methods: In this paper, we applied the structural equation model to data from a cross-sectional sample of 650 participants in low-income communities of New York City, we examined the associations of neighborhood park use vs. park perception and QoL, and whether these associations were mediated through self-reported perceived stress. We also examined whether park use mediated the relationship between park perception and QoL. Results: We found that park use had a significant but weak association with QoL (standardized ß = 0.08, 95% confidence interval (CI): 0.02, 0.15, p = 0.02), but this relationship was not mediated by self-reported stress. Park perception was more strongly associated with QoL than park use (standardized ß = 0.23, 95% CI: 0.16, 0.30, p < 0.01), and this was partly mediated by self-reported stress (indirect effect- standardized ß = 0.08, 95% CI: 0.03, 0.13, p < 0.01) and, to a lesser extent, by park use (indirect effect- standardized ß = 0.01, 95% CI: 0.00, 0.02, p = 0.01). Discussion: Having well-perceived parks appears to be an important factor for QoL independent of park use, suggesting that quality parks may benefit everyone in a community beyond park users. This strengthens the argument in favor of increasing park investment as a strategy to improve population wellbeing.


Subject(s)
Exercise , Quality of Life , Humans , Latent Class Analysis , Cross-Sectional Studies , Parks, Recreational , Perception
8.
BMC Public Health ; 23(1): 127, 2023 01 18.
Article in English | MEDLINE | ID: mdl-36653809

ABSTRACT

BACKGROUND: Measures of the built environment such as neighborhood walkability have been associated with health behaviors such as physical activity, the lack of which in turn may contribute to the development of diseases such as obesity, diabetes, cardiovascular disease, and cancer. However, limited research has examined these measures in association with health-related quality of life (HR-QoL), particularly in minoritized populations. We examined the relationship between perceived neighborhood environment and HR-QoL in a sample of mostly Black and Latino residents in New York City (NYC). METHODS: This study utilized the baseline survey data from the Physical Activity and Redesigned Community Spaces (PARCS) Study among 1252 residents [34.6% Black, 54.1% Latino, 80.1% female, mean(±SD) age = 38.8 ± 12.5) in 54 park neighborhoods in NYC. Perceived built environment was measured using Neighborhood Environment and Walkability Survey, and mental and physical HR-QoL was estimated using Short Form (SF)-12. Using factor analysis, we identified two subscales of neighborhood walkability: enablers (e.g., trails, sidewalks, esthetics) vs. barriers (e.g., high crime and traffic). In addition, we included a third subscale on neighborhood satisfaction. Generalized Estimating Equation models adjusted for demographics and BMI and accounted for the clustering effect within neighborhood. Multiple imputation was used to account for missing data. RESULTS: Mental HR-QoL was associated with barriers of walkability (ß ± SE = - 1.63 ± 0.55, p < 0.01) and neighborhood satisfaction (ß ± SE = 1.55 ± 0.66, p = 0.02), after adjusting for covariates. Physical HR-QoL was associated with only barriers of walkability (ß ± SE = - 1.13 ± 0.57, p < 0.05). CONCLUSIONS: Among NYC residents living in minoritized neighborhoods, mitigating negative aspects of the neighborhood environment may be more crucial than adding positive features in terms of HR-QoL. Our study points to the need to investigate further the role of the built environment in urban, minoritized communities.


Subject(s)
Quality of Life , Walking , Adult , Female , Humans , Male , Middle Aged , Environment Design , Hispanic or Latino , Neighborhood Characteristics , New York City/epidemiology , Residence Characteristics , Black or African American
9.
J Infect Public Health ; 15(4): 460-465, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35249842

ABSTRACT

BACKGROUND: Mask use is a cost-effective measure to decrease COVID-19 transmission. Mask mandates intend to increase mask compliance but are often ambiguous when it comes to public outdoor spaces. METHODS: We used a field audit study to examine mask use in New York City neighborhood parks during COVID-19. 1453 park visitors were observed in 13 parks during July-August 2020 using a modified and validated park use audit tool (System for Observing Play and Recreation in Communities) that included items on general and proper mask use (i.e., mask covering both nose and mouth). Generalized estimating equation regression was used to determine the association between proper mask use and demographic (sex and age) and behavioral (physical and social activity) variables, while adjusting for community-level covariates. RESULTS: Overall, 39.0% of park visitors used masks (24.4% properly, 14.6% improperly). Females (p = 0.023), adults (p = 0.025), and seniors (p = 0.006) showed higher rates of proper mask use compared to males and younger visitors. Physical and social activity were not significantly associated with proper mask use. CONCLUSION: There is a need for improved messaging regarding the proper use of masks among males and younger people. This is particularly important for future surges of new COVID-19 variants or other public health crises similar to COVID-19. Future research should focus on developing and evaluating targeted public health messages regarding mask use.


