Modeling and Simulation of Thermo-Fluid-Electrochemical Ion Flow in Biological Channels

In this article we address the study of ion charge transport in the biological channels separating the intra and extracellular regions of a cell. The focus of the investigation is devoted to including thermal driving forces in the well-known velocity-extended Poisson-Nernst-Planck (vPNP) electrodiffusion model. Two extensions of the vPNP system are proposed: the velocity-extended Thermo-Hydrodynamic model (vTHD) and the velocity-extended Electro-Thermal model (vET). Both formulations are based on the principles of conservation of mass, momentum and energy, and collapse into the vPNP model under thermodynamical equilibrium conditions. Upon introducing a suitable one-dimensional geometrical representation of the channel, we discuss appropriate boundary conditions that depend only on effectively accessible measurable quantities. Then, we describe the novel models, the solution map used to iteratively solve them, and the mixed-hybrid flux-conservative stabilized finite element scheme used to discretize the linearized equations. Finally, we successfully apply our computational algorithms to the simulation of two different realistic biological channels: 1) the Gramicidin-A channel considered in~\cite{JeromeBPJ}; and 2) the bipolar nanofluidic diode considered in~\cite{Siwy7}

Investigating roles for the deubiquitylating enzymes in the PtdIns3-K/PKB pathway in cancer

Phosphatidylinositol 3-kinase (PtdIns3-K) signalling is a crucial survival pathway in multiple malignancies, and an exciting target for drug development. The pathway is subject to multiple regulatory mechanisms including ubiquitylation, a reversible process that can influence protein stability, localisation and activity. A family of approximately 80 deubiquitylating enzymes (DUBs) are responsible for the cleavage of ubiquitin and ubiquitin chains from protein substrates. The DUBs are attractive drug targets and have increasingly been implicated in cellular processes germane to malignancy, including the PtdIns3-K pathway. The aim of this study was to systematically identify DUBs involved in regulating the pathway, with a particular view to identifying potential novel drug targets. The project employed a DUB siRNA library to perform a series of RNAi screens using two complementary approaches. In the first approach, the effects of DUB depletion on the protein level of nine PtdIns3-K pathway components (p110α, p110β, p110γ, p85α, p170, PDK1, PTEN, Akt, and mTOR) were assayed by immunoblotting. DUBs whose depletion either increased or decreased the protein level of these components were subject to further validation. Of particular interest were five DUBs (PRPF8, TNFAIP3, USP32, USP34 and OTUD1) whose depletion decreased the level of PDK1. In addition, depletion of three closely related members of the Josephin family of DUBs (ATXN3, ATXN3L and JOSD1) resulted in an increase in the protein level of the tumour suppressor PTEN. In view of the potential clinical utility of upregulating PTEN, the latter DUBs were prioritised for further investigation. Initial investigation indicates that all three DUBs alter PTEN level at a transcriptional level. Moreover, the effects of ATXN3 appear to be independent of its known function in modulation of histone acetylation status. The second approach utilised a U2OS cell line stably transfected with EGFP tagged FOXO3, in which PtdIns3-K dependent FOXO3 translocation could be assessed by live-cell imaging. This enabled the design of a functional screen in which the effects of DUB depletion on downstream PtdIns3-K signalling were assessed. Among the DUBs identified in this screen was USP45, depletion of which enhanced nuclear translocation of FOXO3-EGFP in response to PtdIns3-K inhibition. Several DUBs regulating FOXO3-EGFP abundance were also identified in this screen, including USP1 and USPL1 whose depletion respectively decreased and increased FOXO3-EGFP levels. The screen additionally identified three DUBs (USP8, OTUD4 and DUB4) whose depletion was synthetically lethal with PI-103 treatment. In summary, several DUB modulators of the PtdIns3-K pathway were identified that, subject to further mechanistic and functional studies, may increase the options available for targeting this vital pathway in malignancy

Cryptosporidium Parvum-Induced Inflammatory Bowel Disease of TCR-β- x TCR-δ-Deficient Mice

