Optimizing network connectivity for mobile health technologies in sub-Saharan Africa.

PubMed

Siedner, Mark J; Lankowski, Alexander; Musinga, Derrick; Jackson, Jonathon; Muzoora, Conrad; Hunt, Peter W; Martin, Jeffrey N; Bangsberg, David R; Haberer, Jessica E

2012-01-01

Mobile health (mHealth) technologies hold incredible promise to improve healthcare delivery in resource-limited settings. Network reliability across large catchment areas can be a major challenge. We performed an analysis of network failure frequency as part of a study of real-time adherence monitoring in rural Uganda. We hypothesized that the addition of short messaging service (SMS+GPRS) to the standard cellular network modality (GPRS) would reduce network disruptions and improve transmission of data. Participants were enrolled in a study of real-time adherence monitoring in southwest Uganda. In June 2011, we began using Wisepill devices that transmit data each time the pill bottle is opened. We defined network failures as medication interruptions of >48 hours duration that were transmitted when network connectivity was re-established. During the course of the study, we upgraded devices from GPRS to GPRS+SMS compatibility. We compared network failure rates between GPRS and GPRS+SMS periods and created geospatial maps to graphically demonstrate patterns of connectivity. One hundred fifty-seven participants met inclusion criteria of seven days of SMS and seven days of SMS+GPRS observation time. Seventy-three percent were female, median age was 40 years (IQR 33-46), 39% reported >1-hour travel time to clinic and 17% had home electricity. One hundred one had GPS coordinates recorded and were included in the geospatial maps. The median number of network failures per person-month for the GPRS and GPRS+SMS modalities were 1.5 (IQR 1.0-2.2) and 0.3 (IQR 0-0.9) respectively, (mean difference 1.2, 95%CI 1.0-1.3, p-value<0.0001). Improvements in network connectivity were notable throughout the region. Study costs increased by approximately $1USD per person-month. Addition of SMS to standard GPRS cellular network connectivity can significantly reduce network connection failures for mobile health applications in remote areas. Projects depending on mobile health data in resource-limited settings should consider this upgrade to optimize mHealth applications.

Sub-cellular force microscopy in single normal and cancer cells.

PubMed

Babahosseini, H; Carmichael, B; Strobl, J S; Mahmoodi, S N; Agah, M

2015-08-07

This work investigates the biomechanical properties of sub-cellular structures of breast cells using atomic force microscopy (AFM). The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity, and the relaxation time of sub-cellular structures. The triple-layered modeling results allow for determination and comparison of the biomechanical properties of the three major sub-cellular structures between normal and cancerous cells: the up plasma membrane/actin cortex, the mid cytoplasm/nucleus, and the low nuclear/integrin sub-domains. The results reveal that the sub-domains become stiffer and significantly more viscous with depth, regardless of cell type. In addition, there is a decreasing trend in the average elastic modulus and apparent viscosity of the all corresponding sub-cellular structures from normal to cancerous cells, which becomes most remarkable in the deeper sub-domain. The presented modeling in this work constitutes a unique AFM-based experimental framework to study the biomechanics of sub-cellular structures. Copyright © 2015 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hajian, Amir; Bond, J. Richard; Battaglia, Nicholas

We measure a significant correlation between the thermal Sunyaev-Zel'dovich effect in the Planck and WMAP maps and an X-ray cluster map based on ROSAT. We use the 100, 143 and 343 GHz Planck maps and the WMAP 94 GHz map to obtain this cluster cross spectrum. We check our measurements for contamination from dusty galaxies using the cross correlations with the 217, 545 and 857 GHz maps from Planck. Our measurement yields a direct characterization of the cluster power spectrum over a wide range of angular scales that is consistent with large cosmological simulations. The amplitude of this signal dependsmore » on cosmological parameters that determine the growth of structure (σ{sub 8} and Ω M) and scales as σ{sub 8}{sup 7.4} and Ω M{sup 1.9} around the multipole (ℓ) ∼ 1000. We constrain σ{sub 8} and Ω M from the cross-power spectrum to be σ{sub 8}(Ω M/0.30){sup 0.26} = 0.8±0.02. Since this cross spectrum produces a tight constraint in the σ{sub 8} and Ω M plane the errors on a σ{sub 8} constraint will be mostly limited by the uncertainties from external constraints. Future cluster catalogs, like those from eRosita and LSST, and pointed multi-wavelength observations of clusters will improve the constraining power of this cross spectrum measurement. In principle this analysis can be extended beyond σ{sub 8} and Ω M to constrain dark energy or the sum of the neutrino masses.« less

Mapping of native inorganic elements and injected nanoparticles in a biological organ with laser-induced plasma

NASA Astrophysics Data System (ADS)

Motto-Ros, V.; Sancey, L.; Ma, Q. L.; Lux, F.; Bai, X. S.; Wang, X. C.; Yu, Jin; Panczer, G.; Tillement, O.

2012-11-01

Emission spectroscopy of laser-induced plasma from a thin section of mouse kidney successfully detected inorganic elements, Na, Ca, Cu, and Gd, naturally contained in the organ or artificially injected in the form of Gd-based nanoparticle. A two-dimensional scan of the sample allowed the laser beam to explore its surface with a resolution of 100 μm, resulting in a quantitative elemental mapping of the organ with sub-mM sensitivity. The compatibility of the setup with standard optical microscopy emphasizes the potential to provide multiple images of a same biological tissue with different types of response which can be elemental, molecular, or cellular.

Combining Observations in the Reflective Solar and Thermal Domains for Improved Mapping of Carbon, Water and Energy FLuxes

NASA Technical Reports Server (NTRS)

Houborg, Rasmus; Anderson, Martha; Kustas, Bill; Rodell, Matthew

2011-01-01

This study investigates the utility of integrating remotely sensed estimates of leaf chlorophyll (C(sub ab)) into a thermal-based Two-Source Energy Balance (TSEB) model that estimates land-surface CO2 and energy fluxes using an analytical, light-use-efficiency (LUE) based model of canopy resistance. Day to day variations in nominal LUE (LUE(sub n)) were assessed for a corn crop field in Maryland U.S.A. through model calibration with CO2 flux tower observations. The optimized daily LUE(sub n) values were then compared to estimates of C(sub ab) integrated from gridded maps of chlorophyll content weighted over the tower flux source area. Changes in Cab exhibited a curvilinear relationship with corresponding changes in daily calibrated LUE(sub n) values derived from the tower flux data, and hourly water, energy and carbon flux estimation accuracies from TSEB were significantly improved when using C(sub ab) for delineating spatio-temporal variations in LUE(sub n). The results demonstrate the synergy between thermal infrared and shortwave reflective wavebands in producing valuable remote sensing data for monitoring of carbon and water fluxes.

Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq

PubMed Central

Loeffler-Wirth, Henry; Hopp, Lydia; Schadendorf, Dirk; Schartl, Manfred; Anderegg, Ulf; Camp, Gray; Treutlein, Barbara; Binder, Hans; Kunz, Manfred

2017-01-01

Recent technological advances in single-cell genomics make it possible to analyze cellular heterogeneity of tumor samples. Here, we applied single-cell RNA-seq to measure the transcriptomes of 307 single cells cultured from three biopsies of three different patients with a BRAF/NRAS wild type, BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant melanoma metastasis, respectively. Analysis based on self-organizing maps identified sub-populations defined by multiple gene expression modules involved in proliferation, oxidative phosphorylation, pigmentation and cellular stroma. Gene expression modules had prognostic relevance when compared with gene expression data from published melanoma samples and patient survival data. We surveyed kinome expression patterns across sub-populations of the BRAF/NRAS wild type sample and found that CDK4 and CDK2 were consistently highly expressed in the majority of cells, suggesting that these kinases might be involved in melanoma progression. Treatment of cells with the CDK4 inhibitor palbociclib restricted cell proliferation to a similar, and in some cases greater, extent than MAPK inhibitors. Finally, we identified a low abundant sub-population in this sample that highly expressed a module containing ABC transporter ABCB5, surface markers CD271 and CD133, and multiple aldehyde dehydrogenases (ALDHs). Patient-derived cultures of the BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant metastases showed more homogeneous single-cell gene expression patterns with gene expression modules for proliferation and ABC transporters. Taken together, our results describe an intertumor and intratumor heterogeneity in melanoma short-term cultures which might be relevant for patient survival, and suggest promising targets for new treatment approaches in melanoma therapy. PMID:27903987

Sub-cellular force microscopy in single normal and cancer cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Babahosseini, H.; Carmichael, B.; Strobl, J.S.

2015-08-07

This work investigates the biomechanical properties of sub-cellular structures of breast cells using atomic force microscopy (AFM). The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity, and the relaxation time of sub-cellular structures. The triple-layered modeling results allow for determination and comparison of the biomechanical properties of the three major sub-cellular structures between normal and cancerous cells: the up plasma membrane/actin cortex, the mid cytoplasm/nucleus, and the low nuclear/integrin sub-domains. The results reveal that the sub-domains become stiffer andmore » significantly more viscous with depth, regardless of cell type. In addition, there is a decreasing trend in the average elastic modulus and apparent viscosity of the all corresponding sub-cellular structures from normal to cancerous cells, which becomes most remarkable in the deeper sub-domain. The presented modeling in this work constitutes a unique AFM-based experimental framework to study the biomechanics of sub-cellular structures. - Highlights: • The cells are modeled as a triple-layered structure using Generalized Maxwell model. • The sub-domains include membrane/cortex, cytoplasm/nucleus, and nuclear/integrin. • Biomechanics of corresponding sub-domains are compared among normal and cancer cells. • Viscoelasticity of sub-domains show a decreasing trend from normal to cancer cells. • The decreasing trend becomes most significant in the deeper sub-domain.« less

Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways

PubMed Central

Kawakami, Eiryo; Singh, Vivek K; Matsubara, Kazuko; Ishii, Takashi; Matsuoka, Yukiko; Hase, Takeshi; Kulkarni, Priya; Siddiqui, Kenaz; Kodilkar, Janhavi; Danve, Nitisha; Subramanian, Indhupriya; Katoh, Manami; Shimizu-Yoshida, Yuki; Ghosh, Samik; Jere, Abhay; Kitano, Hiroaki

2016-01-01

Cellular stress responses require exquisite coordination between intracellular signaling molecules to integrate multiple stimuli and actuate specific cellular behaviors. Deciphering the web of complex interactions underlying stress responses is a key challenge in understanding robust biological systems and has the potential to lead to the discovery of targeted therapeutics for diseases triggered by dysregulation of stress response pathways. We constructed large-scale molecular interaction maps of six major stress response pathways in Saccharomyces cerevisiae (baker’s or budding yeast). Biological findings from over 900 publications were converted into standardized graphical formats and integrated into a common framework. The maps are posted at http://www.yeast-maps.org/yeast-stress-response/ for browse and curation by the research community. On the basis of these maps, we undertook systematic analyses to unravel the underlying architecture of the networks. A series of network analyses revealed that yeast stress response pathways are organized in bow–tie structures, which have been proposed as universal sub-systems for robust biological regulation. Furthermore, we demonstrated a potential role for complexes in stabilizing the conserved core molecules of bow–tie structures. Specifically, complex-mediated reversible reactions, identified by network motif analyses, appeared to have an important role in buffering the concentration and activity of these core molecules. We propose complex-mediated reactions as a key mechanism mediating robust regulation of the yeast stress response. Thus, our comprehensive molecular interaction maps provide not only an integrated knowledge base, but also a platform for systematic network analyses to elucidate the underlying architecture in complex biological systems. PMID:28725465

Mapping Sub-Antarctic Cushion Plants Using Random Forests to Combine Very High Resolution Satellite Imagery and Terrain Modelling

PubMed Central

Bricher, Phillippa K.; Lucieer, Arko; Shaw, Justine; Terauds, Aleks; Bergstrom, Dana M.

2013-01-01

Monitoring changes in the distribution and density of plant species often requires accurate and high-resolution baseline maps of those species. Detecting such change at the landscape scale is often problematic, particularly in remote areas. We examine a new technique to improve accuracy and objectivity in mapping vegetation, combining species distribution modelling and satellite image classification on a remote sub-Antarctic island. In this study, we combine spectral data from very high resolution WorldView-2 satellite imagery and terrain variables from a high resolution digital elevation model to improve mapping accuracy, in both pixel- and object-based classifications. Random forest classification was used to explore the effectiveness of these approaches on mapping the distribution of the critically endangered cushion plant Azorella macquariensis Orchard (Apiaceae) on sub-Antarctic Macquarie Island. Both pixel- and object-based classifications of the distribution of Azorella achieved very high overall validation accuracies (91.6–96.3%, κ = 0.849–0.924). Both two-class and three-class classifications were able to accurately and consistently identify the areas where Azorella was absent, indicating that these maps provide a suitable baseline for monitoring expected change in the distribution of the cushion plants. Detecting such change is critical given the threats this species is currently facing under altering environmental conditions. The method presented here has applications to monitoring a range of species, particularly in remote and isolated environments. PMID:23940805

Sub-Chronic Neuropathological and Biochemical Changes in Mouse Visual System after Repetitive Mild Traumatic Brain Injury

PubMed Central

Tzekov, Radouil; Dawson, Clint; Orlando, Megan; Mouzon, Benoit; Reed, Jon; Evans, James; Crynen, Gogce; Mullan, Michael; Crawford, Fiona

2016-01-01

Repetitive mild traumatic brain injury (r-mTBI) results in neuropathological and biochemical consequences in the human visual system. Using a recently developed mouse model of r-mTBI, with control mice receiving repetitive anesthesia alone (r-sham) we assessed the effects on the retina and optic nerve using histology, immunohistochemistry, proteomic and lipidomic analyses at 3 weeks post injury. Retina tissue was used to determine retinal ganglion cell (RGC) number, while optic nerve tissue was examined for cellularity, myelin content, protein and lipid changes. Increased cellularity and areas of demyelination were clearly detectable in optic nerves in r-mTBI, but not in r-sham. These changes were accompanied by a ~25% decrease in the total number of Brn3a-positive RGCs. Proteomic analysis of the optic nerves demonstrated various changes consistent with a negative effect of r-mTBI on major cellular processes like depolymerization of microtubules, disassembly of filaments and loss of neurons, manifested by decrease of several proteins, including neurofilaments (NEFH, NEFM, NEFL), tubulin (TUBB2A, TUBA4A), microtubule-associated proteins (MAP1A, MAP1B), collagen (COL6A1, COL6A3) and increased expression of other proteins, including heat shock proteins (HSP90B1, HSPB1), APOE and cathepsin D. Lipidomic analysis showed quantitative changes in a number of phospholipid species, including a significant increase in the total amount of lysophosphatidylcholine (LPC), including the molecular species 16:0, a known demyelinating agent. The overall amount of some ether phospholipids, like ether LPC, ether phosphatidylcholine and ether lysophosphatidylethanolamine were also increased, while the majority of individual molecular species of ester phospholipids, like phosphatidylcholine and phosphatidylethanolamine, were decreased. Results from the biochemical analysis correlate well with changes detected by histological and immunohistochemical methods and indicate the involvement of several important molecular pathways. This will allow future identification of therapeutic targets for improving the visual consequences of r-mTBI. PMID:27088355

Probing the cellular damage in bacteria induced by GaN nanoparticles using confocal laser Raman spectroscopy

NASA Astrophysics Data System (ADS)

Sahoo, Prasana; Murthy, P. Sriyutha; Dhara, S.; Venugopalan, V. P.; Das, A.; Tyagi, A. K.

2013-08-01

Understanding the mechanism of nanoparticle (NP) induced toxicity in microbes is of potential importance to a variety of disciplines including disease diagnostics, biomedical implants, and environmental analysis. In this context, toxicity to bacterial cells and inhibition of biofilm formation by GaN NPs and their functional derivatives have been investigated against gram positive and gram negative bacterial species down to single cellular level. High levels of inhibition of biofilm formation (>80 %) was observed on treatments with GaN NPs at sub-micro molar concentrations. These results were substantiated with morphological features investigated with field emission scanning electron microscope, and the observed changes in vibrational modes of microbial cells using Raman spectroscopy. Raman spectra provided molecular interpretation of cell damage by registering signatures of molecular vibrations of individual living microbial cells and mapping the interplay of proteins at the cell membrane. As compared to the untreated cells, Raman spectra of NP-treated cells showed an increase in the intensities of characteristic protein bands, which confirmed membrane damage and subsequent release of cellular contents outside the cells. Raman spectral mapping at single cellular level can facilitate understanding of the mechanistic aspect of toxicity of GaN NPs. The effect may be correlated to passive diffusion causing mechanical damage to the membrane or ingress of Ga3+ (ionic radius 0.076 nm) which can potentially interfere with bacterial metabolism, as it resembles Fe2+ (ionic radius 0.077 nm), which is essential for energy metabolism.

High-resolution x-ray absorption spectroscopy studies of metal compounds in neurodegenerative brain tissue

NASA Astrophysics Data System (ADS)

Collingwood, J. F.; Mikhaylova, A.; Davidson, M. R.; Batich, C.; Streit, W. J.; Eskin, T.; Terry, J.; Barrea, R.; Underhill, R. S.; Dobson, J.

2005-01-01

Fluorescence mapping and microfocus X-ray absorption spectroscopy are used to detect, locate and identify iron biominerals and other inorganic metal accumulations in neurodegenerative brain tissue at sub-cellular resolution (<5 microns). Recent progress in developing the technique is reviewed. Synchrotron X-rays are used to map tissue sections for metals of interest, and XANES and XAFS are used to characterise anomalous concentrations of the metals in-situ so that they can be correlated with tissue structures and disease pathology. Iron anomalies associated with biogenic magnetite, ferritin and haemoglobin are located and identified in an avian tissue model with a pixel resolution ~5 microns. Subsequent studies include brain tissue sections from transgenic Huntington's mice, and the first high-resolution mapping and identification of iron biominerals in human Alzheimer's and control autopsy brain tissue. Technical developments include use of microfocus diffraction to obtain structural information about biominerals in-situ, and depositing sample location grids by lithography for the location of anomalies by conventional microscopy. The combined techniques provide a breakthrough in the study of both intra- and extra-cellular iron compounds and related metals in tissue. The information to be gained from this approach has implications for future diagnosis and treatment of neurodegeneration, and for our understanding of the mechanisms involved.

A grid matrix-based Raman spectroscopic method to characterize different cell milieu in biopsied axillary sentinel lymph nodes of breast cancer patients.

PubMed

Som, Dipasree; Tak, Megha; Setia, Mohit; Patil, Asawari; Sengupta, Amit; Chilakapati, C Murali Krishna; Srivastava, Anurag; Parmar, Vani; Nair, Nita; Sarin, Rajiv; Badwe, R

2016-01-01

Raman spectroscopy which is based upon inelastic scattering of photons has a potential to emerge as a noninvasive bedside in vivo or ex vivo molecular diagnostic tool. There is a need to improve the sensitivity and predictability of Raman spectroscopy. We developed a grid matrix-based tissue mapping protocol to acquire cellular-specific spectra that also involved digital microscopy for localizing malignant and lymphocytic cells in sentinel lymph node biopsy sample. Biosignals acquired from specific cellular milieu were subjected to an advanced supervised analytical method, i.e., cross-correlation and peak-to-peak ratio in addition to PCA and PC-LDA. We observed decreased spectral intensity as well as shift in the spectral peaks of amides and lipid bands in the completely metastatic (cancer cells) lymph nodes with high cellular density. Spectral library of normal lymphocytes and metastatic cancer cells created using the cellular specific mapping technique can be utilized to create an automated smart diagnostic tool for bench side screening of sampled lymph nodes. Spectral library of normal lymphocytes and metastatic cancer cells created using the cellular specific mapping technique can be utilized to develop an automated smart diagnostic tool for bench side screening of sampled lymph nodes supported by ongoing global research in developing better technology and signal and big data processing algorithms.

Exploration of cellular reaction systems.

PubMed

Kirkilionis, Markus

2010-01-01

We discuss and review different ways to map cellular components and their temporal interaction with other such components to different non-spatially explicit mathematical models. The essential choices made in the literature are between discrete and continuous state spaces, between rule and event-based state updates and between deterministic and stochastic series of such updates. The temporal modelling of cellular regulatory networks (dynamic network theory) is compared with static network approaches in two first introductory sections on general network modelling. We concentrate next on deterministic rate-based dynamic regulatory networks and their derivation. In the derivation, we include methods from multiscale analysis and also look at structured large particles, here called macromolecular machines. It is clear that mass-action systems and their derivatives, i.e. networks based on enzyme kinetics, play the most dominant role in the literature. The tools to analyse cellular reaction networks are without doubt most complete for mass-action systems. We devote a long section at the end of the review to make a comprehensive review of related tools and mathematical methods. The emphasis is to show how cellular reaction networks can be analysed with the help of different associated graphs and the dissection into modules, i.e. sub-networks.

In vivo observation of transient photoreceptor movement correlated with oblique light stimulation

NASA Astrophysics Data System (ADS)

Lu, Yiming; Liu, Changgeng; Yao, Xincheng

2018-02-01

Rod-dominated transient retinal phototropism (TRP) has been observed in freshly isolated retinas, promising a noninvasive biomarker for high resolution assessment of retinal physiology. However, in vivo mapping of TRP is challenging due to its fast time course and sub-cellular signal magnitude. By developing a line-scanning and virtually structured detection based super-resolution ophthalmoscope, we report here in vivo observation of TRP in frog retina. In vivo characterization of TRP time course and magnitude were implemented by using variable light stimulus intensities.

A graphene-based physiometer array for the analysis of single biological cells

NASA Astrophysics Data System (ADS)

Paulus, Geraldine L. C.; Nelson, Justin T.; Lee, Katherine Y.; Wang, Qing Hua; Reuel, Nigel F.; Grassbaugh, Brittany R.; Kruss, Sebastian; Landry, Markita P.; Kang, Jeon Woong; Vander Ende, Emma; Zhang, Jingqing; Mu, Bin; Dasari, Ramachandra R.; Opel, Cary F.; Wittrup, K. Dane; Strano, Michael S.

2014-10-01

A significant advantage of a graphene biosensor is that it inherently represents a continuum of independent and aligned sensor-units. We demonstrate a nanoscale version of a micro-physiometer - a device that measures cellular metabolic activity from the local acidification rate. Graphene functions as a matrix of independent pH sensors enabling subcellular detection of proton excretion. Raman spectroscopy shows that aqueous protons p-dope graphene - in agreement with established doping trajectories, and that graphene displays two distinct pKa values (2.9 and 14.2), corresponding to dopants physi- and chemisorbing to graphene respectively. The graphene physiometer allows micron spatial resolution and can differentiate immunoglobulin (IgG)-producing human embryonic kidney (HEK) cells from non-IgG-producing control cells. Population-based analyses allow mapping of phenotypic diversity, variances in metabolic activity, and cellular adhesion. Finally we show this platform can be extended to the detection of other analytes, e.g. dopamine. This work motivates the application of graphene as a unique biosensor for (sub)cellular interrogation.

Mapping the dynamics of force transduction at cell–cell junctions of epithelial clusters

PubMed Central

Ng, Mei Rosa; Besser, Achim; Brugge, Joan S; Danuser, Gaudenz

2014-01-01

Force transduction at cell-cell adhesions regulates tissue development, maintenance and adaptation. We developed computational and experimental approaches to quantify, with both sub-cellular and multi-cellular resolution, the dynamics of force transmission in cell clusters. Applying this technology to spontaneously-forming adherent epithelial cell clusters, we found that basal force fluctuations were coupled to E-cadherin localization at the level of individual cell-cell junctions. At the multi-cellular scale, cell-cell force exchange depended on the cell position within a cluster, and was adaptive to reconfigurations due to cell divisions or positional rearrangements. Importantly, force transmission through a cell required coordinated modulation of cell-matrix adhesion and actomyosin contractility in the cell and its neighbors. These data provide insights into mechanisms that could control mechanical stress homeostasis in dynamic epithelial tissues, and highlight our methods as a resource for the study of mechanotransduction in cell-cell adhesions. DOI: http://dx.doi.org/10.7554/eLife.03282.001 PMID:25479385

A versatile clearing agent for multi-modal brain imaging

PubMed Central

Costantini, Irene; Ghobril, Jean-Pierre; Di Giovanna, Antonino Paolo; Mascaro, Anna Letizia Allegra; Silvestri, Ludovico; Müllenbroich, Marie Caroline; Onofri, Leonardo; Conti, Valerio; Vanzi, Francesco; Sacconi, Leonardo; Guerrini, Renzo; Markram, Henry; Iannello, Giulio; Pavone, Francesco Saverio

2015-01-01

Extensive mapping of neuronal connections in the central nervous system requires high-throughput µm-scale imaging of large volumes. In recent years, different approaches have been developed to overcome the limitations due to tissue light scattering. These methods are generally developed to improve the performance of a specific imaging modality, thus limiting comprehensive neuroanatomical exploration by multi-modal optical techniques. Here, we introduce a versatile brain clearing agent (2,2′-thiodiethanol; TDE) suitable for various applications and imaging techniques. TDE is cost-efficient, water-soluble and low-viscous and, more importantly, it preserves fluorescence, is compatible with immunostaining and does not cause deformations at sub-cellular level. We demonstrate the effectiveness of this method in different applications: in fixed samples by imaging a whole mouse hippocampus with serial two-photon tomography; in combination with CLARITY by reconstructing an entire mouse brain with light sheet microscopy and in translational research by imaging immunostained human dysplastic brain tissue. PMID:25950610

FRET-based genetically-encoded sensors for quantitative monitoring of metabolites.

PubMed

Mohsin, Mohd; Ahmad, Altaf; Iqbal, Muhammad

2015-10-01

Neighboring cells in the same tissue can exist in different states of dynamic activities. After genomics, proteomics and metabolomics, fluxomics is now equally important for generating accurate quantitative information on the cellular and sub-cellular dynamics of ions and metabolite, which is critical for functional understanding of organisms. Various spectrometry techniques are used for monitoring ions and metabolites, although their temporal and spatial resolutions are limited. Discovery of the fluorescent proteins and their variants has revolutionized cell biology. Therefore, novel tools and methods targeting sub-cellular compartments need to be deployed in specific cells and targeted to sub-cellular compartments in order to quantify the target-molecule dynamics directly. We require tools that can measure cellular activities and protein dynamics with sub-cellular resolution. Biosensors based on fluorescence resonance energy transfer (FRET) are genetically encoded and hence can specifically target sub-cellular organelles by fusion to proteins or targetted sequences. Since last decade, FRET-based genetically encoded sensors for molecules involved in energy production, reactive oxygen species and secondary messengers have helped to unravel key aspects of cellular physiology. This review, describing the design and principles of sensors, presents a database of sensors for different analytes/processes, and illustrate examples of application in quantitative live cell imaging.

Nanometer scale thermometry in a living cell

PubMed Central

Kucsko, G.; Maurer, P. C.; Yao, N. Y.; Kubo, M.; Noh, H. J.; Lo, P. K.; Park, H.; Lukin, M. D.

2014-01-01

Sensitive probing of temperature variations on nanometer scales represents an outstanding challenge in many areas of modern science and technology1. In particular, a thermometer capable of sub-degree temperature resolution over a large range of temperatures as well as integration within a living system could provide a powerful new tool for many areas of biological, physical and chemical research; possibilities range from the temperature-induced control of gene expression2–5 and tumor metabolism6 to the cell-selective treatment of disease7,8 and the study of heat dissipation in integrated circuits1. By combining local light-induced heat sources with sensitive nanoscale thermometry, it may also be possible to engineer biological processes at the sub-cellular level2–5. Here, we demonstrate a new approach to nanoscale thermometry that utilizes coherent manipulation of the electronic spin associated with nitrogen-vacancy (NV) color centers in diamond. We show the ability to detect temperature variations down to 1.8 mK (sensitivity of 9mK/Hz) in an ultra-pure bulk diamond sample. Using NV centers in diamond nanocrystals (nanodiamonds, NDs), we directly measure the local thermal environment at length scales down to 200 nm. Finally, by introducing both nanodiamonds and gold nanoparticles into a single human embryonic fibroblast, we demonstrate temperature-gradient control and mapping at the sub-cellular level, enabling unique potential applications in life sciences. PMID:23903748

Isolating specific cell and tissue compartments from 3D images for quantitative regional distribution analysis using novel computer algorithms.

PubMed

Fenrich, Keith K; Zhao, Ethan Y; Wei, Yuan; Garg, Anirudh; Rose, P Ken

2014-04-15

Isolating specific cellular and tissue compartments from 3D image stacks for quantitative distribution analysis is crucial for understanding cellular and tissue physiology under normal and pathological conditions. Current approaches are limited because they are designed to map the distributions of synapses onto the dendrites of stained neurons and/or require specific proprietary software packages for their implementation. To overcome these obstacles, we developed algorithms to Grow and Shrink Volumes of Interest (GSVI) to isolate specific cellular and tissue compartments from 3D image stacks for quantitative analysis and incorporated these algorithms into a user-friendly computer program that is open source and downloadable at no cost. The GSVI algorithm was used to isolate perivascular regions in the cortex of live animals and cell membrane regions of stained spinal motoneurons in histological sections. We tracked the real-time, intravital biodistribution of injected fluorophores with sub-cellular resolution from the vascular lumen to the perivascular and parenchymal space following a vascular microlesion, and mapped the precise distributions of membrane-associated KCC2 and gephyrin immunolabeling in dendritic and somatic regions of spinal motoneurons. Compared to existing approaches, the GSVI approach is specifically designed for isolating perivascular regions and membrane-associated regions for quantitative analysis, is user-friendly, and free. The GSVI algorithm is useful to quantify regional differences of stained biomarkers (e.g., cell membrane-associated channels) in relation to cell functions, and the effects of therapeutic strategies on the redistributions of biomolecules, drugs, and cells in diseased or injured tissues. Copyright © 2014 Elsevier B.V. All rights reserved.

Generic framework for mining cellular automata models on protein-folding simulations.

PubMed

Diaz, N; Tischer, I

2016-05-13

Cellular automata model identification is an important way of building simplified simulation models. In this study, we describe a generic architectural framework to ease the development process of new metaheuristic-based algorithms for cellular automata model identification in protein-folding trajectories. Our framework was developed by a methodology based on design patterns that allow an improved experience for new algorithms development. The usefulness of the proposed framework is demonstrated by the implementation of four algorithms, able to obtain extremely precise cellular automata models of the protein-folding process with a protein contact map representation. Dynamic rules obtained by the proposed approach are discussed, and future use for the new tool is outlined.

Mapped Landmark Algorithm for Precision Landing

NASA Technical Reports Server (NTRS)

Johnson, Andrew; Ansar, Adnan; Matthies, Larry

2007-01-01

A report discusses a computer vision algorithm for position estimation to enable precision landing during planetary descent. The Descent Image Motion Estimation System for the Mars Exploration Rovers has been used as a starting point for creating code for precision, terrain-relative navigation during planetary landing. The algorithm is designed to be general because it handles images taken at different scales and resolutions relative to the map, and can produce mapped landmark matches for any planetary terrain of sufficient texture. These matches provide a measurement of horizontal position relative to a known landing site specified on the surface map. Multiple mapped landmarks generated per image allow for automatic detection and elimination of bad matches. Attitude and position can be generated from each image; this image-based attitude measurement can be used by the onboard navigation filter to improve the attitude estimate, which will improve the position estimates. The algorithm uses normalized correlation of grayscale images, producing precise, sub-pixel images. The algorithm has been broken into two sub-algorithms: (1) FFT Map Matching (see figure), which matches a single large template by correlation in the frequency domain, and (2) Mapped Landmark Refinement, which matches many small templates by correlation in the spatial domain. Each relies on feature selection, the homography transform, and 3D image correlation. The algorithm is implemented in C++ and is rated at Technology Readiness Level (TRL) 4.

Mapping mHealth (mobile health) and mobile penetrations in sub-Saharan Africa for strategic regional collaboration in mHealth scale-up: an application of exploratory spatial data analysis.

PubMed

Lee, Seohyun; Cho, Yoon-Min; Kim, Sun-Young

2017-08-22

Mobile health (mHealth), a term used for healthcare delivery via mobile devices, has gained attention as an innovative technology for better access to healthcare and support for performance of health workers in the global health context. Despite large expansion of mHealth across sub-Saharan Africa, regional collaboration for scale-up has not made progress since last decade. As a groundwork for strategic planning for regional collaboration, the study attempted to identify spatial patterns of mHealth implementation in sub-Saharan Africa using an exploratory spatial data analysis. In order to obtain comprehensive data on the total number of mHelath programs implemented between 2006 and 2016 in each of the 48 sub-Saharan Africa countries, we performed a systematic data collection from various sources, including: the WHO eHealth Database, the World Bank Projects & Operations Database, and the USAID mHealth Database. Additional spatial analysis was performed for mobile cellular subscriptions per 100 people to suggest strategic regional collaboration for improving mobile penetration rates along with the mHealth initiative. Global Moran's I and Local Indicator of Spatial Association (LISA) were calculated for mHealth programs and mobile subscriptions per 100 population to investigate spatial autocorrelation, which indicates the presence of local clustering and spatial disparities. From our systematic data collection, the total number of mHealth programs implemented in sub-Saharan Africa between 2006 and 2016 was 487 (same programs implemented in multiple countries were counted separately). Of these, the eastern region with 17 countries and the western region with 16 countries had 287 and 145 mHealth programs, respectively. Despite low levels of global autocorrelation, LISA enabled us to detect meaningful local clusters. Overall, the eastern part of sub-Saharan Africa shows high-high association for mHealth programs. As for mobile subscription rates per 100 population, the northern area shows extensive low-low association. This study aimed to shed some light on the potential for strategic regional collaboration for scale-up of mHealth and mobile penetration. Firstly, countries in the eastern area with much experience can take the lead role in pursuing regional collaboration for mHealth programs in sub-Saharan Africa. Secondly, collective effort in improving mobile penetration rates for the northern area is recommended.

Anaerobic sludge digestion with a biocatalytic additive. [Lactobacillus acidophilus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, S.; Henry, M.P.; Fedde, P.A.

1982-01-01

Aimed at improving the process operating characteristics of anaerobic digestion for sludge stabilization and SNG production, this study evaluates the effects of a lactobacillus additive under normal, variable, and overload conditions. This whey fermentation product of an acid-tolerant strain of L. acidophilus fortified with CoCO/sub 3/, (NH/sub 4/)/sub 2/HPO/sub 4/, ferrous lactate, and lactic acid provides growth factors, metabolic intermediates, and enzymes needed for substrate degradation and cellular synthesis. Data indicate that the biochemical additive increases methane yield, gas production rate, and volatile solids reduction; decreases volatile acids accumulation; enhances the digester buffer capacity; and improves the fertilizer value andmore » dewatering characteristics of the digested residue. Digester capacities could be potentially doubled when the feed is so treated. Results of field tests with six full-scale digesters confirm observations made with bench-scale digesters.« less

Dynamic positional fate map of the primary heart-forming region.

PubMed

Cui, Cheng; Cheuvront, Tracey J; Lansford, Rusty D; Moreno-Rodriguez, Ricardo A; Schultheiss, Thomas M; Rongish, Brenda J

2009-08-15

Here we show the temporal-spatial orchestration of early heart morphogenesis at cellular level resolution, in vivo, and reconcile conflicting positional fate mapping data regarding the primary heart-forming field(s). We determined the positional fates of precardiac cells using a precision electroporation approach in combination with wide-field time-lapse microscopy in the quail embryo, a warm-blooded vertebrate (HH Stages 4 through 10). Contrary to previous studies, the results demonstrate the existence of a "continuous" circle-shaped heart field that spans the midline, appearing at HH Stage 4, which then expands to form a wide arc of progenitors at HH Stages 5-7. Our time-resolved image data show that a subset of these cardiac progenitor cells do not overlap with the expression of common cardiogenic factors, Nkx-2.5 and Bmp-2, until HH Stage 10, when a tubular heart has formed, calling into question when cardiac fate is specified and by which key factors. Sub-groups and anatomical bands (cohorts) of heart precursor cells dramatically change their relative positions in a process largely driven by endodermal folding and other large-scale tissue deformations. Thus, our novel dynamic positional fate maps resolve the origin of cardiac progenitor cells in amniotes. The data also establish the concept that tissue motion contributes significantly to cellular position fate - i.e., much of the cellular displacement that occurs during assembly of a midline heart tube (HH Stage 9) is NOT due to "migration" (autonomous motility), a commonly held belief. Computational analysis of our time-resolved data lays the foundation for more precise analyses of how cardiac gene regulatory networks correlate with early heart tissue morphogenesis in birds and mammals.

Thorough statistical comparison of machine learning regression models and their ensembles for sub-pixel imperviousness and imperviousness change mapping

NASA Astrophysics Data System (ADS)

Drzewiecki, Wojciech

2017-12-01

We evaluated the performance of nine machine learning regression algorithms and their ensembles for sub-pixel estimation of impervious areas coverages from Landsat imagery. The accuracy of imperviousness mapping in individual time points was assessed based on RMSE, MAE and R2. These measures were also used for the assessment of imperviousness change intensity estimations. The applicability for detection of relevant changes in impervious areas coverages at sub-pixel level was evaluated using overall accuracy, F-measure and ROC Area Under Curve. The results proved that Cubist algorithm may be advised for Landsat-based mapping of imperviousness for single dates. Stochastic gradient boosting of regression trees (GBM) may be also considered for this purpose. However, Random Forest algorithm is endorsed for both imperviousness change detection and mapping of its intensity. In all applications the heterogeneous model ensembles performed at least as well as the best individual models or better. They may be recommended for improving the quality of sub-pixel imperviousness and imperviousness change mapping. The study revealed also limitations of the investigated methodology for detection of subtle changes of imperviousness inside the pixel. None of the tested approaches was able to reliably classify changed and non-changed pixels if the relevant change threshold was set as one or three percent. Also for fi ve percent change threshold most of algorithms did not ensure that the accuracy of change map is higher than the accuracy of random classifi er. For the threshold of relevant change set as ten percent all approaches performed satisfactory.

Movies of cellular and sub-cellular motion by digital holographic microscopy.

PubMed

Mann, Christopher J; Yu, Lingfeng; Kim, Myung K

2006-03-23

Many biological specimens, such as living cells and their intracellular components, often exhibit very little amplitude contrast, making it difficult for conventional bright field microscopes to distinguish them from their surroundings. To overcome this problem phase contrast techniques such as Zernike, Normarsky and dark-field microscopies have been developed to improve specimen visibility without chemically or physically altering them by the process of staining. These techniques have proven to be invaluable tools for studying living cells and furthering scientific understanding of fundamental cellular processes such as mitosis. However a drawback of these techniques is that direct quantitative phase imaging is not possible. Quantitative phase imaging is important because it enables determination of either the refractive index or optical thickness variations from the measured optical path length with sub-wavelength accuracy. Digital holography is an emergent phase contrast technique that offers an excellent approach in obtaining both qualitative and quantitative phase information from the hologram. A CCD camera is used to record a hologram onto a computer and numerical methods are subsequently applied to reconstruct the hologram to enable direct access to both phase and amplitude information. Another attractive feature of digital holography is the ability to focus on multiple focal planes from a single hologram, emulating the focusing control of a conventional microscope. A modified Mach-Zender off-axis setup in transmission is used to record and reconstruct a number of holographic amplitude and phase images of cellular and sub-cellular features. Both cellular and sub-cellular features are imaged with sub-micron, diffraction-limited resolution. Movies of holographic amplitude and phase images of living microbes and cells are created from a series of holograms and reconstructed with numerically adjustable focus, so that the moving object can be accurately tracked with a reconstruction rate of 300ms for each hologram. The holographic movies show paramecium swimming among other microbes as well as displaying some of their intracellular processes. A time lapse movie is also shown for fibroblast cells in the process of migration. Digital holography and movies of digital holography are seen to be useful new tools for visualization of dynamic processes in biological microscopy. Phase imaging digital holography is a promising technique in terms of the lack of coherent noise and the precision with which the optical thickness of a sample can be profiled, which can lead to images with an axial resolution of a few nanometres.

Integration of logistic regression, Markov chain and cellular automata models to simulate urban expansion

NASA Astrophysics Data System (ADS)

Jokar Arsanjani, Jamal; Helbich, Marco; Kainz, Wolfgang; Darvishi Boloorani, Ali

2013-04-01

This research analyses the suburban expansion in the metropolitan area of Tehran, Iran. A hybrid model consisting of logistic regression model, Markov chain (MC), and cellular automata (CA) was designed to improve the performance of the standard logistic regression model. Environmental and socio-economic variables dealing with urban sprawl were operationalised to create a probability surface of spatiotemporal states of built-up land use for the years 2006, 2016, and 2026. For validation, the model was evaluated by means of relative operating characteristic values for different sets of variables. The approach was calibrated for 2006 by cross comparing of actual and simulated land use maps. The achieved outcomes represent a match of 89% between simulated and actual maps of 2006, which was satisfactory to approve the calibration process. Thereafter, the calibrated hybrid approach was implemented for forthcoming years. Finally, future land use maps for 2016 and 2026 were predicted by means of this hybrid approach. The simulated maps illustrate a new wave of suburban development in the vicinity of Tehran at the western border of the metropolis during the next decades.

Exploring the protective effects of calcium-containing carrier against drying-induced cellular injuries of probiotics using single droplet drying technique.

PubMed

Zheng, Xufeng; Fu, Nan; Huang, Song; Jeantet, Romain; Chen, Xiao Dong

2016-12-01

Protective carriers that encapsulate probiotics in spray drying could improve the survival ratio of dried cells through different mechanisms. Unveiling the protective mechanism of each carrier will contribute to a rational design of high performance carrier formulation. This study utilized single droplet drying (SDD) technique to investigate the effects of calcium cation in varied carrier formulation. Inactivation histories of Lactobacillus rhamnosus GG (LGG) in different carriers were compared, and cellular injury history of probiotics during droplet drying was studied for the first time. Adding 1mM CaCl 2 to lactose carrier protected cell viability, mitigated cellular injuries, and enhanced regrowth capability as drying progressed, demonstrating the positive effect of Ca 2+ with possible mechanism of stabilizing sub-cellular structures. At later drying stages, cell survival in Lac/Ca carrier was increased by 0.5-1.5 log on selective media compared to lactose carrier. Supplementing calcium-binding agents lowered the protective effect, shortening the initiation of rapid cell inactivation down to 120s of drying. Adding CaCl 2 to trehalose carrier barely improved cell survival, indicating that the protective effect could be influenced by carrier formulation. Pure trehalose carrier exerted excellent protection on LGG, supporting cells to regrow in liquid rich medium even after 180s of drying. The protection of trehalose may stem from stabilization of sub-cellular structures, which possibly overlap the effect of Ca 2+ . The findings suggested that high performance carrier formulation might be developed by combining carrier materials with different protective mechanisms, for maximizing the survival of active dry probiotics in industrial spray drying operation. Copyright © 2016 Elsevier Ltd. All rights reserved.

A graphene-based physiometer array for the analysis of single biological cells

PubMed Central

Paulus, Geraldine L. C.; Nelson, Justin T.; Lee, Katherine Y.; Wang, Qing Hua; Reuel, Nigel F.; Grassbaugh, Brittany R.; Kruss, Sebastian; Landry, Markita P.; Kang, Jeon Woong; Vander Ende, Emma; Zhang, Jingqing; Mu, Bin; Dasari, Ramachandra R.; Opel, Cary F.; Wittrup, K. Dane; Strano, Michael S.

2014-01-01

A significant advantage of a graphene biosensor is that it inherently represents a continuum of independent and aligned sensor-units. We demonstrate a nanoscale version of a micro-physiometer – a device that measures cellular metabolic activity from the local acidification rate. Graphene functions as a matrix of independent pH sensors enabling subcellular detection of proton excretion. Raman spectroscopy shows that aqueous protons p-dope graphene – in agreement with established doping trajectories, and that graphene displays two distinct pKa values (2.9 and 14.2), corresponding to dopants physi- and chemisorbing to graphene respectively. The graphene physiometer allows micron spatial resolution and can differentiate immunoglobulin (IgG)-producing human embryonic kidney (HEK) cells from non-IgG-producing control cells. Population-based analyses allow mapping of phenotypic diversity, variances in metabolic activity, and cellular adhesion. Finally we show this platform can be extended to the detection of other analytes, e.g. dopamine. This work motivates the application of graphene as a unique biosensor for (sub)cellular interrogation. PMID:25359450

Cellular reflectarray antenna and method of making same

NASA Technical Reports Server (NTRS)

Romanofsky, Robert R (Inventor)

2011-01-01

A method of manufacturing a cellular reflectarray antenna arranged in an m by n matrix of radiating elements for communication with a satellite includes steps of determining a delay .phi.m,n for each of said m by n matrix of elements of said cellular reflectarray antenna using sub-steps of: determining the longitude and latitude of operation, determining elevation and azimuth angles of the reflectarray with respect to the satellite and converting theta.sub.0 (.theta..sub.0) and phi.sub.0 (.phi..sub.0), determining .DELTA..beta..sub.m,n, the pointing vector correction, for a given inter-element spacing and wavelength, determining .DELTA..phi..sub.m,n, the spherical wave front correction factor, for a given radius from the central element and/or from measured data from the feed horn; and, determining a delay .phi.m,n for each of said m by n matrix of elements as a function of .DELTA..beta..sub.m,n and .DELTA..phi..sub.m,n.

Cellular reflectarray antenna and method of making same

NASA Technical Reports Server (NTRS)

Romanofsky, Robert R (Inventor)

2010-01-01

A method of manufacturing a cellular reflectarray antenna arranged in an m by n matrix of radiating elements for communication with a satellite includes steps of determining a delay .phi.m,n for each of said m by n matrix of elements of said cellular reflectarray antenna using sub-steps of: determining the longitude and latitude of operation, determining elevation and azimuth angles of the reflectarray with respect to the satellite and converting theta.sub.0 (.theta..sub.0) and phi.sub.0 (.phi..sub.0), determining .DELTA..beta..sub.m,n, the pointing vector correction, for a given inter-element spacing and wavelength, determining .DELTA..phi..sub.m,n, the spherical wave front correction factor, for a given radius from the central element and/or from measured data from the feed horn; and, determining a delay .phi.m,n for each of said m by n matrix of elements as a function of .DELTA..beta..sub.m,n and .DELTA..phi..sub.m,n..

Lysophosphatidic acid signaling via LPA{sub 1} and LPA{sub 3} regulates cellular functions during tumor progression in pancreatic cancer cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukushima, Kaori; Takahashi, Kaede; Yamasaki, Eri

Lysophosphatidic acid (LPA) signaling via G protein-coupled LPA receptors exhibits a variety of biological effects, such as cell proliferation, motility and differentiation. The aim of this study was to evaluate the roles of LPA{sub 1} and LPA{sub 3} in cellular functions during tumor progression in pancreatic cancer cells. LPA{sub 1} and LPA{sub 3} knockdown cells were generated from PANC-1 cells. The cell motile and invasive activities of PANC-1 cells were inhibited by LPA{sub 1} and LPA{sub 3} knockdown. In gelatin zymography, LPA{sub 1} and LPA{sub 3} knockdown cells indicated the low activation of matrix metalloproteinase-2 (MMP-2) in the presence ofmore » LPA. Next, to assess whether LPA{sub 1} and LPA{sub 3} regulate cellular functions induced by anticancer drug, PANC-1 cells were treated with cisplatin (CDDP) for approximately 6 months. The cell motile and invasive activities of long-term CDDP treated cells were markedly higher than those of PANC-1 cells, correlating with the expression levels of LPAR1 and LPAR3 genes. In soft agar assay, the long-term CDDP treated cells formed markedly large sized colonies. In addition, the cell motile and invasive activities enhanced by CDDP were significantly suppressed by LPA{sub 1} and LPA{sub 3} knockdown as well as colony formation. These results suggest that LPA signaling via LPA{sub 1} and LPA{sub 3} play an important role in the regulation of cellular functions during tumor progression in PANC-1 cells. - Highlights: • The cell motile and invasive activities of PANC-1 cells were stimulated by LPA{sub 1} and LPA{sub 3}. • LPA{sub 1} and LPA{sub 3} enhanced MMP-2 activation in PANC-1 cells. • The expressions of LPAR1 and LPAR3 genes were elevated in PANC-1 cells treated with cisplatin. • The cell motile and invasive activities of PANC-1 cells treated with cisplatin were suppressed by LPA{sub 1} and LPA{sub 3} knockdown. • LPA{sub 1} and LPA{sub 3} are involved in the regulation of cellular functions during tumor progression in PANC-1 cells.« less

Metabolomics for undergraduates: Identification and pathway assignment of mitochondrial metabolites.

PubMed

Marques, Ana Patrícia; Serralheiro, Maria Luisa; Ferreira, António E N; Freire, Ana Ponces; Cordeiro, Carlos; Silva, Marta Sousa

2016-01-01

Metabolomics is a key discipline in systems biology, together with genomics, transcriptomics, and proteomics. In this omics cascade, the metabolome represents the biochemical products that arise from cellular processes and is often regarded as the final response of a biological system to environmental or genetic changes. The overall screening approach to identify all the metabolites in a given biological system is called metabolic fingerprinting. Using high-resolution and high-mass accuracy mass spectrometry, large metabolome coverage, sensitivity, and specificity can be attained. Although the theoretical concepts of this methodology are usually provided in life-science programs, hands-on laboratory experiments are not usually accessible to undergraduate students. Even if the instruments are available, there are not simple laboratory protocols created specifically for teaching metabolomics. We designed a straightforward hands-on laboratory experiment to introduce students to this methodology, relating it to biochemical knowledge through metabolic pathway mapping of the identified metabolites. This study focuses on mitochondrial metabolomics since mitochondria have a well-known, medium-sized cellular sub-metabolome. These features facilitate both data processing and pathway mapping. In this experiment, students isolate mitochondria from potatoes, extract the metabolites, and analyze them by high-resolution mass spectrometry (using an FT-ICR mass spectrometer). The resulting mass list is submitted to an online program for metabolite identification, and compounds associated with mitochondrial pathways can be highlighted in a metabolic network map. © 2015 The International Union of Biochemistry and Molecular Biology.

Antibacterial properties and cytocompatibility of tantalum oxide coatings with different silver content

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Heng-Li; Chang, Yin-Yu, E-mail: yinyu@mail2000.com.tw; Chen, Hung-Jui

Tantalum (Ta) oxides and their coatings have been proved to increase their applications in the biomedical fields by improving osseointegration and wear resistance. In this study, Ta oxide coatings containing different proportions of Ag are deposited on SS304 materials. A twin-gun magnetron sputtering system is used to deposit the tantalum oxide-Ag coating. In this study, Staphylococcus aureus, which exhibits physiological commensalism on the human skin, nares, and mucosal and oral areas, is chosen as the model for in vitro antibacterial analyses via a fluorescence staining method using Syto9. The cytocompatibility and adhesive morphology of human skin fibroblast cells (CCD-966SK) onmore » the coatings are also determined by using the microculture tetrazolium assay. This study shows that Ta{sub 2}O{sub 5} and Ta{sub 2}O{sub 5}-Ag coatings with 12.5 at. % of Ag exhibit improved antibacterial effects against S. aureus and have good skin fibroblast cell cellular biocompatibility.« less

Phase transitions in coupled map lattices and in associated probabilistic cellular automata.

PubMed

Just, Wolfram

2006-10-01

Analytical tools are applied to investigate piecewise linear coupled map lattices in terms of probabilistic cellular automata. The so-called disorder condition of probabilistic cellular automata is closely related with attracting sets in coupled map lattices. The importance of this condition for the suppression of phase transitions is illustrated by spatially one-dimensional systems. Invariant densities and temporal correlations are calculated explicitly. Ising type phase transitions are found for one-dimensional coupled map lattices acting on repelling sets and for a spatially two-dimensional Miller-Huse-like system with stable long time dynamics. Critical exponents are calculated within a finite size scaling approach. The relevance of detailed balance of the resulting probabilistic cellular automaton for the critical behavior is pointed out.

Oceanic tide maps and spherical harmonic coefficients from Geosat altimetry

NASA Technical Reports Server (NTRS)

Cartwright, D. E.; Ray, R. D.; Sanchez, B. V.

1991-01-01

Maps and tables for the global ocean tides, 69 degree N to 68 degree S, derived from two years of Geosat altimetry are presented. Global maps of local and Greenwich admittance of the (altimetric) ocean tide, and maps of amplitude and Greenwich phase lag of the ocean tide are shown for M(sub 2), S(sub 2), N(sub 2), O(sub 1), and K(sub 1). Larger scale maps of amplitude and phases are also shown for regional areas of special interest. Spherical harmonic coefficients of the ocean tide through degree and order 8 are tabulated for the six major constituents.

Care plans using concept maps and their effects on the critical thinking dispositions of nursing students.

PubMed

Atay, Selma; Karabacak, Ukke

2012-06-01

It is expected that nursing education improves abilities of students in solving problems, decision making and critical thinking in different circumstances. This study was performed to analyse the effects of care plans prepared using concept maps on the critical thinking dispositions of students. An experimental group and a control group were made up of a total of 80 freshman and sophomore students from the nursing department of a health school. The study used a pre-test post-test control group design. The critical thinking dispositions of the groups were measured using the California Critical Thinking Disposition Inventory. In addition, the care plans prepared by the experimental group students were evaluated using the criteria for evaluating care plans with concept maps. T-test was used in analysing the data. The results showed that there were no statistically significant differences in the total and sub-scale pre-test scores between the experimental group and control group students. There were also significant differences in the total and sub-scale post-test scores between the experimental group and control group students. There were significant differences between concept map care plan evaluation criteria mean scores of the experimental students. In the light of these findings, it could be argued that the concept mapping strategy improves critical thinking skills of students. © 2012 Blackwell Publishing Asia Pty Ltd.

Microstructural Characterization of a Directionally-Solidified Ni-33 (at. %)Al-31Cr-3Mo Eutectic Alloy as a Function of Withdrawal Rate

NASA Technical Reports Server (NTRS)

Raj, S. V.; Locci, I. E.; Whittenberger, J. D.; Salem, J. A.

2000-01-01

The Ni-33 (at. %)Al-3lCr-3Mo eutectic alloy was directionally-solidified (DS) at different rates, V(sub I), varying between 2.5 to 508 mm/ h. Detailed qualitative and quantitative metallographic and chemical analyses were conducted on the directionally-solidified rods. The microstructures consisted of eutectic colonies with parallel lamellar NiAl/(Cr,Mo) plates for solidification rates at and below 12.7 mm/ h. Cellular eutectic microstructures were observed at higher solidification rates, where the plates exhibited a radial pattern. The microstructures were demonstrated to be fairly uniform throughout a 100 mm length of the DS zone by quantitative metallography. The average cell size, bar-d, decreased with increasing growth rate to a value of 125 microns at 508 mm/ h according to the relation bar-d (microns) approx. = 465 V(sup -0.22, sub I), where V(sub I) is in mm/ h. Both the average NiAl plate thickness, bar-Delta(sub NiAl), and the interlamellar spacing, bar-lambda, were observed to be constant for V(sub I) less than or = 50.8 mm/ h but decreased with increasing growth rate above this value as 0.93 bar-Delta(sub NiAl)(microns) = 61.2 V(sup -0.93, sub I) and bar-lambda (microns) = 47.7 V(sup -0.64, sub I), respectively. The present results are detailed on a microstructural map. Keywords Optical microscopy, microstructure, compounds intermetallic, directional solidification

Cell segmentation in time-lapse fluorescence microscopy with temporally varying sub-cellular fusion protein patterns.

PubMed

Bunyak, Filiz; Palaniappan, Kannappan; Chagin, Vadim; Cardoso, M

2009-01-01

Fluorescently tagged proteins such as GFP-PCNA produce rich dynamically varying textural patterns of foci distributed in the nucleus. This enables the behavioral study of sub-cellular structures during different phases of the cell cycle. The varying punctuate patterns of fluorescence, drastic changes in SNR, shape and position during mitosis and abundance of touching cells, however, require more sophisticated algorithms for reliable automatic cell segmentation and lineage analysis. Since the cell nuclei are non-uniform in appearance, a distribution-based modeling of foreground classes is essential. The recently proposed graph partitioning active contours (GPAC) algorithm supports region descriptors and flexible distance metrics. We extend GPAC for fluorescence-based cell segmentation using regional density functions and dramatically improve its efficiency for segmentation from O(N(4)) to O(N(2)), for an image with N(2) pixels, making it practical and scalable for high throughput microscopy imaging studies.

Scaling of cell size in cellular instabilities of nonpremixed jet flames

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lo Jacono, D.; Monkewitz, P.A.

2007-10-15

Systematic experiments have been undertaken to study the parameter dependence of cellular instability and in particular the scaling of the resulting cell size in CO{sub 2}-diluted H{sub 2}-O{sub 2} jet diffusion flames. Cellular flames are known to arise near the extinction limit when reactant Lewis numbers are relatively low. The Lewis numbers of the investigated near-extinction mixtures, based on the initial mixture strength {phi}{sub m} and ambient conditions, varied in the ranges [1.1-1.3] for oxygen and [0.25-0.29] for hydrogen ({phi}{sub m} is defined here as the fuel-to-oxygen mass ratio, normalized by the stoichiometric ratio). The experiments were carried out bothmore » in an axisymmetric jet (AJ) burner and in a two-dimensional slot burner known as a Wolfhard-Parker (WP) burner with an oxidizer co-flow (mostly 100% O{sub 2}) of fixed low velocity. First, the region of cellular flames adjacent to the extinction limit was characterized in terms of initial H{sub 2} concentration and fuel jet velocity, with all other parameters fixed. Then, the wavelength of the cellular instability, i.e., the cell size, was determined as a function of the fuel jet velocity and the initial mixture strength {phi}{sub m}. For conditions not too close to extinction, this wavelength is found to increase with the square root of the vorticity thickness of the jet shear layer and roughly the 1/5 power of {phi}{sub m}. Very close to extinction, this scaling breaks down and will likely switch to a scaling with the flame thickness, i.e., involving the Damkoehler number. (author)« less

The sub-cellular fate of mercury in the liver of wild mullets (Liza aurata)--Contribution to the understanding of metal-induced cellular toxicity.

