A Novel Semi-Supervised Methodology for Extracting Tumor Type-Specific MRS Sources in Human Brain Data

BackgroundThe clinical investigation of human brain tumors often starts with a non-invasive imaging study, providing information about the tumor extent and location, but little insight into the biochemistry of the analyzed tissue. Magnetic Resonance Spectroscopy can complement imaging by supplying a metabolic fingerprint of the tissue. This study analyzes single-voxel magnetic resonance spectra, which represent signal information in the frequency domain. Given that a single voxel may contain a heterogeneous mix of tissues, signal source identification is a relevant challenge for the problem of tumor type classification from the spectroscopic signal.Methodology/Principal FindingsNon-negative matrix factorization techniques have recently shown their potential for the identification of meaningful sources from brain tissue spectroscopy data. In this study, we use a convex variant of these methods that is capable of handling negatively-valued data and generating sources that can be interpreted as tumor class prototypes. A novel approach to convex non-negative matrix factorization is proposed, in which prior knowledge about class information is utilized in model optimization. Class-specific information is integrated into this semi-supervised process by setting the metric of a latent variable space where the matrix factorization is carried out. The reported experimental study comprises 196 cases from different tumor types drawn from two international, multi-center databases. The results indicate that the proposed approach outperforms a purely unsupervised process by achieving near perfect correlation of the extracted sources with the mean spectra of the tumor types. It also improves tissue type classification.Conclusions/SignificanceWe show that source extraction by unsupervised matrix factorization benefits from the integration of the available class information, so operating in a semi-supervised learning manner, for discriminative source identification and brain tumor labeling from single-voxel spectroscopy data. We are confident that the proposed methodology has wider applicability for biomedical signal processing

How is precision regulated in maintaining trunk posture?

Precision of limb control is associated with increased joint stiffness caused by antagonistic co-activation. The aim of this study was to examine whether this strategy also applies to precision of trunk postural control. To this end, thirteen subjects performed static postural tasks, aiming at a target object with a cursor that responded to 2D trunk angles. By manipulating target dimensions, different levels of precision were imposed in the frontal and sagittal planes. Trunk angle and electromyography (EMG) of abdominal and back muscles were recorded. Repeated measures ANOVAs revealed significant effects of target dimensions on kinematic variability in both movement planes. Specifically, standard deviation (SD) of trunk angle decreased significantly when target size in the same direction decreased, regardless of the precision demands in the other direction. Thus, precision control of trunk posture was directionally specific. However, no consistent effect of precision demands was found on trunk muscle activity, when averaged over time series. Therefore, it was concluded that stiffness regulation by antagonistic co-activation was not used to meet increased precision demands in trunk postural control. Instead, results from additional analyses suggest that precision of trunk angle was controlled in a feedback mode

Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation

<p>Abstract</p> <p>Background</p> <p>External stimulations of cells by hormones, cytokines or growth factors activate signal transduction pathways that subsequently induce a re-arrangement of cellular gene expression. The analysis of such changes is complicated, as they consist of multi-layered temporal responses. While classical analyses based on clustering or gene set enrichment only partly reveal this information, matrix factorization techniques are well suited for a detailed temporal analysis. In signal processing, factorization techniques incorporating data properties like spatial and temporal correlation structure have shown to be robust and computationally efficient. However, such correlation-based methods have so far not be applied in bioinformatics, because large scale biological data rarely imply a natural order that allows the definition of a delayed correlation function.</p> <p>Results</p> <p>We therefore develop the concept of graph-decorrelation. We encode prior knowledge like transcriptional regulation, protein interactions or metabolic pathways in a weighted directed graph. By linking features along this underlying graph, we introduce a partial ordering of the features (e.g. genes) and are thus able to define a graph-delayed correlation function. Using this framework as constraint to the matrix factorization task allows us to set up the fast and robust graph-decorrelation algorithm (GraDe). To analyze alterations in the gene response in <it>IL-6 </it>stimulated primary mouse hepatocytes, we performed a time-course microarray experiment and applied GraDe. In contrast to standard techniques, the extracted time-resolved gene expression profiles showed that <it>IL-6 </it>activates genes involved in cell cycle progression and cell division. Genes linked to metabolic and apoptotic processes are down-regulated indicating that <it>IL-6 </it>mediated priming renders hepatocytes more responsive towards cell proliferation and reduces expenditures for the energy metabolism.</p> <p>Conclusions</p> <p>GraDe provides a novel framework for the decomposition of large-scale 'omics' data. We were able to show that including prior knowledge into the separation task leads to a much more structured and detailed separation of the time-dependent responses upon <it>IL-6 </it>stimulation compared to standard methods. A Matlab implementation of the GraDe algorithm is freely available at <url>http://cmb.helmholtz-muenchen.de/grade</url>.</p