Experimental inoculation of neonatal immunocompetent strains of mice with Cryptosporidium parvum results in a transient, noninflammatory enteric infection. In the present study, we show that inoculation of mice deficient in a 3 and y8 T cells (TCR-3- X TCR-8-deficient mice) with C. parvum results in persistent infection and severe inflammatory bowel disease- like lesions. The most severe lesions in these mice were in the cecum with similar yet less severe lesions in the ileum and proximal colon. The most notable aspect of the histopathology was glandular hyperplasia with abscess formation, extensive fibrosis of the lamina propria with infiltrates of predominately polymorphonuclear cells and macrophages, and a few small aggregates of B cells. Persistently infected mice also developed extensive hepatic periportal fibrosis in association with C. parvum colonization of bile ducts. Lesions observed in TCR- 3- X TCR-8-deficient mice were markedly different than previously described lesions detected in C. parvum-infected TCR-o-deficient mice. Cryptosporidium parvum-infected TCR-o-deficient mice have extensive infiltrations of B cells, whereas TCR-P3- X TCR-8-deficient mice had only a few small aggregates of B cells. These findings indicate that although y8 T cells are not necessary for induction of intestinal inflammation in C. parvum-infected o(4 T- cell-deficient mice, their presence does alter the morphology of the ensuing lesion

The Average Body Surface Area of Adult Cancer Patients in the UK: A Multicentre Retrospective Study

The majority of chemotherapy drugs are dosed based on body surface area (BSA). No standard BSA values for patients being treated in the United Kingdom are available on which to base dose and cost calculations. We therefore retrospectively assessed the BSA of patients receiving chemotherapy treatment at three oncology centres in the UK between 1st January 2005 and 31st December 2005

Relationship of national institutes of health stroke scale to 30-day mortality in medicare beneficiaries with acute ischemic stroke.

BackgroundThe National Institutes of Health Stroke Scale (NIHSS), a well-validated tool for assessing initial stroke severity, has previously been shown to be associated with mortality in acute ischemic stroke. However, the relationship, optimal categorization, and risk discrimination with the NIHSS for predicting 30-day mortality among Medicare beneficiaries with acute ischemic stroke has not been well studied.Methods and resultsWe analyzed data from 33102 fee-for-service Medicare beneficiaries treated at 404 Get With The Guidelines-Stroke hospitals between April 2003 and December 2006 with NIHSS documented. The 30-day mortality rate by NIHSS as a continuous variable and by risk-tree determined or prespecified categories were analyzed, with discrimination of risk quantified by the c-statistic. In this cohort, mean age was 79.0 years and 58% were female. The median NIHSS score was 5 (25th to 75th percentile 2 to 12). There were 4496 deaths in the first 30 days (13.6%). There was a strong graded relation between increasing NIHSS score and higher 30-day mortality. The 30-day mortality rates for acute ischemic stroke by NIHSS categories were as follows: 0 to 7, 4.2%; 8 to 13, 13.9%; 14 to 21, 31.6%; 22 to 42, 53.5%. A model with NIHSS alone provided excellent discrimination whether included as a continuous variable (c-statistic 0.82 [0.81 to 0.83]), 4 categories (c-statistic 0.80 [0.79 to 0.80]), or 3 categories (c-statistic 0.79 [0.78 to 0.79]).ConclusionsThe NIHSS provides substantial prognostic information regarding 30-day mortality risk in Medicare beneficiaries with acute ischemic stroke. This index of stroke severity is a very strong discriminator of mortality risk, even in the absence of other clinical information, whether used as a continuous or categorical risk determinant. (J Am Heart Assoc. 2012;1:42-50.)

Positive Surgical Margins in the 10 Most Common Solid Cancers.