PubMed

Araújo, Olinda; Pereira, Patrícia; Cesário, Rute; Pacheco, Mário; Raimundo, Joana

2015-06-15

Mercury is a recognized harmful pollutant in aquatic systems but still little is known about its sub-cellular partitioning in wild fish. Mercury concentrations in liver homogenate (whole organ load) and in six sub-cellular compartments were determined in wild Liza aurata from two areas - contaminated (LAR) and reference. Water and sediment contamination was also assessed. Fish from LAR displayed higher total mercury (tHg) organ load as well as in sub-cellular compartments than those from the reference area, reflecting environmental differences. However, spatial differences in percentage of tHg were only observed for mitochondria (Mit) and lysosomes plus microsomes (Lys+Mic). At LAR, Lys+Mic exhibited higher levels of tHg than the other fractions. Interestingly, tHg in Mit, granules (Gran) and heat-denaturable proteins was linearly correlated with the whole organ. Low tHg concentrations in heat stable proteins and Gran suggests that accumulated levels might be below the physiological threshold to activate those detoxification fractions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Intracellular L-arginine concentration does not determine NO production in endothelial cells: Implications on the 'L-arginine paradox'

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, Soyoung; Mohan, Srinidi; Fung, Ho-Leung, E-mail: hlfung@buffalo.edu

2011-11-04

Highlights: Black-Right-Pointing-Pointer Our findings provide a possible solution to the 'L-arginine paradox'. Black-Right-Pointing-Pointer Extracellular L-arginine concentration is the major determinant of NO production. Black-Right-Pointing-Pointer Cellular L-arginine action is limited by cellular ARG transport, not the K{sub m} of NOS. Black-Right-Pointing-Pointer We explain how L-arginine supplementation can work to increase endothelial function. -- Abstract: We examined the relative contributory roles of extracellular vs. intracellular L-arginine (ARG) toward cellular activation of endothelial nitric oxide synthase (eNOS) in human endothelial cells. EA.hy926 human endothelial cells were incubated with different concentrations of {sup 15}N{sub 4}-ARG, ARG, or L-arginine ethyl ester (ARG-EE) for 2 h.more » To modulate ARG transport, siRNA for ARG transporter (CAT-1) vs. sham siRNA were transfected into cells. ARG transport activity was assessed by cellular fluxes of ARG, {sup 15}N{sub 4}-ARG, dimethylarginines, and L-citrulline by an LC-MS/MS assay. eNOS activity was determined by nitrite/nitrate accumulation, either via a fluorometric assay or by{sup 15}N-nitrite or estimated {sup 15}N{sub 3}-citrulline concentrations when {sup 15}N{sub 4}-ARG was used to challenge the cells. We found that ARG-EE incubation increased cellular ARG concentration but no increase in nitrite/nitrate was observed, while ARG incubation increased both cellular ARG concentration and nitrite accumulation. Cellular nitrite/nitrate production did not correlate with cellular total ARG concentration. Reduced {sup 15}N{sub 4}-ARG cellular uptake in CAT-1 siRNA transfected cells vs. control was accompanied by reduced eNOS activity, as determined by {sup 15}N-nitrite, total nitrite and {sup 15}N{sub 3}-citrulline formation. Our data suggest that extracellular ARG, not intracellular ARG, is the major determinant of NO production in endothelial cells. It is likely that once transported inside the cell, ARG can no longer gain access to the membrane-bound eNOS. These observations indicate that the 'L-arginine paradox' should not consider intracellular ARG concentration as a reference point.« less

The Contribution of Conceptual Change Texts Accompanied by Concept Mapping to Eleventh-Grade Students Understanding of Cellular Respiration Concepts

ERIC Educational Resources Information Center

Al khawaldeh, Salem A.; Al Olaimat, Ali M.

2010-01-01

The present study conducted to investigate the contribution of conceptual change texts, accompanied by concept mapping instruction to eleventh-grade students' understanding of cellular respiration concepts, and their retention of this understanding. Cellular respiration concepts test was developed as a result of examination of related literature…

Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

PubMed

Farré, Jean-Claude; Kramer, Michael; Ideker, Trey; Subramani, Suresh

2017-07-03

Increasingly, various 'omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new 'omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.

Role of Rotors in the Ablative Therapy of Persistent Atrial Fibrillation

PubMed Central

Schricker, Amir A; Zaman, Junaid; Narayan, Sanjiv M

2015-01-01

Atrial fibrillation (AF) ablation is increasingly used to maintain sinus rhythm yet its results are sub-optimal, especially in patients with persistent AF or prior unsuccessful procedures. Attempts at improvement have often targeted substrates that sustain AF after it is triggered, yet those mechanisms are debated. Many studies now challenge the concept that AF is driven by self-sustaining disordered wavelets, showing instead that localised drivers (rotors) may drive disorder via a process known as fibrillatory conduction. Novel mapping using wide-area recordings, physiological filtering and phase analysis demonstrates rotors in human AF. Contact mapping with focal impulse and rotor modulation (FIRM) shows that localised ablation at sources can improve procedural success in many populations on long-term follow up and some newer approaches to rotor mapping are qualitatively similar. This review critically evaluates the data on rotor mapping and ablation, which advances our conceptual understanding of AF and holds the promise of substantially improving ablative outcomes in patients with persistent AF. PMID:26835100

NASA Tech Briefs, January 2010

NASA Technical Reports Server (NTRS)

2010-01-01

Topics covered include: Cryogenic Flow Sensor; Multi-Sensor Mud Detection; Gas Flow Detection System; Mapping Capacitive Coupling Among Pixels in a Sensor Array; Fiber-Based Laser Transmitter for Oxygen A-Band Spectroscopy and Remote Sensing; Low-Profile, Dual-Wavelength, Dual-Polarized Antenna; Time-Separating Heating and Sensor Functions of Thermistors in Precision Thermal Control Applications; Cellular Reflectarray Antenna; A One-Dimensional Synthetic-Aperture Microwave Radiometer; Electrical Switching of Perovskite Thin-Film Resistors; Two-Dimensional Synthetic-Aperture Radiometer; Ethernet-Enabled Power and Communication Module for Embedded Processors; Electrically Variable Resistive Memory Devices; Improved Attachment in a Hybrid Inflatable Pressure Vessel; Electrostatic Separator for Beneficiation of Lunar Soil; Amorphous Rover; Space-Frame Antenna; Gear-Driven Turnbuckle Actuator; In-Situ Focusing Inside a Thermal Vacuum Chamber; Space-Frame Lunar Lander; Wider-Opening Dewar Flasks for Cryogenic Storage; Silicon Oxycarbide Aerogels for High-Temperature Thermal Insulation; Supercapacitor Electrolyte Solvents with Liquid Range Below -80 C; Designs and Materials for Better Coronagraph Occulting Masks; Fuel-Cell-Powered Vehicle with Hybrid Power Management; Fine-Water-Mist Multiple-Orientation-Discharge Fire Extinguisher; Fuel-Cell Water Separator; Turbulence and the Stabilization Principle; Improved Cloud Condensation Nucleus Spectrometer; Better Modeling of Electrostatic Discharge in an Insulator; Sub-Aperture Interferometers; Terahertz Mapping of Microstructure and Thickness Variations; Multiparallel Three-Dimensional Optical Microscopy; Stabilization of Phase of a Sinusoidal Signal Transmitted Over Optical Fiber; Vacuum-Compatible Wideband White Light and Laser Combiner Source System; Optical Tapers as White-Light WGM Resonators; EPR Imaging at a Few Megahertz Using SQUID Detectors; Reducing Field Distortion in Magnetic Resonance Imaging; Fluorogenic Cell-Based Biosensors for Monitoring Microbes; A Constant-Force Resistive Exercise Unit; GUI to Facilitate Research on Biological Damage from Radiation; On-Demand Urine Analyzer; More-Realistic Digital Modeling of a Human Body; and Advanced Liquid-Cooling Garment Using Highly Thermally Conductive Sheets.

Imaging Small-scale Seafloor and Sub-seafloor Tectonic Fabric Using Satellite Altimetry

NASA Astrophysics Data System (ADS)

Sandwell, D. T.; Müller, D.; Matthews, K. J.; Smith, W. H. F.

2017-12-01

Marine gravity anomalies derived from satellite radar altimetry now provide an unprecedented resolution of about 7 km for mapping small-scale seafloor and sub-seafloor tectonic fabric. These gravity maps are improving rapidly because three satellite altimeters are currently collecting data with dense track coverage: (1) CryoSat-2 has routinely collected altimetry data over ice, land, and ocean since July 2010. The satellite has a long 369-day repeat cycle resulting in an average ground track spacing of 3.5 km at the equator. To date it has completed more than 7 geodetic mappings of the ocean surface. (2) The SARAL AltiKa altimeter began a non-repeat orbit phase in July 2016. AltiKa has a new Ka-band instrument with a factor of 2 better range precision than all previous altimeters. (3) Jason-2 was placed in a geodetic orbit starting July 2017. It has lower inclination coverage to provide improved gravity recovery for N-S trending anomalies. These data combined with sparse soundings will provide a dramatic improvement in predicted bathymetry and thus help guide future deep ocean surveys. The most recent global marine gravity anomaly map based on these geodetic mission data with 2-pass retracking for optimal range precision has an accuracy that is 2-4 times better than the maps derived from Geosat and ERS-1. The new data reveal the detailed fabric of fracture zones, previously unmapped, now extinct oceanic microplates in the central Pacific, and fault networks buried beneath thick sediments along continental margins. By combining satellite altimetry with marine magnetic anomalies and seafloor age dates from rock samples we are able to pinpoint the geometry and age of major plate reorganizations, particularly the enigmatic 100 Ma event, which occurred during the Cretaceous Magnetic Superchron.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christopher Liner

The objective of our work is graduate and undergraduate student training related to improved 3D seismic technology that addresses key challenges related to monitoring movement and containment of CO{sub 2}, specifically better quantification and sensitivity for mapping of caprock integrity, fractures, and other potential leakage pathways. We utilize data and results developed through previous DOE-funded CO{sub 2} characterization project (DE-FG26-06NT42734) at the Dickman Field of Ness County, KS. Dickman is a type locality for the geology that will be encountered for CO{sub 2} sequestration projects from northern Oklahoma across the U.S. midcontinent to Indiana and Illinois. Since its discovery inmore » 1962, the Dickman Field has produced about 1.7 million barrels of oil from porous Mississippian carbonates with a small structural closure at about 4400 ft drilling depth. Project data includes 3.3 square miles of 3D seismic data, 142 wells, with log, some core, and oil/water production data available. Only two wells penetrate the deep saline aquifer. In a previous DOE-funded project, geological and seismic data were integrated to create a geological property model and a flow simulation grid. We believe that sequestration of CO{sub 2} will largely occur in areas of relatively flat geology and simple near surface, similar to Dickman. The challenge is not complex geology, but development of improved, lower-cost methods for detecting natural fractures and subtle faults. Our project used numerical simulation to test methods of gathering multicomponent, full azimuth data ideal for this purpose. Our specific objectives were to apply advanced seismic methods to aide in quantifying reservoir properties and lateral continuity of CO{sub 2} sequestration targets. The purpose of the current project is graduate and undergraduate student training related to improved 3D seismic technology that addresses key challenges related to monitoring movement and containment of CO{sub 2}, specifically better quantification and sensitivity for mapping of caprock integrity, fractures, and other potential leakage pathways. Specifically, our focus is fundamental research on (1) innovative narrow-band seismic data decomposition and interpretation, and (2) numerical simulation of advanced seismic data (multi-component, high density, full azimuth data) ideal for mapping of cap rock integrity and potential leakage pathways.« less

Real-time mapping of the corneal sub-basal nerve plexus by in vivo laser scanning confocal microscopy

NASA Astrophysics Data System (ADS)

Guthoff, Rudolf F.; Zhivov, Andrey; Stachs, Oliver

2010-02-01

The aim of the study was to produce two-dimensional reconstruction maps of the living corneal sub-basal nerve plexus by in vivo laser scanning confocal microscopy in real time. CLSM source data (frame rate 30Hz, 384x384 pixel) were used to create large-scale maps of the scanned area by selecting the Automatic Real Time (ART) composite mode. The mapping algorithm is based on an affine transformation. Microscopy of the sub-basal nerve plexus was performed on normal and LASIK eyes as well as on rabbit eyes. Real-time mapping of the sub-basal nerve plexus was performed in large-scale up to a size of 3.2mm x 3.2mm. The developed method enables a real-time in vivo mapping of the sub-basal nerve plexus which is stringently necessary for statistically firmed conclusions about morphometric plexus alterations.

Knowledge synthesis with maps of neural connectivity.

PubMed

Tallis, Marcelo; Thompson, Richard; Russ, Thomas A; Burns, Gully A P C

2011-01-01

This paper describes software for neuroanatomical knowledge synthesis based on neural connectivity data. This software supports a mature methodology developed since the early 1990s. Over this time, the Swanson laboratory at USC has generated an account of the neural connectivity of the sub-structures of the hypothalamus, amygdala, septum, hippocampus, and bed nucleus of the stria terminalis. This is based on neuroanatomical data maps drawn into a standard brain atlas by experts. In earlier work, we presented an application for visualizing and comparing anatomical macro connections using the Swanson third edition atlas as a framework for accurate registration. Here we describe major improvements to the NeuARt application based on the incorporation of a knowledge representation of experimental design. We also present improvements in the interface and features of the data mapping components within a unified web-application. As a step toward developing an accurate sub-regional account of neural connectivity, we provide navigational access between the data maps and a semantic representation of area-to-area connections that they support. We do so based on an approach called "Knowledge Engineering from Experimental Design" (KEfED) model that is based on experimental variables. We have extended the underlying KEfED representation of tract-tracing experiments by incorporating the definition of a neuronanatomical data map as a measurement variable in the study design. This paper describes the software design of a web-application that allows anatomical data sets to be described within a standard experimental context and thus indexed by non-spatial experimental design features.

A draft map of the mouse pluripotent stem cell spatial proteome

PubMed Central

Christoforou, Andy; Mulvey, Claire M.; Breckels, Lisa M.; Geladaki, Aikaterini; Hurrell, Tracey; Hayward, Penelope C.; Naake, Thomas; Gatto, Laurent; Viner, Rosa; Arias, Alfonso Martinez; Lilley, Kathryn S.

2016-01-01

Knowledge of the subcellular distribution of proteins is vital for understanding cellular mechanisms. Capturing the subcellular proteome in a single experiment has proven challenging, with studies focusing on specific compartments or assigning proteins to subcellular niches with low resolution and/or accuracy. Here we introduce hyperLOPIT, a method that couples extensive fractionation, quantitative high-resolution accurate mass spectrometry with multivariate data analysis. We apply hyperLOPIT to a pluripotent stem cell population whose subcellular proteome has not been extensively studied. We provide localization data on over 5,000 proteins with unprecedented spatial resolution to reveal the organization of organelles, sub-organellar compartments, protein complexes, functional networks and steady-state dynamics of proteins and unexpected subcellular locations. The method paves the way for characterizing the impact of post-transcriptional and post-translational modification on protein location and studies involving proteome-level locational changes on cellular perturbation. An interactive open-source resource is presented that enables exploration of these data. PMID:26754106

Imaging articular cartilage using second harmonic generation microscopy

NASA Astrophysics Data System (ADS)

Mansfield, Jessica C.; Winlove, C. Peter; Knapp, Karen; Matcher, Stephen J.

2006-02-01

Sub cellular resolution images of equine articular cartilage have been obtained using both second harmonic generation microscopy (SHGM) and two-photon fluorescence microscopy (TPFM). The SHGM images clearly map the distribution of the collagen II fibers within the extracellular matrix while the TPFM images show the distribution of endogenous two-photon fluorophores in both the cells and the extracellular matrix, highlighting especially the pericellular matrix and bright 2-3μm diameter features within the cells. To investigate the source of TPF in the extracellular matrix experiments have been carried out to see if it may originate from the proteoglycans. Pure solutions of the following proteoglycans hyaluronan, chondroitin sulfate and aggrecan have been imaged, only the aggrecan produced any TPF and here the intensity was not great enough to account for the TPF in the extracellular matrix. Also cartilage samples were subjected to a process to remove proteoglycans and cellular components. After this process the TPF from the samples had decreased by a factor of two, with respect to the SHG intensity.

Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis.

PubMed

Milewski, Robert J; Kumagai, Yutaro; Fujita, Katsumasa; Standley, Daron M; Smith, Nicholas I

2010-11-19

Macrophages represent the front lines of our immune system; they recognize and engulf pathogens or foreign particles thus initiating the immune response. Imaging macrophages presents unique challenges, as most optical techniques require labeling or staining of the cellular compartments in order to resolve organelles, and such stains or labels have the potential to perturb the cell, particularly in cases where incomplete information exists regarding the precise cellular reaction under observation. Label-free imaging techniques such as Raman microscopy are thus valuable tools for studying the transformations that occur in immune cells upon activation, both on the molecular and organelle levels. Due to extremely low signal levels, however, Raman microscopy requires sophisticated image processing techniques for noise reduction and signal extraction. To date, efficient, automated algorithms for resolving sub-cellular features in noisy, multi-dimensional image sets have not been explored extensively. We show that hybrid z-score normalization and standard regression (Z-LSR) can highlight the spectral differences within the cell and provide image contrast dependent on spectral content. In contrast to typical Raman imaging processing methods using multivariate analysis, such as single value decomposition (SVD), our implementation of the Z-LSR method can operate nearly in real-time. In spite of its computational simplicity, Z-LSR can automatically remove background and bias in the signal, improve the resolution of spatially distributed spectral differences and enable sub-cellular features to be resolved in Raman microscopy images of mouse macrophage cells. Significantly, the Z-LSR processed images automatically exhibited subcellular architectures whereas SVD, in general, requires human assistance in selecting the components of interest. The computational efficiency of Z-LSR enables automated resolution of sub-cellular features in large Raman microscopy data sets without compromise in image quality or information loss in associated spectra. These results motivate further use of label free microscopy techniques in real-time imaging of live immune cells.

Univariate and multivariate methods for chemical mapping of cervical cancer cells

NASA Astrophysics Data System (ADS)

Duraipandian, Shiyamala; Zheng, Wei; Huang, Zhiwei

2012-01-01

Visualization of cells and subcellular organelles are currently carried out using available microscopy methods such as cryoelectron microscopy, and fluorescence microscopy. These methods require external labeling using fluorescent dyes and extensive sample preparations to access the subcellular structures. However, Raman micro-spectroscopy provides a non-invasive, label-free method for imaging the cells with chemical specificity at sub-micrometer spatial resolutions. The scope of this paper is to image the biochemical/molecular distributions in cells associated with cancerous changes. Raman map data sets were acquired from the human cervical carcinoma cell lines (HeLa) after fixation under 785 nm excitation wavelength. The individual spectrum was recorded by raster-scanning the laser beam over the sample with 1μm step size and 10s exposure time. Images revealing nucleic acids, lipids and proteins (phenylalanine, amide I) were reconstructed using univariate methods. In near future, the small pixel to pixel variations will also be imaged using different multivariate methods (PCA, clustering (HCA, K-means, FCM)) to determine the main cellular constitutions. The hyper-spectral image of cell was reconstructed utilizing the spectral contrast at different pixels of the cell (due to the variation in the biochemical distribution) without using fluorescent dyes. Normal cervical squamous cells will also be imaged in order to differentiate normal and cancer cells of cervix using the biochemical changes in different grades of cancer. Based on the information obtained from the pseudo-color maps, constructed from the hyper-spectral cubes, the primary cellular constituents of normal and cervical cancer cells were identified.

Visibility and artifacts of gold fiducial markers used for image guided radiation therapy of pancreatic cancer on MRI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gurney-Champion, Oliver J., E-mail: o.j.gurney-champion@amc.uva.nl; Lens, Eelco; Horst, Astrid van der

2015-05-15

Purpose: In radiation therapy of pancreatic cancer, tumor alignment prior to each treatment fraction is improved when intratumoral gold fiducial markers (from here onwards: markers), which are visible on computed tomography (CT) and cone beam CT, are used. Visibility of these markers on magnetic resonance imaging (MRI) might improve image registration between CT and magnetic resonance (MR) images for tumor delineation purposes. However, concomitant image artifacts induced by markers are undesirable. The extent of visibility and artifact size depend on MRI-sequence parameters. The authors’ goal was to determine for various markers their potential to be visible and to generate artifacts,more » using measures that are independent of the MRI-sequence parameters. Methods: The authors selected ten different markers suitable for endoscopic placement in the pancreas and placed them into a phantom. The markers varied in diameter (0.28–0.6 mm), shape, and iron content (0%–0.5%). For each marker, the authors calculated T{sub 2}{sup ∗}-maps and ΔB{sub 0}-maps using MRI measurements. A decrease in relaxation time T{sub 2}{sup ∗} can cause signal voids, associated with visibility, while a change in the magnetic field B{sub 0} can cause signal shifts, which are associated with artifacts. These shifts inhibit accurate tumor delineation. As a measure for potential visibility, the authors used the volume of low T{sub 2}{sup ∗}, i.e., the volume for which T{sub 2}{sup ∗} differed from the background by >15 ms. As a measure for potential artifacts, the authors used the volume for which |ΔB{sub 0}| > 9.4 × 10{sup −8} T (4 Hz). To test whether there is a correlation between visibility and artifact size, the authors calculated the Spearman’s correlation coefficient (R{sub s}) between the volume of low T{sub 2}{sup ∗} and the volume of high |ΔB{sub 0}|. The authors compared the maps with images obtained using a clinical MR-sequence. Finally, for the best visible marker as well as the marker that showed the smallest artifact, the authors compared the phantom data with in vivo MR-images in four pancreatic cancer patients. Results: The authors found a strong correlation (R{sub s} = 1.00, p < 0.01) between the volume of low T{sub 2}{sup ∗} and the volume with high |ΔB{sub 0}|. Visibility in clinical MR-images increased with lower T{sub 2}{sup ∗}. Signal shift artifacts became worse for markers with high |ΔB{sub 0}|. The marker that was best visible in the phantom, a folded marker with 0.5% iron content, was also visible in vivo, but showed artifacts on diffusion weighted images. The marker with the smallest artifact in the phantom, a small, stretched, ironless marker, was indiscernible on in vivo MR-images. Conclusions: Changes in T{sub 2}{sup ∗} and ΔB{sub 0} are sequence-independent measures for potential visibility and artifact size, respectively. Improved visibility of markers correlates strongly to signal shift artifacts; therefore, marker choice will depend on the clinical purpose. When visibility of the markers is most important, markers that contain iron are optimal, preferably in a folded configuration. For artifact sensitive imaging, small ironless markers are best, preferably in a stretched configuration.« less

Robust imaging and gene delivery to study human lymphoblastoid cell lines.

PubMed

Jolly, Lachlan A; Sun, Ying; Carroll, Renée; Homan, Claire C; Gecz, Jozef

2018-06-20

Lymphoblastoid cell lines (LCLs) have been by far the most prevalent cell type used to study the genetics underlying normal and disease-relevant human phenotypic variation, across personal to epidemiological scales. In contrast, only few studies have explored the use of LCLs in functional genomics and mechanistic studies. Two major reasons are technical, as (1) interrogating the sub-cellular spatial information of LCLs is challenged by their non-adherent nature, and (2) LCLs are refractory to gene transfection. Methodological details relating to techniques that overcome these limitations are scarce, largely inadequate (without additional knowledge and expertise), and optimisation has never been described. Here we compare, optimise, and convey such methods in-depth. We provide a robust method to adhere LCLs to coverslips, which maintained cellular integrity, morphology, and permitted visualisation of sub-cellular structures and protein localisation. Next, we developed the use of lentiviral-based gene delivery to LCLs. Through empirical and combinatorial testing of multiple transduction conditions, we improved transduction efficiency from 3% up to 48%. Furthermore, we established strategies to purify transduced cells, to achieve sustainable cultures containing >85% transduced cells. Collectively, our methodologies provide a vital resource that enables the use of LCLs in functional cell and molecular biology experiments. Potential applications include the characterisation of genetic variants of unknown significance, the interrogation of cellular disease pathways and mechanisms, and high-throughput discovery of genetic modifiers of disease states among others.

Improvements to a Major Digital Archive of Seismic Waveforms from Nuclear Explosions: The Borovoye Seismogram Archive

DTIC Science & Technology

2009-09-30

excitation of surface waves in the Balapan sub-region of the Soviet Semipalatinsk test site in central Asia were noted for anomalous behavior...complete recording history of Semipalatinsk Test Site (STS) explosions, waveform data from the Borovoye archive offer the opportunity to re-evaluate...Figure 2. Map of the Balapan sub-region of the Semipalatinsk Test Site showing locations of 50 tests currently understudy and the boundaries of NE

MO-C-17A-08: Evaluation of Lung Deformation Using Three Dimensional Strain Maps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, T; Huang, Q; Miller, W

2014-06-15

Purpose: To develop a systematic approach to generate three dimensional (3D) strain maps of lung using the displacement vector field (DVF) during the respiratory deformation, and to demonstrate its application in evaluating deformable image registration (DIR). Methods: A DVF based strain tensor at each voxel of interest (VOI) was calculated from the relative displacements between the VOI and each of the six nearest neighbors. The maximum and minimum stretches of a VOI can be determined by the principal strains (E{sub 1}, E{sub 2} and E{sub 3}), which are the eigenvalues and the corresponding strain tensors. Two healthy volunteers enrolled inmore » this study under IRB-approved protocol, each was scanned using 3D Hyperpolarized He-3 tagging-MRI and 3D proton-MRI with TrueFISP sequence at the endof- inhalation (EOI) and the end-of-exhalation (EOE) phases. 3D DVFs of tagging- and proton-MRI were obtained by the direct measurements of the tagging grid trajectory and by the DIR method implemented in commercial software. Results: 3D strain maps were successfully generated for all DVFs. The principal strain E1s were calculated as 0.43±0.05 and 0.17±0.25 for tagging-MRI and proton-MRI, respectively. The large values of E{sub 1} indicate the predominant lung motion in the superior-inferior (SI) direction. Given that the DVFs from the tagging images are considered as the ground truth, the discrepancies in the DIR-based strain maps suggest the inaccuracy of the DIR algorithm. In the E{sub 1} maps of tagging-MRI for subject 1, the fissures were distinguishable by the larger values (0.49±0.02) from the adjacent tissues (0.41±0.03) due to the larger relative displacement between the lung lobes. Conclusion: We have successfully developed a methodology to generate DVF-based 3D strain maps of lung. It can potentially enable us to better understand the pulmonary biomechanics and to evaluate and improve the DIR algorithms for the lung deformation. We are currently studying more subjects to evaluate this tool.« less

GoFFish: A Sub-Graph Centric Framework for Large-Scale Graph Analytics1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simmhan, Yogesh; Kumbhare, Alok; Wickramaarachchi, Charith

2014-08-25

Large scale graph processing is a major research area for Big Data exploration. Vertex centric programming models like Pregel are gaining traction due to their simple abstraction that allows for scalable execution on distributed systems naturally. However, there are limitations to this approach which cause vertex centric algorithms to under-perform due to poor compute to communication overhead ratio and slow convergence of iterative superstep. In this paper we introduce GoFFish a scalable sub-graph centric framework co-designed with a distributed persistent graph storage for large scale graph analytics on commodity clusters. We introduce a sub-graph centric programming abstraction that combines themore » scalability of a vertex centric approach with the flexibility of shared memory sub-graph computation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation.« less

Spatial reconstruction of single-cell gene expression

PubMed Central

Satija, Rahul; Farrell, Jeffrey A.; Gennert, David; Schier, Alexander F.; Regev, Aviv

2015-01-01

Spatial localization is a key determinant of cellular fate and behavior, but spatial RNA assays traditionally rely on staining for a limited number of RNA species. In contrast, single-cell RNA-seq allows for deep profiling of cellular gene expression, but established methods separate cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos, inferring a transcriptome-wide map of spatial patterning. We confirmed Seurat’s accuracy using several experimental approaches, and used it to identify a set of archetypal expression patterns and spatial markers. Additionally, Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems. PMID:25867923

Temporal and spatial heterogeneity of rupture process application in shakemaps of Yushu Ms7.1 earthquake, China

NASA Astrophysics Data System (ADS)

Kun, C.

2015-12-01

Studies have shown that estimates of ground motion parameter from ground motion attenuation relationship often greater than the observed value, mainly because multiple ruptures of the big earthquake reduce the source pulse height of source time function. In the absence of real-time data of the station after the earthquake, this paper attempts to make some constraints from the source, to improve the accuracy of shakemaps. Causative fault of Yushu Ms 7.1 earthquake is vertical approximately (dip 83 °), and source process in time and space was dispersive distinctly. Main shock of Yushu Ms7.1 earthquake can be divided into several sub-events based on source process of this earthquake. Magnitude of each sub-events depended on each area under the curve of source pulse of source time function, and location derived from source process of each sub-event. We use ShakeMap method with considering the site effect to generate shakeMap for each sub-event, respectively. Finally, ShakeMaps of mainshock can be aquired from superposition of shakemaps for all the sub-events in space. Shakemaps based on surface rupture of causative Fault from field survey can also be derived for mainshock with only one magnitude. We compare ShakeMaps of both the above methods with Intensity of investigation. Comparisons show that decomposition method of main shock more accurately reflect the shake of earthquake in near-field, but for far field the shake is controlled by the weakening influence of the source, the estimated Ⅵ area was smaller than the intensity of the actual investigation. Perhaps seismic intensity in far-field may be related to the increasing seismic duration for the two events. In general, decomposition method of main shock based on source process, considering shakemap of each sub-event, is feasible for disaster emergency response, decision-making and rapid Disaster Assessment after the earthquake.

Force-activatable biosensor enables single platelet force mapping directly by fluorescence imaging.

PubMed

Wang, Yongliang; LeVine, Dana N; Gannon, Margaret; Zhao, Yuanchang; Sarkar, Anwesha; Hoch, Bailey; Wang, Xuefeng

2018-02-15

Integrin-transmitted cellular forces are critical for platelet adhesion, activation, aggregation and contraction during hemostasis and thrombosis. Measuring and mapping single platelet forces are desired in both research and clinical applications. Conventional force-to-strain based cell traction force microscopies have low resolution which is not ideal for cellular force mapping in small platelets. To enable platelet force mapping with submicron resolution, we developed a force-activatable biosensor named integrative tension sensor (ITS) which directly converts molecular tensions to fluorescent signals, therefore enabling cellular force mapping directly by fluorescence imaging. With ITS, we mapped cellular forces in single platelets at 0.4µm resolution. We found that platelet force distribution has strong polarization which is sensitive to treatment with the anti-platelet drug tirofiban, suggesting that the ITS force map can report anti-platelet drug efficacy. The ITS also calibrated integrin molecular tensions in platelets and revealed two distinct tension levels: 12-54 piconewton (nominal values) tensions generated during platelet adhesion and tensions above 54 piconewton generated during platelet contraction. Overall, the ITS is a powerful biosensor for the study of platelet mechanobiology, and holds great potential in antithrombotic drug development and assessing platelet activity in health and disease. Copyright © 2017 Elsevier B.V. All rights reserved.

Leveraging electronic health record documentation for Failure Mode and Effects Analysis team identification

PubMed Central

Carson, Matthew B; Lee, Young Ji; Benacka, Corrine; Mutharasan, R. Kannan; Ahmad, Faraz S; Kansal, Preeti; Yancy, Clyde W; Anderson, Allen S; Soulakis, Nicholas D

2017-01-01

Objective: Using Failure Mode and Effects Analysis (FMEA) as an example quality improvement approach, our objective was to evaluate whether secondary use of orders, forms, and notes recorded by the electronic health record (EHR) during daily practice can enhance the accuracy of process maps used to guide improvement. We examined discrepancies between expected and observed activities and individuals involved in a high-risk process and devised diagnostic measures for understanding discrepancies that may be used to inform quality improvement planning. Methods: Inpatient cardiology unit staff developed a process map of discharge from the unit. We matched activities and providers identified on the process map to EHR data. Using four diagnostic measures, we analyzed discrepancies between expectation and observation. Results: EHR data showed that 35% of activities were completed by unexpected providers, including providers from 12 categories not identified as part of the discharge workflow. The EHR also revealed sub-components of process activities not identified on the process map. Additional information from the EHR was used to revise the process map and show differences between expectation and observation. Conclusion: Findings suggest EHR data may reveal gaps in process maps used for quality improvement and identify characteristics about workflow activities that can identify perspectives for inclusion in an FMEA. Organizations with access to EHR data may be able to leverage clinical documentation to enhance process maps used for quality improvement. While focused on FMEA protocols, findings from this study may be applicable to other quality activities that require process maps. PMID:27589944

Universal map for cellular automata

NASA Astrophysics Data System (ADS)

García-Morales, V.

2012-08-01

A universal map is derived for all deterministic 1D cellular automata (CAs) containing no freely adjustable parameters and valid for any alphabet size and any neighborhood range (including non-symmetrical neighborhoods). The map can be extended to an arbitrary number of dimensions and topologies and to arbitrary order in time. Specific CA maps for the famous Conway's Game of Life and Wolfram's 256 elementary CAs are given. An induction method for CAs, based in the universal map, allows mathematical expressions for the orbits of a wide variety of elementary CAs to be systematically derived.

A comparison of radiographic and clinical outcomes of anterior lumbar interbody fusion performed with either a cellular bone allograft containing multipotent adult progenitor cells or recombinant human bone morphogenetic protein-2.

PubMed

Lee, Daniel Dongwhan; Kim, John Yongmin

2017-08-25

Both the map3 Cellular Allogeneic Bone Graft® and recombinant human bone morphogenetic protein 2 (rhBMP-2, Infuse®) were developed to provide an alternative to iliac crest autograft, thus eliminating the morbidity associated with its harvest. The recent literature concerning adverse events associated with the use of rhBMP-2, however, highlights the need for a safe and effective alternative. The multipotent adult progenitor cells (MAPC) found in map3 allograft may provide this alternative. The purpose of this study is to report 1-year outcomes of patients treated via anterior lumbar interbody fusion (ALIF) using either map3 Cellular Allogeneic Bone Graft or rhBMP-2 for bony fusion. This was a retrospective evaluation of 41 patients treated via ALIF with either map3 or rhBMP-2 in a polyetheretherketone cage with posterior stabilization at 1, 2, or 3 consecutive levels (L3-S1). Patients were equally divided between treatment groups. The Oswestry Disability Index (ODI) and visual analog scores (VAS) for pain were documented as part of the standard of care. An independent radiologist assessed bridging of bone, disc height, and lordosis. Primary outcome measures included radiographic analysis of fusion by plain film and CTs. Secondary clinical outcomes included visual analogue scale for neck and arm pain and low back disability index scores. The overall fusion rate was 91%, with no significant difference between groups. Improvements in ODI and VAS were observed among all patients (p < 0.001), with no significant difference between groups for ODI (p = 0.966) or VAS (p = 0.251). There was no significant difference in terms of changes to disc height and lordosis between groups (p < 0.05). The rhBMP-2 group had increased post-operative complications when compared to the map3 group, but the low numbers precluded statistical analysis. Improvements in radiographic and clinical findings were observed in both treatment groups one-year postoperatively. Map3 allograft demonstrated equivalent fusion rates to rhBMP-2. A review of surgical supply costs at the treatment facility favored map3 allograft for the treatment of patients with DDD undergoing an ALIF in 1-3 levels compared to rhBMP-2. Further studies to evaluate long-term outcomes and post-operative complications are required.

High-throughput microscopy must re-invent the microscope rather than speed up its functions

PubMed Central

Oheim, M

2007-01-01

Knowledge gained from the revolutions in genomics and proteomics has helped to identify many of the key molecules involved in cellular signalling. Researchers, both in academia and in the pharmaceutical industry, now screen, at a sub-cellular level, where and when these proteins interact. Fluorescence imaging and molecular labelling combine to provide a powerful tool for real-time functional biochemistry with molecular resolution. However, they traditionally have been work-intensive, required trained personnel, and suffered from low through-put due to sample preparation, loading and handling. The need for speeding up microscopy is apparent from the tremendous complexity of cellular signalling pathways, the inherent biological variability, as well as the possibility that the same molecule plays different roles in different sub-cellular compartments. Research institutes and companies have teamed up to develop imaging cytometers of ever-increasing complexity. However, to truly go high-speed, sub-cellular imaging must free itself from the rigid framework of current microscopes. PMID:17603553

Domain matched epitaxial growth of (111) Ba{sub 0.5}Sr{sub 0.5}TiO{sub 3} thin films on (0001) Al{sub 2}O{sub 3} with ZnO buffer layer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnaprasad, P. S., E-mail: pskrishnaprasu@gmail.com, E-mail: mkj@cusat.ac.in; Jayaraj, M. K., E-mail: pskrishnaprasu@gmail.com, E-mail: mkj@cusat.ac.in; Antony, Aldrin

2015-03-28

Epitaxial (111) Ba{sub 0.5}Sr{sub 0.5}TiO{sub 3} (BST) thin films have been grown by pulsed laser deposition on (0001) Al{sub 2}O{sub 3} substrate with ZnO as buffer layer. The x-ray ω-2θ, Φ-scan and reciprocal space mapping indicate epitaxial nature of BST thin films. The domain matched epitaxial growth of BST thin films over ZnO buffer layer was confirmed using Fourier filtered high resolution transmission electron microscope images of the film-buffer interface. The incorporation of ZnO buffer layer effectively suppressed the lattice mismatch and promoted domain matched epitaxial growth of BST thin films. Coplanar inter digital capacitors fabricated on epitaxial (111) BSTmore » thin films show significantly improved tunable performance over polycrystalline thin films.« less

Applying Intervention Mapping to Develop a Community-Based Intervention Aimed at Improved Psychological and Social Well-Being of Unmarried Teenage Mothers in Uganda

ERIC Educational Resources Information Center

Leerlooijer, Joanne N.; Kok, Gerjo; Weyusya, Joseph; Bos, Arjan E. R.; Ruiter, Robert A. C.; Rijsdijk, Liesbeth E.; Nshakira, Nathan; Bartholomew, Leona K.

2014-01-01

Out-of-wedlock pregnancy among adolescents in sub-Saharan Africa is a major concern, because of its association with health, social, psychological, economic and demographic factors. This article describes the development of the Teenage Mothers Project, a community-based intervention to improve psychological and social well-being of unmarried…

Spatial distributions of AQP5 and AQP0 in embryonic and postnatal mouse lens development

PubMed Central

Petrova, Rosica S.; Schey, Kevin L.; Donaldson, Paul J.; Grey, Angus C.

2015-01-01

The expression of the water channel protein aquaporin (AQP)-5 in adult rodent and human lenses was recently reported using immunohistochemistry, molecular biology, and mass spectrometry techniques, confirming a second transmembrane water channel that is present in lens fibre cells in addition to the abundant AQP0 protein. Interestingly, the sub-cellular distribution and level of post-translational modification of both proteins changes with fibre cell differentiation and location in the adult rodent lens. This study compares the sub-cellular distribution of AQP0 and AQP5 during embryonic and postnatal fibre cell development in the mouse lens to understand how the immunolabelling patterns for both AQPs observed in adult lens are first established. Immunohistochemistry was used to map the cellular and sub-cellular distribution of AQP5 and AQP0 throughout the lens in cryosections from adult (6 weeks to 8 months) and postnatal (0-2 weeks) mouse lenses and in sections from paraffin embedded mouse embryos (E10-E19). All sections were imaged by fluorescence confocal microscopy. Using antibodies directed against the C-terminus of each AQP, AQP5 was abundantly expressed early in development, being found in the cytoplasm of cells of the lens vesicle and surrounding tissues (E10), while AQP0 was detected later (E11), and only in the membranes of elongating primary fibre cells. During the course of subsequent embryonic and postnatal development the pattern of cytoplasmic AQP5 and membranous AQP0 labelling was maintained until postnatal day 6 (P6). From P6 AQP5 labelling became progressively more membranous initially in the lens nucleus and then later in all regions of the lens, while AQP0 labelling was abruptly lost in the lens nucleus due to C-terminal truncation. Our results show that the spatial distribution patterns of AQP0 and AQP5 observed in the adult lens are established during a narrow window of post natal development (P6-P15) that precedes eye opening and coincides with regression of the hyaloid vascular system. Our results support the hypothesis that, in the older fibre cells, insertion of AQP5 into the fibre cell membrane may compensate for any change in the functionality of AQP0 induced by truncation of its C-terminal tail. PMID:25595964

Five-Year Wilkinson Microwave Anisotropy Probe Observations: Data Processing, Sky Maps, and Basic Results

NASA Technical Reports Server (NTRS)

Hinshaw, G.; Weiland, J. L.; Hill, R. S.; Odegard, N.; Larson, D.; Bennett, C. L.; Dunkley, J.; Gold, B.; Greason, M. R.; Jarosik, N.;

Smartphone-based imaging of the corneal endothelium at sub-cellular resolution

NASA Astrophysics Data System (ADS)

Toslak, Devrim; Thapa, Damber; Erol, Muhammet Kazim; Chen, Yanjun; Yao, Xincheng

2017-07-01

This aim of this study was to test the feasibility of smartphone-based specular microscopy of the corneal endothelium at a sub-cellular resolution. Quantitative examination of endothelial cells is essential for evaluating corneal disease such as determining a diagnosis, monitoring progression and assessing treatment. Smartphone-based technology promises a new opportunity to develop affordable devices to foster quantitative examination of endothelial cells in rural and underserved areas. In our study, we incorporated an iPhone 6 and a slit lamp to demonstrate the feasibility of smartphone-based microscopy of the corneal endothelium at a sub-cellular resolution. The sub-cellular resolution images allowed quantitative calculation of the endothelial cell density. Comparative measurements revealed a normal endothelial cell density of 2978 cells/mm2 in the healthy cornea, and a significantly reduced cell density of 1466 cells/mm2 in the diseased cornea with Fuchs' dystrophy. Our ultimate goal is to develop a smartphone-based telemedicine device for low-cost examination of the corneal endothelium, which can benefit patients in rural areas and underdeveloped countries to reduce health care disparities.

Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mountassif, Driss; Fabre, Lucien; Zaid, Younes

Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation inducesmore » a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. - Highlights: • p97{sub R155P} and p97{sub A232E} decrease the ability of p97 to bind to its co-factor Npl4. • p97{sub R155P} has a different isoelectric point than that of p97{sub R95G}, p97{sub A232E} and p97{sub WT}. • Mutation R155P changes principally the conformation of the D2 ring. • Mutation R155P modifies the interface between two protomers within the D2 ring.« less

Determining the sub-cellular localization of proteins within Caenorhabditis elegans body wall muscle.

PubMed

Meissner, Barbara; Rogalski, Teresa; Viveiros, Ryan; Warner, Adam; Plastino, Lorena; Lorch, Adam; Granger, Laure; Segalat, Laurent; Moerman, Donald G

2011-01-01

Determining the sub-cellular localization of a protein within a cell is often an essential step towards understanding its function. In Caenorhabditis elegans, the relatively large size of the body wall muscle cells and the exquisite organization of their sarcomeres offer an opportunity to identify the precise position of proteins within cell substructures. Our goal in this study is to generate a comprehensive "localizome" for C. elegans body wall muscle by GFP-tagging proteins expressed in muscle and determining their location within the cell. For this project, we focused on proteins that we know are expressed in muscle and are orthologs or at least homologs of human proteins. To date we have analyzed the expression of about 227 GFP-tagged proteins that show localized expression in the body wall muscle of this nematode (e.g. dense bodies, M-lines, myofilaments, mitochondria, cell membrane, nucleus or nucleolus). For most proteins analyzed in this study no prior data on sub-cellular localization was available. In addition to discrete sub-cellular localization we observe overlapping patterns of localization including the presence of a protein in the dense body and the nucleus, or the dense body and the M-lines. In total we discern more than 14 sub-cellular localization patterns within nematode body wall muscle. The localization of this large set of proteins within a muscle cell will serve as an invaluable resource in our investigation of muscle sarcomere assembly and function.

PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases

PubMed Central

Forrest, Alistair RR; Taylor, Darrin F; Fink, J Lynn; Gongora, M Milena; Flegg, Cameron; Teasdale, Rohan D; Suzuki, Harukazu; Kanamori, Mutsumi; Kai, Chikatoshi; Hayashizaki, Yoshihide; Grimmond, Sean M

2006-01-01

Background Protein kinases and protein phosphatases are the fundamental components of phosphorylation dependent protein regulatory systems. We have created a database for the protein kinase-like and phosphatase-like loci of mouse that integrates protein sequence, interaction, classification and pathway information with the results of a systematic screen of their sub-cellular localization and tissue specific expression data mined from the GNF tissue atlas of mouse. Results The database lets users query where a specific kinase or phosphatase is expressed at both the tissue and sub-cellular levels. Similarly the interface allows the user to query by tissue, pathway or sub-cellular localization, to reveal which components are co-expressed or co-localized. A review of their expression reveals 30% of these components are detected in all tissues tested while 70% show some level of tissue restriction. Hierarchical clustering of the expression data reveals that expression of these genes can be used to separate the samples into tissues of related lineage, including 3 larger clusters of nervous tissue, developing embryo and cells of the immune system. By overlaying the expression, sub-cellular localization and classification data we examine correlations between class, specificity and tissue restriction and show that tyrosine kinases are more generally expressed in fewer tissues than serine/threonine kinases. Conclusion Together these data demonstrate that cell type specific systems exist to regulate protein phosphorylation and that for accurate modelling and for determination of enzyme substrate relationships the co-location of components needs to be considered. PMID:16504016

Knowledge Synthesis with Maps of Neural Connectivity

PubMed Central

Tallis, Marcelo; Thompson, Richard; Russ, Thomas A.; Burns, Gully A. P. C.

2011-01-01

This paper describes software for neuroanatomical knowledge synthesis based on neural connectivity data. This software supports a mature methodology developed since the early 1990s. Over this time, the Swanson laboratory at USC has generated an account of the neural connectivity of the sub-structures of the hypothalamus, amygdala, septum, hippocampus, and bed nucleus of the stria terminalis. This is based on neuroanatomical data maps drawn into a standard brain atlas by experts. In earlier work, we presented an application for visualizing and comparing anatomical macro connections using the Swanson third edition atlas as a framework for accurate registration. Here we describe major improvements to the NeuARt application based on the incorporation of a knowledge representation of experimental design. We also present improvements in the interface and features of the data mapping components within a unified web-application. As a step toward developing an accurate sub-regional account of neural connectivity, we provide navigational access between the data maps and a semantic representation of area-to-area connections that they support. We do so based on an approach called “Knowledge Engineering from Experimental Design” (KEfED) model that is based on experimental variables. We have extended the underlying KEfED representation of tract-tracing experiments by incorporating the definition of a neuronanatomical data map as a measurement variable in the study design. This paper describes the software design of a web-application that allows anatomical data sets to be described within a standard experimental context and thus indexed by non-spatial experimental design features. PMID:22053155

Distribution of Single-Wall Carbon Nanotubes in the Xenopus laevis Embryo after Microinjection

PubMed Central

Holt, Brian D.; Shawky, Joseph H.; Dahl, Kris Noel; Davidson, Lance A.; Islam, Mohammad F.

2016-01-01

Single-wall carbon nanotubes (SWCNTs) are advanced materials with the potential for a myriad of diverse applications, including biological technologies and largescale usage with the potential for environmental impacts. SWCNTs have been exposed to developing organisms to determine their effects on embryogenesis, and results have been inconsistent arising, in part, from differing material quality, dispersion status, material size, impurity from catalysts, and stability. For this study, we utilized highly purified SWCNT samples with short, uniform lengths (145 ± 17 nm) well dispersed in solution. To test high exposure doses, we microinjected > 500 μg mL-1 SWCNT concentrations into the well-established embryogenesis model, Xenopus laevis, and determined embryo compatibility and sub-cellular localization during development. SWCNTs localized within cellular progeny of the microinjected cells, but heterogeneously distributed throughout the target-injected tissue. Co-registering unique Raman spectral intensity of SWCNTs with images of fluorescently labelled sub-cellular compartments demonstrated that even at the regions of highest SWCNT concentration, there were no gross alterations to sub-cellular microstructures, including filamentous actin, endoplasmic reticulum and vesicles. Furthermore, SWCNTs did not aggregate or localize to the perinuclear sub-cellular region. Combined, these results suggest that purified and dispersed SWCNTs are not toxic to X. laevis animal cap ectoderm and may be suitable candidate materials for biological applications. PMID:26510384

[Effects of sub-micro emulsion composition on cellular disposition of incorporated lipophilic drug].

PubMed

Sun, Xiao-Yi; Xiang, Zhi-Qiang; Wu, Shuo; Lv, Yuan-Yuan; Liang, Wen-Quan

2013-09-01

To investigate the effects of sub-micro emulsion composition on cellular uptake and disposition of incorporated lipophilic drug. Sub-micro emulsions containing 10 % oil, 1.2 % lecithin and 2.25 % glycerol were prepared, and the fluorescent agent coumarin 6 was used as a model drug. The effects of oil types, co-surfactants and cationic lipid on uptake and elimination kinetics of 6-coumarin in HeLa cells were studied. The uptake mechanism of sub-micro emulsions was further investigated. Oil type and Tweens had no influence on the cellular uptake. Modifications of surfactants with Span series increased the cellular influx, among which Span 20 with hydrophilic-lipophilic balance (HLB) value of 8.6 was the best enhancer. The intracellular drug level reached up to (46.09 ± 1.98)ng/μg protein which had significant difference with control group [(38.54 ± 0.34)ng/μg protein]. The positively charged emulsions significantly increased the uptake rate constant and elimination rate constant which were 4 times and 1.5 times of those in anionic groups, respectively. The uptake enhancement was also observed in cationic emulsions, cellular concentrations at plateau were (42.73 ± 0.84)ng/μg protein, which was about 3 times of that in anionic emulsions [(15.71 ± 0.74)ng/μg protein], when extracellular drug concentration kept at 100 ng/ml. Cationic emulsions delivered the payload mainly by direct drug transfer to contacted cells, while the negative ones depended on both drug passive diffusion and clathrin-mediated endocytosis of drug containing oil droplets which accounted for 20% of the intracellular drug. Interfacial characteristic of sub-micro emulsions such as co-surfactants HLB as well as zeta potentials can influence lipophilic drug both in cellular uptake and elimination.

Genome-wide association mapping of provitamin A carotenoid content in cassava

USDA-ARS?s Scientific Manuscript database

Global efforts are underway to develop staple crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency, which is widespread among resource-poor farmers in the developing world. As a staple crop for more than 500 million people in sub-Saharan Africa, cassava ...

The spatial variation of the infrared-to-radio ratio in spiral galaxies

NASA Technical Reports Server (NTRS)

Marsh, K. A.; Helou, G.

1995-01-01

We have produced two-dimensional maps of the intensity ratio, Q(sub 60), of 60 micron infrared to 20 cm radio continuum emission, for a set of 25 nearby galaxies, mostly spirals. The ratio maps were obtained from infrared images made using IRAS data with the maximum correlation method, and radio images made using VLA data. Before taking the ratio, the radio images were processed so as to have the same resolution properties as the infrared images; the final spatial resolution in all cases is approximately 1 min, corresponding to 1 - 2 kpc for most galaxies. This resolution represents a significant improvement over previous studies. Our new high-resolution maps confirm the slow decrease of Q(sub 60) with increasing radial distance from the nucleus, but show additional structure which is probably associated with separate sites of active star formation in the spiral arms. The maps show Q(sub 60) to be more closely related to infrared surface brightness than to the radial distance r in the galaxy disk. We note also that the Q(sub 60) gradients are absent (or at least reduced) for the edge-on galaxies, a property which can be attributed to the dilution of contrast due to the averaging of the additional structure along the line of sight. The results are all in qualitative agreement with the suggestion that the radio image represents a smeared version of the infrared image, as would be expected on the basis of current models in which the infrared-radio correlation is driven by the formation of massive stars, and the intensity distribution of radio emission is smeared as a result of the propagation of energetic electrons accelerated during the supernova phase.

The study of non-fouling and non-specific cellular binding on functionalized surface for mammalian cell identification and manipulation

NASA Astrophysics Data System (ADS)

Zainudin, Nor Syuhada; Hambali, Nor Azura Malini Ahmad; Wahid, Mohamad Halim Abd; Retnasamy, Vithyacharan; Shahimin, Mukhzeer Mohamad

2017-04-01

Surface functionalization has emerged as a powerful tool for mapping limitless surface-cell membrane interaction in diverse biomolecular applications. Inhibition of non-specific biomolecular and cellular adhesion to solid surfaces is critical in improving the performance of some biomedical devices, particularly for in vitro bioassays. Some factors have to be paid particular attention in determining the right surface modification which are the types of surface, the methods and chemical solution that being used during the experimentation and also tools for analyzing the results. Improved surface functionalization technologies that provide better non-fouling performance in conjunction with specific attachment chemistries are sought for these applications. Hence, this paper serves as a review for multiple surface treatment methods including PEG grafting, adsorptive chemistries, self-assembled monolayers (SAMs) and plasma treatments.

The use of Sentinel-2 imagery for seagrass mapping: Kalloni Gulf (Lesvos Island, Greece) case study

NASA Astrophysics Data System (ADS)

Topouzelis, Konstantinos; Charalampis Spondylidis, Spyridon; Papakonstantinou, Apostolos; Soulakellis, Nikolaos

2016-08-01

Seagrass meadows play a significant role in ecosystems by stabilizing sediment and improving water clarity, which enhances seagrass growing conditions. It is high on the priority of EU legislation to map and protect them. The traditional use of medium spatial resolution satellite imagery e.g. Landsat-8 (30m) is very useful for mapping seagrass meadows on a regional scale. However, the availability of Sentinel-2 data, the recent ESA's satellite with its payload Multi-Spectral Instrument (MSI) is expected to improve the mapping accuracy. MSI designed to improve coastline studies due to its enhanced spatial and spectral capabilities e.g. optical bands with 10m spatial resolution. The present work examines the quality of Sentinel-2 images for seagrass mapping, the ability of each band in detection and discrimination of different habitats and estimates the accuracy of seagrass mapping. After pre-processing steps, e.g. radiometric calibration and atmospheric correction, image classified into four classes. Classification classes included sub-bottom composition e.g. seagrass, soft bottom, and hard bottom. Concrete vectors describing the areas covered by seagrass extracted from the high-resolution satellite image and used as in situ measurements. The developed methodology applied in the Gulf of Kalloni, (Lesvos Island - Greece). Results showed that Sentinel-2 images can be robustly used for seagrass mapping due to their spatial resolution, band availability and radiometric accuracy.

Analytical SuperSTEM for extraterrestrial materials research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bradley, J P; Dai, Z R

2009-09-08

Electron-beam studies of extraterrestrial materials with significantly improved spatial resolution, energy resolution and sensitivity are enabled using a 300 keV SuperSTEM scanning transmission electron microscope with a monochromator and two spherical aberration correctors. The improved technical capabilities enable analyses previously not possible. Mineral structures can be directly imaged and analyzed with single-atomic-column resolution, liquids and implanted gases can be detected, and UV-VIS optical properties can be measured. Detection limits for minor/trace elements in thin (<100 nm thick) specimens are improved such that quantitative measurements of some extend to the sub-500 ppm level. Electron energy-loss spectroscopy (EELS) can be carried outmore » with 0.10-0.20 eV energy resolution and atomic-scale spatial resolution such that variations in oxidation state from one atomic column to another can be detected. Petrographic mapping is extended down to the atomic scale using energy-dispersive x-ray spectroscopy (EDS) and energy-filtered transmission electron microscopy (EFTEM) imaging. Technical capabilities and examples of the applications of SuperSTEM to extraterrestrial materials are presented, including the UV spectral properties and organic carbon K-edge fine structure of carbonaceous matter in interplanetary dust particles (IDPs), x-ray elemental maps showing the nanometer-scale distribution of carbon within GEMS (glass with embedded metal and sulfides), the first detection and quantification of trace Ti in GEMS using EDS, and detection of molecular H{sub 2}O in vesicles and implanted H{sub 2} and He in irradiated mineral and glass grains.« less

Mid-infrared thermal imaging for an effective mapping of surface materials and sub-surface detachments in mural paintings: integration of thermography and thermal quasi-reflectography

NASA Astrophysics Data System (ADS)

Daffara, C.; Parisotto, S.; Mariotti, P. I.

2015-06-01

Cultural Heritage is discovering how precious is thermal analysis as a tool to improve the restoration, thanks to its ability to inspect hidden details. In this work a novel dual mode imaging approach, based on the integration of thermography and thermal quasi-reflectography (TQR) in the mid-IR is demonstrated for an effective mapping of surface materials and of sub-surface detachments in mural painting. The tool was validated through a unique application: the "Monocromo" by Leonardo da Vinci in Italy. The dual mode acquisition provided two spatially aligned dataset: the TQR image and the thermal sequence. Main steps of the workflow included: 1) TQR analysis to map surface features and 2) to estimate the emissivity; 3) projection of the TQR frame on reference orthophoto and TQR mosaicking; 4) thermography analysis to map detachments; 5) use TQR to solve spatial referencing and mosaicking for the thermal-processed frames. Referencing of thermal images in the visible is a difficult aspect of the thermography technique that the dual mode approach allows to solve in effective way. We finally obtained the TQR and the thermal maps spatially referenced to the mural painting, thus providing the restorer a valuable tool for the restoration of the detachments.

Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.).

PubMed

Mishra, Awdhesh Kumar; Muthamilarasan, Mehanathan; Khan, Yusuf; Parida, Swarup Kumar; Prasad, Manoj

2014-01-01

WD40 proteins play a crucial role in diverse protein-protein interactions by acting as scaffolding molecules and thus assisting in the proper activity of proteins. Hence, systematic characterization and expression profiling of these WD40 genes in foxtail millet would enable us to understand the networks of WD40 proteins and their biological processes and gene functions. In the present study, a genome-wide survey was conducted and 225 potential WD40 genes were identified. Phylogenetic analysis categorized the WD40 proteins into 5 distinct sub-families (I-V). Gene Ontology annotation revealed the biological roles of the WD40 proteins along with its cellular components and molecular functions. In silico comparative mapping with sorghum, maize and rice demonstrated the orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of WD40 genes. Estimation of synonymous and non-synonymous substitution rates revealed its evolutionary significance in terms of gene-duplication and divergence. Expression profiling against abiotic stresses provided novel insights into specific and/or overlapping expression patterns of SiWD40 genes. Homology modeling enabled three-dimensional structure prediction was performed to understand the molecular functions of WD40 proteins. Although, recent findings had shown the importance of WD40 domains in acting as hubs for cellular networks during many biological processes, it has invited a lesser research attention unlike other common domains. Being a most promiscuous interactors, WD40 domains are versatile in mediating critical cellular functions and hence this genome-wide study especially in the model crop foxtail millet would serve as a blue-print for functional characterization of WD40s in millets and bioenergy grass species. In addition, the present analyses would also assist the research community in choosing the candidate WD40s for comprehensive studies towards crop improvement of millets and biofuel grasses.

Genome-Wide Investigation and Expression Analyses of WD40 Protein Family in the Model Plant Foxtail Millet (Setaria italica L.)

PubMed Central

Mishra, Awdhesh Kumar; Muthamilarasan, Mehanathan; Khan, Yusuf; Parida, Swarup Kumar; Prasad, Manoj

2014-01-01

WD40 proteins play a crucial role in diverse protein-protein interactions by acting as scaffolding molecules and thus assisting in the proper activity of proteins. Hence, systematic characterization and expression profiling of these WD40 genes in foxtail millet would enable us to understand the networks of WD40 proteins and their biological processes and gene functions. In the present study, a genome-wide survey was conducted and 225 potential WD40 genes were identified. Phylogenetic analysis categorized the WD40 proteins into 5 distinct sub-families (I–V). Gene Ontology annotation revealed the biological roles of the WD40 proteins along with its cellular components and molecular functions. In silico comparative mapping with sorghum, maize and rice demonstrated the orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of WD40 genes. Estimation of synonymous and non-synonymous substitution rates revealed its evolutionary significance in terms of gene-duplication and divergence. Expression profiling against abiotic stresses provided novel insights into specific and/or overlapping expression patterns of SiWD40 genes. Homology modeling enabled three-dimensional structure prediction was performed to understand the molecular functions of WD40 proteins. Although, recent findings had shown the importance of WD40 domains in acting as hubs for cellular networks during many biological processes, it has invited a lesser research attention unlike other common domains. Being a most promiscuous interactors, WD40 domains are versatile in mediating critical cellular functions and hence this genome-wide study especially in the model crop foxtail millet would serve as a blue-print for functional characterization of WD40s in millets and bioenergy grass species. In addition, the present analyses would also assist the research community in choosing the candidate WD40s for comprehensive studies towards crop improvement of millets and biofuel grasses. PMID:24466268

REVERBERATION AND PHOTOIONIZATION ESTIMATES OF THE BROAD-LINE REGION RADIUS IN LOW-z QUASARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Negrete, C. Alenka; Dultzin, Deborah; Marziani, Paola

2013-07-01

Black hole mass estimation in quasars, especially at high redshift, involves the use of single-epoch spectra with signal-to-noise ratio and resolution that permit accurate measurement of the width of a broad line assumed to be a reliable virial estimator. Coupled with an estimate of the radius of the broad-line region (BLR) this yields the black hole mass M{sub BH}. The radius of the BLR may be inferred from an extrapolation of the correlation between source luminosity and reverberation-derived r{sub BLR} measures (the so-called Kaspi relation involving about 60 low-z sources). We are exploring a different method for estimating r{sub BLR}more » directly from inferred physical conditions in the BLR of each source. We report here on a comparison of r{sub BLR} estimates that come from our method and from reverberation mapping. Our ''photoionization'' method employs diagnostic line intensity ratios in the rest-frame range 1400-2000 A (Al III {lambda}1860/Si III] {lambda}1892, C IV {lambda}1549/Al III {lambda}1860) that enable derivation of the product of density and ionization parameter with the BLR distance derived from the definition of the ionization parameter. We find good agreement between our estimates of the density, ionization parameter, and r{sub BLR} and those from reverberation mapping. We suggest empirical corrections to improve the agreement between individual photoionization-derived r{sub BLR} values and those obtained from reverberation mapping. The results in this paper can be exploited to estimate M{sub BH} for large samples of high-z quasars using an appropriate virial broadening estimator. We show that the width of the UV intermediate emission lines are consistent with the width of H{beta}, thereby providing a reliable virial broadening estimator that can be measured in large samples of high-z quasars.« less

Confocal Microscopy and Molecular-Specific Optical Contrast Agents for the Detection of Oral Neoplasia

PubMed Central

Carlson, Alicia L.; Gillenwater, Ann M.; Williams, Michelle D.; El-Naggar, Adel K.; Richards-Kortum, R. R.

