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Author Karanth, P.K. openurl 
  Title An island called India: phylogenetic patterns across multiple taxonomic groups reveal endemic radiations Type Journal Article
  Year 2015 Publication Abbreviated Journal Current Science  
  Volume 108 Issue 10 Pages (down) 1847-1851  
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  Call Number CES @ dilipnaidu.gt @ Serial 43063  
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Author Laurenti, M.; Perrone, D.; Verna, A.; Pirri, C.F.; Chiolerio, A. url  openurl
  Title Development of a flexible lead-free piezoelectric transducer for health monitoring in the space environment Type Journal Article
  Year 2015 Publication Abbreviated Journal Micromachines  
  Volume 6 Issue 11 Pages (down) 1729-1744  
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  Notes Cited By :4; Export Date: 2 November 2016 Approved no  
  Call Number IIT-CSF @ alessandro.chiolerio @ Serial 42781  
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Author Albers, J.; Danzer, C.; Rechsteiner, M.; Lehmann, H.; Brandt, L.P.; Hejhal, T.; Catalano, A.; Busenhart, P.; Gonçalves, A.F.; Brandt, S.; Bode, P.K.; Bode-Lesniewska, B.; Wild, P.J.; Frew, I.J. url  openurl
  Title A versatile modular vector system for rapid combinatorial mammalian genetics Type Journal Article
  Year 2015 Publication Abbreviated Journal J Clin Invest  
  Volume 125 Issue 4 Pages (down) 1603-1619  
  Keywords Animals; Apoptosis; Caspase 9; Cells, Cultured; Cloning, Molecular; Clustered Regularly Interspaced Short Palindromic Repeats; Doxycycline; Drug Resistance; Gene Deletion; Gene Knockdown Techniques; Genetic Vectors; Humans; Hypoxia-Inducible Factor 1, alpha Subunit; Lentivirus; Mice; Mice, SCID; PTEN Phosphohydrolase; Recombination, Genetic; research support, non-u.s. gov’t; Retinoblastoma Protein; RNA, Small Interfering; Sarcoma, Experimental; Transduction, Genetic; Tumor Suppressor Protein p53; Xenograft Model Antitumor Assays; Cas9/CRIPSR; Journal club  
  Abstract Here, we describe the multiple lentiviral expression (MuLE) system that allows multiple genetic alterations to be introduced simultaneously into mammalian cells. We created a toolbox of MuLE vectors that constitute a flexible, modular system for the rapid engineering of complex polycistronic lentiviruses, allowing combinatorial gene overexpression, gene knockdown, Cre-mediated gene deletion, or CRISPR/Cas9-mediated (where CRISPR indicates clustered regularly interspaced short palindromic repeats) gene mutation, together with expression of fluorescent or enzymatic reporters for cellular assays and animal imaging. Examples of tumor engineering were used to illustrate the speed and versatility of performing combinatorial genetics using the MuLE system. By transducing cultured primary mouse cells with single MuLE lentiviruses, we engineered tumors containing up to 5 different genetic alterations, identified genetic dependencies of molecularly defined tumors, conducted genetic interaction screens, and induced the simultaneous CRISPR/Cas9-mediated knockout of 3 tumor-suppressor genes. Intramuscular injection of MuLE viruses expressing oncogenic H-RasG12V together with combinations of knockdowns of the tumor suppressors cyclin-dependent kinase inhibitor 2A (Cdkn2a), transformation-related protein 53 (Trp53), and phosphatase and tensin homolog (Pten) allowed the generation of 3 murine sarcoma models, demonstrating that genetically defined autochthonous tumors can be rapidly generated and quantitatively monitored via direct injection of polycistronic MuLE lentiviruses into mouse tissues. Together, our results demonstrate that the MuLE system provides genetic power for the systematic investigation of the molecular mechanisms that underlie human diseases.  
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  Call Number UofT @ mathieu.lemaire @ Serial 45848  
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Author Jones, O.C.; McDonald, I.; Rich, R.M.; Kemper, F.; Boyer, M.L.; Zijlstra, A.A.; Bendo, G.J. url  openurl
  Title A Spitzer Space Telescope survey of extreme asymptotic giant branch stars in M32 Type Journal Article
  Year 2015 Publication Mon.~Not.~R.~Astron.~Soc. Abbreviated Journal  
  Volume 446 Issue 2 Pages (down) 1584-1596  
  Keywords stars: AGB and post-AGB; stars: late-type; stars: mass-loss; galaxies: individual: M32; galaxies: stellar content; infrared: stars  
  Abstract We investigate the population of cool, evolved stars in the Local Group dwarf elliptical galaxy M32, using Infrared Array Camera observations from the Spitzer Space Telescope. We construct deep mid-infrared colour-magnitude diagrams for the resolved stellar populations within 3.5 arcmin of M32's centre, and identify those stars that exhibit infrared excess. Our data are dominated by a population of luminous, dust-producing stars on the asymptotic giant branch (AGB) and extend to approximately 3 mag below the AGB tip. We detect for the first time a sizeable population of `extreme' AGB stars, highly enshrouded by circumstellar dust and likely completely obscured at optical wavelengths. The total dust-injection rate from the extreme AGB candidates is measured to be 7.5 × 10-7 M⊙ yr-1, corresponding to a gas mass-loss rate of 1.5 × 10-4 M⊙ yr-1. These extreme stars may be indicative of an extended star formation epoch between 0.2 and 5 Gyr ago.  