A positive surgical margin (PSM) following cancer resection oftentimes necessitates adjuvant treatments and carries significant financial and prognostic implications. We sought to compare PSM rates for the ten most common solid cancers in the United States, and to assess trends over time. Over 10 million patients were identified in the National Cancer Data Base from 1998-2012, and 6.5 million had surgical margin data. PSM rates were compared between two time periods, 1998-2002 and 2008-2012. PSM was positively correlated with tumor category and grade. Ovarian and prostate cancers had the highest PSM prevalence in women and men, respectively. The highest PSM rates for cancers affecting both genders were seen for oral cavity tumors. PSM rates for breast cancer and lung and bronchus cancer in both men and women declined over the study period. PSM increases were seen for bladder, colon and rectum, and kidney and renal pelvis cancers. This large-scale analysis appraises the magnitude of PSM in the United States in order to focus future efforts on improving oncologic surgical care with the goal of optimizing value and improving patient outcomes

Socioeconomic Status, Psychosocial Factors, Race and Nocturnal Blood Pressure Dipping in a Hispanic Cohort

BACKGROUND Little information is available about the relationship of socioeconomic status (SES) to blunted nocturnal ambulatory blood pressure (ABP) dipping among Hispanics and whether this relationship differs by race. We sought to characterize ABP nondipping and its determinants in a sample of Hispanics. METHODS We enrolled 180 Hispanic participants not on antihypertensive medications. SES was defined by years of educational attainment. All participants underwent 24-hour ABP monitoring. A decrease of <10% in the ratio between average awake and average asleep systolic BP was considered nondipping. RESULTS The mean age of the cohort was 67.1 ± 8.7, mean educational level was 9.4 ± 4.4 years, and 58.9% of the cohort was female. The cohort was comprised of 78.3% Caribbean Hispanics with the rest from Mexico and Central/South America; 41.4% self-identified as white Hispanic, 34.4% self-identified as black Hispanic, and 24.4% did not racially self- identify. The percentage of nondippers was 57.8%. Educational attainment (10.5 years vs. 8.6 years; P <0.01) was significantly higher among dippers than nondippers. In multivariable analyses, each 1-year increase in education was associated with a 9% reduction in the likelihood of being a nondipper (odds ratio [OR], 0.91; 95% confidence interval [CI], 0.84–0.98; P = 0.01). There were significantly greater odds of being a nondipper for black Hispanics than for white Hispanics (OR, 2.83, 95% CI, 1.29–6.23; P = 0.005). Higher SES was significantly protective of nondipping in white Hispanics but not black Hispanics. CONCLUSIONS These results document a substantial prevalence of nondipping in a cohort of predominantly normotensive Hispanics. Dipping status varied significantly by race. Lower SES is significantly associated with nondipping status, and race potentially impacts on this relation

Loss of the deubiquitylase BAP1 alters class I histone deacetylase expression and sensitivity of mesothelioma cells to HDAC inhibitors

Histone deacetylases are important targets for cancer therapeutics, but their regulation is poorly understood. Our data show coordinated transcription of HDAC1 and HDAC2 in lung cancer cell lines, but suggest HDAC2 protein expression is cell-context specific. Through an unbiased siRNA screen we found that BRCA1-associated protein 1 (BAP1) regulates their expression, with HDAC2 reduced and HDAC1 increased in BAP1 depleted cells. BAP1 loss-of-function is increasingly reported in cancers including thoracic malignancies, with frequent mutation in malignant pleural mesothelioma. Endogenous HDAC2 directly correlates with BAP1 across a panel of lung cancer cell lines, and is downregulated in mesothelioma cell lines with genetic BAP1 inactivation. We find that BAP1 regulates HDAC2 by increasing transcript abundance, rather than opposing its ubiquitylation. Importantly, although total cellular HDAC activity is unaffected by transient depletion of HDAC2 or of BAP1 due to HDAC1 compensation, this isoenzyme imbalance sensitizes MSTO-211H cells to HDAC inhibitors. However, other established mesothelioma cell lines with low endogenous HDAC2 have adapted to become more resistant to HDAC inhibition. Our work establishes a mechanism by which BAP1 loss alters sensitivity of cancer cells to HDAC inhibitors. Assessment of BAP1 and HDAC expression may ultimately help identify patients likely to respond to HDAC inhibitors