2009-01-01

Using current clinical diagnostic techniques, it is difficult to visualize tumor morphology and architecture at the cellular level, which is necessary for diagnostic localization of pathologic lesions. Optical imaging techniques have the potential to address this clinical need by providing real-time, sub-cellular resolution images. This paper describes the use of dual mode confocal microscopy and optical molecular-specific contrast agents to image tissue architecture, cellular morphology, and sub-cellular molecular features of normal and neoplastic oral tissues. Fresh tissue slices were prepared from 33 biopsies of clinically normal and abnormal oral mucosa obtained from 14 patients. Reflectance confocal images were acquired after the application of 6% acetic acid, and fluorescence confocal images were acquired after the application of a fluorescence contrast agent targeting the epidermal growth factor receptor (EGFR). The dual imaging modes provided images similar to light microscopy of hematoxylin and eosin and immunohistochemistry staining, but from thick fresh tissue slices. Reflectance images provided information on the architecture of the tissue and the cellular morphology. The nuclear-to-cytoplasmic (N/C) ratio from the reflectance images was at least 7.5 times greater for the carcinoma than the corresponding normal samples, except for one case of highly keratinized carcinoma. Separation of carcinoma from normal and mild dysplasia was achieved using this ratio (p<0.01). Fluorescence images of EGFR expression yielded a mean fluorescence labeling intensity (FLI) that was at least 2.7 times higher for severe dysplasia and carcinoma samples than for the corresponding normal sample, and could be used to distinguish carcinoma from normal and mild dysplasia (p<0.01). Analyzed together, the N/C ratio and the mean FLI may improve the ability to distinguish carcinoma from normal squamous epithelium. PMID:17877424

Secure chaotic map based block cryptosystem with application to camera sensor networks.

PubMed

Guo, Xianfeng; Zhang, Jiashu; Khan, Muhammad Khurram; Alghathbar, Khaled

2011-01-01

Recently, Wang et al. presented an efficient logistic map based block encryption system. The encryption system employs feedback ciphertext to achieve plaintext dependence of sub-keys. Unfortunately, we discovered that their scheme is unable to withstand key stream attack. To improve its security, this paper proposes a novel chaotic map based block cryptosystem. At the same time, a secure architecture for camera sensor network is constructed. The network comprises a set of inexpensive camera sensors to capture the images, a sink node equipped with sufficient computation and storage capabilities and a data processing server. The transmission security between the sink node and the server is gained by utilizing the improved cipher. Both theoretical analysis and simulation results indicate that the improved algorithm can overcome the flaws and maintain all the merits of the original cryptosystem. In addition, computational costs and efficiency of the proposed scheme are encouraging for the practical implementation in the real environment as well as camera sensor network.

Secure Chaotic Map Based Block Cryptosystem with Application to Camera Sensor Networks

PubMed Central

Guo, Xianfeng; Zhang, Jiashu; Khan, Muhammad Khurram; Alghathbar, Khaled

2011-01-01

Recently, Wang et al. presented an efficient logistic map based block encryption system. The encryption system employs feedback ciphertext to achieve plaintext dependence of sub-keys. Unfortunately, we discovered that their scheme is unable to withstand key stream attack. To improve its security, this paper proposes a novel chaotic map based block cryptosystem. At the same time, a secure architecture for camera sensor network is constructed. The network comprises a set of inexpensive camera sensors to capture the images, a sink node equipped with sufficient computation and storage capabilities and a data processing server. The transmission security between the sink node and the server is gained by utilizing the improved cipher. Both theoretical analysis and simulation results indicate that the improved algorithm can overcome the flaws and maintain all the merits of the original cryptosystem. In addition, computational costs and efficiency of the proposed scheme are encouraging for the practical implementation in the real environment as well as camera sensor network. PMID:22319371

An authenticated image encryption scheme based on chaotic maps and memory cellular automata

NASA Astrophysics Data System (ADS)

Bakhshandeh, Atieh; Eslami, Ziba

2013-06-01

This paper introduces a new image encryption scheme based on chaotic maps, cellular automata and permutation-diffusion architecture. In the permutation phase, a piecewise linear chaotic map is utilized to confuse the plain-image and in the diffusion phase, we employ the Logistic map as well as a reversible memory cellular automata to obtain an efficient and secure cryptosystem. The proposed method admits advantages such as highly secure diffusion mechanism, computational efficiency and ease of implementation. A novel property of the proposed scheme is its authentication ability which can detect whether the image is tampered during the transmission or not. This is particularly important in applications where image data or part of it contains highly sensitive information. Results of various analyses manifest high security of this new method and its capability for practical image encryption.

Improve EPA's AIRNow Air Quality Index Maps with NASA/NOAA Satellite Data

NASA Astrophysics Data System (ADS)

Pasch, A.; Zahn, P. H.; DeWinter, J. L.; Haderman, M. D.; White, J. E.; Dickerson, P.; Dye, T. S.; Martin, R. V.

2011-12-01

The U.S. Environmental Protection Agency's (EPA) AIRNow program provides maps of real-time hourly Air Quality Index (AQI) conditions and daily AQI forecasts nationwide (http://www.airnow.gov). The public uses these maps to make decisions concerning their respiratory health. The usefulness of the AIRNow air quality maps depends on the accuracy and spatial coverage of air quality measurements. Currently, the maps use only ground-based measurements, which have significant gaps in coverage in some parts of the United States. As a result, contoured AQI levels have high uncertainty in regions far from monitors. To improve the usefulness of air quality maps, scientists at EPA and Sonoma Technology, Inc. are working in collaboration with the National Aeronautics and Space Administration (NASA), the National Oceanic and Atmospheric Administration (NOAA), and university researchers on a project to incorporate additional measurements into the maps via the AIRNow Satellite Data Processor (ASDP). These measurements include estimated surface PM

Definition of the metric on the space clos{sub ∅}(X) of closed subsets of a metric space X and properties of mappings with values in clos{sub ∅}(R{sup n})

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhukovskii, E S; Panasenko, E A

2014-09-30

The paper is concerned with the extension of tests for superpositional measurability, Filippov's implicit function lemma and the Scorza Dragoni property to set-valued (and, as a corollary, to single-valued) mappings that fail to satisfy the Carathéodory conditions (the upper Carathéodory conditions) and are not continuous (upper semicontinuous) in the phase variable. The corresponding results depend on the introduction of the space clos{sub ∅}(X) of all closed subsets (including the empty set) of an arbitrary metric space X; a metric on clos{sub ∅}(X) is proposed; the space clos{sub ∅}(X) is shown to be complete whenever the original space X is; a criterion for convergence of a sequence ismore » put forward; mappings with values in clos{sub ∅}(X) are studied. Some results on set-valued mappings satisfying the Carathéodory conditions and having compact values in R{sup n} are shown to hold for mappings with values in clos{sub ∅}(R{sup n}), measurable in the first argument, and continuous in the proposed metric in the second argument. Bibliography: 22 titles.« less

Effects of sub-lethal high-pressure homogenization treatment on the outermost cellular structures and the volatile-molecule profiles of two strains of probiotic lactobacilli.

PubMed

Tabanelli, Giulia; Vernocchi, Pamela; Patrignani, Francesca; Del Chierico, Federica; Putignani, Lorenza; Vinderola, Gabriel; Reinheimer, Jorge A; Gardini, Fausto; Lanciotti, Rosalba

2015-01-01

Applying sub-lethal levels of high-pressure homogenization (HPH) to lactic acid bacteria has been proposed as a method of enhancing some of their functional properties. Because the principal targets of HPH are the cell-surface structures, the aim of this study was to examine the effect of sub-lethal HPH treatment on the outermost cellular structures and the proteomic profiles of two known probiotic bacterial strains. Moreover, the effect of HPH treatment on the metabolism of probiotic cells within a dairy product during its refrigerated storage was investigated using SPME-GC-MS. Transmission electron microscopy was used to examine the microstructural changes in the outermost cellular structures due to HPH treatment. These alterations may be involved in the changes in some of the technological and functional properties of the strains that were observed after pressure treatment. Moreover, the proteomic profiles of the probiotic strains treated with HPH and incubated at 37°C for various periods showed different peptide patterns compared with those of the untreated cells. In addition, there were differences in the peaks that were observed in the low-mass spectral region (2000-3000 Da) of the spectral profiles of the control and treated samples. Due to pressure treatment, the volatile-molecule profiles of buttermilk inoculated with treated or control cells and stored at 4°C for 30 days exhibited overall changes in the aroma profile and in the production of molecules that improved its sensory profile, although the two different species imparted specific fingerprints to the product. The results of this study will contribute to understanding the changes that occur in the outermost cellular structures and the metabolism of LAB in response to HPH treatment. The findings of this investigation may contribute to elucidating the relationships between these changes and the alterations of the technological and functional properties of LAB induced by pressure treatment.

Beyond the biomedical: community resources for mental health care in rural Ethiopia.

PubMed

Selamu, Medhin; Asher, Laura; Hanlon, Charlotte; Medhin, Girmay; Hailemariam, Maji; Patel, Vikram; Thornicroft, Graham; Fekadu, Abebaw

2015-01-01

The focus of discussion in addressing the treatment gap is often on biomedical services. However, community resources can benefit health service scale-up in resource-constrained settings. These assets can be captured systematically through resource mapping, a method used in social action research. Resource mapping can be informative in developing complex mental health interventions, particularly in settings with limited formal mental health resources. We employed resource mapping within the Programme for Improving Mental Health Care (PRIME), to systematically gather information on community assets that can support integration of mental healthcare into primary care in rural Ethiopia. A semi-structured instrument was administered to key informants. Community resources were identified for all 58 sub-districts of the study district. The potential utility of these resources for the provision of mental healthcare in the district was considered. The district is rich in community resources: There are over 150 traditional healers, 164 churches and mosques, and 401 religious groups. There were on average 5 eddir groups (traditional funeral associations) per sub-district. Social associations and 51 micro-finance institutions were also identified. On average, two traditional bars were found in each sub-district. The eight health centres and 58 satellite clinics staffed by Health Extension Workers (HEWs) represented all the biomedical health services in the district. In addition the Health Development Army (HDA) are community volunteers who support health promotion and prevention activities. The plan for mental healthcare integration in this district was informed by the resource mapping. Community and religious leaders, HEWs, and HDA may have roles in awareness-raising, detection and referral of people with mental illness, improving access to medical care, supporting treatment adherence, and protecting human rights. The diversity of community structures will be used to support rehabilitation and social reintegration. Alcohol use was identified as a target disorder for community-level intervention.

Beyond the Biomedical: Community Resources for Mental Health Care in Rural Ethiopia

PubMed Central

Selamu, Medhin; Asher, Laura; Hanlon, Charlotte; Medhin, Girmay; Hailemariam, Maji; Patel, Vikram; Thornicroft, Graham; Fekadu, Abebaw

2015-01-01

Background The focus of discussion in addressing the treatment gap is often on biomedical services. However, community resources can benefit health service scale-up in resource-constrained settings. These assets can be captured systematically through resource mapping, a method used in social action research. Resource mapping can be informative in developing complex mental health interventions, particularly in settings with limited formal mental health resources. Method We employed resource mapping within the Programme for Improving Mental Health Care (PRIME), to systematically gather information on community assets that can support integration of mental healthcare into primary care in rural Ethiopia. A semi-structured instrument was administered to key informants. Community resources were identified for all 58 sub-districts of the study district. The potential utility of these resources for the provision of mental healthcare in the district was considered. Results The district is rich in community resources: There are over 150 traditional healers, 164 churches and mosques, and 401 religious groups. There were on average 5 eddir groups (traditional funeral associations) per sub-district. Social associations and 51 micro-finance institutions were also identified. On average, two traditional bars were found in each sub-district. The eight health centres and 58 satellite clinics staffed by Health Extension Workers (HEWs) represented all the biomedical health services in the district. In addition the Health Development Army (HDA) are community volunteers who support health promotion and prevention activities. Discussion The plan for mental healthcare integration in this district was informed by the resource mapping. Community and religious leaders, HEWs, and HDA may have roles in awareness-raising, detection and referral of people with mental illness, improving access to medical care, supporting treatment adherence, and protecting human rights. The diversity of community structures will be used to support rehabilitation and social reintegration. Alcohol use was identified as a target disorder for community-level intervention. PMID:25962075

MapA, an iron-regulated, cytoplasmic membrane protein in the cyanobacterium Synechococcus sp. strain PCC7942.

PubMed

Webb, R; Troyan, T; Sherman, D; Sherman, L A

1994-08-01

Growth of Synechococcus sp. strain PCC 7942 in iron-deficient media leads to the accumulation of an approximately 34-kDa protein. The gene encoding this protein, mapA (membrane-associated protein A), has been cloned and sequenced (GenBank accession number, L01621). The mapA transcript is not detectable in normally grown cultures but is stably accumulated by cells grown in iron-deficient media. However, the promoter sequence for this gene does not resemble other bacterial iron-regulated promoters described to date. The carboxyl-terminal region of the derived amino acid sequence of MapA resembles bacterial proteins involved in iron acquisition, whereas the amino-terminal end of MapA has a high degree of amino acid identity with the abundant, chloroplast envelope protein E37. An approach employing improved cellular fractionation techniques as well as electron microscopy and immunocytochemistry was essential in localizing MapA protein to the cytoplasmic membrane of Synechococcus sp. strain PCC 7942. When these cells were grown under iron-deficient conditions, a significant fraction of MapA could also be localized to the thylakoid membranes.

A photometric study of Enceladus

NASA Technical Reports Server (NTRS)

Verbiscer, Anne J.; Veverka, Joseph

1994-01-01

We have supplemented Voyager imaging data from Enceladus (limited to phase angles of 13 deg-43 deg) with recent Earth-based CCD observations to obtain an improved determination of the Bond albedo, to construct an albedo map of the satellite, and to constrain parameters in Hapke's (1986) photometric equation. A major result is evidence of regional variations in the physical properties of Enceladus' surface. The average global photometric properties are described by single scattering albedo omega(sub 0) average = 0.998 +/- 0.001, macroscopic roughness parameter theta average = 6 +/- 1 deg, and Henyey-Greenstein asymmetry parameter g = -0.399 +/- 0.005. The value of theta average is smaller than the 14 deg found by fitting whole-disk data, which include all terrains on Enceladus. The opposition surge amplitude B(sub 0) = 0.21 +/- 0.07 and regolith compaction parameter h = 0.014 +/- 0.02 are loosely constrained by the scarcity of and uncertainty in near-opposition observations. From the solar phase curve we determine the geometric albedo of Enceladus p(sub v) = 0.99 +/- 0.06 and phase integral q = 0.92 +/- 0.05, which corresponds to a spherical albedo A = p(sub v)q = 0.91 +/- 0.1. Since the spectrum of Enceladus is fairly flat, we can approximate the Bond albedo A(sub B) with the spherical albedo. Our photometric analysis is summarized in terms of an albedo map which generally reproduces the satellite's observed lightcurve and indicates that normal reflectances range from 0.9 on the leading hemisphere to 1.4 on the trailing one. The albedo map also revels an albedo variation of 15% from longitudes 170 deg to 200 deg, corresponding to the boundary between the leading and trailing hemispheres.

Multi-scale continuum modeling of biological processes: from molecular electro-diffusion to sub-cellular signaling transduction

NASA Astrophysics Data System (ADS)

Cheng, Y.; Kekenes-Huskey, P.; Hake, J. E.; Holst, M. J.; McCammon, J. A.; Michailova, A. P.

2012-01-01

This paper presents a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of the time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times, with increasing ionic strength, and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a nonlinear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally derived rodent ventricular myocyte geometries. Results reveal the important role of mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate sub-cellular Ca2+ signals. The model predicts that reduced off-rate in the whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for the integration of molecular-scale information into simulations of cellular-scale systems.

Lysophosphatidic acid receptor-5 negatively regulates cellular responses in mouse fibroblast 3T3 cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Yan; Hirane, Miku; Araki, Mutsumi

2014-04-04

Highlights: • LPA{sub 5} inhibits the cell growth and motile activities of 3T3 cells. • LPA{sub 5} suppresses the cell motile activities stimulated by hydrogen peroxide in 3T3 cells. • Enhancement of LPA{sub 5} on the cell motile activities inhibited by LPA{sub 1} in 3T3 cells. • The expression and activation of Mmp-9 were inhibited by LPA{sub 5} in 3T3 cells. • LPA signaling via LPA{sub 5} acts as a negative regulator of cellular responses in 3T3 cells. - Abstract: Lysophosphatidic acid (LPA) signaling via G protein-coupled LPA receptors (LPA{sub 1}–LPA{sub 6}) mediates a variety of biological functions, including cellmore » migration. Recently, we have reported that LPA{sub 1} inhibited the cell motile activities of mouse fibroblast 3T3 cells. In the present study, to evaluate a role of LPA{sub 5} in cellular responses, Lpar5 knockdown (3T3-L5) cells were generated from 3T3 cells. In cell proliferation assays, LPA markedly stimulated the cell proliferation activities of 3T3-L5 cells, compared with control cells. In cell motility assays with Cell Culture Inserts, the cell motile activities of 3T3-L5 cells were significantly higher than those of control cells. The activity levels of matrix metalloproteinases (MMPs) were measured by gelatin zymography. 3T3-L5 cells stimulated the activation of Mmp-2, correlating with the expression levels of Mmp-2 gene. Moreover, to assess the co-effects of LPA{sub 1} and LPA{sub 5} on cell motile activities, Lpar5 knockdown (3T3a1-L5) cells were also established from Lpar1 over-expressing (3T3a1) cells. 3T3a1-L5 cells increased the cell motile activities of 3T3a1 cells, while the cell motile activities of 3T3a1 cells were significantly lower than those of control cells. These results suggest that LPA{sub 5} may act as a negative regulator of cellular responses in mouse fibroblast 3T3 cells, similar to the case for LPA{sub 1}.« less

Quantitative Susceptibility Mapping: Contrast Mechanisms and Clinical Applications

PubMed Central

Liu, Chunlei; Wei, Hongjiang; Gong, Nan-Jie; Cronin, Matthew; Dibb, Russel; Decker, Kyle

2016-01-01

Quantitative susceptibility mapping (QSM) is a recently developed MRI technique for quantifying the spatial distribution of magnetic susceptibility within biological tissues. It first uses the frequency shift in the MRI signal to map the magnetic field profile within the tissue. The resulting field map is then used to determine the spatial distribution of the underlying magnetic susceptibility by solving an inverse problem. The solution is achieved by deconvolving the field map with a dipole field, under the assumption that the magnetic field is a result of the superposition of the dipole fields generated by all voxels and that each voxel has its unique magnetic susceptibility. QSM provides improved contrast to noise ratio for certain tissues and structures compared to its magnitude counterpart. More importantly, magnetic susceptibility is a direct reflection of the molecular composition and cellular architecture of the tissue. Consequently, by quantifying magnetic susceptibility, QSM is becoming a quantitative imaging approach for characterizing normal and pathological tissue properties. This article reviews the mechanism generating susceptibility contrast within tissues and some associated applications. PMID:26844301

A cellular automaton model for ship traffic flow in waterways

NASA Astrophysics Data System (ADS)

Qi, Le; Zheng, Zhongyi; Gang, Longhui

2017-04-01

With the development of marine traffic, waterways become congested and more complicated traffic phenomena in ship traffic flow are observed. It is important and necessary to build a ship traffic flow model based on cellular automata (CAs) to study the phenomena and improve marine transportation efficiency and safety. Spatial discretization rules for waterways and update rules for ship movement are two important issues that are very different from vehicle traffic. To solve these issues, a CA model for ship traffic flow, called a spatial-logical mapping (SLM) model, is presented. In this model, the spatial discretization rules are improved by adding a mapping rule. And the dynamic ship domain model is considered in the update rules to describe ships' interaction more exactly. Take the ship traffic flow in the Singapore Strait for example, some simulations were carried out and compared. The simulations show that the SLM model could avoid ship pseudo lane-change efficiently, which is caused by traditional spatial discretization rules. The ship velocity change in the SLM model is consistent with the measured data. At finally, from the fundamental diagram, the relationship between traffic ability and the lengths of ships is explored. The number of ships in the waterway declines when the proportion of large ships increases.

Spatial reconstruction of single-cell gene expression data.

PubMed

Satija, Rahul; Farrell, Jeffrey A; Gennert, David; Schier, Alexander F; Regev, Aviv

2015-05-01

Spatial localization is a key determinant of cellular fate and behavior, but methods for spatially resolved, transcriptome-wide gene expression profiling across complex tissues are lacking. RNA staining methods assay only a small number of transcripts, whereas single-cell RNA-seq, which measures global gene expression, separates cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos and generated a transcriptome-wide map of spatial patterning. We confirmed Seurat's accuracy using several experimental approaches, then used the strategy to identify a set of archetypal expression patterns and spatial markers. Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems.

A land-cover map for South and Southeast Asia derived from SPOT-VEGETATION data

USGS Publications Warehouse

Stibig, H.-J.; Belward, A.S.; Roy, P.S.; Rosalina-Wasrin, U.; Agrawal, S.; Joshi, P.K.; ,; Beuchle, R.; Fritz, S.; Mubareka, S.; Giri, C.

2007-01-01

Aim  Our aim was to produce a uniform ‘regional’ land-cover map of South and Southeast Asia based on ‘sub-regional’ mapping results generated in the context of the Global Land Cover 2000 project.Location  The ‘region’ of tropical and sub-tropical South and Southeast Asia stretches from the Himalayas and the southern border of China in the north, to Sri Lanka and Indonesia in the south, and from Pakistan in the west to the islands of New Guinea in the far east.Methods  The regional land-cover map is based on sub-regional digital mapping results derived from SPOT-VEGETATION satellite data for the years 1998–2000. Image processing, digital classification and thematic mapping were performed separately for the three sub-regions of South Asia, continental Southeast Asia, and insular Southeast Asia. Landsat TM images, field data and existing national maps served as references. We used the FAO (Food and Agriculture Organization) Land Cover Classification System (LCCS) for coding the sub-regional land-cover classes and for aggregating the latter to a uniform regional legend. A validation was performed based on a systematic grid of sample points, referring to visual interpretation from high-resolution Landsat imagery. Regional land-cover area estimates were obtained and compared with FAO statistics for the categories ‘forest’ and ‘cropland’.Results  The regional map displays 26 land-cover classes. The LCCS coding provided a standardized class description, independent from local class names; it also allowed us to maintain the link to the detailed sub-regional land-cover classes. The validation of the map displayed a mapping accuracy of 72% for the dominant classes of ‘forest’ and ‘cropland’; regional area estimates for these classes correspond reasonably well to existing regional statistics.Main conclusions  The land-cover map of South and Southeast Asia provides a synoptic view of the distribution of land cover of tropical and sub-tropical Asia, and it delivers reasonable thematic detail and quantitative estimates of the main land-cover proportions. The map may therefore serve for regional stratification or modelling of vegetation cover, but could also support the implementation of forest policies, watershed management or conservation strategies at regional scales.

Reconstruction of an SSR-based Magnaporthe oryzae physical map to locate avirulence gene AvrPi12.

PubMed

Li, Tonghui; Wen, Jianqiang; Zhang, Yaling; Correll, James; Wang, Ling; Pan, Qinghua

2018-05-31

Pathogen avirulence (Avr) genes can evolve rapidly when challenged by the widespread deployment of host genes for resistance. They can be effectively isolated by positional cloning provided a robust and well-populated genetic map is available. An updated, SSR-based physical map of the rice blast pathogen Magnaporthe oryzae (Mo) has been constructed based on 116 of the 120 SSRs used to assemble the last map, along with 18 newly developed ones. A comparison between the two versions of the map has revealed an altered marker content and order within most of the Mo chromosomes. The avirulence gene AvrPi12 was mapped in a population of 219 progeny derived from a cross between the two Mo isolates CHL42 and CHL357. A bulked segregant analysis indicated that the gene was located on chromosome 6, a conclusion borne out by an analysis of the pattern of segregation shown by individual isolates. Six additional PCR-based markers were developed to improve the map resolution in the key region. AvrPi12 was finally located within the sub-telomeric region of chromosome 6, distal to the SSR locus LSM6-5. The improved SSR-based linkage map should be useful as a platform for gene mapping and isolation in Mo. It was used to establish the location of AvrPi12, thereby providing a starting point for its positional cloning.

The protein expression landscape of the Arabidopsis root

PubMed Central

Petricka, Jalean J.; Schauer, Monica A.; Megraw, Molly; Breakfield, Natalie W.; Thompson, J. Will; Georgiev, Stoyan; Soderblom, Erik J.; Ohler, Uwe; Moseley, Martin Arthur; Grossniklaus, Ueli; Benfey, Philip N.

2012-01-01

Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein–protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development. PMID:22447775

Explicit blow-up solutions to the Schroedinger maps from R{sup 2} to the hyperbolic 2-space H{sup 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding Qing

2009-10-15

In this article, we prove that the equation of the Schroedinger maps from R{sup 2} to the hyperbolic 2-space H{sup 2} is SU(1,1)-gauge equivalent to the following 1+2 dimensional nonlinear Schroedinger-type system of three unknown complex functions p, q, r, and a real function u: iq{sub t}+q{sub zz}-2uq+2(pq){sub z}-2pq{sub z}-4|p|{sup 2}q=0, ir{sub t}-r{sub zz}+2ur+2(pr){sub z}-2pr{sub z}+4|p|{sup 2}r=0, ip{sub t}+(qr){sub z}-u{sub z}=0, p{sub z}+p{sub z}=-|q|{sup 2}+|r|{sup 2}, -r{sub z}+q{sub z}=-2(pr+pq), where z is a complex coordinate of the plane R{sup 2} and z is the complex conjugate of z. Although this nonlinear Schroedinger-type system looks complicated, it admits a class ofmore » explicit blow-up smooth solutions: p=0, q=(e{sup i(bzz/2(a+bt))}/a+bt){alpha}z, r=e{sup -i(bzz/2(a+bt))}/(a+bt){alpha}z, u=2{alpha}{sup 2}zz/(a+bt){sup 2}, where a and b are real numbers with ab<0 and {alpha} satisfies {alpha}{sup 2}=b{sup 2}/16. From these facts, we explicitly construct smooth solutions to the Schroedinger maps from R{sup 2} to the hyperbolic 2-space H{sup 2} by using the gauge transformations such that the absolute values of their gradients blow up in finite time. This reveals some blow-up phenomenon of Schroedinger maps.« less

Correlative characterization of primary particles formed in as-cast Al-Mg alloy containing a high level of Sc

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Shi'ang

Primary particles formed in as-cast Al-5Mg-0.6Sc alloy and their role in microstructure and mechanical properties of the alloy were investigated using optical microscopy (OM), scanning electron microscopy (SEM), electron back-scatter diffraction (EBSD) and tensile testing. It was found that primary particles due to a close orientation to matrix could serve as the potent heterogeneous nucleation sites for α-Al during solidification and thus impose a remarkable grain refinement effect. Eutectic structure consisted of layer by layer of ‘Al{sub 3}Sc + α-Al + Al{sub 3}Sc + ⋯’ and cellular-dendritic substructure were simultaneously observed at the particles inside, indicating that these particles couldmore » be identified as the eutectics rather than individual Al{sub 3}Sc phase. A calculating method, based on EBSD results, was introduced for the spatial distribution of these particles in matrix. The results showed that these eutectic particles randomly distributed in matrix. In addition, the formation of primary eutectic particles significant improved the strength of the Al-Mg alloy in as-cast condition, which is ascribed to the structural evolution from coarse dendrites to prefect fine equiaxed grains. On the other hand, these large-sized particles due to the tendency to act as the microcrack sources could cause a harmful effect in the ductility of Al-Mg-Sc alloy. - Highlights: •Primary particles exhibit an ‘Al{sub 3}Sc + α-Al + Al{sub 3}Sc + ⋯’ multilayer feature with a cellular-dendritic mode of growth. •EBSD analyses the mechanism of grain refinement and the distribution of primary particles in α-Al matrix. •A computational method was presented to calculate the habit planes of primary particles.« less

A 3D Image Filter for Parameter-Free Segmentation of Macromolecular Structures from Electron Tomograms

PubMed Central

Ali, Rubbiya A.; Landsberg, Michael J.; Knauth, Emily; Morgan, Garry P.; Marsh, Brad J.; Hankamer, Ben

2012-01-01

3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters—the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms. PMID:22479430

Self-organizing feature maps for dynamic control of radio resources in CDMA microcellular networks

NASA Astrophysics Data System (ADS)

Hortos, William S.

1998-03-01

The application of artificial neural networks to the channel assignment problem for cellular code-division multiple access (CDMA) cellular networks has previously been investigated. CDMA takes advantage of voice activity and spatial isolation because its capacity is only interference limited, unlike time-division multiple access (TDMA) and frequency-division multiple access (FDMA) where capacities are bandwidth-limited. Any reduction in interference in CDMA translates linearly into increased capacity. To satisfy the high demands for new services and improved connectivity for mobile communications, microcellular and picocellular systems are being introduced. For these systems, there is a need to develop robust and efficient management procedures for the allocation of power and spectrum to maximize radio capacity. Topology-conserving mappings play an important role in the biological processing of sensory inputs. The same principles underlying Kohonen's self-organizing feature maps (SOFMs) are applied to the adaptive control of radio resources to minimize interference, hence, maximize capacity in direct-sequence (DS) CDMA networks. The approach based on SOFMs is applied to some published examples of both theoretical and empirical models of DS/CDMA microcellular networks in metropolitan areas. The results of the approach for these examples are informally compared to the performance of algorithms, based on Hopfield- Tank neural networks and on genetic algorithms, for the channel assignment problem.

In vitro biocompatibility study of sub-5 nm silica-coated magnetic iron oxide fluorescent nanoparticles for potential biomedical application.

PubMed

Foglia, Sabrina; Ledda, Mario; Fioretti, Daniela; Iucci, Giovanna; Papi, Massimiliano; Capellini, Giovanni; Lolli, Maria Grazia; Grimaldi, Settimio; Rinaldi, Monica; Lisi, Antonella

2017-04-19

Magnetic iron oxide nanoparticles (IONPs), for their intriguing properties, have attracted a great interest as they can be employed in many different biomedical applications. In this multidisciplinary study, we synthetized and characterized ultrafine 3 nm superparamagnetic water-dispersible nanoparticles. By a facile and inexpensive one-pot approach, nanoparticles were coated with a shell of silica and contemporarily functionalized with fluorescein isothiocyanate (FITC) dye. The obtained sub-5 nm silica-coated magnetic iron oxide fluorescent (sub-5 SIO-Fl) nanoparticles were assayed for cellular uptake, biocompatibility and cytotoxicity in a human colon cancer cellular model. By confocal microscopy analysis we demonstrated that nanoparticles as-synthesized are internalized and do not interfere with the CaCo-2 cell cytoskeletal organization nor with their cellular adhesion. We assessed that they do not exhibit cytotoxicity, providing evidence that they do not affect shape, proliferation, cellular viability, cell cycle distribution and progression. We further demonstrated at molecular level that these nanoparticles do not interfere with the expression of key differentiation markers and do not affect pro-inflammatory cytokines response in Caco-2 cells. Overall, these results showed the in vitro biocompatibility of the sub-5 SIO-Fl nanoparticles promising their safe employ for diagnostic and therapeutic biomedical applications.

The UL24 protein of herpes simplex virus 1 affects the sub-cellular distribution of viral glycoproteins involved in fusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ben Abdeljelil, Nawel; Rochette, Pierre-Alexandre; Pearson, Angela, E-mail: angela.pearson@iaf.inrs.ca

2013-09-15

Mutations in UL24 of herpes simplex virus type 1 can lead to a syncytial phenotype. We hypothesized that UL24 affects the sub-cellular distribution of viral glycoproteins involved in fusion. In non-immortalized human foreskin fibroblasts (HFFs) we detected viral glycoproteins B (gB), gD, gH and gL present in extended blotches throughout the cytoplasm with limited nuclear membrane staining; however, in HFFs infected with a UL24-deficient virus (UL24X), staining for the viral glycoproteins appeared as long, thin streaks running across the cell. Interestingly, there was a decrease in co-localized staining of gB and gD with F-actin at late times in UL24X-infected HFFs.more » Treatment with chemical agents that perturbed the actin cytoskeleton hindered the formation of UL24X-induced syncytia in these cells. These data support a model whereby the UL24 syncytial phenotype results from a mislocalization of viral glycoproteins late in infection. - Highlights: • UL24 affects the sub-cellular distribution of viral glycoproteins required for fusion. • Sub-cellular distribution of viral glycoproteins varies in cell-type dependent manner. • Drugs targeting actin microfilaments affect formation of UL24-related syncytia in HFFs.« less

Functionally Charged Polystyrene Particles Activate Immortalized Mouse Microglia (BV2): Cellular and Genomic Response

EPA Science Inventory

The effect of particle surface charge on the biological activation of immortalized mouse microglia (BV2) was examined. Same size (~850-950 nm) spherical polystyrene microparticles (SPM) with net negative (carboxyl, COOH-) or positive (dimethyl amino, CH₃)₂

Spatially resolved RNA-sequencing of the embryonic heart identifies a role for Wnt/β-catenin signaling in autonomic control of heart rate

PubMed Central

Burkhard, Silja Barbara

2018-01-01

Development of specialized cells and structures in the heart is regulated by spatially -restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development we used tomo-seq, combining high-throughput RNA-sequencing with tissue-sectioning, to establish a genome-wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub-compartments. Pacemaker cells in the sinoatrial region induce heart contractions, but little is known about the mechanisms underlying their development. Using our transcriptome map, we identified spatially restricted Wnt/β-catenin signaling activity in pacemaker cells, which was controlled by Islet-1 activity. Moreover, Wnt/β-catenin signaling controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus, this high-resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. PMID:29400650

Forces and dynamics in epithelial domes of controlled size and shape

NASA Astrophysics Data System (ADS)

Latorre-Ibars, Ernest; Casares, Laura; Gomez-Gonzalez, Manuel; Uroz, Marina; Arroyo, Marino; Trepat, Xavier

Mechanobiology of epithelia plays a central role in morphogenesis, wound healing, and tumor progression. Its current understanding relies on mechanical measurements on flat epithelial layers. However, most epithelia in vivo exhibit a curved 3D shape enclosing a pressurized lumen. Using soft micropatterned substrates we produce massive parallel arrays of epithelial domes with controlled size and basal shape. We measure epithelial traction, tension, and luminal pressure in epithelial domes. The local stress tensor on the freestanding epithelial membrane is then mapped by combining measured luminal pressure and local curvature. We show that tension and cell shape are highly anisotropic and vary along the meridional position of the domes. Finally, we establish constitutive relations between shape, tension, and pressure during perturbations of the contractile machinery, osmotic shocks, and spontaneous fluctuations of dome volume. Our findings contradict a description of the epithelium as a fluid capillary surface. Cells in the dome are unable to relax into a uniform and isotropic tensional state through sub- and supra-cellular rearrangements. Mapping epithelial shape, tension, and pressure will enable quantitative studies of mechanobiology in 3D epithelia of controlled size and shape.

A global interaction network maps a wiring diagram of cellular function

PubMed Central

Costanzo, Michael; VanderSluis, Benjamin; Koch, Elizabeth N.; Baryshnikova, Anastasia; Pons, Carles; Tan, Guihong; Wang, Wen; Usaj, Matej; Hanchard, Julia; Lee, Susan D.; Pelechano, Vicent; Styles, Erin B.; Billmann, Maximilian; van Leeuwen, Jolanda; van Dyk, Nydia; Lin, Zhen-Yuan; Kuzmin, Elena; Nelson, Justin; Piotrowski, Jeff S.; Srikumar, Tharan; Bahr, Sondra; Chen, Yiqun; Deshpande, Raamesh; Kurat, Christoph F.; Li, Sheena C.; Li, Zhijian; Usaj, Mojca Mattiazzi; Okada, Hiroki; Pascoe, Natasha; Luis, Bryan-Joseph San; Sharifpoor, Sara; Shuteriqi, Emira; Simpkins, Scott W.; Snider, Jamie; Suresh, Harsha Garadi; Tan, Yizhao; Zhu, Hongwei; Malod-Dognin, Noel; Janjic, Vuk; Przulj, Natasa; Troyanskaya, Olga G.; Stagljar, Igor; Xia, Tian; Ohya, Yoshikazu; Gingras, Anne-Claude; Raught, Brian; Boutros, Michael; Steinmetz, Lars M.; Moore, Claire L.; Rosebrock, Adam P.; Caudy, Amy A.; Myers, Chad L.; Andrews, Brenda; Boone, Charles

2017-01-01

We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing over 23 million double mutants, identifying ~550,000 negative and ~350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell. PMID:27708008

MODELING THE ANOMALY OF SURFACE NUMBER DENSITIES OF GALAXIES ON THE GALACTIC EXTINCTION MAP DUE TO THEIR FIR EMISSION CONTAMINATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kashiwagi, Toshiya; Suto, Yasushi; Taruya, Atsushi

The most widely used Galactic extinction map is constructed assuming that the observed far-infrared (FIR) fluxes come entirely from Galactic dust. According to the earlier suggestion by Yahata et al., we consider how FIR emission of galaxies affects the SFD map. We first compute the surface number density of Sloan Digital Sky Survey (SDSS) DR7 galaxies as a function of the r-band extinction, A {sub r,} {sub SFD}. We confirm that the surface densities of those galaxies positively correlate with A {sub r,} {sub SFD} for A {sub r,} {sub SFD} < 0.1, as first discovered by Yahata et al.more » for SDSS DR4 galaxies. Next we construct an analytical model to compute the surface density of galaxies, taking into account the contamination of their FIR emission. We adopt a log-normal probability distribution for the ratio of 100 μm and r-band luminosities of each galaxy, y ≡ (νL){sub 100} {sub μm}/(νL) {sub r}. Then we search for the mean and rms values of y that fit the observed anomaly, using the analytical model. The required values to reproduce the anomaly are roughly consistent with those measured from the stacking analysis of SDSS galaxies. Due to the limitation of our statistical modeling, we are not yet able to remove the FIR contamination of galaxies from the extinction map. Nevertheless, the agreement with the model prediction suggests that the FIR emission of galaxies is mainly responsible for the observed anomaly. Whereas the corresponding systematic error in the Galactic extinction map is 0.1-1 mmag, it is directly correlated with galaxy clustering and thus needs to be carefully examined in precision cosmology.« less

Observational Requirements for High-Fidelity Reverberation Mapping

NASA Technical Reports Server (NTRS)

Horne, Keith; Peterson, Bradley M.; Collier, Stefan J.; Netzer, Hagai

2004-01-01

We present a series of simulations to demonstrate that high-fidelity velocity-delay maps of the emission-line regions in active galactic nuclei can be obtained from time-resolved spectrophotometric data sets like those that will arise from the proposed Kronos satellite. While previous reverberation-mapping experiments have established the size scale R of the broad emission-line regions from the mean time delay tau = R/c between the line and continuum variations and have provided strong evidence for supermassive black holes, the detailed structure and kinematics of the broad-line region remain ambiguous and poorly constrained. Here we outline the technical improvements that will be required to successfully map broad-line regions by reverberation techniques. For typical AGN continuum light curves, characterized by power-law power spectra P (f) is proportional to f(exp -alpha) with a = -1.5 +/- 0.5, our simulations show that a small UV/optical spectrometer like Kronos will clearly distinguish between currently viable alternative kinematic models. From spectra sampled at time intervals Delta t and sustained for a total duration T(sub dur), we can reconstruct high-fidelity velocity-delay maps with velocity resolution comparable to that of the spectra, and delay resolution Delta tau approx. 2 Delta t, provided T(sub dur) exceeds the broad-line region light crossing time by at least a factor of three. Even very complicated kinematical models, such as a Keplerian flow with superimposed spiral wave pattern, are resolved in maps from our simulated Kronos datasets. Reverberation mapping with Kronos data is therefore likely deliver the first clear maps of the geometry and kinematics in the broad emission-line regions 1-100 microarcseconds from supermassive black holes.

Amide-based inhibitors of p38alpha MAP kinase. Part 2: design, synthesis and SAR of potent N-pyrimidyl amides.

PubMed

Tester, Richland; Tan, Xuefei; Luedtke, Gregory R; Nashashibi, Imad; Schinzel, Kurt; Liang, Weiling; Jung, Joon; Dugar, Sundeep; Liclican, Albert; Tabora, Jocelyn; Levy, Daniel E; Do, Steven

2010-04-15

Optimization of a tri-substituted N-pyridyl amide led to the discovery of a new class of potent N-pyrimidyl amide based p38alpha MAP kinase inhibitors. Initial SAR studies led to the identification of 5-dihydrofuran as an optimal hydrophobic group. Additional side chain modifications resulted in the introduction of hydrogen bond interactions. Through extensive SAR studies, analogs bearing free amino groups and alternatives to the parent (S)-alpha-methyl benzyl moiety were identified. These compounds exhibited improved cellular activities and maintained balance between p38alpha and CYP3A4 inhibition. Copyright 2010 Elsevier Ltd. All rights reserved.

New Funding Opportunity from the Human Biomolecular Atlas Program (HuBMAP)! | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) aims to develop a framework for functional mapping the human body with cellular resolution to enhance our understanding of cellular organization-function. HuBMAP will accelerate the development of the next generation of tools and techniques to generate 3D tissue maps using validated high-content, high-throughput imaging and omics assays, and establish an open data platform for integrating, visualizing data to build multi-dimensional maps.

THE CO-TO-H{sub 2} CONVERSION FACTOR AND DUST-TO-GAS RATIO ON KILOPARSEC SCALES IN NEARBY GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sandstrom, K. M.; Walter, F.; Leroy, A. K.

2013-11-01

We present ∼kiloparsec spatial resolution maps of the CO-to-H{sub 2} conversion factor (α{sub CO}) and dust-to-gas ratio (DGR) in 26 nearby, star-forming galaxies. We have simultaneously solved for α{sub CO} and the DGR by assuming that the DGR is approximately constant on kiloparsec scales. With this assumption, we can combine maps of dust mass surface density, CO-integrated intensity, and H I column density to solve for both α{sub CO} and the DGR with no assumptions about their value or dependence on metallicity or other parameters. Such a study has just become possible with the availability of high-resolution far-IR maps frommore » the Herschel key program KINGFISH, {sup 12}CO J = (2-1) maps from the IRAM 30 m large program HERACLES, and H I 21 cm line maps from THINGS. We use a fixed ratio between the (2-1) and (1-0) lines to present our α{sub CO} results on the more typically used {sup 12}CO J = (1-0) scale and show using literature measurements that variations in the line ratio do not affect our results. In total, we derive 782 individual solutions for α{sub CO} and the DGR. On average, α{sub CO} = 3.1 M{sub ☉} pc{sup –2} (K km s{sup –1}){sup –1} for our sample with a standard deviation of 0.3 dex. Within galaxies, we observe a generally flat profile of α{sub CO} as a function of galactocentric radius. However, most galaxies exhibit a lower α{sub CO} value in the central kiloparsec—a factor of ∼2 below the galaxy mean, on average. In some cases, the central α{sub CO} value can be factors of 5-10 below the standard Milky Way (MW) value of α{sub CO,{sub MW}} = 4.4 M{sub ☉} pc{sup –2} (K km s{sup –1}){sup –1}. While for α{sub CO} we find only weak correlations with metallicity, the DGR is well-correlated with metallicity, with an approximately linear slope. Finally, we present several recommendations for choosing an appropriate α{sub CO} for studies of nearby galaxies.« less

Interval mapping of high growth (hg), a major locus that increases weight gain in mice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horvat, S.; Medrano, J.F.

1995-04-01

The high growth locus (hg) causes a major increase in weight gain and body size in mice. As a first step to map-based cloning of hg, we developed a genetic map of the hg-containing region using interval mapping of 403 F{sub 2} from a C57BL/6J-hghg x CAST/EiJ cross. The maximum likelihood position of hg was at the chromosome 10 marker D10Mit41 (LOD = 24.8) in the F{sub 2} females and 1.5 cM distal to D10Mit41 (LOD = 9.56) in the F{sub 2} males with corresponding LOD 2 support intervals of 3.7 and 5.4 cM, respectively. The peak LOD scores weremore » significantly higher than the estimated empirical threshold LOD values. The localization of hg by interval mapping was supported by a test cross of F{sub 2} mice recombinant between the LOD 2 support interval and the flanking marker. The interval mapping and test-cross indicate that hg is not allelic with candidate genes Igf1 or decorin (Dcn), a gene that was mapped close to hg in this study. The hg inheritance was recessive in females, although we could not reject recessive or additive inheritance in males. Possible causes for sex differences in peak LOD scores and for the distortion of transmission ratios observed in F{sub 2} males are discussed. The genetic map of the hg region will facilitate further fine mapping and cloning of hg, and allow searches for a homologous quantitative trait locus affecting growth in humans and domestic animals. 48 refs., 3 figs., 3 tabs.« less

Potential Land Mapping for Agricultural Extentification in Mengwi Sub-district to Support Food Balance in Badung Regency, Indonesia

NASA Astrophysics Data System (ADS)

Made Trigunasih, Ni; Lanya, Indayati; Ratna Adi, I. G. P.; Hutauruk, Jeremia; Feronika

2017-12-01

The availability of agricultural land for food crops, especially in Bali, is rapidly declining every year. The availability of rice fields in Badung regency, especially in Mengwi Sub-district until 2040 is no longer exist, this means that Mengwi Sub-district has lost the rice fields. The existence of land conversion will affect food availability for the country, so there will be food deficit. The food balance in Badung Regency in 2015 with Cultivation Index (IP) and initial productivity in each Sub-district showed a food deficit of 32,843.44 tons, then after increasing IP of 2,5 the productivity in Kecamatan Petang and Kuta at 7 tons / ha, and Abiansemal, Mengwi and North Kuta Sub-districts with 8 tons / ha which indicate a surplus in 2020 and 2030 respectively of 25,155.19 tons, and 3,401.79 tons. But in 2040 and 2050 there was a food deficiency of 18,434.78 tons and 11,824.82 tons respectively. Considering that productivity improvement efforts cannot rely solely on intensification approaches, but also need to be done with extensification or expansion of agricultural areas to support food production. This research was conducted in Mengwi Sub-district, Badung Regency. Mengwi Sub-district consists of 20 villages. The objectives of this research are: (1) to map potential land that can be converted to agricultural land of food crops, and (2) to know the amount of food demand to supply food balance in Badung Regency in 2040. Research methodology includes (1) preliminary study, (2) interpretation of satellite images, (3) mapping and measurement of land area, and (4) calculation of additional food availability. The results indicate that the potential land that can be converted to agricultural land for food crops is 132 ha, consists of 128.51 ha of mixed plantation and 3.49 ha of bare land/bush. The result of additional land produced 1601.73 tons of rice that increased the food availability in Mengwi Sub-district to 45425.7 tons. The addition of surplus in 2040 in Mengwi sub-district amounted to 21669.23 tons but did not cover the food deficit in Badung regency in 2040.

Mapping agroecosystem zone using remote sensing for food security analysis in Bantul district Daerah Istimewa Yogyakarta

NASA Astrophysics Data System (ADS)

Murti, Sigit Heru

2017-10-01

Food security is one of the most important issue for Indonesia. The huge population number and high population growing rate has made the food security a critical issue. This paper describe the application of remote sensing data to (1) map agroecosystem zones in Bantul District, Special Region of Yogyakarta, Indonesia in 2012 and (2) analyze the food security in the study area based on the resulting agro-ecosystem map. Bantul District is selected as the pilot area because this area is among the highest food crop production area in the Province. ALOS AVNIR-2 image accquired on 15 June 2010 was integrated with Indonesian Surface map (RBI map), soil types map, and slope steepness map. Population statistics data was also used to calculate the food needs. Field survey was conducted to obtain the crop field productivity information on each agro-ecosystem zone and assess the accuracy of the model. This research indicates that (1) Bantul District can be divided into three agroecosystem zones, where each zone has unique topograhic configuration and soil types composition, and (2) Bantul Distict is categorized as food secure area since the rice production in 2012 managed to cover the food needs of the people with the surplus of 33,208.6 tonnes of rice. However, when the analysis was conducted at sub-district level, there are four subdistrict with food insecurity where the food needs surpass the rice production. These sub-district are Kasihan Sub-district (-5,598.4 t), Banguntapan Sub-district (-2,483.4 t), Pajangan Sub-district (-1,039.6 t) and Dlingo Sub-district (-798.7 t).

MapA, an iron-regulated, cytoplasmic membrane protein in the cyanobacterium Synechococcus sp. strain PCC7942.

PubMed Central

Webb, R; Troyan, T; Sherman, D; Sherman, L A

1994-01-01

Growth of Synechococcus sp. strain PCC 7942 in iron-deficient media leads to the accumulation of an approximately 34-kDa protein. The gene encoding this protein, mapA (membrane-associated protein A), has been cloned and sequenced (GenBank accession number, L01621). The mapA transcript is not detectable in normally grown cultures but is stably accumulated by cells grown in iron-deficient media. However, the promoter sequence for this gene does not resemble other bacterial iron-regulated promoters described to date. The carboxyl-terminal region of the derived amino acid sequence of MapA resembles bacterial proteins involved in iron acquisition, whereas the amino-terminal end of MapA has a high degree of amino acid identity with the abundant, chloroplast envelope protein E37. An approach employing improved cellular fractionation techniques as well as electron microscopy and immunocytochemistry was essential in localizing MapA protein to the cytoplasmic membrane of Synechococcus sp. strain PCC 7942. When these cells were grown under iron-deficient conditions, a significant fraction of MapA could also be localized to the thylakoid membranes. Images PMID:8051004

Bedmap2; Mapping, visualizing and communicating the Antarctic sub-glacial environment.

NASA Astrophysics Data System (ADS)

Fretwell, Peter; Pritchard, Hamish

2013-04-01

Bedmap2; Mapping, visualizing and communicating the Antarctic sub-glacial environment. The Bedmap2 project has been a large cooperative effort to compile, model, map and visualize the ice-rock interface beneath the Antarctic ice sheet. Here we present the final output of that project; the Bedmap2 printed map. The map is an A1, double sided print, showing 2d and 3d visualizations of the dataset. It includes scientific interpretations, cross sections and comparisons with other areas. Paper copies of the colour double sided map will be freely distributed at this session.

Comparative mapping of Pluto's sub-Charon hemisphere - Three least squares models based on mutual event lightcurves

NASA Technical Reports Server (NTRS)

Young, Eliot F.; Binzel, Richard P.

1993-01-01

Observations of Charon transits are used here to derive preliminary maps of Pluto's sub-Charon hemisphere. Three models are used to describe the brightness of Pluto's surface as functions of latitude and longitude. Mapping results are presented using spherical harmonic functions, polynomial functions, and finite elements. A smoothing algorithm applied to the maps is described and the validity and resolution of the maps is tested by reconstruction from synthetic data. A preliminary finding from the maps is that the south polar region has the highest albedo of any location on the planet.

Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM

PubMed Central

Kishchenko, Gregory P.; Danev, Radostin; Fisher, Rebecca; He, Jie; Hsieh, Chyongere; Marko, Michael; Sui, Haixin

2015-01-01

Zernike phase-plate (ZPP) imaging greatly increases contrast in cryo-electron microscopy, however fringe artifacts appear in the images. A computational de-fringing method has been proposed, but it has not been widely employed, perhaps because the importance of de-fringing has not been clearly demonstrated. For testing purposes, we employed Zernike phase-plate imaging in a cryo-electron tomographic study of radial-spoke complexes attached to microtubule doublets. We found that the contrast enhancement by ZPP imaging made nonlinear denoising insensitive to the filtering parameters, such that simple low-frequency band-pass filtering made the same improvement in map quality. We employed sub-tomogram averaging, which compensates for the effect of the “missing wedge” and considerably improves map quality. We found that fringes (caused by the abrupt cut-on of the central hole in the phase plate) can lead to incorrect representation of a structure that is well-known from the literature. The expected structure was restored by amplitude scaling, as proposed in the literature. Our results show that de-fringing is an important part of image-processing for cryo-electron tomography of macromolecular complexes with ZPP imaging. PMID:26210582

Quantitatively Mapping Cellular Viscosity with Detailed Organelle Information via a Designed PET Fluorescent Probe

PubMed Central

Liu, Tianyu; Liu, Xiaogang; Spring, David R.; Qian, Xuhong; Cui, Jingnan; Xu, Zhaochao

2014-01-01

Viscosity is a fundamental physical parameter that influences diffusion in biological processes. The distribution of intracellular viscosity is highly heterogeneous, and it is challenging to obtain a full map of cellular viscosity with detailed organelle information. In this work, we report 1 as the first fluorescent viscosity probe which is able to quantitatively map cellular viscosity with detailed organelle information based on the PET mechanism. This probe exhibited a significant ratiometric fluorescence intensity enhancement as solvent viscosity increases. The emission intensity increase was attributed to combined effects of the inhibition of PET due to restricted conformational access (favorable for FRET, but not for PET), and the decreased PET efficiency caused by viscosity-dependent twisted intramolecular charge transfer (TICT). A full map of subcellular viscosity was successfully constructed via fluorescent ratiometric detection and fluorescence lifetime imaging; it was found that lysosomal regions in a cell possess the highest viscosity, followed by mitochondrial regions. PMID:24957323

Porosity and mechanical properties of zirconium ceramics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buyakova, S., E-mail: sbuyakova@ispms.tsc.ru; Kulkov, S.; Tomsk Polytechnic University

2015-11-17

Has been studied a porous ceramics obtained from ultra-fine powders. Porous ceramic ZrO{sub 2}(MgO), ZrO{sub 2}(Y{sub 2}O{sub 3}) powder was prepared by pressing and subsequent sintering of compacts homologous temperatures ranging from 0.63 to 0.56 during the isothermal holding duration of 1 to 5 hours. The porosity of ceramic samples was from 15 to 80%. The structure of the ceramic materials produced from plasma-sprayed ZrO{sub 2} powder was represented as a system of cell and rod structure elements. Cellular structure formed by stacking hollow powder particles can be easily seen at the images of fracture surfaces of obtained ceramics. Theremore » were three types of pores in ceramics: large cellular hollow spaces, small interparticle pores which are not filled with powder particles and the smallest pores in the shells of cells. The cells generally did not have regular shapes. The size of the interior of the cells many times exceeded the thickness of the walls which was a single-layer packing of ZrO{sub 2} grains. A distinctive feature of all deformation diagrams obtained in the experiment was their nonlinearity at low deformations which was described by the parabolic law. It was shown that the observed nonlinear elasticity for low deformation on deformation diagrams is due to mechanical instability of the cellular elements in the ceramic carcass.« less

No evidence for a local renin-angiotensin system in liver mitochondria

PubMed Central

Astin, Ronan; Bentham, Robert; Djafarzadeh, Siamak; Horscroft, James A.; Kuc, Rhoda E.; Leung, Po Sing; Skipworth, James R. A.; Vicencio, Jose M.; Davenport, Anthony P.; Murray, Andrew J.; Takala, Jukka; Jakob, Stephan M.; Montgomery, Hugh; Szabadkai, Gyorgy

2013-01-01

The circulating, endocrine renin-angiotensin system (RAS) is important to circulatory homeostasis, while ubiquitous tissue and cellular RAS play diverse roles, including metabolic regulation. Indeed, inhibition of RAS is associated with improved cellular oxidative capacity. Recently it has been suggested that an intra-mitochondrial RAS directly impacts on metabolism. Here we sought to rigorously explore this hypothesis. Radiolabelled ligand-binding and unbiased proteomic approaches were applied to purified mitochondrial sub-fractions from rat liver, and the impact of AngII on mitochondrial function assessed. Whilst high-affinity AngII binding sites were found in the mitochondria-associated membrane (MAM) fraction, no RAS components could be detected in purified mitochondria. Moreover, AngII had no effect on the function of isolated mitochondria at physiologically relevant concentrations. We thus found no evidence of endogenous mitochondrial AngII production, and conclude that the effects of AngII on cellular energy metabolism are not mediated through its direct binding to mitochondrial targets. PMID:23959064

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mi; University of Chinese Academy of Sciences, Beijing 100049; Liu, Lianqing, E-mail: lqliu@sia.cn

Highlights: •Nanoscale cellular ultra-structures of macrophages were observed. •The binding affinities of FcγRs were measured directly on macrophages. •The nanoscale distributions of FcγRs were mapped on macrophages. -- Abstract: Fc gamma receptors (FcγR), widely expressed on effector cells (e.g., NK cells, macrophages), play an important role in clinical cancer immunotherapy. The binding of FcγRs to the Fc portions of antibodies that are attached to the target cells can activate the antibody-dependent cell-mediated cytotoxicity (ADCC) killing mechanism which leads to the lysis of target cells. In this work, we used atomic force microscopy (AFM) to observe the cellular ultra-structures and measuremore » the biophysical properties (affinity and distribution) of FcγRs on single macrophages in aqueous environments. AFM imaging was used to obtain the topographies of macrophages, revealing the nanoscale cellular fine structures. For molecular interaction recognition, antibody molecules were attached onto AFM tips via a heterobifunctional polyethylene glycol (PEG) crosslinker. With AFM single-molecule force spectroscopy, the binding affinities of FcγRs were quantitatively measured on single macrophages. Adhesion force mapping method was used to localize the FcγRs, revealing the nanoscale distribution of FcγRs on local areas of macrophages. The experimental results can improve our understanding of FcγRs on macrophages; the established approach will facilitate further research on physiological activities involved in antibody-based immunotherapy.« less

Combining Human and Machine Learning to Map Cropland in the 21st Century's Major Agricultural Frontier

NASA Astrophysics Data System (ADS)

Estes, L. D.; Debats, S. R.; Caylor, K. K.; Evans, T. P.; Gower, D.; McRitchie, D.; Searchinger, T.; Thompson, D. R.; Wood, E. F.; Zeng, L.

