Induction of lymphoidlike stroma and immune escape by tumors that express the chemokine CCL21

Tumor manipulation of host immunity is important for tumor survival and invasion. Many cancers secrete CCL21, a chemoattractant for various leukocytes and lymphoid tissue inducer cells, which drive lymphoid neogenesis. CCL21 expression by melanoma tumors in mice was associated with an immunotolerant microenvironment, which included the induction of lymphoid-like reticular stromal networks, an altered cytokine milieu, and the recruitment of regulatory leukocyte populations. In contrast, CCL21-deficient tumors induced antigen-specific immunity. CCL21-mediated immune tolerance was dependent on host rather than tumor expression of the CCL21 receptor, CCR7, and could protect distant, coimplanted CCL21-deficient tumors and even nonsyngeneic allografts from rejection. We suggest that by altering the tumor microenvironment, CCL21-secreting tumors shift the host immune response from immunogenic to tolerogenic, which facilitates tumor progression

DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association

microRNAs (miRNAs) are small endogenous RNA molecules that are implicated in many biological processes through post-transcriptional regulation of gene expression. The DIANA-microT Web server provides a user-friendly interface for comprehensive computational analysis of miRNA targets in human and mouse. The server has now been extended to support predictions for two widely studied species: Drosophila melanogaster and Caenorhabditis elegans. In the updated version, the Web server enables the association of miRNAs to diseases through bibliographic analysis and provides insights for the potential involvement of miRNAs in biological processes. The nomenclature used to describe mature miRNAs along different miRBase versions has been extensively analyzed, and the naming history of each miRNA has been extracted. This enables the identification of miRNA publications regardless of possible nomenclature changes. User interaction has been further refined allowing users to save results that they wish to analyze further. A connection to the UCSC genome browser is now provided, enabling users to easily preview predicted binding sites in comparison to a wide array of genomic tracks, such as single nucleotide polymorphisms. The Web server is publicly accessible in www.microrna.gr/microT-v4

A SDN-based WiFi-VLC Coupled System for Optimised Service Provision in 5G Networks

Abstract— Visible Light Communication (VLC) is a powerful supplement, which has gained tremendous attention recently and has become a favorable technology in short-range communication scenarios for the Fifth Generation (5G) networks. VLC possesses a number of prominent features to address the highly demanding 5G system requirements for high capacity, high data rate, high spectral efficiency, high energy efficiency, low battery consumption, and low latency. However, this prominent performance is limited by the imperfect reception, since line of sight channel condition may not always exist in practice. This paper presents and experimentally validates a SDN-based VLC system, which is coupled with WiFi access technology in order to improve the network QoS, reassuring zero packet loss reception quality when the user is moving between two consecutive VLC transmitters

PNAS plus: plasmodium falciparum responds to amino acid starvation by entering into a hibernatory state

The human malaria parasite Plasmodium falciparum is auxotrophic for most amino acids. Its amino acid needs are met largely through the degradation of host erythrocyte hemoglobin; however the parasite must acquire isoleucine exogenously, because this amino acid is not present in adult human hemoglobin. We report that when isoleucine is withdrawn from the culture medium of intraerythrocytic P. falciparum, the parasite slows its metabolism and progresses through its developmental cycle at a reduced rate. Isoleucine-starved parasites remain viable for 72 h and resume rapid growth upon resupplementation. Protein degradation during starvation is important for maintenance of this hibernatory state. Microarray analysis of starved parasites revealed a 60% decrease in the rate of progression through the normal transcriptional program but no other apparent stress response. Plasmodium parasites do not possess a TOR nutrient-sensing pathway and have only a rudimentary amino acid starvation-sensing eukaryotic initiation factor 2α (eIF2α) stress response. Isoleucine deprivation results in GCN2-mediated phosphorylation of eIF2α, but kinase-knockout clones still are able to hibernate and recover, indicating that this pathway does not directly promote survival during isoleucine starvation. We conclude that P. falciparum, in the absence of canonical eukaryotic nutrient stress-response pathways, can cope with an inconsistent bloodstream amino acid supply by hibernating and waiting for more nutrient to be provided

