96 research outputs found

    Recognizing the Continuous Nature of Expression Heterogeneity and Clinical Outcomes in Clear Cell Renal Cell Carcinoma

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    Clear cell renal cell carcinoma (ccRCC) has been previously classified into putative discrete prognostic subtypes by gene expression profiling. To investigate the robustness of these proposed subtype classifications, we evaluated 12 public datasets, together with a new dataset of 265 ccRCC gene expression profiles. Consensus clustering showed unstable subtype and principal component analysis (PCA) showed a continuous spectrum both within and between datasets. Considering the lack of discrete delineation and continuous spectrum observed, we developed a continuous quantitative prognosis score (Continuous Linear Enhanced Assessment of RCC, or CLEAR score). Prognostic performance was evaluated in independent cohorts from The Cancer Genome Atlas (TCGA) (n = 414) and EMBL-EBI (n = 53), CLEAR score demonstrated both superior prognostic estimates and inverse correlation with anti-angiogenic tyrosine-kinase inhibition in comparison to previously proposed discrete subtyping classifications. Inverse correlation with high-dose interleukin-2 outcomes was also observed for the CLEAR score. Multiple somatic mutations (VHL, PBRM1, SETD2, KDM5C, TP53, BAP1, PTEN, MTOR) were associated with the CLEAR score. Application of the CLEAR score to independent expression profiling of intratumoral ccRCC regions demonstrated that average intertumoral heterogeneity exceeded intratumoral expression heterogeneity. Wider investigation of cancer biology using continuous approaches may yield insights into tumor heterogeneity; single cell analysis may provide a key foundation for this approach

    Recognizing the Continuous Nature of Expression Heterogeneity and Clinical Outcomes in Clear Cell Renal Cell Carcinoma.

    Get PDF
    Clear cell renal cell carcinoma (ccRCC) has been previously classified into putative discrete prognostic subtypes by gene expression profiling. To investigate the robustness of these proposed subtype classifications, we evaluated 12 public datasets, together with a new dataset of 265 ccRCC gene expression profiles. Consensus clustering showed unstable subtype and principal component analysis (PCA) showed a continuous spectrum both within and between datasets. Considering the lack of discrete delineation and continuous spectrum observed, we developed a continuous quantitative prognosis score (Continuous Linear Enhanced Assessment of RCC, or CLEAR score). Prognostic performance was evaluated in independent cohorts from The Cancer Genome Atlas (TCGA) (n = 414) and EMBL-EBI (n = 53), CLEAR score demonstrated both superior prognostic estimates and inverse correlation with anti-angiogenic tyrosine-kinase inhibition in comparison to previously proposed discrete subtyping classifications. Inverse correlation with high-dose interleukin-2 outcomes was also observed for the CLEAR score. Multiple somatic mutations (VHL, PBRM1, SETD2, KDM5C, TP53, BAP1, PTEN, MTOR) were associated with the CLEAR score. Application of the CLEAR score to independent expression profiling of intratumoral ccRCC regions demonstrated that average intertumoral heterogeneity exceeded intratumoral expression heterogeneity. Wider investigation of cancer biology using continuous approaches may yield insights into tumor heterogeneity; single cell analysis may provide a key foundation for this approach

    Posture modulates implicit hand maps

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    Several forms of somatosensation require that afferent signals be informed by stored representations of body size and shape. Recent results have revealed that position sense relies on a highly distorted body representation. Changes of internal hand posture produce plastic alterations of processing in somatosensory cortex. This study therefore investigated how such postural changes affect implicit body representations underlying position sense. Participants localized the knuckles and tips of each finger in external space in two postures: the fingers splayed (Apart posture) or pressed together (Together posture). Comparison of the relative locations of the judgments of each landmark were used to construct implicit maps of represented hand structure. Spreading the fingers apart produced increases in the implicit representation of hand size, with no apparent effect on hand shape. Thus, changes of internal hand posture produce rapid modulation of how the hand itself is represented, paralleling the known effects on somatosensory cortical processing

    The Cost-Effectiveness and Value of Information of Three Influenza Vaccination Dosing Strategies for Individuals with Human Immunodeficiency Virus

