Podcasts about multiscale

Nachum Ulanovsky is a professor at the Weizman Institute. We talk about his research on spatial navigation in bats, how Nachum started working with bats, the importance of natural behaviour, how to build a 700m long tunnel for neuroscience, and much more.Support the show: https://geni.us/bjks-patreonTimestamps0:00:00: How Nachum started working with bats0:09:29: The technical difficulties of working with bats and in a new species0:16:03: The Egyptian Fruit Bat0:19:42: Wild bats vs lab-born bats / spatial navigation in very large spaces0:26:28: How to build a 700m long tunnel for neuroscience0:44:30: 2 random questions about bats0:53:48: The social lives of bats & social place cells1:05:09: Why are there so many types of cells for spatial navigation?1:13:01: Natural neuroscience1:17:33: A book or paper more people should read1:20:39: Advice for PhD students/postdocsPodcast linksWebsite: https://geni.us/bjks-podTwitter: https://geni.us/bjks-pod-twtNachum's linksWebsite: https://geni.us/ulanovsky-webBen's linksWebsite: https://geni.us/bjks-webGoogle Scholar: https://geni.us/bjks-scholarTwitter: https://geni.us/bjks-twtReferences & linksBracken Cave in Texas, with millions of bats: https://www.youtube.com/watch?v=PNPioS_roREThe Onion video on scientist who wasted life studying anteaters: https://www.youtube.com/watch?v=qXD9HnrNrvkEilam-Altstadter ... (2021). Stereotaxic brain atlas of the Egyptian fruit bat.Eliav ... (2021). Multiscale representation of very large environments in the hippocampus of flying bats. Science.Finkelstein ... (2015). Three-dimensional head-direction coding in the bat brain. Nature.Geva-Sagiv ... (2015). Spatial cognition in bats and rats: from sensory acquisition to multiscale maps and navigation. Nat Rev Neuro.Geva-Sagiv ... (2016). Hippocampal global remapping for different sensory modalities in flying bats. Nat Neuro.Hafting ... (2005). Microstructure of a spatial map in the entorhinal cortex. Nature.Hodgkin & Huxley (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. The J phys.Hubel & Wiesel (1962). Receptive fields, binocular interaction and functional architecture in the cat's visual cortex. The J phys.Lettvin... (1959). What the frog's eye tells the frog's brain. Proceedings of IRE.Miller (1956). The magical number seven, plus or minus two ... Psych Rev.O'Keefe & Dostrovsky (1971). The hippocampus as a spatial map ... Brain research.Omer ... (2018). Social place-cells in the bat hippocampus. Science.Sarel ... (2017). Vectorial representation of spatial goals in the hippocampus of bats. Science.Sarel ... (2022). Natural switches in behaviour rapidly modulate hippocampal coding. Nature.Tsoar ... (2011). Large-scale navigational map in a mammal. PNAS.Ulanovsky ... (2003). Processing of low-probability sounds by cortical neurons. Nature neuroscience.Ulanovsky & Moss (2007). Hippocampal cellular and network activity in freely moving echolocating bats. Nat Neuro.Yartsev & Ulanovsky (2013). Representation of three-dimensional space in the hippocampus of flying bats. Science.

Joshua Nash is a PhD candidate under Dr. Adam Shlien at The Hospital for Sick Children in Toronto, Canada. Joshua's research focuses on leveraging transcriptomics and machine learning to understand the overarching biology of sarcomas and mesenchymal tumours and to develop more molecularly informed and prognosticating diagnostic subtypes. -- What We Do at MIB Agents: PROGRAMS: End-of-Life MISSIONS Gamer Agents Agent Writers Prayer Agents Healing Hearts - Bereaved Parent and Sibling Support Ambassador Agents - Peer Support Warrior Mail Young Adult Survivorship Support Group EDUCATION for physicians, researchers and families: OsteoBites, weekly webinar & podcast with thought leaders and innovators in Osteosarcoma MIB Book: Osteosarcoma: From our Families to Yours RESEARCH: Annual MIB FACTOR Research Conference Funding multiple $100,000 and $50,000 grants annually for OS research MIB Testing & Research Directory The Osteosarcoma Project partner with Broad Institute of MIT and Harvard ... Kids are still dying with 40+ year old treatments. Help us MakeItBetter. https://www.mibagents.org​ Help support MIB Agents, Donate here https://give-usa.keela.co/embed/YAipuSaWxHPJP7RCJ SUBSCRIBE for all the Osteosarcoma Intel

We explore connections between FEP and enactivism, including tensions raised in a paper critiquing FEP from an enactivist perspective. Dr. Maxwell Ramstead provides background on enactivism emerging from autopoiesis, with a focus on embodied cognition and rejecting information processing/computational views of mind. Chris shares his journey from robotics into FEP, starting as a skeptic but becoming convinced it's the right framework. He notes there are both "high road" and "low road" versions, ranging from embodied to more radically anti-representational stances. He doesn't see a definitive fork between dynamical systems and information theory as the source of conflict. Rather, the notion of operational closure in enactivism seems to be the main sticking point. The group explores definitional issues around structure/organization, boundaries, and operational closure. Maxwell argues the generative model in FEP captures organizational dependencies akin to operational closure. The Markov blanket formalism models structural interfaces. We discuss the concept of goals in cognitive systems - Chris advocates an intentional stance perspective - using notions of goals/intentions if they help explain system dynamics. Goals emerge from beliefs about dynamical trajectories. Prof Friston provides an elegant explanation of how goal-directed behavior naturally falls out of the FEP mathematics in a particular "goldilocks" regime of system scale/dynamics. The conversation explores the idea that many systems simply act "as if" they have goals or models, without necessarily possessing explicit representations. This helps resolve tensions between enactivist and computational perspectives. Throughout the dialogue, Maxwell presses philosophical points about the FEP abolishing what he perceives as false dichotomies in cognitive science such as internalism/externalism. He is critical of enactivists' commitment to bright line divides between subject areas. Prof. Karl Friston - Inventor of the free energy principle https://scholar.google.com/citations?user=q_4u0aoAAAAJ Prof. Chris Buckley - Professor of Neural Computation at Sussex University https://scholar.google.co.uk/citations?user=nWuZ0XcAAAAJ&hl=en Dr. Maxwell Ramstead - Director of Research at VERSES https://scholar.google.ca/citations?user=ILpGOMkAAAAJ&hl=fr We address critique in this paper: Laying down a forking path: Tensions between enaction and the free energy principle (Ezequiel A. Di Paolo, Evan Thompson, Randall D. Beere) https://philosophymindscience.org/index.php/phimisci/article/download/9187/8975 Other refs: Multiscale integration: beyond internalism and externalism (Maxwell J D Ramstead) https://pubmed.ncbi.nlm.nih.gov/33627890/ MLST panel: Dr. Tim Scarfe and Dr. Keith Duggar TOC (auto generated): 0:00 - Introduction 0:41 - Defining enactivism and its variants 6:58 - The source of the conflict between dynamical systems and information theory 8:56 - Operational closure in enactivism 10:03 - Goals and intentions 12:35 - The link between dynamical systems and information theory 15:02 - Path integrals and non-equilibrium dynamics 18:38 - Operational closure defined 21:52 - Structure vs. organization in enactivism 24:24 - Markov blankets as interfaces 28:48 - Operational closure in FEP 30:28 - Structure and organization again 31:08 - Dynamics vs. information theory 33:55 - Goals and intentions emerge in the FEP mathematics 36:58 - The Good Regulator Theorem 49:30 - enactivism and its relation to ecological psychology 52:00 - Goals, intentions and beliefs 55:21 - Boundaries and meaning 58:55 - Enactivism's rejection of information theory 1:02:08 - Beliefs vs goals 1:05:06 - Ecological psychology and FEP 1:08:41 - The Good Regulator Theorem 1:18:38 - How goal-directed behavior emerges 1:23:13 - Ontological vs metaphysical boundaries 1:25:20 - Boundaries as maps 1:31:08 - Connections to the maximum entropy principle 1:33:45 - Relations to quantum and relational physics

