Analysis of an efficient parallel implementation of active-set Newton algorithm

[EN] This paper presents an analysis of an efficient parallel implementation of the active-set Newton algorithm (ASNA), which is used to estimate the nonnegative weights of linear combinations of the atoms in a large-scale dictionary to approximate an observation vector by minimizing the Kullback¿Leibler divergence between the observation vector and the approximation. The performance of ASNA has been proved in previous works against other state-of-the-art methods. The implementations analysed in this paper have been developed in C, using parallel programming techniques to obtain a better performance in multicore architectures than the original MATLAB implementation. Also a hardware analysis is performed to check the influence of CPU frequency and number of CPU cores in the different implementations proposed. The new implementations allow ASNA algorithm to tackle real-time problems due to the execution time reduction obtained.This work has been partially supported by Programa de FPU del MECD, by MINECO and FEDER from Spain, under the projects TEC2015-67387- C4-1-R, and by project PROMETEO FASE II 2014/003 of Generalitat Valenciana. The authors want to thank Dr. Konstantinos Drossos for some very useful mind changing discussions. This work has been conducted in Laboratory of Signal Processing, Tampere University of Technology.San Juan-Sebastian, P.; Virtanen, T.; García Mollá, VM.; Vidal Maciá, AM. (2018). Analysis of an efficient parallel implementation of active-set Newton algorithm. The Journal of Supercomputing. 75(3):1298-1309. https://doi.org/10.1007/s11227-018-2423-5S12981309753Raj B, Smaragdis P (2005) Latent variable decomposition of spectrograms for single channel speaker separation. In: Proceedings of the IEEE Workshop on Applications of Signal Processing to Audio and Acoustics (WASPAA 2005), New Paltz, NyBertin N, Badeau R, Vincent E (2010) Enforcing harmonicity and smoothness in Bayesian non-negative matrix factorization applied to polyphonic music transcription. IEEE Trans Audio Speech Lang Process 18(3):538–549Dikmen O, Mesaros A (2013) Sound event detection using non-negative dictionaries learned from annotated overlapping events. In: IEEE Workshop on Applications of Signal Processing to Audio and Acoustics (WASPAA 2013). New Paltz, NYLawson CL, Hanson RJ (1995) Solving least squares problems. Society for Industrial and Applied Mathematics, PhiladelphiaVirtanen T (2007) Monaural sound source separation by nonnegative matrix factorization with temporal continuity and sparseness criteria. IEEE Trans Audio Speech Lang Process 15(3):1066–1074Virtanen T, Gemmeke J, Raj B (2013) Active-set Newton algorithm for overcomplete non-negative representations of audio. IEEE Trans Audio Speech Lang Process 21(11):2277–2289Cemgil AT (2009) Bayesian inference for nonnegative matrix factorisation models. Comput Intell Neurosci 2009:785152Cichocki A, Zdunek R, Phan AH, Amari S (2009) Nonnegative matrix and tensor factorizations. Wiley, New YorkMATLAB (2014) The Mathworks Inc., MATLAB R2014B, Natnick MATuomas Virtanen, Original MATLAB implementation of ASNA algorithm. http://www.cs.tut.fi/~tuomasv/software.htmlCarabias-Orti J, Rodriguez-Serrano F, Vera-Candeas P, Canadas-Quesada F, Ruiz-Reyes N (2013) Constrained non-negative sparse coding using learnt instrument templates for realtime music transcription. Eng Appl Artif Intell 26:1671–1680San Juan P, Virtanen T, Garcia-Molla Victor M, Vidal Antonio M (2016) Efficient parallel implementation of active-set newton algorithm for non-negative sparse representations. In: 16th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2016), Rota, SpainJuan P San, Efficient implementations of ASNA algorithm. https://gitlab.com/P.SanJuan/ASNAOpenMP v4.5 specification (2015). http://www.openmp.org/wpcontent/uploads/openmp-4.5.pdfGemmeke JF, Hurmalainen A, Virtanen T, Sun Y (2011) Toward a practical implementation of exemplar-based noise robust ASR. In: Signal Processing Conference, 19th European, IEEE, pp 1490–149

Low precision matrix multiplication for efficient deep learning in NVIDIA Carmel processors