Subject(s)
COVID-19 , Adult , Female , Humans , Male , New York City/epidemiology , Pandemics , SARS-CoV-2
10.
J Racial Ethn Health Disparities ; 9(4): 1454-1463, 2022 08.
Article in English | MEDLINE | ID: mdl-34152587

ABSTRACT

Hispanics in the USA, particularly those of Caribbean descent, experience high levels of diet-related diseases and dietary risk factors. Restaurants are an increasingly important yet understudied source of food and may present opportunities to positively influence urban food environments. We sought to explore food environments further, by examining the association between neighborhood characteristics and restaurant consumer nutrition environments within New York City's Hispanic Caribbean (HC) restaurant environments. We applied an adapted version of the Nutrition Environment Measurements Survey for Restaurants (NEMS-R) to evaluate a random sample of HC restaurants (n=89). NEMS-HCR scores (continuous and categorized as low, medium, and high based on data distribution) were examined against area sociodemographic characteristics using bivariate and logistic regression analysis. HC restaurants located in Hispanic geographic enclaves had a higher proportion of fried menu items (p<0.01) but presented fewer environmental barriers to healthy eating, compared with those in areas with lower Hispanic concentrations. No significant differences in NEMS-R scores were found by other neighborhood characteristics. Size was the only significant factor predicting high NEMS-HCR scores, where small restaurants were less likely to have scores in the high category (NEMS-HCR score>6), compared with their medium (aOR: 6.6, 95% CI: 1.8-24.6) and large counterparts (aOR: 5.6, 95% CI: 1.5-21.4). This research is the first to examine the association between restaurant location and consumer nutrition environments, providing information to contribute to future interventions and policies seeking to improve urban food environments in communities disproportionately affected by diet-related conditions, as in the case of HC communities in New York City.


Subject(s)
Diet, Healthy , Restaurants , Hispanic or Latino , Humans , New York City , Nutrition Surveys
11.
Ann Epidemiol ; 63: 68-74, 2021 11.
Article in English | MEDLINE | ID: mdl-34343614

ABSTRACT

PURPOSE: To examine whether there was an association of leucocyte telomere length (LTL) with all-cause, cardiovascular (CVD)- and cancer-specific mortality risks among U.S. adults; and whether these associations vary with race and ethnicity and age. METHODS: We conducted a retrospective cohort using data from the National Health and Nutrition Examination Survey, 1999 to 2002 and the 2015 Linked Mortality File on adults 25 years or older (n = 6,526 and 1,753 deaths). Cox proportional hazards regression was used to quantify the association of LTL with each outcome adjusting for baseline sociodemographic and health-related characteristics. We tested a three-way interaction for LTL, race and ethnicity, and age groups. RESULTS: After adjustment, the rate of dying for all-cause and CVD-specific mortality was at least 24% lower for a 1 kilobase increase in LTL. When compared with adults with the shortest telomere, the rates of dying were at least 17% lower for all-cause and CVD-specific mortality for those with longer telomere. For all-cause mortality, increase LTL was associated with lower rate of dying among non-Hispanic Blacks 45 years or older, and non-Hispanic Whites 65 years or older. CONCLUSIONS: We found that increase telomere length was associated with lower all-cause and CVD-specific mortality rates among U.S. adults. For all-cause mortality, this association varies within racial and ethnic groups across age groups.


