Fast Truncated SVD of Sparse and Dense Matrices on Graphics Processors

We investigate the solution of low-rank matrix approximation problems using the truncated SVD. For this purpose, we develop and optimize GPU implementations for the randomized SVD and a blocked variant of the Lanczos approach. Our work takes advantage of the fact that the two methods are composed of very similar linear algebra building blocks, which can be assembled using numerical kernels from existing high-performance linear algebra libraries. Furthermore, the experiments with several sparse matrices arising in representative real-world applications and synthetic dense test matrices reveal a performance advantage of the block Lanczos algorithm when targeting the same approximation accuracy.Comment: 16 pages, 4 figure

Virtual reality exercise intradialysis to improve physical function: A feasibility randomized trial

[EN] Objective The main objective of this investigation was to assess feasibility of conducting a future RCT with an intradialysis non-immersive virtual reality exercise intervention. The secondary aim was to explore the impact of either conventional or VR exercise on physical function. Design Feasibility randomized trial. Participants Eighteen subjects who participated in a 16-week intradialysis combined exercise program. Interventions The program lasted four additional weeks of either combined exercise or virtual reality exercise. Main outcome measures Physical function was measured through several reliable tests (sit-to-stand-to-sit tests 10 and 60, gait speed, one-leg heel-rise tests, and 6-minute walk test) at baseline, after 16 weeks of intradialysis combined exercise and by the end of four additional weeks of exercise. Adherence to the exercise programs was registered. Results There was a significant time effect, so that physical function improved in both groups. By the end of the 20 weeks, function improved as measured through the sit-to-stand-to-sit tests 10 and 60, gait speed, one-leg heel-rise left leg, and the 6-minute walk test. Changes that did not occur due to error in the test were seen after 20 weeks were achieved in the sit-to-stand-to-sit test 60, gait speed, one-leg heel-rise test for the left leg, and 6-minute walking test. Conclusion Virtual reality was a feasible intervention. Both interventions improved physical function. Adherence was not significantly different between groups.Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain, Grant/Award Number: Consolidacion de Indicadores CEU-UCH 2016-2017/ISegura-Orti, E.; Perez-Dominguez, B.; Ortega-Pérez De Villar, L.; Melendez-Oliva, E.; Martínez-Gramaje, J.; García-Maset, R.; Gil-Gómez, J. (2019). Virtual reality exercise intradialysis to improve physical function: A feasibility randomized trial. Scandinavian Journal of Medicine and Science in Sports. 29(1):89-94. https://doi.org/10.1111/sms.13304S8994291Segura-Ortí, E., Gordon, P. L., Doyle, J. W., & Johansen, K. L. (2017). Correlates of Physical Functioning and Performance Across the Spectrum of Kidney Function. Clinical Nursing Research, 27(5), 579-596. doi:10.1177/1054773816689282Segura-Orti, E., & Johansen, K. L. (2010). Exercise in End-Stage Renal Disease. Seminars in Dialysis, 23(4), 422-430. doi:10.1111/j.1525-139x.2010.00766.xDelgado, C., & Johansen, K. L. (2011). Barriers to exercise participation among dialysis patients. Nephrology Dialysis Transplantation, 27(3), 1152-1157. doi:10.1093/ndt/gfr404Heiwe, S., & Tollin, H. (2012). Patients’ perspectives on the implementation of intra-dialytic cycling—a phenomenographic study. Implementation