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    Influenza vaccine immunogenicity is diminished in patients living with HIV/AIDS. We evaluated the cost-effectiveness and expected value of perfect information (EVPI) of three alternative influenza vaccine dosing strategies intended to increase immunogenicity in those patients.A randomized, multi-centered, controlled, vaccine trial was conducted at 12 CIHR Canadian HIV Trials Network sites. Three dosing strategies with seasonal, inactivated trivalent, non-adjuvanted intramuscular vaccine were used in HIV infected adults: two standard doses over 28 days (Strategy A), two double doses over 28 days (Strategy B) and a single standard dose of influenza vaccine (Strategy C), administered prior to the 2008 influenza season. The comparator in our analysis was practice in the previous year, in which 82.8% of HIV/AIDS received standard-dose vaccination (Strategy D). A Markov cohort model was developed to estimate the monthly probability of Influenza-like Illness (ILI) over one influenza season. Costs and quality-adjusted life years, extrapolated to the lifetime of the hypothetical study cohorts, were estimated in calculating incremental cost-effectiveness ratios (ICER) and EVPI in conducting further research.298 patients with median CD4 of 470 cells/Β΅l and 76% with viral load suppression were randomized. Strategy C was the most cost-effective strategy for the overall trial population and for suppressed and unsuppressed individuals. Mean ICERs for Strategy A for unsuppressed patients could also be considered cost-effective. The level of uncertainty regarding the decision to implement strategy A versus C for unsuppressed individuals was high. The maximum acceptable cost of reducing decision uncertainty in implementing strategy A for individuals with unsuppressed pVL was $418,000--below the cost of conducting a larger-scale trial.Our results do not support a policy to implement increased antigen dose or booster dosing strategies with seasonal, inactivated trivalent, non-adjuvanted intramuscular vaccine for individuals with HIV in Canada.ClinicalTrials.gov NCT00764998

    Complex Coacervate-based Materials for Biomedicine

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    There has been increasing interest in complex coacervates for deriving and trans- porting biomaterials. Complex coacervates are a dense, polyelectrolyte-rich liq- uid that results from the electrostatic complexation of oppositely charged macroions. Coacervates have long been used as a strategy for encapsulation, par- ticularly in food and personal care products. More recent efforts have focused on the utility of this class of materials for the encapsulation of small molecules, pro- teins, RNA, DNA, and other biomaterials for applications ranging from sensing to biomedicine. Furthermore, coacervate-related materials have found utility in other areas of biomedicine, including cartilage mimics, tissue culture scaffolds, and adhesives for wet, biological environments. Here, we discuss the self- assembly of complex coacervate-based materials, current challenges in the intel- ligent design of these materials, and their utility applications in the broad field of biomedicine

    Acoustic attenuation spectroscopy and helium ion microscopy study of rehydration of dairy powder

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    Complete hydration is essential for the production of structured dairy products from powders. It is essential that the ingredients used hydrate completely. Determination of an end point of rehydration is non-trivial, but ultrasound-based methodologies have demonstrated potential in this area and are well suited to measuring bulk samples in situ. Here, acoustic attenuation spectroscopy (AAS) is used to monitor rehydration of skim milk powder, and recombined systems of micellar casein isolate with lactose and whey protein isolate. Dynamic light scattering, zeta-potential measurements and AAS as a function of pH characterise each component around its isoelectric point to assess its functionality. Scanning helium ion microscopy was used to image the dry powders, without any conductive coating, producing resolution equivalent to scanning electron microscopy, but with much larger focal lengths and fewer imaging artefacts. Imaging the powders provides information on particle size and morphology which can affect dissolution behaviour. Reconstituted skim milk powder and recombined samples were monitored showing there are changes occurring over several hours. Attenuation coefficients are shown to predict the end point of hydration. Model fitting is used to extract volume fractions and average particle sizes of large and small particle populations in recombined samples over time. AAS is demonstrated to be capable of tracking the dynamics in rehydrating dispersions over time. Physical parameters such as the volume fraction and particle size of the dispersed phase can be determined

    Influenza vaccination for immunocompromised patients: systematic review and meta-analysis from a public health policy perspective.

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    Immunocompromised patients are vulnerable to severe or complicated influenza infection. Vaccination is widely recommended for this group. This systematic review and meta-analysis assesses influenza vaccination for immunocompromised patients in terms of preventing influenza-like illness and laboratory confirmed influenza, serological response and adverse events
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