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https://www.readbyqxmd.com/read/28227835/multi-chip-dataflow-architecture-for-massive-scale-biophysically-accurate-neuron-simulation
#1
Jaco Hofmann, Amir Zjajo, Carlo Galuzzi, Rene van Leuken, Jaco Hofmann, Amir Zjajo, Carlo Galuzzi, Rene van Leuken, Carlo Galuzzi, Rene Van Leuken, Jaco Hofmann, Amir Zjajo
State-of-the-art neuron simulators are capable of simulating at most few tens/hundreds of neurons in real-time due to the exponential growth in the communication costs with the number of simulated neurons. In this paper, we present a novel, reconfigurable, multi-chip system architecture based on localized communication, which effectively reduces the communication cost to a linear growth. The system is very flexible and it allows to tune, at run-time, various parameters, e.g. the intracellular concentration of chemical compounds, the interconnection scheme between the neurons...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226616/a-real-time-hybrid-neuron-network-for-highly-parallel-cognitive-systems
#2
Gerrit Jan Christiaanse, Amir Zjajo, Carlo Galuzzi, Rene van Leuken, Gerrit Jan Christiaanse, Amir Zjajo, Carlo Galuzzi, Rene van Leuken, Carlo Galuzzi, Gerrit Jan Christiaanse, Rene van Leuken, Amir Zjajo
For comprehensive understanding of how neurons communicate with each other, new tools need to be developed that can accurately mimic the behaviour of such neurons and neuron networks under `real-time' constraints. In this paper, we propose an easily customisable, highly pipelined, neuron network design, which executes optimally scheduled floating-point operations for maximal amount of biophysically plausible neurons per FPGA family type. To reduce the required amount of resources without adverse effect on the calculation latency, a single exponent instance is used for multiple neuron calculation operations...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226461/role-of-cytosolic-calcium-diffusion-in-cardiac-purkinje-cells
#3
Bijay Limbu, Kushal Shah, Makarand Deo, Bijay Limbu, Kushal Shah, Makarand Deo, Bijay Limbu, Makar Deo, Kushal Shah
The Cardiac Purkinje cells (PCs) exhibit distinct calcium (Ca(2)+) homeostasis than that in ventricular myocytes (VMs). Due to lack of t-tubules in PCs, the Ca(2)+ ions entering the cell have to diffuse through the cytoplasm to reach the sarcoplasmic reticulum (SR) before triggering Ca(2)+-induced-Ca(2)+-release (CICR). In recent experimental studies PCs have been shown to be more susceptible to action potential (AP) abnormalities than the VMs, however the exact mechanisms are poorly understood. In this study, we utilize morphologically realistic detailed biophysical mathematical model of a murine PC to systematically examine the role intracellular Ca(2)+ diffusion in the APs of PCs...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226216/overcoming-immune-dysregulation-with-immunoengineered-nanobiomaterials
#4
Evan A Scott, Nicholas B Karabin, Punn Augsornworawat
The immune system is governed by an immensely complex network of cells and both intracellular and extracellular molecular factors. It must respond to an ever-growing number of biochemical and biophysical inputs by eliciting appropriate and specific responses in order to maintain homeostasis. But as with any complex system, a plethora of false positives and false negatives can occur to generate dysregulated responses. Dysregulated immune responses are essential components of diverse inflammation-driven pathologies, including cancer, heart disease, and autoimmune disorders...
February 9, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28225803/bacterial-expression-correct-membrane-targeting-and-functional-folding-of-the-hiv-1-membrane-protein-vpu-using-a-periplasmic-signal-peptide
#5
Arpan Deb, William A Johnson, Alexander P Kline, Boston J Scott, Lydia R Meador, Dustin Srinivas, Jose M Martin-Garcia, Katerina Dörner, Chad R Borges, Rajeev Misra, Brenda G Hogue, Petra Fromme, Tsafrir S Mor
Viral protein U (Vpu) is a type-III integral membrane protein encoded by Human Immunodeficiency Virus-1 (HIV- 1). It is expressed in infected host cells and plays several roles in viral progeny escape from infected cells, including down-regulation of CD4 receptors. But key structure/function questions remain regarding the mechanisms by which the Vpu protein contributes to HIV-1 pathogenesis. Here we describe expression of Vpu in bacteria, its purification and characterization. We report the successful expression of PelB-Vpu in Escherichia coli using the leader peptide pectate lyase B (PelB) from Erwinia carotovora...