A fast sparse block circulant matrix vector product

In the context of computed tomography (CT), iterative image reconstruction techniques are gaining attention because high-quality images are becoming computationally feasible. They involve the solution of large systems of equations, whose cost is dominated by the sparse matrix vector product (SpMV). Our work considers the case of the sparse matrices being block circulant, which arises when taking advantage of the rotational symmetry in the tomographic system. Besides the straightforward storage saving, we exploit the circulant structure to rewrite the poor-performance SpMVs into a high-performance product between sparse and dense matrices. This paper describes the implementations developed for multi-core CPUs and GPUs, and presents experimental results with typical CT matrices. The presented approach is up to ten times faster than without exploiting the circulant structure.Romero Alcalde, E.; Tomás Domínguez, AE.; Soriano Asensi, A.; Blanquer Espert, I. (2014). A fast sparse block circulant matrix vector product. En Euro-Par 2014 Parallel Processing. Springer. 548-559. doi:10.1007/978-3-319-09873-9_46S548559Bian, J., Siewerdsen, J.H., Han, X., Sidky, E.Y., Prince, J.L., Pelizzari, C.A., Pal, X.: Evaluation of sparse-view reconstruction from flat-panel-detector cone-beam ct. Physics in Medicine and Biology 55, 6575–6599 (2010)Dalton, S., Bell, N.: CUSP: A C++ templated sparse matrix library version 0.4.0 (2014), http://cusplibrary.github.com/Feldkamp, L., Davis, L., Kress, J.: Practical cone-beam algorithm. Journal of the Optical Society of America 1, 612–619 (1984)Ganine, V., Legrand, M., Michalska, H., Pierre, C.: A sparse preconditioned iterative method for vibration analysis of geometrically mistuned bladed disks. Computers & Structures 87(5-6), 342–354 (2009)Hara, A.K., Paden, R.G., Silva, A.C., Kujak, J.L., Lawder, H.J., Pavlicek, W.: Iterative reconstruction technique for reducing body radiation dose at CT: Feasibility study. American Journal of Roentgenology 193, 764–771 (2009)Heroux, M.A., Bartlett, R.A., Howle, V.E., Hoekstra, R.J., Hu, J.J., Kolda, T.G., Lehoucq, R.B., Long, K.R., Pawlowski, R.P., Phipps, E.T., Salinger, A.G., Thornquist, H.K., Tuminaro, R.S., Willenbring, J.M., Williams, A., Stanley, K.S.: An overview of the Trilinos project. ACM Trans. Math. Softw. 31(3), 397–423 (2005)Im, E.J., Yelick, K., Vuduc, R.: Sparsity: Optimization framework for sparse matrix kernels. International Journal of High Performance Computing Applications 18(1), 135–158 (2004)Jones, E., Oliphant, T., Peterson, P., et al.: SciPy: Open source scientific tools for Python (2001), http://www.scipy.org/Kaveh, A., Rahami, H.: Block circulant matrices and applications in free vibration analysis of cyclically repetitive structures. Acta Mechanica 217(1-2), 51–62 (2011)Kourtis, K., Goumas, G., Koziris, N.: Optimizing sparse matrix-vector multiplication using index and value compression. In: Proceedings of the 5th Conference on Computing Frontiers, CF 2008, pp. 87–96. ACM, New York (2008)Krotkiewski, M., Dabrowski, M.: Parallel symmetric sparse matrix–vector product on scalar multi-core CPUs. Parallel Computing 36(4), 181–198 (2010)Lee, B., Vuduc, R., Demmel, J., Yelick, K.: Performance models for evaluation and automatic tuning of symmetric sparse matrix-vector multiply. In: International Conference on Parallel Processing, ICPP 2004, vol. 1, pp. 169–176 (2004)Leroux, J.D., Selivanov, V., Fontaine, R., Lecomte, R.: Accelerated iterative image