Subject(s)
Cardiovascular Diseases , Ethnicity , Adult , Cardiovascular Diseases/genetics , Humans , Nutrition Surveys , Retrospective Studies , Telomere , United States/epidemiology
12.
Front Public Health ; 9: 656988, 2021.
Article in English | MEDLINE | ID: mdl-33959584

ABSTRACT

Physical and social environments of parks and neighborhoods influence park use, but the extent of their relative influence remains unclear. This cross-sectional study examined the relationship between the physical and social environment of parks and both observed and self-reported park use in low-income neighborhoods in New York City. We conducted community- (n = 54 parks) and individual-level (n = 904 residents) analyses. At the community level, observed park use was measured using a validated park audit tool and regressed on the number of facilities and programmed activities in parks, violent crime, stop-and-frisk incidents, and traffic accidents. At the individual level, self-reported park use was regressed on perceived park quality, crime, traffic-related walkability, park use by others, and social cohesion and trust. Data were collected in 2016-2018 and analyzed in 2019-2020. At the community level, observed park use was negatively associated with stop-and-frisk (ß = -0.04; SE = 0.02; p < 0.05) and positively associated with the number of park facilities (ß = 1.46; SE = 0.57; p < 0.05) and events (ß = 0.16; SE = 0.16; p < 0.01). At the individual level, self-reported park use was positively associated with the social cohesion and trust scale (ß = 0.02; SE = 0.01; p < 0.05). These results indicate that physical and social attributes of parks, but not perceptions of parks, were significantly associated with park use. The social environment of neighborhoods at both community and individual levels was significantly related to park use. Policies for increasing park use should focus on improving the social environment of parks and surrounding communities, not only parks' physical attributes. These findings can inform urban planning and public health interventions aimed at improving the well-being of residents in low-income communities.


Subject(s)
Environment Design , Social Environment , Cross-Sectional Studies , Humans , New York City , Self Report
13.
Soc Sci Med ; 270: 113560, 2021 02.
Article in English | MEDLINE | ID: mdl-33385623

ABSTRACT

Race/ethnicity is associated with adverse birth outcomes in the United States. However, mostly mother's race/ethnicity has been considered. We examined the associations of mother's and parents' race/ethnicity with low birth weight, small for gestational age, preterm birth and infant mortality among New York City women between 2012 and 2017. We also examined the independent and joint effects of neighborhood racial/ethnic composition. We found that mother's and parents' race/ethnicity are associated with adverse birth outcomes; these associations are outcome-specific; and neighborhood racial/ethnic composition is not only associated with such outcomes but also modifies the association of mother's and parents' race/ethnicity with these outcomes. Our findings underscore the need to consider the race/ethnicity of women's partners and their neighborhoods calling attention to the role of context where individuals reside, and their daily interactions take place. These findings may have implications beyond New York City as our society becomes more racial/ethnic diverse and interracial/ethnic marriage becomes more common in the United States.


Subject(s)
Ethnicity , Premature Birth , Female , Humans , Infant , Infant, Newborn , Marriage , New York City/epidemiology , Pregnancy , Premature Birth/epidemiology , Residence Characteristics , United States/epidemiology
14.
JCO Clin Cancer Inform ; 4: 958-971, 2020 10.
Article in English | MEDLINE | ID: mdl-33119407

ABSTRACT

PURPOSE: Investigations of the molecular basis for the development, progression, and treatment of cancer increasingly use complementary genomic assays to gather multiomic data, but management and analysis of such data remain complex. The cBioPortal for cancer genomics currently provides multiomic data from > 260 public studies, including The Cancer Genome Atlas (TCGA) data sets, but integration of different data types remains challenging and error prone for computational methods and tools using these resources. Recent advances in data infrastructure within the Bioconductor project enable a novel and powerful approach to creating fully integrated representations of these multiomic, pan-cancer databases. METHODS: We provide a set of R/Bioconductor packages for working with TCGA legacy data and cBioPortal data, with special considerations for loading time; efficient representations in and out of memory; analysis platform; and an integrative framework, such as MultiAssayExperiment. Large methylation data sets are provided through out-of-memory data representation to provide responsive loading times and analysis capabilities on machines with limited memory. RESULTS: We developed the curatedTCGAData and cBioPortalData R/Bioconductor packages to provide integrated multiomic data sets from the TCGA legacy database and the cBioPortal web application programming interface using the MultiAssayExperiment data structure. This suite of tools provides coordination of diverse experimental assays with clinicopathological data with minimal data management burden, as demonstrated through several greatly simplified multiomic and pan-cancer analyses. CONCLUSION: These integrated representations enable analysts and tool developers to apply general statistical and plotting methods to extensive multiomic data through user-friendly commands and documented examples.