2017: PloS One
https://www.readbyqxmd.com/read/28225654/germicidal-efficacy-and-mammalian-skin-safety-of-222-nm-uv-light
#6
Manuela Buonanno, Brian Ponnaiya, David Welch, Milda Stanislauskas, Gerhard Randers-Pehrson, Lubomir Smilenov, Franklin D Lowy, David M Owens, David J Brenner
We have previously shown that 207-nm ultraviolet (UV) light has similar antimicrobial properties as typical germicidal UV light (254 nm), but without inducing mammalian skin damage. The biophysical rationale is based on the limited penetration distance of 207-nm light in biological samples (e.g. stratum corneum) compared with that of 254-nm light. Here we extended our previous studies to 222-nm light and tested the hypothesis that there exists a narrow wavelength window in the far-UVC region, from around 200-222 nm, which is significantly harmful to bacteria, but without damaging cells in tissues...
February 22, 2017: Radiation Research
https://www.readbyqxmd.com/read/28225152/topical-phenytoin-for-treating-pressure-ulcers
#7
REVIEW
Xiang Yong Hao, Hong Ling Li, He Su, Hui Cai, Tian Kang Guo, Ruifeng Liu, Lei Jiang, Yan Fei Shen
BACKGROUND: Pressure ulcers are common in clinical practice and pose a significant health problem worldwide. Apart from causing suffering to patients, they also result in longer hospital stays and increase the cost of health care. A variety of methods are used for treating pressure ulcers, including pressure relief, patient repositioning, biophysical strategies, nutritional supplementation, debridement, topical negative pressure, and local treatments including dressings, ointments and creams such as bacitracin, silver sulphadiazine, neomycin, and phenytoin...
February 22, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28223913/neuromorphic-implementation-of-attractor-dynamics-in-a-two-variable-winner-take-all-circuit-with-nmdars-a-simulation-study
#8
Hongzhi You, Da-Hui Wang
Neural networks configured with winner-take-all (WTA) competition and N-methyl-D-aspartate receptor (NMDAR)-mediated synaptic dynamics are endowed with various dynamic characteristics of attractors underlying many cognitive functions. This paper presents a novel method for neuromorphic implementation of a two-variable WTA circuit with NMDARs aimed at implementing decision-making, working memory and hysteresis in visual perceptions. The method proposed is a dynamical system approach of circuit synthesis based on a biophysically plausible WTA model...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28223358/structural-and-biochemical-analysis-of-escherichia-coli-obge-a-central-regulator-of-bacterial-persistence
#9
Sotirios Gkekas, Ranjan Kumar Singh, Alexander V Shkumatov, Joris Messens, Maarten Fauvart, Natalie Verstraeten, Jan Michiels, Wim Versées
The Obg protein family belongs to the TRAFAC (translation factor) class of P-loop GTPases and is conserved from bacteria to eukaryotes. Essential roles in many different cellular processes have been suggested for the Obg protein from Escherichia coli (ObgE), and we recently showed that it is a central regulator of bacterial persistence. Here, we report the first crystal structure of ObgE at 1.85 Å resolution in the GDP-bound state, showing the characteristic N-terminal domain and a central G domain that are common to all Obg proteins...
February 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28223224/transient-receptor-potential-canonical-type-3-channels-interactions-role-and-relevance-a-vascular-focus
#10
REVIEW
T Hilton Grayson, Timothy V Murphy, Shaun L Sandow
Transient receptor potential canonical type 3 channels (TRPC3) are expressed in neural, cardiac, respiratory and vascular tissues, with both similarities and differences between human and animal models for the same cell types. In common with all members of the six subfamilies of TRP channels, TRPC3 are non-voltage gated, non-selective cation channels that are mainly permeated by Ca(2+), and have distinct molecular, biophysical, anatomical and functional properties. TRP channels are present in excitable and non-excitable cells where they sense and respond to a wide variety of physical and chemical stimuli...