2016-12-01

In the coming decades, large areas of new cropland will be created to meet the world's rapidly growing food demands. Much of this new cropland will be in sub-Saharan Africa, where food needs will increase most and the area of remaining potential farmland is greatest. If we are to understand the impacts of global change, it is critical to accurately identify Africa's existing croplands and how they are changing. Yet the continent's smallholder-dominated agricultural systems are unusually challenging for remote sensing analyses, making accurate area estimates difficult to obtain, let alone important details related to field size and geometry. Fortunately, the rapidly growing archives of moderate to high-resolution satellite imagery hosted on open servers now offer an unprecedented opportunity to improve landcover maps. We present a system that integrates two critical components needed to capitalize on this opportunity: 1) human image interpretation and 2) machine learning (ML). Human judgment is needed to accurately delineate training sites within noisy imagery and a highly variable cover type, while ML provides the ability to scale and to interpret large feature spaces that defy human comprehension. Because large amounts of training data are needed (a major impediment for analysts), we use a crowdsourcing platform that connects amazon.com's Mechanical Turk service to satellite imagery hosted on open image servers. Workers map visible fields at pre-assigned sites, and are paid according to their mapping accuracy. Initial tests show overall high map accuracy and mapping rates >1800 km2/hour. The ML classifier uses random forests and randomized quasi-exhaustive feature selection, and is highly effective in classifying diverse agricultural types in southern Africa (AUC > 0.9). We connect the ML and crowdsourcing components to make an interactive learning framework. The ML algorithm performs an initial classification using a first batch of crowd-sourced maps, using thresholds of posterior probabilities to segregate sub-images classified with high or low confidence. Workers are then directed to collect new training data in low confidence sub-images, after which classification is repeated and re-assessed, and the entire process iterated until maximum possible accuracy is realized.

Analysis of uniformity of as prepared and irradiated S.I. GaAs radiation detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nava, F.; Vanni, P.; Canali, C.

1998-06-01

SI (semi-insulating) LEC (Liquid Encapsulated Czochralsky) GaAs (gallium arsenide) Schottky barrier detectors have been irradiated with high energy protons (24 GeV/c, fluence up to 16.45 {times} 10{sup 13} p/cm{sup 2}). The detectors have been characterized in terms of I/V curves, charge collection efficiency (cce) for incident 5.48 MeV {alpha}-, 2 MeV proton and minimum ionizing {beta}-particles and of cce maps by microprobe technique IBIC (Ion Beam Induced Charge). At the highest fluence a significant degradation of the electron and hole collection efficiencies and a remarkable improvement of the Full Width Half Maximum (FWHM) energy resolution have been measured with {alpha}-more » and proton particles. Furthermore, the reduction in the cce is greater than the one measured with {beta}-particles and the energy resolution worsens with increasing the applied bias, V{sub a}, above the voltage V{sub d} necessary to extend the electric field al the way to the ohmic contact. On the contrary, in the unirradiated detectors the charge collection efficiencies with {alpha}-, {beta}- and proton particles are quite similar and the energy resolution improves with increasing V{sub a} > V{sub d}. IBIC spectra and IBIC space maps obtained by scanning a focused (8 {micro}m{sup 2}) 2 MeV proton microbeam on front (Schottky) and back (ohmic) contacts, support the observed electric field dependence of the energy resolution both in unirradiated and most irradiated detectors. The results obtained let them explain the effect of the electric field strength and the plasma on the collection of the charge carriers and the FWHM energy resolution.« less

Mapping Agricultural Fields in Sub-Saharan Africa with a Computer Vision Approach

NASA Astrophysics Data System (ADS)

Debats, S. R.; Luo, D.; Estes, L. D.; Fuchs, T.; Caylor, K. K.

2014-12-01

Sub-Saharan Africa is an important focus for food security research, because it is experiencing unprecedented population growth, agricultural activities are largely dominated by smallholder production, and the region is already home to 25% of the world's undernourished. One of the greatest challenges to monitoring and improving food security in this region is obtaining an accurate accounting of the spatial distribution of agriculture. Households are the primary units of agricultural production in smallholder communities and typically rely on small fields of less than 2 hectares. Field sizes are directly related to household crop productivity, management choices, and adoption of new technologies. As population and agriculture expand, it becomes increasingly important to understand both the distribution of field sizes as well as how agricultural communities are spatially embedded in the landscape. In addition, household surveys, a common tool for tracking agricultural productivity in Sub-Saharan Africa, would greatly benefit from spatially explicit accounting of fields. Current gridded land cover data sets do not provide information on individual agricultural fields or the distribution of field sizes. Therefore, we employ cutting edge approaches from the field of computer vision to map fields across Sub-Saharan Africa, including semantic segmentation, discriminative classifiers, and automatic feature selection. Our approach aims to not only improve the binary classification accuracy of cropland, but also to isolate distinct fields, thereby capturing crucial information on size and geometry. Our research focuses on the development of descriptive features across scales to increase the accuracy and geographic range of our computer vision algorithm. Relevant data sets include high-resolution remote sensing imagery and Landsat (30-m) multi-spectral imagery. Training data for field boundaries is derived from hand-digitized data sets as well as crowdsourcing.

Geomorphology and depositional sub-environments of Assateague Island MD/VA

USGS Publications Warehouse

Morton, Robert A.; Bracone, Jeremy E.; Cooke, Brian

2007-01-01

The U.S. Geological Survey is studying coastal hazards and coastal change to improve our understanding of coastal ecosystems and to develop better capabilities of predicting future coastal change. One approach to understanding the dynamics of coastal systems is to monitor changes in barrier-island sub-environments through time. This involves examining morphological and topographic change at time scales ranging from millennia to years and space scales ranging from tens of kilometers to meters. Of particular interest are the processes that produce those changes and determining whether or not those processes are likely to persist into the future. In these analyses of hazards and change, both natural and anthropogenic influences are considered. Quantifying past magnitudes and rates of coastal change and knowing the principal factors that govern those changes are critical to predicting what changes are likely to occur under different scenarios, such as short-term impacts of extreme storms or long-term impacts of sea-level rise. Assateague Island MD/VA was selected for detailed mapping of barrier island morphology and topography because the island offers a diversity of depositional sub-environments that are representative of other barrier islands along the middle Atlantic coast. The geomorphology and sub-environment map emphasizes the origins of the surficial features and it also serves as a basis for documenting which sub-environments are relatively stable, such as the barrier island core, and those that are highly dynamic, such as the beach and active overwash zones.

THE DARKEST SHADOWS: DEEP MID-INFRARED EXTINCTION MAPPING OF A MASSIVE PROTOCLUSTER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butler, Michael J.; Tan, Jonathan C.; Kainulainen, Jouni

We use deep 8 μm Spitzer-IRAC imaging of massive Infrared Dark Cloud (IRDC) G028.37+00.07 to construct a mid-infrared (MIR) extinction map that probes mass surface densities up to Σ ∼ 1 g cm{sup –2} (A{sub V} ∼ 200 mag), amongst the highest values yet probed by extinction mapping. Merging with an NIR extinction map of the region creates a high dynamic range map that reveals structures down to A{sub V} ∼ 1 mag. We utilize the map to: (1) measure a cloud mass ∼7 × 10{sup 4} M {sub ☉} within a radius of ∼8 pc. {sup 13}CO kinematics indicate thatmore » the cloud is gravitationally bound. It thus has the potential to form one of the most massive young star clusters known in the Galaxy. (2) Characterize the structures of 16 massive cores within the IRDC, finding they can be fit by singular polytropic spheres with ρ∝r{sup −k{sub ρ}} and k {sub ρ} = 1.3 ± 0.3. They have Σ-bar ≃0.1--0.4 g cm{sup −2}—relatively low values that, along with their measured cold temperatures, suggest that magnetic fields, rather than accretion-powered radiative heating, are important for controlling fragmentation of these cores. (3) Determine the Σ (equivalently column density or A{sub V} ) probability distribution function (PDF) for a region that is nearly complete for A{sub V} > 3 mag. The PDF is well fit by a single log-normal with mean A-bar {sub V}≃9 mag, high compared to other known clouds. It does not exhibit a separate high-end power law tail, which has been claimed to indicate the importance of self-gravity. However, we suggest that the PDF does result from a self-similar, self-gravitating hierarchy of structures present over a wide range of scales in the cloud.« less

Cellular content of biomolecules in sub-seafloor microbial communities

NASA Astrophysics Data System (ADS)

Braun, Stefan; Morono, Yuki; Becker, Kevin W.; Hinrichs, Kai-Uwe; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-09-01

Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density centrifugation. Amino acids, amino sugars, muramic acid, and intact polar lipids were analyzed in both whole sediment and cell extract, and cell separation was optimized and evaluated in terms of purity, separation efficiency, taxonomic resemblance, and compatibility to high-performance liquid chromatography and mass spectrometry for biomolecule analyses. Because cell extracts from density centrifugation still contained considerable amounts of detrital particles and non-cellular biomolecules, we further purified cells from two samples by fluorescence-activated cell sorting (FACS). Cells from these highly purified cell extracts had an average content of amino acids and lipids of 23-28 fg cell-1 and 2.3 fg cell-1, respectively, with an estimated carbon content of 19-24 fg cell-1. In the sediment, the amount of biomolecules associated with vegetative cells was up to 70-fold lower than the total biomolecule content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates of microbial biomass.

Chaos analysis of viscoelastic chaotic flows of polymeric fluids in a micro-channel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lim, C. P.; Lam, Y. C., E-mail: myclam@ntu.edu.sg; BioSystems and Micromechanics

2015-07-15

Many fluids, including biological fluids such as mucus and blood, are viscoelastic. Through the introduction of chaotic flows in a micro-channel and the construction of maps of characteristic chaos parameters, differences in viscoelastic properties of these fluids can be measured. This is demonstrated by creating viscoelastic chaotic flows induced in an H-shaped micro-channel through the steady infusion of a polymeric fluid of polyethylene oxide (PEO) and another immiscible fluid (silicone oil). A protocol for chaos analysis was established and demonstrated for the analysis of the chaotic flows generated by two polymeric fluids of different molecular weight but with similar relaxationmore » times. The flows were shown to be chaotic through the computation of their correlation dimension (D{sub 2}) and the largest Lyapunov exponent (λ{sub 1}), with D{sub 2} being fractional and λ{sub 1} being positive. Contour maps of D{sub 2} and λ{sub 1} of the respective fluids in the operating space, which is defined by the combination of polymeric fluids and silicone oil flow rates, were constructed to represent the characteristic of the chaotic flows generated. It was observed that, albeit being similar, the fluids have generally distinct characteristic maps with some similar trends. The differences in the D{sub 2} and λ{sub 1} maps are indicative of the difference in the molecular weight of the polymers in the fluids because the driving force of the viscoelastic chaotic flows is of molecular origin. This approach in constructing the characteristic maps of chaos parameters can be employed as a diagnostic tool for biological fluids and, more generally, chaotic signals.« less

Time-resolved multicolor two-photon excitation fluorescence microscopy of cells and tissues

NASA Astrophysics Data System (ADS)

Zheng, Wei

2014-11-01

Multilabeling which maps the distribution of different targets is an indispensable technique in many biochemical and biophysical studies. Two-photon excitation fluorescence (TPEF) microscopy of endogenous fluorophores combining with conventional fluorescence labeling techniques such as genetically encoded fluorescent protein (FP) and fluorescent dyes staining could be a powerful tool for imaging living cells. However, the challenge is that the excitation and emission wavelength of these endogenous fluorophores and fluorescent labels are very different. A multi-color ultrafast source is required for the excitation of multiple fluorescence molecules. In this study, we developed a two-photon imaging system with excitations from the pump femtosecond laser and the selected supercontinuum generated from a photonic crystal fiber (PCF). Multiple endogenous fluorophores, fluorescent proteins and fluorescent dyes were excited in their optimal wavelengths simultaneously. A time- and spectral-resolved detection system was used to record the TPEF signals. This detection technique separated the TPEF signals from multiple sources in time and wavelength domains. Cellular organelles such as nucleus, mitochondria, microtubule and endoplasmic reticulum, were clearly revealed in the TPEF images. The simultaneous imaging of multiple fluorophores of cells will greatly aid the study of sub-cellular compartments and protein localization.

Scanning micro-Hall probe mapping of magnetic flux distributions and current densities in YBa{sub 2}Cu{sub 3}O{sub 7}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xing, W.; Heinrich, B.; Zhou, H.

1994-12-31

Mapping of the magnetic flux density B{sub z} (perpendicular to the film plane) for a YBa{sub 2}Cu{sub 3}O{sub 7} thin-film sample was carried out using a scanning micro-Hall probe. The sheet magnetization and sheet current densities were calculated from the B{sub z} distributions. From the known sheet magnetization, the tangential (B{sub x,y}) and normal components of the flux density B were calculated in the vicinity of the film. It was found that the sheet current density was mostly determined by 2B{sub x,y}/d, where d is the film thickness. The evolution of flux penetration as a function of applied field willmore » be shown.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giuliani, Sarah E; Frank, Ashley M; Corgliano, Danielle M

Abstract Background: Transporter proteins are one of an organism s primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and regulatory networks. The functional annotation of most transporters is currently limited to general classification into families. The development of capabilities to map ligands with specific transporters would improve our knowledge of the function of these proteins, improve the annotation of related genomes, and facilitate predictions for their role in cellular responses to environmental changes. Results: To improve the utility of the functional annotation for ABC transporters, we expressed and purifiedmore » the set of solute binding proteins from Rhodopseudomonas palustris and characterized their ligand-binding specificity. Our approach utilized ligand libraries consisting of environmental and cellular metabolic compounds, and fluorescence thermal shift based high throughput ligand binding screens. This process resulted in the identification of specific binding ligands for approximately 64% of the purified and screened proteins. The collection of binding ligands is representative of common functionalities associated with many bacterial organisms as well as specific capabilities linked to the ecological niche occupied by R. palustris. Conclusion: The functional screen identified specific ligands that bound to ABC transporter periplasmic binding subunits from R. palustris. These assignments provide unique insight for the metabolic capabilities of this organism and are consistent with the ecological niche of strain isolation. This functional insight can be used to improve the annotation of related organisms and provides a route to evaluate the evolution of this important and diverse group of transporter proteins.« less

Subnormalized states and trace-nonincreasing maps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cappellini, Valerio; Sommers, Hans-Juergen; Zyczkowski, Karol

2007-05-15

We investigate the set of completely positive, trace-nonincreasing linear maps acting on the set M{sub N} of mixed quantum states of size N. Extremal point of this set of maps are characterized and its volume with respect to the Hilbert-Schmidt (HS) (Euclidean) measure is computed explicitly for an arbitrary N. The spectra of partially reduced rescaled dynamical matrices associated with trace-nonincreasing completely positive maps belong to the N cube inscribed in the set of subnormalized states of size N. As a by-product we derive the measure in M{sub N} induced by partial trace of mixed quantum states distributed uniformly withmore » respect to the HS measure in M{sub N{sup 2}}.« less

The Shuttle Radar Topography Mission: A Global DEM

NASA Technical Reports Server (NTRS)

Farr, Tom G.; Kobrick, Mike

2000-01-01

Digital topographic data are critical for a variety of civilian, commercial, and military applications. Scientists use Digital Elevation Models (DEM) to map drainage patterns and ecosystems, and to monitor land surface changes over time. The mountain-building effects of tectonics and the climatic effects of erosion can also be modeled with DEW The data's military applications include mission planning and rehearsal, modeling and simulation. Commercial applications include determining locations for cellular phone towers, enhanced ground proximity warning systems for aircraft, and improved maps for backpackers. The Shuttle Radar Topography Mission (SRTM) (Fig. 1), is a cooperative project between NASA and the National Imagery and Mapping Agency (NIMA) of the U.S. Department of Defense. The mission is designed to use a single-pass radar interferometer to produce a digital elevation model of the Earth's land surface between about 60 degrees north and south latitude. The DEM will have 30 m pixel spacing and about 15 m vertical errors.

Ground-Based Robotic Sensing of an Agricultural Sub-Canopy Environment

NASA Astrophysics Data System (ADS)

Burns, A.; Peschel, J.

2015-12-01

Airborne remote sensing is a useful method for measuring agricultural crop parameters over large areas; however, the approach becomes limited to above-canopy characterization as a crop matures due to reduced visual access of the sub-canopy environment. During the growth cycle of an agricultural crop, such as soybeans, the micrometeorology of the sub-canopy environment can significantly impact pod development and reduced yields may result. Larger-scale environmental conditions aside, the physical structure and configuration of the sub-canopy matrix will logically influence local climate conditions for a single plant; understanding the state and development of the sub-canopy could inform crop models and improve best practices but there are currently no low-cost methods to quantify the sub-canopy environment at a high spatial and temporal resolution over an entire growth cycle. This work describes the modification of a small tactical and semi-autonomous, ground-based robotic platform with sensors capable of mapping the physical structure of an agricultural row crop sub-canopy; a soybean crop is used as a case study. Point cloud data representing the sub-canopy structure are stored in LAS format and can be used for modeling and visualization in standard GIS software packages.

Using Leaf Chlorophyll to Parameterize Light-Use-Efficiency Within a Thermal-Based Carbon, Water and Energy Exchange Model

NASA Technical Reports Server (NTRS)

Houlborg, Rasmus; Anderson, Martha C.; Daughtry, C. S. T.; Kustas, W. P.; Rodell, Matthew

2010-01-01

Chlorophylls absorb photosynthetically active radiation and thus function as vital pigments for photosynthesis, which makes leaf chlorophyll content (C(sub ab) useful for monitoring vegetation productivity and an important indicator of the overall plant physiological condition. This study investigates the utility of integrating remotely sensed estimates of C(sub ab) into a thermal-based Two-Source Energy Balance (TSEB) model that estimates land-surface CO2 and energy fluxes using an analytical, light-use-efficiency (LUE) based model of canopy resistance. The LUE model component computes canopy-scale carbon assimilation and transpiration fluxes and incorporates LUE modifications from a nominal (species-dependent) value (LUE(sub n)) in response to short term variations in environmental conditions, However LUE(sub n) may need adjustment on a daily timescale to accommodate changes in plant phenology, physiological condition and nutrient status. Day to day variations in LUE(sub n) were assessed for a heterogeneous corn crop field in Maryland, U,S.A. through model calibration with eddy covariance CO2 flux tower observations. The optimized daily LUE(sub n) values were then compared to estimates of C(sub ab) integrated from gridded maps of chlorophyll content weighted over the tower flux source area. The time continuous maps of daily C(sub ab) over the study field were generated by focusing in-situ measurements with retrievals generated with an integrated radiative transfer modeling tool (accurate to within +/-10%) using at-sensor radiances in green, red and near-infrared wavelengths acquired with an aircraft imaging system. The resultant daily changes in C(sub ab) within the tower flux source area generally correlated well with corresponding changes in daily calibrated LUE(sub n) derived from the tower flux data, and hourly water, energy and carbon flux estimation accuracies from TSEB were significantly improved when using C(sub ab) for delineating spatio-temporal variations in LUE(sub n). The results demonstrate the synergy between thermal infrared and shortwave reflective wavebands in producing valuable remote sensing data for operational monitoring of carbon and water fluxes.

High School Biology: A Group Approach to Concept Mapping.

ERIC Educational Resources Information Center

Brown, David S.

2003-01-01

Explains concept mapping as an instructional method in cooperative learning environments, and describes a study investigating the effectiveness of concept mapping on student learning during a photosynthesis and cellular respiration unit. Reports on the positive effects of concept mapping in the experimental group. (Contains 16 references.) (YDS)

Integration of sewer system maps in topographically based sub-basin delineation in suburban areas

NASA Astrophysics Data System (ADS)

Jankowfsky, Sonja; Branger, Flora; Braud, Isabelle; Rodriguez, Fabrice

2010-05-01

Due to the increase of urbanization, suburban areas experience a fast change in land use. The impact of such modifications on the watershed hydrological cycle must be quantified. To achieve this goal, distributed hydrological models offer the possibility to take into account land use change, and more particularly to consider urbanized areas and anthropogenic features such as roads or ditches and their impact on the hydrological cycle. A detailed definition of the hydrographical drainage network and a corresponding delineation of sub-basins is therefore necessary as input to distributed models. Sub-basins in natural catchments are usually delineated using standard GIS based terrain analysis. The drainage network in urbanised watersheds is often modified, due to sewer systems, ditches, retention basins, etc.. Therefore, its delineation is not only determined by topography. The simple application of terrain analysis algorithms to delineate sub-basins in suburban areas can consequently lead to erroneous sub-basin borders. This study presents an improved approach for sub-basin delineation in suburban areas. It applies to small catchments connected to a sewage plant, located outside the catchment boundary. The approach assumes that subsurface flow follows topography. The method requires a digital elevation model (DEM), maps of land use, cadastre, sewer system and the location of measurement stations and retention basins. Firstly, the topographic catchment border must be defined for the concerning flow measurement station. Standard GIS based algorithms, like the d8-flow direction algorithm (O'Callaghan and Mark, 1984) can be applied using a high resolution DEM. Secondly, the artificial catchment outlets have to be determined. Each catchment has one natural outlet - the measurement station on the river- but it can have several artificial outlets towards a sewage station. Once the outlets are determined, a first approximation of the "theoretical maximal contributing area" can be made. It encompasses the whole connected sewer system and the topographic catchment boundary. The area of interest is therefore defined. The next step is the determination of the extended drainage network, consisting of the natural river, ditches, combined and separated sewer systems and retention basins. This requires a detailed analysis of sewer system data, field work (mapping of ditches and inlets into the natural river). Contacts with local authorities are also required to keep up-to-date about recent changes. Pure wastewater and drinking water pipes are not integrated in the drainage network. In order to have a unique drainage network for the model, choices might have to be made in case of several coexisting drainage pipes. The urban sub-basins are then delineated with the help of a cadastral map (Rodriguez et al., 2003) or an aerial photography. Each cadastral unit is connected to the closest drainage pipe, following the principle of proximity and gravity. The assembly of all cadastral units connected to one network reach represents one urban sub-basin. The sub-basins in the rural part are calculated using the d8 flow direction and watershed delineation algorithm with "stream burning" (Hutchinson, 1989). One sub-basin is delineated for each reach of the extended drainage network. Some manual corrections of the calculated sub-basins are necessary. Finally, the urban and rural sub-basins are merged by subtraction of the urban area from the rural area and subsequent union of both maps. This method was applied to the Chaudanne catchment, a sub-basin of the Yzeron catchment (ca. 4 km2) in the suburban region of Lyon city, France. The method leads to a 30 % extended catchment area, as compared to the topographic catchment area. For each river inlet the sub-basin area could be determined, as well as for each retention basin. This information can be directly used for the dimensioning of retention basins, pipe diameters, etc.

Sirt1 protects against oxidative stress-induced renal tubular cell apoptosis by the bidirectional regulation of catalase expression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasegawa, Kazuhiro; Wakino, Shu; Yoshioka, Kyoko

2008-07-18

NAD{sup +}-dependent protein deacetylase Sirt1 regulates cellular apoptosis. We examined the role of Sirt1 in renal tubular cell apoptosis by using HK-2 cells, proximal tubular cell lines with or without reactive oxygen species (ROS), H{sub 2}O{sub 2}. Without any ROS, Sirt1 inhibitors enhanced apoptosis and the expression of ROS scavenger, catalase, and Sirt1 overexpression downregulated catalase. When apoptosis was induced with H{sub 2}O{sub 2}, Sirt1 was upregulated with the concomitant increase in catalase expression. Sirt1 overexpression rescued H{sub 2}O{sub 2}-induced apoptosis through the upregulation of catalase. H{sub 2}O{sub 2} induced the nuclear accumulation of forkhead transcription factor, FoxO3a and themore » gene silencing of FoxO3a enhanced H{sub 2}O{sub 2}-induced apoptosis. In conclusion, endogenous Sirt1 maintains cell survival by regulating catalase expression and by preventing the depletion of ROS required for cell survival. In contrast, excess ROS upregulates Sirt1, which activates FoxO3a and catalase leading to rescuing apoptosis. Thus, Sirt1 constitutes a determinant of renal tubular cell apoptosis by regulating cellular ROS levels.« less

Mission Adaptive UAS Platform for Earth Science Resource Assessment

NASA Technical Reports Server (NTRS)

Dunagan, S.; Fladeland, M.; Ippolito, C.; Knudson, M.

2015-01-01

NASA Ames Research Center has led a number of important Earth science remote sensing missions including several directed at the assessment of natural resources. A key asset for accessing high risk airspace has been the 180 kg class SIERRA UAS platform, providing mission durations of up to 8 hrs at altitudes up to 3 km. Recent improvements to this mission capability are embodied in the incipient SIERRA-B variant. Two resource mapping problems having unusual mission characteristics requiring a mission adaptive capability are explored here. One example involves the requirement for careful control over solar angle geometry for passive reflectance measurements. This challenges the management of resources in the coastal ocean where solar angle combines with sea state to produce surface glint that can obscure the ocean color signal. Furthermore, as for all scanning imager applications, the primary flight control priority to fly the UAS directly to the next waypoint should compromise with the requirement to minimize roll and crab effects in the imagery. A second example involves the mapping of natural resources in the Earth's crust using precision magnetometry. In this case the vehicle flight path must be oriented to optimize magnetic flux gradients over a spatial domain having continually emerging features, while optimizing the efficiency of the spatial mapping task. These requirements were highlighted in several recent Earth Science missions including the October 2013 OCEANIA mission directed at improving the capability for hyperspectral reflectance measurements in the coastal ocean, and the Surprise Valley Mission directed at mapping sub-surface mineral composition and faults, using high-sensitivity magentometry. This paper reports the development of specific aircraft control approaches to incorporate the unusual and demanding requirements to manage solar angle, aircraft attitude and flight path orientation, and efficient (directly geo-rectified) surface and sub-surface mapping, including the near-time optimization of these sometimes conflicting requirements. *

Improving axial resolution in confocal microscopy with new high refractive index mounting media.

PubMed

Fouquet, Coralie; Gilles, Jean-François; Heck, Nicolas; Dos Santos, Marc; Schwartzmann, Richard; Cannaya, Vidjeacoumary; Morel, Marie-Pierre; Davidson, Robert Stephen; Trembleau, Alain; Bolte, Susanne

2015-01-01

Resolution, high signal intensity and elevated signal to noise ratio (SNR) are key issues for biologists who aim at studying the localisation of biological structures at the cellular and subcellular levels using confocal microscopy. The resolution required to separate sub-cellular biological structures is often near to the resolving power of the microscope. When optimally used, confocal microscopes may reach resolutions of 180 nm laterally and 500 nm axially, however, axial resolution in depth is often impaired by spherical aberration that may occur due to refractive index mismatches. Spherical aberration results in broadening of the point-spread function (PSF), a decrease in peak signal intensity when imaging in depth and a focal shift that leads to the distortion of the image along the z-axis and thus in a scaling error. In this study, we use the novel mounting medium CFM3 (Citifluor Ltd., UK) with a refractive index of 1.518 to minimize the effects of spherical aberration. This mounting medium is compatible with most common fluorochromes and fluorescent proteins. We compare its performance with established mounting media, harbouring refractive indices below 1.500, by estimating lateral and axial resolution with sub-resolution fluorescent beads. We show furthermore that the use of the high refractive index media renders the tissue transparent and improves considerably the axial resolution and imaging depth in immuno-labelled or fluorescent protein labelled fixed mouse brain tissue. We thus propose to use those novel high refractive index mounting media, whenever optimal axial resolution is required.

CONSTRAINING THE MILKY WAY POTENTIAL WITH A SIX-DIMENSIONAL PHASE-SPACE MAP OF THE GD-1 STELLAR STREAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koposov, Sergey E.; Rix, Hans-Walter; Hogg, David W., E-mail: koposov@ast.cam.ac.u

2010-03-20

The narrow GD-1 stream of stars, spanning 60{sup 0} on the sky at a distance of {approx}10 kpc from the Sun and {approx}15 kpc from the Galactic center, is presumed to be debris from a tidally disrupted star cluster that traces out a test-particle orbit in the Milky Way halo. We combine Sloan Digital Sky Survey (SDSS) photometry, USNO-B astrometry, and SDSS and Calar Alto spectroscopy to construct a complete, empirical six-dimensional (6D) phase-space map of the stream. We find that an eccentric orbit in a flattened isothermal potential describes this phase-space map well. Even after marginalizing over the streammore » orbital parameters and the distance from the Sun to the Galactic center, the orbital fit to GD-1 places strong constraints on the circular velocity at the Sun's radius V{sub c} = 224 +- 13 km s{sup -1} and total potential flattening q{sub P}HI = 0.87{sup +0.07}{sub -0.04}. When we drop any informative priors on V{sub c} , the GD-1 constraint becomes V{sub c} = 221 +- 18 km s{sup -1}. Our 6D map of GD-1, therefore, yields the best current constraint on V{sub c} and the only strong constraint on q{sub P}HI at Galactocentric radii near R {approx} 15 kpc. Much, if not all, of the total potential flattening may be attributed to the mass in the stellar disk, so the GD-1 constraints on the flattening of the halo itself are weak: q{sub P}HI{sub ,halo} > 0.89 at 90% confidence. The greatest uncertainty in the 6D map and the orbital analysis stems from the photometric distances, which will be obviated by GAIA.« less

Induction of sister chromatid exchanges and inhibition of cellular proliferation in vitro. I. Caffeine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guglielmi, G.E.; Vogt, T.F.; Tice, R.R.

1982-01-01

While many agents have been examined for their ability to induce SCE's, complete dose-response information has often been lacking. We have reexamined the ability of one such compound - caffeine - to induce SCEs and also to inhibit cellular proliferation in human peripheral lymphocytes in vitro. An acute exposure to caffeine prior to the DNA synthetic period did not affect either SCE frequency or the rate of cellular proliferation. Chronic exposure to caffeine throughout the culture period lead to both a dose-dependent increase in SCEs (SCE/sub d/ or doubling dose = 2.4 mM; SCE/sub 10/ or the dose capable ofmore » inducing 10 SCE = 1.4 mM) and a dose-dependent inhibition of cellular proliferation (IC/sub 50/ or the 50% inhibition concentration = 2.6 mM). The relative proportion of first generation metaphase cells, an assessment of proliferative inhibiton, increased linearly with increasing caffeine concentrations. However, SCE frequency increased nonlinearly over the same range of caffeine concentrations. Examination of the ratio of nonsymmetrical to symmetrical SCEs in third generation metaphase cells indicated that caffeine induced SCEs in equal frequency in each of three successive generations. The dependency of SCE induction and cellular proliferative inhibition on caffeine's presence during the DNA synthetic period suggests that caffeine may act as an antimetabolite in normal human cells.« less

Transient Expression and Cellular Localization of Recombinant Proteins in Cultured Insect Cells.

PubMed

Fabrick, Jeffrey A; Hull, J Joe

2017-04-20

Heterologous protein expression systems are used for the production of recombinant proteins, the interpretation of cellular trafficking/localization, and the determination of the biochemical function of proteins at the sub-organismal level. Although baculovirus expression systems are increasingly used for protein production in numerous biotechnological, pharmaceutical, and industrial applications, nonlytic systems that do not involve viral infection have clear benefits but are often overlooked and underutilized. Here, we describe a method for generating nonlytic expression vectors and transient recombinant protein expression. This protocol allows for the efficient cellular localization of recombinant proteins and can be used to rapidly discern protein trafficking within the cell. We show the expression of four recombinant proteins in a commercially available insect cell line, including two aquaporin proteins from the insect Bemisia tabaci, as well as subcellular marker proteins specific for the cell plasma membrane and for intracellular lysosomes. All recombinant proteins were produced as chimeras with fluorescent protein markers at their carboxyl termini, which allows for the direct detection of the recombinant proteins. The double transfection of cells with plasmids harboring constructs for the genes of interest and a known subcellular marker allows for live cell imaging and improved validation of cellular protein localization.

Cellular Factors Shape 3D Genome Landscape

Cancer.gov

Researchers, using novel large-scale imaging technology, have mapped the spatial location of individual genes in the nucleus of human cells and identified 50 cellular factors required for the proper 3D positioning of genes. These spatial locations play important roles in gene expression, DNA repair, genome stability, and other cellular activities.

An image encryption algorithm based on 3D cellular automata and chaotic maps

NASA Astrophysics Data System (ADS)

Del Rey, A. Martín; Sánchez, G. Rodríguez

2015-05-01

A novel encryption algorithm to cipher digital images is presented in this work. The digital image is rendering into a three-dimensional (3D) lattice and the protocol consists of two phases: the confusion phase where 24 chaotic Cat maps are applied and the diffusion phase where a 3D cellular automata is evolved. The encryption method is shown to be secure against the most important cryptanalytic attacks.

Multi-scale Imaging of Cellular and Sub-cellular Structures using Scanning Probe Recognition Microscopy.

NASA Astrophysics Data System (ADS)

Chen, Q.; Rice, A. F.

2005-03-01

Scanning Probe Recognition Microscopy is a new scanning probe capability under development within our group to reliably return to and directly interact with a specific nanobiological feature of interest. In previous work, we have successfully recognized and classified tubular versus globular biological objects from experimental atomic force microscope images using a method based on normalized central moments [ref. 1]. In this paper we extend this work to include recognition schemes appropriate for cellular and sub-cellular structures. Globular cells containing tubular actin filaments are under investigation. Thus there are differences in external/internal shapes and scales. Continuous Wavelet Transform with a differential Gaussian mother wavelet is employed for multi- scale analysis. [ref. 1] Q. Chen, V. Ayres and L. Udpa, ``Biological Investigation Using Scanning Probe Recognition Microscopy,'' Proceedings 3rd IEEE Conference on Nanotechnology, vol. 2, p 863-865 (2003).

Use of volumetric features for temporal comparison of mass lesions in full field digital mammograms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bozek, Jelena, E-mail: jelena.bozek@fer.hr; Grgic, Mislav; Kallenberg, Michiel

2014-02-15

Purpose: Temporal comparison of lesions might improve classification between benign and malignant lesions in full-field digital mammograms (FFDM). The authors compare the use of volumetric features for lesion classification, which are computed from dense tissue thickness maps, to the use of mammographic lesion area. Use of dense tissue thickness maps for lesion characterization is advantageous, since it results in lesion features that are invariant to acquisition parameters. Methods: The dataset used in the analysis consisted of 60 temporal mammogram pairs comprising 120 mediolateral oblique or craniocaudal views with a total of 65 lesions, of which 41 were benign and 24more » malignant. The authors analyzed the performance of four volumetric features, area, and four other commonly used features obtained from temporal mammogram pairs, current mammograms, and prior mammograms. The authors evaluated the individual performance of all features and of different feature sets. The authors used linear discriminant analysis with leave-one-out cross validation to classify different feature sets. Results: Volumetric features from temporal mammogram pairs achieved the best individual performance, as measured by the area under the receiver operating characteristic curve (A{sub z} value). Volume change (A{sub z} = 0.88) achieved higher A{sub z} value than projected lesion area change (A{sub z} = 0.78) in the temporal comparison of lesions. Best performance was achieved with a set that consisted of a set of features extracted from the current exam combined with four volumetric features representing changes with respect to the prior mammogram (A{sub z} = 0.90). This was significantly better (p = 0.005) than the performance obtained using features from the current exam only (A{sub z} = 0.77). Conclusions: Volumetric features from temporal mammogram pairs combined with features from the single exam significantly improve discrimination of benign and malignant lesions in FFDM mammograms compared to using only single exam features. In the comparison with prior mammograms, use of volumetric change may lead to better performance than use of lesion area change.« less

Sub-cellular mRNA localization modulates the regulation of gene expression by small RNAs in bacteria

NASA Astrophysics Data System (ADS)

Teimouri, Hamid; Korkmazhan, Elgin; Stavans, Joel; Levine, Erel

2017-10-01

Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that demonstrate that families of mRNAs show non-trivial sub-cellular distributions raise the question of how localization may affect the regulatory activity of sRNAs. Here we address this question within a simple mathematical model. We show that the non-uniform spatial distributions of mRNA can alter the threshold-linear response that characterizes sRNAs that act stoichiometrically, and modulate the hierarchy among targets co-regulated by the same sRNA. We also identify conditions where the sub-cellular organization of cofactors in the sRNA pathway can induce spatial heterogeneity on sRNA targets. Our results suggest that under certain conditions, interpretation and modeling of natural and synthetic gene regulatory circuits need to take into account the spatial organization of the transcripts of participating genes.

Enhancement of two dimensional electron gas concentrations due to Si{sub 3}N{sub 4} passivation on Al{sub 0.3}Ga{sub 0.7}N/GaN heterostructure: strain and interface capacitance analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dinara, Syed Mukulika, E-mail: smdinara.iit@gmail.com; Jana, Sanjay Kr.; Ghosh, Saptarsi

2015-04-15

Enhancement of two dimensional electron gas (2DEG) concentrations at Al{sub 0.3}Ga{sub 0.7}N/GaN hetero interface after a-Si{sub 3}N{sub 4} (SiN) passivation has been investigated from non-destructive High Resolution X-ray Diffraction (HRXRD) analysis, depletion depth and capacitance-voltage (C-V) profile measurement. The crystalline quality and strained in-plane lattice parameters of Al{sub 0.3}Ga{sub 0.7}N and GaN were evaluated from double axis (002) symmetric (ω-2θ) diffraction scan and double axis (105) asymmetric reciprocal space mapping (DA RSM) which revealed that the tensile strain of the Al{sub 0.3}Ga{sub 0.7}N layer increased by 15.6% after SiN passivation. In accordance with the predictions from theoretical solution of Schrödinger-Poisson’smore » equations, both electrochemical capacitance voltage (ECV) depletion depth profile and C-V characteristics analyses were performed which implied effective 9.5% increase in 2DEG carrier density after passivation. The enhancement of polarization charges results from increased tensile strain in the Al{sub 0.3}Ga{sub 0.7}N layer and also due to the decreased surface states at the interface of SiN/Al{sub 0.3}Ga{sub 0.7}N layer, effectively improving the carrier confinement at the interface.« less

Laser-emission imaging of nuclear biomarkers for high-contrast cancer screening and immunodiagnosis

PubMed Central

Chen, Yu-Cheng; Tan, Xiaotian; Sun, Qihan; Chen, Qiushu; Wang, Wenjie; Fan, Xudong

2017-01-01

Detection of nuclear biomarkers such as nucleic acids and nuclear proteins is critical for early-stage cancer diagnosis and prognosis. Conventional methods relying on morphological assessment of cell nuclei in histopathology slides may be subjective, whereas colorimetric immunohistochemical and fluorescence-based imaging are limited by strong light absorption, broad-emission bands and low contrast. Here, we describe the development and use of a scanning laser-emission-based microscope that maps lasing emissions from nuclear biomarkers in human tissues. 41 tissue samples from 35 patients labelled with site-specific and biomarker-specific antibody-conjugated dyes were sandwiched in a Fabry-Pérot microcavity while an excitation laser beam built a laser-emission image. We observed multiple sub-cellular lasing emissions from cancer cell nuclei, with a threshold of tens of μJ/mm2, sub-micron resolution (<700 nm), and a lasing band in the few-nanometre range. Different lasing thresholds of nuclei in cancer and normal tissues enabled the identification and multiplexed detection of nuclear proteomic biomarkers, with a high sensitivity for early-stage cancer diagnosis. Laser-emission-based cancer screening and immunodiagnosis might find use in precision medicine and facilitate research in cell biology. PMID:29204310

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shrivastava, Pragya; Dalai, Sridhar; Vijayalakshmi, S.

With an increasing demand of biocompatible bone substitutes for the treatment of bone diseases and bone tissue regeneration, bioactive glass composites are being tested to improvise the osteoconductive as well as osteoinductive properties. Nanobioactive glass (nBG) composites, having composition of SiO{sub 2} 70 mol%, CaO 26 mol % and P{sub 2}O{sub 5} 4 mol% were prepared by Freeze drying method using PEG-PPG-PEG co-polymer. Polymer addition improves the mechanical strength and porosity of the scaffold of nBG. Nano Bioactive glass composites upon implantation undergo specific reactions leading to the formation of crystalline hydroxyapatite (HA). This is tested in vitro using Simulatedmore » Body Fluid (SBF). This high strength hydroxyapatite (HA) layer acts as osteoconductive in cellular environment, by acting as mineral base of bones, onto which new bone cells proliferate leading to new bone formation. Strength of the nBG composites as well as HA is in the range of cortical and cancellous bone, thus proving significant for bone tissue regeneration substitutes.« less

SUB1 Plays a Negative Role during Starvation Induced Sporulation Program in Saccharomyces cerevisiae

PubMed Central

Gupta, Ritu; Vijayraghavan, Usha

2015-01-01

Saccharomyces cerevisiae Sub1 is involved in several cellular processes such as, transcription initiation, elongation, mRNA processing and DNA repair. It has also been reported to provide cellular resistance during conditions of oxidative DNA damage and osmotic stress. Here, we report a novel role of SUB1 during starvation stress-induced sporulation, which leads to meiosis and spore formation in diploid yeast cells. Deletion of SUB1 gene significantly increased sporulation efficiency as compared to the wild-type cells in S288c genetic background. Whereas, the sporulation functions of the sub1(Y66A) missense mutant were similar to Sub1. SUB1 transcript and protein levels are downregulated during sporulation, in highly synchronized and sporulation proficient wild-type SK1 cells. The changes in Sub1 levels during sporulation cascade correlate with the induction of middle sporulation gene expression. Deletion of SUB1 increased middle sporulation gene transcript levels with no effect on their induction kinetics. In wild-type cells, Sub1 associates with chromatin at these loci in a temporal pattern that correlates with their enhanced gene expression seen in sub1Δ cells. We show that SUB1 genetically interacts with HOS2, which led us to speculate that Sub1 might function with Set3 repressor complex during sporulation. Positive Cofactor 4, human homolog of Sub1, complemented the sub1Δ sporulation phenotype, suggesting conservation of function. Taken together, our results suggest that SUB1 acts as a negative regulator of sporulation. PMID:26147804

SUB1 Plays a Negative Role during Starvation Induced Sporulation Program in Saccharomyces cerevisiae.

PubMed

Gupta, Ritu; Sadhale, Parag P; Vijayraghavan, Usha

2015-01-01

Saccharomyces cerevisiae Sub1 is involved in several cellular processes such as, transcription initiation, elongation, mRNA processing and DNA repair. It has also been reported to provide cellular resistance during conditions of oxidative DNA damage and osmotic stress. Here, we report a novel role of SUB1 during starvation stress-induced sporulation, which leads to meiosis and spore formation in diploid yeast cells. Deletion of SUB1 gene significantly increased sporulation efficiency as compared to the wild-type cells in S288c genetic background. Whereas, the sporulation functions of the sub1(Y66A) missense mutant were similar to Sub1. SUB1 transcript and protein levels are downregulated during sporulation, in highly synchronized and sporulation proficient wild-type SK1 cells. The changes in Sub1 levels during sporulation cascade correlate with the induction of middle sporulation gene expression. Deletion of SUB1 increased middle sporulation gene transcript levels with no effect on their induction kinetics. In wild-type cells, Sub1 associates with chromatin at these loci in a temporal pattern that correlates with their enhanced gene expression seen in sub1Δ cells. We show that SUB1 genetically interacts with HOS2, which led us to speculate that Sub1 might function with Set3 repressor complex during sporulation. Positive Cofactor 4, human homolog of Sub1, complemented the sub1Δ sporulation phenotype, suggesting conservation of function. Taken together, our results suggest that SUB1 acts as a negative regulator of sporulation.

Geographical Inequalities in Use of Improved Drinking Water Supply and Sanitation across Sub-Saharan Africa: Mapping and Spatial Analysis of Cross-sectional Survey Data

PubMed Central

Pullan, Rachel L.; Freeman, Matthew C.; Gething, Peter W.; Brooker, Simon J.

2014-01-01

Background Understanding geographic inequalities in coverage of drinking-water supply and sanitation (WSS) will help track progress towards universal coverage of water and sanitation by identifying marginalized populations, thus helping to control a large number of infectious diseases. This paper uses household survey data to develop comprehensive maps of WSS coverage at high spatial resolution for sub-Saharan Africa (SSA). Analysis is extended to investigate geographic heterogeneity and relative geographic inequality within countries. Methods and Findings Cluster-level data on household reported use of improved drinking-water supply, sanitation, and open defecation were abstracted from 138 national surveys undertaken from 1991–2012 in 41 countries. Spatially explicit logistic regression models were developed and fitted within a Bayesian framework, and used to predict coverage at the second administrative level (admin2, e.g., district) across SSA for 2012. Results reveal substantial geographical inequalities in predicted use of water and sanitation that exceed urban-rural disparities. The average range in coverage seen between admin2 within countries was 55% for improved drinking water, 54% for use of improved sanitation, and 59% for dependence upon open defecation. There was also some evidence that countries with higher levels of inequality relative to coverage in use of an improved drinking-water source also experienced higher levels of inequality in use of improved sanitation (rural populations r = 0.47, p = 0.002; urban populations r = 0.39, p = 0.01). Results are limited by the quantity of WSS data available, which varies considerably by country, and by the reliability and utility of available indicators. Conclusions This study identifies important geographic inequalities in use of WSS previously hidden within national statistics, confirming the necessity for targeted policies and metrics that reach the most marginalized populations. The presented maps and analysis approach can provide a mechanism for monitoring future reductions in inequality within countries, reflecting priorities of the post-2015 development agenda. Please see later in the article for the Editors' Summary PMID:24714528

Geographical inequalities in use of improved drinking water supply and sanitation across Sub-Saharan Africa: mapping and spatial analysis of cross-sectional survey data.

PubMed

Pullan, Rachel L; Freeman, Matthew C; Gething, Peter W; Brooker, Simon J

2014-04-01

Understanding geographic inequalities in coverage of drinking-water supply and sanitation (WSS) will help track progress towards universal coverage of water and sanitation by identifying marginalized populations, thus helping to control a large number of infectious diseases. This paper uses household survey data to develop comprehensive maps of WSS coverage at high spatial resolution for sub-Saharan Africa (SSA). Analysis is extended to investigate geographic heterogeneity and relative geographic inequality within countries. Cluster-level data on household reported use of improved drinking-water supply, sanitation, and open defecation were abstracted from 138 national surveys undertaken from 1991-2012 in 41 countries. Spatially explicit logistic regression models were developed and fitted within a Bayesian framework, and used to predict coverage at the second administrative level (admin2, e.g., district) across SSA for 2012. Results reveal substantial geographical inequalities in predicted use of water and sanitation that exceed urban-rural disparities. The average range in coverage seen between admin2 within countries was 55% for improved drinking water, 54% for use of improved sanitation, and 59% for dependence upon open defecation. There was also some evidence that countries with higher levels of inequality relative to coverage in use of an improved drinking-water source also experienced higher levels of inequality in use of improved sanitation (rural populations r = 0.47, p = 0.002; urban populations r = 0.39, p = 0.01). Results are limited by the quantity of WSS data available, which varies considerably by country, and by the reliability and utility of available indicators. This study identifies important geographic inequalities in use of WSS previously hidden within national statistics, confirming the necessity for targeted policies and metrics that reach the most marginalized populations. The presented maps and analysis approach can provide a mechanism for monitoring future reductions in inequality within countries, reflecting priorities of the post-2015 development agenda. Please see later in the article for the Editors' Summary.

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States* | Office of Cancer Genomics

Cancer.gov

The systematic sequencing of the cancer genome has led to the identification of numerous genetic alterations in cancer. However, a deeper understanding of the functional consequences of these alterations is necessary to guide appropriate therapeutic strategies. Here, we describe Onco-GPS (OncoGenic Positioning System), a data-driven analysis framework to organize individual tumor samples with shared oncogenic alterations onto a reference map defined by their underlying cellular states.

Oxidative stress suppression by luteolin-induced heme oxygenase-1 expression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Gui-bo; Sun, Xiao; Wang, Min

Luteolin, a flavonoid that exhibits antioxidative properties, exerts myocardial protection effects. However, the underlying molecular mechanisms are not yet fully understood. To investigate the effects of luteolin on myocardial injury protection and its possible mechanisms, a myocardial injury model was established with intragastric administration of 4 mg/kg isoproterenol (ISO) to male Sprague–Dawley rats (200–220 g) daily for 2 days. We found that pretreatment of luteolin (160, 80 and 40 mg/kg, i.g., respectively) daily for 15 days can prevent ISO-induced myocardial damage, including decrease of serum cardiac enzymes, improvement electrocardiography and heart vacuolation. Luteolin also improved the free radical scavenging andmore » antioxidant potential, suggesting one possible mechanism of luteolin-induced cardio-protection is mediated by blocking the oxidative stress. To clarify the mechanisms, we performed the in vitro study by hydrogen peroxide (H{sub 2}O{sub 2})-induced cytotoxicty model in H9c2 cells. We found that luteolin pretreatment prevented apoptosis, increased the expression of heme oxygenase-1 (HO-1), and enhanced the binding of Nrf2 to the antioxidant response element, providing an adaptive survival response against H{sub 2}O{sub 2}-derived oxidative cytotoxicity. The addition of Znpp, a selective HO-1 competitive inhibitor, reduced the cytoprotective ability of luteolin, indicating the vital role of HO-1 on these effects. Luteolin also activated Akt and ERK, whereas the addition of LY294002 and U0126, the pharmacologic inhibitors of PI3K and ERK, attenuated luteolin-induced HO-1 expression and cytoprotective effect. Taken together, the above findings suggest that luteolin protects against myocardial injury and enhances cellular antioxidant defense capacity through the activation of Akt and ERK signal pathways that leads to Nrf2 activation, and subsequently HO-1 induction. -- Highlights: ► Luteolin prevents isoproterenol-induced myocardial damage. ► Luteolin enhances cellular antioxidant defense capacity. ► Luteolin increases the expression of heme oxygenase-1 protein levels. ► Luteolin activates Akt and ERK signal pathways.« less

DO QUIESCENT AND ACTIVE GALAXIES HAVE DIFFERENT M{sub BH}-{sigma}{sub *} RELATIONS?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woo, Jong-Hak; Park, Daeseong; Kang, Wol-Rang

To investigate the validity of the assumption that quiescent galaxies and active galaxies follow the same black hole mass (M{sub BH})-stellar velocity dispersion ({sigma}{sub *}) relation, as required for the calibration of M{sub BH} estimators for broad line active galactic nuclei (AGNs), we determine and compare the M{sub BH}-{sigma}{sub *} relations, respectively, for quiescent and active galaxies. For the quiescent galaxy sample, composed of 72 dynamical M{sub BH} measurements, we update {sigma}{sub *} for 28 galaxies using homogeneous H-band measurements that are corrected for galaxy rotation. For active galaxies, we collect 25 reverberation-mapped AGNs and improve {sigma}{sub *} measurement formore » two objects. Combining the two samples, we determine the virial factor f, first by scaling the active galaxy sample to the M{sub BH}-{sigma}{sub *} relation of quiescent galaxies, and second by simultaneously fitting the quiescent and active galaxy samples, as f=5.1{sub -1.1}{sup +1.5} and f=5.9{sub -1.5}{sup +2.1}, respectively. The M{sub BH}-{sigma}{sub *} relation of active galaxies appears to be shallower than that of quiescent galaxies. However, the discrepancy is caused by a difference in the accessible M{sub BH} distribution at given {sigma}{sub *}, primarily due to the difficulty of measuring reliable stellar velocity dispersion for the host galaxies of luminous AGNs. Accounting for the selection effects, we find that active and quiescent galaxies are consistent with following intrinsically the same M{sub BH}-{sigma}{sub *} relation.« less

Hot deformation behaviors and processing maps of B{sub 4}C/Al6061 neutron absorber composites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yu-Li

In this study, the hot deformation behaviors of 30 wt.% B{sub 4}C/Al6061 neutron absorber composites (NACs) have been investigated by conducting isothermal compression tests at temperatures ranging from 653 K to 803 K and strain rates from 0.01 to 10 s{sup −1}. It was found that, during hot compression, the B{sub 4}C/Al6061 NACs exhibited a steady flow characteristic which can be expressed by the Zener-Hollomon parameter as a hyperbolic-sine function of flow stress. High average activation energy (185.62 kJ/mol) of B{sub 4}C/Al6061 NACs is noted in current study owing to the high content of B{sub 4}C particle. The optimum hotmore » working conditions for B{sub 4}C/Al6061 NACs are found to be 760–803 K/0.01–0.05 s{sup −1} based on processing map and microstructure evolution. Typical material instabilities are thought to be attributed to void formation, adiabatic shear bands (ASB), particle debonding, and matrix cracking. Finally, the effect of the plastic deformation zones (PDZs) on the microstructure evolution in this 30 wt.% B{sub 4}C/Al6061 composite is found to be very important. - Highlights: •The hot deformation behavior of the 30 wt.% B{sub 4}C/Al6061 NACs was first analyzed. •The 3D efficiency map and the instability map are developed. •The optimum hot working conditions were identified and validated by SEM and TEM. •The hot deformation schematic diagram of 30 wt.% B{sub 4}C/Al6061 NACs is developed.« less

Mapping Sub-Saharan African Agriculture in High-Resolution Satellite Imagery with Computer Vision & Machine Learning

NASA Astrophysics Data System (ADS)

Debats, Stephanie Renee

Smallholder farms dominate in many parts of the world, including Sub-Saharan Africa. These systems are characterized by small, heterogeneous, and often indistinct field patterns, requiring a specialized methodology to map agricultural landcover. In this thesis, we developed a benchmark labeled data set of high-resolution satellite imagery of agricultural fields in South Africa. We presented a new approach to mapping agricultural fields, based on efficient extraction of a vast set of simple, highly correlated, and interdependent features, followed by a random forest classifier. The algorithm achieved similar high performance across agricultural types, including spectrally indistinct smallholder fields, and demonstrated the ability to generalize across large geographic areas. In sensitivity analyses, we determined multi-temporal images provided greater performance gains than the addition of multi-spectral bands. We also demonstrated how active learning can be incorporated in the algorithm to create smaller, more efficient training data sets, which reduced computational resources, minimized the need for humans to hand-label data, and boosted performance. We designed a patch-based uncertainty metric to drive the active learning framework, based on the regular grid of a crowdsourcing platform, and demonstrated how subject matter experts can be replaced with fleets of crowdsourcing workers. Our active learning algorithm achieved similar performance as an algorithm trained with randomly selected data, but with 62% less data samples. This thesis furthers the goal of providing accurate agricultural landcover maps, at a scale that is relevant for the dominant smallholder class. Accurate maps are crucial for monitoring and promoting agricultural production. Furthermore, improved agricultural landcover maps will aid a host of other applications, including landcover change assessments, cadastral surveys to strengthen smallholder land rights, and constraints for crop modeling and famine prediction.

Coastal habitat mapping in the Aegean Sea using high resolution orthophoto maps

NASA Astrophysics Data System (ADS)

Topouzelis, Konstantinos; Papakonstantinou, Apostolos; Doukari, Michaela; Stamatis, Panagiotis; Makri, Despina; Katsanevakis, Stelios

2017-09-01

The significance of coastal habitat mapping lies in the need to prevent from anthropogenic interventions and other factors. Until 2015, Landsat-8 (30m) imagery were used as medium spatial resolution satellite imagery. So far, Sentinel-2 satellite imagery is very useful for more detailed regional scale mapping. However, the use of high resolution orthophoto maps, which are determined from UAV data, is expected to improve the mapping accuracy. This is due to small spatial resolution of the orthophoto maps (30 cm). This paper outlines the integration of UAS for data acquisition and Structure from Motion (SfM) pipeline for the visualization of selected coastal areas in the Aegean Sea. Additionally, the produced orthophoto maps analyzed through an object-based image analysis (OBIA) and nearest-neighbor classification for mapping the coastal habitats. Classification classes included the main general habitat types, i.e. seagrass, soft bottom, and hard bottom The developed methodology applied at the Koumbara beach (Ios Island - Greece). Results showed that UAS's data revealed the sub-bottom complexity in large shallow areas since they provide such information in the spatial resolution that permits the mapping of seagrass meadows with extreme detail. The produced habitat vectors are ideal as reference data for studies with satellite data of lower spatial resolution.

Dependence of Coronary 3-Dimensional Dose Maps on Coronary Topologies and Beam Set in Breast Radiation Therapy: A Study Based on CT Angiographies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moignier, Alexandra, E-mail: alexandra.moignier@gmail.com; Broggio, David; Derreumaux, Sylvie

2014-05-01

Purpose: In left-side breast radiation therapy (RT), doses to the left main (LM) and left anterior descending (LAD) coronary arteries are usually assessed after delineation by prior anatomic knowledge on the treatment planning computed tomography (CT) scan. In this study, dose sensitivity due to interindividual coronary topology variation was assessed, and hot spots were located. Methods and Materials: Twenty-two detailed heart models, created from heart computed tomography angiographies, were fitted into a single representative female thorax. Two breast RT protocols were then simulated into a treatment planning system: the first protocol comprised tangential and tumoral bed beams (TGs{sub T}B) atmore » 50 + 16 Gy, the second protocol added internal mammary chain beams at 50 Gy to TGs{sub T}B (TGs{sub T}B{sub I}MC). For the heart, the LAD, and the LM, several dose indicators were calculated: dose-volume histograms, mean dose (D{sub mean}), minimal dose received by the most irradiated 2% of the volume (D{sub 2%}), and 3-dimensional (3D) dose maps. Variations of these indicators with anatomies were studied. Results: For the LM, the intermodel dispersion of D{sub mean} and D{sub 2%} was 10% and 11%, respectively, with TGs{sub T}B and 40% and 80%, respectively, with TGs{sub T}B{sub I}MC. For the LAD, these dispersions were 19% (D{sub mean}) and 49% (D{sub 2%}) with TGs{sub T}B and 35% (D{sub mean}) and 76% (D{sub 2%}) with TGs{sub T}B{sub I}MC. The 3D dose maps revealed that the internal mammary chain beams induced hot spots between 20 and 30 Gy on the LM and the proximal LAD for some coronary topologies. Without IMC beams, hot spots between 5 and 26 Gy are located on the middle and distal LAD. Conclusions: Coronary dose distributions with hot spot location and dose level can change significantly depending on coronary topology, as highlighted by 3D coronary dose maps. In clinical practice, coronary imaging may be required for a relevant coronary dose assessment, especially in cases of internal mammary chain irradiation.« less

GALAXY CLUSTERS DISCOVERED VIA THE SUNYAEV-ZEL'DOVICH EFFECT IN THE FIRST 720 SQUARE DEGREES OF THE SOUTH POLE TELESCOPE SURVEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reichardt, C. L.; Stalder, B.; Ashby, M. L. N.

