177 research outputs found

    Building Virtual Private Networks to Support Mobile VPN users in a Group with Quality of Service Guarantees

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    Flexible, secure and cost effective in comparison to traditional solutions, IP-VPNs exhibit many of the traits enterprises are seeking today. Mobile VPN users have special requirements relating to resource adoption and customization. In this paper we have discussed how mobile agent technology can be applied to IP-VPN in finding a route for a tunnel with QoS features and also how can it provide service capabilities to mobile users. In our approach, we have considered the requirement from a group of VPN users. We have developed a framework to use active packets that can help us in discovering an optimal QoS route based on the available bandwidth and link cost. Also we have described an alternative approach for resource management between two agents. Taking into account, the structuring mechanisms enabled by standard mobile agent platforms, like regions, agencies grouped within regions, and places belonging to agencies, we have applied these structural principles to our target mobile communications environment. We have assumed that service providers have access to node’s control environment, algorithms and states. A possible framework for supporting mobile user groups after the deployment of the VPN issuggested in this paper. We have considered the concept of Place Oriented VPNs that are based on agent technology and can be built on top of existing VPN infrastructure

    Evolutionary origins of insulin resistance: a behavioral switch hypothesis

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    <p>Abstract</p> <p>Background</p> <p>Insulin resistance, which can lead to a number of diseases including type 2 diabetes and coronary heart disease, is believed to have evolved as an adaptation to periodic starvation. The "thrifty gene" and "thrifty phenotype" hypotheses constitute the dominant paradigm for over four decades. With an increasing understanding of the diverse effects of impairment of the insulin signaling pathway, the existing hypotheses are proving inadequate.</p> <p>Presentation of the hypothesis</p> <p>We propose a hypothesis that insulin resistance is a socio-ecological adaptation that mediates two phenotypic transitions, (i) a transition in reproductive strategy from "r" (large number of offspring with little investment in each) to "K" (smaller number of offspring with more investment in each) and (ii) a transition from "stronger to smarter" or "soldier to diplomat" i.e. from relatively more muscle dependent to brain dependent lifestyle. A common switch could have evolved for the two transitions since the appropriate environmental conditions for the two transitions are highly overlapping and interacting.</p> <p>Testing the hypothesis</p> <p>Gestational insulin resistance diverts more energy through the placenta, resulting in increased investment per offspring. On the other hand, insulin resistance is associated with reduced ovulation. The insulin signaling pathway is also related to longevity. Insulin resistance diverts more nutrients to the brain as compared to muscle. Also, hyperinsulinemia has direct positive effects on cognitive functions of the brain. The hypothesis gets support from known patterns in human clinical data and recent research on the molecular interactions in the insulin signaling pathway. Further we state many predictions of the hypothesis that can be tested experimentally or epidemiologically.</p> <p>Implications of the hypothesis</p> <p>The hypothesis can bring about a significant change in the line of treatment as well as public health policies for the control of metabolic syndrome.</p

    Designed β-hairpin peptides with defined tight turn stereochemistry

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    The conformational analysis of two synthetic octapeptides, Boc-Leu-Val-Val-D-Pro-L-Ala-Leu-Val-Val-OMe (1) and Boc-Leu-Val-Val-D-Pro-D-Ala-Leu-Val-Val-OMe (2) has been carried out in order to investigate the effect of &#946;-turn stereochemistry on designed &#946;-hairpin structures. Five hundred megahertz 1H NMR studies establish that both peptides 1 and 2 adopt predominantly &#946;-hairpin conformations in methanol solution. Specific nuclear Overhauser effects provide evidence for a type II&#8242; &#946;-turn conformation for the D-Pro-L-Ala segment in 1, while the NMR data suggest that the type I D-Pro-D-Ala &#946;-turn conformation predominates in peptide 2. Evidence for a minor conformation in peptide 2, in slow exchange on the NMR time scale, is also presented. Interstrand registry is demonstrated in both peptides 1 and 2. The crystal structure of 1 reveals two independent molecules in the crystallographic asymmetric unit, both of which adopt &#946;-hairpin conformations nucleated by D-Pro-L-Ala type II&#8242; &#946;-turns and are stabilized by three cross-strand hydrogen bonds. CD spectra for peptides 1 and 2 show marked differences, presumably as a consequence of the superposition of spectral bands arising from both &#946;-turn and &#946;-strand conformations