[EN] We introduce a high performance, multi-threaded realization of the gemm kernel for the ARMv8.2 architecture that operates with 16-bit (half precision)/queryKindly check and confirm whether the corresponding author is correctly identified. floating point operands. Our code is especially designed for efficient machine learning inference (and to a certain extent, also training) with deep neural networks. The results on the NVIDIA Carmel multicore processor, which implements the ARMv8.2 architecture, show considerable performance gains for the gemm kernel, close to the theoretical peak acceleration that could be expected when moving from 32-bit arithmetic/data to 16-bit. Combined with the type of convolution operator arising in convolutional neural networks, the speed-ups are more modest though still relevant.This work was supported by projects TIN2017-82972-R and RTI2018-093684-B-I00 from the Ministerio de Ciencia, Innovacion y Universidades, project S2018/TCS-4423 of the Comunidad de Madrid, project PR65/19-22445 of the UCM, and project Prometeo/2019/109 of the Generalitat Valenciana.San Juan-Sebastian, P.; Rodríguez-Sánchez, R.; Igual, FD.; Alonso-Jordá, P.; Quintana-Ortí, ES. (2021). Low precision matrix multiplication for efficient deep learning in NVIDIA Carmel processors. The Journal of Supercomputing. 77(10):11257-11269. https://doi.org/10.1007/s11227-021-03636-41125711269771

Generalization of the K-SVD algorithm for minimization of ß-divergence

[EN] In this paper, we propose, describe, and test a modification of the K-SVD algorithm. Given a set of training data, the proposed algorithm computes an overcomplete dictionary by minimizing the ß-divergence () between the data and its representation as linear combinations of atoms of the dictionary, under strict sparsity restrictions. For the special case , the proposed algorithm minimizes the Frobenius norm and, therefore, for the proposed algorithm is equivalent to the original K-SVD algorithm. We describe the modifications needed and discuss the possible shortcomings of the new algorithm. The algorithm is tested with random matrices and with an example based on speech separation.This work has been partially supported by the EU together with the Spanish Government through TEC2015-67387-C4-1-R (MINECO/FEDER) and by Programa de FPU del Ministerio de Educacion, Cultura y Deporte FPU13/03828 (Spain).García Mollá, VM.; San Juan-Sebastian, P.; Virtanen, T.; Vidal Maciá, AM.; Alonso-Jordá, P. (2019). Generalization of the K-SVD algorithm for minimization of ß-divergence. Digital Signal Processing. 92:47-53. https://doi.org/10.1016/j.dsp.2019.05.001S47539

Additive Manufacturing of Fe-Mn-Si-Based Shape Memory Alloys: State of the Art, Challenges and Opportunities

Additive manufacturing (AM) constitutes the new paradigm in materials processing and its use on metals and alloys opens new unforeseen possibilities, but is facing several challenges regarding the design of the microstructure, which is particularly awkward in the case of functional materials, like shape memory alloys (SMA), as they require a robust microstructure to withstand the constraints appearing during their shape change. In the present work, the attention is focused on the AM of the important Fe-Mn-Si-based SMA family, which is attracting a great technological interest in many industrial sectors. Initially, an overview on the design concepts of this SMA family is offered, with special emphasis to the problems arising during AM. Then, such concepts are considered in order to experimentally develop the AM production of the Fe-20Mn-6Si-9Cr-5Ni (wt%) SMA through laser powder bed fusion (LPBF). The complete methodology is approached, from the gas atomization of powders to the LPBF production and the final thermal treatments to functionalize the SMA. The microstructure is characterized by scanning and transmission electron microscopy after each step of the processing route. The reversibility of the ε martensitic transformation and its evolution on cycling are studied by internal friction and electron microscopy. An outstanding 14% of fully reversible thermal transformation of ε martensite is obtained. The present results show that, in spite of the still remaining challenges, AM by LPBF offers a good approach to produce this family of Fe-Mn-Si-based SMA, opening new opportunities for its applications.This research was supported by the Industry Department of the Basque Government through the ELKARTEK-MINERVA (KK-2022/000082) project, and also from the GIU-021/24 from the University of the Basque Country UPV/EHU. This work made use of the electron microscopes installed at the General Service of Electron Microscopy of Materials, of the SGIKER—UPV/EHU, and the Zeiss at LORTEK technology center. Lucía Del-Río acknowledges the Pre-Doctoral grant (PRE_2022_1_0109) from the Education Department of the Basque Government

