Word-Graph Based Applications for Handwriting Documents: Impact of Word-Graph Size on Their Performances

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-19390-8 29Computer Assisted Transcription of Text Images (CATTI) and Key-Word Spotting (KWS) applications aim at transcribing and indexing handwritten documents respectively. They both are approached by means of Word Graphs (WG) obtained using segmentation-free handwritten text recognition technology based on N-gram Language Models and Hidden Markov Models. A large WG contains most of the relevant information of the original text (line) image needed for CATTI and KWS but, if it is too large, the computational cost of generating and using it can become unaffordable. Conversely, if it is too small, relevant information may be lost, leading to a reduction of CATTI/KWS in performance accuracy. We study the trade-off between WG size and CATTI &KWS performance in terms of effectiveness and efficiency. Results show that small, computationally cheap WGs can be used without loosing the excellent CATTI/KWS performance achieved with huge WGs.Work partially supported by the Spanish MICINN projects STraDA (TIN2012-37475-C02-01) and by the EU 7th FP tranScriptorium project (Ref:600707).Toselli, AH.; Romero Gómez, V.; Vidal Ruiz, E. (2015). Word-Graph Based Applications for Handwriting Documents: Impact of Word-Graph Size on Their Performances. En Pattern Recognition and Image Analysis. Springer. 253-261. https://doi.org/10.1007/978-3-319-19390-8_29S253261Romero, V., Toselli, A.H., Vidal, E.: Multimodal Interactive Handwritten Text Transcription. Series in Machine Perception and Artificial Intelligence (MPAI). World Scientific Publishing, Singapore (2012)Toselli, A.H., Vidal, E., Romero, V., Frinken, V.: Word-graph based keyword spotting and indexing of handwritten document images. Technical report, Universitat Politècnica de València (2013)Oerder, M., Ney, H.: Word graphs: an efficient interface between continuous-speech recognition and language understanding. In: IEEE International Conference on Acoustics, Speech, and Signal Processing, vol. 2, pp. 119–122, April 1993Bazzi, I., Schwartz, R., Makhoul, J.: An omnifont open-vocabulary OCR system for English and Arabic. IEEE Trans. Pattern Anal. Mach. Intell. 21(6), 495–504 (1999)Jelinek, F.: Statistical Methods for Speech Recognition. MIT Press, Cambridge (1998)Ström, N.: Generation and minimization of word graphs in continuous speech recognition. In: Proceedings of IEEE Workshop on ASR 1995, Snowbird, Utah, pp. 125–126 (1995)Ortmanns, S., Ney, H., Aubert, X.: A word graph algorithm for large vocabulary continuous speech recognition. Comput. Speech Lang. 11(1), 43–72 (1997)Wessel, F., Schluter, R., Macherey, K., Ney, H.: Confidence measures for large vocabulary continuous speech recognition. IEEE Trans. Speech Audio Process. 9(3), 288–298 (2001)Robertson, S.: A new interpretation of average precision. In: Proceedings of the International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2008), pp. 689–690. ACM, USA (2008)Manning, C.D., Raghavan, P., Schutze, H.: Introduction to Information Retrieval. Cambridge University Press, USA (2008)Romero, V., Toselli, A.H., Rodríguez, L., Vidal, E.: Computer assisted transcription for ancient text images. In: Kamel, M.S., Campilho, A. (eds.) ICIAR 2007. LNCS, vol. 4633, pp. 1182–1193. Springer, Heidelberg (2007)Fischer, A., Wuthrich, M., Liwicki, M., Frinken, V., Bunke, H., Viehhauser, G., Stolz, M.: Automatic transcription of handwritten medieval documents. In: 15th International Conference on Virtual Systems and Multimedia, VSMM 2009, pp. 137–142 (2009)Pesch, H., Hamdani, M., Forster, J., Ney, H.: Analysis of preprocessing techniques for latin handwriting recognition. In: ICFHR, pp. 280–284 (2012)Evermann, G.: Minimum Word Error Rate Decoding. Ph.D. thesis, Churchill College, University of Cambridge (1999

Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair.