    Evaluation of accuracy of various impression techniques and impression materials in recording multiple implants placed unilaterally in a partially edentulous mandible- An in vitro study

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    Various factors like implant angulation, type of impression material and tray type affects the implant impression accuracy. To date limited in-vitro studies were carried out on the implant impression accuracy of unilateral partially edentulous arches. The aim of this research was to evaluate the effects of 0o, 15o and 25o implant angulations on impression accuracy in simulated master casts of unilateral partially edentulous situation using different impression materials and tray selections. 30 replicas (N = 30) of a resin matrix (control) containing four implant analogues placed unilaterally from the midline till the region of second molar at an angulation of 00, 00, 150 and 250 to the vertical axis of the ridge respectively were obtained by using three impression techniques (stock metal tray, closed custom tray, and open nonsplinted custom tray) and two different impression materials (Polyvinyl-siloxane and polyether). Specific dimensions of the resultant casts were measured using coordinated measuring microscope. Mean linear changes were calculated and statistically analyzed using analysis of variance (ANOVA) and Tukey?s post-hoc procedures (p< 0.05). The casts obtained from all three impression techniques had significant differences in dimensions (p<0.05) as compared to that of master model irrespective of impression materials. Comparing the techniques with regard to the parallel implants, no statistical significant difference (p<0.05) was observed with custom tray techniques (closed/open). Whereas while comparing parallel versus non parallel, open tray technique showed superior accuracy compared to closed tray technique as the angulation increased more than 15 degrees. The influence of material and technique appeared to be significant for highly non axial implant angulations (p< 0.05), and increased angulation tended to decrease impression accuracy. The open tray technique was more accurate with highly nonaxially oriented implants for the small sample size investigated

    Iodine status during pregnancy in India and related neonatal and infant outcomes

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    Objective: To document iodine status in Indian pregnancies, associations with maternal diet and demographics, and offspring developmental measures. Design: Longitudinal study following mothers through pregnancy and offspring up to 24 months. Setting: Rural health-care centre (Vadu) and urban antenatal clinic (Pune) in the Maharashtra region of India. Subjects: Pregnant mothers at 17 (n 132) and 34 weeks’ (n 151) gestation and their infants from birth to the age of 24 months. Results: Median urinary iodine concentration (UIC) was 203 and 211 μg/l at 17 and 34 weeks of pregnancy, respectively (range 26–800 μg/l). Using the UIC distribution adjusted for within-person variation, extreme UIC quartiles were compared for predictors and outcomes. There was no correlation between UIC at 17 and 34 weeks, but 24 % of those with UIC in the lowest quartile at 17 weeks had UIC in the same lowest quartile at 34 weeks. Maternal educational, socio-economic status and milk products consumption (frequency) were different between the lowest and highest quartile of UIC at 34 weeks. Selected offspring developmental outcomes differed between the lowest and highest UIC quartiles (abdominal circumference at 24 months, subscapular and triceps skinfolds at 12 and 24 months). However, UIC was only a weak predictor of subscapular skinfold at 12 months and of triceps skinfold at 24 months. Conclusions: Median UIC in this pregnant population suggested adequate dietary provision at both gestational stages studied. Occasional high results found in spot samples may indicate intermittent consumption of iodine-rich foods. Maternal UIC had limited influence on offspring developmental outcomes