Microbes Bind Complement Inhibitor Factor H via a Common Site

To cause infections microbes need to evade host defense systems, one of these being the evolutionarily old and important arm of innate immunity, the alternative pathway of complement. It can attack all kinds of targets and is tightly controlled in plasma and on host cells by plasma complement regulator factor H (FH). FH binds simultaneously to host cell surface structures such as heparin or glycosaminoglycans via domain 20 and to the main complement opsonin C3b via domain 19. Many pathogenic microbes protect themselves from complement by recruiting host FH. We analyzed how and why different microbes bind FH via domains 19–20 (FH19-20). We used a selection of FH19-20 point mutants to reveal the binding sites of several microbial proteins and whole microbes (Haemophilus influenzae, Bordetella pertussis, Pseudomonas aeruginosa, Streptococcus pneumonia, Candida albicans, Borrelia burgdorferi, and Borrelia hermsii). We show that all studied microbes use the same binding region located on one side of domain 20. Binding of FH to the microbial proteins was inhibited with heparin showing that the common microbial binding site overlaps with the heparin site needed for efficient binding of FH to host cells. Surprisingly, the microbial proteins enhanced binding of FH19-20 to C3b and down-regulation of complement activation. We show that this is caused by formation of a tripartite complex between the microbial protein, FH, and C3b. In this study we reveal that seven microbes representing different phyla utilize a common binding site on the domain 20 of FH for complement evasion. Binding via this site not only mimics the glycosaminoglycans of the host cells, but also enhances function of FH on the microbial surfaces via the novel mechanism of tripartite complex formation. This is a unique example of convergent evolution resulting in enhanced immune evasion of important pathogens viautilization of a “superevasion site.

A Structured Model of Video Reproduces Primary Visual Cortical Organisation

The visual system must learn to infer the presence of objects and features in the world from the images it encounters, and as such it must, either implicitly or explicitly, model the way these elements interact to create the image. Do the response properties of cells in the mammalian visual system reflect this constraint? To address this question, we constructed a probabilistic model in which the identity and attributes of simple visual elements were represented explicitly and learnt the parameters of this model from unparsed, natural video sequences. After learning, the behaviour and grouping of variables in the probabilistic model corresponded closely to functional and anatomical properties of simple and complex cells in the primary visual cortex (V1). In particular, feature identity variables were activated in a way that resembled the activity of complex cells, while feature attribute variables responded much like simple cells. Furthermore, the grouping of the attributes within the model closely parallelled the reported anatomical grouping of simple cells in cat V1. Thus, this generative model makes explicit an interpretation of complex and simple cells as elements in the segmentation of a visual scene into basic independent features, along with a parametrisation of their moment-by-moment appearances. We speculate that such a segmentation may form the initial stage of a hierarchical system that progressively separates the identity and appearance of more articulated visual elements, culminating in view-invariant object recognition

Affective computing in virtual reality: emotion recognition from brain and heartbeat dynamics using wearable sensors