Repair of double strand DNA breaks (DSBs) can result in gene disruption or gene modification via homology directed repair (HDR) from donor DNA. Altering cellular responses to DSBs may rebalance editing outcomes towards HDR and away from other repair outcomes. Here, we utilize a pooled CRISPR screen to define host cell involvement in HDR between a Cas9 DSB and a plasmid double stranded donor DNA (dsDonor). We find that the Fanconi Anemia (FA) pathway is required for dsDonor HDR and that other genes act to repress HDR. Small molecule inhibition of one of these repressors, CDC7, by XL413 and other inhibitors increases the efficiency of HDR by up to 3.5 fold in many contexts, including primary T cells. XL413 stimulates HDR during a reversible slowing of S-phase that is unexplored for Cas9-induced HDR. We anticipate that XL413 and other such rationally developed inhibitors will be useful tools for gene modification

High energy emission from microquasars

The microquasar phenomenon is associated with the production of jets by X-ray binaries and, as such, may be associated with the majority of such systems. In this chapter we briefly outline the associations, definite, probable, possible, and speculative, between such jets and X-ray, gamma-ray and particle emission.Comment: Contributing chapter to the book Cosmic Gamma-Ray Sources, K.S. Cheng and G.E. Romero (eds.), to be published by Kluwer Academic Publishers, Dordrecht, 2004. (19 pages

Dynamic capacity provision for wireless sensors connectivity: A profit optimization approach