    Overview of the PAN/CLEF 2015 Evaluation Lab

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    The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-24027-5_49This paper presents an overview of the PAN/CLEF evaluation lab. During the last decade, PAN has been established as the main forum of text mining research focusing on the identification of personal traits of authors left behind in texts unintentionally. PAN 2015 comprises three tasks: plagiarism detection, author identification and author profiling studying important variations of these problems. In plagiarism detection, community-driven corpus construction is introduced as a new way of developing evaluation resources with diversity. In author identification, cross-topic and cross-genre author verification (where the texts of known and unknown authorship do not match in topic and/or genre) is introduced. A new corpus was built for this challenging, yet realistic, task covering four languages. In author profiling, in addition to usual author demographics, such as gender and age, five personality traits are introduced (openness, conscientiousness, extraversion, agreeableness, and neuroticism) and a new corpus of Twitter messages covering four languages was developed. In total, 53 teams participated in all three tasks of PAN 2015 and, following the practice of previous editions, software submissions were required and evaluated within the TIRA experimentation framework.Stamatatos, E.; Potthast, M.; Rangel, F.; Rosso, P.; Stein, B. (2015). Overview of the PAN/CLEF 2015 Evaluation Lab. En Experimental IR Meets Multilinguality, Multimodality, and Interaction: 6th International Conference of the CLEF Association, CLEF'15, Toulouse, France, September 8-11, 2015, Proceedings. Springer International Publishing. 518-538. doi:10.1007/978-3-319-24027-5_49S518538Álvarez-Carmona, M.A., López-Monroy, A.P., Montes-Y-Gómez, M., Villaseñor-Pineda, L., Jair-Escalante, H.: INAOE’s participation at PAN 2015: author profiling task–notebook for PAN at CLEF 2015. In: CLEF 2013 Working Notes. CEUR (2015)Argamon, S., Koppel, M., Fine, J., Shimoni, A.R.: Gender, Genre, and Writing Style in Formal Written Texts. TEXT 23, 321–346 (2003)Bagnall, D.: Author identification using multi-headed recurrent neural networks. In: CLEF 2015 Working Notes. CEUR (2015)Burger, J.D., Henderson, J., Kim, G., Zarrella, G.: Discriminating gender on twitter. In: Proceedings of EMNLP 2011. ACL (2011)Burrows, S., Potthast, M., Stein, B.: Paraphrase Acquisition via Crowdsourcing and Machine Learning. ACM TIST 4(3), 43:1–43:21 (2013)Castillo, E., Cervantes, O., Vilariño, D., Pinto, D., León, S.: Unsupervised method for the authorship identification task. In: CLEF 2014 Labs and Workshops, Notebook Papers. CEUR (2014)Celli, F., Lepri, B., Biel, J.I., Gatica-Perez, D., Riccardi, G., Pianesi, F.: The workshop on computational personality recognition 2014. In: Proceedings of ACM MM 2014 (2014)Celli, F., Pianesi, F., Stillwell, D., Kosinski, M.: Workshop on computational personality recognition: shared task. In: Proceedings of WCPR at ICWSM 2013 (2013)Celli, F., Polonio, L.: Relationships between personality and interactions in facebook. In: Social Networking: Recent Trends, Emerging Issues and Future Outlook. Nova Science Publishers, Inc. (2013)Chaski, C.E.: Who’s at the Keyboard: Authorship Attribution in Digital Evidence Invesigations. International Journal of Digital Evidence 4 (2005)Chittaranjan, G., Blom, J., Gatica-Perez, D.: Mining Large-scale Smartphone Data for Personality