[EN] Affective Computing has emerged as an important field of study that aims to develop systems that can automatically recognize emotions. Up to the present, elicitation has been carried out with nonimmersive stimuli. This study, on the other hand, aims to develop an emotion recognition system for affective states evoked through Immersive Virtual Environments. Four alternative virtual rooms were designed to elicit four possible arousal-valence combinations, as described in each quadrant of the Circumplex Model of Affects. An experiment involving the recording of the electroencephalography (EEG) and electrocardiography (ECG) of sixty participants was carried out. A set of features was extracted from these signals using various state-of-the-art metrics that quantify brain and cardiovascular linear and nonlinear dynamics, which were input into a Support Vector Machine classifier to predict the subject's arousal and valence perception. The model's accuracy was 75.00% along the arousal dimension and 71.21% along the valence dimension. Our findings validate the use of Immersive Virtual Environments to elicit and automatically recognize different emotional states from neural and cardiac dynamics; this development could have novel applications in fields as diverse as Architecture, Health, Education and Videogames.This work was supported by the Ministerio de Economia y Competitividad. Spain (Project TIN2013-45736-R).Marín-Morales, J.; Higuera-Trujillo, JL.; Greco, A.; Guixeres Provinciale, J.; Llinares Millán, MDC.; Scilingo, EP.; Alcañiz Raya, ML.... (2018). Affective computing in virtual reality: emotion recognition from brain and heartbeat dynamics using wearable sensors. Scientific Reports. 8:1-15. https://doi.org/10.1038/s41598-018-32063-4S1158Picard, R. W. Affective computing. (MIT press, 1997).Picard, R. W. Affective Computing: Challenges. Int. J. Hum. Comput. Stud. 59, 55–64 (2003).Jerritta, S., Murugappan, M., Nagarajan, R. & Wan, K. Physiological signals based human emotion Recognition: a review. Signal Process. its Appl. (CSPA), 2011 IEEE 7th Int. Colloq. 410–415, https://doi.org/10.1109/CSPA.2011.5759912 (2011).Harms, M. B., Martin, A. & Wallace, G. L. Facial emotion recognition in autism spectrum disorders: A review of behavioral and neuroimaging studies. Neuropsychol. Rev. 20, 290–322 (2010).Koolagudi, S. G. & Rao, K. S. Emotion recognition from speech: A review. Int. J. Speech Technol. 15, 99–117 (2012).Gross, J. J. & Levenson, R. W. Emotion elicitation using films. Cogn. Emot. 9, 87–108 (1995).Lindal, P. J. & Hartig, T. Architectural variation, building height, and the restorative quality of urban residential streetscapes. J. Environ. Psychol. 33, 26–36 (2013).Ulrich, R. View through a window may influence recovery from surgery. Science (80-.). 224, 420–421 (1984).Fernández-Caballero, A. et al. Smart environment architecture for emotion detection and regulation. J. Biomed. Inform. 64, 55–73 (2016).Ekman, P. Basic Emotions. Handbook of cognition and emotion 45–60, https://doi.org/10.1017/S0140525X0800349X (1999).Posner, J., Russell, J. A. & Peterson, B. S. The circumplex model of affect: an integrative approach to affective neuroscience, cognitive development, and psychopathology. Dev. Psychopathol. 17, 715–34 (2005).Russell, J. A. & Mehrabian, A. Evidence for a three-factor theory of emotions. J. Res. Pers. 11, 273–294 (1977).Calvo, R. A. & D’Mello, S. Affect detection: An interdisciplinary review of models, methods, and their applications. IEEE Trans. Affect. Comput. 1, 18–37 (2010).Valenza, G. et al. Combining electroencephalographic activity and instantaneous heart rate for assessing brain–heart dynamics during visual emotional elicitation in healthy subjects. Philos. Trans. R. Soc. A Math. Phys. Eng. Sci. 374, 20150176 (2016).Valenza, G., Lanata, A. & Scilingo, E. P. The role of nonlinear dynamics in affective valence and arousal recognition. IEEE Trans. Affect. Comput. 3, 237–249 (2012).Valenza, G., Citi, L., Lanatá, A., Scilingo, E. P. & Barbieri, R. Revealing real-time emotional responses: a personalized assessment based on heartbeat dynamics. Sci. Rep. 4, 4998 (2014).Valenza, G. et al. Wearable monitoring for mood recognition in bipolar disorder based on history-dependent long-term heart rate variability analysis. IEEE J. Biomed. Heal. Informatics 18, 1625–1635 (2014).Piwek, L., Ellis, D. A., Andrews, S. & Joinson, A. The Rise of Consumer Health Wearables: Promises and Barriers. PLoS Med. 13, 1–9 (2016).Xu, J., Mitra, S., Van Hoof, C., Yazicioglu, R. & Makinwa, K. A. A. Active Electrodes for Wearable EEG Acquisition: Review and Electronics Design Methodology. IEEE Rev. Biomed. Eng. 3333, 1–1 (2017).Kumari, P., Mathew, L. & Syal, P. Increasing trend of wearables and multimodal interface for human activity monitoring: A review. Biosens. Bioelectron. 