Representativeness of breast cancer cases in an integrated health care delivery system.

BackgroundIntegrated health care delivery systems, with their comprehensive and integrated electronic medical records (EMR), are well-poised to conduct research that leverages the detailed clinical data within the EMRs. However, information regarding the representativeness of these clinical populations is limited, and thus the generalizability of research findings is uncertain.MethodsUsing data from the population-based California Cancer Registry, we compared age-adjusted distributions of patient and neighborhood characteristics for three groups of breast cancer patients: 1) those diagnosed within Kaiser Permanente Northern California (KPNC), 2) non-KPNC patients from NCI-designated cancer centers, and 3) those from all other hospitals.ResultsKPNC patients represented 32 % (N = 36,109); cancer center patients represented 7 % (N = 7805); and all other hospitals represented 61 % (N = 68,330) of the total breast cancer patients from this geographic area during 1996-2009. Compared with cases from all other hospitals, KPNC had slightly fewer non-Hispanic Whites (70.6 % versus 74.4 %) but more Blacks (8.1 % versus 5.0 %), slightly more patients in the 50-69 age range and fewer in the younger and older age groups, a slightly lower proportion of in situ but higher proportion of stage I disease (41.6 % versus 38.9 %), were slightly less likely to reside in the lowest (4.2 % versus 6.5 %) and highest (36.2 % versus 39.0 %) socioeconomic status neighborhoods, and more likely to live in suburban metropolitan areas and neighborhoods with more racial/ethnic minorities. Cancer center patients differed substantially from patients from KPNC and all other hospitals on all characteristics assessed. All differences were statistically significant (p < .001).ConclusionsAlthough much of clinical research discoveries are based in academic medical centers, patients from large, integrated medical centers are likely more representative of the underlying population, providing support for the generalizability of cancer research based on electronic data from these centers

Pretreatment of citrus by-products affects polyphenol recovery:a review

A large amount of citrus waste is generated annually. This waste is of great economic worth, since it contains high levels of polyphenols, which have attracted scientific interest due to their potent antimicrobial and antiradical activities. Pretreatment is a crucial step that precedes the extraction process and influences the yields and quality of polyphenols. This review emphasizes the effect of different drying processes, such as freeze drying, hot-air drying, vacuum drying, microwave drying, infrared drying, and high-speed drying, on the polyphenol retention in citrus by-products. Further treatments of the dried citrus by-products for assisting the liberation of bound polyphenols are also provided and comprehensively discussed

Synergistic drug combinations from electronic health records and gene expression.

ObjectiveUsing electronic health records (EHRs) and biomolecular data, we sought to discover drug pairs with synergistic repurposing potential. EHRs provide real-world treatment and outcome patterns, while complementary biomolecular data, including disease-specific gene expression and drug-protein interactions, provide mechanistic understanding.MethodWe applied Group Lasso INTERaction NETwork (glinternet), an overlap group lasso penalty on a logistic regression model, with pairwise interactions to identify variables and interacting drug pairs associated with reduced 5-year mortality using EHRs of 9945 breast cancer patients. We identified differentially expressed genes from 14 case-control human breast cancer gene expression datasets and integrated them with drug-protein networks. Drugs in the network were scored according to their association with breast cancer individually or in pairs. Lastly, we determined whether synergistic drug pairs found in the EHRs were enriched among synergistic drug pairs from gene-expression data using a method similar to gene set enrichment analysis.ResultsFrom EHRs, we discovered 3 drug-class pairs associated with lower mortality: anti-inflammatories and hormone antagonists, anti-inflammatories and lipid modifiers, and lipid modifiers and obstructive airway drugs. The first 2 pairs were also enriched among pairs discovered using gene expression data and are supported by molecular interactions in drug-protein networks and preclinical and epidemiologic evidence.ConclusionsThis is a proof-of-concept study demonstrating that a combination of complementary data sources, such as EHRs and gene expression, can corroborate discoveries and provide mechanistic insight into drug synergism for repurposing

Discrete wetland groundwater discharges revealed with a three-dimensional temperature model and botanical indicators (Boxford, UK)