2013-02-15

We present a catalog of galaxy cluster candidates, selected through their Sunyaev-Zel'dovich (SZ) effect signature in the first 720 deg{sup 2} of the South Pole Telescope (SPT) survey. This area was mapped with the SPT in the 2008 and 2009 austral winters to a depth of {approx}18 {mu}K{sub CMB}-arcmin at 150 GHz; 550 deg{sup 2} of it was also mapped to {approx}44 {mu}K{sub CMB}-arcmin at 95 GHz. Based on optical imaging of all 224 candidates and near-infrared imaging of the majority of candidates, we have found optical and/or infrared counterparts for 158, which we then classify as confirmed galaxy clusters.more » Of these 158 clusters, 135 were first identified as clusters in SPT data, including 117 new discoveries reported in this work. This catalog triples the number of confirmed galaxy clusters discovered through the SZ effect. We report photometrically derived (and in some cases spectroscopic) redshifts for confirmed clusters and redshift lower limits for the remaining candidates. The catalog extends to high redshift with a median redshift of z = 0.55 and maximum confirmed redshift of z = 1.37. Forty-five of the clusters have counterparts in the ROSAT bright or faint source catalogs from which we estimate X-ray fluxes. Based on simulations, we expect the catalog to be nearly 100% complete above M {sub 500} Almost-Equal-To 5 Multiplication-Sign 10{sup 14} M {sub Sun} h {sup -1} {sub 70} at z {approx}> 0.6. There are 121 candidates detected at signal-to-noise ratio greater than five, at which the catalog purity is measured to be 95%. From this high-purity subsample, we exclude the z < 0.3 clusters and use the remaining 100 candidates to improve cosmological constraints following the method presented by Benson et al. Adding the cluster data to CMB + BAO + H {sub 0} data leads to a preference for non-zero neutrino masses while only slightly reducing the upper limit on the sum of neutrino masses to {Sigma}m {sub {nu}} < 0.38 eV (95% CL). For a spatially flat wCDM cosmological model, the addition of this catalog to the CMB + BAO + H {sub 0} + SNe results yields {sigma}{sub 8} = 0.807 {+-} 0.027 and w = -1.010 {+-} 0.058, improving the constraints on these parameters by a factor of 1.4 and 1.3, respectively. The larger cluster catalog presented in this work leads to slight improvements in cosmological constraints from those presented by Benson et al. These cosmological constraints are currently limited by uncertainty in the cluster mass calibration, not the size or quality of the cluster catalog. A multi-wavelength observation program to improve the cluster mass calibration will make it possible to realize the full potential of the final 2500 deg{sup 2} SPT cluster catalog to constrain cosmology.« less

a Fast and Flexible Method for Meta-Map Building for Icp Based Slam

NASA Astrophysics Data System (ADS)

Kurian, A.; Morin, K. W.

2016-06-01

Recent developments in LiDAR sensors make mobile mapping fast and cost effective. These sensors generate a large amount of data which in turn improves the coverage and details of the map. Due to the limited range of the sensor, one has to collect a series of scans to build the entire map of the environment. If we have good GNSS coverage, building a map is a well addressed problem. But in an indoor environment, we have limited GNSS reception and an inertial solution, if available, can quickly diverge. In such situations, simultaneous localization and mapping (SLAM) is used to generate a navigation solution and map concurrently. SLAM using point clouds possesses a number of computational challenges even with modern hardware due to the shear amount of data. In this paper, we propose two strategies for minimizing the cost of computation and storage when a 3D point cloud is used for navigation and real-time map building. We have used the 3D point cloud generated by Leica Geosystems's Pegasus Backpack which is equipped with Velodyne VLP-16 LiDARs scanners. To improve the speed of the conventional iterative closest point (ICP) algorithm, we propose a point cloud sub-sampling strategy which does not throw away any key features and yet significantly reduces the number of points that needs to be processed and stored. In order to speed up the correspondence finding step, a dual kd-tree and circular buffer architecture is proposed. We have shown that the proposed method can run in real time and has excellent navigation accuracy characteristics.

Sub-pixel mapping of hyperspectral imagery using super-resolution

NASA Astrophysics Data System (ADS)

Sharma, Shreya; Sharma, Shakti; Buddhiraju, Krishna M.

2016-04-01

With the development of remote sensing technologies, it has become possible to obtain an overview of landscape elements which helps in studying the changes on earth's surface due to climate, geological, geomorphological and human activities. Remote sensing measures the electromagnetic radiations from the earth's surface and match the spectral similarity between the observed signature and the known standard signatures of the various targets. However, problem lies when image classification techniques assume pixels to be pure. In hyperspectral imagery, images have high spectral resolution but poor spatial resolution. Therefore, the spectra obtained is often contaminated due to the presence of mixed pixels and causes misclassification. To utilise this high spectral information, spatial resolution has to be enhanced. Many factors make the spatial resolution one of the most expensive and hardest to improve in imaging systems. To solve this problem, post-processing of hyperspectral images is done to retrieve more information from the already acquired images. The algorithm to enhance spatial resolution of the images by dividing them into sub-pixels is known as super-resolution and several researches have been done in this domain.In this paper, we propose a new method for super-resolution based on ant colony optimization and review the popular methods of sub-pixel mapping of hyperspectral images along with their comparative analysis.

Developing Land Use Land Cover Maps for the Lower Mekong Basin to Aid SWAT Hydrologic Modeling

NASA Astrophysics Data System (ADS)

Spruce, J.; Bolten, J. D.; Srinivasan, R.

2017-12-01

This presentation discusses research to develop Land Use Land Cover (LULC) maps for the Lower Mekong Basin (LMB). Funded by a NASA ROSES Disasters grant, the main objective was to produce updated LULC maps to aid the Mekong River Commission's (MRC's) Soil and Water Assessment Tool (SWAT) hydrologic model. In producing needed LULC maps, temporally processed MODIS monthly NDVI data for 2010 were used as the primary data source for classifying regionally prominent forest and agricultural types. The MODIS NDVI data was derived from processing MOD09 and MYD09 8-day reflectance data with the Time Series Product Tool, a custom software package. Circa 2010 Landsat multispectral data from the dry season were processed into top of atmosphere reflectance mosaics and then classified to derive certain locally common LULC types, such as urban areas and industrial forest plantations. Unsupervised ISODATA clustering was used to derive most LULC classifications. GIS techniques were used to merge MODIS and Landsat classifications into final LULC maps for Sub-Basins (SBs) 1-8 of the LMB. The final LULC maps were produced at 250-meter resolution and delivered to the MRC for use in SWAT modeling for the LMB. A map accuracy assessment was performed for the SB 7 LULC map with 14 classes. This assessment was performed by comparing random locations for sampled LULC types to geospatial reference data such as Landsat RGBs, MODIS NDVI phenologic profiles, high resolution satellite data from Google Map/Earth, and other reference data from the MRC (e.g., crop calendars). LULC accuracy assessment results for SB 7 indicated an overall agreement to reference data of 81% at full scheme specificity. However, by grouping 3 deciduous forest classes into 1 class, the overall agreement improved to 87%. The project enabled updated LULC maps, plus more specific rice types were classified compared to the previous LULC maps. The LULC maps from this project should improve the use of SWAT for modeling hydrology in the LMB, plus improve water and disaster management in a region vulnerable to flooding, droughts, and anthropogenic change (e.g., from dam building and other LULC change).

MAP Attitude Control System Design and Analysis

NASA Technical Reports Server (NTRS)

Andrews, S. F.; Campbell, C. E.; Ericsson-Jackson, A. J.; Markley, F. L.; ODonnell, J. R., Jr.

1997-01-01

The Microwave Anisotropy Probe (MAP) is a follow-on to the Differential Microwave Radiometer (DMR) instrument on the Cosmic Background Explorer (COBE) spacecraft. The MAP spacecraft will perform its mission in a Lissajous orbit around the Earth-Sun L(sub 2) Lagrange point to suppress potential instrument disturbances. To make a full-sky map of cosmic microwave background fluctuations, a combination fast spin and slow precession motion will be used. MAP requires a propulsion system to reach L(sub 2), to unload system momentum, and to perform stationkeeping maneuvers once at L(sub 2). A minimum hardware, power and thermal safe control mode must also be provided. Sufficient attitude knowledge must be provided to yield instrument pointing to a standard deviation of 1.8 arc-minutes. The short development time and tight budgets require a new way of designing, simulating, and analyzing the Attitude Control System (ACS). This paper presents the design and analysis of the control system to meet these requirements.

Geomorphometry of Drainage Basin for Natural Resources Management Using High Resolution Satellite Data an Indian Example

NASA Astrophysics Data System (ADS)

Venkateswarlu, P.; Reddy, M. A.; Prasad, A. T.

2003-12-01

Application of Remote Sensing and Geographic Information System for the development of land and water resources action plan at micro level for appropriate management of land/water resources of a watershed in rain fed region of Prakasam District in Andhra Pradesh, India forms the focal theme of this paper. The quantitative description of drainage basin geometry can be effectively determined using Remote Sensing and GIS techniques. Each of the sixty-two sub-watersheds of the study area have been studied in terms of the Morphometric parameters - Stream length, Bifurcation ratio, Length ratio, Drainage density, Stream frequency, Texture ratio, Form factor, Area Perimeters, Circularity ratio and Elongation ratio and prioritized all the sub-watersheds under study. The prioritization of sub sheds based on morphometry is compared with sediment yield prioritization and found nearly same for the study area. The information obtained from the thematic maps are integrated and action plans are suggested for land and water resources development on a sustainable basis. Landuse/Landcover, Hydrogeomorphology and Soil thematic maps were generated. In addition slope and Drainage maps were prepared from Survey of India toposheets. Based on the computerized database created using ARC/INFO software, information derived in terms of natural resources and their spatial distribution was then integrated with the socio economic data to formulate an action plan, which includes suggestion of alternative Landuse/Landcover practices. Such a plan is useful for natural resources management and for improving the socio-economic status of rural population on a sustainable basis. Keywords: Natural Resources, Remote Sensing, Morphometry sustainable development.

Nanoscale quantification of intracellular element concentration by X-ray fluorescence microscopy combined with X-ray phase contrast nanotomography

NASA Astrophysics Data System (ADS)

Gramaccioni, Chiara; Yang, Yang; Procopio, Alessandra; Pacureanu, Alexandra; Bohic, Sylvain; Malucelli, Emil; Iotti, Stefano; Farruggia, Giovanna; Bukreeva, Inna; Notargiacomo, Andrea; Fratini, Michela; Valenti, Piera; Rosa, Luigi; Berlutti, Francesca; Cloetens, Peter; Lagomarsino, Stefano

2018-01-01

We present here a correlative X-ray microscopy approach for quantitative single cell imaging of molar concentrations. By combining the elemental content provided by X-ray fluorescence microscopy and the morphology information extracted from X-ray phase nanotomography, we determine the intracellular molarity distributions. This correlative method was demonstrated on a freeze-dried human phagocytic cell to obtain the absolute elemental concentration maps of K, P, and Fe. The cell morphology results showed a very good agreement with atomic-force microscopy measurements. This work opens the way for non-destructive single cell chemical analysis down to the sub-cellular level using exclusively synchrotron radiation techniques. It will be of high interest in the case where it is difficult to access the morphology using atomic-force microscopy, for example, on frozen-hydrated cells or tissues.

Transient expression and cellular localization of recombinant proteins in cultured insect cells

USDA-ARS?s Scientific Manuscript database

Heterologous protein expression systems are used for production of recombinant proteins, interpretation of cellular trafficking/localization, and for the determination of biochemical function of proteins at the sub-organismal level. Although baculovirus expression systems are increasingly used for ...

Global Detection of Live Virtual Machine Migration Based on Cellular Neural Networks

PubMed Central

Xie, Kang; Yang, Yixian; Zhang, Ling; Jing, Maohua; Xin, Yang; Li, Zhongxian

2014-01-01

In order to meet the demands of operation monitoring of large scale, autoscaling, and heterogeneous virtual resources in the existing cloud computing, a new method of live virtual machine (VM) migration detection algorithm based on the cellular neural networks (CNNs), is presented. Through analyzing the detection process, the parameter relationship of CNN is mapped as an optimization problem, in which improved particle swarm optimization algorithm based on bubble sort is used to solve the problem. Experimental results demonstrate that the proposed method can display the VM migration processing intuitively. Compared with the best fit heuristic algorithm, this approach reduces the processing time, and emerging evidence has indicated that this new approach is affordable to parallelism and analog very large scale integration (VLSI) implementation allowing the VM migration detection to be performed better. PMID:24959631

Global detection of live virtual machine migration based on cellular neural networks.

PubMed

Xie, Kang; Yang, Yixian; Zhang, Ling; Jing, Maohua; Xin, Yang; Li, Zhongxian

2014-01-01

In order to meet the demands of operation monitoring of large scale, autoscaling, and heterogeneous virtual resources in the existing cloud computing, a new method of live virtual machine (VM) migration detection algorithm based on the cellular neural networks (CNNs), is presented. Through analyzing the detection process, the parameter relationship of CNN is mapped as an optimization problem, in which improved particle swarm optimization algorithm based on bubble sort is used to solve the problem. Experimental results demonstrate that the proposed method can display the VM migration processing intuitively. Compared with the best fit heuristic algorithm, this approach reduces the processing time, and emerging evidence has indicated that this new approach is affordable to parallelism and analog very large scale integration (VLSI) implementation allowing the VM migration detection to be performed better.

A novel image encryption algorithm using chaos and reversible cellular automata

NASA Astrophysics Data System (ADS)

Wang, Xingyuan; Luan, Dapeng

2013-11-01

In this paper, a novel image encryption scheme is proposed based on reversible cellular automata (RCA) combining chaos. In this algorithm, an intertwining logistic map with complex behavior and periodic boundary reversible cellular automata are used. We split each pixel of image into units of 4 bits, then adopt pseudorandom key stream generated by the intertwining logistic map to permute these units in confusion stage. And in diffusion stage, two-dimensional reversible cellular automata which are discrete dynamical systems are applied to iterate many rounds to achieve diffusion on bit-level, in which we only consider the higher 4 bits in a pixel because the higher 4 bits carry almost the information of an image. Theoretical analysis and experimental results demonstrate the proposed algorithm achieves a high security level and processes good performance against common attacks like differential attack and statistical attack. This algorithm belongs to the class of symmetric systems.

Grain boundary engineering to control the discontinuous precipitation in multicomponent U10Mo alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devaraj, Arun; Kovarik, Libor; Kautz, Elizabeth

Grain boundaries in metallic alloys often play a crucial role, not only in determining the mechanical properties or thermal stability of alloys, but also in dictating the phase transformation kinetics during thermomechanical processing. We demonstrate that locally stabilized structure and compositional segregation at grain boundaries—“grain boundary complexions”—in a complex multicomponent alloy can be modified to influence the kinetics of cellular transformation during subsequent thermomechanical processing. Using aberration-corrected scanning transmission electron microscopy and atom probe tomography analysis of a metallic nuclear fuel highly relevant to worldwide nuclear non-proliferation efforts —uranium-10 wt% molybdenum (U-10Mo) alloy, new evidence for the existence of grainmore » boundary complexion is provided. We then modified the concentration of impurities dissolved in Υ-UMo grain interiors and/or segregated to Υ-UMo grain boundaries by changing the homogenization treatment, and these effects were used used to retard the kinetics of cellular transformation during subsequent sub-eutectoid annealing in this U-10-Mo alloy during sub-eutectoid annealing. Thus, this work provided insights on tailoring the final microstructure of the U-10Mo alloy, which can potentially improve the irradiation performance of this important class of alloy fuels.« less

On dealing with multiple correlation peaks in PIV

NASA Astrophysics Data System (ADS)

Masullo, A.; Theunissen, R.

2018-05-01

A novel algorithm to analyse PIV images in the presence of strong in-plane displacement gradients and reduce sub-grid filtering is proposed in this paper. Interrogation windows subjected to strong in-plane displacement gradients often produce correlation maps presenting multiple peaks. Standard multi-grid procedures discard such ambiguous correlation windows using a signal to noise (SNR) filter. The proposed algorithm improves the standard multi-grid algorithm allowing the detection of splintered peaks in a correlation map through an automatic threshold, producing multiple displacement vectors for each correlation area. Vector locations are chosen by translating images according to the peak displacements and by selecting the areas with the strongest match. The method is assessed on synthetic images of a boundary layer of varying intensity and a sinusoidal displacement field of changing wavelength. An experimental case of a flow exhibiting strong velocity gradients is also provided to show the improvements brought by this technique.

Strengthening accountability for improved maternal and newborn health: A mapping of studies in Sub-Saharan Africa.

PubMed

Martin Hilber, Adriane; Blake, Carolyn; Bohle, Leah F; Bandali, Sarah; Agbon, Esther; Hulton, Louise

2016-12-01

To describe the types of maternal and newborn health program accountability mechanisms implemented and evaluated in recent years in Sub-Saharan Africa, how these have been implemented, their effectiveness, and future prospects to improve governance and MNH outcomes. A structured review selected 38 peer-reviewed papers between 2006 and 2016 in Sub-Saharan Africa to include in the analysis. Performance accountability in MNH through maternal and perinatal death surveillance was the most common accountability mechanism used. Political and democratic accountability through advocacy, human rights, and global tracking of progress on indicators achieved greatest results when multiple stakeholders were involved. Financial accountability can be effective but depend on external support. Overall, this review shows that accountability is more effective when clear expectations are backed by social and political advocacy and multistakeholder engagement, and supported by incentives for positive action. There are few accountability mechanisms in MNH in Sub-Saharan Africa between decision-makers and those affected by those decisions with both the power and the will to enforce answerability. Increasing accountability depends not only on how mechanisms are enforced but also, on how providers and managers understand accountability. Copyright © 2016 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

Interaction of HSP20 with a viral RdRp changes its sub-cellular localization and distribution pattern in plants.

PubMed

Li, Jing; Xiang, Cong-Ying; Yang, Jian; Chen, Jian-Ping; Zhang, Heng-Mu

2015-09-11

Small heat shock proteins (sHSPs) perform a fundamental role in protecting cells against a wide array of stresses but their biological function during viral infection remains unknown. Rice stripe virus (RSV) causes a severe disease of rice in Eastern Asia. OsHSP20 and its homologue (NbHSP20) were used as baits in yeast two-hybrid (YTH) assays to screen an RSV cDNA library and were found to interact with the viral RNA-dependent RNA polymerase (RdRp) of RSV. Interactions were confirmed by pull-down and BiFC assays. Further analysis showed that the N-terminus (residues 1-296) of the RdRp was crucial for the interaction between the HSP20s and viral RdRp and responsible for the alteration of the sub-cellular localization and distribution pattern of HSP20s in protoplasts of rice and epidermal cells of Nicotiana benthamiana. This is the first report that a plant virus or a viral protein alters the expression pattern or sub-cellular distribution of sHSPs.

Femtosecond laser nanosurgery of sub-cellular structures in HeLa cells by employing Third Harmonic Generation imaging modality as diagnostic tool.

PubMed

Tserevelakis, George J; Psycharakis, Stylianos; Resan, Bojan; Brunner, Felix; Gavgiotaki, Evagelia; Weingarten, Kurt; Filippidis, George

2012-02-01

Femtosecond laser assisted nanosurgery of microscopic biological specimens is a relatively new technique which allows the selective disruption of sub-cellular structures without causing any undesirable damage to the surrounding regions. The targeted structures have to be stained in order to be clearly visualized for the nanosurgery procedure. However, the validation of the final nanosurgery result is difficult, since the targeted structure could be simply photobleached rather than selectively destroyed. This fact comprises a main drawback of this technique. In our study we employed a multimodal system which integrates non-linear imaging modalities with nanosurgery capabilities, for the selective disruption of sub-cellular structures in HeLa cancer cells. Third Harmonic Generation (THG) imaging modality was used as a tool for the identification of structures that were subjected to nanosurgery experiments. No staining of the biological samples was required, since THG is an intrinsic property of matter. Furthermore, cells' viability after nanosurgery processing was verified via Two Photon Excitation Fluorescence (TPEF) measurements. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrating views on support for mid-level health worker performance: a concept mapping study with regional health system actors in rural Guatemala.

PubMed

Hernández, Alison R; Hurtig, Anna-Karin; Dahlblom, Kjerstin; San Sebastián, Miguel

2015-10-08

Mid-level health workers are on the front-lines in underserved areas in many LMICs, and their performance is critical for improving the health of vulnerable populations. However, improving performance in low-resource settings is complex and highly dependent on the organizational context of local health systems. This study aims to examine the views of actors from different levels of a regional health system in Guatemala on actions to support the performance of auxiliary nurses, a cadre of mid-level health workers with a prominent role in public sector service delivery. A concept mapping study was carried out to develop an integrated view on organizational support and identify locally relevant strategies for strengthening performance. A total of 93 regional and district managers, and primary and secondary care health workers participated in generating ideas on actions needed to support auxiliary nurses' performance. Ideas were consolidated into 30 action items, which were structured through sorting and rating exercises, involving a total of 135 of managers and health workers. Maps depicting participants' integrated views on domains of action and dynamics in sub-groups' interests were generated using a sequence of multivariate statistical analyses, and interpreted by regional managers. The combined input of health system actors provided a multi-faceted view of actions needed to support performance, which were organized in six domains, including: Communication and coordination, Tools to orient work, Organizational climate of support, Motivation through recognition, Professional development and Skills development. The nature of relationships across hierarchical levels was identified as a cross-cutting theme. Pattern matching and go-zone maps indicated directions for action based on areas of consensus and difference across sub-groups of actors. This study indicates that auxiliary nurses' performance is interconnected with the performance of other health system actors who require support, including managers and community-level collaborators. Organizational climate is critical for making auxiliary nurses feel supported, and greater attention to improving the quality of hierarchical relationships is needed in LMIC settings. The participatory nature of the concept-mapping process enabled health system actors to collaborate in co-production of context-specific knowledge needed to guide efforts to strengthen performance in a vulnerable region.

Improving Axial Resolution in Confocal Microscopy with New High Refractive Index Mounting Media

PubMed Central

Fouquet, Coralie; Gilles, Jean-François; Heck, Nicolas; Dos Santos, Marc; Schwartzmann, Richard; Cannaya, Vidjeacoumary; Morel, Marie-Pierre; Davidson, Robert Stephen; Trembleau, Alain; Bolte, Susanne

2015-01-01

Resolution, high signal intensity and elevated signal to noise ratio (SNR) are key issues for biologists who aim at studying the localisation of biological structures at the cellular and subcellular levels using confocal microscopy. The resolution required to separate sub-cellular biological structures is often near to the resolving power of the microscope. When optimally used, confocal microscopes may reach resolutions of 180 nm laterally and 500 nm axially, however, axial resolution in depth is often impaired by spherical aberration that may occur due to refractive index mismatches. Spherical aberration results in broadening of the point-spread function (PSF), a decrease in peak signal intensity when imaging in depth and a focal shift that leads to the distortion of the image along the z-axis and thus in a scaling error. In this study, we use the novel mounting medium CFM3 (Citifluor Ltd., UK) with a refractive index of 1.518 to minimize the effects of spherical aberration. This mounting medium is compatible with most common fluorochromes and fluorescent proteins. We compare its performance with established mounting media, harbouring refractive indices below 1.500, by estimating lateral and axial resolution with sub-resolution fluorescent beads. We show furthermore that the use of the high refractive index media renders the tissue transparent and improves considerably the axial resolution and imaging depth in immuno-labelled or fluorescent protein labelled fixed mouse brain tissue. We thus propose to use those novel high refractive index mounting media, whenever optimal axial resolution is required. PMID:25822785

A High-Resolution Proteomic Landscaping of Primary Human Dental Stem Cells: Identification of SHED- and PDLSC-Specific Biomarkers.

PubMed

Taraslia, Vasiliki; Lymperi, Stefania; Pantazopoulou, Vasiliki; Anagnostopoulos, Athanasios K; Papassideri, Issidora S; Basdra, Efthimia K; Bei, Marianna; Kontakiotis, Evangelos G; Tsangaris, George Th; Stravopodis, Dimitrios J; Anastasiadou, Ema

2018-01-05

Dental stem cells (DSCs) have emerged as a promising tool for basic research and clinical practice. A variety of adult stem cell (ASC) populations can be isolated from different areas within the dental tissue, which, due to their cellular and molecular characteristics, could give rise to different outcomes when used in potential applications. In this study, we performed a high-throughput molecular comparison of two primary human adult dental stem cell (hADSC) sub-populations: Stem Cells from Human Exfoliated Deciduous Teeth (SHEDs) and Periodontal Ligament Stem Cells (PDLSCs). A detailed proteomic mapping of SHEDs and PDLSCs, via employment of nano-LC tandem-mass spectrometry (MS/MS) revealed 2032 identified proteins in SHEDs and 3235 in PDLSCs. In total, 1516 proteins were expressed in both populations, while 517 were unique for SHEDs and 1721 were exclusively expressed in PDLSCs. Further analysis of the recorded proteins suggested that SHEDs predominantly expressed molecules that are involved in organizing the cytoskeletal network, cellular migration and adhesion, whereas PDLSCs are highly energy-producing cells, vastly expressing proteins that are implicated in various aspects of cell metabolism and proliferation. Applying the Rho-GDI signaling pathway as a paradigm, we propose potential biomarkers for SHEDs and for PDLSCs, reflecting their unique features, properties and engaged molecular pathways.

A High-Resolution Proteomic Landscaping of Primary Human Dental Stem Cells: Identification of SHED- and PDLSC-Specific Biomarkers

PubMed Central

Taraslia, Vasiliki; Lymperi, Stefania; Pantazopoulou, Vasiliki; Anagnostopoulos, Athanasios K.; Basdra, Efthimia K.; Bei, Marianna; Kontakiotis, Evangelos G.; Tsangaris, George Th.; Stravopodis, Dimitrios J.; Anastasiadou, Ema

2018-01-01

Dental stem cells (DSCs) have emerged as a promising tool for basic research and clinical practice. A variety of adult stem cell (ASC) populations can be isolated from different areas within the dental tissue, which, due to their cellular and molecular characteristics, could give rise to different outcomes when used in potential applications. In this study, we performed a high-throughput molecular comparison of two primary human adult dental stem cell (hADSC) sub-populations: Stem Cells from Human Exfoliated Deciduous Teeth (SHEDs) and Periodontal Ligament Stem Cells (PDLSCs). A detailed proteomic mapping of SHEDs and PDLSCs, via employment of nano-LC tandem-mass spectrometry (MS/MS) revealed 2032 identified proteins in SHEDs and 3235 in PDLSCs. In total, 1516 proteins were expressed in both populations, while 517 were unique for SHEDs and 1721 were exclusively expressed in PDLSCs. Further analysis of the recorded proteins suggested that SHEDs predominantly expressed molecules that are involved in organizing the cytoskeletal network, cellular migration and adhesion, whereas PDLSCs are highly energy-producing cells, vastly expressing proteins that are implicated in various aspects of cell metabolism and proliferation. Applying the Rho-GDI signaling pathway as a paradigm, we propose potential biomarkers for SHEDs and for PDLSCs, reflecting their unique features, properties and engaged molecular pathways. PMID:29304003

Atrial fibrillation driven by micro-anatomic intramural re-entry revealed by simultaneous sub-epicardial and sub-endocardial optical mapping in explanted human hearts.

PubMed

Hansen, Brian J; Zhao, Jichao; Csepe, Thomas A; Moore, Brandon T; Li, Ning; Jayne, Laura A; Kalyanasundaram, Anuradha; Lim, Praise; Bratasz, Anna; Powell, Kimerly A; Simonetti, Orlando P; Higgins, Robert S D; Kilic, Ahmet; Mohler, Peter J; Janssen, Paul M L; Weiss, Raul; Hummel, John D; Fedorov, Vadim V

2015-09-14

The complex architecture of the human atria may create physical substrates for sustained re-entry to drive atrial fibrillation (AF). The existence of sustained, anatomically defined AF drivers in humans has been challenged partly due to the lack of simultaneous endocardial-epicardial (Endo-Epi) mapping coupled with high-resolution 3D structural imaging. Coronary-perfused human right atria from explanted diseased hearts (n = 8, 43-72 years old) were optically mapped simultaneously by three high-resolution CMOS cameras (two aligned Endo-Epi views (330 µm2 resolution) and one panoramic view). 3D gadolinium-enhanced magnetic resonance imaging (GE-MRI, 80 µm3 resolution) revealed the atrial wall structure varied in thickness (1.0 ± 0.7-6.8 ± 2.4 mm), transmural fiber angle differences, and interstitial fibrosis causing transmural activation delay from 23 ± 11 to 43 ± 22 ms at increased pacing rates. Sustained AF (>90 min) was induced by burst pacing during pinacidil (30-100 µM) perfusion. Dual-sided sub-Endo-sub-Epi optical mapping revealed that AF was driven by spatially and temporally stable intramural re-entry with 107 ± 50 ms cycle length and transmural activation delay of 67 ± 31 ms. Intramural re-entrant drivers were captured primarily by sub-Endo mapping, while sub-Epi mapping visualized re-entry or 'breakthrough' patterns. Re-entrant drivers were anchored on 3D micro-anatomic tracks (15.4 ± 2.2 × 6.0 ± 2.3 mm2, 2.9 ± 0.9 mm depth) formed by atrial musculature characterized by increased transmural fiber angle differences and interstitial fibrosis. Targeted radiofrequency ablation of the tracks verified these re-entries as drivers of AF. Integrated 3D structural-functional mapping of diseased human right atria ex vivo revealed that the complex atrial microstructure caused significant differences between Endo vs. Epi activation during pacing and sustained AF driven by intramural re-entry anchored to fibrosis-insulated atrial bundles. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2015. For permissions please email: journals.permissions@oup.com.

Atrial fibrillation driven by micro-anatomic intramural re-entry revealed by simultaneous sub-epicardial and sub-endocardial optical mapping in explanted human hearts

PubMed Central

Hansen, Brian J.; Zhao, Jichao; Csepe, Thomas A.; Moore, Brandon T.; Li, Ning; Jayne, Laura A.; Kalyanasundaram, Anuradha; Lim, Praise; Bratasz, Anna; Powell, Kimerly A.; Simonetti, Orlando P.; Higgins, Robert S.D.; Kilic, Ahmet; Mohler, Peter J.; Janssen, Paul M.L.; Weiss, Raul; Hummel, John D.; Fedorov, Vadim V.

2015-01-01

Aims The complex architecture of the human atria may create physical substrates for sustained re-entry to drive atrial fibrillation (AF). The existence of sustained, anatomically defined AF drivers in humans has been challenged partly due to the lack of simultaneous endocardial–epicardial (Endo–Epi) mapping coupled with high-resolution 3D structural imaging. Methods and results Coronary-perfused human right atria from explanted diseased hearts (n = 8, 43–72 years old) were optically mapped simultaneously by three high-resolution CMOS cameras (two aligned Endo–Epi views (330 µm2 resolution) and one panoramic view). 3D gadolinium-enhanced magnetic resonance imaging (GE-MRI, 80 µm3 resolution) revealed the atrial wall structure varied in thickness (1.0 ± 0.7–6.8 ± 2.4 mm), transmural fiber angle differences, and interstitial fibrosis causing transmural activation delay from 23 ± 11 to 43 ± 22 ms at increased pacing rates. Sustained AF (>90 min) was induced by burst pacing during pinacidil (30–100 µM) perfusion. Dual-sided sub-Endo–sub-Epi optical mapping revealed that AF was driven by spatially and temporally stable intramural re-entry with 107 ± 50 ms cycle length and transmural activation delay of 67 ± 31 ms. Intramural re-entrant drivers were captured primarily by sub-Endo mapping, while sub-Epi mapping visualized re-entry or ‘breakthrough’ patterns. Re-entrant drivers were anchored on 3D micro-anatomic tracks (15.4 ± 2.2 × 6.0 ± 2.3 mm2, 2.9 ± 0.9 mm depth) formed by atrial musculature characterized by increased transmural fiber angle differences and interstitial fibrosis. Targeted radiofrequency ablation of the tracks verified these re-entries as drivers of AF. Conclusions Integrated 3D structural–functional mapping of diseased human right atria ex vivo revealed that the complex atrial microstructure caused significant differences between Endo vs. Epi activation during pacing and sustained AF driven by intramural re-entry anchored to fibrosis-insulated atrial bundles. PMID:26059724

Minimal entropy approximation for cellular automata

NASA Astrophysics Data System (ADS)

Fukś, Henryk

2014-02-01

We present a method for the construction of approximate orbits of measures under the action of cellular automata which is complementary to the local structure theory. The local structure theory is based on the idea of Bayesian extension, that is, construction of a probability measure consistent with given block probabilities and maximizing entropy. If instead of maximizing entropy one minimizes it, one can develop another method for the construction of approximate orbits, at the heart of which is the iteration of finite-dimensional maps, called minimal entropy maps. We present numerical evidence that the minimal entropy approximation sometimes outperforms the local structure theory in characterizing the properties of cellular automata. The density response curve for elementary CA rule 26 is used to illustrate this claim.

WE-AB-204-12: Dosimetry at the Sub-Cellular Scale of Auger-Electron Emitter 99m-Tc in a Mouse Single Thyroid Follicle Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taborda, A; Benabdallah, N; Desbree, A

2015-06-15

Purpose: To perform a dosimetry study at the sub-cellular scale of Auger-electron emitter 99m-Tc using a mouse single thyroid cellular model to investigate the contribution of the 99m-Tc Auger-electrons to the absorbed dose and possible link to the thyroid stunning in in vivo experiments in mice, recently reported in literature. Methods: The simulation of S-values for Auger-electron emitting radionuclides was performed using both the recent MCNP6 software and the Geant4-DNA extension of the Geant4 toolkit. The dosimetric calculations were validated through comparison with results from literature, using a simple model of a single cell consisting of two concentric spheres ofmore » unit density water and for six Auger-electron emitting radionuclides. Furthermore, the S-values were calculated using a single thyroid follicle model for uniformly distributed 123-I and 125-I radionuclides and compared with published S-values. After validation, the simulation of the S-values was performed for the 99m-Tc radionuclide within the several mouse thyroid follicle cellular compartments, considering the radiative and non-radiative transitions of the 99m-Tc radiation spectrum. Results: The calculated S-values using MCNP6 are in good agreement with the results from literature, validating its use for the 99m-Tc S-values calculations. The most significant absorbed dose corresponds to the case where the radionuclide is uniformly distributed in the follicular cell’s nucleus, with a S-value of 7.8 mGy/disintegration, due mainly to the absorbed Auger-electrons. The results show that, at a sub-cellular scale, the emitted X-rays and gamma particles do not contribute significantly to the absorbed dose. Conclusion: In this work, MCNP6 was validated for dosimetric studies at the sub-cellular scale. It was shown that the contribution of the Auger-electrons to the absorbed dose is important at this scale compared to the emitted photons’ contribution and can’t be neglected. The obtained S-values of Auger-electron emitting 99m-Tc radionuclide will be presented and discussed.« less

Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alexopoulos, E.; Kanjee, U.; Snider, J.

2010-02-11

The decameric inducible lysine decarboxylase (LdcI) from Escherichia coli has been crystallized in space groups C2 and C222{sub 1}; the Ta{sub 6}Br{sub 12}{sup 2+} cluster was used to derivatize the C2 crystals. The method of single isomorphous replacement with anomalous scattering (SIRAS) as implemented in SHELXD was used to solve the Ta{sub 6}Br{sub 12}{sup 2+}-derivatized structure to 5 {angstrom} resolution. Many of the Ta{sub 6}Br{sub 12}{sup 2+}-binding sites had twofold and fivefold noncrystallographic symmetry. Taking advantage of this feature, phase modification was performed in DM. The electron-density map of LdcI displays many features in agreement with the low-resolution negative-stain electron-densitymore » map [Snider et al. (2006), J. Biol. Chem. 281, 1532-1546].« less

A Synergy Cropland of China by Fusing Multiple Existing Maps and Statistics.

PubMed

Lu, Miao; Wu, Wenbin; You, Liangzhi; Chen, Di; Zhang, Li; Yang, Peng; Tang, Huajun

2017-07-12

Accurate information on cropland extent is critical for scientific research and resource management. Several cropland products from remotely sensed datasets are available. Nevertheless, significant inconsistency exists among these products and the cropland areas estimated from these products differ considerably from statistics. In this study, we propose a hierarchical optimization synergy approach (HOSA) to develop a hybrid cropland map of China, circa 2010, by fusing five existing cropland products, i.e., GlobeLand30, Climate Change Initiative Land Cover (CCI-LC), GlobCover 2009, MODIS Collection 5 (MODIS C5), and MODIS Cropland, and sub-national statistics of cropland area. HOSA simplifies the widely used method of score assignment into two steps, including determination of optimal agreement level and identification of the best product combination. The accuracy assessment indicates that the synergy map has higher accuracy of spatial locations and better consistency with statistics than the five existing datasets individually. This suggests that the synergy approach can improve the accuracy of cropland mapping and enhance consistency with statistics.

(abstract) Monitoring Seasonal State and Mapping Species in Alaskan Taiga Using Imaging Radar as Input to CO(sub 2) Flux Models

NASA Technical Reports Server (NTRS)

Way, J. B.; Rignot, E.; McDonald, K.; Adams, P.; Viereck, L.

1993-01-01

Changes in the seasonal CO(sub 2) flux of the boreal forests may result from increased atmospheric CO(sub 2) concentrations and associated atmospheric warming. To monitor this potential change, a combination of remote sensing information and ecophysiological models are required. In this paper we address the use of synthetic aperture radar (SAR) data to provide some of the input to the ecophysiological models: forest type, freeze/thaw state which limits the growing season for conifers, and leaf on/off state which limits the growing season for deciduous species. AIRSAR data collected in March 1988 during an early thaw event and May 1991 during spring breakup are used to generate species maps and to determine the sensitivity of SAR to canopy freeze/thaw transitions. These data are also used to validate a microwave scattering model which is then used to determine the sensitivity of SAR to leaf on/off and soil freeze/thaw transitions. Finally, a CO(sub 2) flux algorithm which utilizes SAR data and an ecophysiological model to estimate CO(sub 2) flux is presented. CO(sub 2) flux maps are generated from which areal estimates of CO(sub 2) flux are derived.

Sub-cellular localisation studies may spuriously detect the Yes-associated protein, YAP, in nucleoli leading to potentially invalid conclusions of its function.

PubMed

Finch, Megan L; Passman, Adam M; Strauss, Robyn P; Yeoh, George C; Callus, Bernard A

2015-01-01

The Yes-associated protein (YAP) is a potent transcriptional co-activator that functions as a nuclear effector of the Hippo signaling pathway. YAP is oncogenic and its activity is linked to its cellular abundance and nuclear localisation. Activation of the Hippo pathway restricts YAP nuclear entry via its phosphorylation by Lats kinases and consequent cytoplasmic retention bound to 14-3-3 proteins. We examined YAP expression in liver progenitor cells (LPCs) and surprisingly found that transformed LPCs did not show an increase in YAP abundance compared to the non-transformed LPCs from which they were derived. We then sought to ascertain whether nuclear YAP was more abundant in transformed LPCs. We used an antibody that we confirmed was specific for YAP by immunoblotting to determine YAP's sub-cellular localisation by immunofluorescence. This antibody showed diffuse staining for YAP within the cytosol and nuclei, but, noticeably, it showed intense staining of the nucleoli of LPCs. This staining was non-specific, as shRNA treatment of cells abolished YAP expression to undetectable levels by Western blot yet the nucleolar staining remained. Similar spurious YAP nucleolar staining was also seen in mouse embryonic fibroblasts and mouse liver tissue, indicating that this antibody is unsuitable for immunological applications to determine YAP sub-cellular localisation in mouse cells or tissues. Interestingly nucleolar staining was not evident in D645 cells suggesting the antibody may be suitable for use in human cells. Given the large body of published work on YAP in recent years, many of which utilise this antibody, this study raises concerns regarding its use for determining sub-cellular localisation. From a broader perspective, it serves as a timely reminder of the need to perform appropriate controls to ensure the validity of published data.

Sub-Cellular Localisation Studies May Spuriously Detect the Yes-Associated Protein, YAP, in Nucleoli Leading to Potentially Invalid Conclusions of Its Function

PubMed Central

Finch, Megan L.; Passman, Adam M.; Strauss, Robyn P.; Yeoh, George C.; Callus, Bernard A.

2015-01-01

The Yes-associated protein (YAP) is a potent transcriptional co-activator that functions as a nuclear effector of the Hippo signaling pathway. YAP is oncogenic and its activity is linked to its cellular abundance and nuclear localisation. Activation of the Hippo pathway restricts YAP nuclear entry via its phosphorylation by Lats kinases and consequent cytoplasmic retention bound to 14-3-3 proteins. We examined YAP expression in liver progenitor cells (LPCs) and surprisingly found that transformed LPCs did not show an increase in YAP abundance compared to the non-transformed LPCs from which they were derived. We then sought to ascertain whether nuclear YAP was more abundant in transformed LPCs. We used an antibody that we confirmed was specific for YAP by immunoblotting to determine YAP’s sub-cellular localisation by immunofluorescence. This antibody showed diffuse staining for YAP within the cytosol and nuclei, but, noticeably, it showed intense staining of the nucleoli of LPCs. This staining was non-specific, as shRNA treatment of cells abolished YAP expression to undetectable levels by Western blot yet the nucleolar staining remained. Similar spurious YAP nucleolar staining was also seen in mouse embryonic fibroblasts and mouse liver tissue, indicating that this antibody is unsuitable for immunological applications to determine YAP sub-cellular localisation in mouse cells or tissues. Interestingly nucleolar staining was not evident in D645 cells suggesting the antibody may be suitable for use in human cells. Given the large body of published work on YAP in recent years, many of which utilise this antibody, this study raises concerns regarding its use for determining sub-cellular localisation. From a broader perspective, it serves as a timely reminder of the need to perform appropriate controls to ensure the validity of published data. PMID:25658431

Sci-Thur PM - Colourful Interactions: Highlights 04: A Fast Quantitative MRI Acquisition and Processing Pipeline for Radiation Treatment Planning and Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jutras, Jean-David

MRI-only Radiation Treatment Planning (RTP) is becoming increasingly popular because of a simplified work-flow, and less inconvenience to the patient who avoids multiple scans. The advantages of MRI-based RTP over traditional CT-based RTP lie in its superior soft-tissue contrast, and absence of ionizing radiation dose. The lack of electron-density information in MRI can be addressed by automatic tissue classification. To distinguish bone from air, which both appear dark in MRI, an ultra-short echo time (UTE) pulse sequence may be used. Quantitative MRI parametric maps can provide improved tissue segmentation/classification and better sensitivity in monitoring disease progression and treatment outcome thanmore » standard weighted images. Superior tumor contrast can be achieved on pure T{sub 1} images compared to conventional T{sub 1}-weighted images acquired in the same scan duration and voxel resolution. In this study, we have developed a robust and fast quantitative MRI acquisition and post-processing work-flow that integrates these latest advances into the MRI-based RTP of brain lesions. Using 3D multi-echo FLASH images at two different optimized flip angles (both acquired in under 9 min, and 1mm isotropic resolution), parametric maps of T{sub 1}, proton-density (M{sub 0}), and T{sub 2}{sup *} are obtained with high contrast-to-noise ratio, and negligible geometrical distortions, water-fat shifts and susceptibility effects. An additional 3D UTE MRI dataset is acquired (in under 4 min) and post-processed to classify tissues for dose simulation. The pipeline was tested on four healthy volunteers and a clinical trial on brain cancer patients is underway.« less

Imaging of single cells and tissue using MeV ions

NASA Astrophysics Data System (ADS)

Watt, F.; Bettiol, A. A.; van Kan, J. A.; Ynsa, M. D.; Minqin, Ren; Rajendran, R.; Huifang, Cui; Fwu-Shen, Sheu; Jenner, A. M.

2009-06-01

With the attainment of sub-100 nm high energy (MeV) ion beams, comes the opportunity to image cells and tissue at nano-dimensions. The advantage of MeV ion imaging is that the ions will penetrate whole cells, or relatively thick tissue sections, without any significant loss of resolution. In this paper, we demonstrate that whole cells (cultured N2A neuroblastoma cells ATCC) and tissue sections (rabbit pancreas tissue) can be imaged at sub-100 nm resolutions using scanning transmission ion microscopy (STIM), and that sub-cellular structural details can be identified. In addition to STIM imaging we have also demonstrated for the first time, that sub-cellular proton induced fluorescence imaging (on cultured N2A neuroblastoma cells ATCC) can also be carried out at resolutions of 200 nm, compared with 300-400 nm resolutions achieved by conventional optical fluorescence imaging. The combination of both techniques offers a potentially powerful tool in the quest for elucidating cell function, particularly when it should be possible in the near future to image down to sub-50 nm.

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.

PubMed

Pengelly, Reuben J; Tapper, William; Gibson, Jane; Knut, Marcin; Tearle, Rick; Collins, Andrew; Ennis, Sarah

2015-09-03

An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution. We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure. WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.

1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time.

PubMed

Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M; Queisser, Gillian

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator-which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics.

1D-3D hybrid modeling—from multi-compartment models to full resolution models in space and time

PubMed Central

Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M.; Queisser, Gillian

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator—which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics. PMID:25120463

THE CELLULAR AND GENOMIC RESPONSE OF AN IMMORTALIZED MICROGLIA CELL LINE (BV2) TO CONCENTRATED AMBIENT PARTICULATE MATTER

EPA Science Inventory

This manuscript describes cellular and genomic evidence that microglia exposed to concentrated air pollutants (CAPs). These were CAPs achieved from a previous study in which sub-chronically exposed transgenic animals develop neurodegeneration (Veronesi et al., Inhalation Tox,...

Structure characterization of MHEMT heterostructure elements with In{sub 0.4}Ga{sub 0.6}As quantum well grown by molecular beam epitaxy on GaAs substrate using reciprocal space mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aleshin, A. N., E-mail: a.n.aleshin@mail.ru; Bugaev, A. S.; Ermakova, M. A.

2016-03-15

The crystallographic parameters of elements of a metamorphic high-electron-mobility transistor (MHEMT) heterostructure with In{sub 0.4}Ga{sub 0.6}As quantum well are determined using reciprocal space mapping. The heterostructure has been grown by molecular-beam epitaxy (MBE) on the vicinal surface of a GaAs substrate with a deviation angle of 2° from the (001) plane. The structure consists of a metamorphic step-graded buffer (composed of six layers, including an inverse step), a high-temperature buffer of constant composition, and active high-electron-mobility transistor (HEMT) layers. The InAs content in the metamorphic buffer layers varies from 0.1 to 0.48. Reciprocal space mapping has been performed for themore » 004 and 224 reflections (the latter in glancing exit geometry). Based on map processing, the lateral and vertical lattice parameters of In{sub x}Ga{sub 1–x}As ternary solid solutions of variable composition have been determined. The degree of layer lattice relaxation and the compressive stress are found within the linear elasticity theory. The high-temperature buffer layer of constant composition (on which active MHEMT layers are directly formed) is shown to have the highest (close to 100%) degree of relaxation in comparison with all other heterostructure layers and a minimum compressive stress.« less

Organizational readiness for knowledge translation in chronic care: a Delphi study.

PubMed

Attieh, Randa; Gagnon, Marie-Pierre; Estabrooks, Carole A; Légaré, France; Ouimet, Mathieu; Vazquez, Patricia; Nuño, Roberto

2014-11-08

Health-care organizations need to be ready prior to implement evidence-based interventions. In this study, we sought to achieve consensus on a framework to assess the readiness of health-care organizations to implement evidence-based interventions in the context of chronic care. We conducted a web-based modified Delphi study between March and May 2013. We contacted 76 potentially eligible international experts working in the fields of organizational readiness (OR), knowledge translation (KT), and chronic care to comment upon the 76 elements resulting from our proposed conceptual map. This conceptual map was based on a systematic review of the existing frameworks of Organizational Readiness for Change (ORC) in health-care. We developed a conceptual map that proposed a set of core concepts and their associated 17 dimensions and 59 sub-dimensions. Experts rated their agreement concerning the applicability and importance of ORC elements on a 5-point Likert scale, where 1 indicates total disagreement and 5 indicates total agreement. Two rounds were needed to get a consensus from the experts. Consensus was a priori defined as strong (≥75%) or moderate (60-74%). Simple descriptive statistics was used. In total, 14 participants completed the first round and 10 completed the two rounds. Panel members reached consensus on the applicability and importance of 6 out of 17 dimensions and 28 out of 59 sub-dimensions to assess OR for KT in the context of chronic care. A strong level of consensus (≥75%) was attained on the Organizational contextual factors, Leadership/participation, Organizational support, and Motivation dimensions. The Organizational climate for change and Change content dimensions reached a moderate consensus (60-74%). Experts also reached consensus on 28 out of 59 sub-dimensions to assess OR for KT. Twenty-one sub-dimensions reached a strong consensus (≥75%) and seven a moderate consensus (60-74%). This study results provided the most important and applicable dimensions and sub-dimensions for assessing OR-KT in the context of chronic care. They can be used to guide the design of an assessment tool to improve knowledge translation in the field of chronic care.

Sphingosine-1-phosphate stimulates rat primary chondrocyte proliferation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Mi-Kyoung; Lee, Ha Young; Kwak, Jong-Young

2006-06-23

Rat primary chondrocytes express the sphingosine-1-phosphate (S1P) receptor, S1P{sub 2}, S1P{sub 3}, S1P{sub 4}, but not S1P{sub 1}. When chondrocytes were stimulated with S1P or phytosphingosine-1-phosphate (PhS1P, an S1P{sub 1}- and S1P{sub 4}-selective agonist), phospholipase C-mediated cytosolic calcium increase was dramatically induced. S1P and PhS1P also stimulated two kinds of mitogen-activated protein kinases, extracellular signal-regulated kinase (ERK) and p38 kinase in chondrocytes. In terms of the two phospholipids-mediated functional modulation of chondrocytes, S1P and PhS1P stimulated cellular proliferation. The two phospholipids-induced chondrocyte proliferations were almost completely blocked by PD98059 but not by SB203580, suggesting that ERK but not p38 kinasemore » is essentially required for the proliferation. Pertussis toxin almost completely inhibited the two phospholipids-induced cellular proliferation and ERK activation, indicating the crucial role of G{sub i} protein. This study demonstrates the physiological role of two important phospholipids (S1P and PhS1P) on the modulation of rat primary chondrocyte proliferation, and the crucial role played by ERK in the process.« less

Mapping Vinyl Cyanide and Other Nitriles in Titan’s Atmosphere Using ALMA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lai, J. C.-Y.; Cordiner, M. A.; Nixon, C. A.

Vinyl cyanide (C{sub 2}H{sub 3}CN) is theorized to form in Titan’s atmosphere via high-altitude photochemistry and is of interest regarding the astrobiology of cold planetary surfaces due to its predicted ability to form cell membrane-like structures (azotosomes) in liquid methane. In this work, we follow up on the initial spectroscopic detection of C{sub 2}H{sub 3}CN on Titan by Palmer et al. with the detection of three new C{sub 2}H{sub 3}CN rotational emission lines at submillimeter frequencies. These new, high-resolution detections have allowed for the first spatial distribution mapping of C{sub 2}H{sub 3}CN on Titan. We present simultaneous observations of C{submore » 2}H{sub 5}CN, HC{sub 3}N, and CH{sub 3}CN emission, and obtain the first (tentative) detection of C{sub 3}H{sub 8} (propane) at radio wavelengths. We present disk-averaged vertical abundance profiles, two-dimensional spatial maps, and latitudinal flux profiles for the observed nitriles. Similarly to HC{sub 3}N and C{sub 2}H{sub 5}CN, which are theorized to be short-lived in Titan’s atmosphere, C{sub 2}H{sub 3}CN is most abundant over the southern (winter) pole, whereas the longer-lived CH{sub 3}CN is more concentrated in the north. This abundance pattern is consistent with the combined effects of high-altitude photochemical production, poleward advection, and the subsequent reversal of Titan’s atmospheric circulation system following the recent transition from northern to southern winter. We confirm that C{sub 2}H{sub 3}CN and C{sub 2}H{sub 5}CN are most abundant at altitudes above 200 km. Using a 300 km step model, the average abundance of C{sub 2}H{sub 3}CN is found to be 3.03 ± 0.29 ppb, with a C{sub 2}H{sub 5}CN/C{sub 2}H{sub 3}CN abundance ratio of 2.43 ± 0.26. Our HC{sub 3}N and CH{sub 3}CN spectra can be accurately modeled using abundance gradients above the tropopause, with fractional scale-heights of 2.05 ± 0.16 and 1.63 ± 0.02, respectively.« less

Sparse feature selection methods identify unexpected global cellular response to strontium-containing materials

PubMed Central

Autefage, Hélène; Littmann, Elena; Hedegaard, Martin A. B.; Von Erlach, Thomas; O’Donnell, Matthew; Burden, Frank R.; Winkler, David A.; Stevens, Molly M.

2015-01-01

Despite the increasing sophistication of biomaterials design and functional characterization studies, little is known regarding cells’ global response to biomaterials. Here, we combined nontargeted holistic biological and physical science techniques to evaluate how simple strontium ion incorporation within the well-described biomaterial 45S5 bioactive glass (BG) influences the global response of human mesenchymal stem cells. Our objective analyses of whole gene-expression profiles, confirmed by standard molecular biology techniques, revealed that strontium-substituted BG up-regulated the isoprenoid pathway, suggesting an influence on both sterol metabolite synthesis and protein prenylation processes. This up-regulation was accompanied by increases in cellular and membrane cholesterol and lipid raft contents as determined by Raman spectroscopy mapping and total internal reflection fluorescence microscopy analyses and by an increase in cellular content of phosphorylated myosin II light chain. Our unexpected findings of this strong metabolic pathway regulation as a response to biomaterial composition highlight the benefits of discovery-driven nonreductionist approaches to gain a deeper understanding of global cell–material interactions and suggest alternative research routes for evaluating biomaterials to improve their design. PMID:25831522

Transcriptome landscape of Synechococcus elongatus PCC 7942 for nitrogen starvation responses using RNA-seq

PubMed Central

Choi, Sun Young; Park, Byeonghyeok; Choi, In-Geol; Sim, Sang Jun; Lee, Sun-Mi; Um, Youngsoon; Woo, Han Min

2016-01-01

The development of high-throughput technology using RNA-seq has allowed understanding of cellular mechanisms and regulations of bacterial transcription. In addition, transcriptome analysis with RNA-seq has been used to accelerate strain improvement through systems metabolic engineering. Synechococcus elongatus PCC 7942, a photosynthetic bacterium, has remarkable potential for biochemical and biofuel production due to photoautotrophic cell growth and direct CO2 conversion. Here, we performed a transcriptome analysis of S. elongatus PCC 7942 using RNA-seq to understand the changes of cellular metabolism and regulation for nitrogen starvation responses. As a result, differentially expressed genes (DEGs) were identified and functionally categorized. With mapping onto metabolic pathways, we probed transcriptional perturbation and regulation of carbon and nitrogen metabolisms relating to nitrogen starvation responses. Experimental evidence such as chlorophyll a and phycobilisome content and the measurement of CO2 uptake rate validated the transcriptome analysis. The analysis suggests that S. elongatus PCC 7942 reacts to nitrogen starvation by not only rearranging the cellular transport capacity involved in carbon and nitrogen assimilation pathways but also by reducing protein synthesis and photosynthesis activities. PMID:27488818

Hyperoside attenuates hydrogen peroxide-induced L02 cell damage via MAPK-dependent Keap{sub 1}-Nrf{sub 2}-ARE signaling pathway

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xing, Hai-Yan; Liu, Yao; Chen, Jian-Hong

Highlights: {yields} Hyperoside attenuated H{sub 2}O{sub 2}-induced L02 cell damage. {yields} Hyperoside up-regulated HO-1 expression at both mRNA and protein levels. {yields} Hyperoside activated both Nrf{sub 2} nuclear translocation and gene expression. {yields} Hyperoside may inhibit Keap{sub 1} mRNA translation or protein degradation. {yields} Phosphorylation of ERK and p38 is involved in hyperoside-mediated Nrf{sub 2} activation. -- Abstract: The flavonoid hyperoside has been reported to elicit cytoprotection against oxidative stress partly by increasing the activity of antioxidant enzymes, such as glutathione peroxidase, superoxide dismutase and catalase. However, the cellular and molecular mechanisms underlying this effect remain unclear. Here, hepatic L02more » cells exposed to H{sub 2}O{sub 2} (100 {mu}M) were used to demonstrate that hyperoside protected cells by significantly inhibiting overproduction of intracellular ROS, depletion of the mitochondrial membrane potential and leakage of lactate dehydrogenase. Hyperoside further enhanced the cellular antioxidant defense system through increasing the activity of heme oxygenase-1 (HO-1), and by up-regulating HO-1 expression. Meanwhile, real time PCR, western blot and immunofluorescence studies revealed that hyperoside stimulated nuclear translocation of the Nrf{sub 2} transcription factor in a dose-dependent manner, and this effect was significantly suppressed by pharmacological inhibition of the mitogen-activated protein kinases (MAPK) p38 and ERK. Collectively, our data provide the first description of the mechanism underlying hyperoside's ability to attenuate H{sub 2}O{sub 2}-induced cell damage, namely this compound interacts with the MAPK-dependent Keap{sub 1}-Nrf{sub 2}-ARE signaling pathway to up-regulate HO-1 expression and enhance intracellular antioxidant activity.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandit, Shubhrangshu; Preston, Thomas J.; Orr-Ewing, Andrew J., E-mail: a.orr-ewing@bristol.ac.uk

Photodissociation of gaseous bromocyclopropane via its A-band continuum has been studied at excitation wavelengths ranging from 230 nm to 267 nm. Velocity-map images of ground-state bromine atoms (Br), spin-orbit excited bromine atoms (Br{sup ∗}), and C{sub 3}H{sub 5} hydrocarbon radicals reveal the kinetic energies of these various photofragments. Both Br and Br{sup ∗} atoms are predominantly generated via repulsive excited electronic states in a prompt photodissociation process in which the hydrocarbon co-fragment is a cyclopropyl radical. However, the images obtained at the mass of the hydrocarbon radical fragment identify a channel with total kinetic energy greater than that deduced frommore » the Br and Br{sup ∗} images, and with a kinetic energy distribution that exceeds the energetic limit for Br + cyclopropyl radical products. The velocity-map images of these C{sub 3}H{sub 5} fragments have lower angular anisotropies than measured for Br and Br{sup ∗}, indicating molecular restructuring during dissociation. The high kinetic energy C{sub 3}H{sub 5} signals are assigned to allyl radicals generated by a minor photochemical pathway which involves concerted C–Br bond dissociation and cyclopropyl ring-opening following single ultraviolet (UV)-photon absorption. Slow photofragments also contribute to the velocity map images obtained at the C{sub 3}H{sub 5} radical mass, but the corresponding slow Br atoms are not observed. These features in the images are attributed to C{sub 3}H{sub 5}{sup +} from the photodissociation of the C{sub 3}H{sub 5}Br{sup +} molecular cation following two-photon ionization of the parent compound. This assignment is confirmed by 118-nm vacuum ultraviolet ionization studies that prepare the molecular cation in its ground electronic state prior to UV photodissociation.« less

Improving risk models for avian influenza: the role of intensive poultry farming and flooded land during the 2004 Thailand epidemic.

PubMed

Van Boeckel, Thomas P; Thanapongtharm, Weerapong; Robinson, Timothy; Biradar, Chandrashekhar M; Xiao, Xiangming; Gilbert, Marius

2012-01-01

Since 1996 when Highly Pathogenic Avian Influenza type H5N1 first emerged in southern China, numerous studies sought risk factors and produced risk maps based on environmental and anthropogenic predictors. However little attention has been paid to the link between the level of intensification of poultry production and the risk of outbreak. This study revised H5N1 risk mapping in Central and Western Thailand during the second wave of the 2004 epidemic. Production structure was quantified using a disaggregation methodology based on the number of poultry per holding. Population densities of extensively- and intensively-raised ducks and chickens were derived both at the sub-district and at the village levels. LandSat images were used to derive another previously neglected potential predictor of HPAI H5N1 risk: the proportion of water in the landscape resulting from floods. We used Monte Carlo simulation of Boosted Regression Trees models of predictor variables to characterize the risk of HPAI H5N1. Maps of mean risk and uncertainty were derived both at the sub-district and the village levels. The overall accuracy of Boosted Regression Trees models was comparable to that of logistic regression approaches. The proportion of area flooded made the highest contribution to predicting the risk of outbreak, followed by the densities of intensively-raised ducks, extensively-raised ducks and human population. Our results showed that as little as 15% of flooded land in villages is sufficient to reach the maximum level of risk associated with this variable. The spatial pattern of predicted risk is similar to previous work: areas at risk are mainly located along the flood plain of the Chao Phraya river and to the south-east of Bangkok. Using high-resolution village-level poultry census data, rather than sub-district data, the spatial accuracy of predictions was enhanced to highlight local variations in risk. Such maps provide useful information to guide intervention.