90, 298–307 (2017).He, C., Yao, Y. & Ye, X. An Emotion Recognition System Based on Physiological Signals Obtained by Wearable Sensors. In Wearable Sensors and Robots: Proceedings of International Conference on Wearable Sensors and Robots 2015 (eds Yang, C., Virk, G. S. & Yang, H.) 15–25. https://doi.org/10.1007/978-981-10-2404-7_2 (Springer Singapore, 2017).Nakisa, B., Rastgoo, M. N., Tjondronegoro, D. & Chandran, V. Evolutionary computation algorithms for feature selection of EEG-based emotion recognition using mobile sensors. Expert Syst. Appl. 93, 143–155 (2018).Kory Jacqueline, D. & Sidney, K. Affect Elicitation for Affective Computing. In The Oxford Handbook of Affective Computing 371–383 (2014).Ekman, P. The directed facial action task. In Handbook of emotion elicitation and assessment 47–53 (2007).Harmon-Jones, E., Amodio, D. M. & Zinner, L. R. Social psychological methods of emotion elicitation. Handb. Emot. elicitation Assess. 91–105, https://doi.org/10.2224/sbp.2007.35.7.863 (2007)Roberts, N. A., Tsai, J. L. & Coan, J. A. Emotion elicitation using dyadic interaction task. Handbook of Emotion Elicitation and Assessment 106–123 (2007).Nardelli, M., Valenza, G., Greco, A., Lanata, A. & Scilingo, E. P. Recognizing emotions induced by affective sounds through heart rate variability. IEEE Trans. Affect. Comput. 6, 385–394 (2015).Kim, J. Emotion Recognition Using Speech and Physiological Changes. Robust Speech Recognit. Underst. 265–280 (2007).Soleymani, M., Pantic, M. & Pun, T. Multimodal emotion recognition in response to videos (Extended abstract). 2015 Int. Conf. Affect. Comput. Intell. Interact. ACII 2015 3, 491–497 (2015).Baños, R. M. et al. Immersion and Emotion: Their Impact on the Sense of Presence. CyberPsychology Behav. 7, 734–741 (2004).Giglioli, I. A. C., Pravettoni, G., Martín, D. L. S., Parra, E. & Raya, M. A. A novel integrating virtual reality approach for the assessment of the attachment behavioral system. Front. Psychol. 8, 1–7 (2017).Marín-Morales, J., Torrecilla, C., Guixeres, J. & Llinares, C. Methodological bases for a new platform for the measurement of human behaviour in virtual environments. DYNA 92, 34–38 (2017).Vince, J. Introduction to virtual reality. (Media, Springer Science & Business, 2004).Alcañiz, M., Baños, R., Botella, C. & Rey, B. The EMMA Project: Emotions as a Determinant of Presence. PsychNology J. 1, 141–150 (2003).Vecchiato, G. et al. Neurophysiological correlates of embodiment and motivational factors during the perception of virtual architectural environments. Cogn. Process. 16, 425–429 (2015).Slater, M. & Wilbur, S. A Framework for Immersive Virtual Environments (FIVE): Speculations on the Role of Presence in Virtual Environments. Presence Teleoperators Virtual Environ. 6, 603–616 (1997).Riva, G. et al. Affective Interactions Using Virtual Reality: The Link between Presence and Emotions. CyberPsychology Behav. 10, 45–56 (2007).Baños, R. M. et al Changing induced moods via virtual reality. In International Conference on Persuasive Technology (ed. Springer, Berlin, H.) 7–15, https://doi.org/10.1007/11755494_3 (2006).Baños, R. M. et al. Positive mood induction procedures for virtual environments designed for elderly people. Interact. Comput. 24, 131–138 (2012).Gorini, A. et al. Emotional Response to Virtual Reality Exposure across Different Cultures: The Role of the AttributionProcess. CyberPsychology Behav. 12, 699–705 (2009).Gorini, A., Capideville, C. S., De Leo, G., Mantovani, F. & Riva, G. The Role of Immersion and Narrative in Mediated Presence: The Virtual Hospital Experience. Cyberpsychology, Behav. Soc. Netw. 14, 99–105 (2011).Chirico, A. et al. Effectiveness of Immersive Videos in Inducing Awe: An Experimental Study. Sci. Rep. 7, 1–11 (2017).Blascovich, J. et al. Immersive Virtual Environment Technology as a Methodological Tool for Social Psychology. Psychol. Inq. 7965, 103–124 (2012).Peperkorn, H. M., Alpers, G. W. & Mühlberger, A. Triggers of fear: Perceptual cues versus conceptual information in spider phobia. J. Clin. Psychol. 70, 704–714 (2014).McCall, C., Hildebrandt, L. K., Bornemann, B. & Singer, T. Physiophenomenology in retrospect: Memory reliably reflects physiological arousal during a prior threatening experience. Conscious. Cogn. 38, 60–70 (2015).Hildebrandt, L. K., Mccall, C., Engen, H. G. & Singer, T. Cognitive flexibility, heart rate variability, and resilience predict fine-grained regulation of arousal during prolonged threat. Psychophysiology 53, 880–890 (2016).Notzon, S. et al. Psychophysiological effects of an iTBS modulated virtual reality challenge including participants with spider phobia. Biol. Psychol. 