[EN] We model a wireless sensors' connectivity scenario mathematically and analyze it using capacity provision mechanisms, with the objective of maximizing the profits of a network operator. The scenario has several sensors' clusters with each one having one sink node, which uploads the sensing data gathered in the cluster through the wireless connectivity of a network operator. The scenario is analyzed both as a static game and as a dynamic game, each one with two stages, using game theory. The sinks' behavior is characterized with a utility function related to the mean service time and the price paid to the operator for the service. The objective of the operator is to maximize its profits by optimizing the network capacity. In the static game, the sinks' subscription decision is modeled using a population game. In the dynamic game, the sinks' behavior is modeled using an evolutionary game and the replicator dynamic, while the operator optimal capacity is obtained solving an optimal control problem. The scenario is shown feasible from an economic point of view. In addition, the dynamic capacity provision optimization is shown as a valid mechanism for maximizing the operator profits, as well as a useful tool to analyze evolving scenarios. Finally, the dynamic analysis opens the possibility to study more complex scenarios using the differential game extension.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by the Spanish Ministry of Economy and Competitiveness through project TIN2013-47272-C2-1-R; AEI/FEDER, UE through project TEC2017-85830-C2-1-P; and co-supported by the European Social Fund BES-2014-068998.Sanchis-Cano, Á.; Guijarro, L.; Condoluci, M. (2018). Dynamic capacity provision for wireless sensors connectivity: A profit optimization approach. International Journal of Distributed Sensor Networks (Online). 14(4):1-14. https://doi.org/10.1177/1550147718772544S114144Weiser, M. (1991). The Computer for the 21st Century. Scientific American, 265(3), 94-104. doi:10.1038/scientificamerican0991-94Gubbi, J., Buyya, R., Marusic, S., & Palaniswami, M. (2013). Internet of Things (IoT): A vision, architectural elements, and future directions. Future Generation Computer Systems, 29(7), 1645-1660. doi:10.1016/j.future.2013.01.010Perera, C., Zaslavsky, A., Christen, P., & Georgakopoulos, D. (2013). Sensing as a service model for smart cities supported by Internet of Things. Transactions on Emerging Telecommunications Technologies, 25(1), 81-93. doi:10.1002/ett.2704Wang, N., Hossain, E., & Bhargava, V. K. (2016). Joint Downlink Cell Association and Bandwidth Allocation for Wireless Backhauling in Two-Tier HetNets With Large-Scale Antenna Arrays. IEEE Transactions on Wireless Communications, 15(5), 3251-3268. doi:10.1109/twc.2016.2519401Chowdhury, M. Z., Jang, Y. M., & Haas, Z. J. (2013). Call admission control based on adaptive bandwidth allocation for wireless networks. Journal of Communications and Networks, 15(1), 15-24. doi:10.1109/jcn.2013.000005Nan, G., Mao, Z., Yu, M., Li, M., Wang, H., & Zhang, Y. (2014). Stackelberg Game for Bandwidth Allocation in Cloud-Based Wireless Live-Streaming Social Networks. IEEE Systems Journal, 8(1), 256-267. doi:10.1109/jsyst.2013.2253420Zhu, K., Niyato, D., Wang, P., & Han, Z. (2012). Dynamic Spectrum Leasing and Service Selection in Spectrum Secondary Market of Cognitive Radio Networks. IEEE Transactions on Wireless Communications, 11(3), 1136-1145. doi:10.1109/twc.2012.010312.110732Vamvakas, P., Tsiropoulou, E. E., & Papavassiliou, S. (2017). Dynamic Provider Selection & Power Resource Management in Competitive Wireless Communication Markets. Mobile Networks and Applications, 23(1), 86-99. doi:10.1007/s11036-017-0885-yNiyato, D., Hoang, D. T., Luong, N. C., Wang, P., Kim, D. I., & Han, Z. (2016). Smart data pricing models for the internet of things: a bundling strategy approach. IEEE Network, 30(2), 18-25. doi:10.1109/mnet.2016.7437020Guijarro, L., Pla, V., Vidal, J. R., & Naldi, M. (2016). Maximum-Profit Two-Sided Pricing in Service Platforms Based on Wireless Sensor Networks. IEEE Wireless Communications Letters, 5(1), 8-11. doi:10.1109/lwc.2015.2487259Romero, J., Guijarro, L., Pla, V., & Vidal, J. R. (2017). Price competition between a macrocell and a small-cell service provider with limited resources and optimal bandwidth user subscription: a game-theoretical model. Telecommunication Systems, 67(2), 195-209. doi:10.1007/s11235-017-0331-2Al Daoud, A., Alanyali, M., & Starobinski, D. (2010). Pricing Strategies for Spectrum Lease in Secondary Markets. IEEE/ACM Transactions on Networking, 18(2), 462-475. doi:10.1109/tnet.2009.2031176Do, C. T., Tran, N. H., Huh, E.-N., Hong, C. S., Niyato, D., & Han, Z. (2016). Dynamics of service selection and provider pricing game in heterogeneous cloud market. Journal of Network and Computer Applications, 69, 152-165. doi:10.1016/j.jnca.2016.04.012Tsiropoulou, E. E., Vamvakas, P., & Papavassiliou, S. (2017). Joint Customized Price and Power Control for Energy-Efficient Multi-Service Wireless Networks via S-Modular Theory. IEEE Transactions on Green Communications and Networking, 1(1), 17-28. doi:10.1109/tgcn.2017.2678207Sanchis-Cano, A., Romero, J., Sacoto-Cabrera, E., & Guijarro, L. (2017). Economic Feasibility of Wireless Sensor Network-Based Service Provision in a Duopoly Setting with a Monopolist Operator. Sensors, 17(12), 2727. doi:10.3390/s17122727Weber, T. A. (2011). Optimal Control Theory with Applications in Economics. doi:10.7551/mitpress/9780262015738.001.0001Mandjes, M. (2003). Pricing strategies under heterogeneous service requirements. Computer Networks, 42(2), 231-249. doi:10.1016/s1389-1286(03)00191-9Shariatmadari, H., Ratasuk, R., Iraji, S., Laya, A., Taleb, T., Jäntti, R., & Ghosh, A. (2015). Machine-type communications: current status and future perspectives toward 5G systems. IEEE Communications Magazine, 53(9), 10-17. doi:10.1109/mcom.2015.7263367Ng, C.-H., & Soong, B.-H. (2008). Queueing Modelling Fundamentals. doi:10.1002/9780470994672Mendelson, H. (1985). Pricing computer services: queueing effects. Communications of the ACM, 28(3), 312-321. doi:10.1145/3166.3171Altman, E., Boulogne, T., El-Azouzi, R., Jiménez, T., & Wynter, L. (2006). A survey on networking games in telecommunications. Computers & Operations Research, 33(2), 286-311. doi:10.1016/j.cor.2004.06.005Belleflamme, P., & Peitz, M. (2015). Industrial Organization. doi:10.1017/cbo9781107707139Reynolds, S. S. (1987). Capacity Investment, Preemption and Commitment in an Infinite Horizon Model. International Economic Review, 28(1), 69. doi:10.2307/2526860Barron, E. N. (2013). Game Theory. doi:10.1002/9781118547168Sandholm, W. (2009). Pairwise Comparison Dynamics and Evolutionary Foundations for Nash Equilibrium. Games, 1(1), 3-17. doi:10.3390/g1010003Schlag, K. H. (1998). Why Imitate, and If So, How? Journal of Economic Theory, 78(1), 130-156. doi:10.1006/jeth.1997.234