Improving Risk Models for Avian Influenza: The Role of Intensive Poultry Farming and Flooded Land during the 2004 Thailand Epidemic

PubMed Central

Van Boeckel, Thomas P.; Thanapongtharm, Weerapong; Robinson, Timothy; Biradar, Chandrashekhar M.; Xiao, Xiangming; Gilbert, Marius

2012-01-01

Since 1996 when Highly Pathogenic Avian Influenza type H5N1 first emerged in southern China, numerous studies sought risk factors and produced risk maps based on environmental and anthropogenic predictors. However little attention has been paid to the link between the level of intensification of poultry production and the risk of outbreak. This study revised H5N1 risk mapping in Central and Western Thailand during the second wave of the 2004 epidemic. Production structure was quantified using a disaggregation methodology based on the number of poultry per holding. Population densities of extensively- and intensively-raised ducks and chickens were derived both at the sub-district and at the village levels. LandSat images were used to derive another previously neglected potential predictor of HPAI H5N1 risk: the proportion of water in the landscape resulting from floods. We used Monte Carlo simulation of Boosted Regression Trees models of predictor variables to characterize the risk of HPAI H5N1. Maps of mean risk and uncertainty were derived both at the sub-district and the village levels. The overall accuracy of Boosted Regression Trees models was comparable to that of logistic regression approaches. The proportion of area flooded made the highest contribution to predicting the risk of outbreak, followed by the densities of intensively-raised ducks, extensively-raised ducks and human population. Our results showed that as little as 15% of flooded land in villages is sufficient to reach the maximum level of risk associated with this variable. The spatial pattern of predicted risk is similar to previous work: areas at risk are mainly located along the flood plain of the Chao Phraya river and to the south-east of Bangkok. Using high-resolution village-level poultry census data, rather than sub-district data, the spatial accuracy of predictions was enhanced to highlight local variations in risk. Such maps provide useful information to guide intervention. PMID:23185352

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

PubMed Central

2014-01-01

Background Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation. Results The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes. Conclusion The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps. PMID:24581289

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map.

PubMed

van Dijk, Thijs; Pagliarani, Giulia; Pikunova, Anna; Noordijk, Yolanda; Yilmaz-Temel, Hulya; Meulenbroek, Bert; Visser, Richard G F; van de Weg, Eric

2014-03-01

Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation. The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes. The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps.

An online operational rainfall-monitoring resource for epidemic malaria early warning systems in Africa

USGS Publications Warehouse

Grover-Kopec, Emily; Kawano, Mika; Klaver, Robert W.; Blumenthal, Benno; Ceccato, Pietro; Connor, Stephen J.

2005-01-01

Periodic epidemics of malaria are a major public health problem for many sub-Saharan African countries. Populations in epidemic prone areas have a poorly developed immunity to malaria and the disease remains life threatening to all age groups. The impact of epidemics could be minimized by prediction and improved prevention through timely vector control and deployment of appropriate drugs. Malaria Early Warning Systems are advocated as a means of improving the opportunity for preparedness and timely response.Rainfall is one of the major factors triggering epidemics in warm semi-arid and desert-fringe areas. Explosive epidemics often occur in these regions after excessive rains and, where these follow periods of drought and poor food security, can be especially severe. Consequently, rainfall monitoring forms one of the essential elements for the development of integrated Malaria Early Warning Systems for sub-Saharan Africa, as outlined by the World Health Organization.The Roll Back Malaria Technical Resource Network on Prevention and Control of Epidemics recommended that a simple indicator of changes in epidemic risk in regions of marginal transmission, consisting primarily of rainfall anomaly maps, could provide immediate benefit to early warning efforts. In response to these recommendations, the Famine Early Warning Systems Network produced maps that combine information about dekadal rainfall anomalies, and epidemic malaria risk, available via their Africa Data Dissemination Service. These maps were later made available in a format that is directly compatible with HealthMapper, the mapping and surveillance software developed by the WHO's Communicable Disease Surveillance and Response Department. A new monitoring interface has recently been developed at the International Research Institute for Climate Prediction (IRI) that enables the user to gain a more contextual perspective of the current rainfall estimates by comparing them to previous seasons and climatological averages. These resources are available at no cost to the user and are updated on a routine basis.

Elution of Labile Fluorescent Dye from Nanoparticles during Biological Use

PubMed Central

Tenuta, Tiziana; Monopoli, Marco P.; Kim, JongAh; Salvati, Anna; Dawson, Kenneth A.; Sandin, Peter; Lynch, Iseult

2011-01-01

Cells act as extremely efficient filters for elution of unbound fluorescent tags or impurities associated with nanoparticles, including those that cannot be removed by extensive cleaning. This has consequences for quantification of nanoparticle uptake and sub-cellular localization in vitro and in vivo as a result of the presence of significant amount of labile dye even following extensive cleaning by dialysis. Polyacrylamide gel electrophoresis (PAGE) can be used to monitor the elution of unbound fluorescent probes from nanoparticles, either commercially available or synthesized in-house, and to ensure their complete purification for biological studies, including cellular uptake and sub-cellular localisation. Very different fluorescence distribution within cells is observed after short dialysis times versus following extensive dialysis against a solvent in which the free dye is more soluble, due to the contribution from free dye. In the absence of an understanding of the presence of residual free dye in (most) labeled nanoparticle solutions, the total fluorescence intensity in cells following exposure to nanoparticle solutions could be mis-ascribed to the presence of nanoparticles through the cell, rather than correctly assigned to either a combination of free-dye and nanoparticle-bound dye, or even entirely to free dye depending on the exposure conditions (i.e. aggregation of the particles etc). Where all of the dye is nanoparticle-bound, the particles are highly localized in sub-cellular organelles, likely lysosomes, whereas in a system containing significant amounts of free dye, the fluorescence is distributed through the cell due to the free diffusion of the molecule dye across all cellular barriers and into the cytoplasm. PMID:21998668

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren Limei; Schuchardt, Frank; Shen Yujun

An absorbent mixture of magnesium hydroxide (Mg(OH){sub 2}) and phosphoric acid (H{sub 3}PO{sub 4}) was added to compost mixtures of pig manure with cornstalk in different molar ratios (T1, 1:1; T2, 1:2; T3, 1:3) in order to examine its effect on controlling ammonia losses during composting. Based on the principle of struvite precipitation, and with an unamended trial as control (CK), an in-vessel composting experiment was conducted in fermenters (60 L with forced aeration) in which the absorbent mixture was added with proportions of 3.8%, 7.3% and 8.9% of dry weight for T1, T2 and T3, respectively. The results showedmore » that the total nitrogen loss was reduced from 35% to 12%, 5% and 1% of initial N mass, respectively. In the final compost, the total nitrogen content in T1, T2 and T3 was improved by 10, 14, 12 g kg{sup -1}, and NH{sub 4}{sup +}-N in T1, T2 and T3 was improved by 8, 9, and 10 g kg{sup -1}, respectively, compared with the unamended trial. The results of the germination index test showed that the maturity of treatment T2 was best among the four treatments in the final compost, followed by T1, CK and T3. The results of X-ray diffraction (XRD) confirmed the formation of magnesium ammonium phosphate hexahydrate (MgNH{sub 4}PO{sub 4}.6H{sub 2}O:MAP) in the T1, T2 and T3 compost. Based on these results, the adsorbent mixture of Mg(OH){sub 2} + H{sub 3}PO{sub 4} could control nitrogen loss effectively during composting via struvite crystallization. However, an excess of phosphoric acid (1:3) had a negative influence on composting properties. The pH value decreased which led to reduced microorganism activity, and which finally resulted in reduced biodegradation of the organic matter.« less

First Year Wilkinson Microwave Anisotropy Probe (WMAP)Observations: Preliminary Maps and Basic Results

NASA Technical Reports Server (NTRS)

Bennett, C. L.; Halpern, M.; Hinshaw, G.; Jarosik, N.; Kogut, A.; Limon, M.; Meyer, S. S.; Page, L.; Spergel, D. N.; Tucker, G. S.

2003-01-01

We present full sky microwave maps in five frequency bands (23 to 94 GHz) from the WMAP first year sky survey. Calibration errors are less than 0.5% and the low systematic error level is well specified. The cosmic microwave background (CMB) is separated from the foregrounds using multifrequency data. The sky maps are consistent with the 7 in. full-width at half-maximum (FWHM) Cosmic Background Explorer (COBE) maps. We report more precise, but consistent, dipole and quadrupole values. The CMB anisotropy obeys Gaussian statistics with -58 less than f(sub NL) less than 134 (95% CL). The 2 less than or = l less than or = 900 anisotropy power spectrum is cosmic variance limited for l less than 354 with a signal-to-noise ratio greater than 1 per mode to l = 658. The temperature-polarization cross-power spectrum reveals both acoustic features and a large angle correlation from reionization. The optical depth of reionization is tau = 0.17 +/- 0.04, which implies a reionization epoch of t(sub r) = 180(sup +220, sub -80) Myr (95% CL) after the Big Bang at a redshift of z(sub r) = 20(sup +10, sub -9) (95% CL) for a range of ionization scenarios. This early reionization is incompatible with the presence of a significant warm dark matter density. A best-fit cosmological model to the CMB and other measures of large scale structure works remarkably well with only a few parameters. The age of the best-fit universe is t(sub 0) = 13.7 +/- 0.2 Gyr old. Decoupling was t(sub dec) = 379(sup +8, sub -7)kyr after the Big Bang at a redshift of z(sub dec) = 1089 +/- 1. The thickness of the decoupling surface was Delta(sub z(sub dec)) = 195 +/- 2. The matter density of the universe is Omega(sub m)h(sup 2) = 0.135(sup +0.008, sub -0.009) the baryon density is Omega(sub b)h(sup 2) = 0.0224 +/- 0.0009, and the total mass-energy of the universe is Omega(sub tot) = 1.02 +/- 0.02. There is progressively less fluctuation power on smaller scales, from WMAP to fine scale CMB measurements to galaxies and finally to the Ly-alpha forest. This is accounted for with a running spectral index, significant at the approx. 2(sigma) level. The spectral index of scalar fluctuations is fit as n(sub s) = 0.93 +/-0.03 at wavenumber k(sub o) = 0.05/Mpc ((sub eff) approx. = 700), with a slope of dn(sub s)/d I(sub nk) = -0.031(sup + 0.016, sub -0.018) in the best-fit model.

Impact of cell size on inventory and mapping errors in a cellular geographic information system

NASA Technical Reports Server (NTRS)

Wehde, M. E. (Principal Investigator)

1979-01-01

The author has identified the following significant results. The effect of grid position was found insignificant for maps but highly significant for isolated mapping units. A modelable relationship between mapping error and cell size was observed for the map segment analyzed. Map data structure was also analyzed with an interboundary distance distribution approach. Map data structure and the impact of cell size on that structure were observed. The existence of a model allowing prediction of mapping error based on map structure was hypothesized and two generations of models were tested under simplifying assumptions.

High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations.

PubMed

2014-12-11

Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400-500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selection-enhanced breeding of this important crop. Copyright © 2015 International Cassava Genetic Map Consortium (ICGMC).

Photocrosslinking approaches to interactome mapping

PubMed Central

Pham, Nam D.; Parker, Randy B.; Kohler, Jennifer J.

2012-01-01

Photocrosslinking approaches can be used to map interactome networks within the context of living cells. Photocrosslinking methods rely on use of metabolic engineering or genetic code expansion to incorporate photocrosslinking analogs of amino acids or sugars into cellular biomolecules. Immunological and mass spectrometry techniques are used to analyze crosslinked complexes, thereby defining specific interactomes. Because photocrosslinking can be conducted in native, cellular settings, it can be used to define context-dependent interactions. Photocrosslinking methods are also ideally suited for determining interactome dynamics, mapping interaction interfaces, and identifying transient interactions in which intrinsically disordered proteins and glycoproteins engage. Here we discuss the application of cell-based photocrosslinking to the study of specific problems in immune cell signaling, transcription, membrane protein dynamics, nucleocytoplasmic transport, and chaperone-assisted protein folding. PMID:23149092

Synchrotron radiation induced X-ray emission studies of the antioxidant mechanism of the organoselenium drug ebselen.

PubMed

Aitken, Jade B; Lay, Peter A; Duong, T T Hong; Aran, Roshanak; Witting, Paul K; Harris, Hugh H; Lai, Barry; Vogt, Stefan; Giles, Gregory I

2012-04-01

Synchrotron radiation induced X-ray emission (SRIXE) spectroscopy was used to map the cellular uptake of the organoselenium-based antioxidant drug ebselen using differentiated ND15 cells as a neuronal model. The cellular SRIXE spectra, acquired using a hard X-ray microprobe beam (12.8-keV), showed a large enhancement of fluorescence at the K(α) line for Se (11.2-keV) following treatment with ebselen (10 μM) at time periods from 60 to 240 min. Drug uptake was quantified and ebselen was shown to induce time-dependent changes in cellular elemental content that were characteristic of oxidative stress with the efflux of K, Cl, and Ca species. The SRIXE cellular Se distribution map revealed that ebselen was predominantly localized to a discreet region of the cell which, by comparison with the K and P elemental maps, is postulated to correspond to the endoplasmic reticulum. On the basis of these findings, it is hypothesized that a major outcome of ebselen redox catalysis is the induction of cellular stress. A mechanism of action of ebselen is proposed that involves the cell responding to drug-induced stress by increasing the expression of antioxidant genes. This hypothesis is supported by the observation that ebselen also regulated the homeostasis of the transition metals Mn, Cu, Fe, and Zn, with increases in transition metal uptake paralleling known induction times for the expression of antioxidant metalloenzymes. © SBIC 2012

Forward and backward tone mapping of high dynamic range images based on subband architecture

NASA Astrophysics Data System (ADS)

Bouzidi, Ines; Ouled Zaid, Azza

2015-01-01

This paper presents a novel High Dynamic Range (HDR) tone mapping (TM) system based on sub-band architecture. Standard wavelet filters of Daubechies, Symlets, Coiflets and Biorthogonal were used to estimate the proposed system performance in terms of Low Dynamic Range (LDR) image quality and reconstructed HDR image fidelity. During TM stage, the HDR image is firstly decomposed in sub-bands using symmetrical analysis-synthesis filter bank. The transform coefficients are then rescaled using a predefined gain map. The inverse Tone Mapping (iTM) stage is straightforward. Indeed, the LDR image passes through the same sub-band architecture. But, instead of reducing the dynamic range, the LDR content is boosted to an HDR representation. Moreover, in our TM sheme, we included an optimization module to select the gain map components that minimize the reconstruction error, and consequently resulting in high fidelity HDR content. Comparisons with recent state-of-the-art methods have shown that our method provides better results in terms of visual quality and HDR reconstruction fidelity using objective and subjective evaluations.

OCT in the field of laryngology: further perspectives

NASA Astrophysics Data System (ADS)

Just, T.; Pau, H. W.; Lankenau, E.; Hüttmann, G.

2011-03-01

Early detection of cancerous lesions of the larynx may be the best method of improving patient quality of life and survival rates. New in-vivo technologies may be of great clinical relevance in improving the accuracy of sampling during microlaryngeal surgery. Optical coherence tomography (OCT) is an optical imaging technique that clearly identifies basement membrane violation caused by laryngeal cancer. With a microscope-based spectral domain OCT (SD-OCT) we reached in vivo a fairly accurate assessment of benign and dysplastic laryngeal lesions. Recent improvements in OCT technology have led to the development of high-speed OCT systems displaying millions of pixels per second. These systems allow non-contact real-time imaging of large sections of laryngeal tissue. Polarization contrast OCT (PS-OCT) may provide additional information about the lamina propria of the true vocal cord because of the birefringence of connective tissue. We present microscope-based high-speed SD-OCT images with and without polarization contrast and 3D volumes of selected laryngeal pathologies in order to demonstrate our current concepts for the intended intraoperative application. High-speed SD-OCT and polarization contrast can also be complemented by our recently developed rigid confocal endoscopic system to obtain cellular and sub-cellular information about the tissue. Further perspectives will be presented.

Characterization of Aquaporin 4 Protein Expression and Localization in Tissues of the Dogfish (Squalus acanthias)

PubMed Central

Cutler, Christopher P.; Harmon, Sheena; Walsh, Jonathon; Burch, Kia

2012-01-01

The role of aquaporin water channels such as aquaporin 4 (Aqp4) in elasmobranchs such as the dogfish Squalus acanthias is completely unknown. This investigation set out to determine the expression and cellular and sub-cellular localization of Aqp4 protein in dogfish tissues. Two polyclonal antibodies were generated (AQP4/1 and AQP4/2) and these showed somewhat different characteristics in Western blotting and immunohistochemistry. Western blots using the AQP4/1 antibody showed two bands (35.5 and 49.5 kDa) in most tissues in a similar fashion to mammals. Liver had an additional band of 57 kDa and rectal gland two further faint bands of 37.5 and 38.5 kDa. However, unlike in mammals, Aqp4 protein was ubiquitously expressed in all tissues including gill and liver. The AQP4/2 antibody appeared much less specific in Western blots. Both antibodies were used in immunohistochemistry and showed similar cellular localizations, although the AQP4/2 antibody had a more restricted sub-cellular distribution compared to AQP4/1 and therefore appeared to be more specific for Aqp4. In kidney a sub-set of tubules were stained which may represent intermediate tubule segments (In-III–In-VI). AQP4/1 and AQP4/2 antibodies localized to the same tubules segments in serial sections although the intensity and sub-cellular distribution were different. AQP4/2 showed a basal or basolateral membrane distribution whereas AQP4/1 was often distributed throughout the whole cell including the nuclear region. In rectal gland and cardiac stomach Aqp4 was localized to secretory tubules but again AQP/1 and AQP/2 exhibited different sub-cellular distributions. In gill, both antibodies stained large cells in the primary filament and secondary lamellae. Again AQP4/1 antibody stained most or all the cell including the nucleus, whereas AQP4/2 had a plasma membrane or plasma membrane and cytoplasmic distribution. Two types of large mitochondrial rich transport cells are known to exist in elasmobranchs, that express either Na, K-ATPase, or V-type ATPase ion transporters. Using Na, K-ATPase, and V-type ATPase antibodies, Aqp4 was colocalized with these proteins using the AQP4/1 antibody. Results show Aqp4 is expressed in both (and all) branchial Na, K-ATPase, and V-type ATPase expressing cells. PMID:22363294

Characterization of Aquaporin 4 Protein Expression and Localization in Tissues of the Dogfish (Squalus acanthias).

PubMed

Cutler, Christopher P; Harmon, Sheena; Walsh, Jonathon; Burch, Kia

2012-01-01

The role of aquaporin water channels such as aquaporin 4 (Aqp4) in elasmobranchs such as the dogfish Squalus acanthias is completely unknown. This investigation set out to determine the expression and cellular and sub-cellular localization of Aqp4 protein in dogfish tissues. Two polyclonal antibodies were generated (AQP4/1 and AQP4/2) and these showed somewhat different characteristics in Western blotting and immunohistochemistry. Western blots using the AQP4/1 antibody showed two bands (35.5 and 49.5 kDa) in most tissues in a similar fashion to mammals. Liver had an additional band of 57 kDa and rectal gland two further faint bands of 37.5 and 38.5 kDa. However, unlike in mammals, Aqp4 protein was ubiquitously expressed in all tissues including gill and liver. The AQP4/2 antibody appeared much less specific in Western blots. Both antibodies were used in immunohistochemistry and showed similar cellular localizations, although the AQP4/2 antibody had a more restricted sub-cellular distribution compared to AQP4/1 and therefore appeared to be more specific for Aqp4. In kidney a sub-set of tubules were stained which may represent intermediate tubule segments (In-III-In-VI). AQP4/1 and AQP4/2 antibodies localized to the same tubules segments in serial sections although the intensity and sub-cellular distribution were different. AQP4/2 showed a basal or basolateral membrane distribution whereas AQP4/1 was often distributed throughout the whole cell including the nuclear region. In rectal gland and cardiac stomach Aqp4 was localized to secretory tubules but again AQP/1 and AQP/2 exhibited different sub-cellular distributions. In gill, both antibodies stained large cells in the primary filament and secondary lamellae. Again AQP4/1 antibody stained most or all the cell including the nucleus, whereas AQP4/2 had a plasma membrane or plasma membrane and cytoplasmic distribution. Two types of large mitochondrial rich transport cells are known to exist in elasmobranchs, that express either Na, K-ATPase, or V-type ATPase ion transporters. Using Na, K-ATPase, and V-type ATPase antibodies, Aqp4 was colocalized with these proteins using the AQP4/1 antibody. Results show Aqp4 is expressed in both (and all) branchial Na, K-ATPase, and V-type ATPase expressing cells.

On Pulsating and Cellular Forms of Hydrodynamic Instability in Liquid-Propellant Combustion

NASA Technical Reports Server (NTRS)

Margolis, Stephen B.; Sacksteder, Kurt (Technical Monitor)

1998-01-01

An extended Landau-Levich model of liquid-propellant combustion, one that allows for a local dependence of the burning rate on the (gas) pressure at the liquid-gas interface, exhibits not only the classical hydrodynamic cellular instability attributed to Landau but also a pulsating hydrodynamic instability associated with sufficiently negative pressure sensitivities. Exploiting the realistic limit of small values of the gas-to-liquid density ratio p, analytical formulas for both neutral stability boundaries may be obtained by expanding all quantities in appropriate powers of p in each of three distinguished wave-number regimes. In particular, composite analytical expressions are derived for the neutral stability boundaries A(sub p)(k), where A, is the pressure sensitivity of the burning rate and k is the wave number of the disturbance. For the cellular boundary, the results demonstrate explicitly the stabilizing effect of gravity on long-wave disturbances, the stabilizing effect of viscosity (both liquid and gas) and surface tension on short-wave perturbations, and the instability associated with intermediate wave numbers for negative values of A(sub p), which is characteristic of many hydroxylammonium nitrate-based liquid propellants over certain pressure ranges. In contrast, the pulsating hydrodynamic stability boundary is insensitive to gravitational and surface-tension effects but is more sensitive to the effects of liquid viscosity because, for typical nonzero values of the latter, the pulsating boundary decreases to larger negative values of A(sub p) as k increases through O(l) values. Thus, liquid-propellant combustion is predicted to be stable (that is, steady and planar) only for a range of negative pressure sensitivities that lie below the cellular boundary that exists for sufficiently small negative values of A(sub p) and above the pulsating boundary that exists for larger negative values of this parameter.

Large-Scale, High-Resolution Neurophysiological Maps Underlying fMRI of Macaque Temporal Lobe

PubMed Central

Papanastassiou, Alex M.; DiCarlo, James J.

2013-01-01

Maps obtained by functional magnetic resonance imaging (fMRI) are thought to reflect the underlying spatial layout of neural activity. However, previous studies have not been able to directly compare fMRI maps to high-resolution neurophysiological maps, particularly in higher level visual areas. Here, we used a novel stereo microfocal x-ray system to localize thousands of neural recordings across monkey inferior temporal cortex (IT), construct large-scale maps of neuronal object selectivity at subvoxel resolution, and compare those neurophysiology maps with fMRI maps from the same subjects. While neurophysiology maps contained reliable structure at the sub-millimeter scale, fMRI maps of object selectivity contained information at larger scales (>2.5 mm) and were only partly correlated with raw neurophysiology maps collected in the same subjects. However, spatial smoothing of neurophysiology maps more than doubled that correlation, while a variety of alternative transforms led to no significant improvement. Furthermore, raw spiking signals, once spatially smoothed, were as predictive of fMRI maps as local field potential signals. Thus, fMRI of the inferior temporal lobe reflects a spatially low-passed version of neurophysiology signals. These findings strongly validate the widespread use of fMRI for detecting large (>2.5 mm) neuronal domains of object selectivity but show that a complete understanding of even the most pure domains (e.g., faces vs nonface objects) requires investigation at fine scales that can currently only be obtained with invasive neurophysiological methods. PMID:24048850

WIDE FIELD CO MAPPING IN THE REGION OF IRAS 19312+1950

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakashima, Jun-ichi; Ladeyschikov, Dmitry A.; Sobolev, Andrej M.

2016-07-01

We report the results of wide field CO mapping in the region of IRAS 19312+1950. This Infrared Astronomical Satellite ( IRAS ) object exhibits SiO/H{sub 2}O/OH maser emission, and is embedded in a chemically rich molecular component, the origin of which is still unknown. In order to reveal the entire structure and gas mass of the surrounding molecular component for the first time, we have mapped a wide region around IRAS 19312+1950 in the {sup 12}CO J = 1–0, {sup 13}CO J = 1–0 and C{sup 18}O J = 1–0 lines using the Nobeyama 45 m telescope. In conjunction withmore » archival CO maps, we investigated a region up to 20′ × 20′ in size around this IRAS object. We calculated the CO gas mass assuming local thermal equilibrium, the stellar velocity through the interstellar medium assuming an analytic model of bow shock, and the absolute luminosity, using the latest archival data and trigonometric parallax distance. The derived gas mass (225 M {sub ⊙}–478 M {sub ⊙}) of the molecular component and the relatively large luminosity (2.63 × 10{sup 4} L {sub ☉}) suggest that the central SiO/H{sub 2}O/OH maser source is a red supergiant rather than an asymptotic giant branch (AGB) star or post-AGB star.« less

The radio continuum-star formation rate relation in WSRT sings galaxies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heesen, Volker; Brinks, Elias; Leroy, Adam K.

2014-05-01

We present a study of the spatially resolved radio continuum-star formation rate (RC-SFR) relation using state-of-the-art star formation tracers in a sample of 17 THINGS galaxies. We use SFR surface density (Σ{sub SFR}) maps created by a linear combination of GALEX far-UV (FUV) and Spitzer 24 μm maps. We use RC maps at λλ22 and 18 cm from the WSRT SINGS survey and Hα emission maps to correct for thermal RC emission. We compare azimuthally averaged radial profiles of the RC and FUV/mid-IR (MIR) based Σ{sub SFR} maps and study pixel-by-pixel correlations at fixed linear scales of 1.2 and 0.7more » kpc. The ratio of the integrated SFRs from the RC emission to that of the FUV/MIR-based SF tracers is R{sub int}=0.78±0.38, consistent with the relation by Condon. We find a tight correlation between the radial profiles of the radio and FUV/MIR-based Σ{sub SFR} for the entire extent of the disk. The ratio R of the azimuthally averaged radio to FUV/MIR-based Σ{sub SFR} agrees with the integrated ratio and has only quasi-random fluctuations with galactocentric radius that are relatively small (25%). Pixel-by-pixel plots show a tight correlation in log-log diagrams of radio to FUV/MIR-based Σ{sub SFR}, with a typical standard deviation of a factor of two. Averaged over our sample we find (Σ{sub SFR}){sub RC}∝(Σ{sub SFR}){sub hyb}{sup 0.63±0.25}, implying that data points with high Σ{sub SFR} are relatively radio dim, whereas the reverse is true for low Σ{sub SFR}. We interpret this as a result of spectral aging of cosmic-ray electrons (CREs), which are diffusing away from the star formation sites where they are injected into the interstellar medium. This is supported by our finding that the radio spectral index is a second parameter in pixel-by-pixel plots: those data points dominated by young CREs are relatively radio dim, while those dominated by old CREs are slightly more RC bright than what would be expected from a linear extrapolation. We studied the ratio R of radio to FUV/MIR-based integrated SFR as a function of global galaxy parameters and found no clear correlation. This suggests that we can use RC emission as a universal star formation tracer for galaxies with a similar degree of accuracy as other tracers, if we restrict ourselves to global or azimuthally averaged measurements. We can reconcile our finding of an almost linear RC-SFR relation and sub-linear resolved (on 1 kpc scale) RC-Σ{sub SFR} relation by proposing a non-linear magnetic field-SFR relation, B∝SFR{sub hyb}{sup 0.30±0.02}, which holds both globally and locally.« less

Herpes simplex virus 2 VP22 phosphorylation induced by cellular and viral kinases does not influence intracellular localization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geiss, Brian J.; Cano, Gina L.; Tavis, John E.

2004-12-05

Phosphorylation of the herpes simplex virus (HSV) VP22 protein is regulated by cellular kinases and the UL13 viral kinase, but the sites at which these enzymes induce phosphorylation of HSV-2 VP22 are not known. Using serine-to-alanine mutants to map phosphorylation sites on HSV-2 VP22 in cells, we made three major observations. First, phosphorylation by a cellular kinase mapped to serines 70, 71, and/or 72 within CKII consensus sites analogous to previously identified phosphorylation sites in HSV-1 VP22. Second, we mapped UL13-mediated phosphorylation of HSV-2 VP22 to serines 28 and 34, describing for the first time UL13-dependent phosphorylation sites on VP22.more » Third, previously identified VP22-associated cellular kinase sites in HSV-1 VP22 (serines 292 and 294) were not phosphorylated in HSV-2 VP22 (serines 291 and 293). VP22 expressed alone accumulated in the cytoplasm and to a lesser extent in the nucleus. Phosphorylation by endogenous cellular kinase(s) did not alter the localization of VP22. Co-expression of HSV-2 VP22 with active UL13, but not with enzymatically inactive UL13, resulted in nuclear accumulation of VP22 and altered nuclear morphology. Surprisingly, redistribution of VP22 to the nucleus occurred independently of UL13-induced phosphorylation of VP22. The altered nuclear morphology of UL13-expressing cells was not due to apoptosis. These results demonstrate that phosphorylation of HSV-2 VP22 at multiple serine residues is induced by UL13 and cellular kinase(s), and that the nuclear/cytoplasmic distribution of VP22 is independent of its phosphorylation status but is controlled indirectly by UL13 kinase activity.« less

Cellular and humoral immune responses in sheep vaccinated with candidate antigens MAP2698c and MAP3567 from Mycobacterium avium subspecies paratuberculosis

PubMed Central

Gurung, Ratna B.; Purdie, Auriol C.; Whittington, Richard J.; Begg, Douglas J.

2014-01-01

Control of Johne's disease, caused by Mycobacterium avium subspecies paratuberculosis (MAP) in ruminants using commercially available vaccine reduces production losses, mortality, fecal shedding and histopathological lesions but does not provide complete protection from infection and interferes with serological diagnosis of Johne's disease and bovine tuberculosis. At this time no recombinant antigens have been found to provide superior protection compared to whole killed or live-attenuated MAP vaccines. Therefore, there is a need to evaluate more candidate MAP antigens. In this study recombinant MAP antigens MAP2698c and MAP3567 were formulated with four different MONTANIDE™ (ISA 50V2, 61VG, 71VG, and 201VG) adjuvants and evaluated for their ability to produce specific immune responses in vaccinated sheep. The cellular immune response was measured with an interferon-gamma (IFN-γ) release assay and the humoral immune response was measured by antibody detection enzyme linked immunosorbent assay. Recombinant vaccine formulation with the antigen MAP2698c and MONTANIDE™ ISA 201VG adjuvant produced strong whole-MAP as well as MAP2698c-specific IFN-γ responses in a high proportion of the vaccinated sheep. The formulation caused less severe injection site lesions in comparison to other formulations. The findings from this study suggest that the MAP2698c + 201VG should be evaluated in a challenge trial to determine the efficacy of this vaccine candidate. PMID:25077074

Simulating the large-scale structure of HI intensity maps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seehars, Sebastian; Paranjape, Aseem; Witzemann, Amadeus

Intensity mapping of neutral hydrogen (HI) is a promising observational probe of cosmology and large-scale structure. We present wide field simulations of HI intensity maps based on N-body simulations of a 2.6 Gpc / h box with 2048{sup 3} particles (particle mass 1.6 × 10{sup 11} M{sub ⊙} / h). Using a conditional mass function to populate the simulated dark matter density field with halos below the mass resolution of the simulation (10{sup 8} M{sub ⊙} / h < M{sub halo} < 10{sup 13} M{sub ⊙} / h), we assign HI to those halos according to a phenomenological halo to HI mass relation. The simulations span a redshift range of 0.35 ∼< z ∼< 0.9 in redshift bins of width Δ z ≈ 0.05 andmore » cover a quarter of the sky at an angular resolution of about 7'. We use the simulated intensity maps to study the impact of non-linear effects and redshift space distortions on the angular clustering of HI. Focusing on the autocorrelations of the maps, we apply and compare several estimators for the angular power spectrum and its covariance. We verify that these estimators agree with analytic predictions on large scales and study the validity of approximations based on Gaussian random fields, particularly in the context of the covariance. We discuss how our results and the simulated maps can be useful for planning and interpreting future HI intensity mapping surveys.« less

Method for coding low entrophy data

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu (Inventor)

1995-01-01

A method of lossless data compression for efficient coding of an electronic signal of information sources of very low information rate is disclosed. In this method, S represents a non-negative source symbol set, (s(sub 0), s(sub 1), s(sub 2), ..., s(sub N-1)) of N symbols with s(sub i) = i. The difference between binary digital data is mapped into symbol set S. Consecutive symbols in symbol set S are then paired into a new symbol set Gamma which defines a non-negative symbol set containing the symbols (gamma(sub m)) obtained as the extension of the original symbol set S. These pairs are then mapped into a comma code which is defined as a coding scheme in which every codeword is terminated with the same comma pattern, such as a 1. This allows a direct coding and decoding of the n-bit positive integer digital data differences without the use of codebooks.

Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alexopoulos, Eftichia; Department of Medical Biophysics, University of Toronto, Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto Medical Discovery Tower, 101 College Street, Toronto, Ontario M5G 1L7; Kanjee, Usheer

2008-08-01

The structure of the decameric inducible lysine decarboxylase from E. coli was determined by SIRAS using a hexatantalum dodecabromide (Ta{sub 6}Br{sub 12}{sup 2+}) derivative. Model building and refinement are under way. The decameric inducible lysine decarboxylase (LdcI) from Escherichia coli has been crystallized in space groups C2 and C222{sub 1}; the Ta{sub 6}Br{sub 12}{sup 2+} cluster was used to derivatize the C2 crystals. The method of single isomorphous replacement with anomalous scattering (SIRAS) as implemented in SHELXD was used to solve the Ta{sub 6}Br{sub 12}{sup 2+}-derivatized structure to 5 Å resolution. Many of the Ta{sub 6}Br{sub 12}{sup 2+}-binding sites hadmore » twofold and fivefold noncrystallographic symmetry. Taking advantage of this feature, phase modification was performed in DM. The electron-density map of LdcI displays many features in agreement with the low-resolution negative-stain electron-density map [Snider et al. (2006 ▶), J. Biol. Chem.281, 1532–1546].« less

Monitoring seasonal state and mapping species in Alaskan taiga using imaging radar as input to CO[sub 2] flux models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Way, J.B.; Rignot, E.; McDonald, K.

1993-06-01

Changes in the seasonal CO[sub 2] flux of the boreal forests may result from increased atmospheric CO[sub 2] concentrations and associated atmospheric warming. To monitor this potential change, a combination of remote sensing information and ecophysiological models are required. In this paper we address the use of synthetic aperture radar (SAR) data to provide some of the input to the ecophysiological models: forest type, freeze/thaw state which limits the growing season for conifers, and leaf on/off state which limits the growing season for deciduous species. AIRSAR data collected in March 1988 during an early thaw event and May 1991 duringmore » spring breakup are used to generate species maps and to determine the sensitivity of SAR to canopy freeze/thaw transitions. These data are also used to validate a microwave scattering model which is then used to determine the sensitivity of SAR to leaf on/off and soil freeze/thaw transitions. Finally, a CO[sub 2] flux algorithm which utilizes SAR data and an ecophysiological model to estimate CO[sub 2] flux is presented. CO[sub 2] flux maps are generated from which areal estimates of CO[sub 2] flux are derived. This work was carried out at the Jet Propulsion Laboratory under contract to the NASA.« less

The Effect of Rainfall Measurement Technique and Its Spatiotemporal Resolution on Discharge Predictions in the Netherlands

NASA Astrophysics Data System (ADS)

Uijlenhoet, R.; Brauer, C.; Overeem, A.; Sassi, M.; Rios Gaona, M. F.

2014-12-01

Several rainfall measurement techniques are available for hydrological applications, each with its own spatial and temporal resolution. We investigated the effect of these spatiotemporal resolutions on discharge simulations in lowland catchments by forcing a novel rainfall-runoff model (WALRUS) with rainfall data from gauges, radars and microwave links. The hydrological model used for this analysis is the recently developed Wageningen Lowland Runoff Simulator (WALRUS). WALRUS is a rainfall-runoff model accounting for hydrological processes relevant to areas with shallow groundwater (e.g. groundwater-surface water feedback). Here, we used WALRUS for case studies in a freely draining lowland catchment and a polder with controlled water levels. We used rain gauge networks with automatic (hourly resolution but low spatial density) and manual gauges (high spatial density but daily resolution). Operational (real-time) and climatological (gauge-adjusted) C-band radar products and country-wide rainfall maps derived from microwave link data from a cellular telecommunication network were also used. Discharges simulated with these different inputs were compared to observations. We also investigated the effect of spatiotemporal resolution with a high-resolution X-band radar data set for catchments with different sizes. Uncertainty in rainfall forcing is a major source of uncertainty in discharge predictions, both with lumped and with distributed models. For lumped rainfall-runoff models, the main source of input uncertainty is associated with the way in which (effective) catchment-average rainfall is estimated. When catchments are divided into sub-catchments, rainfall spatial variability can become more important, especially during convective rainfall events, leading to spatially varying catchment wetness and spatially varying contribution of quick flow routes. Improving rainfall measurements and their spatiotemporal resolution can improve the performance of rainfall-runoff models, indicating their potential for reducing flood damage through real-time control.

Imaging cellular and subcellular structure of human brain tissue using micro computed tomography

NASA Astrophysics Data System (ADS)

Khimchenko, Anna; Bikis, Christos; Schweighauser, Gabriel; Hench, Jürgen; Joita-Pacureanu, Alexandra-Teodora; Thalmann, Peter; Deyhle, Hans; Osmani, Bekim; Chicherova, Natalia; Hieber, Simone E.; Cloetens, Peter; Müller-Gerbl, Magdalena; Schulz, Georg; Müller, Bert

2017-09-01

Brain tissues have been an attractive subject for investigations in neuropathology, neuroscience, and neurobiol- ogy. Nevertheless, existing imaging methodologies have intrinsic limitations in three-dimensional (3D) label-free visualisation of extended tissue samples down to (sub)cellular level. For a long time, these morphological features were visualised by electron or light microscopies. In addition to being time-consuming, microscopic investigation includes specimen fixation, embedding, sectioning, staining, and imaging with the associated artefacts. More- over, optical microscopy remains hampered by a fundamental limit in the spatial resolution that is imposed by the diffraction of visible light wavefront. In contrast, various tomography approaches do not require a complex specimen preparation and can now reach a true (sub)cellular resolution. Even laboratory-based micro computed tomography in the absorption-contrast mode of formalin-fixed paraffin-embedded (FFPE) human cerebellum yields an image contrast comparable to conventional histological sections. Data of a superior image quality was obtained by means of synchrotron radiation-based single-distance X-ray phase-contrast tomography enabling the visualisation of non-stained Purkinje cells down to the subcellular level and automated cell counting. The question arises, whether the data quality of the hard X-ray tomography can be superior to optical microscopy. Herein, we discuss the label-free investigation of the human brain ultramorphology be means of synchrotron radiation-based hard X-ray magnified phase-contrast in-line tomography at the nano-imaging beamline ID16A (ESRF, Grenoble, France). As an example, we present images of FFPE human cerebellum block. Hard X-ray tomography can provide detailed information on human tissues in health and disease with a spatial resolution below the optical limit, improving understanding of the neuro-degenerative diseases.

Dose-shaping using targeted sparse optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayre, George A.; Ruan, Dan

2013-07-15

Purpose: Dose volume histograms (DVHs) are common tools in radiation therapy treatment planning to characterize plan quality. As statistical metrics, DVHs provide a compact summary of the underlying plan at the cost of losing spatial information: the same or similar dose-volume histograms can arise from substantially different spatial dose maps. This is exactly the reason why physicians and physicists scrutinize dose maps even after they satisfy all DVH endpoints numerically. However, up to this point, little has been done to control spatial phenomena, such as the spatial distribution of hot spots, which has significant clinical implications. To this end, themore » authors propose a novel objective function that enables a more direct tradeoff between target coverage, organ-sparing, and planning target volume (PTV) homogeneity, and presents our findings from four prostate cases, a pancreas case, and a head-and-neck case to illustrate the advantages and general applicability of our method.Methods: In designing the energy minimization objective (E{sub tot}{sup sparse}), the authors utilized the following robust cost functions: (1) an asymmetric linear well function to allow differential penalties for underdose, relaxation of prescription dose, and overdose in the PTV; (2) a two-piece linear function to heavily penalize high dose and mildly penalize low and intermediate dose in organs-at risk (OARs); and (3) a total variation energy, i.e., the L{sub 1} norm applied to the first-order approximation of the dose gradient in the PTV. By minimizing a weighted sum of these robust costs, general conformity to dose prescription and dose-gradient prescription is achieved while encouraging prescription violations to follow a Laplace distribution. In contrast, conventional quadratic objectives are associated with a Gaussian distribution of violations, which is less forgiving to large violations of prescription than the Laplace distribution. As a result, the proposed objective E{sub tot}{sup sparse} improves tradeoff between planning goals by 'sacrificing' voxels that have already been violated to improve PTV coverage, PTV homogeneity, and/or OAR-sparing. In doing so, overall plan quality is increased since these large violations only arise if a net reduction in E{sub tot}{sup sparse} occurs as a result. For example, large violations to dose prescription in the PTV in E{sub tot}{sup sparse}-optimized plans will naturally localize to voxels in and around PTV-OAR overlaps where OAR-sparing may be increased without compromising target coverage. The authors compared the results of our method and the corresponding clinical plans using analyses of DVH plots, dose maps, and two quantitative metrics that quantify PTV homogeneity and overdose. These metrics do not penalize underdose since E{sub tot}{sup sparse}-optimized plans were planned such that their target coverage was similar or better than that of the clinical plans. Finally, plan deliverability was assessed with the 2D modulation index.Results: The proposed method was implemented using IBM's CPLEX optimization package (ILOG CPLEX, Sunnyvale, CA) and required 1-4 min to solve with a 12-core Intel i7 processor. In the testing procedure, the authors optimized for several points on the Pareto surface of four 7-field 6MV prostate cases that were optimized for different levels of PTV homogeneity and OAR-sparing. The generated results were compared against each other and the clinical plan by analyzing their DVH plots and dose maps. After developing intuition by planning the four prostate cases, which had relatively few tradeoffs, the authors applied our method to a 7-field 6 MV pancreas case and a 9-field 6MV head-and-neck case to test the potential impact of our method on more challenging cases. The authors found that our formulation: (1) provided excellent flexibility for balancing OAR-sparing with PTV homogeneity; and (2) permitted the dose planner more control over the evolution of the PTV's spatial dose distribution than conventional objective functions. In particular, E{sub tot}{sup sparse}-optimized plans for the pancreas case and head-and-neck case exhibited substantially improved sparing of the spinal cord and parotid glands, respectively, while maintaining or improving sparing for other OARs and markedly improving PTV homogeneity. Plan deliverability for E{sub tot}{sup sparse}-optimized plans was shown to be better than their associated clinical plans, according to the two-dimensional modulation index.Conclusions: These results suggest that our formulation may be used to improve dose-shaping and OAR-sparing for complicated disease sites, such as the pancreas or head and neck. Furthermore, our objective function and constraints are linear and constitute a linear program, which converges to the global minimum quickly, and can be easily implemented in treatment planning software. Thus, the authors expect fast translation of our method to the clinic where it may have a positive impact on plan quality for challenging disease sites.« less

THE EINSTEIN CROSS: CONSTRAINT ON DARK MATTER FROM STELLAR DYNAMICS AND GRAVITATIONAL LENSING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van de Ven, Glenn; Falcon-Barroso, Jesus; McDermid, Richard M.

2010-08-20

We present two-dimensional line-of-sight stellar kinematics of the lens galaxy in the Einstein Cross, obtained with the GEMINI 8 m telescope, using the GMOS integral-field spectrograph. The stellar kinematics extend to a radius of 4'' (with 0.''2 spaxels), covering about two-thirds of the effective (or half-light) radius R{sub e} {approx_equal} 6'' of this early-type spiral galaxy at redshift z{sub l} {approx_equal} 0.04, of which the bulge is lensing a background quasar at redshift z{sub s} {approx_equal} 1.7. The velocity map shows regular rotation up to {approx}100 km s{sup -1} around the minor axis of the bulge, consistent with axisymmetry. Themore » velocity dispersion map shows a weak gradient increasing toward a central (R < 1'') value of {sigma}{sub 0} = 170 {+-} 9 km s{sup -1}. We deproject the observed surface brightness from Hubble Space Telescope imaging to obtain a realistic luminosity density of the lens galaxy, which in turn is used to build axisymmetric dynamical models that fit the observed kinematic maps. We also construct a gravitational lens model that accurately fits the positions and relative fluxes of the four quasar images. We combine these independent constraints from stellar dynamics and gravitational lensing to study the total mass distribution in the inner parts of the lens galaxy. We find that the resulting luminous and total mass distribution are nearly identical around the Einstein radius R{sub E} = 0.''89, with a slope that is close to isothermal, but which becomes shallower toward the center if indeed mass follows light. The dynamical model fits to the observed kinematic maps result in a total mass-to-light ratio Y{sub dyn} = 3.7 {+-} 0.5 Y{sub sun,I} (in the I band). This is consistent with the Einstein mass M{sub E} = 1.54 x 10{sup 10} M {sub sun} divided by the (projected) luminosity within R{sub E} , which yields a total mass-to-light ratio of Y {sub E} = 3.4 Y{sub sun,I}, with an error of at most a few percent. We estimate from stellar population model fits to colors of the lens galaxy a stellar mass-to-light ratio Y{sub *} from 2.8 to 4.1 Y{sub sun,I}. Although a constant dark matter fraction of 20% is not excluded, dark matter may play no significant role in the bulge of this {approx}L {sub *} early-type spiral galaxy.« less

Community context and sub-neighborhood scale detail to explain dengue, chikungunya and Zika patterns in Cali, Colombia.

PubMed

Krystosik, Amy R; Curtis, Andrew; Buritica, Paola; Ajayakumar, Jayakrishnan; Squires, Robert; Dávalos, Diana; Pacheco, Robinson; Bhatta, Madhav P; James, Mark A

2017-01-01

Cali, Colombia has experienced chikungunya and Zika outbreaks and hypoendemic dengue. Studies have explained Cali's dengue patterns but lack the sub-neighborhood-scale detail investigated here. Spatial-video geonarratives (SVG) with Ministry of Health officials and Community Health Workers were collected in hotspots, providing perspective on perceptions of why dengue, chikungunya and Zika hotspots exist, impediments to control, and social outcomes. Using spatial video and Google Street View, sub-neighborhood features possibly contributing to incidence were mapped to create risk surfaces, later compared with dengue, chikungunya and Zika case data. SVG captured insights in 24 neighborhoods. Trash and water risks in Calipso were mapped using SVG results. Perceived risk factors included proximity to standing water, canals, poverty, invasions, localized violence and military migration. These risks overlapped case density maps and identified areas that are suitable for transmission but are possibly underreporting to the surveillance system. Resulting risk maps with local context could be leveraged to increase vector-control efficiency- targeting key areas of environmental risk.

Methods of Real Time Image Enhancement of Flash LIDAR Data and Navigating a Vehicle Using Flash LIDAR Data

NASA Technical Reports Server (NTRS)

Vanek, Michael D. (Inventor)

2014-01-01

A method for creating a digital elevation map ("DEM") from frames of flash LIDAR data includes generating a first distance R(sub i) from a first detector i to a first point on a surface S(sub i). After defining a map with a mesh THETA having cells k, a first array S(k), a second array M(k), and a third array D(k) are initialized. The first array corresponds to the surface, the second array corresponds to the elevation map, and the third array D(k) receives an output for the DEM. The surface is projected onto the mesh THETA, so that a second distance R(sub k) from a second point on the mesh THETA to the detector can be found. From this, a height may be calculated, which permits the generation of a digital elevation map. Also, using sequential frames of flash LIDAR data, vehicle control is possible using an offset between successive frames.

Effect of deformable registration on the dose calculated in radiation therapy planning CT scans of lung cancer patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cunliffe, Alexandra R.; Armato, Samuel G.; White, Bradley

2015-01-15

Purpose: To characterize the effects of deformable image registration of serial computed tomography (CT) scans on the radiation dose calculated from a treatment planning scan. Methods: Eighteen patients who received curative doses (≥60 Gy, 2 Gy/fraction) of photon radiation therapy for lung cancer treatment were retrospectively identified. For each patient, a diagnostic-quality pretherapy (4–75 days) CT scan and a treatment planning scan with an associated dose map were collected. To establish correspondence between scan pairs, a researcher manually identified anatomically corresponding landmark point pairs between the two scans. Pretherapy scans then were coregistered with planning scans (and associated dose maps)more » using the demons deformable registration algorithm and two variants of the Fraunhofer MEVIS algorithm (“Fast” and “EMPIRE10”). Landmark points in each pretherapy scan were automatically mapped to the planning scan using the displacement vector field output from each of the three algorithms. The Euclidean distance between manually and automatically mapped landmark points (d{sub E}) and the absolute difference in planned dose (|ΔD|) were calculated. Using regression modeling, |ΔD| was modeled as a function of d{sub E}, dose (D), dose standard deviation (SD{sub dose}) in an eight-pixel neighborhood, and the registration algorithm used. Results: Over 1400 landmark point pairs were identified, with 58–93 (median: 84) points identified per patient. Average |ΔD| across patients was 3.5 Gy (range: 0.9–10.6 Gy). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, with an average d{sub E} across patients of 5.2 mm (compared with >7 mm for the other two algorithms). Consequently, average |ΔD| was also lowest using the Fraunhofer MEVIS EMPIRE10 algorithm. |ΔD| increased significantly as a function of d{sub E} (0.42 Gy/mm), D (0.05 Gy/Gy), SD{sub dose} (1.4 Gy/Gy), and the algorithm used (≤1 Gy). Conclusions: An average error of <4 Gy in radiation dose was introduced when points were mapped between CT scan pairs using deformable registration, with the majority of points yielding dose-mapping error <2 Gy (approximately 3% of the total prescribed dose). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, resulting in the smallest errors in mapped dose. Dose differences following registration increased significantly with increasing spatial registration errors, dose, and dose gradient (i.e., SD{sub dose}). This model provides a measurement of the uncertainty in the radiation dose when points are mapped between serial CT scans through deformable registration.« less

Integration of Optical Manipulation and Electrophysiological Tools to Modulate and Record Activity in Neural Networks

NASA Astrophysics Data System (ADS)

Difato, F.; Schibalsky, L.; Benfenati, F.; Blau, A.

2011-07-01

We present an optical system that combines IR (1064 nm) holographic optical tweezers with a sub-nanosecond-pulsed UV (355 nm) laser microdissector for the optical manipulation of single neurons and entire networks both on transparent and non-transparent substrates in vitro. The phase-modulated laser beam can illuminate the sample concurrently or independently from above or below assuring compatibility with different types of microelectrode array and patch-clamp electrophysiology. By combining electrophysiological and optical tools, neural activity in response to localized stimuli or injury can be studied and quantified at sub-cellular, cellular, and network level.

Cadmium accumulation, sub-cellular distribution and chemical forms in rice seedling in the presence of sulfur.

PubMed

Zhang, Wen; Lin, Kuangfei; Zhou, Jian; Zhang, Wei; Liu, Lili; Zhang, Qianqian

2014-01-01

Changes in cadmium (Cd) accumulation, distribution, and chemical form in rice seedling in the joint presence of different concentrations of sulfur (S) remain almost unknown. Therefore, the indoor experiments were performed to determine the accumulation, sub-cellular distribution and chemical forms of Cd under three S levels in rice seedling for the first time. The result showed that Cd accumulation in rice roots was more than in shoots. Sub-cellular distribution of Cd in rice roots and shoots indicated that the largest proportion of Cd accumulated in cell walls and soluble fractions. As S supply increased, the proportion of Cd in cell walls reduced, while it increased in the soluble fractions. The majority of Cd existed in inorganic form, and then gradually changed to organic forms that included pectates and proteins with increased S supply. The results showed that S supply significantly influenced Cd accumulation, distribution, and chemical forms, suggesting that S might provide the material for the synthesis of sulfhydryl protein and thereby affect Cd stress on plants. These observations provided a basic understanding of potential ecotoxicological effects of joint Cd and S exposure in the environment. Copyright © 2013 Elsevier B.V. All rights reserved.

Therapeutics incorporating blood constituents.

PubMed

Charoenphol, Phapanin; Oswalt, Katie; Bishop, Corey J

2018-04-05

Blood deficiency and dysfunctionality can result in adverse events, which can primarily be treated by transfusion of blood or the re-introduction of properly functioning sub-components. Blood constituents can be engineered on the sub-cellular (i.e., DNA recombinant technology) and cellular level (i.e., cellular hitchhiking for drug delivery) for supplementing and enhancing therapeutic efficacy, in addition to rectifying dysfunctioning mechanisms (i.e., clotting). Herein, we report the progress of blood-based therapeutics, with an emphasis on recent applications of blood transfusion, blood cell-based therapies and biomimetic carriers. Clinically translated technologies and commercial products of blood-based therapeutics are subsequently highlighted and perspectives on challenges and future prospects are discussed. Blood-based therapeutics is a burgeoning field and has advanced considerably in recent years. Blood and its constituents, with and without modification (i.e., combinatorial), have been utilized in a broad spectrum of pre-clinical and clinically-translated treatments. This review article summarizes the most up-to-date progress of blood-based therapeutics in the following contexts: synthetic blood substitutes, acellular/non-recombinant therapies, cell-based therapies, and therapeutic sub-components. The article subsequently discusses clinically-translated technologies and future prospects thereof. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Gene expression responses of HeLa cells to chemical species generated by an atmospheric plasma flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yokoyama, Mayo, E-mail: yokoyama@plasma.ifs.tohoku.ac.jp; Johkura, Kohei, E-mail: kohei@shinshu-u.ac.jp; Sato, Takehiko, E-mail: sato@ifs.tohoku.ac.jp

2014-08-08

Highlights: • Response of HeLa cells to a plasma-irradiated medium was revealed by DNA microarray. • Gene expression pattern was basically different from that in a H{sub 2}O{sub 2}-added medium. • Prominently up-/down-regulated genes were partly shared by the two media. • Gene ontology analysis showed both similar and different responses in the two media. • Candidate genes involved in response to ROS were detected in each medium. - Abstract: Plasma irradiation generates many factors able to affect the cellular condition, and this feature has been studied for its application in the field of medicine. We previously reported that hydrogenmore » peroxide (H{sub 2}O{sub 2}) was the major cause of HeLa cell death among the chemical species generated by high level irradiation of a culture medium by atmospheric plasma. To assess the effect of plasma-induced factors on the response of live cells, HeLa cells were exposed to a medium irradiated by a non-lethal plasma flow level, and their gene expression was broadly analyzed by DNA microarray in comparison with that in a corresponding concentration of 51 μM H{sub 2}O{sub 2}. As a result, though the cell viability was sufficiently maintained at more than 90% in both cases, the plasma-medium had a greater impact on it than the H{sub 2}O{sub 2}-medium. Hierarchical clustering analysis revealed fundamentally different cellular responses between these two media. A larger population of genes was upregulated in the plasma-medium, whereas genes were downregulated in the H{sub 2}O{sub 2}-medium. However, a part of the genes that showed prominent differential expression was shared by them, including an immediate early gene ID2. In gene ontology analysis of upregulated genes, the plasma-medium showed more diverse ontologies than the H{sub 2}O{sub 2}-medium, whereas ontologies such as “response to stimulus” were common, and several genes corresponded to “response to reactive oxygen species.” Genes of AP-1 proteins, e.g., JUN and FOS, were detected and notably elevated in the plasma-medium. These results showed that the medium irradiated with a non-lethal level of plasma flow altered various gene expressions of HeLa cells by giving not only common effects with H{sub 2}O{sub 2} but also some distinctive actions. This study suggests that in addition to H{sub 2}O{sub 2}, other chemical species able to affect the cellular responses exist in the plasma-irradiated medium and provide unique features for it, probably increasing the oxidative stress level.« less

Multipurpose prevention technologies for sexual and reproductive health: mapping global needs for introduction of new preventive products.

PubMed

Schelar, Erin; Polis, Chelsea B; Essam, Timothy; Looker, Katharine J; Bruni, Laia; Chrisman, Cara J; Manning, Judy

2016-01-01

Worldwide, women face sexual and reproductive health (SRH) risks including unintended pregnancy and sexually transmitted infections (STIs) including HIV. Multipurpose prevention technologies (MPTs) combine protection against two or more SRH risks into one product. Male and female condoms are the only currently available MPT products, but several other forms of MPTs are in development. We examined the global distribution of selected SRH issues to determine where various risks have the greatest geographical overlap. We examined four indicators relevant to MPTs in development: HIV prevalence, herpes simplex virus type 2 prevalence (HSV-2), human papillomavirus prevalence (HPV) and the proportion of women with unmet need for modern contraception. Using ArcGIS Desktop, we mapped these indicators individually and in combination on choropleth and graduated symbol maps. We conducted a principal components analysis to reduce data and enable visual mapping of all four indicators on one graphic to identify overlap. Our findings document the greatest overlapping risks in Sub-Saharan Africa, and we specify countries in greatest need by specific MPT indication. These results can inform strategic planning for MPT introduction, market segmentation and demand generation; data limitations also highlight the need for improved (non-HIV) STI surveillance globally. MPTs are products in development with the potential to empower women to prevent two or more SRH risks. Geographic analysis of overlapping SRH risks demonstrates particularly high need in Sub-Saharan Africa. This study can help to inform strategic planning for MPT introduction, market segmentation and demand generation. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Multicolor Super-Resolution Fluorescence Imaging via Multi-Parameter Fluorophore Detection

PubMed Central

Bates, Mark; Dempsey, Graham T; Chen, Kok Hao; Zhuang, Xiaowei

2012-01-01

Understanding the complexity of the cellular environment will benefit from the ability to unambiguously resolve multiple cellular components, simultaneously and with nanometer-scale spatial resolution. Multicolor super-resolution fluorescence microscopy techniques have been developed to achieve this goal, yet challenges remain in terms of the number of targets that can be simultaneously imaged and the crosstalk between color channels. Herein, we demonstrate multicolor stochastic optical reconstruction microscopy (STORM) based on a multi-parameter detection strategy, which uses both the fluorescence activation wavelength and the emission color to discriminate between photo-activatable fluorescent probes. First, we obtained two-color super-resolution images using the near-infrared cyanine dye Alexa 750 in conjunction with a red cyanine dye Alexa 647, and quantified color crosstalk levels and image registration accuracy. Combinatorial pairing of these two switchable dyes with fluorophores which enhance photo-activation enabled multi-parameter detection of six different probes. Using this approach, we obtained six-color super-resolution fluorescence images of a model sample. The combination of multiple fluorescence detection parameters for improved fluorophore discrimination promises to substantially enhance our ability to visualize multiple cellular targets with sub-diffraction-limit resolution. PMID:22213647

Context Specificity of Stress-activated Mitogen-activated Protein (MAP) Kinase Signaling: The Story as Told by Caenorhabditis elegans*

PubMed Central

Andrusiak, Matthew G.; Jin, Yishi

2016-01-01

Stress-associated p38 and JNK mitogen-activated protein (MAP) kinase signaling cascades trigger specific cellular responses and are involved in multiple disease states. At the root of MAP kinase signaling complexity is the differential use of common components on a context-specific basis. The roundworm Caenorhabditis elegans was developed as a system to study genes required for development and nervous system function. The powerful genetics of C. elegans in combination with molecular and cellular dissections has led to a greater understanding of how p38 and JNK signaling affects many biological processes under normal and stress conditions. This review focuses on the studies revealing context specificity of different stress-activated MAPK components in C. elegans. PMID:26907690

Accumulation and sub-cellular partitioning of metals and As in the clam Venerupis corrugata: Different strategies towards different elements.