Studies. Personal and Ubiquitous Computing 17(3), 433–450 (2013)Fréry, J., Largeron, C., Juganaru-Mathieu, M.: UJM at clef in author identification. In: CLEF 2014 Labs and Workshops, Notebook Papers. CEUR (2014)Gollub, T., Potthast, M., Beyer, A., Busse, M., Rangel, F., Rosso, P., Stamatatos, E., Stein, B.: Recent trends in digital text forensics and its evaluation. In: Forner, P., Müller, H., Paredes, R., Rosso, P., Stein, B. (eds.) CLEF 2013. LNCS, vol. 8138, pp. 282–302. Springer, Heidelberg (2013)Gollub, T., Stein, B., Burrows, S.: Ousting ivory tower research: towards a web framework for providing experiments as a service. In: Proceedings of SIGIR 2012. ACM (2012)Hagen, M., Potthast, M., Stein, B.: Source retrieval for plagiarism detection from large web corpora: recent approaches. In: CLEF 2015 Working Notes. CEUR (2015)van Halteren, H.: Linguistic profiling for author recognition and verification. In: Proceedings of ACL 2004. ACL (2004)Holmes, J., Meyerhoff, M.: The Handbook of Language and Gender. Blackwell Handbooks in Linguistics. Wiley (2003)Jankowska, M., Keselj, V., Milios, E.: CNG text classification for authorship profiling task–notebook for PAN at CLEF 2013. In: CLEF 2013 Working Notes. CEUR (2013)Juola, P.: Authorship Attribution. Foundations and Trends in Information Retrieval 1, 234–334 (2008)Juola, P.: How a Computer Program Helped Reveal J.K. Rowling as Author of A Cuckoo’s Calling. Scientific American (2013)Juola, P., Stamatatos, E.: Overview of the author identification task at PAN-2013. In: CLEF 2013 Working Notes. CEUR (2013)Kalimeri, K., Lepri, B., Pianesi, F.: Going beyond traits: multimodal classification of personality states in the wild. In: Proceedings of ICMI 2013. ACM (2013)Koppel, M., Argamon, S., Shimoni, A.R.: Automatically Categorizing Written Texts by Author Gender. Literary and Linguistic Computing 17(4) (2002)Koppel, M., Schler, J., Bonchek-Dokow, E.: Measuring Differentiability: Unmasking Pseudonymous Authors. J. Mach. Learn. Res. 8, 1261–1276 (2007)Koppel, M., Winter, Y.: Determining if Two Documents are Written by the same Author. Journal of the American Society for Information Science and Technology 65(1), 178–187 (2014)Kosinski, M., Bachrach, Y., Kohli, P., Stillwell, D., Graepel, T.: Manifestations of User Personality in Website Choice and Behaviour on Online Social Networks. Machine Learning (2013)López-Monroy, A.P., y Gómez, M.M., Jair-Escalante, H., Villaseñor-Pineda, L.: Using intra-profile information for author profiling–notebook for PAN at CLEF 2014. In: CLEF 2014 Working Notes. CEUR (2014)Lopez-Monroy, A.P., Montes-Y-Gomez, M., Escalante, H.J., Villasenor-Pineda, L., Villatoro-Tello, E.: INAOE’s participation at PAN 2013: author profiling task-notebook for PAN at CLEF 2013. In: CLEF 2013 Working Notes. CEUR (2013)Luyckx, K., Daelemans, W.: Authorship attribution and verification with many authors and limited data. In: Proceedings of COLING 2008 (2008)Maharjan, S., Shrestha, P., Solorio, T., Hasan, R.: A straightforward author profiling approach in mapreduce. In: Bazzan, A.L.C., Pichara, K. (eds.) IBERAMIA 2014. LNCS, vol. 8864, pp. 95–107. Springer, Heidelberg (2014)Mairesse, F., Walker, M.A., Mehl, M.R., Moore, R.K.: Using Linguistic Cues for the Automatic Recognition of Personality in Conversation and Text. Journal of Artificial Intelligence Research 30(1), 457–500 (2007)Eissen, S.M., Stein, B.: Intrinsic plagiarism detection. In: Lalmas, M., MacFarlane, A., Rüger, S.M., Tombros, A., Tsikrika, T., Yavlinsky, A. (eds.) ECIR 