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  Notes refereed; Owner: ciska; Added to JabRef: 2015.04.15 Approved no  
  Call Number ASIAA @ ciska @ Serial 41992  
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Author Émond, K.; Sainte-Marie, B.; Galbraith, P.S.; Bêty, J. url  openurl
  Title Top-down vs. bottom-up drivers of recruitment in a key marine invertebrate: Investigating early life stages of snow crab Type Journal Article
  Year 2015 Publication Abbreviated Journal ICES Journal of Marine Science  
  Volume 72 Issue 5 Pages (down) 1336-1348  
  Keywords cannibalism; climate; groundfish predation; larval production; population dynamics; recruitment; snow crab  
  Abstract Many snow crab fisheries have fluctuated widely over time in a quasi-cyclic way due to highly variable recruitment. The causes of this variability are still debated. Bottom-up processes related to climate variability may strongly affect growth and survival during early life, whereas top-down predator effects may be a major source of juvenile mortality. Moreover, intrinsic density-dependent processes, which have received much less attention, are hypothetically responsible for the cycles in recruitment. This study explored how climate, larval production, intercohort cannibalism and groundfish predation may have affected recruitment of early juvenile snow crab in the northwest Gulf of St Lawrence (eastern Canada) over a period of 23 years. Abundance of early juvenile snow crabs (2.5-22.9 mm in carapace width), representing the first 3 years of benthic life, came from an annual trawl survey and was used to determine cohort strength. Analyses revealed a cyclic pattern in abundance of 0+ crabs that may arise from cohort resonant effects. This pattern consisted of three recruitment pulses but was reduced to two pulses by age 2+, while the interannual variability of cohort strength was dampened. This reconfiguration of the earliest recruitment pattern was dictated primarily by bottom water temperature and cannibalism, which progressively overruled the pre-settlement factors of larval production and surface water temperature that best explained abundance of 0+ crabs. The results strongly suggest that bottom-up and density-dependent processes prevail over top-down control in setting the long-term trends and higher-frequency oscillations of snow crab early recruitment patterns. © 2015 International Council for the Exploration of the Sea 2015. All rights reserved. For Permissions, please email: journals.permissions@oup.com.  
  Address Department of Fisheries and Oceans, Maurice Lamontagne Institute, 850 Route de la Mer, Mont-Joli, QC, Canada  
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  Notes Export Date: 17 March 2016 Approved no  
  Call Number McgGll @ elizabethburgess @ Serial 42532  
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Author Skirnisdottir, I.; Seidal, T.; Åkerud, H. url  openurl
  Title Differences in Clinical and Biological Features Between Type I and Type II Tumors in FIGO Stages I-II Epithelial Ovarian Carcinoma Type Journal Article
  Year 2015 Publication Abbreviated Journal Int J Gynecol Cancer  
  Volume 25 Issue 7 Pages (down) 1239-1247  
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  Abstract OBJECTIVE: The objective of this study was to compare immunohistochemical profile for the apoptosis regulators p53, C-MYC, bax, PUMA, and PTEN and the cell cycle regulatory proteins p21 and p27, as well as clinical factors between types I and II tumors. METHODS: In total, 131 patients in FIGO (International Federation of Gynecology and Obstetrics) stages I-II were divided into 2 groups of patients after type I tumors (n = 79) and type II tumors (n = 52). Differences in the immunohistochemical profile for the cell cycle-related proteins, detected by tissue microarrays and immune-histochemistry, were compared. For statistical tests, the Pearson χ test and the logistic regression model were used. All tests were 2-sided, and the level of statistical significance was P ≤ 0.05. RESULTS: In multivariate logistic regression analysis with recurrent disease as endpoint, FIGO stage (odds ratio [OR], 4.7), type I/II tumors (OR, 3.8), body mass index (BMI) (OR, 3.5), and p53 status (OR, 4.2) all were found to be independent predictive factors. In 2 different multivariate logistic regression analyses with type I/II tumors as endpoint, both p53p21 (OR, 2.9) and p27 status (OR, 3.0) were associated with type II tumors. Differently, C-MYC status (OR, 0.4) was associated with type I tumors. Furthermore, age (OR, 1.04), BMI (OR, 0.4), and recurrent disease (OR, 4.3) all were associated to type II tumors. In survival analysis, there was a trend (P = 0.054) toward better disease-free survival for patients with type I tumors. CONCLUSIONS: Concomitant positivity for p53 and negativity for p21, positivity for p27, and negativity for C-MYC in an epithelial ovarian tumor might strengthen the diagnostic option of type II tumor ovarian carcinoma. Patients with type II tumors were older, had lower BMI, and had more often recurrent disease than patients with type I tumors.  