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.12.548724v1?rss=1 Authors: Semeia, L., Nourhashemi, M., Mahmoudzadeh, M., Wallois, F., Sippel, K., Preissl, H. Abstract: In nature, biological systems such as the human brain are characterized by complex and non-linear dynamics. One way of quantifying signal complexity is Multiscale Entropy (MSE), which is suitable for structures with long-range correlation at different time scales. In developmental neuroscience, MSE can be taken as an index of brain maturation, and can differentiate between healthy and pathological development. In our current work, we explored the developmental trends of MSE on the basis of 30 simultaneous EEG-fNIRS recordings in premature infants between 27 and 34 weeks of gestational age (wGA). To explore potential factors impacting MSE, we determined the relation between MSE and the EEG Power Spectrum Density (PSD) and Spontaneous Activity Transients (SATs). As a result, via wGA, the MSE calculated on the EEG increases, thus reflecting the maturational processes in the brain networks, whereas in the fNIRS, MSE decreases, which might indicate a maturation of the brain blood supply. Moreover, we propose that the EEG power in the beta band (13-30 Hz) might be the main contributor to MSE in the EEG. Finally, we highlight the importance of SATs in determining MSE as calculated from the fNIRS recordings. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Humans get in the way of snakes finding love over long distances, and then we talk about a cool new gecko that glides, or does it paraglide? Become a Patreon: https://www.patreon.com/herphighlights Merch: https://www.redbubble.com/people/herphighlights/shop Full reference list available here: http://www.herphighlights.podbean.com Main Paper References: Bauder, J. M., Peterman, W. E., Spear, S. F., Jenkins, C. L., Whiteley, A. R., & McGarigal, K. (2021). Multiscale assessment of functional connectivity: Landscape genetics of eastern indigo snakes in an anthropogenically fragmented landscape in central Florida. Molecular Ecology, 30(14), 3422–3438. doi: 10.1111/mec.15979 Species of the Bi-Week: Lalremsanga, H. T., Muansanga, L., Vabeiryureilai, M., & Mirza, Z. A. (2023). A new species of Parachute Gecko of the subgenus Ptychozoon (Sauria: Gekkonidae: Gekko) from the Indo-Burma region. Salamandra, 59(2). Editing and Music: Podcast edited by Emmy – https://www.fiverr.com/emmyk10  Intro/outro – Treehouse by Ed Nelson Species Bi-week theme – Michael Timothy Other Music – The Passion HiFi, https://www.thepassionhifi.com

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.09.548296v1?rss=1 Authors: Karimi-Rouzbahani, H. Abstract: Distinct neural processes are often encoded across distinct time scales of neural activations. However, it has remained unclear if this multiscale coding strategy is also implemented for separate features of the same process. One difficulty is that the conventional methods of time scale analysis provide imperfect estimations of time scales when several components are active during a single process. Developing a novel decoding-based time scale estimation method, we detected distinct time scales for simultaneously present features of visual stimuli in electroencephalography. We observed that orientation and colour of grating stimuli were encoded in shorter whereas the spatial frequency and contrast of those stimuli were encoded in longer time scales. The conventional autocorrelation-based estimation of time scale was unable to detect these distinguishable time scales. These results provide new evidence for a multiscale multiplexed neural code in the human visual system and introduces a flexible method for estimating neural time scales. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.27.538651v1?rss=1 Authors: Xiao, C., Sun, Y., Huang, H., Song, Z., Yue, X., David, T., Xu, S. Abstract: Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.31.535073v1?rss=1 Authors: Wischnewski, M., Tran, H., Zhao, Z., Shirinpour, S., Haigh, Z. J., Rotteveel, J., Alekseichuk, I., Zimmermann, J., Opitz, A. Abstract: The gradual shifting of preferred neural spiking relative to local field potentials (LFPs), known as phase precession, plays a prominent role in neural coding. Correlations between the phase precession and behavior have been observed throughout various brain regions. As such, phase precession is suggested to be a global neural mechanism that promotes local neuroplasticity. However, causal evidence and neuroplastic mechanisms of phase precession are lacking so far. Here we show a causal link between LFP dynamics and phase precession. In three experiments, we modulated LFPs in humans, a non-human primate, and computational models using alternating current stimulation. We show that continuous stimulation of motor cortex oscillations in humans lead to a gradual phase shift of maximal corticospinal excitability by ~90 degrees. Further, exogenous alternating current stimulation induced phase precession in a subset of neurons (~17%) in the non-human primate. Multiscale modeling of realistic neural circuits suggests that alternating current stimulation-induced phase precession is driven by NMDA-mediated synaptic plasticity. Altogether, the three experiments provide mechanistic and causal evidence for phase precession as a global neocortical process. Alternating current-induced phase precession and consequently synaptic plasticity is crucial for the development of novel therapeutic neuromodulation methods. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.26.529328v1?rss=1 Authors: Cao, T., Pang, J. C., Segal, A., Chen, Y.-C., Aquino, K. M., Breakspear, M., Fornito, A. Abstract: Voxel-based morphometry (VBM) and surface-based morphometry (SBM) are two widely used neuroimaging techniques for investigating brain anatomy. These techniques rely on statistical inferences at individual points (voxels or vertices), clusters of points, or a priori regions-of-interest. They are powerful tools for describing brain anatomy, but offer little insights into the generative processes that shape a particular set of findings. Moreover, they are restricted to a single spatial resolution scale, precluding the opportunity to distinguish anatomical variations that are expressed across multiple scales. Drawing on concepts from classical physics, here we develop an approach, called mode-based morphometry (MBM), that can describe any empirical map of anatomical variations in terms of the fundamental, resonant modes--eigenmodes--of brain anatomy, each tied to a specific spatial scale. Hence, MBM naturally yields a multiscale characterization of the empirical map, affording new opportunities for investigating the spatial frequency content of neuroanatomical variability. Using simulated and empirical data, we show that the validity and reliability of MBM are either comparable or superior to classical vertex-based SBM for capturing differences in cortical thickness maps between two experimental groups. Our approach thus offers a robust, accurate, and informative method for characterizing empirical maps of neuroanatomical variability that can be directly linked to a generative physical process. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

In this episode, we sit down with Amber Case of the Plurigrid project. In the conversation, we talk about the intersection of open source software economic models, cybernetics, anthropology, and how combining the three can open up new possibilities in distributed energy resources management and distributed, resilient, microgrids. We hope you enjoy the episode.

While today's video recognition systems parse snapshots or short clips accurately, they cannot connect the dots and reason across a longer range of time yet. Most existing video architectures can only process 3,000% more compute to do the same. On a wide range of settings, the increased temporal support enabled by MeMViT brings large gains in recognition accuracy consistently. MeMViT obtains state-of-the-art results on the AVA, EPIC-Kitchens-100 action classification, and action anticipation datasets. 2022: Chao-Yuan Wu, Yanghao Li, Karttikeya Mangalam, Haoqi Fan, Bo Xiong, J. Malik, Christoph Feichtenhofer Ranked #2 on Action Anticipation on EPIC-KITCHENS-100 (using extra training data) https://arxiv.org/pdf/2201.08383v2.pdf

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.12.02.518906v1?rss=1 Authors: Hansen, J. Y., Shafiei, G., Voigt, K., Liang, E., Cox, S. M., Leyton, M., Jamadar, S. D., Misic, B. Abstract: The brain is composed of disparate neural populations that communicate and interact with one another. Although fiber bundles, similarities in molecular architecture, and synchronized neural activity all represent brain connectivity, a comprehensive study of how these connectivity modes jointly reflect brain structure and function remains missing. Here we systematically integrate seven multimodal, multiscale brain connectivity profiles derived from gene expression, neurotransmitter receptor density, cellular morphology, glucose metabolism, haemodynamic activity, and electrophysiology. We uncover a compact set of universal organizational principles through which brain geometry and neuroanatomy shape emergent connectivity modes. Connectivity modes also exhibit unique and diverse connection patterns, hub profiles, dominant gradients, and modular organization. Throughout, we observe a consistent primacy of molecular connectivity modes---namely correlated gene expression and receptor similarity---that map well onto multiple phenomena including the rich club and patterns of cortical abnormalities across 13 neurological, psychiatric, and neurodevelopmental disorders. Finally, we fuse all seven connectivity modes into a single multimodal network and show that it maps onto major organizational features of the brain including structural conenctivity, intrinsic functional networks, and cytoarchitectonic classes. Altogether, this work contributes to next-generation connectomics and the integrative study of inter-regional relationships. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.23.517696v1?rss=1 Authors: Pascoa dos Santos, F., Vohryzek, J., Verschure, P. Abstract: Stroke-related disruptions in functional connectivity (FC) often spread beyond lesioned areas and, given the localized nature of lesions, it is unclear how the recovery of FC is orchestrated on a global scale. Since recovery is accompanied by long-term changes in excitability, we propose excitatory-inhibitory (E-I) homeostasis as a driving mechanism. We present a large-scale model of the neocortex, with synaptic scaling of local inhibition, showing how E-I homeostasis can drive the post-lesion restoration of FC and linking it to changes in excitability. We show that functional networks could reorganize to recover disrupted modularity and small-worldness, but not network dynamics, suggesting the need to consider forms of plasticity beyond synaptic scaling of inhibition. On average, we observed widespread increases in excitability, with the emergence of complex lesion-dependent patterns related to biomarkers of relevant side effects of stroke, such as epilepsy, depression and chronic pain. In summary, our results show that the effects of E-I homeostasis extend beyond local E-I balance, driving the restoration of global properties of FC, and relating to post-stroke symptomatology. Therefore, we suggest the framework of E-I homeostasis as a relevant theoretical foundation for the study of stroke recovery and for understanding the emergence of meaningful features of FC from local dynamics. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

https://psychiatry.dev/wp-content/uploads/speaker/post-10878.mp3?cb=1669043940.mp3 Playback speed: 0.8x 1x 1.3x 1.6x 2x Download: Multiscale imaging informs translational mouse modeling of neurological disease – PubMed Review Yundi Wang et al. Neuron. 2022. Multiscale neurophysiology reveals thatFull EntryMultiscale imaging informs translational mouse modeling of neurological disease – PubMed