Characterization of protons accelerated from a 3 TW table-top laser system

[EN] We report on benchmark tests of a 3 TW/50 fs, table-top laser system specifically developed for proton acceleration with an intrinsic pump rate up to 100 Hz. In two series of single-shot measurements differing in pulse energy and contrast the successful operation of the diode pumped laser is demonstrated. Protons have been accelerated up to 1.6 MeV in interactions of laser pulses focused on aluminium and mylar foils between 0.8 and 25 mu m thickness. Their spectral distributions and maximum energies are consistent with former experiments under similar conditions. These results show the suitability of our system and provide a reference for studies of laser targets at high repetition rate and possible applications.This project has been funded by Centro para el Desarrollo Tecnologico Industrial (CDTI, Spain) within the INNPRONTA program, grant no. IPT-20111027, by EUROSTARS project E9113, and by the Spanish Ministry for Economy and Competitiveness within the Retos-Colaboracion 2015 initiative, ref. RTC-2015-3278-1.Bellido-Millán, PJ.; Lera, R.; Seimetz, M.; Ruiz-De La Cruz, A.; Torres Peiró, S.; Galán, M.; Mur, P.... (2017). Characterization of protons accelerated from a 3 TW table-top laser system. Journal of Instrumentation. 12:1-12. https://doi.org/10.1088/1748-0221/12/05/T05001S11212Daido, H., Nishiuchi, M., & Pirozhkov, A. S. (2012). Review of laser-driven ion sources and their applications. Reports on Progress in Physics, 75(5), 056401. doi:10.1088/0034-4885/75/5/056401Macchi, A., Borghesi, M., & Passoni, M. (2013). Ion acceleration by superintense laser-plasma interaction. Reviews of Modern Physics, 85(2), 751-793. doi:10.1103/revmodphys.85.751Ledingham, K., Bolton, P., Shikazono, N., & Ma, C.-M. (2014). Towards Laser Driven Hadron Cancer Radiotherapy: A Review of Progress. Applied Sciences, 4(3), 402-443. doi:10.3390/app4030402Kraft, S. D., Richter, C., Zeil, K., Baumann, M., Beyreuther, E., Bock, S., … Pawelke, J. (2010). Dose-dependent biological damage of tumour cells by laser-accelerated proton beams. New Journal of Physics, 12(8), 085003. doi:10.1088/1367-2630/12/8/085003Yogo, A., Sato, K., Nishikino, M., Mori, M., Teshima, T., Numasaki, H., … Daido, H. (2009). Application of laser-accelerated protons to the demonstration of DNA double-strand breaks in human cancer cells. Applied Physics Letters, 94(18), 181502. doi:10.1063/1.3126452Fritzler, S., Malka, V., Grillon, G., Rousseau, J. P., Burgy, F., Lefebvre, E., … Ledingham, K. W. D. (2003). Proton beams generated with high-intensity lasers: Applications to medical isotope production. Applied Physics Letters, 83(15), 3039-3041. doi:10.1063/1.1616661Kishimura, H., Morishita, H., Okano, Y. H., Okano, Y., Hironaka, Y., Kondo, K., … Nemoto, K. (2004). Enhanced generation of fast protons from a polymer-coated metal foil by a femtosecond intense laser field. Applied Physics Letters, 85(14), 2736-2738. doi:10.1063/1.1803915Nakamura, S., Iwashita, Y., Noda, A., Shirai, T., Tongu, H., Fukumi, A., … Wada, Y. (2006). Real-Time Optimization of Proton Production by Intense Short-Pulse Laser with Time-of-Flight Measurement. Japanese Journal of Applied Physics, 45(No. 34), L913-L916. doi:10.1143/jjap.45.l913Nishiuchi, M., Fukumi, A., Daido, H., Li, Z., Sagisaka, A., Ogura, K., … Nakamura, S. (2006). The laser proton acceleration in the strong charge separation regime. Physics Letters A, 357(4-5), 339-344. doi:10.1016/j.physleta.2006.04.053Yogo, A., Daido, H., Fukumi, A., Li, Z., Ogura, K., Sagisaka, A., … Itoh, A. (2007). Laser prepulse dependency of proton-energy distributions in ultraintense laser-foil interactions with an online time-of-flight technique. Physics of Plasmas, 14(4), 043104. doi:10.1063/1.2721066Robinson, A. P. L., Foster, P., Adams, D., Carroll, D. C., Dromey, B., Hawkes, S., … Neely, D. (2009). Spectral modification of laser-accelerated proton beams by self-generated magnetic fields. New Journal of Physics, 11(8), 083018. doi:10.1088/1367-2630/11/8/083018Nemoto, K., Maksimchuk, A., Banerjee, S., Flippo, K., Mourou, G., Umstadter, D., & Bychenkov, V. Y. (2001). Laser-triggered ion acceleration and table top isotope production. Applied Physics Letters, 78(5), 595-597. doi:10.1063/1.1343845Lee, K., Park, S. H., Cha, Y.