February 13, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28223017/novel-bcl2-inhibitor-disarib-induces-apoptosis-by-disruption-of-bcl2-bak-interaction
#11
Supriya V Vartak, Divyaanka Iyer, T R Santhoshkumar, Sheetal Sharma, Archita Mishra, Gunaseelan Goldsmith, Mrinal Srivastava, Shikha Srivastava, Subhas S Karki, Avadhesha Surolia, Bibha Choudhary, Sathees C Raghavan
Apoptosis is a highly regulated pathway of programmed cell death relying on the fine balance between pro and antiapoptotic binding partners. Overexpression of the antiapoptotic protein BCL2 in several cancers makes it an ideal target for chemotherapy, with minimum side effects. In one of our previous studies, we designed, synthesized and characterized Disarib, a BCL2-specific small molecule inhibitor. Interestingly, Disarib showed a novel mode of BCL2 inhibition, by predominantly binding to its BH1 domain, as compared to the BH3-specific action of other known BCL2 inhibitors...
February 18, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28222010/optical-tweezers-studies-of-transcription-by-eukaryotic-rna-polymerases
#12
Ana Lisica, Stephan W Grill
Transcription is the first step in the expression of genetic information and it is carried out by large macromolecular enzymes called RNA polymerases. Transcription has been studied for many years and with a myriad of experimental techniques, ranging from bulk studies to high-resolution transcript sequencing. In this review, we emphasise the advantages of using single-molecule techniques, particularly optical tweezers, to study transcription dynamics. We give an overview of the latest results in the single-molecule transcription field, focusing on transcription by eukaryotic RNA polymerases...
February 21, 2017: Biomolecular Concepts
https://www.readbyqxmd.com/read/28221776/the-horizon-of-materiobiology-a-perspective-on-material-guided-cell-behaviors-and-tissue-engineering
#13
Yulin Li, Yin Xiao, Changsheng Liu
Although the biological functions of cell and tissue can be regulated by biochemical factors (e.g., growth factors, hormones), the biophysical effects of materials on the regulation of biological activity are receiving more attention. In this Review, we systematically summarize the recent progress on how biomaterials with controllable properties (e.g., compositional/degradable dynamics, mechanical properties, 2D topography, and 3D geometry) can regulate cell behaviors (e.g., cell adhesion, spreading, proliferation, cell alignment, and the differentiation or self-maintenance of stem cells) and tissue/organ functions...
February 21, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28220680/an-environmental-sociology-for-the-anthropocene
#14
Gary Bowden
Attention to the relationship between nature and society has been a defining feature of environmental sociology since its inception. Early research, incorporating insights from ecology, argued for the need to (1) theorize the causal connections between nature and society and (2) contextualize those connections in terms of biophysical limits resulting from resource scarcity. Over the past two decades, partly in response to new forms of existential threat such as climate change, the treatment of nature and society as distinct entities has given way to a focus on socio-natural assemblages...
February 2017: Canadian Review of Sociology, Revue Canadienne de Sociologie
https://www.readbyqxmd.com/read/28220607/neurological-and-spinal-manifestations-of-the-ehlers-danlos-syndromes
#15
Fraser C Henderson, Claudiu Austin, Edward Benzel, Paolo Bolognese, Richard Ellenbogen, Clair A Francomano, Candace Ireton, Petra Klinge, Myles Koby, Donlin Long, Sunil Patel, Eric L Singman, Nicol C Voermans
The Ehlers-Danlos syndromes (EDS) are a heterogeneous group of heritable connective tissue disorders characterized by joint hypermobility, skin extensibility, and tissue fragility. This communication briefly reports upon the neurological manifestations that arise including the weakness of the ligaments of the craniocervical junction and spine, early disc degeneration, and the weakness of the epineurium and perineurium surrounding peripheral nerves. Entrapment, deformation, and biophysical deformative stresses exerted upon the nervous system may alter gene expression, neuronal function and phenotypic expression...