Wetlands provide unique goods and services, as habitats of high biodiversity. Hydrology is the principal control on wetland functioning; hence, understanding the water source is fundamental. However, groundwater inflows may be discrete and easily missed. Research techniques are required with low cost and minimal impact in sensitive settings. In this study, the effectiveness of using a three-dimensional (3D) temperature model and botanical indicators to characterise groundwater discharge is explored at the CEH (Centre for Ecology and Hydrology) River Lambourn Observatory, Boxford, UK. This comprises a 10 ha lowland riparian wetland, designated for its scientific interest and conservation value. Temperature data were collected in winter at multiple depths down to 0.9 m over approximately 3.6 ha and transformed into a 3D model via ordinary kriging. Anomalous warm zones indicated distinct areas of groundwater upwelling which were concurrent with relic channel structures. Lateral heat propagation from the channels was minimal and restricted to within 5–10 m. Vertical temperature sections within the channels suggest varying degrees of groundwater discharge along their length. Hydrochemical analysis showed that warmer peat waters were akin to deeper aquifer waters, confirming the temperature anomalies as areas of groundwater discharge. Subsequently, a targeted vegetation survey identified Carex paniculata as an indicator of groundwater discharge. The upwelling groundwater contains high concentrations of nitrate which is considered to support the spatially restricted growth of Carex paniculata against a background of poor fen communities located in reducing higher-phosphate waters

Measurement of the Proton Spin Structure Function g1p with a Pure Hydrogen Target

A measurement of the proton spin structure function g1p(x,Q^2) in deep-inelastic scattering is presented. The data were taken with the 27.6 GeV longitudinally polarised positron beam at HERA incident on a longitudinally polarised pure hydrogen gas target internal to the storage ring. The kinematic range is 0.021<x<0.85 and 0.8 GeV^2<Q^2<20 GeV^2. The integral Int_{0.021}^{0.85} g1p(x)dx evaluated at Q0^2 of 2.5 GeV^2 is 0.122+/-0.003(stat.)+/-0.010(syst.).Comment: 7 pages, 3 figures, 1 table, RevTeX late

Flavor decomposition of the sea quark helicity distributions in the nucleon from semi-inclusive deep-inelastic scattering

Double-spin asymmetries of semi-inclusive cross sections for the production of identified pions and kaons have been measured in deep-inelastic scattering of polarized positrons on a polarized deuterium target. Five helicity distributions including those for three sea quark flavors were extracted from these data together with re-analyzed previous data for identified pions from a hydrogen target. These distributions are consistent with zero for all three sea flavors. A recently predicted flavor asymmetry in the polarization of the light quark sea appears to be disfavored by the data.Comment: 5 pages, 3 figure

Evidence for Quark-Hadron Duality in the Proton Spin Asymmetry A1A_1

Spin-dependent lepton-nucleon scattering data have been used to investigate the validity of the concept of quark-hadron duality for the spin asymmetry $A_1$. Longitudinally polarised positrons were scattered off a longitudinally polarised hydrogen target for values of $Q^2$ between 1.2 and 12 GeV$^2$ and values of $W^2$ between 1 and 4 GeV$^2$. The average double-spin asymmetry in the nucleon resonance region is found to agree with that measured in deep-inelastic scattering at the same values of the Bjorken scaling variable $x$. This finding implies that the description of $A_1$ in terms of quark degrees of freedom is valid also in the nucleon resonance region for values of $Q^2$ above 1.6 GeV$^2$.Comment: 5 pages, 1 eps figure, table added, new references added, in print in Phys. Rev. Let

Measurement of the Spin Asymmetry in the Photoproduction of Pairs of High-pT Hadrons at HERMES

We present a measurement of the longitudinal spin asymmetry A_|| in photoproduction of pairs of hadrons with high transverse momentum p_T. Data were accumulated by the HERMES experiment using a 27.5 GeV polarized positron beam and a polarized hydrogen target internal to the HERA storage ring. For h+h- pairs with p_T^h_1 > 1.5 GeV/c and p_T^h_2 > 1.0 GeV/c, the measured asymmetry is A_|| = -0.28 +/- 0.12 (stat.) +/- 0.02 (syst.). This negative value is in contrast to the positive asymmetries typically measured in deep inelastic scattering from protons, and is interpreted to arise from a positive gluon polarization.Comment: 5 pages (latex), 4 figures (eps

Observation of a Coherence Length Effect in Exclusive Rho^0 Electroproduction

Exclusive incoherent electroproduction of the rho^0(770) meson from 1H, 2H, 3He, and 14N targets has been studied by the HERMES experiment at squared four-momentum transfer Q**2>0.4 GeV**2 and positron energy loss nu from 9 to 20 GeV. The ratio of the 14N to 1H cross sections per nucleon, known as the nuclear transparency, was found to decrease with increasing coherence length of quark-antiquark fluctuations of the virtual photon. The data provide clear evidence of the interaction of the quark- antiquark fluctuations with the nuclear medium.Comment: RevTeX, 5 pages, 3 figure