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.09.14.507986v1?rss=1 Authors: Makani, A., Akhavan, A., Shahbazi, F., Noruzi, M., Zare, M. Abstract: The effects of aging on the brain can be studied by examining the changes in complexity of brain signals and fluid cognitive abilities. This paper is a relatively large-scale study in which the complexity of the resting-state MEG (rsMEG) signal was investigated in 602 healthy participants (298 females and 304 males) aged 18 to 87. In order to quantify the brain signals' complexity, the multiscale entropy is applied. This study investigates the relationship between age and fluid intelligence with brain complexity and the variations of the complexity asymmetry between the left-right brain hemispheres across the life span. In the analysis of the brain signals, the gender difference was considered. The results showed that the complexity of rsMEG decreases across the lifespan. However, the complexity difference between the left-right brain hemispheres positively correlates with age. Furthermore, the results demonstrated that fluid intelligence and age have a positive correlation. Finally, the frequency analysis revealed a significant increase in the relative power of low and high gamma rhythms in females compared to males in all age groups. Copy rights belong to original authors. Visit the link for more info Podcast created by PaperPlayer

CLICK HERE to listen to episode audio (4:38).Sections below are the following: Transcript of Audio Audio Notes and Acknowledgments ImagesExtra Information Sources Related Water Radio Episodes For Virginia Teachers (Relevant SOLs, etc.). Unless otherwise noted, all Web addresses mentioned were functional as of 4-15-22. TRANSCRIPT OF AUDIO From the Cumberland Gap to the Atlantic Ocean, this is Virginia Water Radio for the week of April 18, 2022.  This update of an episode from July 2017 is part of a series this year of episodes related to trees and shrubs. MUSIC – ~14 sec That's part of “The Ash Grove,” a traditional Welsh tune performed by Madeline MacNeil, on her 2002 album, “Songs of Earth & Sea.”  Born in Norfolk and raised in Richmond, Ms. MacNeil was a well-known and highly regarded musician based in Virginia's Shenandoah Valley until her passing in 2020. The music opens an episode where we revisit the status of North American ash trees and explore the water impacts of pest damage to trees generally. As noted in the July 2017 episode on ashes, North America is home to 16 native ash species, with six of those occurring naturally in Virginia.  The two most common ash species in Virginia are White Ash, which tends toward upland habitats, and Green Ash, which is often found along streams and rivers.  In those areas, Green Ash can be a significant portion of the vegetation and help create habitats, improve water quality, and stabilize flows.  Both species provide food for a variety of animals and both have been widely planted in cities and towns. Since the early 2000s, ash tree populations have been devastated by the spread of the Emerald Ash Borer, a beetle native to Asia.  As of April 2022, the insect had been found in at least 35 states and the District of Columbia, and in nearly all of Virginia.  In an affected tree, the insect's larvae create a network of tunnels that impair the tree's transport of water and nutrients, eventually killing the tree.  Once an area's invaded, ashes are unlikely to survive for more than a few years without expensive chemical treatment of individual trees.  At the scale of whole forests, researchers and managers are exploring the use of parasitoid wasps as a biological control method. The Emerald Ash Borer is only one of many pest species threatening different trees in Virginia and elsewhere.  Several of these pests have been the subject of research on their water-related, or hydrologic, impacts.  Researchers are interested in how loss of tree leaves or death of trees can affect evaporation, soil moisture, water-table levels, streamflows, water chemistry, and snowpack.  Those water-cycle processes are in turn connected to ecosystem pathways of carbon, nutrients, and energy, all being affected by climate changes.  From all of these connections, little ash-boring beetles become part of a biosphere-sized story. Thanks to Janita Baker of Blue Lion Dulcimers and Guitars for permission to use Madeline MacNeil's music,” and we close with about 25 more seconds of “The Ash Grove.” MUSIC – ~24 sec – instrumental. SHIP'S BELL Virginia Water Radio is produced by the Virginia Water Resources Research Center, part of Virginia Tech's College of Natural Resources and Environment.  For more Virginia water sounds, music, or information, visit us online at virginiawaterradio.org, or call the Water Center at (540) 231-5624.  Thanks to Ben Cosgrove for his version of “Shenandoah” to open and close this episode.  In Blacksburg, I'm Alan Raflo, thanking you for listening, and wishing you health, wisdom, and good water. AUDIO NOTES AND ACKNOWLEDGEMENTS This Virginia Water Radio episode builds upon and updates information in Episode 376, 7-10-17. “The Ash Grove/O Spirit Sweet of Summertime” is from Madeline MacNeil's 2002 album “Songs of Earth & Sea”; copyright held by Janita Baker, used with permission.  More information about Madeline MacNeil is available from Ms. Baker's “Blue Lion Dulcimers & Guitars” Web site, online at https://www.bluelioninstruments.com/Maddie.html. Virginia Water Radio thanks Daniel McLaughlin, of the Virginia Tech Department of Forest Resources and Environmental Conservation and the Virginia Water Resources Research Center, for his help with this episode. Click here if you'd like to hear the full version (2 min./22 sec.) of the “Shenandoah” arrangement/performance by Ben Cosgrove that opens and closes this episode.  More information about Mr. Cosgrove is available online at http://www.bencosgrove.com. IMAGES Emerald Ash Borer-infected White Ash tree that cracked and fell in a Blacksburg, Va., neighborhood in 2021.  Photo taken April 19, 2022.Nationwide range maps for ash tree species and the Emerald Ash Borer, as of January 2021.  Map from the U.S. Department of Agriculture/Animal and Plant Health Inspection Service, “Emerald Ash Borer,” online at https://www.aphis.usda.gov/aphis/ourfocus/planthealth/plant-pest-and-disease-programs/pests-and-diseases/emerald-ash-borer/emerald-ash-borer.Adult Emerald Ash Borer.  Photo from the the U.S. Department of Agriculture/Animal and Plant Health Inspection Service, “Emerald Ash Borer,” online at https://www.aphis.usda.gov/aphis/ourfocus/planthealth/plant-pest-and-disease-programs/pests-and-diseases/emerald-ash-borer/emerald-ash-borer. EXTRA INFORMATION ABOUT THE EMERALD ASH BORER The following information is quoted from the Virginia Department of Forestry, “Emerald Ash Borer in Virginia—An Introduction,” online at https://vdof.maps.arcgis.com/apps/MapSeries/index.html?appid=e2660c30d9cd46cc988cc72415101590. From Background Tab: “After only 1-5 years of infestation, the larvae create extensive tunnels under the bark that disrupt the tree's ability to transport water and nutrients, which eventually girdles and kills the tree. The length of this process depends on tree age, health, and EAB density in the area but no ash tree is safe - 99% of infested ash will die.” From Distribution Tab: “In the U.S., EAB targets 16 species of native ash trees (Fraxinus spp.) and white fringetree (Chionanthus virginicus).  In Virginia, white ash (Fraxinus americana) and green ash (Fraxinus pennsylvanica) are the most commonly found, though there are four other species that have limited ranges (pumpkin, black, blue, and Carolina ash). In the wild, ash often prefers wetter environments and are dominant species along rivers and streambanks.  Ash decline and death may have a negative impact on streambank stabilization and waterways in these rural areas.  Though only a small percentage of Virginia's forests are composed of ash (2-3%), urban areas can have tree inventories tallying up to 13% ash.  This is where dead ash poses the most risk!” From Biological Control Tab: “Biological control (or “biocontrol”) is a management strategy that involves releasing natural enemies from the pest's native range to control the pest at a given location.  Researchers identified wasps in the early 2000s from Eastern Asia that had co-evolved with emerald ash borers as a parasite to control its populations.  They then conducted extensive research in quarantined U.S. labs to study their life cycle, environmental parameters, and host species.  After nearly a decade of trials, only four wasp species passed the strict requirements set by the USDA-APHIS (Animal and Plant Health Inspection Service) and were approved for release.  APHIS now rears these wasps in large quantities then collaborates with federal, state, and local governments, as well as land owners to release them at approved sites.  These tiny stingless wasps lay eggs in EAB eggs or larvae, effectively killing the EAB host, and are commonly called “parasitoids.” ...These wasps do not harm humans in any way, they only target emerald ash borer as a host. The use of these biocontrol agents in suppressing EAB has shown promising results, but it will take years of controlled releases and research before we see successful parasitism and a reduction of the EAB population.” SOURCES Used for Audio Samuel H. Austin, Riparian Forest Handbook 1: Appreciating and Evaluating Stream Side Forests, Virginia Department of Forestry, Charlottesville, 2000. J. A. Biederman et al., “Multiscale observations of snow accumulation and peak snowpack following widespread, insect-induced lodgepole pine mortality,” Ecohydrology, Vol. 7 (2014), pages 150-162. J. A. Biederman et al., Increased evaporation following widespread tree mortality limits streamflow response,” Water Resources Research, Vol. 50 (2014), pages 5295-5409. S. T. Brantley et al., “Changes to southern Appalachian water yield and stormflow after loss of a foundation species,” Ecohydrology, Vol. 8 (2015), pages 518-528. T. R. Cianciolo et al., “Hydrologic variability in black ash wetlands: Implications for vulnerability to emerald ash borer,” Hydrological Processes, Vol. 35 (2021), e14014. D. W. Clow et al., “Responses of soil and water chemistry to mountain pine beetle induced tree mortality in Grand County, Colorado, USA,” Applied Geochemistry, Vol. 26 (2011), pages 174-178. Anthony D'Amato et al., “Ecological and hydrological impacts of the emerald ash borer on black ash forests,” Northeast Climate Science Center, online at https://necsc.umass.edu/projects/ecological-and-hydrological-impacts-emerald-ash-borer-black-ash-forests. M. J. Daley et al., “Water use by eastern hemlock (Tsuga Canadensis) and black birch (Betula lenta): implications of effects of the hemlock wooly adelgid,” Canadian Journal of Forest Research, Vol. 37 (2007), pages 2031-2040. J. S. Diamond et al., “Forested versus herbaceous wetlands: Can management mitigate ecohydrologic regime shifts from invasive emerald ash borer?”  Journal of Environmental Management, Vol. 222 (2018), pages 436-446. Emerald Ash Borer Information Network, online at http://www.emeraldashborer.info/index.php.  Virginia information is online at http://www.emeraldashborer.info/state/virginia.php.  Information by county for each state is available in the table online at http://www.emeraldashborer.info/state-dectection-table.php. Gary M. Lovett et al., “Forest Ecosystem Responses to Exotic Pests and Pathogens in Eastern North America,” Bioscience Vol. 56, No. 5 (May 2006), pages 395-405. Steven G. Pallardy, Physiology of Woody Plants, Third Edition, Elsevier/Academic Press, Burlington, Mass., 2008. D. E. Reed et al., “Bark beetle-induced tree mortality alters stand energy budgets due to water budget changes,” “Theoretical and Applied Climatology, Vol., 131 (2018), pages 153-165. W. M. Robertson et al., “Soil moisture response to white ash mortality following emerald ash borer invasion,” Environmental Earth Sciences, Vol. 77 (2018). Anita K. Rose and James S. Meadows, “Status and Trends of Bottomland Hardwood Forests in the Mid‑Atlantic Region,” USDA/Forest Service Southern Research Station, Asheville, N.C., November 2016; available online at https://www.treesearch.fs.fed.us/pubs/53238. Scott Salom and Eric Day and Scott Salomn, “Hemlock Wooly Adelgid,” Virginia Cooperative Extension (Publication 3006-1451/ENTO-228NP), Blacksburg, Va., 2016, online at https://vtechworks.lib.vt.edu/handle/10919/75419. U.S. Department of Agriculture/Forest Service/Northern Research Station [Newtown Square, Penn.], “Forest Disturbance Processes/Invasive Species,” online at https://www.nrs.fs.fed.us/disturbance/invasive_species/.” U.S. Department of Agriculture/Natural Resources Conservation Service, “Plants Data Base,” online at https://plants.usda.gov/java/nameSearch. U.S. Department of Agriculture/Animal and Plant Health Inspection Service (APHIS):“Asian Longhorned Beetle,” online at https://www.aphis.usda.gov/aphis/resources/pests-diseases/asian-longhorned-beetle;“Emerald Ash Borer,” online at https://www.aphis.usda.gov/aphis/ourfocus/planthealth/plant-pest-and-disease-programs/pests-and-diseases/emerald-ash-borer;“Gypsy Moth,” online at https://www.aphis.usda.gov/aphis/ourfocus/planthealth/plant-pest-and-disease-programs/pests-and-diseases/gypsy-moth. Virginia Departme

