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https://www.readbyqxmd.com/read/28814063/icave-an-open-source-tool-for-visualizing-biomolecular-networks-in-3d-stereoscopic-3d-and-immersive-3d
#1
Vaja Liluashvili, Selim Kalayci, Eugene Fluder, Manda Wilson, Aaron Gabow, Zeynep H Gümüs
Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28809897/topology-optimized-metasurfaces-impact-of-initial-geometric-layout
#2
Jianji Yang, Jonathan A Fan
Topology optimization is a powerful iterative inverse design technique in metasurface engineering and can transform an initial layout into a high-performance device. With this method, devices are optimized within a local design phase space, making the identification of suitable initial geometries essential. In this Letter, we examine the impact of initial geometric layout on the performance of large-angle (75 deg) topology-optimized metagrating deflectors. We find that when conventional metasurface designs based on dielectric nanoposts are used as initial layouts for topology optimization, the final devices have efficiencies around 65%...
August 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28809703/motion-based-rapid-serial-visual-presentation-for-gaze-independent-brain-computer-interfaces
#3
Dong-Ok Won, Han-Jeong Hwang, Dong-Min Kim, Klaus-Robert Muller, Seong-Whan Lee
Most event-related potential (ERP)-based braincomputer interface (BCI) spellers primarily use matrix layouts, and generally require moderate eye movement for successful operation. The fundamental objective of this study is to enhance the perceptibility of target characters by introducing motion stimuli to classical rapid serial visual presentation (RSVP) spellers that do not require any eye movement, thereby applying them to paralyzed patients with oculomotor dysfunctions. To test the feasibility of the proposed motion-based RSVP paradigm, we implemented three RSVP spellers: i) fixed-direction motion (FM-RSVP), ii) random-direction motion (RM-RSVP), and iii) (the conventional) non-motion stimulation (NM-RSVP), and evaluated the effect of the three different stimulation methods on spelling performance...
August 11, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28806960/16-channel-biphasic-current-mode-programmable-charge-balanced-neural-stimulation
#4
Xiaoran Li, Shunan Zhong, James Morizio
BACKGROUND: Neural stimulation is an important method used to activate or inhibit action potentials of the neuronal anatomical targets found in the brain, central nerve and peripheral nerve. The neural stimulator system produces biphasic pulses that deliver balanced charge into tissue from single or multichannel electrodes. The timing and amplitude of these biphasic pulses are precisely controlled by the neural stimulator software or imbedded algorithms. Amplitude mismatch between the anodic current and cathodic current of the biphasic pulse will cause permanently damage for the neural tissues...
August 14, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28806487/gut-microbiome-response-to-short-term-dietary-interventions-in-reactive-hypoglycemia-subjects
#5
Sara Quercia, Silvia Turroni, Jessica Fiori, Matteo Soverini, Simone Rampelli, Elena Biagi, Andrea Castagnetti, Clarissa Consolandi, Marco Severgnini, Mario Pianesi, Francesco Fallucca, Paolo Pozzilli, Patrizia Brigidi, Marco Candela
BACKGROUND: Reactive hypoglycemia (RH) is a metabolic disorder that provokes severe hypoglycemic episodes after meal. Over recent years, the gut microbiota (GM) has been recognized as potential target for the control of metabolic diseases, and the possibility to correct GM dysbioses through diet, favoring the recovery of metabolic homeostasis, has been considered. METHODS: We investigate the impact of two short-term (3-day) nutritional interventions, based on the macrobiotic Ma-Pi 2 diet and a control Mediterranean diet, on the structure and functionality of the GM in 12 patients affected by RH...
August 14, 2017: Diabetes/metabolism Research and Reviews
https://www.readbyqxmd.com/read/28805041/direct-microrolling-processing-on-a-silicon-wafer
#6
Kanna Aoki, Keita Ishiguro, Masaki Denokami, Yuya Tanahashi, Kentaro Furusawa, Norihiko Sekine, Tadafumi Adschiri, Minoru Fujii
Although, varieties of micro- to nanoscale fabrication technologies have been invented and refined for silicon (Si) processing because Si is the basic material of integrated circuits, the layouts are based on layer-by-layer approaches, making it difficult to realize three-dimensional (3D) structures with complicated shapes normal to the planar surface (along the out-of-plane direction) of the wafers used. Here, a novel and direct Si-processing technology that enables to bend thin layers of Si surfaces into various 3D curved structures at the micrometer scale is introduced...
August 14, 2017: Small
https://www.readbyqxmd.com/read/28804783/functional-corticostriatal-connection-topographies-predict-goal-directed-behaviour-in-humans
#7
Andre F Marquand, Koen V Haak, Christian F Beckmann
Anatomical tracing studies in non-human primates have suggested that corticostriatal connectivity is topographically organized: nearby locations in striatum are connected with nearby locations in cortex. The topographic organization of corticostriatal connectivity is thought to underpin many goal-directed behaviours, but these topographies have not been completely characterised in humans and their relationship to uniquely human behaviours remains to be fully determined. Instead, the dominant approach employs parcellations that cannot model the continuous nature of the topography, nor accommodate overlapping cortical projections in the striatum...