-H., Lee, J. Y., Lee, Y. W., Yea, K.-H., & Jeong, Y. U. (2008). Generation of intense proton beams from plastic targets irradiated by an ultraintense laser pulse. Physical Review E, 78(5). doi:10.1103/physreve.78.056403Yogo, A., Daido, H., Bulanov, S. V., Nemoto, K., Oishi, Y., Nayuki, T., … Tajima, T. (2008). Laser ion acceleration via control of the near-critical density target. Physical Review E, 77(1). doi:10.1103/physreve.77.016401Lee, K., Lee, J. Y., Park, S. H., Cha, Y.-H., Lee, Y. W., Kim, K. N., & Jeong, Y. U. (2011). Dominant front-side acceleration of energetic proton beams from plastic targets irradiated by an ultraintense laser pulse. Physics of Plasmas, 18(1), 013101. doi:10.1063/1.3496058OKIHARA, S., SENTOKU, Y., SUEDA, K., SHIMIZU, S., SATO, F., MIYANAGA, N., … SAKABE, S. (2002). Energetic Proton Generation in a Thin Plastic Foil Irradiated by Intense Femtosecond Lasers. Journal of Nuclear Science and Technology, 39(1), 1-5. doi:10.1080/18811248.2002.9715150McKenna, P., Ledingham, K. W. D., Spencer, I., McCany, T., Singhal, R. P., Ziener, C., … Clark, E. L. (2002). Characterization of multiterawatt laser-solid interactions for proton acceleration. Review of Scientific Instruments, 73(12), 4176-4184. doi:10.1063/1.1516855Spencer, I., Ledingham, K. W. D., McKenna, P., McCanny, T., Singhal, R. P., Foster, P. S., … Davies, J. R. (2003). Experimental study of proton emission from 60-fs, 200-mJ high-repetition-rate tabletop-laser pulses interacting with solid targets. Physical Review E, 67(4). doi:10.1103/physreve.67.046402Kaluza, M., Schreiber, J., Santala, M. I. K., Tsakiris, G. D., Eidmann, K., Meyer-ter-Vehn, J., & Witte, K. J. (2004). Influence of the Laser Prepulse on Proton Acceleration in Thin-Foil Experiments. Physical Review Letters, 93(4). doi:10.1103/physrevlett.93.045003Ceccotti, T., Lévy, A., Popescu, H., Réau, F., D’Oliveira, P., Monot, P., … Martin, P. (2007). Proton Acceleration with High-Intensity Ultrahigh-Contrast Laser Pulses. Physical Review Letters, 99(18). doi:10.1103/physrevlett.99.185002Neely, D., Foster, P., Robinson, A., Lindau, F., Lundh, O., Persson, A., … McKenna, P. (2006). Enhanced proton beams from ultrathin targets driven by high contrast laser pulses. Applied Physics Letters, 89(2), 021502. doi:10.1063/1.2220011Steinke, S., Henig, A., Schnürer, M., Sokollik, T., Nickles, P. V., Jung, D., … Habs, D. (2010). Efficient ion acceleration by collective laser-driven electron dynamics with ultra-thin foil targets. Laser and Particle Beams, 28(1), 215-221. doi:10.1017/s0263034610000157Strickland, D., & Mourou, G. (1985). Compression of amplified chirped optical pulses. Optics Communications, 56(3), 219-221. doi:10.1016/0030-4018(85)90120-8Yogo, A., Kondo, K., Mori, M., Kiriyama, H., Ogura, K., Shimomura, T., … Bolton, P. R. (2014). Insertable pulse cleaning module with a saturable absorber pair and a compensating amplifier for high-intensity ultrashort-pulse lasers. Optics Express, 22(2), 2060. doi:10.1364/oe.22.002060Trisorio, A., Grabielle, S., Divall, M., Forget, N., & Hauri, C. P. (2012). Self-referenced spectral interferometry for ultrashort infrared pulse characterization. Optics Letters, 37(14), 2892. doi:10.1364/ol.37.002892Seimetz, M., Bellido, P., Soriano, A., Garcia Lopez, J., Jimenez-Ramos, M. C., Fernandez, B., … Benlloch, J. M. (2015). Calibration and Performance Tests of Detectors for Laser-Accelerated Protons. IEEE Transactions on Nuclear Science, 62(6), 3216-3224. doi:10.1109/tns.2015.2480682Nürnberg, F., Schollmeier, M., Brambrink, E., Blažević, A., Carroll, D. C., Flippo, K., … Roth, M. (2009). Radiochromic film imaging spectroscopy of laser-accelerated proton beams. Review of Scientific Instruments, 80(3), 033301. doi:10.1063/1.3086424Oishi, Y., Nayuki, T., Fujii, T., Takizawa, Y., Wang, X., Yamazaki, T., … Andreev, A. A. (2005). Dependence