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  Call Number UofT @ ankit.sinha @ Serial 44930  
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Author Ignatchenko, V.; Ignatchenko, A.; Sinha, A.; Boutros, P.C.; Kislinger, T. url  openurl
  Title VennDIS: a JavaFX-based Venn and Euler diagram software to generate publication quality figures Type Journal Article
  Year 2015 Publication Abbreviated Journal Proteomics  
  Volume 15 Issue 7 Pages (down) 1239-1244  
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  Abstract Venn diagrams are graphical representations of the relationships among multiple sets of objects and are often used to illustrate similarities and differences among genomic and proteomic datasets. All currently existing tools for producing Venn diagrams evince one of two traits; they require expertise in specific statistical software packages (such as R), or lack the flexibility required to produce publication-quality figures. We describe a simple tool that addresses both shortcomings, Venn Diagram Interactive Software (VennDIS), a JavaFX-based solution for producing highly customizable, publication-quality Venn, and Euler diagrams of up to five sets. The strengths of VennDIS are its simple graphical user interface and its large array of customization options, including the ability to modify attributes such as font, style and position of the labels, background color, size of the circle/ellipse, and outline color. It is platform independent and provides real-time visualization of figure modifications. The created figures can be saved as XML files for future modification or exported as high-resolution images for direct use in publications.  
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  Call Number UofT @ ankit.sinha @ Serial 45271  
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Author Surinova, S.; Choi, M.; Tao, S.; Schüffler, P.J.; Chang, C.Y.; Clough, T.; Vysloužil, K.; Khoylou, M.; Srovnal, J.; Liu, Y.; Matondo, M.; Hüttenhain, R.; Weisser, H.; Buhmann, J.M.; Hajdúch, M.; Brenner, H.; Vitek, O.; Aebersold, R. url  openurl
  Title Prediction of colorectal cancer diagnosis based on circulating plasma proteins Type Journal Article
  Year 2015 Publication Abbreviated Journal EMBO Mol Med  
  Volume 7 Issue 9 Pages (down) 1166-1178  
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  Abstract Non-invasive detection of colorectal cancer with blood-based markers is a critical clinical need. Here we describe a phased mass spectrometry-based approach for the discovery, screening, and validation of circulating protein biomarkers with diagnostic value. Initially, we profiled human primary tumor tissue epithelia and characterized about 300 secreted and cell surface candidate glycoproteins. These candidates were then screened in patient systemic circulation to identify detectable candidates in blood plasma. An 88-plex targeting method was established to systematically monitor these proteins in two large and independent cohorts of plasma samples, which generated quantitative clinical datasets at an unprecedented scale. The data were deployed to develop and evaluate a five-protein biomarker signature for colorectal cancer detection.  
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  Call Number UofT @ ankit.sinha @ Serial 45345  
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Author Andeen, N.K.; Nguyen, T.Q.; Steegh, F.; Hudkins, K.L.; Najafian, B.; Alpers, C.E. url  openurl
  Title The phenotypes of podocytes and parietal epithelial cells may overlap in diabetic nephropathy Type Journal Article
  Year 2015 Publication Abbreviated Journal Kidney Int  
  Volume 88 Issue 5 Pages (down) 1099-1107  
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  Abstract Reversal of diabetic nephropathy (DN) has been achieved in humans and mice, but only rarely and under special circumstances. As progression of DN is related to podocyte loss, reversal of DN requires restoration of podocytes. Here, we identified and quantified potential glomerular progenitor cells that could be a source for restored podocytes. DN was identified in 31 human renal biopsy cases and separated into morphologically early or advanced lesions. Markers of podocytes (WT-1, p57), parietal epithelial cells (PECs) (claudin-1), and cell proliferation (Ki-67) were identified by immunohistochemistry. Podocyte density was progressively reduced with DN. Cells marking as podocytes (p57) were present infrequently on Bowman’s capsule in controls, but significantly increased in histologically early DN. Ki-67-expressing cells were identified on the glomerular tuft and Bowman’s capsule in DN, but rarely in controls. Cells marking as PECs were present on the glomerular tuft, particularly in morphologically advanced DN. These findings show evidence of phenotypic plasticity in podocyte and PEC populations and are consistent with studies in the BTBR ob/ob murine model in which reversibility of DN occurs with podocytes potentially regenerating from PEC precursors. Thus, our findings support, but do not prove, that podocytes may regenerate from PEC progenitors in human DN. If so, progression of DN may represent a modifiable net balance between podocyte loss and regeneration.  
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  Call Number UofT @ mathieu.lemaire @ Serial 45953  
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Author Schölz, C.; Lyon, D.; Refsgaard, J.C.; Jensen, L.J.; Choudhary, C.; Weinert, B.T. url  openurl
  Title Avoiding abundance bias in the functional annotation of post-translationally modified proteins Type Journal Article
  Year 2015 Publication Abbreviated Journal Nat Methods  
  Volume 12 Issue 11 Pages (down) 1003-1004  
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  Call Number UofT @ ankit.sinha @ Serial 45272  
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