Subject(s)
Computational Biology , Data Management , Databases, Genetic , Genomics , Humans , Software
15.
Am J Clin Nutr ; 108(2): 237-242, 2018 08 01.
Article in English | MEDLINE | ID: mdl-29982268

ABSTRACT

Background: Despite great progress in prevention and control, ischemic heart disease (IHD) remains a leading cause of global morbidity and mortality. Diet plays a key role in IHD, but a comprehensive delineation of the role of dietary factors in IHD is not yet quite complete. Objective: The aim of this study was to test the long-standing hypothesis that copper is protective and zinc harmful in IHD. Design: We used separate-sample instrumental variable analysis with genetic instruments (Mendelian randomization). We obtained single nucleotide polymorphisms (SNPs) from a genome wide association study, strongly (P value < 5 × 10-8) and independently associated with erythrocyte copper and zinc. We applied these genetic predictors of copper and zinc to the largest, most extensively genotyped IHD case (n ≤ 76014)-control (n ≤ 264785) study, based largely on CARDIoGRAMplusC4D 1000 Genomes and the UK Biobank SOFT CAD, to obtain SNP-specific Wald estimates for the effects of copper and zinc on IHD, which were combined through the use of inverse variance weighting. Sensitivity analysis included use of the MR-Egger method, and reanalysis including SNPs independently associated with erythrocyte copper and zinc at P value < 5 × 10-6. Results: Genetically instrumented copper was negatively associated with IHD (OR: 0.94; 95% CI: 0.90, 0.98). Genetically instrumented zinc was positively associated with IHD (OR: 1.06; 95% CI: 1.02, 1.11). Sensitivity analysis via MR-Egger gave no indication of unknown pleiotropy; less strongly associated SNPs gave similar results for copper. Conclusion: Genetic validation of a long-standing hypothesis suggests that further investigation of the effects, particularly of copper, on IHD may provide a practical means of reducing the leading cause of mortality and morbidity.


Subject(s)
Copper/administration & dosage , Mendelian Randomization Analysis , Myocardial Infarction/genetics , Myocardial Ischemia/genetics , Zinc/administration & dosage , Copper/blood , Genome-Wide Association Study , Humans , Polymorphism, Single Nucleotide , Zinc/blood
17.
Cancer Res ; 77(21): e39-e42, 2017 11 01.
Article in English | MEDLINE | ID: mdl-29092936

ABSTRACT

Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide the unrestricted multiple 'omics data for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable, and reproducible statistical analysis of multiomics data and enhances data science applications of multiple omics datasets. Cancer Res; 77(21); e39-42. ©2017 AACR.


Subject(s)
Genomics , Neoplasms/genetics , Software , Computational Biology , Datasets as Topic , Genome, Human , Humans
18.
J Clin Diagn Res ; 11(3): OC13-OC16, 2017 Mar.
Article in English | MEDLINE | ID: mdl-28511427

ABSTRACT

INTRODUCTION: Diabetic dyslipidaemia is characterised by hypertriglyceridaemia, low High Density Lipoprotein (HDL), postprandial lipimea, small and dense LDL particles is considered to be a major predisposing factor for various macrovascular complications. Omega-3 fatty acids are fish oil derivative introduced in the market for dyslipidaemia associated with increased triglyceride level. AIM: To study the effect of omega-3 fatty acids on lipid profile in Type II diabetes patients. MATERIALS AND METHODS: This study was prospective, single blind, randomized comparative trial. Hundred patients were randomized into three groups. Group I received metformin 500 mg twice daily and placebo, Group II received metformin 500 mg twice daily and omega-3 fatty acids (1 gram) once daily and the Group III received metformin 500 mg twice daily and omega-3 fatty acids (1 gram) twice daily. ANOVA test was applied for analysis. RESULTS: Group II was effective in reducing the triglyceride level from 144.59±14.18 mg/dl to 101±13.31 mg/dl which was significant as compared to Group I from 147.67±18.57 mg/dl to 145.8±19.86 mg/dl respectively. Group III containing 1 g of omega-3 fatty acids twice daily showed decrease from 144.83±22.17 mg/dl to 86±17.46 mg/dl and was more effective in reducing triglyceride levels than Group II containing 1 gram of omega-3 fatty acids once daily. CONCLUSION: Omega-3 fatty acids can be given in conjunction with metformin to reduce triglyceride levels in diabetic dyslipidaemia without any adverse drug reactions or any drug interaction. Omega-3 fatty acids were effective in reducing the triglyceride level significantly as compared to placebo. Two grams of omega-3 fatty acids were more effective than 1 gram of omega-3 fatty acids in reducing triglyceride levels.

