330 Mount Auburn St Primary Care Center
Cambridge MA 02138
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TopFed: TCGA tailored federated query processing and linking to LOD. - Journal of biomedical semantics
The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to catalogue genetic mutations responsible for cancer using genome analysis techniques. One of the aims of this project is to create a comprehensive and open repository of cancer related molecular analysis, to be exploited by bioinformaticians towards advancing cancer knowledge. However, devising bioinformatics applications to analyse such large dataset is still challenging, as it often requires downloading large archives and parsing the relevant text files. Therefore, it is making it difficult to enable virtual data integration in order to collect the critical co-variates necessary for analysis.We address these issues by transforming the TCGA data into the Semantic Web standard Resource Description Format (RDF), link it to relevant datasets in the Linked Open Data (LOD) cloud and further propose an efficient data distribution strategy to host the resulting 20.4 billion triples data via several SPARQL endpoints. Having the TCGA data distributed across multiple SPARQL endpoints, we enable biomedical scientists to query and retrieve information from these SPARQL endpoints by proposing a TCGA tailored federated SPARQL query processing engine named TopFed.We compare TopFed with a well established federation engine FedX in terms of source selection and query execution time by using 10 different federated SPARQL queries with varying requirements. Our evaluation results show that TopFed selects on average less than half of the sources (with 100% recall) with query execution time equal to one third to that of FedX.With TopFed, we aim to offer biomedical scientists a single-point-of-access through which distributed TCGA data can be accessed in unison. We believe the proposed system can greatly help researchers in the biomedical domain to carry out their research effectively with TCGA as the amount and diversity of data exceeds the ability of local resources to handle its retrieval and parsing.
Disparities in access to surgical care within a lower income country: an alarming inequity. - World journal of surgery
Surgical care is not uniformly available worldwide. Inequities in surgical care and access may also vary within countries, and the present study aimed to explore these disparities in Pakistan.The National Health Survey of Pakistan was analyzed. The proportion of people with a history of abdominal surgery (AS) was calculated and associated factors were determined by weighted multivariate logistic regression. Factors tested were age, gender, urban/rural residence, province, literacy, community development index (CDI), and economic status (ES). The CDI was developed for each sampling unit from select household and individual data. The ES was constructed from ownership of assets.A total of 59 million adults were represented. Abdominal surgery had been performed in 3.2 % adults (95 % confidence interval [CI] = 2.67, 3.84), which corresponded to an annual rate of 85.9 abdominal surgeries per 100,000 population. Wide disparities were noted, with annual rates of AS varying from 37.8 to 215.6 per 100,000 population. Urban residents were independently twice as likely as rural populations to have had AS (95 % CI = 1.3, 2.8). Higher age (OR = 2.6; 95 % CI = 1.7, 4.0), female gender (OR = 1.5; 95 % CI = 1.1, 2.1), and higher ES (OR = 1.9; 95 % CI = 1.2, 2.9) were also independently associated with AS. In rural populations ES was the only factor associated with surgery, whereas in urban populations gender and CDI had important roles to play.Access to surgical care is disparate and grossly inadequate in Pakistan. This likely contributes to significant preventable morbidity and death. Physical access to surgical facilities, especially in rural areas and for those with a low CDI, is an important concern and should be prioritized in any forthcoming national policies.
Intensive insulin therapy in brain injury: a meta-analysis. - Journal of neurotrauma
Many studies have addressed the question of whether intensive insulin therapy (IIT) provides better outcomes for brain-injured patients than does conventional insulin therapy (CIT), with conflicting results. We performed a systematic review and meta-analysis of the literature to estimate the effect of IIT on patients with brain injury. We searched MEDLINE, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), and citations of key articles and selected "all randomized controlled trials" (RCTs) comparing the effect of IIT to CIT among adult patients with acute brain injury (traumatic brain injury, stroke, subarachnoid hemorrhage, and encephalitis). Of the 2807 studies, we identified 9 RCTs with a total of 1160 patients for analysis. IIT did not appear to decrease the risk of in-hospital or late mortality (RR=1.04, 95% CI=0.75, 1.43 and RR=1.07, 95%CI=0.91, 1.27 respectively). No significant heterogeneity was found (I(2)=0.0%). IIT also did not have a protective effect on long-term neurological outcomes (LTNO) (RR=1.10, 95% CI=0.96, 1.27). IIT, however, did decrease the rate of infections (RR=0.76, 95% CI=0.58, 0.98). Heterogeneity was present (I(2)=64%), which was eliminated upon sensitivity analysis bringing the RR to 0.66 (95% CI=0.55, 0.80, I(2)=0%). IIT increased the rate of hypoglycemic episodes (RR=1.72, 95% CI=1.20, 2.46) however there was intractable heterogeneity present (I(2)=89%), which did not resolve upon sensitivity analysis. We found no evidence of publication bias by Egger's test (p=0.50). To conclude, IIT has no mortality or LTNO benefit to patients with brain injury, but is beneficial at decreasing infection rates.
Never giving up: outcomes and presentation of emergency general surgery in geriatric octogenarian and nonagenarian patients. - American journal of surgery
Aging of the population necessitates consideration of the increasing number of older adults requiring emergency care. The objective of this study was to compare outcomes and presentation of octogenarian and/or nonagenarian emergency general surgery (EGS) patients with younger adults.Based on a standardized definition of EGS, patients in the 2007 to 2011 Healthcare Cost and Utilization Project-Nationwide Inpatient Sample were queried for primary EGS diagnoses. Included patients were categorized into older (â‰¥80 years) vs younger (<80 years) adults based on a marked increase in mortality around aged 80 years. Using propensity scores, risk-adjusted differences in major morbidity, mortality, length of stay (LOS), and cost were compared.Of 3,707,465 included patients, 17.2% (n = 637,588) were â‰¥80 years. Relative to younger adults, older patients most frequently presented for gastrointestinal-bleeding (odds ratio [95% confidence intervals]: 2.81 [2.79 to 2.82]) and gastrostomy care (2.46 [2.39 to 2.53]). Despite higher odds of mortality (1.67 [1.63 to 1.69]), older adults exhibited lower risk-adjusted odds of morbidity (.87 [.86 to .88]), shorter LOS (4.50 vs 5.14Â days), and lower total hospital costs ($10,700 vs $12,500).Octogenarian and/or nonagenarian patients present differently than younger adults. Reductions in complications, LOS, and cost among surviving older adults allude to a "survivorship tendency" to never give up, despite collectively higher mortality risk.Copyright Â© 2016 Elsevier Inc. All rights reserved.
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