on laser intensity and pulse duration in proton acceleration by irradiation of ultrashort laser pulses on a Cu foil target. Physics of Plasmas, 12(7), 073102. doi:10.1063/1.1943436Nishiuchi, M., Daito, I., Ikegami, M., Daido, H., Mori, M., Orimo, S., … Yoshiyuki, T. (2009). Focusing and spectral enhancement of a repetition-rated, laser-driven, divergent multi-MeV proton beam using permanent quadrupole magnets. Applied Physics Letters, 94(6), 061107. doi:10.1063/1.3078291Antici, P., Fuchs, J., d’ Humières, E., Lefebvre, E., Borghesi, M., Brambrink, E., … Pépin, H. (2007). Energetic protons generated by ultrahigh contrast laser pulses interacting with ultrathin targets. Physics of Plasmas, 14(3), 030701. doi:10.1063/1.2480610Green, J. S., Carroll, D. C., Brenner, C., Dromey, B., Foster, P. S., Kar, S., … Zepf, M. (2010). Enhanced proton flux in the MeV range by defocused laser irradiation. New Journal of Physics, 12(8), 085012. doi:10.1088/1367-2630/12/8/085012Zeil, K., Kraft, S. D., Bock, S., Bussmann, M., Cowan, T. E., Kluge, T., … Schramm, U. (2010). The scaling of proton energies in ultrashort pulse laser plasma acceleration. New Journal of Physics, 12(4), 045015. doi:10.1088/1367-2630/12/4/045015Nishiuchi, M., Daido, H., Yogo, A., Orimo, S., Ogura, K., Ma, J., … Azuma, H. (2008). Efficient production of a collimated MeV proton beam from a polyimide target driven by an intense femtosecond laser pulse. Physics of Plasmas, 15(5), 053104. doi:10.1063/1.2928161Macchi, A., Sgattoni, A., Sinigardi, S., Borghesi, M., & Passoni, M. (2013). Advanced strategies for ion acceleration using high-power lasers. Plasma Physics and Controlled Fusion, 55(12), 124020. doi:10.1088/0741-3335/55/12/124020Fuchs, J., Antici, P., d’ Humières, E., Lefebvre, E., Borghesi, M., Brambrink, E., … Audebert, P. (2005). Laser-driven proton scaling laws and new paths towards energy increase. Nature Physics, 2(1), 48-54. doi:10.1038/nphys199Schwoerer, H., Pfotenhauer, S., Jäckel, O., Amthor, K.-U., Liesfeld, B., Ziegler, W., … Esirkepov, T. (2006). Laser-plasma acceleration of quasi-monoenergetic protons from microstructured targets. Nature, 439(7075), 445-448. doi:10.1038/nature04492Margarone, D., Klimo, O., Kim, I. J., Prokůpek, J., Limpouch, J., Jeong, T. M., … Korn, G. (2012). Laser-Driven Proton Acceleration Enhancement by Nanostructured Foils. Physical Review Letters, 109(23). doi:10.1103/physrevlett.109.234801Flippo, K. A., d’ Humières, E., Gaillard, S. A., Rassuchine, J., Gautier, D. C., Schollmeier, M., … Hegelich, B. M. (2008). Increased efficiency of short-pulse laser-generated proton beams from novel flat-top cone targets. Physics of Plasmas, 15(5), 056709. doi:10.1063/1.291812

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Common variants in Alzheimer's disease and risk stratification by polygenic risk scores.

Funder: Funder: Fundación bancaria ‘La Caixa’ Number: LCF/PR/PR16/51110003 Funder: Grifols SA Number: LCF/PR/PR16/51110003 Funder: European Union/EFPIA Innovative Medicines Initiative Joint Number: 115975 Funder: JPco-fuND FP-829-029 Number: 733051061Genetic discoveries of Alzheimer's disease are the drivers of our understanding, and together with polygenetic risk stratification can contribute towards planning of feasible and efficient preventive and curative clinical trials. We first perform a large genetic association study by merging all available case-control datasets and by-proxy study results (discovery n = 409,435 and validation size n = 58,190). Here, we add six variants associated with Alzheimer's disease risk (near APP, CHRNE, PRKD3/NDUFAF7, PLCG2 and two exonic variants in the SHARPIN gene). Assessment of the polygenic risk score and stratifying by APOE reveal a 4 to 5.5 years difference in median age at onset of Alzheimer's disease patients in APOE ɛ4 carriers. Because of this study, the underlying mechanisms of APP can be studied to refine the amyloid cascade and the polygenic risk score provides a tool to select individuals at high risk of Alzheimer's disease