112, 66–76 (2015).Amaral, C. P., Simões, M. A., Mouga, S., Andrade, J. & Castelo-Branco, M. A novel Brain Computer Interface for classification of social joint attention in autism and comparison of 3 experimental setups: A feasibility study. J. Neurosci. Methods 290, 105–115 (2017).Eudave, L. & Valencia, M. Physiological response while driving in an immersive virtual environment. 2017 IEEE 14th Int. Conf. Wearable Implant. Body Sens. Networks 145–148, https://doi.org/10.1109/BSN.2017.7936028 (2017).Sharma, G. et al. Influence of landmarks on wayfinding and brain connectivity in immersive virtual reality environment. Front. Psychol. 8, 1–12 (2017).Bian, Y. et al. A framework for physiological indicators of flow in VR games: construction and preliminary evaluation. Pers. Ubiquitous Comput. 20, 821–832 (2016).Egan, D. et al. An evaluation of Heart Rate and Electrodermal Activity as an Objective QoE Evaluation method for Immersive Virtual Reality Environments. 3–8, https://doi.org/10.1109/QoMEX.2016.7498964 (2016).Meehan, M., Razzaque, S., Insko, B., Whitton, M. & Brooks, F. P. Review of four studies on the use of physiological reaction as a measure of presence in stressful virtual environments. Appl. Psychophysiol. Biofeedback 30, 239–258 (2005).Higuera-Trujillo, J. L., López-Tarruella Maldonado, J. & Llinares Millán, C. Psychological and physiological human responses to simulated and real environments: A comparison between Photographs, 360° Panoramas, and Virtual Reality. Appl. Ergon. 65, 398–409 (2016).Felnhofer, A. et al. Is virtual reality emotionally arousing? Investigating five emotion inducing virtual park scenarios. Int. J. Hum. Comput. Stud. 82, 48–56 (2015).Anderson, A. P. et al. Relaxation with Immersive Natural Scenes Presented Using Virtual Reality. Aerosp. Med. Hum. Perform. 88, 520–526 (2017).Higuera, J. L. et al. Emotional cartography in design: A novel technique to represent emotional states altered by spaces. In D and E 2016: 10th International Conference on Design and Emotion 561–566 (2016).Kroenke, K., Spitzer, R. L. & Williams, J. B. W. The PHQ-9: Validity of a brief depression severity measure. J. Gen. Intern. Med. 16, 606–613 (2001).Bradley, M. M. & Lang, P. J. Measuring emotion: The self-assessment manikin and the semantic differential. J. Behav. Ther. Exp. Psychiatry 25, 49–59 (1994).Lang, P. J., Bradley, M. M. & Cuthbert, B. N. International Affective Picture System (IAPS): Technical Manual and Affective Ratings. NIMH Cent. Study Emot. Atten. 39–58, https://doi.org/10.1027/0269-8803/a000147 (1997).Nanda, U., Pati, D., Ghamari, H. & Bajema, R. Lessons from neuroscience: form follows function, emotions follow form. Intell. Build. Int. 5, 61–78 (2013).Russell, J. A. A circumplex model of affect. J. Pers. Soc. Psychol. 39, 1161–1178 (1980).Sejima, K. Kazuyo Sejima. 1988–1996. El Croquis 15 (1996).Ochiai, H. et al. Physiological and Psychological Effects of Forest Therapy on Middle-Aged Males with High-NormalBlood Pressure. Int. J. Environ. Res. Public Health 12, 2532–2542 (2015).Noguchi, H. & Sakaguchi, T. Effect of illuminance and color temperature on lowering of physiological activity. Appl. Hum. Sci. 18, 117–123 (1999).Küller, R., Mikellides, B. & Janssens, J. Color, arousal, and performance—A comparison of three experiments. Color Res. Appl. 34, 141–152 (2009).Yildirim, K., Hidayetoglu, M. L. & Capanoglu, A. Effects of interior colors on mood and preference: comparisons of two living rooms. Percept. Mot. Skills 112, 509–524 (2011).Hogg, J., Goodman, S., Porter, T., Mikellides, B. & Preddy, D. E. Dimensions and determinants of judgements of colour samples and a simulated interior space by architects and non‐architects. Br. J. Psychol. 70, 231–242 (1979).Jalil, N. A., Yunus, R. M. & Said, N. S. Environmental Colour Impact upon Human Behaviour: A Review. Procedia - Soc. Behav. Sci. 35, 54–62 (2012).Jacobs, K. W. & Hustmyer, F. E. Effects of four psychological primary colors on GSR, heart rate and respiration rate. Percept. Mot. Skills 38, 763–766 (1974).Jin, H. R., Yu, M., Kim, D. W., Kim, N. G. & Chung, A. S. W. Study on Physiological Responses to Color Stimulation. In International Association of Societies of Design Research (ed. Poggenpohl, S.) 1969–1979 (Korean Society of Design Science, 2009).Vartanian, O. et al. Impact of contour on aesthetic judgments and approach-avoidance decisions in architecture. Proc. Natl. Acad. Sci. 110, 1–8 (2013).Tsunetsugu, Y., Miyazaki, Y. & Sato, H. Visual effects of interior design in actual-size living rooms on physiological responses. Build. Environ. 40, 1341–1346 (2005).Stamps, A. E. Physical Determinants of Preferences for Residential Facades. Environ. Behav. 31, 723–751 (1999).Berlyne, D. E. Novelty, Complexity, and Hedonic Value. Percept. Psychophys. 