PubMed

Velez, Cátia; Figueira, Etelvina; Soares, Amadeu M V M; Freitas, Rosa

2016-08-01

The main goal of the present study was to assess accumulation, tolerance and sub-cellular partitioning of As, Hg, Cd and Pb in Venerupis corrugata. Results showed an increase of elements accumulation in V. corrugata with the increase of exposure. However, organisms presented higher capacity to accumulate Hg, Cd and Pb (BCF ≥ 12.8) than As (BCF ≤ 2.1) and higher accumulation rate for Cd and Pb than for Hg and As. With the increase of Hg exposure concentrations clams tended to increase the amount of metal bound to metal-sensitive fractions, which may explain the mortality recorded at the highest exposure concentration. Cd sub-cellular partitioning showed that with the increase of exposure concentrations V. corrugata increased the amount of metal in the cellular debris fraction, probably bound to the cellular membranes which explain the mortality recorded at the highest concentration. Results on As partitioning demonstrated that most of the metalloid was associated with fractions in the biologically detoxified metal compartment (BDM). Since high mortality was observed in clams exposed to As our results may indicate that this strategy was not enough to prevent clams from toxic effects and mortality occurred. When exposed to Pb most of the metal was in the BDM compartment, but in this case the metal was mostly in the metal-rich granules fraction which seemed to be efficient in preventing clams from toxicity, and no mortality was recorded. Our study further revealed that As and Hg were the most available elements to be biomagnified through the food chain. Copyright © 2016 Elsevier Ltd. All rights reserved.

Arc/Arg3.1 mRNA expression reveals a sub-cellular trace of prior sound exposure in adult primary auditory cortex

PubMed Central

Ivanova, Tamara; Matthews, Andrew; Gross, Christina; Mappus, Rudolph C.; Gollnick, Clare; Swanson, Andrew; Bassell, Gary J.; Liu, Robert C.

2011-01-01

Acquiring the behavioral significance of a sound has repeatedly been shown to correlate with long term changes in response properties of neurons in the adult primary auditory cortex. However, the molecular and cellular basis for such changes is still poorly understood. To address this, we have begun examining the auditory cortical expression of an activity-dependent effector immediate early gene (IEG) with documented roles in synaptic plasticity and memory consolidation in the hippocampus: Arc/Arg3.1. For initial characterization, we applied a repeated 10 minute (24 hour separation) sound exposure paradigm to determine the strength and consistency of sound-evoked Arc/Arg3.1 mRNA expression in the absence of explicit behavioral contingencies for the sound. We used 3D surface reconstruction methods in conjunction with fluorescent in-situ hybridization (FISH) to assess the layer-specific sub-cellular compartmental expression of Arc/Arg3.1 mRNA. We unexpectedly found that both the intranuclear and cytoplasmic patterns of expression depended on the prior history of sound stimulation. Specifically, the percentage of neurons with expression only in the cytoplasm increased for repeated versus singular sound exposure, while intranuclear expression decreased. In contrast, the total cellular expression did not differ, consistent with prior IEG studies of primary auditory cortex. Our results were specific for cortical layers 3–6, as there was virtually no sound driven Arc/Arg3.1 mRNA in layers 1–2 immediately after stimulation. Our results are consistent with the kinetics and/or detectability of cortical sub-cellular Arc/Arg3.1 mRNA expression being altered by the initial exposure to the sound, suggesting exposure-induced modifications in the cytoplasmic Arc/Arg3.1 mRNA pool. PMID:21334422

Phase coexistence and domain configuration in Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-0.34PbTiO{sub 3} single crystal revealed by synchrotron-based X-ray diffractive three-dimensional reciprocal space mapping and piezoresponse force microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Ruixue; Yang, Bin, E-mail: binyang@hit.edu.cn; Sun, Enwei

The crystalline phases and domain configuration in the morphotropic phase boundary composition Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-0.34PbTiO{sub 3} (PMN-0.34PT) single crystal have been investigated by synchrotron-based X-ray 3D Reciprocal Space Mapping (3D-RSM) and Piezoresponse Force Microscopy. The coexistence of tetragonal (T) and monoclinic M{sub C} phases in this PMN-0.34PT single crystal is confirmed. The affiliation of each diffraction spot in the 3D-RSM was identified with the assistance of qualitative simulation. Most importantly, the twinning structure between different domains in such a mixed phase PMN-PT crystal is firmly clarified, and the spatial distribution of different twin domains is demonstrated. In addition, themore » lattice parameters of T and M{sub C} phases in PMN-0.34PT single crystal as well as the tilting angles of crystal lattices caused by the interfacial lattice mismatch are determined.« less

Uses, misuses, new uses and fundamental limitations of magnetic resonance imaging in cognitive science

PubMed Central

2016-01-01

When blood oxygenation level-dependent (BOLD) contrast functional magnetic resonance imaging (fMRI) was discovered in the early 1990s, it provoked an explosion of interest in exploring human cognition, using brain mapping techniques based on MRI. Standards for data acquisition and analysis were rapidly put in place, in order to assist comparison of results across laboratories. Recently, MRI data acquisition capabilities have improved dramatically, inviting a rethink of strategies for relating functional brain activity at the systems level with its neuronal substrates and functional connections. This paper reviews the established capabilities of BOLD contrast fMRI, the perceived weaknesses of major methods of analysis, and current results that may provide insights into improved brain modelling. These results have inspired the use of in vivo myeloarchitecture for localizing brain activity, individual subject analysis without spatial smoothing and mapping of changes in cerebral blood volume instead of BOLD activation changes. The apparent fundamental limitations of all methods based on nuclear magnetic resonance are also discussed. This article is part of the themed issue ‘Interpreting BOLD: a dialogue between cognitive and cellular neuroscience’. PMID:27574303

Uses, misuses, new uses and fundamental limitations of magnetic resonance imaging in cognitive science.

PubMed

Turner, Robert

2016-10-05

When blood oxygenation level-dependent (BOLD) contrast functional magnetic resonance imaging (fMRI) was discovered in the early 1990s, it provoked an explosion of interest in exploring human cognition, using brain mapping techniques based on MRI. Standards for data acquisition and analysis were rapidly put in place, in order to assist comparison of results across laboratories. Recently, MRI data acquisition capabilities have improved dramatically, inviting a rethink of strategies for relating functional brain activity at the systems level with its neuronal substrates and functional connections. This paper reviews the established capabilities of BOLD contrast fMRI, the perceived weaknesses of major methods of analysis, and current results that may provide insights into improved brain modelling. These results have inspired the use of in vivo myeloarchitecture for localizing brain activity, individual subject analysis without spatial smoothing and mapping of changes in cerebral blood volume instead of BOLD activation changes. The apparent fundamental limitations of all methods based on nuclear magnetic resonance are also discussed.This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'. © 2016 The Authors.

Longitudinal atlas for normative human brain development and aging over the lifespan using quantitative susceptibility mapping.

PubMed

Zhang, Yuyao; Wei, Hongjiang; Cronin, Matthew J; He, Naying; Yan, Fuhua; Liu, Chunlei

2018-05-01

Longitudinal brain atlases play an important role in the study of human brain development and cognition. Existing atlases are mainly based on anatomical features derived from T1-and T2-weighted MRI. A 4D developmental quantitative susceptibility mapping (QSM) atlas may facilitate the estimation of age-related iron changes in deep gray matter nuclei and myelin changes in white matter. To this end, group-wise co-registered QSM templates were generated over various age intervals from age 1-83 years old. Registration was achieved by combining both T1-weighted and QSM images. Based on the proposed template, we created an accurate deep gray matter nuclei parcellation map (DGM map). Notably, we segmented thalamus into 5 sub-regions, i.e. the anterior nuclei, the median nuclei, the lateral nuclei, the pulvinar and the internal medullary lamina. Furthermore, we built a "whole brain QSM parcellation map" by combining existing cortical parcellation and white-matter atlases with the proposed DGM map. Based on the proposed QSM atlas, the segmentation accuracy of iron-rich nuclei using QSM is significantly improved, especially for children and adolescent subjects. The age-related progression of magnetic susceptibility in each of the deep gray matter nuclei, the hippocampus, and the amygdala was estimated. Our automated atlas-based analysis provided a systematic confirmation of previous findings on susceptibility progression with age resulting from manual ROI drawings in deep gray matter nuclei. The susceptibility development in the hippocampus and the amygdala follow an iron accumulation model; while in the thalamus sub-regions, the susceptibility development exhibits a variety of trends. It is envisioned that the newly developed 4D QSM atlas will serve as a template for studying brain iron deposition and myelination/demyelination in both normal aging and various brain diseases. Copyright © 2018 Elsevier Inc. All rights reserved.

Optimizing spectral wave estimates with adjoint-based sensitivity maps

NASA Astrophysics Data System (ADS)

Orzech, Mark; Veeramony, Jay; Flampouris, Stylianos

2014-04-01

A discrete numerical adjoint has recently been developed for the stochastic wave model SWAN. In the present study, this adjoint code is used to construct spectral sensitivity maps for two nearshore domains. The maps display the correlations of spectral energy levels throughout the domain with the observed energy levels at a selected location or region of interest (LOI/ROI), providing a full spectrum of values at all locations in the domain. We investigate the effectiveness of sensitivity maps based on significant wave height ( H s ) in determining alternate offshore instrument deployment sites when a chosen nearshore location or region is inaccessible. Wave and bathymetry datasets are employed from one shallower, small-scale domain (Duck, NC) and one deeper, larger-scale domain (San Diego, CA). The effects of seasonal changes in wave climate, errors in bathymetry, and multiple assimilation points on sensitivity map shapes and model performance are investigated. Model accuracy is evaluated by comparing spectral statistics as well as with an RMS skill score, which estimates a mean model-data error across all spectral bins. Results indicate that data assimilation from identified high-sensitivity alternate locations consistently improves model performance at nearshore LOIs, while assimilation from low-sensitivity locations results in lesser or no improvement. Use of sub-sampled or alongshore-averaged bathymetry has a domain-specific effect on model performance when assimilating from a high-sensitivity alternate location. When multiple alternate assimilation locations are used from areas of lower sensitivity, model performance may be worse than with a single, high-sensitivity assimilation point.

Accuracies of the synthesized monochromatic CT numbers and effective atomic numbers obtained with a rapid kVp switching dual energy CT scanner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goodsitt, Mitchell M.; Christodoulou, Emmanuel G.; Larson, Sandra C.

2011-04-15

Purpose: This study was performed to investigate the accuracies of the synthesized monochromatic images and effective atomic number maps obtained with the new GE Discovery CT750 HD CT scanner. Methods: A Gammex-RMI model 467 tissue characterization phantom and the CT number linearity section of a Phantom Laboratory Catphan 600 phantom were scanned using the dual energy (DE) feature on the GE CT750 HD scanner. Synthesized monochromatic images at various energies between 40 and 120 keV and effective atomic number (Z{sub eff}) maps were generated. Regions of interest were placed within these images/maps to measure the average monochromatic CT numbers andmore » average Z{sub eff} of the materials within these phantoms. The true Z{sub eff} values were either supplied by the phantom manufacturer or computed using Mayneord's equation. The linear attenuation coefficients for the true CT numbers were computed using the NIST XCOM program with the input of manufacturer supplied elemental compositions and densities. The effects of small variations in the assumed true densities of the materials were also investigated. Finally, the effect of body size on the accuracies of the synthesized monochromatic CT numbers was investigated using a custom lumbar section phantom with and without an external fat-mimicking ring. Results: Other than the Z{sub eff} of the simulated lung inserts in the tissue characterization phantom, which could not be measured by DECT, the Z{sub eff} values of all of the other materials in the tissue characterization and Catphan phantoms were accurate to 15%. The accuracies of the synthesized monochromatic CT numbers of the materials in both phantoms varied with energy and material. For the 40-120 keV range, RMS errors between the measured and true CT numbers in the Catphan are 8-25 HU when the true CT numbers were computed using the nominal plastic densities. These RMS errors improve to 3-12 HU for assumed true densities within the nominal density {+-}0.02 g/cc range. The RMS errors between the measured and true CT numbers of the tissue mimicking materials in the tissue characterization phantom over the 40-120 keV range varied from about 6 HU-248 HU and did not improve as dramatically with small changes in assumed true density. Conclusions: Initial tests indicate that the Z{sub eff} values computed with DECT on this scanner are reasonably accurate; however, the synthesized monochromatic CT numbers can be very inaccurate, especially for dense tissue mimicking materials at low energies. Furthermore, the synthesized monochromatic CT numbers of materials still depend on the amount of the surrounding tissues especially at low keV, demonstrating that the numbers are not truly monochromatic. Further research is needed to develop DE methods that produce more accurate synthesized monochromatic CT numbers.« less

Recalibration of the M {sub BH}– σ {sub ⋆} Relation for AGN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Batiste, Merida; Bentz, Misty C.; Raimundo, Sandra I.

2017-03-20

We present a recalibration of the M {sub BH}– σ {sub ⋆} relation, based on a sample of 16 reverberation-mapped galaxies with newly determined bulge stellar velocity dispersions ( σ {sub ⋆}) from integral-field spectroscopy (IFS), and a sample of 32 quiescent galaxies with publicly available IFS. For both samples, σ {sub ⋆} is determined via two different methods that are popular in the literature, and we provide fits for each sample based on both sets of σ {sub ⋆}. We find the fit to the active galactic nucleus sample is shallower than the fit to the quiescent galaxy sample,more » and that the slopes for each sample are in agreement with previous investigations. However, the intercepts to the quiescent galaxy relations are notably higher than those found in previous studies, due to the systematically lower σ {sub ⋆} measurements that we obtain from IFS. We find that this may be driven, in part, by poorly constrained measurements of bulge effective radius ( r{sub e}) for the quiescent galaxy sample, which may bias the σ {sub ⋆} measurements low. We use these quiescent galaxy parameterizations, as well as one from the literature, to recalculate the virial scaling factor f . We assess the potential biases in each measurement, and suggest f = 4.82 ± 1.67 as the best currently available estimate. However, we caution that the details of how σ {sub ⋆} is measured can significantly affect f , and there is still much room for improvement.« less

Multi-Compartment T2 Relaxometry Using a Spatially Constrained Multi-Gaussian Model

PubMed Central

Raj, Ashish; Pandya, Sneha; Shen, Xiaobo; LoCastro, Eve; Nguyen, Thanh D.; Gauthier, Susan A.

2014-01-01

The brain’s myelin content can be mapped by T2-relaxometry, which resolves multiple differentially relaxing T2 pools from multi-echo MRI. Unfortunately, the conventional fitting procedure is a hard and numerically ill-posed problem. Consequently, the T2 distributions and myelin maps become very sensitive to noise and are frequently difficult to interpret diagnostically. Although regularization can improve stability, it is generally not adequate, particularly at relatively low signal to noise ratio (SNR) of around 100–200. The purpose of this study was to obtain a fitting algorithm which is able to overcome these difficulties and generate usable myelin maps from noisy acquisitions in a realistic scan time. To this end, we restrict the T2 distribution to only 3 distinct resolvable tissue compartments, modeled as Gaussians: myelin water, intra/extra-cellular water and a slow relaxing cerebrospinal fluid compartment. We also impose spatial smoothness expectation that volume fractions and T2 relaxation times of tissue compartments change smoothly within coherent brain regions. The method greatly improves robustness to noise, reduces spatial variations, improves definition of white matter fibers, and enhances detection of demyelinating lesions. Due to efficient design, the additional spatial aspect does not cause an increase in processing time. The proposed method was applied to fast spiral acquisitions on which conventional fitting gives uninterpretable results. While these fast acquisitions suffer from noise and inhomogeneity artifacts, our preliminary results indicate the potential of spatially constrained 3-pool T2 relaxometry. PMID:24896833

The goya mouse mutant reveals distinct newly identified roles for MAP3K1 in the development and survival of cochlear sensory hair cells.

PubMed

Parker, Andrew; Cross, Sally H; Jackson, Ian J; Hardisty-Hughes, Rachel; Morse, Susan; Nicholson, George; Coghill, Emma; Bowl, Michael R; Brown, Steve D M

2015-12-01

Mitogen-activated protein kinase, MAP3K1, plays an important role in a number of cellular processes, including epithelial migration during eye organogenesis. In addition, studies in keratinocytes indicate that MAP3K1 signalling through JNK is important for actin stress fibre formation and cell migration. However, MAP3K1 can also act independently of JNK in the regulation of cell proliferation and apoptosis. We have identified a mouse mutant, goya, which exhibits the eyes-open-at-birth and microphthalmia phenotypes. In addition, these mice also have hearing loss. The goya mice carry a splice site mutation in the Map3k1 gene. We show that goya and kinase-deficient Map3k1 homozygotes initially develop supernumerary cochlear outer hair cells (OHCs) that subsequently degenerate, and a progressive profound hearing loss is observed by 9 weeks of age. Heterozygote mice also develop supernumerary OHCs, but no cellular degeneration or hearing loss is observed. MAP3K1 is expressed in a number of inner-ear cell types, including outer and inner hair cells, stria vascularis and spiral ganglion. Investigation of targets downstream of MAP3K1 identified an increase in p38 phosphorylation (Thr180/Tyr182) in multiple cochlear tissues. We also show that the extra OHCs do not arise from aberrant control of proliferation via p27KIP1. The identification of the goya mutant reveals a signalling molecule involved with hair-cell development and survival. Mammalian hair cells do not have the ability to regenerate after damage, which can lead to irreversible sensorineural hearing loss. Given the observed goya phenotype, and the many diverse cellular processes that MAP3K1 is known to act upon, further investigation of this model might help to elaborate upon the mechanisms underlying sensory hair cell specification, and pathways important for their survival. In addition, MAP3K1 is revealed as a new candidate gene for human sensorineural hearing loss. © 2015. Published by The Company of Biologists Ltd.

Precise GPS orbits for geodesy

NASA Technical Reports Server (NTRS)

Colombo, Oscar L.

1994-01-01

The Global Positioning System (GPS) has become, in recent years, the main space-based system for surveying and navigation in many military, commercial, cadastral, mapping, and scientific applications. Better receivers, interferometric techniques (DGPS), and advances in post-processing methods have made possible to position fixed or moving receivers with sub-decimeter accuracies in a global reference frame. Improved methods for obtaining the orbits of the GPS satellites have played a major role in these achievements; this paper gives a personal view of the main developments in GPS orbit determination.

High resolution mapping of the binding site on human IgG1 for Fc gamma RI, Fc gamma RII, Fc gamma RIII, and FcRn and design of IgG1 variants with improved binding to the Fc gamma R.

PubMed

Shields, R L; Namenuk, A K; Hong, K; Meng, Y G; Rae, J; Briggs, J; Xie, D; Lai, J; Stadlen, A; Li, B; Fox, J A; Presta, L G

2001-03-02

Immunoglobulin G (IgG) Fc receptors play a critical role in linking IgG antibody-mediated immune responses with cellular effector functions. A high resolution map of the binding site on human IgG1 for human Fc gamma RI, Fc gamma RIIA, Fc gamma RIIB, Fc gamma RIIIA, and FcRn receptors has been determined. A common set of IgG1 residues is involved in binding to all Fc gamma R; Fc gamma RII and Fc gamma RIII also utilize residues outside this common set. In addition to residues which, when altered, abrogated binding to one or more of the receptors, several residues were found that improved binding only to specific receptors or simultaneously improved binding to one type of receptor and reduced binding to another type. Select IgG1 variants with improved binding to Fc gamma RIIIA exhibited up to 100% enhancement in antibody-dependent cell cytotoxicity using human effector cells; these variants included changes at residues not found at the binding interface in the IgG/Fc gamma RIIIA co-crystal structure (Sondermann, P., Huber, R., Oosthuizen, V., and Jacob, U. (2000) Nature 406, 267-273). These engineered antibodies may have important implications for improving antibody therapeutic efficacy.

Hermite-Hadamard type inequality for φ{sub h}-convex stochastic processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarıkaya, Mehmet Zeki, E-mail: sarikayamz@gmail.com; Kiriş, Mehmet Eyüp, E-mail: kiris@aku.edu.tr; Çelik, Nuri, E-mail: ncelik@bartin.edu.tr

2016-04-18

The main aim of the present paper is to introduce φ{sub h}-convex stochastic processes and we investigate main properties of these mappings. Moreover, we prove the Hadamard-type inequalities for φ{sub h}-convex stochastic processes. We also give some new general inequalities for φ{sub h}-convex stochastic processes.

Extending the Operational Envelope of a Turbofan Engine Simulation into the Sub-Idle Region

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Hamley, Andrew J.; Guo, Ten-Huei; Litt, Jonathan S.

2016-01-01

In many non-linear gas turbine simulations, operation in the sub-idle region can lead to model instability. This paper lays out a method for extending the operational envelope of a map based gas turbine simulation to include the sub-idle region. This method develops a multi-simulation solution where the baseline component maps are extrapolated below the idle level and an alternate model is developed to serve as a safety net when the baseline model becomes unstable or unreliable. Sub-idle model development takes place in two distinct operational areas, windmilling/shutdown and purge/cranking/ startup. These models are based on derived steady state operating points with transient values extrapolated between initial (known) and final (assumed) states. Model transitioning logic is developed to predict baseline model sub-idle instability, and transition smoothly and stably to the backup sub-idle model. Results from the simulation show a realistic approximation of sub-idle behavior as compared to generic sub-idle engine performance that allows the engine to operate continuously and stably from shutdown to full power.

Extending the Operational Envelope of a Turbofan Engine Simulation into the Sub-Idle Region

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes Walter; Hamley, Andrew J.; Guo, Ten-Huei; Litt, Jonathan S.

2016-01-01

In many non-linear gas turbine simulations, operation in the sub-idle region can lead to model instability. This paper lays out a method for extending the operational envelope of a map based gas turbine simulation to include the sub-idle region. This method develops a multi-simulation solution where the baseline component maps are extrapolated below the idle level and an alternate model is developed to serve as a safety net when the baseline model becomes unstable or unreliable. Sub-idle model development takes place in two distinct operational areas, windmilling/shutdown and purge/cranking/startup. These models are based on derived steady state operating points with transient values extrapolated between initial (known) and final (assumed) states. Model transitioning logic is developed to predict baseline model sub-idle instability, and transition smoothly and stably to the backup sub-idle model. Results from the simulation show a realistic approximation of sub-idle behavior as compared to generic sub-idle engine performance that allows the engine to operate continuously and stably from shutdown to full power.

Mapping whole-brain activity with cellular resolution by light-sheet microscopy and high-throughput image analysis (Conference Presentation)

NASA Astrophysics Data System (ADS)

Silvestri, Ludovico; Rudinskiy, Nikita; Paciscopi, Marco; Müllenbroich, Marie Caroline; Costantini, Irene; Sacconi, Leonardo; Frasconi, Paolo; Hyman, Bradley T.; Pavone, Francesco S.

2016-03-01

Mapping neuronal activity patterns across the whole brain with cellular resolution is a challenging task for state-of-the-art imaging methods. Indeed, despite a number of technological efforts, quantitative cellular-resolution activation maps of the whole brain have not yet been obtained. Many techniques are limited by coarse resolution or by a narrow field of view. High-throughput imaging methods, such as light sheet microscopy, can be used to image large specimens with high resolution and in reasonable times. However, the bottleneck is then moved from image acquisition to image analysis, since many TeraBytes of data have to be processed to extract meaningful information. Here, we present a full experimental pipeline to quantify neuronal activity in the entire mouse brain with cellular resolution, based on a combination of genetics, optics and computer science. We used a transgenic mouse strain (Arc-dVenus mouse) in which neurons which have been active in the last hours before brain fixation are fluorescently labelled. Samples were cleared with CLARITY and imaged with a custom-made confocal light sheet microscope. To perform an automatic localization of fluorescent cells on the large images produced, we used a novel computational approach called semantic deconvolution. The combined approach presented here allows quantifying the amount of Arc-expressing neurons throughout the whole mouse brain. When applied to cohorts of mice subject to different stimuli and/or environmental conditions, this method helps finding correlations in activity between different neuronal populations, opening the possibility to infer a sort of brain-wide 'functional connectivity' with cellular resolution.

Digitising the Past: The Beginning of a New Future at the Royal Tropical Institute of The Netherlands

ERIC Educational Resources Information Center

Levi, Peter

2010-01-01

Purpose: The purpose of this paper is to describe a project to digitise maps at the Royal Tropical Institute, or Koninklijk Instituut voor de Tropen (KIT), of The Netherlands. KIT has an extensive collection of maps and nautical charts of (sub-) tropical regions, including general maps and topographical map series, city maps, thematic maps and…

PDADMAC flocculation of Chinese hamster ovary cells: enabling a centrifuge-less harvest process for monoclonal antibodies.

PubMed

McNerney, Thomas; Thomas, Anne; Senczuk, Anna; Petty, Krista; Zhao, Xiaoyang; Piper, Rob; Carvalho, Juliane; Hammond, Matthew; Sawant, Satin; Bussiere, Jeanine

2015-01-01

High titer (>10 g/L) monoclonal antibody (mAb) cell culture processes are typically achieved by maintaining high viable cell densities over longer culture durations. A corresponding increase in the solids and sub-micron cellular debris particle levels are also observed. This higher burden of solids (≥15%) and sub-micron particles typically exceeds the capabilities of a continuous centrifuge to effectively remove the solids without a substantial loss of product and/or the capacity of the harvest filtration train (depth filter followed by membrane filter) used to clarify the centrate. We discuss here the use of a novel and simple two-polymer flocculation method used to harvest mAb from high cell mass cell culture processes. The addition of the polycationic polymer, poly diallyldimethylammonium chloride (PDADMAC) to the cell culture broth flocculates negatively-charged cells and cellular debris via an ionic interaction mechanism. Incorporation of a non-ionic polymer such as polyethylene glycol (PEG) into the PDADMAC flocculation results in larger flocculated particles with faster settling rate compared to PDADMAC-only flocculation. PDADMAC also flocculates the negatively-charged sub-micron particles to produce a feed stream with a significantly higher harvest filter train throughput compared to a typical centrifuged harvest feed stream. Cell culture process variability such as lactate production, cellular debris and cellular densities were investigated to determine the effect on flocculation. Since PDADMAC is cytotoxic, purification process clearance and toxicity assessment were performed.

PDADMAC flocculation of Chinese hamster ovary cells: Enabling a centrifuge-less harvest process for monoclonal antibodies

PubMed Central

McNerney, Thomas; Thomas, Anne; Senczuk, Anna; Petty, Krista; Zhao, Xiaoyang; Piper, Rob; Carvalho, Juliane; Hammond, Matthew; Sawant, Satin; Bussiere, Jeanine

2015-01-01

High titer (>10 g/L) monoclonal antibody (mAb) cell culture processes are typically achieved by maintaining high viable cell densities over longer culture durations. A corresponding increase in the solids and sub-micron cellular debris particle levels are also observed. This higher burden of solids (≥15%) and sub-micron particles typically exceeds the capabilities of a continuous centrifuge to effectively remove the solids without a substantial loss of product and/or the capacity of the harvest filtration train (depth filter followed by membrane filter) used to clarify the centrate. We discuss here the use of a novel and simple two-polymer flocculation method used to harvest mAb from high cell mass cell culture processes. The addition of the polycationic polymer, poly diallyldimethylammonium chloride (PDADMAC) to the cell culture broth flocculates negatively-charged cells and cellular debris via an ionic interaction mechanism. Incorporation of a non-ionic polymer such as polyethylene glycol (PEG) into the PDADMAC flocculation results in larger flocculated particles with faster settling rate compared to PDADMAC-only flocculation. PDADMAC also flocculates the negatively-charged sub-micron particles to produce a feed stream with a significantly higher harvest filter train throughput compared to a typical centrifuged harvest feed stream. Cell culture process variability such as lactate production, cellular debris and cellular densities were investigated to determine the effect on flocculation. Since PDADMAC is cytotoxic, purification process clearance and toxicity assessment were performed. PMID:25706650

Scanning micro-Hall probe mapping of magnetic flux distributions and current densities in YBa2Cu3O7 thin films

NASA Technical Reports Server (NTRS)

Xing, W.; Heinrich, B.; Zhou, HU; Fife, A. A.; Cragg, A. R.; Grant, P. D.

1995-01-01

Mapping of the magnetic flux density B(sub z) (perpendicular to the film plane) for a YBa2Cu3O7 thin-film sample was carried out using a scanning micro-Hall probe. The sheet magnetization and sheet current densities were calculated from the B(sub z) distributions. From the known sheet magnetization, the tangential (B(sub x,y)) and normal components of the flux density B were calculated in the vicinity of the film. It was found that the sheet current density was mostly determined by 2B(sub x,y)/d, where d is the film thickness. The evolution of flux penetration as a function of applied field will be shown.

Dynamic maps of UV damage formation and repair for the human genome

PubMed Central

Hu, Jinchuan; Adebali, Ogun; Adar, Sheera; Sancar, Aziz

2017-01-01

Formation and repair of UV-induced DNA damage in human cells are affected by cellular context. To study factors influencing damage formation and repair genome-wide, we developed a highly sensitive single-nucleotide resolution damage mapping method [high-sensitivity damage sequencing (HS–Damage-seq)]. Damage maps of both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] from UV-irradiated cellular and naked DNA revealed that the effect of transcription factor binding on bulky adducts formation varies, depending on the specific transcription factor, damage type, and strand. We also generated time-resolved UV damage maps of both CPDs and (6-4)PPs by HS–Damage-seq and compared them to the complementary repair maps of the human genome obtained by excision repair sequencing to gain insight into factors that affect UV-induced DNA damage and repair and ultimately UV carcinogenesis. The combination of the two methods revealed that, whereas UV-induced damage is virtually uniform throughout the genome, repair is affected by chromatin states, transcription, and transcription factor binding, in a manner that depends on the type of DNA damage. PMID:28607063

Dynamic maps of UV damage formation and repair for the human genome.

PubMed

Hu, Jinchuan; Adebali, Ogun; Adar, Sheera; Sancar, Aziz

2017-06-27

Formation and repair of UV-induced DNA damage in human cells are affected by cellular context. To study factors influencing damage formation and repair genome-wide, we developed a highly sensitive single-nucleotide resolution damage mapping method [high-sensitivity damage sequencing (HS-Damage-seq)]. Damage maps of both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] from UV-irradiated cellular and naked DNA revealed that the effect of transcription factor binding on bulky adducts formation varies, depending on the specific transcription factor, damage type, and strand. We also generated time-resolved UV damage maps of both CPDs and (6-4)PPs by HS-Damage-seq and compared them to the complementary repair maps of the human genome obtained by excision repair sequencing to gain insight into factors that affect UV-induced DNA damage and repair and ultimately UV carcinogenesis. The combination of the two methods revealed that, whereas UV-induced damage is virtually uniform throughout the genome, repair is affected by chromatin states, transcription, and transcription factor binding, in a manner that depends on the type of DNA damage.

The Development of 3d Sub-Surface Mapping Scheme and its Application to Martian Lobate Debris Aprons

NASA Astrophysics Data System (ADS)

Baik, H.; Kim, J.

2017-07-01

The Shallow Subsurface Radar (SHARAD), a sounding radar equipped on the Mars Reconnaissance Orbiter (MRO), has produced highly valuable information about the Martian subsurface. In particular, the complicated substructures of Mars such as polar deposit, pedestal crater and the other geomorphic features involving possible subsurface ice body has been successfully investigated by SHARAD. In this study, we established a 3D subsurface mapping strategy employing the multiple SHARAD profiles. A number of interpretation components of SHARAD signals were integrated into a subsurface mapping scheme using radargram information and topographic data, then applied over a few mid latitude Lobate Debris Aprons (LDAs). From the identified subsurface layers of LDA, and the GIS data base incorporating the other interpretation outcomes, we are expecting to trace the origin of LDAs. Also, the subsurface mapping scheme developed in this study will be further applied to other interesting Martian geological features such as inter crater structures, aeolian deposits and fluvial sediments. To achieve higher precision sub-surface mapping, the clutter simulation employing the high resolution topographic data and the upgraded clustering algorithms assuming multiple sub-surface layers will be also developed.

Physical biology of human brain development.

PubMed

Budday, Silvia; Steinmann, Paul; Kuhl, Ellen

2015-01-01

Neurodevelopment is a complex, dynamic process that involves a precisely orchestrated sequence of genetic, environmental, biochemical, and physical events. Developmental biology and genetics have shaped our understanding of the molecular and cellular mechanisms during neurodevelopment. Recent studies suggest that physical forces play a central role in translating these cellular mechanisms into the complex surface morphology of the human brain. However, the precise impact of neuronal differentiation, migration, and connection on the physical forces during cortical folding remains unknown. Here we review the cellular mechanisms of neurodevelopment with a view toward surface morphogenesis, pattern selection, and evolution of shape. We revisit cortical folding as the instability problem of constrained differential growth in a multi-layered system. To identify the contributing factors of differential growth, we map out the timeline of neurodevelopment in humans and highlight the cellular events associated with extreme radial and tangential expansion. We demonstrate how computational modeling of differential growth can bridge the scales-from phenomena on the cellular level toward form and function on the organ level-to make quantitative, personalized predictions. Physics-based models can quantify cortical stresses, identify critical folding conditions, rationalize pattern selection, and predict gyral wavelengths and gyrification indices. We illustrate that physical forces can explain cortical malformations as emergent properties of developmental disorders. Combining biology and physics holds promise to advance our understanding of human brain development and enable early diagnostics of cortical malformations with the ultimate goal to improve treatment of neurodevelopmental disorders including epilepsy, autism spectrum disorders, and schizophrenia.

Anaerobic sludge digestion with a biocatalytic additive

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, S.; Henry, M.P.; Fedde, P.A.

1982-01-01

The objective of this research was to evaluate the effects of a lactobacillus additive an anaerobic sludge digestion under normal, variable, and overload operating conditions. The additive was a whey fermentation product of an acid-tolerant strain of Lactobacillus acidophilus fortified with CaCO/sub 3/, (NH/sub 4/)/sub 2/HPO/sub 4/, ferrous lactate, and lactic acid. The lactobacillus additive is multifunctional in nature and provides growth factors, metabolic intermediates, and enzymes needed for substrate degradation and cellular synthesis. The experimental work consisted of several pairs of parallel mesophilic (35/sup 0/C) digestion runs (control and test) conducted in five experimental phases. Baseline runs without themore » additive showed that the two experimental digesters had the same methane content, gas production rate (GPR), and ethane yield. The effect of the additive was to increase methane yield and GPR by about 5% (which was statistically significant) during digester operation at a loading rate (LR) of 3.2 kg VS/m/sup 3/-day and a hydraulic retention time (HRT) of 14 days. Data collected from the various experimental phases showed that the biochemical additive increased methane yield, gas production rate, and VS reduction, and decreased volatile acids accumulation. In addition, it enhanced digester buffer capacity and improved the fertilizer value and dewatering characteristics of the digested residue.« less

Constraints on μ-distortion fluctuations and primordial non-Gaussianity from Planck data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khatri, Rishi; Sunyaev, Rashid, E-mail: khatri@mpa-garching.mpg.de, E-mail: sunyaev@mpa-garching.mpg.de

2015-09-01

We use the Planck HFI channel maps to make an all sky map of μ-distortion fluctuations. Our μ-type distortion map is dominated by the y-type distortion contamination from the hot gas in the low redshift Universe and we can thus only place upper limits on the μ-type distortion fluctuations. For the amplitude of μ-type distortions on 10' scales we get the limit on root mean square (rms) value μ{sub rms}{sup 10'}< 6.4× 10{sup −6}, a limit 14 times stronger than the COBE-FIRAS (95% confidence) limit on the mean of ( μ )<90× 10{sup −6}. Using our maps we also place strong upper limits on themore » auto angular power spectrum of μ, C{sub ℓ}{sup μμ} and the cross angular power spectrum of μ with the CMB temperature anisotropies, C{sub ℓ}{sup μ T}. The strongest observational limits are on the largest scales, ℓ(ℓ+1)/(2π)C{sub ℓ}{sup μμ}|{sub ℓ=2−26}<(2.3± 1.0)× 10{sup −12} and ℓ(ℓ+1)/(2π)C{sub ℓ}{sup μ T}|{sub ℓ=2−26}<(2.6± 2.6)× 10{sup −12} K. Our observational limits can be used to constrain new physics which can create spatially varying energy release in the early Universe between redshifts 5× 10{sup 4∼<} z∼< 2× 10{sup 6}. We specifically apply our observational results to constrain the primordial non-Gaussianity of the local type, when the source of μ-distortion is Silk damping, for very squeezed configurations with the wavenumber for the short wavelength mode 46 ∼< k{sub S} ∼< 10{sup 4} Mpc{sup −1} and for the long wavelength mode k{sub L}≈ 10{sup −3} Mpc{sup −1}. Our limits on the primordial non-Gaussianity parameters are f{sub NL}<10{sup 5}, τ{sub NL}<1.4× 10{sup 11} for k{sub S}/k{sub L}≈ 5× 10{sup 4}− 10{sup 7}. We also give a new derivation of the evolution of the μ-distortion fluctuations through the y-distortion era and the recombination epoch until today resulting in very simple expressions for the cross and auto power spectra in the squeezed limit. We also introduce mixing of Bose-Einstein spectra due to Silk damping and y{sup BE}-type distortions. The μ-type distortion map and masks are now publicly available.« less

Growth control of the oxidation state in vanadium oxide thin films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Shinbuhm; Meyer, Tricia L.; Lee, Ho Nyung, E-mail: hnlee@ornl.gov

2014-12-01

Precise control of the chemical valence or oxidation state of vanadium in vanadium oxide thin films is highly desirable for not only fundamental research but also technological applications that utilize the subtle change in the physical properties originating from the metal-insulator transition (MIT) near room temperature. However, due to the multivalent nature of vanadium and the lack of a good understanding on growth control of the oxidation state, stabilization of phase pure vanadium oxides with a single oxidation state is extremely challenging. Here, we systematically varied the growth conditions to clearly map out the growth window for preparing phase puremore » epitaxial vanadium oxides by pulsed laser deposition for providing a guideline to grow high quality thin films with well-defined oxidation states of V{sub 2}{sup +3}O{sub 3}, V{sup +4}O{sub 2}, and V{sub 2}{sup +5}O{sub 5}. A well pronounced MIT was only observed in VO{sub 2} films grown in a very narrow range of oxygen partial pressure P(O{sub 2}). The films grown either in lower (<10 mTorr) or higher P(O{sub 2}) (>25 mTorr) result in V{sub 2}O{sub 3} and V{sub 2}O{sub 5} phases, respectively, thereby suppressing the MIT for both cases. We have also found that the resistivity ratio before and after the MIT of VO{sub 2} thin films can be further enhanced by one order of magnitude when the films are further oxidized by post-annealing at a well-controlled oxidizing ambient. This result indicates that stabilizing vanadium into a single valence state has to compromise with insufficient oxidation of an as grown thin film and, thereby, a subsequent oxidation is required for an improved MIT behavior.« less

Altered Cell Mechanics from the Inside: Dispersed Single Wall Carbon Nanotubes Integrate with and Restructure Actin

PubMed Central

Holt, Brian D.; Shams, Hengameh; Horst, Travis A.; Basu, Saurav; Rape, Andrew D.; Wang, Yu-Li; Rohde, Gustavo K.; Mofrad, Mohammad R. K.; Islam, Mohammad F.; Dahl, Kris Noel

2012-01-01

With a range of desirable mechanical and optical properties, single wall carbon nanotubes (SWCNTs) are a promising material for nanobiotechnologies. SWCNTs also have potential as biomaterials for modulation of cellular structures. Previously, we showed that highly purified, dispersed SWCNTs grossly alter F-actin inside cells. F-actin plays critical roles in the maintenance of cell structure, force transduction, transport and cytokinesis. Thus, quantification of SWCNT-actin interactions ranging from molecular, sub-cellular and cellular levels with both structure and function is critical for developing SWCNT-based biotechnologies. Further, this interaction can be exploited, using SWCNTs as a unique actin-altering material. Here, we utilized molecular dynamics simulations to explore the interactions of SWCNTs with actin filaments. Fluorescence lifetime imaging microscopy confirmed that SWCNTs were located within ~5 nm of F-actin in cells but did not interact with G-actin. SWCNTs did not alter myosin II sub-cellular localization, and SWCNT treatment in cells led to significantly shorter actin filaments. Functionally, cells with internalized SWCNTs had greatly reduced cell traction force. Combined, these results demonstrate direct, specific SWCNT alteration of F-actin structures which can be exploited for SWCNT-based biotechnologies and utilized as a new method to probe fundamental actin-related cellular processes and biophysics. PMID:24955540

Quantitative Assessment of Heterogeneity in Tumor Metabolism Using FDG-PET

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vriens, Dennis, E-mail: d.vriens@nucmed.umcn.nl; Disselhorst, Jonathan A.; Oyen, Wim J.G.

2012-04-01

Purpose: [{sup 18}F]-fluorodeoxyglucose-positron emission tomography (FDG-PET) images are usually quantitatively analyzed in 'whole-tumor' volumes of interest. Also parameters determined with dynamic PET acquisitions, such as the Patlak glucose metabolic rate (MR{sub glc}) and pharmacokinetic rate constants of two-tissue compartment modeling, are most often derived per lesion. We propose segmentation of tumors to determine tumor heterogeneity, potentially useful for dose-painting in radiotherapy and elucidating mechanisms of FDG uptake. Methods and Materials: In 41 patients with 104 lesions, dynamic FDG-PET was performed. On MR{sub glc} images, tumors were segmented in quartiles of background subtracted maximum MR{sub glc} (0%-25%, 25%-50%, 50%-75%, and 75%-100%).more » Pharmacokinetic analysis was performed using an irreversible two-tissue compartment model in the three segments with highest MR{sub glc} to determine the rate constants of FDG metabolism. Results: From the highest to the lowest quartile, significant decreases of uptake (K{sub 1}), washout (k{sub 2}), and phosphorylation (k{sub 3}) rate constants were seen with significant increases in tissue blood volume fraction (V{sub b}). Conclusions: Tumor regions with highest MR{sub glc} are characterized by high cellular uptake and phosphorylation rate constants with relatively low blood volume fractions. In regions with less metabolic activity, the blood volume fraction increases and cellular uptake, washout, and phosphorylation rate constants decrease. These results support the hypothesis that regional tumor glucose phosphorylation rate is not dependent on the transport of nutrients (i.e., FDG) to the tumor.« less

High-Resolution AES Mapping and TEM Study of Cu(In,Ga)Se2 Thin Film Growth: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkins, C. L.; Yan, Y.; Jones, K.

2001-10-01

Presented at 2001 NCPV Program Review Meeting: TEM and high-resolution AES mapping data on CIGS samples. The chalcopyrite Cu(In,Ga)Se{sub 2} (CIGS) shows promise as an absorber layer in thin polycrystalline solar cells, however, details of the PVD growth of this complicated material remain in a developing stage. Previous workers have postulated the existence of a thin film of liquid Cu{sub x}Se on the growing CIGS film, and that this layer acts as a reservoir of copper as well as a layer in which rapid mass transport is possible. In this paper we present transmission electron microscopy (TEM) and high resolutionmore » Auger electron spectroscopy (AES) mapping data taken on samples that had their growth interrupted at a stage when Cu{sub x}Se was expected to be present. The AES maps show CIGS grains which are highly enriched in copper relative to the rest of the CIGS film, and that these same areas contain almost no indium, results consistent with the presence of CuxSe. Small-area diffraction analysis and energy dispersive spectroscopy (EDS) performed on these same samples independently confirm the presence of Cu{sub x}Se at the surface of growing CIGS films.« less

Assessment of groundwater vulnerability using DRASTIC Model and GIS : A case study of two sub-districts in Banda Aceh city, Indonesia

NASA Astrophysics Data System (ADS)

Machdar, I.; Zulfikar, T.; Rinaldi, W.; Alfiansyah, Y.

2018-03-01

This present study assessed the groundwater vulnerability to protect aquifer in part of Banda Aceh City (the sub-district of Banda Raya and Lueng Bata), Indonesia. The study provides an additional tool for local planner and manager as for managing and protecting groundwater resources. The study area covers 1,164 ha and total population was estimated around 50,000 inhabitants. DRASTIC model in a GIS (Geographic Information System) environment was used in this study to generate vulnerability maps. The maps were created by applied seven criteria as standard in DRASTIC approach, i.e. depth to groundwater, recharge, aquifer type, soil properties, topography, impact of the vadose zone, and hydraulic conductivity. The vulnerability maps provides five categories of vulnerability, i.e. less, low, medium, high, and very high. It was found that the village areas, labelled with the high groundwater pollution potential, are mainly in the area of Lamlagang and the part of Geuce Kaye Jatoe and Geuce Komplek (Banda Raya sub-district) and the part of Batoh and Suka Damai (Lueng Bata sub-distric) This study prompts that the DRASTIC approach is helpful and efficient instrument for assessing groundwater vulnerability. The generated map can be an effective tool for local administrators in groundwater management as well.

High-resolution linkage map and chromosome-scale genome assembly for cassava ( Manihot esculenta Crantz) from 10 populations

DOE PAGES

Lyons, Jessica

2014-12-11

Cassava Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400–500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculent Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480more » meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. Here, we used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selectionenhanced breeding of this important crop.« less

High-resolution linkage map and chromosome-scale genome assembly for cassava ( Manihot esculenta Crantz) from 10 populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyons, Jessica

Cassava Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400–500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculent Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480more » meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. Here, we used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selectionenhanced breeding of this important crop.« less

Detecting the Extent of Cellular Decomposition after Sub-Eutectoid Annealing in Rolled UMo Foils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kautz, Elizabeth J.; Jana, Saumyadeep; Devaraj, Arun

2017-07-31

This report presents an automated image processing approach to quantifying microstructure image data, specifically the extent of eutectoid (cellular) decomposition in rolled U-10Mo foils. An image processing approach is used here to be able to quantitatively describe microstructure image data in order to relate microstructure to processing parameters (time, temperature, deformation).

HERACLES: THE HERA CO LINE EXTRAGALACTIC SURVEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leroy, Adam K.; Walter, Fabian; Bigiel, Frank

2009-06-15

We present the Heterodyne Receiver Array CO Line Extragalactic Survey, an atlas of CO emission from 18 nearby galaxies that are also part of The H I Nearby Galaxy Survey and the Spitzer Infrared Nearby Galaxies Survey. We used the HERA multipixel receiver on the IRAM 30-m telescope to map the CO J = 2 {yields} 1 line over the full optical disk (defined by the isophotal radius r {sub 25}) of each target, at 13'' angular resolution and 2.6 km s{sup -1} velocity resolution. Here we describe the observations and reduction of the data and show channel maps, azimuthallymore » averaged profiles, integrated intensity maps, and peak intensity maps. The implied H{sub 2} masses range from 7 x 10{sup 6} to 6 x 10{sup 9} M {sub sun}, with four low metallicity dwarf irregular galaxies yielding only upper limits. In the cases where CO is detected, the integrated H{sub 2}-to-H I ratios range from 0.02 to 1.13 and H{sub 2}-to-stellar mass ratios from 0.01 to 0.25. Exponential scale lengths of the CO emission for our targets are in the range 0.8-3.2 kpc, or 0.2 {+-} 0.05r {sub 25}. The intensity-weighted mean velocity of CO matches that of H I very well, with a 1{sigma} scatter of only 6 km s{sup -1}. The CO J = 2 {yields} 1/J = 1 {yields} 0 line ratio varies over a range similar to that found in the Milky Way and other nearby galaxies, {approx}0.6-1.0, with higher values found in the centers of galaxies. The typical line ratio, {approx}0.8, could be produced by optically thick gas with an excitation temperature of {approx}10 K.« less

Function-specific and Enhanced Brain Structural Connectivity Mapping via Joint Modeling of Diffusion and Functional MRI.

PubMed

Chu, Shu-Hsien; Parhi, Keshab K; Lenglet, Christophe

2018-03-16

A joint structural-functional brain network model is presented, which enables the discovery of function-specific brain circuits, and recovers structural connections that are under-estimated by diffusion MRI (dMRI). Incorporating information from functional MRI (fMRI) into diffusion MRI to estimate brain circuits is a challenging task. Usually, seed regions for tractography are selected from fMRI activation maps to extract the white matter pathways of interest. The proposed method jointly analyzes whole brain dMRI and fMRI data, allowing the estimation of complete function-specific structural networks instead of interactively investigating the connectivity of individual cortical/sub-cortical areas. Additionally, tractography techniques are prone to limitations, which can result in erroneous pathways. The proposed framework explicitly models the interactions between structural and functional connectivity measures thereby improving anatomical circuit estimation. Results on Human Connectome Project (HCP) data demonstrate the benefits of the approach by successfully identifying function-specific anatomical circuits, such as the language and resting-state networks. In contrast to correlation-based or independent component analysis (ICA) functional connectivity mapping, detailed anatomical connectivity patterns are revealed for each functional module. Results on a phantom (Fibercup) also indicate improvements in structural connectivity mapping by rejecting false-positive connections with insufficient support from fMRI, and enhancing under-estimated connectivity with strong functional correlation.

Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation.

PubMed

Dillinger, Stefan; Straub, Tobias; Németh, Attila

2017-01-01

Mammalian chromosomes are organized in structural and functional domains of 0.1-10 Mb, which are characterized by high self-association frequencies in the nuclear space and different contact probabilities with nuclear sub-compartments. They exhibit distinct chromatin modification patterns, gene expression levels and replication timing. Recently, nucleolus-associated chromosomal domains (NADs) have been discovered, yet their precise genomic organization and dynamics are still largely unknown. Here, we use nucleolus genomics and single-cell experiments to address these questions in human embryonic fibroblasts during replicative senescence. Genome-wide mapping reveals 1,646 NADs in proliferating cells, which cover about 38% of the annotated human genome. They are mainly heterochromatic and correlate with late replicating loci. Using Hi-C data analysis, we show that interactions of NADs dominate interphase chromosome contacts in the 10-50 Mb distance range. Interestingly, only minute changes in nucleolar association are observed upon senescence. These spatial rearrangements in subdomains smaller than 100 kb are accompanied with local transcriptional changes. In contrast, large centromeric and pericentromeric satellite repeat clusters extensively dissociate from nucleoli in senescent cells. Accordingly, H3K9me3-marked heterochromatin gets remodelled at the perinucleolar space as revealed by immunofluorescence analyses. Collectively, this study identifies connections between the nucleolus, 3D genome structure, and cellular aging at the level of interphase chromosome organization.

Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation

PubMed Central

Dillinger, Stefan

2017-01-01

Mammalian chromosomes are organized in structural and functional domains of 0.1–10 Mb, which are characterized by high self-association frequencies in the nuclear space and different contact probabilities with nuclear sub-compartments. They exhibit distinct chromatin modification patterns, gene expression levels and replication timing. Recently, nucleolus-associated chromosomal domains (NADs) have been discovered, yet their precise genomic organization and dynamics are still largely unknown. Here, we use nucleolus genomics and single-cell experiments to address these questions in human embryonic fibroblasts during replicative senescence. Genome-wide mapping reveals 1,646 NADs in proliferating cells, which cover about 38% of the annotated human genome. They are mainly heterochromatic and correlate with late replicating loci. Using Hi-C data analysis, we show that interactions of NADs dominate interphase chromosome contacts in the 10–50 Mb distance range. Interestingly, only minute changes in nucleolar association are observed upon senescence. These spatial rearrangements in subdomains smaller than 100 kb are accompanied with local transcriptional changes. In contrast, large centromeric and pericentromeric satellite repeat clusters extensively dissociate from nucleoli in senescent cells. Accordingly, H3K9me3-marked heterochromatin gets remodelled at the perinucleolar space as revealed by immunofluorescence analyses. Collectively, this study identifies connections between the nucleolus, 3D genome structure, and cellular aging at the level of interphase chromosome organization. PMID:28575119

Lineage mapping and characterization of the native progenitor population in cellular allograft.

PubMed

Neman, Josh; Duenas, Vincent; Kowolik, Claudia; Hambrecht, Amanda; Chen, Mike; Jandial, Rahul

2013-02-01

The gold standard for bone grafting remains the autograft. However, the attractiveness of autograft is counterbalanced by donor site morbidity. To mimic autograft-and its fundamental properties of osteoconductivity, osteoinductivity, and osteogenicity-novel bone grafting materials such as cellular allograft (Osteocel Plus) are composed of allograft in which the progenitor cells are preserved. However, the true identity of these cells remains obscure largely due to the lack of specific bona fide antigenic markers for stem versus progenitor cells. To characterize the stem and progenitor population in cellular allograft, Osteocel Plus. To determine whether cells endogenous to a cellular allograft undergo extensive self-renewal (a functional hallmark of stem cells), we employed a novel use of lineage mapping using a modern and refined replication incompetent lentiviral library with high complexity to uniquely label single cells with indelible genetic tags faithfully passed on to all progeny, allowing identification of highly proliferative clones. We used genetic and proteomic profiling as well as functional assays to show that these cells are capable of multipotential differentiation (the second functional hallmark of stem cells). Use of these two functional hallmarks enabled us to establish the existence of a stem and progenitor cell population in cellular allografts. Specifically, we employed (1) cellular dissociation and (2) in vitro expansion and differentiation capacity of cells released from cellular allograft. We determined differential gene expression profiling of a bona fide human mesenchymal stem cell line and cells from cellular allograft using focused PCR arrays mesenchymal stem cell (MSC) and osteogenesis associated. Proteomic profiling of cells from cellular allograft was performed using (1) immunofluorescence for BMP-2, Runx2 SMADs, CD44, Stro-1, Collagen, RANKL, Osterix Osteocalcin, and Ki67; (2) flow cytometry for Ki67, CD44, Stro-1, Thy1, CD146, and Osteocalcin; and (3) enzyme-linked immunosorbent assays (ELISA) for BMP-2, Osteocalcin, RANKL, Osteoprotegrin, and Osteocalcin. Clonal analysis of cells from cellular allograft was performed utilizing advance lentivirus lineage mapping techniques and massive parallel sequencing. Alizarin Red, Alcian Blue, and Oil red O staining assessed tripotential differentiation capacity. Serial trypsinization of allograft cellular bone matrix yielded approximately 1×105 cells per mL with viability greater than 90%. Cells expressed a panel of 84 MSC-associated genes in a pattern similar to but not identical to pure MSCs; specifically, 59 of 84 genes showed less than a 2.5-fold change in both cell types. Protein analysis showed that cellular allograft -derived cells maintained in nondifferentiation media expressed the early osteo-progenitor markers BMP-2, SMADs, and Runx2. Corresponding flow cytometry data for MSC markers revealed the presence of Stro-1 (49%), CD44 (99%), CD90 (42%), and CD146 (97%). Lineage mapping indicated that 62% of clones persisted and generated progeny through 10 passages, strongly suggesting the presence of bona fide stem cells. Passage 10 clones also exhibited tri-lineage differentiation capacity into osteogenic (Alizarin Red with H&E counterstain), chondrogenic (Alcian Blue), and adipogenic (Oil red O). Cells that did not proliferate through 10 passages presumably differentiated along an osteo-progenitor lineage. These data indicate that cellular allograft (Osteocel Plus) contains a heterogeneous population of cells with most cells demonstrating the capacity for extensive self-renewal and multipotential differentiation, which are hallmarks of stem cells. Whether stem cell-enriched allografts function comparably to autograft will require further studies, and their efficacy in facilitating arthrodesis will depend on randomized clinical studies. Copyright © 2013 Elsevier Inc. All rights reserved.

Computer simulation of a cellular automata model for the immune response in a retrovirus system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandey, R.B.

1989-02-01

Immune response in a retrovirus system is modeled by a network of three binary cell elements to take into account some of the main functional features of T4 cells, T8 cells, and viruses. Two different intercell interactions are introduced, one of which leads to three fixed points while the other yields bistable fixed points oscillating between a healthy state and a sick state in a mean field treatment. Evolution of these cells is studied for quenched and annealed random interactions on a simple cubic lattice with a nearest neighbor interaction using inhomogenous cellular automata. Populations of T4 cells and viralmore » cells oscillate together with damping (with constant amplitude) for annealed (quenched) interaction on increasing the value of mixing probability B from zero to a characteristic value B/sub ca/ (B/sub cq/). For higher B, the average number of T4 cells increases while that of the viral infected cells decreases monotonically on increasing B, suggesting a phase transition at B/sub ca/ (B/sub cq/).« less

The Cellular Automata for modelling of spreading of lava flow on the earth surface

NASA Astrophysics Data System (ADS)

Jarna, A.

2012-12-01

Volcanic risk assessment is a very important scientific, political and economic issue in densely populated areas close to active volcanoes. Development of effective tools for early prediction of a potential volcanic hazard and management of crises are paramount. However, to this date volcanic hazard maps represent the most appropriate way to illustrate the geographical area that can potentially be affected by a volcanic event. Volcanic hazard maps are usually produced by mapping out old volcanic deposits, however dynamic lava flow simulation gaining popularity and can give crucial information to corroborate other methodologies. The methodology which is used here for the generation of volcanic hazard maps is based on numerical simulation of eruptive processes by the principle of Cellular Automata (CA). The python script is integrated into ArcToolbox in ArcMap (ESRI) and the user can select several input and output parameters which influence surface morphology, size and shape of the flow, flow thickness, flow velocity and length of lava flows. Once the input parameters are selected, the software computes and generates hazard maps on the fly. The results can be exported to Google Maps (.klm format) to visualize the results of the computation. For validation of the simulation code are used data from a real lava flow. Comparison of the simulation results with real lava flows mapped out from satellite images will be presented.

The heparin-binding domain of HB-EGF as an efficient cell-penetrating peptide for drug delivery.