Science, 7(1). doi:10.1186/1748-5908-7-68Konstantinidou, E., Koukouvou, G., Kouidi, E., Deligiannis, A., & Tourkantonis, A. (2002). Exercise training in patients with end-stage renal disease on hemodialysis: Comparison of three rehabilitation programs. Journal of Rehabilitation Medicine, 34(1), 40-45. doi:10.1080/165019702317242695Corbetta, D., Imeri, F., & Gatti, R. (2015). Rehabilitation that incorporates virtual reality is more effective than standard rehabilitation for improving walking speed, balance and mobility after stroke: a systematic review. Journal of Physiotherapy, 61(3), 117-124. doi:10.1016/j.jphys.2015.05.017Peruzzi, A., Cereatti, A., Della Croce, U., & Mirelman, A. (2016). Effects of a virtual reality and treadmill training on gait of subjects with multiple sclerosis: a pilot study. Multiple Sclerosis and Related Disorders, 5, 91-96. doi:10.1016/j.msard.2015.11.002Brien, M., & Sveistrup, H. (2011). An Intensive Virtual Reality Program Improves Functional Balance and Mobility of Adolescents With Cerebral Palsy. Pediatric Physical Therapy, 23(3), 258-266. doi:10.1097/pep.0b013e318227ca0fOrtega‐Pérez de VillarL Pérez‐ DomínguezB Segura‐OrtíE et al.Use of virtual reality game as part of exercise program for chronic kidney disease patients undergoing haemodialysis.2015.Cho, H., & Sohng, K.-Y. (2014). The Effect of a Virtual Reality Exercise Program on Physical Fitness, Body Composition, and Fatigue in Hemodialysis Patients. Journal of Physical Therapy Science, 26(10), 1661-1665. doi:10.1589/jpts.26.1661OrtegaL.Comparison of two exercise programs for hemodialysis patients intradialysis vs home based program. absolute and relative reliability of physical performance[tesis doctoral]. Universidad CEU Cardenal Herrera. Facultad de Ciencias de la Salud;2017.Guralnik, J. M., Ferrucci, L., Simonsick, E. M., Salive, M. E., & Wallace, R. B. (1995). Lower-Extremity Function in Persons over the Age of 70 Years as a Predictor of Subsequent Disability. New England Journal of Medicine, 332(9), 556-562. doi:10.1056/nejm199503023320902Segura-Ortí, E., & Martínez-Olmos, F. J. (2011). Test-Retest Reliability and Minimal Detectable Change Scores for Sit-to-Stand-to-Sit Tests, the Six-Minute Walk Test, the One-Leg Heel-Rise Test, and Handgrip Strength in People Undergoing Hemodialysis. Physical Therapy, 91(8), 1244-1252. doi:10.2522/ptj.20100141Segura-Ortí, E. (2017). Fisioterapia sobre ejercicio en pacientes en hemodiálisis. Fisioterapia, 39(4), 137-139. doi:10.1016/j.ft.2017.05.003Bohm, C., Stewart, K., Onyskie-Marcus, J., Esliger, D., Kriellaars, D., & Rigatto, C. (2014). Effects of intradialytic cycling compared with pedometry on physical function in chronic outpatient hemodialysis: a prospective randomized trial. Nephrology Dialysis Transplantation, 29(10), 1947-1955. doi:10.1093/ndt/gfu248KOUFAKI, P., NASH, P. F., & MERCER, T. H. (2002). Assessing the efficacy of exercise training in patients with chronic disease. Medicine & Science in Sports & Exercise, 34(8), 1234-1241. doi:10.1097/00005768-200208000-00002Cappy, C. S., Jablonka, J., & Schroeder, E. T. (1999). The effects of exercise during hemodialysis on physical performance and nutrition assessment. Journal of Renal Nutrition, 9(2), 63-70. doi:10.1016/s1051-2276(99)90002-xHeadley, S., Germain, M., Mailloux, P., Mulhern, J., Ashworth, B., Burris, J., … Jones, M. (2002). Resistance training improves strength and functional measures in patients with end-stage renal disease. American Journal of Kidney Diseases, 40(2), 355-364. doi:10.1053/ajkd.2002.34520Painter, P., Carlson, L., Carey, S., Paul, S. M., & Myll, J. (2000). Low-functioning