19.
J Ultrasound Med ; 36(11): 2245-2256, 2017 Nov.
Article in English | MEDLINE | ID: mdl-28407281

ABSTRACT

OBJECTIVES: To evaluate the value of multiparametric quantitative ultrasound imaging in assessing chronic kidney disease (CKD) using kidney biopsy pathologic findings as reference standards. METHODS: We prospectively measured multiparametric quantitative ultrasound markers with grayscale, spectral Doppler, and acoustic radiation force impulse imaging in 25 patients with CKD before kidney biopsy and 10 healthy volunteers. Based on all pathologic (glomerulosclerosis, interstitial fibrosis/tubular atrophy, arteriosclerosis, and edema) scores, the patients with CKD were classified into mild (no grade 3 and <2 of grade 2) and moderate to severe (at least 2 of grade 2 or 1 of grade 3) CKD groups. Multiparametric quantitative ultrasound parameters included kidney length, cortical thickness, pixel intensity, parenchymal shear wave velocity, intrarenal artery peak systolic velocity (PSV), end-diastolic velocity (EDV), and resistive index. We tested the difference in quantitative ultrasound parameters among mild CKD, moderate to severe CKD, and healthy controls using analysis of variance, analyzed correlations of quantitative ultrasound parameters with pathologic scores and the estimated glomerular filtration rate (GFR) using Pearson correlation coefficients, and examined the diagnostic performance of quantitative ultrasound parameters in determining moderate CKD and an estimated GFR of less than 60 mL/min/1.73 m2 using receiver operating characteristic curve analysis. RESULTS: There were significant differences in cortical thickness, pixel intensity, PSV, and EDV among the 3 groups (all P < .01). Among quantitative ultrasound parameters, the top areas under the receiver operating characteristic curves for PSV and EDV were 0.88 and 0.97, respectively, for determining pathologic moderate to severe CKD, and 0.76 and 0.86 for estimated GFR of less than 60 mL/min/1.73 m2 . Moderate to good correlations were found for PSV, EDV, and pixel intensity with pathologic scores and estimated GFR. CONCLUSIONS: The PSV, EDV, and pixel intensity are valuable in determining moderate to severe CKD. The value of shear wave velocity in assessing CKD needs further investigation.


Subject(s)
Renal Insufficiency, Chronic/diagnostic imaging , Ultrasonography/methods , Adult , Evaluation Studies as Topic , Female , Glomerular Filtration Rate , Humans , Kidney/diagnostic imaging , Middle Aged , Prospective Studies
20.
J Clin Diagn Res ; 10(12): OD10-OD11, 2016 Dec.
Article in English | MEDLINE | ID: mdl-28208914

ABSTRACT

Neurosurgical interventions are rarely associated with meningitis with a very low incidence rate ranging from 1.1% to 2.5%. Gram negative bacillary meningitis first described in the 1940's, previously uncommon has been increasing in the recent past associated with advanced age, immunosuppression and neurosurgery. Enterobacter meningitis though relatively uncommon is recently increasing in incidence and treatment is frequently complicated due to resistance to antibiotics making this a challenging, difficult to treat infection that may be associated with adverse clinical outcomes. Here, we describe a case of a 27-year-old patient diagnosed with brain sarcoma at the age of four years, who presented with Enterobacter meningitis following a neurosurgical intervention for resection of a recurrent brain tumor (meningioma on pathology) and had a prolonged hospital stay with a difficult to treat infection.

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