You can read the original post with more links at https://botany.one/2022/04/integrative-and-multiscale-modelling-special-issue-call-for-papers/

Die Forschung braucht Tierversuche, wenn sie Medikamente entwickeln will. Dass die Zahl der Tierversuche reduziert wird, ist allerdings erklärtes politisches Ziel. Doch in der Praxis ist es meist gar nicht so einfach, über ethische Grenzen zu entscheiden, weil Grundlagenforschung sich oft erst Jahrzehnte später auszahlt. Nach welchen Kriterien wird also festgesetzt, dass Tierleid in Kauf genommen werden darf? Wie weit sind innovative Ersatzmethoden wie Organs-on-a-chip und 3D-Modelle des menschlichen Gewebes? Wissenschaftsjournalistin Nele Rößler hat in Plön und Göttingen Forscher*innen besucht, die Tierversuche durchführen und sie nach emotionalen Konflikten gefragt. Sie hat mit Ethikerinnen und Tierschützerinnen gesprochen und erzählt im Gespräch mit Host Maja Bahtijarević, wie sich das Thema historisch gewandelt hat, wie es in anderen Ländern gehandhabt wird - und was all das mit unserer Einstellung zur Massentierhaltung zu tun hat. Die Hintergrundinformationen • Nobelpreise und Tierversuche | Mai Thi Nguyen-Kim: Sind Tierversuche ethisch vertretbar? Die kleinste gemeinsame Wirklichkeit, S. 303, Droemer-Verlag, März 2021 • Rechtliche Grundlage zu Tierversuchen | BMJV: Das Deutsche Tierschutzgesetz, 1972, letzte Änderung des Gesetzes August, 2021 https://www.gesetze-im-internet.de/tierschg/BJNR012770972.html • Rahmenbedingungen für Tierversuche in Deutschland | BfR: Fragen und Antworten zu Tierversuchen und Alternativmethoden, September 2020 https://www.bfr.bund.de/de/fragen_und_antworten_zu_tierversuchen_und_alternativmethoden-196366.html • Einsatz von Tierversuchen bei der Entwicklung von Cochlea-Implantaten | Keppeler et al: Multiscale photonic imaging of the native and implanted cochlea in PNAS, Mai 2021 https://www.pnas.org/content/118/18/e2014472118 • Heimliche Filmaufnahmen von Affenversuchen am MPI in Tübingen | stern-TV : Tierversuche am Max Planck-Institut-Reportage 1-6, 2016 https://www.youtube.com/watch?v=MY03Tj3g6sw • Schließungen von Hamburger Tierversuchslabor | NDR: Keine Tierversuche mehr: LPT zieht Klage zurück, November 2020 https://www.ndr.de/aktuelllueneburg4702.html • Verwendete Tierarten, Schweregrad der Versuche, Versuchsschwerpunkt | BMEL: Verwendung von Versuchstieren im Jahr 2019, August 2021 https://www.bmel.de/DE/themen/tiere/tierschutz/versuchstierzahlen2019.html • Geschichte der Tierexperimente | RP-Online: Erste Experimente bereits in der Antike, Januar 2017 https://rp-online.de/nrw/staedte/duesseldorf/erste-experimente-bereits-in-der-antike_aid-17054905 • TGN1412: Gefährliches Medikament trotz Tierversuchen | H.Attarwala: TGN1412: From Discovery to Disaster, Journal of Young Pharmacists Volume 2, Issue 3, Sommer 2010 https://www.sciencedirect.com/science/article/abs/pii/S0975148310230248?via%3Dihub • Übertragbarkeit von Tierversuchen auf den Menschen | Tierversuche verstehen (Initiative von Forschungseinrichtungen in Deutschland), November 2018 https://www.tierversuche-verstehen.de/faktencheck-92-prozent-der-tierversuche-sind-nicht-uebertragbar/ • Meta-Analyse zur Aussagekraft von Tierversuchen | Matthew Clark und Thomas Steger-Hartmann: A big data approach to the concordance of the toxicity of pharmaceuticals in animals and humans. Regulatory Toxicology and Pharmacology, Juli 2018 https://reader.elsevier.com/reader/sd/pii/S0273230018301272?token=5918D7FBE359782FBA0C6693B42D60B29A0308056DC5CE5FE4AACD0B4F0B2A4EC9519A59993E72CBE493FA4E6D7537C6&originRegion=eu-west-1&originCreation=20210922213953 • Organ-on-a-Chip als Alternative zu Tierversuchen | Fraunhofer Gesellschaft: Medikamente schneller entwickeln und Tierversuche vermeiden: Ermöglichen soll es die Organ-on-a-Chip-Technologie. https://www.fraunhofer.de/de/forschung/aktuelles-aus-derforschung/biooekonomie/gesundheit/organs-on-a-chip.html • Niederlande im Umgang mit Tierversuchen | Julia Merlot: Alternativmethoden werden Tierversuche nie ganz ersetzen. Spiegel, August 2020 https://www.spiegel.de/wissenschaft/medizin/tierversuche-darum-kann-es-keinen-schnellen-ausstieg-geben-a-fe2714bc-7daa-4e5d-a3db-674ec6e6a485 • Verhältnis Tiernutzung in Deutschland | BMEL: Tierverbrauch und zu wissenschaftlichen Zwecken verwendete Tierarten. 2014 https://www.dfg.de/download/pdf/dfg_im_profil/geschaeftsstelle/publikationen/tierversuche_forschung.pdf • Ernährungsgewohnheiten der Deutschen | BMEL-Ernährungsreport: Deutschland, wie es isst. 2021 https://www.bmel.de/SharedDocs/Downloads/DE/Broschueren/ernaehrungsreport-2021.pdf?__blob=publicationFile&v=5