reconstruction methods based on block-circulant system matrix derived from a cylindrical image representation. In: Nuclear Science Symposium Conference Record, NSS 2007, vol. 4, pp. 2764–2771. IEEE (2007)NVIDIA: CUSPARSE library (2014), https://developer.nvidia.com/cusparsePan, X., Sidky, E.Y., Vannier, M.: Why do commercial CT scanners still employ traditional, filtered back-projection for image reconstruction? Inverse Problems 25, 123009 (2008)Rodríguez-Alvarez, M.J., Soriano, A., Iborra, A., Sánchez, F., González, A.J., Conde, P., Hernández, L., Moliner, L., Orero, A., Vidal, L.F., Benlloch, J.M.: Expectation maximization (EM) algorithms using polar symmetries for computed tomography CT image reconstruction. Computers in Biology and Medicine 43(8), 1053–1061 (2013)Sheep, L., Vardi, Y.: Maximum likelihood reconstruction for emmision tomography. IEEE Transactions on Medical Imaging 1, 113–122 (1982)Sidky, E.Y., Pan, X.: Image reconstruction in circular cone-beam computed tomography by constrained, total-variation minimization. Physics in Medicine and Biology 53, 4777–4807 (2008)Soriano, A., Rodríguez-Alvarez, M.J., Iborra, A., Sánchez, F., Carles, M., Conde, P., González, A.J., Hernández, L., Moliner, L., Orero, A., Vidal, L.F., Benlloch, J.M.: EM tomographic image reconstruction using polar voxels. Journal of Instrumentation 8, C01004 (2013)Thibaudeau, C., Leroux, J.D., Pratte, J.F., Fontaine, R., Lecomte, R.: Cylindrical and spherical ray-tracing for ct iterative reconstruction. In: 2011 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), pp. 4378–4381 (2011)Vuduc, R., Demmel, J.W., Yelick, K.A.: OSKI: A library of automatically tuned sparse matrix kernels. Journal of Physics: Conference Series 16(1), 521 (2005)Vuduc, R.W., Moon, H.-J.: Fast sparse matrix-vector multiplication by exploiting variable block structure. In: Yang, L.T., Rana, O.F., Di Martino, B., Dongarra, J. (eds.) HPCC 2005. LNCS, vol. 3726, pp. 807–816. Springer, Heidelberg (2005)Williams, S., Oliker, L., Vuduc, R., Shalf, J., Yelick, K., Demmel, J.: Optimization of sparse matrix-vector multiplication on emerging multicore platforms. Parallel Computing 35(3), 178–194 (2009

DIANA-microT web server: elucidating microRNA functions through target prediction

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT

Three-dimensional Access Point Assignment in Hybrid VLC, mmWave and WiFi Wireless Access Networks:2020 IEEE International Conference on Communications, ICC 2020

To improve data speed and reliability, hybrid wireless networks combine two different Radio Access Technologies (RATs), such as Visible Light Communications (VLC), millimetre wave (mmWave), Wireless Fidelity (WiFi), 4G Long Term Evolution (LTE), etc. The Internet of Radio Light (IoRL) is a cutting-edge system paradigm to combine three RATs for taking advantage the vast VLC and mmWave spectrum with the ubiquitous coverage of WiFi. In this respect, this work introduces a new convex optimisation-based solution method to optimise the three-dimensional (3D) Access Point Assignment (APA) problem of the IoRL system under individual user positioning, priority and minimum Quality-of-Service (QoS) constraints. We use both the IoRL real-world testbed and large-scale Maltab simulations to evaluate that our solution converges in linear time, and attains higher throughput-vs-fairness trade-off than existing efforts. © 2020 IEEE

Accurate microRNA target prediction correlates with protein repression levels

MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and diseas