hemodialysis patients improve with exercise training. American Journal of Kidney Diseases, 36(3), 600-608. doi:10.1053/ajkd.2000.16200Segura-Ortí, E., Kouidi, E., & Lisón, J. F. (2009). Effect of resistance exercise during hemodialysis on physical function and quality of life: randomized controlled trial. Clinical Nephrology, 71(05), 527-537. doi:10.5414/cnp71527Esteve Simó, V., Junqué, A., Fulquet, M., Duarte, V., Saurina, A., Pou, M., … Ramírez de Arellano, M. (2014). Complete Low-Intensity Endurance Training Programme in Haemodialysis Patients: Improving the Care of Renal Patients. Nephron Clinical Practice, 128(3-4), 387-393. doi:10.1159/000369253Johansen, K. L., Painter, P. L., Sakkas, G. K., Gordon, P., Doyle, J., & Shubert, T. (2006). Effects of Resistance Exercise Training and Nandrolone Decanoate on Body Composition and Muscle Function among Patients Who Receive Hemodialysis: A Randomized, Controlled Trial. Journal of the American Society of Nephrology, 17(8), 2307-2314. doi:10.1681/asn.2006010034Tao, X., Chow, S. K. Y., & Wong, F. K. (2017). The effects of a nurse-supervised home exercise programme on improving patients’ perceptions of the benefits and barriers to exercise: A randomised controlled trial. Journal of Clinical Nursing, 26(17-18), 2765-2775. doi:10.1111/jocn.13798Rossi, A. P., Burris, D. D., Lucas, F. L., Crocker, G. A., & Wasserman, J. C. (2014). Effects of a Renal Rehabilitation Exercise Program in Patients with CKD: A Randomized, Controlled Trial. Clinical Journal of the American Society of Nephrology, 9(12), 2052-2058. doi:10.2215/cjn.11791113Boone, A. E., Foreman, M. H., & Engsberg, J. R. (2017). Development of a novel virtual reality gait intervention. Gait & Posture, 52, 202-204. doi:10.1016/j.gaitpost.2016.11.025Orcy, R. B., Dias, P. S., Seus, T. L., Barcellos, F. C., & Bohlke, M. (2012). Combined Resistance and Aerobic Exercise is Better than Resistance Training Alone to Improve Functional Performance of Haemodialysis Patients - Results of a Randomized Controlled Trial. Physiotherapy Research International, 17(4), 235-243. doi:10.1002/pri.1526Oliveros R, M. S., Avendaño, M., Bunout, D., Hirsch, S., De La Maza, M. P., Pedreros, C., & Müller, H. (2011). Estudio piloto sobre entrenamiento físico durante hemodiálisis. Revista médica de Chile, 139(8), 1046-1053. doi:10.4067/s0034-98872011000800010Silva, S. F. da, Pereira, A. A., Silva, W. A. H. da, Simôes, R., & Barros Neto, J. de R. (2013). Physical therapy during hemodialyse in patients with chronic kidney disease. Jornal Brasileiro de Nefrologia, 35(3), 170-176. doi:10.5935/0101-2800.20130028Bulckaen, M., Capitanini, A., Lange, S., Caciula, A., Giuntoli, F., & Cupisti, A. (2011). Implementation of exercise training programs in a hemodialysis unit: effects on physical performance. Journal of Nephrology, 24(6), 790-797. doi:10.5301/jn.2011.6386Cook, S. A., MacLaughlin, H., & Macdougall, I. C. (2007). A structured weight management programme can achieve improved functional ability and significant weight loss in obese patients with chronic kidney disease. Nephrology Dialysis Transplantation, 23(1), 263-268. doi:10.1093/ndt/gfm511PérezDF.Comparación de los efectos de un programa de ejercicio intradiálisis frente a un programa de ejercicio domiciliario[tesis doctoral]. Universidad CEU Cardenal Herrera Facultad de Ciencias de la Salud;2017.Wilkinson, T. J., Shur, N. F., & Smith, A. C. (2016). «Exercise as medicine» in chronic kidney disease. Scandinavian Journal of Medicine & Science in Sports, 26(8), 985-988. doi:10.1111/sms.1271