Die Forschung braucht Tierversuche, wenn sie Medikamente entwickeln will. Dass die Zahl der Tierversuche reduziert wird, ist allerdings erklärtes politisches Ziel. Doch in der Praxis ist es meist gar nicht so einfach, über ethische Grenzen zu entscheiden, weil Grundlagenforschung sich oft erst Jahrzehnte später auszahlt. Nach welchen Kriterien wird also festgesetzt, dass Tierleid in Kauf genommen werden darf? Wie weit sind innovative Ersatzmethoden wie Organs-on-a-chip und 3D-Modelle des menschlichen Gewebes? Wissenschaftsjournalistin Nele Rößler hat in Plön und Göttingen Forscher*innen besucht, die Tierversuche durchführen und sie nach emotionalen Konflikten gefragt. Sie hat mit Ethikerinnen und Tierschützerinnen gesprochen und erzählt im Gespräch mit Host Maja Bahtijarević, wie sich das Thema historisch gewandelt hat, wie es in anderen Ländern gehandhabt wird - und was all das mit unserer Einstellung zur Massentierhaltung zu tun hat. Die Hintergrundinformationen • Nobelpreise und Tierversuche | Mai Thi Nguyen-Kim: Sind Tierversuche ethisch vertretbar? Die kleinste gemeinsame Wirklichkeit, S. 303, Droemer-Verlag, März 2021 • Rechtliche Grundlage zu Tierversuchen | BMJV: Das Deutsche Tierschutzgesetz, 1972, letzte Änderung des Gesetzes August, 2021 https://www.gesetze-im-internet.de/tierschg/BJNR012770972.html • Rahmenbedingungen für Tierversuche in Deutschland | BfR: Fragen und Antworten zu Tierversuchen und Alternativmethoden, September 2020 https://www.bfr.bund.de/de/fragen_und_antworten_zu_tierversuchen_und_alternativmethoden-196366.html • Einsatz von Tierversuchen bei der Entwicklung von Cochlea-Implantaten | Keppeler et al: Multiscale photonic imaging of the native and implanted cochlea in PNAS, Mai 2021 https://www.pnas.org/content/118/18/e2014472118 • Heimliche Filmaufnahmen von Affenversuchen am MPI in Tübingen | stern-TV : Tierversuche am Max Planck-Institut-Reportage 1-6, 2016 https://www.youtube.com/watch?v=MY03Tj3g6sw • Schließungen von Hamburger Tierversuchslabor | NDR: Keine Tierversuche mehr: LPT zieht Klage zurück, November 2020 https://www.ndr.de/aktuelllueneburg4702.html • Verwendete Tierarten, Schweregrad der Versuche, Versuchsschwerpunkt | BMEL: Verwendung von Versuchstieren im Jahr 2019, August 2021 https://www.bmel.de/DE/themen/tiere/tierschutz/versuchstierzahlen2019.html • Geschichte der Tierexperimente | RP-Online: Erste Experimente bereits in der Antike, Januar 2017 https://rp-online.de/nrw/staedte/duesseldorf/erste-experimente-bereits-in-der-antike_aid-17054905 • TGN1412: Gefährliches Medikament trotz Tierversuchen | H.Attarwala: TGN1412: From Discovery to Disaster, Journal of Young Pharmacists Volume 2, Issue 3, Sommer 2010 https://www.sciencedirect.com/science/article/abs/pii/S0975148310230248?via%3Dihub • Übertragbarkeit von Tierversuchen auf den Menschen | Tierversuche verstehen (Initiative von Forschungseinrichtungen in Deutschland), November 2018 https://www.tierversuche-verstehen.de/faktencheck-92-prozent-der-tierversuche-sind-nicht-uebertragbar/ • Meta-Analyse zur Aussagekraft von Tierversuchen | Matthew Clark und Thomas Steger-Hartmann: A big data approach to the concordance of the toxicity of pharmaceuticals in animals and humans. Regulatory Toxicology and Pharmacology, Juli 2018 https://reader.elsevier.com/reader/sd/pii/S0273230018301272?token=5918D7FBE359782FBA0C6693B42D60B29A0308056DC5CE5FE4AACD0B4F0B2A4EC9519A59993E72CBE493FA4E6D7537C6&originRegion=eu-west-1&originCreation=20210922213953 • Organ-on-a-Chip als Alternative zu Tierversuchen | Fraunhofer Gesellschaft: Medikamente schneller entwickeln und Tierversuche vermeiden: Ermöglichen soll es die Organ-on-a-Chip-Technologie. https://www.fraunhofer.de/de/forschung/aktuelles-aus-derforschung/biooekonomie/gesundheit/organs-on-a-chip.html • Niederlande im Umgang mit Tierversuchen | Julia Merlot: Alternativmethoden werden Tierversuche nie ganz ersetzen. Spiegel, August 2020 https://www.spiegel.de/wissenschaft/medizin/tierversuche-darum-kann-es-keinen-schnellen-ausstieg-geben-a-fe2714bc-7daa-4e5d-a3db-674ec6e6a485 • Verhältnis Tiernutzung in Deutschland | BMEL: Tierverbrauch und zu wissenschaftlichen Zwecken verwendete Tierarten. 2014 https://www.dfg.de/download/pdf/dfg_im_profil/geschaeftsstelle/publikationen/tierversuche_forschung.pdf • Ernährungsgewohnheiten der Deutschen | BMEL-Ernährungsreport: Deutschland, wie es isst. 2021 https://www.bmel.de/SharedDocs/Downloads/DE/Broschueren/ernaehrungsreport-2021.pdf?__blob=publicationFile&v=5

En el último programa de este 2020 hemos cambiado un poco el formato. Te traemos una tertulia con tres invitados hablando de ordenación del territorio e infraestructura verde. Hemos tenido a Luis Quesada, Jose Vicente Sánchez Cabrera y Manuel Borobio.*** Patrocinado por Geoinnnova, la Asociación de profesional del Territorio y del Medio Ambiente https://www.geoinnova.org***Manuel Borobio, Jose Vicente Sánchez Cabrera y Luis QuesadaManuel Borobio: Arquitecto experto en ordenación del territorio y gestión de datos. Ha trabajado en la administración pública a nivel local y autonómico.* https://www.abtemas.es/* @manuelborobioLuis Quesada Muelas: Director de Geoinnova, Geógrafo. Experto en Ordenación del Territorio, Medio Ambiente y Sistemas de Información Geográfica.* @luquemuJose Vicente Sánchez Cabrera: Licenciado en Geografía y experto en Desarrollo Local, profesor asociado de la Universidad de Valencia y ha sido Presidente del Colegio de Geógrafos de la Comunidad Valenciana.Consejo de empleo: Este programa también te llega gracias a www.TrabajaenMedioAmbiente.com donde pueden encontrar una bolsa de empleo para buscar o subir tus ofertas de empleo y además ofrecemos consultorías individuales para encontrar trabajo en medio ambiente.Nuestro consejo esta semana es que cuando redactes tu CV, presentación, etc se la des a leer a alguien externo para que te dé su opinión sin tus sesgos.Temas tratados: * Pasado y prehistoria de la Infraestructura verde y la ordenación del territorio* La Infraestructura verde aplicada a la gestión territorial:  * municipal * Ejemplo de Vitoria * supramunicipal * Ejemplo: Valencia, Cantabria, Galicia* ¿Existe normativa aplicable? ¿Está toda junta o desperdigada? * Fallos detectados* Problemas * De concepto * De aterrizaje sobre el terreno * De técnicos* Planes a futuroEnlaces comentados durante el programa* https://geoinnova.org/blog-territorio/* https://www.podcastidae.com/programa/estrategias-de-biodiversidad-e-infraestructura-verde-con-jordi-cortina-actualidad-y-empleo-ambiental-79/* Estrategia Nacional de Infraestructura Verde y de la Conectividad y Restauración Ecológicas. https://www.miteco.gob.es/es/biodiversidad/temas/ecosistemas-y-conectividad/conectividad-fragmentacion-de-habitats-y-restauracion/Infr_verde.aspx Sección de herramientas - Por GeoinnovaLas recomendaciones de herramientas hoy nos las trae Roberto Matellanes, ambientólogo, del blog “Gis and Beers” @GIS_and_Beers, y profesor de Sistemas de Información Geográfica en Geoinnova.* MULTISCALE https://www.arcgis.com/home/item.html?id=e406a43e6ba84512aaeaff3fb7c59ef2Esta sección te llega gracias a nuestro patrocinador, Geoinnova, la Asociación de Profesionales del Territorio y del Medio Ambiente y que puedes encontrar en www.Geoinnova.orgPodcast Recomendados* Podcast SEO desde cero* Podcast “Encierrate con la Ciencia” vuelve"Actualidad y Empleo Ambiental" #ActualidadyEmpleoAmbiental https://www.podcastidae.com/podcast/actualidad-y-empleo-ambiental/ es un podcast de la Red Podcastidae https://www.podcastidae.com . Dirigido y presentado por:* Juan María Arenas. Doctor en Ecología y Restauración de ecosistemas. CEO de Oikos MSP https://www.oikosmsp.com.* Enoch Martinez. Ambientólogo y profesional del Medio Ambiente. Director de https://www.trabajaenmedioambiente.com y https://www.podcastidae.com