August 2017: Nature Human Behaviour
https://www.readbyqxmd.com/read/28797083/the-transcriptional-response-to-the-olive-fruit-fly-bactrocera-oleae-reveals-extended-differences-between-tolerant-and-susceptible-olive-olea-europaea-l-varieties
#8
Filomena Grasso, Mariangela Coppola, Fabrizio Carbone, Luciana Baldoni, Fiammetta Alagna, Gaetano Perrotta, Antonio J Pérez-Pulido, Antonio Garonna, Paolo Facella, Loretta Daddiego, Loredana Lopez, Alessia Vitiello, Rosa Rao, Giandomenico Corrado
The olive fruit fly Bactrocera oleae (Diptera: Tephritidae) is the most devastating pest of cultivated olive (Olea europaea L.). Intraspecific variation in plant resistance to B. oleae has been described only at phenotypic level. In this work, we used a transcriptomic approach to study the molecular response to the olive fruit fly in two olive cultivars with contrasting level of susceptibility. Using next-generation pyrosequencing, we first generated a catalogue of more than 80,000 sequences expressed in drupes from approximately 700k reads...
2017: PloS One
https://www.readbyqxmd.com/read/28792517/comparison-of-alternative-approaches-for-analysing-multi-level-rna-seq-data
#9
Irina Mohorianu, Amanda Bretman, Damian T Smith, Emily K Fowler, Tamas Dalmay, Tracey Chapman
RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D...
2017: PloS One
https://www.readbyqxmd.com/read/28790782/revelations-of-an-overt-water-contamination
#10
Gurpreet Singh, S K Kaushik, S Mukherji
BACKGROUND: Contaminated water sources are major cause of water borne diseases of public health importance. Usually, contamination is suspected after an increase in patient load. METHODS: Two health teams investigated the episode. First team conducted sanitary survey, and second team undertook water safety and morbidity survey. On-site testing was carried out from source till consumer end. Investigation was also undertaken to identify factors which masked the situation...
July 2017: Medical Journal, Armed Forces India
https://www.readbyqxmd.com/read/28790358/environmental-concern-based-site-screening-of-carbon-dioxide-geological-storage-in-china
#11
Bofeng Cai, Qi Li, Guizhen Liu, Lancui Liu, Taotao Jin, Hui Shi
Environmental impacts and risks related to carbon dioxide (CO2) capture and storage (CCS) projects may have direct effects on the decision-making process during CCS site selection. This paper proposes a novel method of environmental optimization for CCS site selection using China's ecological red line approach. Moreover, this paper established a GIS based spatial analysis model of environmental optimization during CCS site selection by a large database. The comprehensive data coverage of environmental elements and fine 1 km spatial resolution were used in the database...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28776234/combination-of-antibody-coated-physical-based-microfluidic-chip-with-wave-shaped-arrays-for-isolating-circulating-tumor-cells
#12
Hongmei Chen, Baoshan Cao, Hongda Chen, Yu-Sheng Lin, Jingjing Zhang
Circulating tumor cells (CTCs) are found in the peripheral blood of patients with metastatic cancers, which have critical significance in cancer prognosis and diagnostics. Enumeration is significantly valuable since number of CTCs is strongly correlated to severity of disease. This article is proposed and demonstrated an antibody-coated, size-based microfluidic chip with wave-shaped arrays could efficiently capture CTCs combining two separation methods of both size- and deformability-based and affinity-based segregation...
September 2017: Biomedical Microdevices
https://www.readbyqxmd.com/read/28774178/quantized-transport-strain-induced-perfectly-conducting-modes-and-valley-filtering-on-shape-optimized-graphene-corbino-devices
#13
Gareth W Jones, Dario Andres Bahamon, Antonio H Castro Neto, Vitor M Pereira
The extreme mechanical resilience of graphene and the peculiar coupling it hosts between lattice and electronic degrees of freedom have spawned a strong impetus toward strain-engineered graphene where, on the one hand, strain augments the richness of its phenomenology and makes possible new concepts for electronic devices, and on the other hand, new and extreme physics might take place. Here, we demonstrate that the shape of substrates supporting graphene sheets can be optimized for approachable experiments where strain-induced pseudomagnetic fields (PMF) can be tailored by pressure for directionally selective electronic transmission and pinching-off of current flow down to the quantum channel limit...
August 9, 2017: Nano Letters
https://www.readbyqxmd.com/read/28774041/lamb-wave-based-tomographic-imaging-techniques-for-hole-edge-corrosion-monitoring-in-plate-structures
#14
Dengjiang Wang, Weifang Zhang, Xiangyu Wang, Bo Sun
This study presents a novel monitoring method for hole-edge corrosion damage in plate structures based on Lamb wave tomographic imaging techniques. An experimental procedure with a cross-hole layout using 16 piezoelectric transducers (PZTs) was designed. The A0 mode of the Lamb wave was selected, which is sensitive to thickness-loss damage. The iterative algebraic reconstruction technique (ART) method was used to locate and quantify the corrosion damage at the edge of the hole. Hydrofluoric acid with a concentration of 20% was used to corrode the specimen artificially...