Mapping and assessment of ecosystems and their services. Urban ecosystems

Action 5 of the EU Biodiversity Strategy to 2020 requires member states to Map and Assess the state of Ecosystems and their Services (MAES). This report provides guidance for mapping and assessment of urban ecosystems. The MAES urban pilot is a collaboration between the European Commission, the European Environment Agency, volunteering Member States and cities, and stakeholders. Its ultimate goal is to deliver a knowledge base for policy and management of urban ecosystems by analysing urban green infrastructure, condition of urban ecosystems and ecosystem services. This report presents guidance for mapping urban ecosystems and includes an indicator framework to assess the condition of urban ecosystems and urban ecosystem services. The scientific framework of mapping and assessment is designed to support in particular urban planning policy and policy on green infrastructure at urban, metropolitan and regional scales. The results are based on the following different sources of information: a literature survey of 54 scientific articles, an online-survey (on urban ecosystems, related policies and planning instruments and with participation of 42 cities), ten case studies (Portugal: Cascais, Oeiras, Lisbon; Italy: Padua, Trento, Rome; The Netherlands: Utrecht; Poland: Poznań; Spain: Barcelona; Norway: Oslo), and a two-day expert workshop. The case studies constituted the core of the MAES urban pilot. They provided real examples and applications of how mapping and assessment can be organized to support policy; on top, they provided the necessary expertise to select a set of final indicators for condition and ecosystem services. Urban ecosystems or cities are defined here as socio-ecological systems which are composed of green infrastructure and built infrastructure. Urban green infrastructure (GI) is understood in this report as the multi-functional network of urban green spaces situated within the boundary of the urban ecosystem. Urban green spaces are the structural components of urban GI. This study has shown that there is a large scope for urban ecosystem assessments. Firstly, urban policies increasingly use urban green infrastructure and nature-based solutions in their planning process. Secondly, an increasing amount of data at multiple spatial scales is becoming available to support these policies, to provide a baseline, and to compare or benchmark cities with respect to the extent and management of the urban ecosystem. Concrete examples are given on how to delineate urban ecosystems, how to choose an appropriate spatial scale, and how to map urban ecosystems based on a combination of national or European datasets (including Urban Atlas) and locally collected information (e.g., location of trees). Also examples of typologies for urban green spaces are presented. This report presents an indicator framework which is composed of indicators to assess for urban ecosystem condition and for urban ecosystem services. These are the result of a rigorous selection process and ensure consistent mapping and assessment across Europe. The MAES urban pilot will continue with work on the interface between research and policy. The framework presented in this report needs to be tested and validated across Europe, e.g. on its applicability at city scale, on how far the methodology for measuring ecosystem condition and ecosystem service delivery in urban areas can be used to assess urban green infrastructure and nature-based solutions

The TNFR1 antagonist Atrosimab reduces neuronal loss, glial activation and memory deficits in an acute mouse model of neurodegeneration

Abstract Tumor necrosis factor alpha (TNF-α) and its key role in modulating immune responses has been widely recognized as a therapeutic target for inflammatory and neurodegenerative diseases. Even though inhibition of TNF-α is beneficial for the treatment of certain inflammatory diseases, total neutralization of TNF-α largely failed in the treatment of neurodegenerative diseases. TNF-α exerts distinct functions depending on interaction with its two TNF receptors, whereby TNF receptor 1 (TNFR1) is associated with neuroinflammation and apoptosis and TNF receptor 2 (TNFR2) with neuroprotection and immune regulation. Here, we investigated the effect of administering the TNFR1-specific antagonist Atrosimab, as strategy to block TNFR1 signaling while maintaining TNFR2 signaling unaltered, in an acute mouse model for neurodegeneration. In this model, a NMDA-induced lesion that mimics various hallmarks of neurodegenerative diseases, such as memory loss and cell death, was created in the nucleus basalis magnocellularis and Atrosimab or control protein was administered centrally. We showed that Atrosimab attenuated cognitive impairments and reduced neuroinflammation and neuronal cell death. Our results demonstrate that Atrosimab is effective in ameliorating disease symptoms in an acute neurodegenerative mouse model. Altogether, our study indicates that Atrosimab may be a promising candidate for the development of a therapeutic strategy for the treatment of neurodegenerative diseases

Influence of diamond crystal orientation on the interaction with biological matter

Diamond has been a popular material for a variety of biological applications due to its favorable chemical, optical, mechanical and biocompatible properties. While the lattice orientation of crystalline material is known to alter the interaction between solids and biological materials, the effect of diamond's crystal orientation on biological applications is completely unknown. Here, we experimentally evaluate the influence of the crystal orientation by investigating the interaction between the , and surfaces of the single crystal diamond with biomolecules, cell culture medium, mammalian cells and bacteria. We show that the crystal orientation significantly alters these biological interactions. Most surprising is the two orders of magnitude difference in the number of bacteria adhering on surface compared to surface when both the surfaces were maintained under the same condition. We also observe differences in how small biomolecules attach to the surfaces. Neurons or HeLa cells on the other hand do not have clear preferences for either of the surfaces. To explain the observed differences, we theoretically estimated the surface charge for these three low index diamond surfaces and followed by the surface composition analysis using x-ray photoelectron spectroscopy (XPS). We conclude that the differences in negative surface charge, atomic composition and functional groups of the different surface orientations lead to significant variations in how the single crystal diamond surface interacts with the studied biological entities. (c) 2020 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Real-time Soundprism