2006. LNCS, vol. 3936, pp. 565–569. Springer, Heidelberg (2006)Mohammadi, G., Vinciarelli, A.: Automatic personality perception: Prediction of Trait Attribution Based on Prosodic Features. IEEE Transactions on Affective Computing 3(3), 273–284 (2012)Moreau, E., Jayapal, A., Lynch, G., Vogel, C.: Author verification: basic stacked generalization applied to predictions from a set of heterogeneous learners. In: CLEF 2015 Working Notes. CEUR (2015)Nguyen, D., Gravel, R., Trieschnigg, D., Meder, T.: “How old do you think I am?”; a study of language and age in twitter. In: Proceedings of ICWSM 2013. AAAI (2013)Oberlander, J., Nowson, S.: Whose thumb is it anyway?: classifying author personality from weblog text. In: Proceedings of COLING 2006. ACL (2006)Peñas, A., Rodrigo, A.: A simple measure to assess non-response. In: Proceedings of HLT 2011. ACL (2011)Pennebaker, J.W., Mehl, M.R., Niederhoffer, K.G.: Psychological Aspects of Natural Language Use: Our Words. Our Selves. Annual Review of Psychology 54(1), 547–577 (2003)Potthast, M., Barrón-Cedeño, A., Eiselt, A., Stein, B., Rosso, P.: Overview of the 2nd international competition on plagiarism detection. In: CLEF 2010 Working Notes. CEUR (2010)Potthast, M., Barrón-Cedeño, A., Stein, B., Rosso, P.: Cross-Language Plagiarism Detection. Language Resources and Evaluation (LRE) 45, 45–62 (2011)Potthast, M., Eiselt, A., Barrón-Cedeño, A., Stein, B., Rosso, P.: Overview of the 3rd international competition on plagiarism detection. In: CLEF 2011 Working Notes (2011)Potthast, M., Gollub, T., Hagen, M., Graßegger, J., Kiesel, J., Michel, M., Oberländer, A., Tippmann, M., Barrón-Cedeño, A., Gupta, P., Rosso, P., Stein, B.: Overview of the 4th international competition on plagiarism detection. In: CLEF 2012 Working Notes. CEUR (2012)Potthast, M., Gollub, T., Hagen, M., Tippmann, M., Kiesel, J., Rosso, P., Stamatatos, E., Stein, B.: Overview of the 5th international competition on plagiarism detection. In: CLEF 2013 Working Notes. CEUR (2013)Potthast, M., Gollub, T., Rangel, F., Rosso, P., Stamatatos, E., Stein, B.: Improving the reproducibility of PAN’s shared tasks: plagiarism detection, author identification, and author profiling. In: Kanoulas, E., Lupu, M., Clough, P., Sanderson, M., Hall, M., Hanbury, A., Toms, E. (eds.) CLEF 2014. LNCS, vol. 8685, pp. 268–299. Springer, Heidelberg (2014)Potthast, M., Hagen, M., Beyer, A., Busse, M., Tippmann, M., Rosso, P., Stein, B.: Overview of the 6th international competition on plagiarism detection. In: CLEF 2014 Working Notes. CEUR (2014)Potthast, M., Göring, S., Rosso, P., Stein, B.: Towards data submissions for shared tasks: first experiences for the task of text alignment. In: CLEF 2015 Working Notes. CEUR (2015)Potthast, M., Hagen, M., Stein, B., Graßegger, J., Michel, M., Tippmann, M., Welsch, C.: ChatNoir: a search engine for the clueweb09 corpus. In: Proceedings of SIGIR 2012. ACM (2012)Potthast, M., Hagen, M., Völske, M., Stein, B.: Crowdsourcing interaction logs to understand text reuse from the web. In: Proceedings of ACL 2013. ACL (2013)Potthast, M., Stein, B., Barrón-Cedeño, A., Rosso, P.: An evaluation framework for plagiarism detection. In: Proceedings of COLING 2010. ACL (2010)Potthast, M., Stein, B., Eiselt, A., Barrón-Cedeño, A., Rosso, P.: Overview of the 1st international competition on plagiarism detection. In: Proceedings of PAN at SEPLN 2009. CEUR (2009)Quercia, D., Lambiotte, R., Stillwell, D., Kosinski, M., Crowcroft, J.: The personality of popular facebook users. In: Proceedings of CSCW 