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.19.390187v1?rss=1 Authors: Casalino, L., Dommer, A. C., Gaieb, Z., Barros, E. P., Sztain, T., Ahn, S.-H., Trifan, A., Brace, A., Ma, H., Lee, H., Turilli, M., Bogetti, A., Khalid, S., Chong, L., Simmerling, C., Hardy, D., Maia, J., Phillips, J., Kurth, T., Stern, A., Huang, L., McCalpain, J., Tatineni, M., Gibbs, T., Stone, J. E., Jha, S., Ramanathan, A., Amaro, R. E. Abstract: We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.386524v1?rss=1 Authors: Hanson, B. S., Read, D. J. Abstract: Many biophysical systems and proteins undergo mesoscopic conformational changes in order to perform their biological function. However, these conformational changes often result from a cascade of atomistic interactions within a much larger overall object. For simulations of such systems, the computational cost of retaining high-resolution structural and dynamical information whilst at the same time observing large scale motions over long times is high. Furthermore, this cost is only going to increase as ever larger biological objects are observed experimentally at high resolution. With insight from the theory of Markov state models and transition state theory, we derive a generalised mechano-kinetic simulation framework which aims to compensate for these disparate time scales. The framework models continuous dynamical motion at coarse-grained length scales whilst simultaneously including fine-detail, chemical reactions or conformational changes implicitly using a kinetic model. The kinetic model is coupled to the dynamic model in a highly generalised manner, such that it can be applied to any defined continuous energy landscape, and indeed, any existing dynamic simulation framework. We present a series of analytical examples to validate the framework, and showcase its capabilities for studying more complex systems by designing a simulation of minimalist molecular motor. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.15.383661v1?rss=1 Authors: Kuchroo, M., Huang, J., Wong, P., Grenier, J.-C., Shung, D., Tong, A., Lucas, C., Klein, J., Burkhardt, D., Gigante, S., Godavarthi, A., Israelow, B., Mao, T., Oh, J. E., Silva, J., Takahashi, T., Odio, C. D., Casanovas-Massana, A., Fournier, J., IMPACT Team, Y., Farhadian, S., Dela Cruz, C. S., Ko, A. I., Wilson, F. P., Hussin, J., Wolf, G., Iwasaki, A., Krishnaswamy, S. Abstract: The biomedical community is producing increasingly high dimensional datasets, integrated from hundreds of patient samples, which current computational techniques struggle to explore. To uncover biological meaning from these complex datasets, we present an approach called Multiscale PHATE, which learns abstracted biological features from data that can be directly predictive of disease. Built on a continuous coarse graining process called diffusion condensation, Multiscale PHATE creates a tree of data granularities that can be cut at coarse levels for high level summarizations of data, as well as at fine levels for detailed representations on subsets. We apply Multiscale PHATE to study the immune response to COVID-19 in 54 million cells from 168 hospitalized patients. Through our analysis of patient samples, we identify CD16hiCD66lo neutrophil and IFN{gamma}+GranzymeB+ Th17 cell responses enriched in patients who die. Further, we show that population groupings Multiscale PHATE discovers can be directly fed into a classifier to predict disease outcome. We also use Multiscale PHATE-derived features to construct two different manifolds of patients, one from abstracted flow cytometry features and another directly on patient clinical features, both associating immune subsets and clinical markers with outcome. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.10.375493v1?rss=1 Authors: Vander Roest, A. S., Liu, C., Morck, M. M., Kooiker, K. B., Jung, G., Song, D., Dawood, A., Jhingran, A., Pardon, G., Ranjbarvaziri, S., Fajardo, G., Zhao, M., Campbell, K. S., Pruitt, B., Spudich, J. A., Ruppel, K. M., Bernstein, D. Abstract: Hypertrophic cardiomyopathy (HCM) is the most common inherited form of heart disease, associated with over 1000 mutations, many in {beta}-cardiac myosin (MYH7). Molecular studies of myosin with different HCM mutations have revealed a diversity of effects on ATPase and load-sensitive rate of detachment from actin. It has been difficult to predict how such diverse molecular effects combine to influence forces at the cellular level and further influence cellular phenotypes. This study focused on the P710R mutation that dramatically decreases in vitro motility and actin-activated ATPase, in contrast to other MYH7 mutations. Optical trap measurements of single myosin molecules revealed that this mutation reduced the step size of the myosin motor and the load-sensitivity of the actin detachment rate. Conversely, this mutation destabilized the super-relaxed state in larger, two-headed myosin constructs, freeing more heads to generate force. Micropatterned hiPSC-cardiomyocytes CRISPR-edited with the P710R mutation produced significantly increased force (measured by traction force microscopy) compared with isogenic control cells. The P710R mutation also caused cardiomyocyte hypertrophy and cytoskeletal remodeling, as measured by immunostaining and electron microscopy. Cellular hypertrophy was prevented in the P710R cells by inhibition of ERK or Akt. Finally, we used a computational model that integrates measured molecular changes to demonstrate that predicted force traces match the forces measured in cells. These results confirm a key role for regulation of the super-relaxed state in driving hypercontractility in HCM and demonstrate the value of a multiscale approach in revealing key mechanisms of disease. Copy rights belong to original authors. Visit the link for more info

Following on from our episode on ergonomic designs, this one takes a closer look at the more prevalent reasons players are choosing fanned fret, multiscale guitars. What are the benefits of a fanned fret guitar? Is a multiscale guitar better for certain styles of playing?