[EN] This paper presents a parallel real-time sound source separation system for decomposing an audio signal captured with a single microphone in so many audio signals as the number of instruments that are really playing. This approach is usually known as Soundprism. The application scenario of the system is for a concert hall in which users, instead of listening to the mixed audio, want to receive the audio of just an instrument, focusing on a particular performance. The challenge is even greater since we are interested in a real-time system on handheld devices, i.e., devices characterized by both low power consumption and mobility. The results presented show that it is possible to obtain real-time results in the tested scenarios using an ARM processor aided by a GPU, when this one is present.This work has been supported by the "Ministerio de Economia y Competitividad" of Spain and FEDER under projects TEC2015-67387-C4-{1,2,3}-R.Muñoz-Montoro, AJ.; Ranilla, J.; Vera-Candeas, P.; Combarro, EF.; Alonso-Jordá, P. (2019). Real-time Soundprism. The Journal of Supercomputing. 75(3):1594-1609. https://doi.org/10.1007/s11227-018-2703-0S15941609753Alonso P, Cortina R, Rodríguez-Serrano FJ, Vera-Candeas P, Alonso-González M, Ranilla J (2017) Parallel online time warping for real-time audio-to-score alignment in multi-core systems. J Supercomput 73:126. https://doi.org/10.1007/s11227-016-1647-5Carabias-Orti JJ, Cobos M, Vera-Candeas P, Rodríguez-Serrano FJ (2013) Nonnegative signal factorization with learnt instrument models for sound source separation in close-microphone recordings. EURASIP J Adv Signal Process 2013:184. https://doi.org/10.1186/1687-6180-2013-184Carabias-Orti JJ, Rodriguez-Serrano FJ, Vera-Candeas P, Canadas-Quesada FJ, Ruiz-Reyes N (2015) An audio to score alignment framework using spectral factorization and dynamic time warping. In: 16th International Society for Music Information Retrieval Conference, pp 742–748Díaz-Gracia N, Cocaña-Fernández A, Alonso-González M, Martínez-Zaldívar FJ, Cortina R, García-Mollá VM, Alonso P, Ranilla J (2014) NNMFPACK: a versatile approach to an NNMF parallel library. In: Proceedings of the 2014 International Conference on Computational and Mathematical Methods in Science and Engineering, pp 456–465Díaz-Gracia N, Cocaña-Fernández A, Alonso-González M, Martínez-Zaldívar FJ, Cortina R, García-Mollá VM, Vidal AM (2015) Improving NNMFPACK with heterogeneous and efficient kernels for $$\beta$$ β -divergence metrics. J Supercomput 71:1846–1856. https://doi.org/10.1007/s11227-014-1363-yDriedger J, Grohganz H, Prätzlich T, Ewert S, Müller M (2013) Score-informed audio decomposition and applications. In: Proceedings of the 21st ACM International Conference on Multimedia, pp 541–544Duan Z, Pardo B (2011) Soundprism: an online system for score-informed source separation of music audio. IEEE J Sel Top Signal Process 5(6):1205–1215Duong NQ, Vincent E, Gribonval R (2010) Under-determined reverberant audio source separation using a full-rank spatial covariance model. IEEE Trans Audio Speech 18(7):1830–1840. https://doi.org/10.1109/TASL.2010.2050716Ewert S, Müller M (2011) Estimating note intensities in music recordings. In: Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing, pp 385–388Ewert S, Pardo B, Mueller M, Plumbley MD (2014) Score-informed source separation for musical audio recordings: an overview. IEEE Signal Process Mag 31:116–124. https://doi.org/10.1109/MSP.2013.2296076Fastl H, Zwicker E (2007) Psychoacoustics. Springer, BerlinGanseman J, Scheunders P, Mysore GJ, Abel JS (2010) Source separation by score synthesis. Int Comput Music Conf 2010:1–4Goto M, Hashiguchi H, Nishimura T, Oka R (2002) RWC music database: popular, classical and jazz music databases. In: ISMIR, vol 2, pp 287–288Goto M (2004) Development of the RWC music database. In: Proceedings of the 18th International Congress on Acoustics (ICA 2004), ppp 553–556Hennequin R, David B, Badeau R (2011) Score informed audio source separation using a parametric model of non-negative spectrogram. In: 2011 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) pp 45–48. https://doi.org/10.1109/ICASSP.2011.5946324Itoyama K, Goto M, Komatani K et al (2008) Instrument equalizer for query-by-example retrieval: improving sound source separation based on integrated harmonic and inharmonic models. In: ISMIR. https://doi.org/10.1136/bmj.324.7341.827Marxer R, Janer J, Bonada J (2012) Low-latency instrument separation in polyphonic audio using timbre models. In: International Conference on Latent Variable Analysis and Signal Separation, pp 314–321Miron M, Carabias-Orti JJ, Janer J (2015) Improving score-informed source separation for classical music through note refinement. In: ISMIR, pp 448–454Ozerov A, Févotte C (2010) Multichannel nonnegative matrix factorization in convolutive mixtures for audio source separation. IEEE Trans Audio Speech Lang Process 18:550–563. https://doi.org/10.1109/TASL.2009.2031510Ozerov A, Vincent E, Bimbot F (2012) A general flexible framework for the handling of prior information in audio source separation. IEEE Trans Audio Speech Lang Process 20:1118–1133. https://doi.org/10.1109/TASL.2011.2172425Pätynen J, Pulkki V, Lokki T (2008) Anechoic recording system for symphony orchestra. Acta Acust United Acust 94:856–865. https://doi.org/10.3813/AAA.918104Raphael C (2008) A classifier-based approach to score-guided source separation of musical audio. Comput Music J 32:51–59. https://doi.org/10.1162/comj.2008.32.1.51Rodriguez-Serrano FJ, Duan Z, Vera-Candeas P, Pardo B, Carabias-Orti JJ (2015) Online score-informed source separation with adaptive instrument models. J New Music Res 44:83–96. https://doi.org/10.1080/09298215.2014.989174Rodriguez-Serrano FJ, Carabias-Orti JJ, Vera-Candeas P, Martinez-Munoz D (2016) Tempo driven audio-to-score alignment using spectral decomposition and online dynamic time warping. ACM Trans Intell Syst Technol 8:1–20. https://doi.org/10.1145/2926717Sawada H, Araki S, Makino S (2011) Underdetermined convolutive blind source separation via frequency bin-wise clustering and permutation alignment. IEEE Trans Audio Speech Lang Process 19(3):516–527. https://doi.org/10.1109/TASL.2010.2051355Vincent E, Araki S, Theis F et al (2012) The signal separation evaluation campaign (2007–2010): achievements and remaining challenges. Signal Process 92:1928–1936. https://doi.org/10.1016/j.sigpro.2011.10.007Vincent E, Bertin N, Gribonval R, Bimbot F (2014) From blind to guided audio source separation: how models and side information can improve the separation of sound. IEEE Signal Process Mag 31:107–115. https://doi.org/10.1109/MSP.2013.229744

Breathing-Dependent Redox Activity in a Tetrathiafulvalene-Based Metal-Organic Framework

“Breathing” metal–organic frameworks (MOFs) that involve changes in their structural and physical properties upon an external stimulus are an interesting class of crystalline materials due to their range of potential applications including chemical sensors. The addition of redox activity opens up a new pathway for multifunctional “breathing” frameworks. Herein, we report the continuous breathing behavior of a tetrathiafulvalene (TTF)-based MOF, namely MUV-2, showing a reversible swelling (up to ca. 40% of the volume cell) upon solvent adsorption. Importantly, the planarity of the TTF linkers is influenced by the breathing behavior of the MOF, directly impacting on its electrochemical properties and thus opening the way for the development of new electrochemical sensors. Quantum chemical calculations and Raman spectroscopy have been used to provide insights into the tunability of the oxidation potential