Predictability of evolutionary trajectories in fitness landscapes

Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness landscape. We report an exhaustive analysis of fitness landscapes constructed with an off-lattice model of protein folding where fitness is equated with robustness to misfolding. This model mimics the essential features of the interactions between amino acids, is consistent with the key paradigms of protein folding and reproduces the universal distribution of evolutionary rates among orthologous proteins. We introduce mean path divergence as a quantitative measure of the degree to which the starting and ending points determine the path of evolution in fitness landscapes. Global measures of landscape roughness are good predictors of path divergence in all studied landscapes: the mean path divergence is greater in smooth landscapes than in rough ones. The model-derived and experimental landscapes are significantly smoother than random landscapes and resemble additive landscapes perturbed with moderate amounts of noise; thus, these landscapes are substantially robust to mutation. The model landscapes show a deficit of suboptimal peaks even compared with noisy additive landscapes with similar overall roughness. We suggest that smoothness and the substantial deficit of peaks in the fitness landscapes of protein evolution are fundamental consequences of the physics of protein folding.Comment: 14 pages, 7 figure

Paleo-landscapes of the Northern Patagonian Massif, Argentina

Fil: Aguilera, Emilia Yolanda. Instituto de Geomorfología y Suelos (IGS). Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Rabassa, Jorge. Laboratorio de Geomorfología y Cuaternario. CADIC. Universidad Nacional de Tierra del Fuego; ArgentinaFil: Aragón, Eugenio. Centro de Investigaciones Geológicas (CIG). Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; Argentin

An FPGA Implementation to Detect Selective Cationic Antibacterial Peptides

Exhaustive prediction of physicochemical properties of peptide sequences is used in different areas of biological research. One example is the identification of selective cationic antibacterial peptides (SCAPs), which may be used in the treatment of different diseases. Due to the discrete nature of peptide sequences, the physicochemical properties calculation is considered a high-performance computing problem. A competitive solution for this class of problems is to embed algorithms into dedicated hardware. In the present work we present the adaptation, design and implementation of an algorithm for SCAPs prediction into a Field Programmable Gate Array (FPGA) platform. Four physicochemical properties codes useful in the identification of peptide sequences with potential selective antibacterial activity were implemented into an FPGA board. The speed-up gained in a single-copy implementation was up to 108 times compared with a single Intel processor cycle for cycle. The inherent scalability of our design allows for replication of this code into multiple FPGA cards and consequently improvements in speed are possible. Our results show the first embedded SCAPs prediction solution described and constitutes the grounds to efficiently perform the exhaustive analysis of the sequence-physicochemical properties relationship of peptides

Cervical epithelial damage promotes Ureaplasma parvum ascending infection, intrauterine inflammation and preterm birth induction in mice

Around 40% of preterm births are attributed to ascending intrauterine infection, and Ureaplasma parvum (UP) is commonly isolated in these cases. Here we present a mouse model of ascending UP infection that resembles human disease, using vaginal inoculation combined with mild cervical injury induced by a common spermicide (Nonoxynol-9, as a surrogate for any mechanism of cervical epithelial damage). We measure bacterial load in a non-invasive manner using a luciferase-expressing UP strain, and post-mortem by qPCR and bacterial titration. Cervical exposure to Nonoxynol-9, 24 h pre-inoculation, facilitates intrauterine UP infection, upregulates pro-inflammatory cytokines, and increases preterm birth rates from 13 to 28%. Our results highlight the crucial role of the cervical epithelium as a barrier against ascending infection. In addition, we expect the mouse model will facilitate further research on the potential links between UP infection and preterm birth

Evolving cell models for systems and synthetic biology

This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm’s results as well as of the resulting evolved cell models

Drosophila Genome-Wide RNAi Screen Identifies Multiple Regulators of HIF–Dependent Transcription in Hypoxia

Hypoxia-inducible factors (HIFs) are a family of evolutionary conserved alpha-beta heterodimeric transcription factors that induce a wide range of genes in response to low oxygen tension. Molecular mechanisms that mediate oxygen-dependent HIF regulation operate at the level of the alpha subunit, controlling protein stability, subcellular localization, and transcriptional coactivator recruitment. We have conducted an unbiased genome-wide RNA interference (RNAi) screen in Drosophila cells aimed to the identification of genes required for HIF activity. After 3 rounds of selection, 30 genes emerged as critical HIF regulators in hypoxia, most of which had not been previously associated with HIF biology. The list of genes includes components of chromatin remodeling complexes, transcription elongation factors, and translational regulators. One remarkable hit was the argonaute 1 (ago1) gene, a central element of the microRNA (miRNA) translational silencing machinery. Further studies confirmed the physiological role of the miRNA machinery in HIF–dependent transcription. This study reveals the occurrence of novel mechanisms of HIF regulation, which might contribute to developing novel strategies for therapeutic intervention of HIF–related pathologies, including heart attack, cancer, and stroke