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.21.349589v1?rss=1 Authors: Kelty-Stephen, D., Furmanek, M. P., Mangalam, M. Abstract: Intermittency is a flexible control process entailing context-sensitive engagement with task constraints. The present work aims to situate the intermittency of dexterous behavior explicitly in multifractal modeling for non-Gaussian cascade processes. Multiscale probability density function (PDF) analysis of the center of pressure (CoP) fluctuations during quiet upright standing yields non-Gaussianity parameters lambda exhibiting task-sensitive curvilinear relationships with timescale. The present reanalysis aims for a finer-grained accounting of how non-Gaussian cascade processes might align with known, separable postural processes. It uses parallel decomposition of non-Gaussianity lambda-vs.-timescale and CoP. Orthogonal polynomials decompose lambda curvilinearity, and rambling-trembling analysis decomposes CoP into relatively more intentional rambling (displacement to new equilibrium points) and less intentional trembling sway (deviations around new equilibrium points). Modeling orthogonal polynomials of non-Gaussianity's lambda-vs.-timescale allows us to differentiate linear from quadratic decay, each of which indicates scale-invariant and scale-dependent cascades, respectively. We tested whether scale-dependent and scale-invariant cascades serve different roles, that is, responding to destabilizing task demands and supporting the proactive movement to a new equilibrium point, respectively. We also tested whether these cascades appear more clearly in rambling rather than trembling sway. More generally, we test whether multifractal nonlinear correlations supports this capacity of postural control to this two-step differentiation: both into rambling vs. trembling, then into scale-dependent vs. scale-invariant cascades within rambling sway. The results supported these hypotheses. Thus, the present work aligns specific aspects of task setting with aspects of cascade dynamics and confirms multifractal foundations of the organism-task relationship. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.14.338681v1?rss=1 Authors: Turner, N. L., Macrina, T., Bae, J. A., Yang, R., Wilson, A. M., Schneider-Mizell, C., Lee, K., Lu, R., Wu, J., Bodor, A. L., Bleckert, A. A., Brittain, D., Froudarakis, E., Dorkenwald, S., Collman, F., Kemnitz, N., Ih, D., Silversmith, W. M., Zung, J., Zlateski, A., Tartavull, I., Yu, S.-c., Popovych, S., Mu, S., Wong, W., Jordan, C. S., Castro, M., Buchanan, J., Bumbarger, D. J., Takeno, M., Torres, R., Mahalingam, G., Elabbady, L., Li, Y., Cobos, E., Zhou, P., Suckow, S., Becker, L., Paninski, L., Polleux, F., Reimer, J., Tolias, A. S., Reid, R. C., Macarico da Costa, N., Seung, H. S. Abstract: We present a semi-automated reconstruction of L2/3 mouse primary visual cortex from 3 million cubic microns of electron microscopic images, including pyramidal and inhibitory neurons, astrocytes, microglia, oligodendrocytes and precursors, pericytes, vasculature, mitochondria, and synapses. Visual responses of a subset of pyramidal cells are included. The data are being made publicly available, along with tools for programmatic and 3D interactive access. The density of synaptic inputs onto inhibitory neurons varies across cell classes and compartments. We uncover a compartment-specific correlation between mitochondrial coverage and synapse density. Frequencies of connectivity motifs in the graph of pyramidal cells are predicted quite accurately from node degrees using the configuration model of random graphs. Cells receiving more connections from nearby cells exhibit stronger and more reliable visual responses. These example findings illustrate the resource's utility for relating structure and function of cortical circuits as well as for neuronal cell biology. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.02.323915v1?rss=1 Authors: Yu, A., Pak, A. J., He, P., Monje-Galvan, V., Casalino, L., Gaieb, Z., Dommer, A. C., Amaro, R. E., Voth, G. A. Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely bottom-up coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.02.323030v1?rss=1 Authors: Bazinet, V., Vos de Wael, R., Hagmann, P., Bernhardt, B. C., Misic, B. Abstract: Signaling events in brain networks unfold over multiple topological scales. Areas may exchange information over local circuits, primarily encompassing direct neighbours and areas with similar functions. Alternatively, areas may exchange information over global circuits, encompassing more distant neighbours with increasingly dissimilar functions. In the present report, we study communication in cortico-cortical networks by characterizing a region's structural embedding over a continuous range of topological scales. We find that the centrality of a brain region varies across scales and that connection diversity determines scale preference, with less diverse unimodal regions showing preference for local communication and more diverse multimodal regions showing preferences for global communication. These preferences manifest as scale-specific structure-function relationships, with unimodal areas showing optimal coupling at local scales and multimodal regions showing optimal coupling at global scales. Altogether, the present findings reveal how functional hierarchies emerge from hidden but highly structured multiscale connection patterns. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.22.307959v1?rss=1 Authors: Svedruzic, Z. M., Vrbnjak, K., Martinovic, M., Miletic, V. Abstract: Significance: The majority of drugs that target membrane-embedded protease gamma-secretase show unusual biphasic activation-inhibition dose-response in cells, model animals, and humans. Semagacestat and avagacestat are two biphasic-drugs that can facilitate cognitive decline in patients with Alzheimers disease. Initial mechanistic studies showed that the biphasic-drugs, and pathogenic mutations, can produce the same type of changes in {gamma}-secretase activity. Results: DAPT, semagacestat LY-411,575, and avagacestat are four drugs that show different binding constants, and biphasic activation-inhibition dose-response curves, for amyloid-beta-40 products in SHSY-5 cells. Multiscale molecular dynamics studies showed that all four drugs bind to the most mobile parts in presenilin structure, at different ends of the 29 A long active site tunnel. Combined results from structure-activity studies, showed that the biphasic dose-response curves are a result of modulation of gamma-secretase activity by concurrent binding of multiple drug molecules at each end of the active site tunnel. The drugs activate gamma-secretase by forcing the active site tunnel to open, when the rate-limiting step is the tunnel opening, and formation of the enzyme-substrate complex. The drugs inhibit gamma-secretase as uncompetitive inhibitors, by binding next to the substrate to dynamic enzyme structures that regulate processive catalysis. The drugs can modulate the production of different amyloid-beta catalytic intermediates, by penetrating into the active site tunnel to different depth with different binding affinity. The drugs and pathogenic mutations affect the same dynamic processes in gamma-secretase structure. Conclusions: Biphasic-drugs like disease-causing mutations can reduce the catalytic capacity of gamma-secretase and facilitate pathogenic changes in amyloid metabolism. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.24.265488v1?rss=1 Authors: Hudson, M. L., Samudrala, R. Abstract: Drug repurposing, the practice of utilizing existing drugs for novel clinical indications, has tremendous potential for improving human health outcomes and increasing therapeutic development efficiency. The goal of multidisease multitarget drug repurposing, also known as shotgun drug repurposing, is to develop platforms that assess the therapeutic potential of each existing drug for every clinical indication. Our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget repurposing implements several pipelines via large scale modelling and simulation of interactions between comprehensive libraries of drugs/compounds and protein structures. In these pipelines, each drug is described by an interaction signature that is then compared to all other signatures that are then sorted and ranked based on similarity. Pipelines within the platform are benchmarked based on their ability to recover known drugs for all indications in our library, and predictions are generated based on the hypothesis that (novel) drugs with similar signatures may be repurposed for the same indication(s). The drug-protein interactions in the platform used to create the drug-proteome signatures may be determined by any screening or docking method but the primary approach used thus far has been an in house similarity docking protocol. In this study, we calculated drug-proteome interaction signatures using the publicly available molecular docking method Autodock Vina and created hybrid decision tree pipelines that combined our original bio- and cheminformatic approach with the goal of assessing and benchmarking their drug repurposing capabilities and performance. The hybrid decision tree pipeline outperformed the corresponding two docking-based pipelines it was synthesized from, yielding an average indication accuracy of 13.3% at the top10 cutoff (the most stringent), relative to 10.9% and 7.1% for its constituent pipelines, and a random control accuracy of 2.2%. We demonstrate that docking based virtual screening pipelines have unique performance characteristics and that the CANDO shotgun repurposing paradigm is not dependent on a specific docking method. Our results also provide further evidence that multiple CANDO pipelines can be synthesized to enhance drug repurposing predictive capability relative to their constituent pipelines. Overall, this study indicates that pipelines consisting of varied docking based signature generation methods can capture unique and useful signal for accurate comparison of drug-proteome interaction signatures, leading to improvements in the benchmarking and predictive performance of the CANDO shotgun drug repurposing platform. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.248690v1?rss=1 Authors: Seitz, C., Casalino, L., Konecny, R., Huber, G., Amaro, R. E., McCammon, J. A. Abstract: Influenza neuraminidase is an important drug target. Glycans are present on neuraminidase, and are generally considered to inhibit antibody binding via their glycan shield. In this work we studied the effect of glycans on the binding kinetics of antiviral drugs to the influenza neuraminidase. We created all-atom in silico systems of influenza neuraminidase with experimentally-derived glycoprofiles consisting of four systems with different glycan conformations and one system without glycans. Using Brownian dynamics simulations, we observe a two- to eight-fold decrease in the rate of ligand binding to the primary binding site of neuraminidase due to the presence of glycans. These glycans are capable of covering much of the surface area of neuraminidase, and the ligand binding inhibition is derived from glycans sterically occluding the primary binding site on a neighboring monomer. Our work also indicates that drugs preferentially bind to the primary binding site (i.e. the active site) over the secondary binding site, and we propose a binding mechanism illustrating this. These results help illuminate the complex interplay between glycans and ligand binding on the influenza membrane protein neuraminidase. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.06.05.136895v1?rss=1 Authors: Furmanek, M. P., Mangalam, M., Kelty-Stephen, D. G., Juras, G. Abstract: Healthy human postural sway exhibits strong intermittency, reflecting a richly interactive foundation of postural control. From a linear perspective, intermittent fluctuations might be interpreted as engagement and disengagement of complementary control processes at distinct timescales or from a nonlinear perspective, as cascade-like interactions across many timescales at once. The diverse control processes entailed by cascade-like multiplicative dynamics suggest specific non-Gaussian distributional properties at different timescales. Multiscale probability density function (PDF) analysis showed that when standing quietly, stable sand-filled loading of the upper extremities would elicit non-Gaussianity profiles showing a negative-quadratic crossover between short and long timescales. Unstable water-filled loading of the upper extremities would elicit simpler monotonic decreases in non-Gaussianity, that is, a positive-quadratic cancellation of the negative-quadratic crossover. Multiple known indices of postural sway governed the appearance or disappearance of the crossover. Finally, both loading conditions elicited Levy-like distributions over progressively larger timescales. These results provide evidence that postural instability recruits shorter-timescale processes into the non-Gaussian cascade processes, that indices of postural sway moderate this recruitment, and that postural control under unstable loading shows stronger statistical hallmarks of cascade structure. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.05.19.104760v1?rss=1 Authors: Mangalam, M., Kelty-Stephen, D. G. Abstract: Quiet standing exhibits strongly intermittent variability reflecting a richly interactive foundation. This intermittency can be understood in various ways. First, variability can be intermittent through the engagement and disengagement of complementary control processes at distinct scales. A second and perhaps a deeper way to understand this intermittency is through the possibility that closed-loop control depends on the cascade-like interactions across many timescales at once. These diverse control processes suggest specific non-Gaussian distributional properties at different timescales. Multiscale probability density (PDF) analysis shows that quiet standing on a stable surface exhibits a crossover between low non-Gaussianity (consistent with exponential distributions) at shorter timescales reflecting open-loop control, increasing towards higher non-Gaussianity and subsequently decreasing (consistent with cascade-driven Levy-like distributions) at longer scales. Destabilizing quiet standing elicits non-Gaussianity that begins high and decreases across timescales (consistent with cascade-driven Levy-like distribution), reflecting closed-loop postural corrections at more of the shorter timescales. Finally, indices of postural sway govern the appearance or disappearance of crossovers, suggesting that tempering of non-Gaussianity across log-timescale in stable-surface condition is mostly a function of endogenous postural control. These results provide new evidence that cascading interactions across longer-timescales supporting postural corrections can even recruit shorter-timescale processes with novel task constraints. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.05.14.097196v1?rss=1 Authors: Zhang, M., Saggar, M. Abstract: The brain is a complex, nonlinear system, exhibiting ever-evolving patterns of activities even without external inputs or tasks. Such intrinsic or resting neural dynamics has been found to play critical roles in the normal functioning of the brain and psychiatric disorders. It remains a challenge, however, to link the intrinsic dynamics to the underlying structure, in part, due to the nonlinearity. Here we use a nonlinear-dynamical model to examine how the complexity of intrinsic neural dynamics, in terms of multistability and temporal diversity, is sculpted by structural properties across scales. Our model combines a population-level model (Wilson-Cowan) with additional biophysical constraints (from the Wong-Wang-Deco model). We show that multistability can emerge at the whole-brain level even when individual brain regions are by themselves monostable. The multi-functionality and memory capacity associated with multistability are thus synergistic properties of the whole-brain, irreducible to properties of its parts. The exact size of the functional repertoire and memory capacity is a joint product of the nonlinearity in the local dynamics and the topology of the large-scale network. Similarly, temporal diversity of the brain is determined by both local structural differences and the topology of the global network. Together, this work unravels an intertwined and circular relationship between local and global properties in defining the intrinsic dynamic organization of the brain. Looking forward, the model can be used to probe the multiscale mechanisms underlying psychiatric disorders and the effective scales for treatment. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.05.08.084947v1?rss=1 Authors: Dai, K., Gratiy, S., Billeh, Y. N., Xu, R., Cai, B., Cain, N., Rimehaug, A. E., Stasik, A. J., Einevoll, G. T., Mihalas, S., Koch, C., Arkhipov, A. Abstract: Experimental studies in neuroscience are producing data at a rapidly increasing rate, providing exciting opportunities and formidable challenges to existing theoretical and modeling approaches. To turn massive datasets into predictive quantitative frameworks, the field needs software solutions for systematic integration of data into realistic, multiscale models. Here we describe the Brain Modeling ToolKit (BMTK), a software suite for building models and performing simulations at multiple levels of resolution, from biophysically detailed multi-compartmental, to point-neuron, to population-statistical approaches. Leveraging the SONATA file format and existing software such as NEURON, NEST, and others, BMTK offers consistent user experience across multiple levels of resolution. It permits highly sophisticated simulations to be set up with little coding required, thus lowering entry barriers to new users. We illustrate successful applications of BMTK to large-scale simulations of a cortical area. BMTK is an open-source package provided as a resource supporting modeling-based discovery in the community. Copy rights belong to original authors. Visit the link for more info