2012. ACM (2012)Rammstedt, B., John, O.: Measuring Personality in One Minute or Less: A 10 Item Short Version of the Big Five Inventory in English and German. Journal of Research in Personality (2007)Rangel, F., Rosso, P.: On the impact of emotions on author profiling. In: Information Processing & Management, Special Issue on Emotion and Sentiment in Social and Expressive Media (2014) (in press)Rangel, F., Rosso, P., Celli, F., Potthast, M., Stein, B., Daelemans, W.: Overview of the 3rd author profiling task at PAN 2015. In: CLEF 2015 Working Notes. CEUR (2015)Rangel, F., Rosso, P., Chugur, I., Potthast, M., Trenkmann, M., Stein, B., Verhoeven, B., Daelemans, W.: Overview of the 2nd author profiling task at PAN 2014. In: CLEF 2014 Working Notes. CEUR (2014)Rangel, F., Rosso, P., Koppel, M., Stamatatos, E., Inches, G.: Overview of the author profiling task at PAN 2013–notebook for PAN at CLEF 2013. In: CLEF 2013 Working Notes. CEUR (2013)Sapkota, U., Bethard, S., Montes-y-Gómez, M., Solorio, T.: Not all character N-grams are created equal: a study in authorship attribution. In: Proceedings of NAACL 2015. ACL (2015)Sapkota, U., Solorio, T., Montes-y-Gómez, M., Bethard, S., Rosso, P.: Cross-topic authorship attribution: will out-of-topic data help? In: Proceedings of COLING 2014 (2014)Schler, J., Koppel, M., Argamon, S., Pennebaker, J.W.: Effects of age and gender on blogging. In: AAAI Spring Symposium: Computational Approaches to Analyzing Weblogs. AAAI (2006)Schwartz, H.A., Eichstaedt, J.C., Kern, M.L., Dziurzynski, L., Ramones, S.M., Agrawal, M., Shah, A., Kosinski, M., Stillwell, D., Seligman, M.E., et al.: Personality, Gender, and Age in the Language of Social Media: The Open-Vocabulary Approach. PloS one 8(9), 773–791 (2013)Stamatatos, E.: A Survey of Modern Authorship Attribution Methods. Journal of the American Society for Information Science and Technology 60, 538–556 (2009)Stamatatos, E.: On the Robustness of Authorship Attribution Based on Character N-gram Features. Journal of Law and Policy 21, 421–439 (2013)Stamatatos, E., Daelemans, W., Verhoeven, B., Juola, P., López-López, A., Potthast, M., Stein, B.: Overview of the author identification task at PAN 2015. In: Working Notes Papers of the CLEF 2015 Evaluation Labs. CEUR (2015)Stamatatos, E., Daelemans, W., Verhoeven, B., Stein, B., Potthast, M., Juola, P., Sánchez-Pérez, M.A., Barrón-Cedeño, A.: Overview of the author identification task at PAN 2014. In: CLEF 2014 Working Notes. CEUR (2014)Stamatatos, E., Fakotakis, N., Kokkinakis, G.: Automatic Text Categorization in Terms of Genre and Author. Comput. Linguist. 26(4), 471–495 (2000)Stein, B., Lipka, N., Prettenhofer, P.: Intrinsic Plagiarism Analysis. Language Resources and Evaluation (LRE) 45, 63–82 (2011)Stein, B., Meyer zu Eißen, S.: Near similarity search and plagiarism analysis. In: Proceedings of GFKL 2005. Springer (2006)Sushant, S.A., Argamon, S., Dhawle, S., Pennebaker, J.W.: Lexical predictors of personality type. In: Proceedings of Joint Interface/CSNA 2005Verhoeven, B., Daelemans, W.: Clips stylometry investigation (CSI) corpus: a dutch corpus for the detection of age, gender, personality, sentiment and deception in text. In: Proceedings of LREC 2014. ACL (2014)Weren, E., Kauer, A., Mizusaki, L., Moreira, V., de Oliveira, P., Wives, L.: Examining Multiple Features for Author Profiling. Journal of Information and Data Management (2014)Zhang, C., Zhang, P.: Predicting gender from blog posts. Tech. rep., Technical Report. University of Massachusetts Amherst, USA (2010