November 12, 2016: Materials
https://www.readbyqxmd.com/read/28773154/strain-wave-acquisition-by-a-fiber-optic-coherent-sensor-for-impact-monitoring
#15
Claudio Sbarufatti, Alessio Beligni, Andrea Gilioli, Maddalena Ferrario, Marco Mattarei, Mario Martinelli, Marco Giglio
A novel fiber optic sensing technology for high frequency dynamics detection is proposed in this paper, specifically tailored for structural health monitoring applications based on strain wave analysis, for both passive impact identification and active Lamb wave monitoring. The sensing solution relies on a fiber optic-based interferometric architecture associated to an innovative coherent detection scheme, which retrieves in a completely passive way the high-frequency phase information of the received optical signal...
July 13, 2017: Materials
https://www.readbyqxmd.com/read/28773024/mechanical-behavior-of-steel-fiber-reinforced-concrete-beams-bonded-with-external-carbon-fiber-sheets
#16
Viktor Gribniak, Vytautas Tamulenas, Pui-Lam Ng, Aleksandr K Arnautov, Eugenijus Gudonis, Ieva Misiunaite
This study investigates the mechanical behavior of steel fiber-reinforced concrete (SFRC) beams internally reinforced with steel bars and externally bonded with carbon fiber-reinforced polymer (CFRP) sheets fixed by adhesive and hybrid jointing techniques. In particular, attention is paid to the load resistance and failure modes of composite beams. The steel fibers were used to avoiding the rip-off failure of the concrete cover. The CFRP sheets were fixed to the concrete surface by epoxy adhesive as well as combined with various configurations of small-diameter steel pins for mechanical fastening to form a hybrid connection...
June 17, 2017: Materials
https://www.readbyqxmd.com/read/28772485/optimal-electrode-selection-for-electrical-resistance-tomography-in-carbon-fiber-reinforced-polymer-composites
#17
Luis Waldo Escalona Galvis, Paulina Diaz-Montiel, Satchi Venkataraman
Electrical Resistance Tomography (ERT) offers a non-destructive evaluation (NDE) technique that takes advantage of the inherent electrical properties in carbon fiber reinforced polymer (CFRP) composites for internal damage characterization. This paper investigates a method of optimum selection of sensing configurations for delamination detection in thick cross-ply laminates using ERT. Reduction in the number of sensing locations and measurements is necessary to minimize hardware and computational effort. The present work explores the use of an effective independence (EI) measure originally proposed for sensor location optimization in experimental vibration modal analysis...
February 4, 2017: Materials
https://www.readbyqxmd.com/read/28771695/challenges-for-visualizing-three-dimensional-data-in-genomic-browsers
#18
REVIEW
Mike Goodstadt, Marc A Marti-Renom
Genomic interactions reveal the spatial organization of genomes and genomic domains, which is known to play key roles in cell function. Physical proximity can be represented as two-dimensional heat maps or matrices. From these, three-dimensional (3D) conformations of chromatin can be computed revealing coherent structures that highlight the importance of non-sequential relationships across genomic features. Mainstream genomic browsers have been classically developed to display compact, stacked tracks based on a linear, sequential, per-chromosome coordinate system...
August 3, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28771583/predicting-the-effect-of-seine-rope-layout-pattern-and-haul-in-procedure-on-the-effectiveness-of-demersal-seine-fishing-a-computer-simulation-based-approach
#19
Nina A H Madsen, Karl G Aarsæther, Bent Herrmann
Demersal Seining is an active fishing method applying two long seine ropes and a seine net. Demersal seining relies on fish responding to the seine rope as it moves during the fishing process. The seine ropes and net are deployed in a specific pattern encircling an area on the seabed. In some variants of demersal seining the haul-in procedure includes a towing phase where the fishing vessel moves forward before starting to winch in the seine ropes. The initial seine rope encircled area, the gradual change in it during the haul-in process and the fish's reaction to the moving seine ropes play an important role in the catch performance of demersal seine fishing...
2017: PloS One
https://www.readbyqxmd.com/read/28765594/evaluation-of-realistic-layouts-for-next-generation-on-scalp-meg-spatial-information-density-maps
#20
Bushra Riaz, Christoph Pfeiffer, Justin F Schneiderman
While commercial magnetoencephalography (MEG) systems are the functional neuroimaging state-of-the-art in terms of spatio-temporal resolution, MEG sensors have not changed significantly since the 1990s. Interest in newer sensors that operate at less extreme temperatures, e.g., high critical temperature (high-T c) SQUIDs, optically-pumped magnetometers, etc., is growing because they enable significant reductions in head-to-sensor standoff (on-scalp MEG). Various metrics quantify the advantages of on-scalp MEG, but a single straightforward one is lacking...
August 1, 2017: Scientific Reports
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