In this twelfth episode, Jeff Kaditz, Founder/CEO of Q Bio begins with coronavirus chat. He goes on to explain that most medical knowledge today is probably incorrect or heavily biased. That there’s almost nothing a doctor does that couldn’t have been done 200 years ago in terms of the information. Read the transcript He presents his vision to run ‘search engines for the body’ and turn healthcare into hard science. Topics we discussed in this episode Coronavirus possibly a once in a hundred year pandemic unfolding Present confusion around the impact of coronavirus Home tests for coronavirus Need for an analytics platform for measuring change in the human body Human health is more of a long tail distribution than a normal distribution Absurdity that we reduce complicated diseases to a single variable measured at a single point in time Applying modern information theory and data science to understanding human health Physical exam of the future gathers genetic, chemical and structural information Building a healthcare system that actually gets better and more efficient over time Transforming healthcare and health into hard science and an information science Getting to the point of being able to test body hypotheticals Envisioning a triage layer in front of the existing primary care system Building the ultimate clinical decision support tool for the future Clinical studies are flawed The more people that have lived, the better we should be at understanding what’s going on in our bodies Age of the digitization of biology Lab assays bake the query into the assay In the near future the query becomes software, not the actual physical process of gathering information Will become feasible and cheap to just measure everything about the human body on some regular interval Healthcare will truly become a pure information science Most medical knowledge today is probably incorrect and it’s probably heavily biased Need to take multi-scale measurements like physics does No reason why we shouldn’t be able to stay as young as we want indefinitely Body is an entropy fighting system which eventually loses the battle The end goal should be getting to more proactive or preventative medicine In the future we will know why we got sick Show links Q Bio (Website) CNN "Australian leader warns coronavirus outbreak is a 'once-in-100 year' crisis" (News Article) COVID-19: No Longer Business as Usual (Article) Modelling When Will Existing Hospital Beds Fill With COVID-19 Patients, by US State (Google Sheet) Elon Musk "Panic is Dumb" (Tweet) Reuter's "'It's ridiculous': Trump travel ban sows panic in European airports" (News Article) Everlywell COVID-19 Test (Website) COVID-19 in Italy: Momentous Decisions and Many Uncertainties (LANCET Paper) "WHO Says The Coronavirus Global Death Rate Is 3.4%, Higher Than Earlier Figures" (Article) Elon Musk Ant-Malarial Drug for Coronavirus (Tweet) Elon Musk Ant-Malarial Drug for Coronavirus (Tweet 2) Brad Perkins on a New Healthcare Industry Emerging From Computing (Podcast Guest #001) Why Software Is Eating the World (Article) LifeSpan by David Sinclair (Book) 2019–20 Coronavirus Pandemic (Wikipedia Entry) Forward (Website) Parsley Health (Website) Human Longevity, Inc (Website) Health Nucleus (Website) Nathan Price on ‘Scientific Wellness’ as Dominant Paradigm of 21st Century Healthcare (Podcast Guest #007)

TIME TO GET EDUCATED. Jason is a local luthier who specializes in multiscale instruments. We take a deep nerdy dive on this one and I definitely learned a ton. I might even have to jump back in and relearn some of the things I forgot! It is seriously very good. Check out his stuff at http://www.jayemarguitars.com/ Learn more about your ad choices. Visit megaphone.fm/adchoices

This week, we have another episode in English for you. A couple of weeks ago, Jeanette had the pleasure of interviewing Prof. Dr. Tobias Moser, who is the spokesperson of the new Göttingen cluster of excellence with the title: "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells". The aim of the cluster is to connect photonics, molecular biosciences, neuroscience and cardiovascular research to get a better understanding of excitable cells, which play a very important role in both disorders of the heart and the brain. He explained how the application process for such a cluster works and what the opportunities and challenges are. Then, of course, you are also going to hear about the research goal of the cluster, and in the end he told Jeanette a bit about his personal background and how he became a medical researcher in Göttingen. You are also going to hear about an exciting new project that is part of the cluster of excellence, the Hertha Sponer College, which will be launched very soon and aims at making interdisciplinary education in medics, physics and biology available to students and young researchers in these fields. More information about the cluster: https://www.uni-goettingen.de/en/579892.html

Guest: Dr. Tannishtha Reya is a Professor of Pharmacology and Medicine at the University of California, San Diego. Her lab  focuses on understanding the signaling pathways that regulate the choice between stem cell renewal and…

Jim Harding, Founder & CEO of MultiScale Health Networks, joins David Johnson for Episode 13 of Market Corner Conversations. Jim discusses how he applied his experience as a serial tech entrepreneur ... The post MARKET CORNER CONVERSATIONS: JIM HARDING, FOUNDER & CEO, MULTISCALE HEALTH NETWORKS appeared first on 4sight Health.

If you pour a liter of water in an already half filled two liter bottle, you’ll usually fill it up completely. But what if the bottle wasn’t filled with liquids, but with sand and air? The mathematics you need to calculate such processes is complex and requires a so-called multiscale approach: calculating the interactions between … Continue reading "44 – Mathematical analysis of multiscale systems"

Dr. Chris Barrett is Executive Director and Professor at the Biocomplexity Institute of Virginia Tech, as well as a Professor in the Department of Computer Science at Virginia Tech. Chris lives on a small farm in the Blue Ridge area of Virginia, and the they daily chores keep him quite busy. He also enjoys playing guitar and riding his motorcycle in his free time. At the Biocomplexity Institute, Chris and his colleagues are using computational methods to better understand our very complicated, interdependent, and multiscale world. They are studying how information is created, transmitted, and manipulated in living systems. Their goal is to take these large, multiscale, massively-interacting systems that have billions of interacting pieces and bring it into a state where people can begin to understand and make sense of them. Chris received a M.S. in Engineering Science and a Ph.D. in Bioinformation Systems from the California Institute of Technology. He also earned a U.S. Navy Aerospace Experimental Psychology Post PhD certification. Before coming to Virginia Tech, Chris led a research group at the Naval Air Development Center, and he later led the Basic and Applied Simulation Science Group at the Los Alamos National Laboratory. Chris has received many awards and honors throughout his career, including Distinguished Service Awards from the U.S. Navy, Los Alamos National Laboratory, the Alliance for Transportation Research, and the Royal Institute of Technology in Stockholm. He was also named a Jubilee Professor in Computer Science and Engineering at Chalmers University in Gothenburg, Sweden. In our interview Chris tells us more about his life and science.