    Loss of CIC promotes mitotic dysregulation and chromosome segregation defects

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    Background: CIC is a transcriptional repressor inactivated by loss-of-function mutations in several cancer types, including gliomas, lung cancers, and gastric adenocarcinomas. CIC alterations and/or loss of CIC activity have been associated with poorer outcomes and more aggressive phenotypes across cancer types, which is consistent with the notion that CIC functions as a tumour suppressor across a wide range of contexts. Results: Using mammalian cells lacking functional CIC, we found that CIC deficiency was associated with chromosome segregation (CS) defects, resulting in chromosomal instability and aneuploidy. These CS defects were associated with transcriptional dysregulation of spindle assembly checkpoint and cell cycle regulators. We also identified novel CIC interacting proteins, including core members of the SWI/SNF complex, and showed that they cooperatively regulated the expression of genes involved in cell cycle regulation. Finally, we showed that loss of CIC and ARID1A cooperatively increased CS defects and reduced cell viability. Conclusions: Our study ascribes a novel role to CIC as an important regulator of the cell cycle and demonstrates that loss of CIC can lead to chromosomal instability and aneuploidy in human and murine cells through defects in CS, providing insight into the underlying mechanisms of CIC's increasingly apparent role as a "pan-cancer" tumour suppressor

    Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

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    Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32% of DLBCL and 89% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4% and 13.4% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis

    Steroid Hormone Control of Cell Death and Cell Survival: Molecular Insights Using RNAi

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    The insect steroid hormone ecdysone triggers programmed cell death of obsolete larval tissues during metamorphosis and provides a model system for understanding steroid hormone control of cell death and cell survival. Previous genome-wide expression studies of Drosophila larval salivary glands resulted in the identification of many genes associated with ecdysone-induced cell death and cell survival, but functional verification was lacking. In this study, we test functionally 460 of these genes using RNA interference in ecdysone-treated Drosophila l(2)mbn cells. Cell viability, cell morphology, cell proliferation, and apoptosis assays confirmed the effects of known genes and additionally resulted in the identification of six new pro-death related genes, including sorting nexin-like gene SH3PX1 and Sox box protein Sox14, and 18 new pro-survival genes. Identified genes were further characterized to determine their ecdysone dependency and potential function in cell death regulation. We found that the pro-survival function of five genes (Ras85D, Cp1, CG13784, CG32016, and CG33087), was dependent on ecdysone signaling. The TUNEL assay revealed an additional two genes (Kap-α3 and Smr) with an ecdysone-dependent cell survival function that was associated with reduced cell death. In vitro, Sox14 RNAi reduced the percentage of TUNEL-positive l(2)mbn cells (p<0.05) following ecdysone treatment, and Sox14 overexpression was sufficient to induce apoptosis. In vivo analyses of Sox14-RNAi animals revealed multiple phenotypes characteristic of aberrant or reduced ecdysone signaling, including defects in larval midgut and salivary gland destruction. These studies identify Sox14 as a positive regulator of ecdysone-mediated cell death and provide new insights into the molecular mechanisms underlying the ecdysone signaling network governing cell death and cell survival
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