8, 279–286 (1970).Krueger, R. A. & Casey, M. Focus groups: a practical guide for applied research. (Sage Publications, 2000).Acharya, U. R., Joseph, K. P., Kannathal, N., Lim, C. M. & Suri, J. S. Heart rate variability: A review. Med. Biol. Eng. Comput. 44, 1031–1051 (2006).Tarvainen, M. P., Niskanen, J. P., Lipponen, J. A., Ranta-aho, P. O. & Karjalainen, P. A. Kubios HRV - Heart rate variability analysis software. Comput. Methods Programs Biomed. 113, 210–220 (2014).Pan, J. & Tompkins, W. J. A real-time QRS detection algorithm. Biomed. Eng. IEEE Trans. 1, 230–236 (1985).Tarvainen, M. P., Ranta-aho, P. O. & Karjalainen, P. A. An advanced detrending method with application to HRV analysis. IEEE Trans. Biomed. Eng. 49, 172–175 (2002).Valenza, G. et al. Predicting Mood Changes in Bipolar Disorder Through HeartbeatNonlinear Dynamics. IEEE J. Biomed. Heal. Informatics 20, 1034–1043 (2016).Pincus, S. & Viscarello, R. Approximate Entropy A regularity measure for fetal heart rate analysis. Obstet. Gynecol. 79, 249–255 (1992).Richman, J. & Moorman, J. Physiological time-series analysis using approximate entropy and sample entropy. Am J Physiol Hear. Circ Physiol 278, H2039–H2049 (2000).Peng, C.-K., Havlin, S., Stanley, H. E. & Goldberger, A. L. Quantification of scaling exponents and crossover phenomena in nonstationary heartbeat time series. Chaos 5, 82–87 (1995).Grassberger, P. & Procaccia, I. Characterization of strange attractors. Phys. Rev. Lett. 50, 346–349 (1983).Delorme, A. & Makeig, S. EEGLAB: An open source toolbox for analysis of single-trial EEG dynamics including independent component analysis. J. Neurosci. Methods 134, 9–21 (2004).Colomer Granero, A. et al. A Comparison of Physiological Signal Analysis Techniques and Classifiers for Automatic Emotional Evaluation of Audiovisual Contents. Front. Comput. Neurosci. 10, 1–14 (2016).Kober, S. E., Kurzmann, J. & Neuper, C. Cortical correlate of spatial presence in 2D and 3D interactive virtual reality: An EEG study. Int. J. Psychophysiol. 83, 365–374 (2012).Hyvärinen, A. & Oja, E. Independent component analysis: Algorithms and applications. Neural Networks 13, 411–430 (2000).Welch, P. D. The Use of Fast Fourier Transform for the Estimation of Power Spectra: A Method Based on Time Aver. aging Over Short, Modified Periodograms. IEEE Trans. AUDIO Electroacoust. 15, 70–73 (1967).Mormann, F., Lehnertz, K., David, P. & Elger, E. C. Mean phase coherence as a measure for phase synchronization and its application to the EEG of epilepsy patients. Phys. D Nonlinear Phenom. 144, 358–369 (2000).Jolliffe, I. T. Principal Component Analysis, Second Edition. Encycl. Stat. Behav. Sci. 30, 487 (2002).Schöllkopf, B., Smola, A. J., Williamson, R. C. & Bartlett, P. L. New support vector algorithms. Neural Comput 12, 1207–1245 (2000).Yan, K. & Zhang, D. Feature selection and analysis on correlated gas sensor data with recursive feature elimination. Sensors Actuators, B Chem. 212, 353–363 (2015).Chang, C.-C. & Lin, C.-J. Libsvm: A Library for Support Vector Machines. ACM Trans. Intell. Syst. Technol. 2, 1–27 (2011).Lewis, P. A., Critchley, H. D., Rotshtein, P. & Dolan, R. J. Neural correlates of processing valence and arousal in affective words. Cereb. Cortex 17, 742–748 (2007).McCall, C., Hildebrandt, L. K., Hartmann, R., Baczkowski, B. M. & Singer, T. Introducing the Wunderkammer as a tool for emotion research: Unconstrained gaze and movement patterns in three emotionally evocative virtual worlds. Comput. Human Behav. 59, 93–107 (2016).Blake, J. & Gurocak, H. B. Haptic glove with MR brakes for virtual reality. IEEE/ASME Trans. Mechatronics 14, 606–615 (2009).Heydarian, A. et al. Immersive virtual environments versus physical built environments: A benchmarking study for building design and user-built environment explorations. Autom. Constr. 54, 116–126 (2015).Kuliga, S. F., Thrash, T., Dalton, R. C. & Hölscher, C. Virtual reality as an empirical research tool - Exploring user experience in a real building and a corresponding virtual model. Comput. Environ. Urban Syst. 54, 363–375 (2015).Yeom, D., Choi, J.-H. & Zhu, Y. Investigation of the Physiological Differences between Immersive Virtual Environment and Indoor Enviorment in a Building. Indoor adn Built Enviornment 0, Accept (2017).Combrisson, E. & Jerbi, K. Exceeding chance level by chance: The caveat of theoretical chance levels in brain signal classification and statistical assessment of decoding accuracy. J. Neurosci. Methods 250, 126–136 (2015).He, C., Yao, Y. & Ye, X. An Emotion Recognition System Based on Physiological Signals Obtained by Wearable Sensors. In Wearable Sensors and Robots: Proceedings of International Conference on Wearable Sensors and Robots 2015 (eds. Yang, C., Virk, G. S. & Yang, H.) 15–25, https://doi.org/10.1007/978-981-10-2404-7_2 (Springer Singapore, 2017)