February 21, 2017: American Journal of Medical Genetics. Part C, Seminars in Medical Genetics
https://www.readbyqxmd.com/read/28218967/representation-of-critical-natural-capital-in-china
#16
Yihe Lü, Liwei Zhang, Yuan Zeng, Bojie Fu, Charlotte Whitham, Shuguang Liu, Bingfang Wu
Traditional means of assessing representativeness of conservation value in protected areas depend on measures of structural biodiversity. The effectiveness of priority conservation areas at representing critical natural capital (CNC) (i.e., an essential and renewable subset of natural capital) remains largely unknown. We analyzed the representativeness of CNC-conservation priority areas in national nature reserves (i.e., nature reserves under jurisdiction of the central government with large spatial distribution across the provinces) in China with a new biophysical-based composite indicator approach...
February 20, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/28218303/a-combination-of-mutational-and-computational-scanning-guides-the-design-of-an-artificial-ligand-binding-controlled-lipase
#17
Marco Kaschner, Oliver Schillinger, Timo Fettweiss, Christina Nutschel, Frank Krause, Alexander Fulton, Birgit Strodel, Andreas Stadler, Karl-Erich Jaeger, Ulrich Krauss
Allostery, i.e. the control of enzyme activity by a small molecule at a location distant from the enzyme's active site, represents a mechanism essential for sustaining life. The rational design of allostery is a non-trivial task but can be achieved by fusion of a sensory domain, which responds to environmental stimuli with a change in its structure. Hereby, the site of domain fusion is difficult to predict. We here explore the possibility to rationally engineer allostery into the naturally not allosterically regulated Bacillus subtilis lipase A, by fusion of the citrate-binding sensor-domain of the CitA sensory-kinase of Klebsiella pneumoniae...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28217771/detection-inhibition-and-disintegration-of-amyloid-fibrils-the-role-of-optical-probes-and-macrocyclic-receptors
#18
Achikanath C Bhasikuttan, Jyotirmayee Mohanty
Amyloid fibrils are formed by the aberrant aggregation of proteins into highly ordered β-sheet structures and are believed to be the root cause of several neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Prion diseases, etc. and have been the subject of extensive biochemical, biophysical and clinical studies. Developing methods for the early detection of fibril formation using optical spectroscopic techniques and inhibition/disintegration of amyloid fibrils/plaques by introducing small molecules have been a major challenge to establish a clinically facile therapeutic intervention to combat these neurodegenerative diseases...
February 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28216658/timing-the-day-what-makes-bacterial-clocks-tick
#19
REVIEW
Carl Hirschie Johnson, Chi Zhao, Yao Xu, Tetsuya Mori
Chronobiological studies of prokaryotic organisms have generally lagged far behind the study of endogenous circadian clocks in eukaryotes, in which such systems are essentially ubiquitous. However, despite only being studied during the past 25 years, cyanobacteria have become important model organisms for the study of circadian rhythms and, presently, their timekeeping mechanism is the best understood of any system in terms of biochemistry, structural biology, biophysics and adaptive importance. Nevertheless, intrinsic daily rhythmicity among bacteria other than cyanobacteria is essentially unknown; some tantalizing information suggests widespread daily timekeeping among Eubacteria and Archaea through mechanisms that share common elements with the cyanobacterial clock but are distinct...
February 20, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28216637/mutations-underlying-episodic-ataxia-type-1-antagonize-kv1-1-rna-editing
#20
Elizabeth A Ferrick-Kiddie, Joshua J C Rosenthal, Gregory D Ayers, Ronald B Emeson
Adenosine-to-inosine RNA editing in transcripts encoding the voltage-gated potassium channel Kv1.1 converts an isoleucine to valine codon for amino acid 400, speeding channel recovery from inactivation. Numerous Kv1.1 mutations have been associated with the human disorder Episodic Ataxia Type-1 (EA1), characterized by stress-induced ataxia, myokymia, and increased prevalence of seizures. Three EA1 mutations, V404I, I407M, and V408A, are located within the RNA duplex structure required for RNA editing. Each mutation decreased RNA editing both in vitro and using an in vivo mouse model bearing the V408A allele...
February 20, 2017: Scientific Reports
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