Biomass burning aerosols in most climate models are too absorbing

Uncertainty in the representation of biomass burning (BB) aerosol composition and optical properties in climate models contributes to a range in modeled aerosol effects on incoming solar radiation. Depending on the model, the top-of-the-atmosphere BB aerosol effect can range from cooling to warming. By relating aerosol absorption relative to extinction and carbonaceous aerosol composition from observational datasets to nine state-of-the-art Earth System Models/Chemical Transport Models,we identify varying degrees of overestimation in BB aerosol absorptivity by these models. Modifications to BB aerosol refractive index, size, and mixing state improve the Community Atmosphere Model version 5 (CAM5) agreement with observations, leading to a global change in BB direct radiative effect of -0.07 W m-2,and regional changes of -2 W m-2(Africa) and -0.5 W m-2(South America/Temperate). Our findings suggest that current modeled BB contributes less to warming than previously thought, largely due to treatments of aerosol mixing state

Statistical and integrative system-level analysis of DNA methylation data

Epigenetics plays a key role in cellular development and function. Alterations to the epigenome are thought to capture and mediate the effects of genetic and environmental risk factors on complex disease. Currently, DNA methylation is the only epigenetic mark that can be measured reliably and genome-wide in large numbers of samples. This Review discusses some of the key statistical challenges and algorithms associated with drawing inferences from DNA methylation data, including cell-type heterogeneity, feature selection, reverse causation and system-level analyses that require integration with other data types such as gene expression, genotype, transcription factor binding and other epigenetic information