PubMed

Luo, Zhao; Cao, Xue-Wei; Li, Chen; Wu, Miao-Dan; Yang, Xu-Zhong; Zhao, Jian; Wang, Fu-Jun

2016-11-01

Cell-penetrating peptides (CPPs) have been shown to be potential drug carriers for cancer therapy. The inherently low immunogenicity and cytotoxicity of human-derived CPPs make them more suitable for intracellular drug delivery compared to other delivery vehicles. In this work, the protein transduction ability of a novel CPP (termed HBP) derived from the heparin-binding domain of HB-EGF was evaluated. Our data shows, for the first time, that HBP possesses similar properties to typical CPPs and is a potent drug delivery vector for improving the antitumor activity of impermeable MAP30. The intrinsic bioactivities of recombinant MAP30-HBP were well preserved compared to those of free MAP30. Furthermore, HBP conjugated to the C-terminus of MAP30 promoted the cellular uptake of recombinant MAP30-HBP. Moreover, the fusion of HBP to MAP30 gave rise to significantly enhanced cytotoxic effects in all of the tumor cell lines tested. In HeLa cells, this cytotoxicity was mainly caused by the induction of cell apoptosis. Further investigation revealed that HBP enhanced MAP30-induced apoptosis through the activation of the mitochondrial- and death receptor-mediated signaling pathways. In addition, the MAP30-HBP fusion protein caused more HeLa cells to become arrested in S phase compared to MAP30 alone. These results highlight the MAP30-HBP fusion protein as a promising drug candidate for cancer therapy and demonstrate HBP, a novel CPP derived from human HB-EGF, as a new potential vector for antitumor drug delivery. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome*

PubMed Central

Jadot, Michel; Boonen, Marielle; Thirion, Jaqueline; Wang, Nan; Xing, Jinchuan; Zhao, Caifeng; Tannous, Abla; Qian, Meiqian; Zheng, Haiyan; Everett, John K.; Moore, Dirk F.; Sleat, David E.; Lobel, Peter

2017-01-01

Accurate knowledge of the intracellular location of proteins is important for numerous areas of biomedical research including assessing fidelity of putative protein-protein interactions, modeling cellular processes at a system-wide level and investigating metabolic and disease pathways. Many proteins have not been localized, or have been incompletely localized, partly because most studies do not account for entire subcellular distribution. Thus, proteins are frequently assigned to one organelle whereas a significant fraction may reside elsewhere. As a step toward a comprehensive cellular map, we used subcellular fractionation with classic balance sheet analysis and isobaric labeling/quantitative mass spectrometry to assign locations to >6000 rat liver proteins. We provide quantitative data and error estimates describing the distribution of each protein among the eight major cellular compartments: nucleus, mitochondria, lysosomes, peroxisomes, endoplasmic reticulum, Golgi, plasma membrane and cytosol. Accounting for total intracellular distribution improves quality of organelle assignments and assigns proteins with multiple locations. Protein assignments and supporting data are available online through the Prolocate website (http://prolocate.cabm.rutgers.edu). As an example of the utility of this data set, we have used organelle assignments to help analyze whole exome sequencing data from an infant dying at 6 months of age from a suspected neurodegenerative lysosomal storage disorder of unknown etiology. Sequencing data was prioritized using lists of lysosomal proteins comprising well-established residents of this organelle as well as novel candidates identified in this study. The latter included copper transporter 1, encoded by SLC31A1, which we localized to both the plasma membrane and lysosome. The patient harbors two predicted loss of function mutations in SLC31A1, suggesting that this may represent a heretofore undescribed recessive lysosomal storage disease gene. PMID:27923875

Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome.

PubMed

Jadot, Michel; Boonen, Marielle; Thirion, Jaqueline; Wang, Nan; Xing, Jinchuan; Zhao, Caifeng; Tannous, Abla; Qian, Meiqian; Zheng, Haiyan; Everett, John K; Moore, Dirk F; Sleat, David E; Lobel, Peter

2017-02-01

Accurate knowledge of the intracellular location of proteins is important for numerous areas of biomedical research including assessing fidelity of putative protein-protein interactions, modeling cellular processes at a system-wide level and investigating metabolic and disease pathways. Many proteins have not been localized, or have been incompletely localized, partly because most studies do not account for entire subcellular distribution. Thus, proteins are frequently assigned to one organelle whereas a significant fraction may reside elsewhere. As a step toward a comprehensive cellular map, we used subcellular fractionation with classic balance sheet analysis and isobaric labeling/quantitative mass spectrometry to assign locations to >6000 rat liver proteins. We provide quantitative data and error estimates describing the distribution of each protein among the eight major cellular compartments: nucleus, mitochondria, lysosomes, peroxisomes, endoplasmic reticulum, Golgi, plasma membrane and cytosol. Accounting for total intracellular distribution improves quality of organelle assignments and assigns proteins with multiple locations. Protein assignments and supporting data are available online through the Prolocate website (http://prolocate.cabm.rutgers.edu). As an example of the utility of this data set, we have used organelle assignments to help analyze whole exome sequencing data from an infant dying at 6 months of age from a suspected neurodegenerative lysosomal storage disorder of unknown etiology. Sequencing data was prioritized using lists of lysosomal proteins comprising well-established residents of this organelle as well as novel candidates identified in this study. The latter included copper transporter 1, encoded by SLC31A1, which we localized to both the plasma membrane and lysosome. The patient harbors two predicted loss of function mutations in SLC31A1, suggesting that this may represent a heretofore undescribed recessive lysosomal storage disease gene. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Supporting performance and configuration management of GTE cellular networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Ming; Lafond, C.; Jakobson, G.

GTE Laboratories, in cooperation with GTE Mobilnet, has developed and deployed PERFFEX (PERFormance Expert), an intelligent system for performance and configuration management of cellular networks. PERFEX assists cellular network performance and radio engineers in the analysis of large volumes of cellular network performance and configuration data. It helps them locate and determine the probable causes of performance problems, and provides intelligent suggestions about how to correct them. The system combines an expert cellular network performance tuning capability with a map-based graphical user interface, data visualization programs, and a set of special cellular engineering tools. PERFEX is in daily use atmore » more than 25 GTE Mobile Switching Centers. Since the first deployment of the system in late 1993, PERFEX has become a major GTE cellular network performance optimization tool.« less

Sub-Selective Quantization for Learning Binary Codes in Large-Scale Image Search.

PubMed

Li, Yeqing; Liu, Wei; Huang, Junzhou

2018-06-01

Recently with the explosive growth of visual content on the Internet, large-scale image search has attracted intensive attention. It has been shown that mapping high-dimensional image descriptors to compact binary codes can lead to considerable efficiency gains in both storage and performing similarity computation of images. However, most existing methods still suffer from expensive training devoted to large-scale binary code learning. To address this issue, we propose a sub-selection based matrix manipulation algorithm, which can significantly reduce the computational cost of code learning. As case studies, we apply the sub-selection algorithm to several popular quantization techniques including cases using linear and nonlinear mappings. Crucially, we can justify the resulting sub-selective quantization by proving its theoretic properties. Extensive experiments are carried out on three image benchmarks with up to one million samples, corroborating the efficacy of the sub-selective quantization method in terms of image retrieval.

Comparison of Sub-Pixel Classification Approaches for Crop-Specific Mapping

EPA Science Inventory

This paper examined two non-linear models, Multilayer Perceptron (MLP) regression and Regression Tree (RT), for estimating sub-pixel crop proportions using time-series MODIS-NDVI data. The sub-pixel proportions were estimated for three major crop types including corn, soybean, a...

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Junjing; Vine, David J.; Chen, Si

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ~90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. Finally, this combined approach offers a way to study the role of trace elements in their structural context.« less

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

DOE PAGES

Deng, Junjing; Vine, David J.; Chen, Si; ...

2015-02-24

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ~90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. Finally, this combined approach offers a way to study the role of trace elements in their structural context.« less

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Junjing; Vine, David J.; Chen, Si

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and similar to 90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. This combined approach offers a way to study the role of trace elements in their structural context.« less

Quantification of asymmetric microtubule nucleation at sub-cellular structures

PubMed Central

Zhu, Xiaodong; Kaverina, Irina

2012-01-01

Cell polarization is important for multiple physiological processes. In polarized cells, microtubules (MTs) are organized into a spatially polarized array. Generally, in non-differentiated cells, it is assumed that MTs are symmetrically nucleated exclusively from centrosome (microtubule organizing center, MTOC) and then reorganized into the asymmetric array. We have recently identified the Golgi complex as an additional MTOC that asymmetrically nucleates MTs toward one side of the cell. Methods used for alternative MTOC identification include microtubule re-growth after complete drug-induced depolymerization and tracking of growing microtubules using fluorescence labeled MT +TIP binding proteins in living cells. These approaches can be used for quantification of MT nucleation sites at diverse sub-cellular structures. PMID:21773933

Context Specificity of Stress-activated Mitogen-activated Protein (MAP) Kinase Signaling: The Story as Told by Caenorhabditis elegans.

PubMed

Andrusiak, Matthew G; Jin, Yishi

2016-04-08

Stress-associated p38 and JNK mitogen-activated protein (MAP) kinase signaling cascades trigger specific cellular responses and are involved in multiple disease states. At the root of MAP kinase signaling complexity is the differential use of common components on a context-specific basis. The roundwormCaenorhabditis eleganswas developed as a system to study genes required for development and nervous system function. The powerful genetics ofC. elegansin combination with molecular and cellular dissections has led to a greater understanding of how p38 and JNK signaling affects many biological processes under normal and stress conditions. This review focuses on the studies revealing context specificity of different stress-activated MAPK components inC. elegans. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis.

PubMed

Gorman, Bryan R; Lu, Junjie; Baccei, Anna; Lowry, Nathan C; Purvis, Jeremy E; Mangoubi, Rami S; Lerou, Paul H

2014-01-01

Human pluripotent stem (hPS) cells are a potential source of cells for medical therapy and an ideal system to study fate decisions in early development. However, hPS cells cultured in vitro exhibit a high degree of heterogeneity, presenting an obstacle to clinical translation. hPS cells grow in spatially patterned colony structures, necessitating quantitative single-cell image analysis. We offer a tool for analyzing the spatial population context of hPS cells that integrates automated fluorescent microscopy with an analysis pipeline. It enables high-throughput detection of colonies at low resolution, with single-cellular and sub-cellular analysis at high resolutions, generating seamless in situ maps of single-cellular data organized by colony. We demonstrate the tool's utility by analyzing inter- and intra-colony heterogeneity of hPS cell cycle regulation and pluripotency marker expression. We measured the heterogeneity within individual colonies by analyzing cell cycle as a function of distance. Cells loosely associated with the outside of the colony are more likely to be in G1, reflecting a less pluripotent state, while cells within the first pluripotent layer are more likely to be in G2, possibly reflecting a G2/M block. Our multi-scale analysis tool groups colony regions into density classes, and cells belonging to those classes have distinct distributions of pluripotency markers and respond differently to DNA damage induction. Lastly, we demonstrate that our pipeline can robustly handle high-content, high-resolution single molecular mRNA FISH data by using novel image processing techniques. Overall, the imaging informatics pipeline presented offers a novel approach to the analysis of hPS cells that includes not only single cell features but also colony wide, and more generally, multi-scale spatial configuration.

Action-at-a-distance metamaterials: Distributed local actuation through far-field global forces

NASA Astrophysics Data System (ADS)

Hedayati, R.; Mirzaali, M. J.; Vergani, L.; Zadpoor, A. A.

2018-03-01

Mechanical metamaterials are a sub-category of designer materials where the geometry of the material at the small-scale is rationally designed to give rise to unusual properties and functionalities. Here, we propose the concept of "action-at-a-distance" metamaterials where a specific pattern of local deformation is programmed into the fabric of (cellular) materials. The desired pattern of local actuation could then be achieved simply through the application of one single global and far-field force. We proposed graded designs of auxetic and conventional unit cells with changing Poisson's ratios as a way of making "action-at-a-distance" metamaterials. We explored five types of graded designs including linear, two types of radial gradients, checkered, and striped. Specimens were fabricated with indirect additive manufacturing and tested under compression, tension, and shear. Full-field strain maps measured with digital image correlation confirmed different patterns of local actuation under similar far-field strains. These materials have potential applications in soft (wearable) robotics and exosuits.

Spectral fractionation detection of gold nanorod contrast agents using optical coherence tomography

PubMed Central

Jia, Yali; Liu, Gangjun; Gordon, Andrew Y.; Gao, Simon S.; Pechauer, Alex D.; Stoddard, Jonathan; McGill, Trevor J.; Jayagopal, Ashwath; Huang, David

2015-01-01

We demonstrate the proof of concept of a novel Fourier-domain optical coherence tomography contrast mechanism using gold nanorod contrast agents and a spectral fractionation processing technique. The methodology detects the spectral shift of the backscattered light from the nanorods by comparing the ratio between the short and long wavelength halves of the optical coherence tomography signal intensity. Spectral fractionation further divides the halves into sub-bands to improve spectral contrast and suppress speckle noise. Herein, we show that this technique can detect gold nanorods in intralipid tissue phantoms. Furthermore, cellular labeling by gold nanorods was demonstrated using retinal pigment epithelial cells in vitro. PMID:25836459

Vitamin D endocrine system after short-term space flight

NASA Technical Reports Server (NTRS)

Rhoten, William B. (Principal Investigator); Sergeev, Igor N. (Principal Investigator)

1996-01-01

The exposure of the body to microgravity during space flight causes a series of well-documented changes in Ca(2+) metabolism, yet the cellular/molecular mechanisms leading to these changes are poorly understood. There is some evidence for microgravity-induced alterations in the vitamin D endocrine system, which is known to be primarily involved in the regulation of Ca(2+) metabolism. Vitamin D-dependent Ca(2+) binding proteins, or calbindins, are believed to have a significant role in maintaining cellular Ca(2+) homeostasis. We used immunocytochemical, biochemical and molecular approaches to analyze the expression of calbindin-D(sub 28k) and calbindin-D(sub 9k) in kidneys and intestines of rats flown for 9 days aboard the Spacelab 3 mission. The effects of microgravity on calbindins in rats in space vs. 'grounded' animals (synchronous Animal Enclosure Module controls and tail suspension controls) were compared. Exposure to microgravity resulted in a significant decrease in calbindin-D(sub 28k) content in kidneys and calbindin-D(sub 9k) in the intestine of flight and suspended animals, as measured by enzyme-linked immunosorbent assay (ELISA). Immunocytochemistry (ICC) in combination with quantitative computer image analysis was used to measure in situ the expression of calbindins in kidneys and intestine, and insulin in pancreas. There was a large decrease in the distal tubular cell-associated calbindin-D(sub 28k) and absorptive cell-associated calbindin-D(sub 9k) immunoreactivity in the space and suspension kidneys and intestine, as compared with matched ground controls. No consistent differences in pancreatic insulin immunoreactivity between space, suspension and ground controls was observed. There were significant correlations between results by quantitative ICC and ELISA. Western blot analysis showed no consistent changes in the low levels of intestinal and renal vitamin D receptors. These findings suggest that a decreased expression of calbindins after a short-term exposure to microgravity and modelled weightlessness, may affect cellular Ca(2+) homeostasis and contribute to Ca(2+) and bone metabolism disorders induced by space flight.

BAC sequencing using pooled methods.

PubMed

Saski, Christopher A; Feltus, F Alex; Parida, Laxmi; Haiminen, Niina

2015-01-01

Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly.

Seismic properties of the crust and uppermost mantle of North America

NASA Technical Reports Server (NTRS)

Braile, L. W.; Hinze, W. J.; Vonfrese, R. R. B.; Keller, G. R.

1983-01-01

Seismic refraction profiles for the North American continent were compiled. The crustal models compiled data on the upper mantle seismic velocity (P sub n), the crustal thickness (H sub c) and the average seismic velocity of the crystalline crust (V sub p). Compressional wave parameters were compared with shear wave data derived from surface wave dispersion models and indicate an average value for Poisson's ratio of 0.252 for the crust and of 0.273 for the uppermost mantle. Contour maps illustrate lateral variations in crustal thickness, upper mantle velocity and average seismic velocity of the crystalline crust. The distribution of seismic parameters are compared with a smoothed free air anomaly map of North America and indicate that a complidated mechanism of isostatic compensation exists for the North American continent. Several features on the seismic contour maps also correlate with regional magnetic anomalies.

Titan Global Map - June 2015

NASA Image and Video Library

2015-10-09

This global digital map of Saturn's moon Titan was created using images taken by NASA's Cassini spacecraft's imaging science subsystem (ISS). The map was produced in June 2015 using data collected through Cassini's flyby on April 7, 2014, known as "T100." The images were taken using a filter centered at 938 nanometers, allowing researchers to examine variations in albedo (or inherent brightness) across the surface of Titan. Because of the scattering of light by Titan's dense atmosphere, no topographic shading is visible in these images. The map is an equidistant projection and has a scale of 2.5 miles (4 kilometers) per pixel. Actual resolution varies greatly across the map, with the best coverage (close to the map scale) along the equator near the center of the map at 180 degrees west longitude. The lowest resolution coverage can be seen in the northern mid-latitudes on the sub-Saturn hemisphere. Mapping coverage in the northern polar region has greatly improved since the previous version of this map in 2011 (see PIA14908). Large dark areas, now known to be liquid-hydrocarbon-filled lakes and seas, have since been documented at high latitudes. Titan's north pole was not well illuminated early in Cassini's mission, because it was winter in the northern hemisphere when the spacecraft arrived at Saturn. Cassini has been better able to observe northern latitudes in more recent years due to seasonal changes in solar illumination. This map is an update to the previous versions released in April 2011 and February 2009 (see PIA11149). Data from the past four years (the most recent data in the map is from April 2014) has completely filled in missing data in the north polar region and replaces the earlier imagery of the Xanadu region with higher quality data. A data gap of about 3 to 5 percent of Titan's surface still remains, located in the northern mid-latitudes on the sub-Saturn hemisphere of Titan. The uniform gray area in the northern hemisphere indicates a gap in the imaging coverage of Titan's surface, to date. The missing data will be imaged by Cassini during flybys on December 15, 2016 and March 5, 2017. The mean radius of Titan used for projection of this map is 1,600 miles (2,575 kilometers). Titan is assumed to be spherical until a control network -- a model of the moon's shape based on multiple images tied together at defined points on the surface -- is created at some point in the future. http://photojournal.jpl.nasa.gov/catalog/PIA19658

Acrylamide inhibits cellular differentiation of human neuroblastoma and glioblastoma cells.

PubMed

Chen, Jong-Hang; Chou, Chin-Cheng

2015-08-01

This study explores human neuroblastoma (SH-SY5Y) and human glioblastoma (U-1240 MG) cellular differentiation changes under exposure to acrylamide (ACR). Differentiation of SH-SY5Y and U-1240 MG cells were induced by retinoic acid (RA) and butyric acid (BA), respectively. Morphological observations and MTT assay showed that the induced cellular differentiation and cell proliferation were inhibited by ACR in a time- and dose-dependent manner. ACR co-treatment with RA attenuated SH-SY5Y expressions of neurofilament protein-L (NF-L), microtubule-associated protein 1b (MAP1b; 1.2 to 0.7, p < 0.001), MAP2c (2.2 to 0.8, p < 0.05), and Janus kinase1 (JAK1; 1.9 to 0.6, p < 0.001), while ACR co-treatment with BA attenuated U-1240 MG expressions of glial fibrillary acidic protein (GFAP), MAP1b (1.2 to 0.6, p < 0.001), MAP2c (1.5 to 0.7, p < 0.01), and JAK1 (2.1 to 0.5, p < 0.001), respectively. ACR also decreased the phosphorylation of extracellular-signal-regulated kinases (ERK) and c-Jun N-terminal kinases (JNK) in U-1240 MG cells, while caffeine reversed this suppression of ERK and JNK phosphorylation caused by ACR treatment. These results showed that RA-induced neurogenesis of SH-SY5Y and BA-induced astrogliogenesis of U-1240 MG cells were attenuated by ACR and were associated with down-regulation of MAPs expression and JAK-STAT signaling. Copyright © 2015 Elsevier Ltd. All rights reserved.

Community context and sub-neighborhood scale detail to explain dengue, chikungunya and Zika patterns in Cali, Colombia

PubMed Central

Curtis, Andrew; Buritica, Paola; Ajayakumar, Jayakrishnan; Squires, Robert; Dávalos, Diana; Pacheco, Robinson; Bhatta, Madhav P.; James, Mark A.

2017-01-01

Background Cali, Colombia has experienced chikungunya and Zika outbreaks and hypoendemic dengue. Studies have explained Cali’s dengue patterns but lack the sub-neighborhood-scale detail investigated here. Methods Spatial-video geonarratives (SVG) with Ministry of Health officials and Community Health Workers were collected in hotspots, providing perspective on perceptions of why dengue, chikungunya and Zika hotspots exist, impediments to control, and social outcomes. Using spatial video and Google Street View, sub-neighborhood features possibly contributing to incidence were mapped to create risk surfaces, later compared with dengue, chikungunya and Zika case data. Results SVG captured insights in 24 neighborhoods. Trash and water risks in Calipso were mapped using SVG results. Perceived risk factors included proximity to standing water, canals, poverty, invasions, localized violence and military migration. These risks overlapped case density maps and identified areas that are suitable for transmission but are possibly underreporting to the surveillance system. Conclusion Resulting risk maps with local context could be leveraged to increase vector-control efficiency- targeting key areas of environmental risk. PMID:28767730

Semi-automated Approach to Mapping Sub-hectare Agricultural Fields using Very High Resolution Data in a High-Performance Computing Environment

NASA Astrophysics Data System (ADS)

Wooten, M.; Neigh, C. S. R.; Carroll, M.; McCarty, J. L.

2017-12-01

In areas susceptible to drought such as sub-Saharan Africa, Crop Area (CA) and agricultural mapping have become increasingly important as strain on natural ecosystems increases. In Ethiopia alone, the population has grown four-fold in the last 70 years, and rapidly growing human populations bring added stress to ecosystems as more wildlands are converted to pastures and subsistence agriculture. Monitoring change in agriculture is one of the more essential goals of famine early warning systems. However, due to the sub-hectare size of rainfed agricultural fields in regions such as Tigray, Ethiopia, moderate resolution satellite imagery is insufficient at capturing these smallholder farms. Thanks to the increasing density of observations and ease of access to very high resolution (VHR) data, we have developed a generalized method for mapping CA with VHR data and have used this to generate wall-to-wall CA map for the entire Tigray region and samples in Myanmar, Senegal, and Vietnam. Here we present the methodology and early results as well as potential future applications.

Mapping the Distribution of Potential Land Drought in Batam Island Using the Integration of Remote Sensing and Geographic Information Systems (GIS)

NASA Astrophysics Data System (ADS)

Lubis, M. Z.; Taki, H. M.; Anurogo, W.; Pamungkas, D. S.; Wicaksono, P.; Aprilliyanti, T.

2017-12-01

Potential land drought mapping on Batam is needed to determine the distribution of areas that are very potential to the physical drought of the land. It is because the drought is always threatening on the long dry season. This research integrates remote sensing science with Geographic Information System (GIS). This research aims to map the distribution of land drought potential in Batam Island. The parameters used in this research are land use, Land Surface Temperature (LST), Potential dryness of land on the Batam island. The resulting map indicates the existence of five potential drought classes on the island of Batam. The area of very low drought potential is 2629.45 ha, mostly located in the Sungai Beduk sub-district. High drought potential with an area of 7081.39 ha is located in Sekupang sub-district. The distribution of very high land drought potential is in Batam city and Nongsa sub-district with area of 15600.12 ha. The coefficient of determination (R 2) is 0.6279. This indicates a strong positive relationship between field LST and modelled LST.

The influence of changes in land use and landscape patterns on soil erosion in a watershed.

PubMed

Zhang, Shanghong; Fan, Weiwei; Li, Yueqiang; Yi, Yujun

2017-01-01

It is very important to have a good understanding of the relation between soil erosion and landscape patterns so that soil and water conservation in river basins can be optimized. In this study, this relationship was explored, using the Liusha River Watershed, China, as a case study. A distributed water and sediment model based on the Soil and Water Assessment Tool (SWAT) was developed to simulate soil erosion from different land use types in each sub-basin of the Liusha River Watershed. Observed runoff and sediment data from 1985 to 2005 and land use maps from 1986, 1995, and 2000 were used to calibrate and validate the model. The erosion modulus for each sub-basin was calculated from SWAT model results using the different land use maps and 12 landscape indices were chosen and calculated to describe the land use in each sub-basin for the different years. The variations in instead of the absolute amounts of the erosion modulus and the landscape indices for each sub-basin were used as the dependent and independent variables, respectively, for the regression equations derived from multiple linear regression. The results indicated that the variations in the erosion modulus were closely related to changes in the large patch index, patch cohesion index, modified Simpson's evenness index, and the aggregation index. From the regression equation and the corresponding landscape indices, it was found that watershed erosion can be reduced by decreasing the physical connectivity between patches, improving the evenness of the landscape patch types, enriching landscape types, and enhancing the degree of aggregation between the landscape patches. These findings will be useful for water and soil conservation and for optimizing the management of watershed landscapes. Copyright © 2016 Elsevier B.V. All rights reserved.

Primordial non-Gaussianity with μ-type and y -type spectral distortions: exploiting Cosmic Microwave Background polarization and dealing with secondary sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ravenni, Andrea; Liguori, Michele; Bartolo, Nicola

Cross-correlations between Cosmic Microwave Background (CMB) temperature and y -spectral distortion anisotropies have been previously proposed as a way to measure the local bispectrum parameter f {sub NL}{sup loc}. in a range of scales inaccessible to either CMB ( T , E ) bispectra or μ T correlations. This is useful e.g. to test scale dependence of primordial non-Gaussianity. Unfortunately, the primordial y T signal is strongly contaminated by the late-time correlation between the Integrated Sachs Wolfe and Sunyaev-Zel'dovich (SZ) effects. Moreover, SZ itself generates a large noise contribution in the y -parameter map. We consider two original ways tomore » address these issues. In order to remove the bias due to the SZ-CMB temperature coupling, while also providing additional signal, we include in the analysis the cross-correlation between y -distortions and CMB polarization . In order to reduce the noise, we propose to clean the y -map by subtracting a SZ template, reconstructed via cross-correlation with external tracers (CMB and galaxy-lensing signals). We combine this SZ template subtraction with the previously suggested solution of directly masking detected clusters. Our final forecasts show that, using y -distortions, a PRISM-like survey can achieve 1σ( f {sub NL}{sup loc}.) = 300, while an ideal experiment will achieve 1σ( f {sub NL}{sup loc}.) = 130 with improvements of a factor between 2.1 and 3.8, depending on the considered survey, from adding the y E signal, and a further 20–30 % from template cleaning. These forecasts are much worse than current f {sub NL}{sup loc}. boundaries from Planck , but we stress that they refer to completely different scales.« less

Evidence for network evolution in an arabidopsis interactome map

USDA-ARS?s Scientific Manuscript database

Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the pl...

Hierarchical brain mapping via a generalized Dirichlet solution for mapping brain manifolds

NASA Astrophysics Data System (ADS)

Joshi, Sarang C.; Miller, Michael I.; Christensen, Gary E.; Banerjee, Ayan; Coogan, Tom; Grenander, Ulf

1995-08-01

In this paper we present a coarse-to-fine approach for the transformation of digital anatomical textbooks from the ideal to the individual that unifies the work on landmark deformations and volume based transformation. The Hierarchical approach is linked to the Biological problem itself, coming out of the various kinds of information which is provided by the anatomists. This information is in the form of points, lines, surfaces and sub-volumes corresponding to 0, 1, 2, and 3 dimensional sub-manifolds respectively. The algorithm is driven by these sub- manifolds. We follow the approach that the highest dimensional transformation is a result from the solution of a sequence of lower dimensional problems driven by successive refinements or partitions of the images into various Biologically meaningful sub-structures.

Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure.

PubMed

Hsiao, Chiaowen; Liu, Mengya; Stanton, Rick; McGee, Monnie; Qian, Yu; Scheuermann, Richard H

2016-01-01

Flow cytometry (FCM) is a fluorescence-based single-cell experimental technology that is routinely applied in biomedical research for identifying cellular biomarkers of normal physiological responses and abnormal disease states. While many computational methods have been developed that focus on identifying cell populations in individual FCM samples, very few have addressed how the identified cell populations can be matched across samples for comparative analysis. This article presents FlowMap-FR, a novel method for cell population mapping across FCM samples. FlowMap-FR is based on the Friedman-Rafsky nonparametric test statistic (FR statistic), which quantifies the equivalence of multivariate distributions. As applied to FCM data by FlowMap-FR, the FR statistic objectively quantifies the similarity between cell populations based on the shapes, sizes, and positions of fluorescence data distributions in the multidimensional feature space. To test and evaluate the performance of FlowMap-FR, we simulated the kinds of biological and technical sample variations that are commonly observed in FCM data. The results show that FlowMap-FR is able to effectively identify equivalent cell populations between samples under scenarios of proportion differences and modest position shifts. As a statistical test, FlowMap-FR can be used to determine whether the expression of a cellular marker is statistically different between two cell populations, suggesting candidates for new cellular phenotypes by providing an objective statistical measure. In addition, FlowMap-FR can indicate situations in which inappropriate splitting or merging of cell populations has occurred during gating procedures. We compared the FR statistic with the symmetric version of Kullback-Leibler divergence measure used in a previous population matching method with both simulated and real data. The FR statistic outperforms the symmetric version of KL-distance in distinguishing equivalent from nonequivalent cell populations. FlowMap-FR was also employed as a distance metric to match cell populations delineated by manual gating across 30 FCM samples from a benchmark FlowCAP data set. An F-measure of 0.88 was obtained, indicating high precision and recall of the FR-based population matching results. FlowMap-FR has been implemented as a standalone R/Bioconductor package so that it can be easily incorporated into current FCM data analytical workflows. © The Authors. Published by Wiley Periodicals, Inc. on behalf of ISAC.

Substance P receptor desensitization requires receptor activation but not phospholipase C

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugiya, Hiroshi; Putney, J.W. Jr.

1988-08-01

Previous studies have shown that exposure of parotid acinar cells to substance P at 37{degree}C results in activation of phospholipase C, formation of ({sup 3}H)inositol 1,4,5-trisphosphate (IP{sub 3}), and persistent desensitization of the substance P response. In cells treated with antimycin in medium containing glucose, ATP was decreased to {approximately}20% of control values, IP{sub 3} formation was completely inhibited, but desensitization was unaffected. When cells were treated with antimycin in the absence of glucose, cellular ATP was decreased to {approximately}5% of control values, and both IP{sub 3} formation and desensitization were blocked. A series of substance P-related peptides increased themore » formation of ({sup 3}H)IP{sub 3} and induced desensitization of the substance P response with a similar rank order of potencies. The substance P antagonist, (D-Pro{sup 2}, D-Try{sup 7,9})-substance P, inhibited substance P-induced IP{sub 3} formation and desensitization but did not induce desensitization. These results suggest that the desensitization of substance P-induced IP{sub 3} formation requires agonist activation of a P-type substance P receptor, and that one or more cellular ATP-dependent processes are required for this reaction. However, activation of phospholipase C and the generation of inositol phosphates does not seem to be a prerequisite for desensitization.« less

Au-rich filamentary behavior and associated subband gap optical absorption in hyperdoped Si

NASA Astrophysics Data System (ADS)

Yang, W.; Akey, A. J.; Smillie, L. A.; Mailoa, J. P.; Johnson, B. C.; McCallum, J. C.; Macdonald, D.; Buonassisi, T.; Aziz, M. J.; Williams, J. S.

2017-12-01

Au-hyperdoped Si, synthesized by ion implantation and pulsed laser melting, is known to exhibit a strong sub-band gap photoresponse that scales monotonically with the Au concentration. However, there is thought to be a limit to this behavior since ultrahigh Au concentrations (>1 ×1020c m-3 ) are expected to induce cellular breakdown during the rapid resolidification of Si, a process that is associated with significant lateral impurity precipitation. This work shows that the cellular morphology observed in Au-hyperdoped Si differs from that in conventional, steady-state cellular breakdown. In particular, Rutherford backscattering spectrometry combined with channeling and transmission electron microscopy revealed an inhomogeneous Au distribution and a subsurface network of Au-rich filaments, within which the Au impurities largely reside on substitutional positions in the crystalline Si lattice, at concentrations as high as ˜3 at. %. The measured substitutional Au dose, regardless of the presence of Au-rich filaments, correlates strongly with the sub-band gap optical absorptance. Upon subsequent thermal treatment, the supersaturated Au forms precipitates, while the Au substitutionality and the sub-band gap optical absorption both decrease. These results offer insight into a metastable filamentary regime in Au-hyperdoped Si that has important implications for Si-based infrared optoelectronics.

Comparative RNA-Seq transcriptome analyses reveal distinct metabolic pathways in diabetic nerve and kidney disease.

PubMed

Hinder, Lucy M; Park, Meeyoung; Rumora, Amy E; Hur, Junguk; Eichinger, Felix; Pennathur, Subramaniam; Kretzler, Matthias; Brosius, Frank C; Feldman, Eva L

2017-09-01

Treating insulin resistance with pioglitazone normalizes renal function and improves small nerve fibre function and architecture; however, it does not affect large myelinated nerve fibre function in mouse models of type 2 diabetes (T2DM), indicating that pioglitazone affects the body in a tissue-specific manner. To identify distinct molecular pathways regulating diabetic peripheral neuropathy (DPN) and nephropathy (DN), as well those affected by pioglitazone, we assessed DPN and DN gene transcript expression in control and diabetic mice with or without pioglitazone treatment. Differential expression analysis and self-organizing maps were then used in parallel to analyse transcriptome data. Differential expression analysis showed that gene expression promoting cell death and the inflammatory response was reversed in the kidney glomeruli but unchanged or exacerbated in sciatic nerve by pioglitazone. Self-organizing map analysis revealed that mitochondrial dysfunction was normalized in kidney and nerve by treatment; however, conserved pathways were opposite in their directionality of regulation. Collectively, our data suggest inflammation may drive large fibre dysfunction, while mitochondrial dysfunction may drive small fibre dysfunction in T2DM. Moreover, targeting both of these pathways is likely to improve DN. This study supports growing evidence that systemic metabolic changes in T2DM are associated with distinct tissue-specific metabolic reprogramming in kidney and nerve and that these changes play a critical role in DN and small fibre DPN pathogenesis. These data also highlight the potential dangers of a 'one size fits all' approach to T2DM therapeutics, as the same drug may simultaneously alleviate one complication while exacerbating another. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Late-assembly of human ribosomal protein S20 in the cytoplasm is essential for the functioning of the small subunit ribosome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tai, Lin-Ru; Chou, Chang-Wei; Wu, Jing-Ying

2013-11-15

Using immuno-fluorescent probing and Western blotting analysis, we reveal the exclusive cytoplasm nature of the small subunit ribosomal protein S20. To illustrate the importance of the cellular compartmentation of S20 to the function of small subunit 40S, we created a nuclear resident S20{sub NLS} mutant gene and examined polysome profile of cells that had been transfected with the S20{sub NLS} gene. As a result, we observed the formation of recombinant 40S carried S20{sub NLS} but this recombinant 40S was never found in the polysome, suggesting such a recombinant 40S was translation incompetent. Moreover, by the tactic of the energy depletionmore » and restoration, we were able to restrain the nuclear-resided S20{sub NLS} in the cytoplasm. Yet, along a progressive energy restoration, we observed the presence of recombinant 40S subunits carrying the S20{sub NLS} in the polysome. This proves that S20 needs to be cytoplasmic in order to make a functional 40S subunit. Furthermore, it also implies that the assembly order of ribosomal protein in eukaryote is orderly regulated. - Highlights: • The step of S20 assembled on 40S is happened in the cytoplasm. • A small subunit assembled with a nuclear S20{sub NLS} is translational incompetence. • Using energy depletion and recovery to manipulate the cellular compartment of S20{sub NLS}. • Cytoplasm-retained S20{sub NLS} is crucial for creating a functional small subunit.« less

Mapping evidence of interventions and strategies to bridge the gap in the implementation of the prevention of mother-to-child transmission of HIV programme policy in sub-Saharan countries: A scoping review.

PubMed

Ngidi, Wilbroda H; Naidoo, Joanne R; Ncama, Busisiwe P; Luvuno, Zamasomi P B; Mashamba-Thompson, Tivani P

2017-05-29

Prevention of mother-to-child transmission (PMTCT) of HIV is a life-saving public health intervention. Sub-Saharan African (SSA) countries have made significant progress in the programme, but little is known about the strategies used by them to eliminate mother-to-child transmission of HIV. To map evidence of strategies and interventions employed by SSA in bridging the implementation gap in the rapidly changing PMTCT of HIV programme policy. Electronic search of the databases MEDLINE, PubMed and SABINET for articles published in English between 2001 and August 2016. Key words included 'Sub-Saharan African countries', 'implementation strategies', 'interventions to bridge implementation gap', 'prevention of mother-to-child transmission of HIV' and 'closing implementation gap'. Of a total of 743 articles, 25 articles that met the inclusion criteria were included in the study. Manual content analysis resulted in the identification of three categories of strategies: (1) health system (referral systems, integration of services, supportive leadership, systematic quality-improvement approaches that vigorously monitors programme performance); (2) health service delivery (task shifting, networking, shared platform for learning, local capacity building, supportive supervision); as well as (3) community-level strategies (community health workers, technology use - mHealth, family-centred approaches, male involvement, culturally appropriate interventions). There are strategies that exist in SSA countries. Future research should examine multifaceted scientific models to prioritise the highest impact and be evaluated for effectiveness and efficiency.

A Far-ultraviolet Fluorescent Molecular Hydrogen Emission Map of the Milky Way Galaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jo, Young-Soo; Min, Kyoung-Wook; Seon, Kwang-Il

We present the far-ultraviolet (FUV) fluorescent molecular hydrogen (H{sub 2}) emission map of the Milky Way Galaxy obtained with FIMS/SPEAR covering ∼76% of the sky. The extinction-corrected intensity of the fluorescent H{sub 2} emission has a strong linear correlation with the well-known tracers of the cold interstellar medium (ISM), including color excess E(B–V) , neutral hydrogen column density N (H i), and H α emission. The all-sky H{sub 2} column density map was also obtained using a simple photodissociation region model and interstellar radiation fields derived from UV star catalogs. We estimated the fraction of H{sub 2} ( f {submore » H2}) and the gas-to-dust ratio (GDR) of the diffuse ISM. The f {sub H2} gradually increases from <1% at optically thin regions where E(B–V) < 0.1 to ∼50% for E(B–V)  = 3. The estimated GDR is ∼5.1 × 10{sup 21} atoms cm{sup −2} mag{sup −1}, in agreement with the standard value of 5.8 × 10{sup 21} atoms cm{sup −2} mag{sup −1}.« less

Superparamagnetic iron oxide polyacrylic acid coated γ-Fe{sub 2}O{sub 3} nanoparticles do not affect kidney function but cause acute effect on the cardiovascular function in healthy mice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iversen, Nina K., E-mail: nina.iversen@biology.au.dk; Interdisciplinary Nanoscience Center, Aarhus University; Frische, Sebastian

This study describes the distribution of intravenously injected polyacrylic acid (PAA) coated γ-Fe{sub 2}O{sub 3} NPs (10 mg kg{sup −1}) at the organ, cellular and subcellular levels in healthy BALB/cJ mice and in parallel addresses the effects of NP injection on kidney function, blood pressure and vascular contractility. Magnetic resonance imaging (MRI) and transmission electron microscopy (TEM) showed accumulation of NPs in the liver within 1 h after intravenous infusion, accommodated by intracellular uptake in endothelial and Kupffer cells with subsequent intracellular uptake in renal cells, particularly the cytoplasm of the proximal tubule, in podocytes and mesangial cells. The renofunctionalmore » effects of NPs were evaluated by arterial acid–base status and measurements of glomerular filtration rate (GFR) after instrumentation with chronically indwelling catheters. Arterial pH was 7.46 ± 0.02 and 7.41 ± 0.02 in mice 0.5 h after injections of saline or NP, and did not change over the next 12 h. In addition, the injections of NP did not affect arterial PCO{sub 2} or [HCO{sub 3}{sup −}] either. Twenty-four and 96 h after NP injections, the GFR averaged 0.35 ± 0.04 and 0.35 ± 0.01 ml min{sup −1} g{sup −1}, respectively, values which were statistically comparable with controls (0.29 ± 0.02 and 0.33 ± 0.1 ml{sup –1} min{sup –1} 25 g{sup –1}). Mean arterial blood pressure (MAP) decreased 12–24 h after NP injections (111.1 ± 11.5 vs 123.0 ± 6.1 min{sup −1}) associated with a decreased contractility of small mesenteric arteries revealed by myography to characterize endothelial function. In conclusion, our study demonstrates that accumulation of superparamagnetic iron oxide nanoparticles does not affect kidney function in healthy mice but temporarily decreases blood pressure. -- Highlights: ► PAA coated γ-Fe{sub 2}O{sub 3} nanoparticles were injected intravenously into healthy mice. ► We examine the distribution and physiological effects of nanoparticle accumulation. ► No effects of accumulation in kidney on acid-base status or GFR. ► Acute hypotension associated with decreased contractility of small vessels. ► We demonstrate physiological effects of PAA γ-Fe{sub 2}O{sub 3} NP for medical purposes.« less

Mapping of reciprocal space of La{sub 0.30}CoO{sub 2} in 3D: Analysis of superstructure diffractions and intergrowths with Co{sub 3}O{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brázda, Petr, E-mail: brazda@fzu.cz; Palatinus, Lukáš; Klementová, Mariana

2015-07-15

We have used electron diffraction tomography and powder X-ray diffraction to elucidate the structural properties of layered cobaltate γ-La{sub 0.30}CoO{sub 2}. The structure consists of hexagonal sheets of edge-sharing CoO{sub 6} octahedra interleaved by lanthanum monolayers. The La{sup 3+} cations occupy only one third of available P2 sites, forming a 2-dimensional a√3×a√3 superstructure in a–b plane. The results show that there exists no order in the mutual relative shift between the neighbouring La interlayers within the a–b plane. This is manifested in the observed monotonous decrease of the diffracted intensity of the superstructure diffractions along c{sup ⁎} in both X-raymore » and electron diffraction data. The observed lack of stacking order differentiates the La{sub x}CoO{sub 2} from its Ca and Sr analogues where at least a partial stacking order of the cationic interlayers is manifested in experimental data published in literature. - Highlights: • We use electron diffraction tomography for reciprocal space mapping of La{sub 0.30}CoO{sub 2}. • We observed a complete disorder of the stacking of Lanthanum interlayers. • Co{sub 3}O{sub 4} intergrown with La{sub 0.30}CoO{sub 2} crystals brings about fake superstructure diffractions. • Twinning of Co{sub 3}O{sub 4} enhances the problem of fake superstructure diffractions.« less

Two-photon excited autofluorescence imaging of freshly isolated frog retinas.

PubMed

Lu, Rong-Wen; Li, Yi-Chao; Ye, Tong; Strang, Christianne; Keyser, Kent; Curcio, Christine A; Yao, Xin-Cheng

2011-06-01

The purpose of this study was to investigate cellular sources of autofluorescence signals in freshly isolated frog (Rana pipiens) retinas. Equipped with an ultrafast laser, a laser scanning two-photon excitation fluorescence microscope was employed for sub-cellular resolution examination of both sliced and flat-mounted retinas. Two-photon imaging of retinal slices revealed autofluorescence signals over multiple functional layers, including the photoreceptor layer (PRL), outer nuclear layer (ONL), outer plexiform layer (OPL), inner nuclear layer (INL), inner plexiform layer (IPL), and ganglion cell layer (GCL). Using flat-mounted retinas, depth-resolved imaging of individual retinal layers further confirmed multiple sources of autofluorescence signals. Cellular structures were clearly observed at the PRL, ONL, INL, and GCL. At the PRL, the autofluorescence was dominantly recorded from the intracellular compartment of the photoreceptors; while mixed intracellular and extracellular autofluorescence signals were observed at the ONL, INL, and GCL. High resolution autofluorescence imaging clearly revealed mosaic organization of rod and cone photoreceptors; and sub-cellular bright autofluorescence spots, which might relate to connecting cilium, was observed in the cone photoreceptors only. Moreover, single-cone and double-cone outer segments could be directly differentiated.

Optical monitoring of thermal effects in RPE during heating

NASA Astrophysics Data System (ADS)

Schuele, G.; Huie, Ph.; Yellachich, D.; Molnar, F. E.; O'Conell-Rodwell, C.; Vitkin, E.; Perelman, L. T.; Palanker, D.

2005-04-01

Fast and non-invasive detection of cellular stress is useful for fundamental research and practical applications in medicine and biology. Using Light Scattering Spectroscopy we extract information about changes in refractive index and size of the cellular organelles. Particle sizes down to 50nm in diameter can be detected using light within the spectral range of 450-850 nm. We monitor the heat-induced sub-cellular structural changes in human RPE cells and, for comparison, in transfected NIH-3T3 cells which express luciferase linked to the heat shock protein (HSP). Using inverse light scattering fitting algorithm, we reconstruct the size distribution of the sub-micron organelles from the light scattering spectrum. The most significant (up to 70%) and rapid (20sec) temperature-related changes can be linked to an increase of refractive index of the 160nm sized mitochondria. The start of this effect coincides with the onset of HSP expression. This technique provides an insight into metabolic processes within organelles larger than 50nm without exogenous staining and opens doors for non-invasive real-time assessment of cellular stress, which can be used for monitoring of retinal laser treatments like transpupillary thermo therapy or PDT.

Imaging interfacial electrical transport in graphene–MoS{sub 2} heterostructures with electron-beam-induced-currents

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, E. R., E-mail: ewhite@physics.ucla.edu; Kerelsky, Alexander; Hubbard, William A.

2015-11-30

Heterostructure devices with specific and extraordinary properties can be fabricated by stacking two-dimensional crystals. Cleanliness at the inter-crystal interfaces within a heterostructure is crucial for maximizing device performance. However, because these interfaces are buried, characterizing their impact on device function is challenging. Here, we show that electron-beam induced current (EBIC) mapping can be used to image interfacial contamination and to characterize the quality of buried heterostructure interfaces with nanometer-scale spatial resolution. We applied EBIC and photocurrent imaging to map photo-sensitive graphene-MoS{sub 2} heterostructures. The EBIC maps, together with concurrently acquired scanning transmission electron microscopy images, reveal how a device's photocurrentmore » collection efficiency is adversely affected by nanoscale debris invisible to optical-resolution photocurrent mapping.« less

Schematic microscopic approach to the description of M1 transitions between mixed-symmetry and fully symmetric collective states in {gamma}-soft nuclei based on RPA-IBM boson mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jolos, R. V.; Shirikova, N. Yu.; Voronov, V. V.

A schematic microscopic method is developed to calculate the M1 transition probabilities between the mixed-symmetry and the fully symmetric states in {gamma}-soft nuclei. The method is based on the random-phase approximation-interacting boson model (RPA-IBM) boson mapping of the most collective isoscalar boson. All other boson modes with higher excitation energies, including the mixed-symmetry boson, are described in the framework of RPA. As an example the M1 transition probabilities are calculated for the {sup 124-134}Xe isotopes and compared with the experimental data. The results agree well with the data for the ratio B(M1;1{sub ms}{sup +}{yields}2{sub 2}{sup +})/B(M1;1{sub ms}{sup +}{yields}0{sub 1}{sup +}).more » However, the calculated ratio B(M1;2{sub ms}{sup +}{yields}2{sub 1}{sup +})/B(M1;1{sub ms}{sup +}{yields}0{sub 1}{sup +}) shows a significantly weaker dependence on the mass number than the experimental data.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Zhichen; Li, Di; Qian, Lei

We present 2.5-square-degree C{sub 2}H N = 1–0 and N{sub 2}H{sup +} J = 1–0 maps of the ρ Ophiuchi molecular cloud complex. These are the first large-scale maps of the ρ Ophiuchi molecular cloud complex with these two tracers. The C{sub 2}H emission is spatially more extended than the N{sub 2}H{sup +} emission. One faint N{sub 2}H{sup +} clump, Oph-M, and one C{sub 2}H ring, Oph-RingSW, are identified for the first time. The observed C{sub 2}H-to-N{sub 2}H{sup +} abundance ratio ([C{sub 2}H]/[N{sub 2}H{sup +}]) varies between 5 and 110. We modeled the C{sub 2}H and N{sub 2}H{sup +} abundancesmore » with 1D chemical models, which show a clear decline of [C{sub 2}H]/[N{sub 2}H{sup +}] with chemical age. Such an evolutionary trend is little affected by temperatures when they are below 40 K. At high density ( n {sub H} > 10{sup 5} cm{sup −3}), however, the time it takes for the abundance ratio to drop at least one order of magnitude becomes less than the dynamical time (e.g., turbulence crossing time of ∼10{sup 5} yr). The observed [C{sub 2}H]/[N{sub 2}H{sup +}] difference between L1688 and L1689 can be explained by L1688 having chemically younger gas in relatively less dense regions. The observed [C{sub 2}H]/[N{sub 2}H{sup +}] values are the results of time evolution, accelerated at higher densities. For the relatively low density regions in L1688 where only C{sub 2}H emission was detected, the gas should be chemically younger.« less

Raman microscopy of individual living human embryonic stem cells

NASA Astrophysics Data System (ADS)

Novikov, S. M.; Beermann, J.; Bozhevolnyi, S. I.; Harkness, L. M.; Kassem, M.

2010-04-01

We demonstrate the possibility of mapping the distribution of different biomolecules in living human embryonic stem cells grown on glass substrates, without the need for fluorescent markers. In our work we improve the quality of measurements by finding a buffer that gives low fluorescence, growing cells on glass substrates (whose Raman signals are relatively weak compared to that of the cells) and having the backside covered with gold to improve the image contrast under direct white light illumination. The experimental setup used for Raman microscopy is the commercially available confocal scanning Raman microscope (Alpha300R) from Witec and sub-μm spatially resolved Raman images were obtained using a 532 nm excitation wavelength.

ALMA MEASUREMENTS OF THE HNC AND HC{sub 3}N DISTRIBUTIONS IN TITAN'S ATMOSPHERE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cordiner, M. A.; Nixon, C. A.; Serigano, J.

2014-11-10

We present spectrally and spatially resolved maps of HNC and HC{sub 3}N emission from Titan's atmosphere, obtained using the Atacama Large Millimeter/submillimeter Array on 2013 November 17. These maps show anisotropic spatial distributions for both molecules, with resolved emission peaks in Titan's northern and southern hemispheres. The HC{sub 3}N maps indicate enhanced concentrations of this molecule over the poles, consistent with previous studies of Titan's photochemistry and atmospheric circulation. Differences between the spectrally integrated flux distributions of HNC and HC{sub 3}N show that these species are not co-spatial. The observed spectral line shapes are consistent with HNC being concentrated predominantlymore » in the mesosphere and above (at altitudes z ≳ 400 km), whereas HC{sub 3}N is abundant at a broader range of altitudes (z ≈ 70-600 km). From spatial variations in the HC{sub 3}N line profile, the locations of the HC{sub 3}N emission peaks are shown to be variable as a function of altitude. The peaks in the integrated emission from HNC and the line core (upper atmosphere) component of HC{sub 3}N (at z ≳ 300 km) are found to be asymmetric with respect to Titan's polar axis, indicating that the mesosphere may be more longitudinally variable than previously thought. The spatially integrated HNC and HC{sub 3}N spectra are modeled using the NEMESIS planetary atmosphere code and the resulting best-fitting disk-averaged vertical mixing ratio profiles are found to be in reasonable agreement with previous measurements for these species. Vertical column densities of the best-fitting gradient models for HNC and HC{sub 3}N are 1.9 × 10{sup 13} cm{sup –2} and 2.3 × 10{sup 14} cm{sup –2}, respectively.« less

Color image encryption based on hybrid hyper-chaotic system and cellular automata

NASA Astrophysics Data System (ADS)

Yaghouti Niyat, Abolfazl; Moattar, Mohammad Hossein; Niazi Torshiz, Masood

2017-03-01

This paper proposes an image encryption scheme based on Cellular Automata (CA). CA is a self-organizing structure with a set of cells in which each cell is updated by certain rules that are dependent on a limited number of neighboring cells. The major disadvantages of cellular automata in cryptography include limited number of reversal rules and inability to produce long sequences of states by these rules. In this paper, a non-uniform cellular automata framework is proposed to solve this problem. This proposed scheme consists of confusion and diffusion steps. In confusion step, the positions of the original image pixels are replaced by chaos mapping. Key image is created using non-uniform cellular automata and then the hyper-chaotic mapping is used to select random numbers from the image key for encryption. The main contribution of the paper is the application of hyper chaotic functions and non-uniform CA for robust key image generation. Security analysis and experimental results show that the proposed method has a very large key space and is resistive against noise and attacks. The correlation between adjacent pixels in the encrypted image is reduced and the amount of entropy is equal to 7.9991 which is very close to 8 which is ideal.

An assessment of the quality of care for children in eighteen randomly selected district and sub-district hospitals in Bangladesh

PubMed Central

2012-01-01

Background Quality hospital care is important in ensuring that the needs of severely ill children are met to avert child mortality. However, the quality of hospital care for children in developing countries has often been found poor. As the first step of a country road map for improving hospital care for children, we assessed the baseline situation with respect to the quality of care provided to children under-five years age in district and sub-district level hospitals in Bangladesh. Methods Using adapted World Health Organization (WHO) hospital assessment tools and standards, an assessment of 18 randomly selected district (n=6) and sub-district (n=12) hospitals was undertaken. Teams of trained assessors used direct case observation, record review, interviews, and Management Information System (MIS) data to assess the quality of clinical case management and monitoring; infrastructure, processes and hospital administration; essential hospital and laboratory supports, drugs and equipment. Results Findings demonstrate that the overall quality of care provided in these hospitals was poor. No hospital had a functioning triage system to prioritise those children most in need of immediate care. Laboratory supports and essential equipment were deficient. Only one hospital had all of the essential drugs for paediatric care. Less than a third of hospitals had a back-up power supply, and just under half had functioning arrangements for safe-drinking water. Clinical case management was found to be sub-optimal for prevalent illnesses, as was the quality of neonatal care. Conclusion Action is needed to improve the quality of paediatric care in hospital settings in Bangladesh, with a particular need to invest in improving newborn care. PMID:23268650

Accurate Mobile Urban Mapping via Digital Map-Based SLAM †

PubMed Central

Roh, Hyunchul; Jeong, Jinyong; Cho, Younggun; Kim, Ayoung

2016-01-01

This paper presents accurate urban map generation using digital map-based Simultaneous Localization and Mapping (SLAM). Throughout this work, our main objective is generating a 3D and lane map aiming for sub-meter accuracy. In conventional mapping approaches, achieving extremely high accuracy was performed by either (i) exploiting costly airborne sensors or (ii) surveying with a static mapping system in a stationary platform. Mobile scanning systems recently have gathered popularity but are mostly limited by the availability of the Global Positioning System (GPS). We focus on the fact that the availability of GPS and urban structures are both sporadic but complementary. By modeling both GPS and digital map data as measurements and integrating them with other sensor measurements, we leverage SLAM for an accurate mobile mapping system. Our proposed algorithm generates an efficient graph SLAM and achieves a framework running in real-time and targeting sub-meter accuracy with a mobile platform. Integrated with the SLAM framework, we implement a motion-adaptive model for the Inverse Perspective Mapping (IPM). Using motion estimation derived from SLAM, the experimental results show that the proposed approaches provide stable bird’s-eye view images, even with significant motion during the drive. Our real-time map generation framework is validated via a long-distance urban test and evaluated at randomly sampled points using Real-Time Kinematic (RTK)-GPS. PMID:27548175

Common genetic variation drives molecular heterogeneity in human iPSCs.

PubMed

Kilpinen, Helena; Goncalves, Angela; Leha, Andreas; Afzal, Vackar; Alasoo, Kaur; Ashford, Sofie; Bala, Sendu; Bensaddek, Dalila; Casale, Francesco Paolo; Culley, Oliver J; Danecek, Petr; Faulconbridge, Adam; Harrison, Peter W; Kathuria, Annie; McCarthy, Davis; McCarthy, Shane A; Meleckyte, Ruta; Memari, Yasin; Moens, Nathalie; Soares, Filipa; Mann, Alice; Streeter, Ian; Agu, Chukwuma A; Alderton, Alex; Nelson, Rachel; Harper, Sarah; Patel, Minal; White, Alistair; Patel, Sharad R; Clarke, Laura; Halai, Reena; Kirton, Christopher M; Kolb-Kokocinski, Anja; Beales, Philip; Birney, Ewan; Danovi, Davide; Lamond, Angus I; Ouwehand, Willem H; Vallier, Ludovic; Watt, Fiona M; Durbin, Richard; Stegle, Oliver; Gaffney, Daniel J

2017-06-15

Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells.

Common genetic variation drives molecular heterogeneity in human iPSCs

PubMed Central

Leha, Andreas; Afzal, Vackar; Alasoo, Kaur; Ashford, Sofie; Bala, Sendu; Bensaddek, Dalila; Casale, Francesco Paolo; Culley, Oliver J; Danecek, Petr; Faulconbridge, Adam; Harrison, Peter W; Kathuria, Annie; McCarthy, Davis; McCarthy, Shane A; Meleckyte, Ruta; Memari, Yasin; Moens, Nathalie; Soares, Filipa; Mann, Alice; Streeter, Ian; Agu, Chukwuma A; Alderton, Alex; Nelson, Rachel; Harper, Sarah; Patel, Minal; White, Alistair; Patel, Sharad R; Clarke, Laura; Halai, Reena; Kirton, Christopher M; Kolb-Kokocinski, Anja; Beales, Philip; Birney, Ewan; Danovi, Davide; Lamond, Angus I; Ouwehand, Willem H; Vallier, Ludovic; Watt, Fiona M; Durbin, Richard

2017-01-01

Induced pluripotent stem cell (iPSC) technology has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterisation of many existing iPSC lines limits their potential use for research and therapy. Here, we describe the systematic generation, genotyping and phenotyping of 711 iPSC lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative (HipSci: http://www.hipsci.org). Our study outlines the major sources of genetic and phenotypic variation in iPSCs and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPSC phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of rare, genomic copy number mutations that are repeatedly observed in iPSC reprogramming and present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells. PMID:28489815

Force-activatable coating enables high-resolution cellular force imaging directly on regular cell culture surfaces.

PubMed

Sarkar, Anwesha; Zhao, Yuanchang; Wang, Yongliang; Wang, Xuefeng

2018-06-25

Integrin-transmitted cellular forces are crucial mechanical signals regulating a vast range of cell functions. Although various methods have been developed to visualize and quantify cellular forces at the cell-matrix interface, a method with high performance and low technical barrier is still in demand. Here we developed a force-activatable coating (FAC), which can be simply coated on regular cell culture apparatus' surfaces by physical adsorption, and turn these surfaces to force reporting platforms that enable cellular force mapping directly by fluorescence imaging. The FAC molecule consists of an adhesive domain for surface coating and a force-reporting domain which can be activated to fluoresce by integrin molecular tension. The tension threshold required for FAC activation is tunable in 10-60 piconewton (pN), allowing the selective imaging of cellular force contributed by integrin tension at different force levels. We tested the performance of two FACs with tension thresholds of 12 and 54 pN (nominal values), respectively, on both glass and polystyrene surfaces. Cellular forces were successfully mapped by fluorescence imaging on all the surfaces. FAC-coated surfaces also enable co-imaging of cellular forces and cell structures in both live cells and immunostained cells, therefore opening a new avenue for the study of the interplay of force and structure. We demonstrated the co-imaging of integrin tension and talin clustering in live cells, and concluded that talin clustering always occurs before the generation of integrin tension above 54 pN, reinforcing the notion that talin is an important adaptor protein for integrin tension transmission. Overall, FAC provides a highly convenient approach that is accessible to general biological laboratories for the study of cellular forces with high sensitivity and resolution, thus holding the potential to greatly boost the research of cell mechanobiology.

Mission Adaptive Uas Capabilities for Earth Science and Resource Assessment

NASA Astrophysics Data System (ADS)

Dunagan, S.; Fladeland, M.; Ippolito, C.; Knudson, M.; Young, Z.

2015-04-01

Unmanned aircraft systems (UAS) are important assets for accessing high risk airspace and incorporate technologies for sensor coordination, onboard processing, tele-communication, unconventional flight control, and ground based monitoring and optimization. These capabilities permit adaptive mission management in the face of complex requirements and chaotic external influences. NASA Ames Research Center has led a number of Earth science remote sensing missions directed at the assessment of natural resources and here we describe two resource mapping problems having mission characteristics requiring a mission adaptive capability extensible to other resource assessment challenges. One example involves the requirement for careful control over solar angle geometry for passive reflectance measurements. This constraint exists when collecting imaging spectroscopy data over vegetation for time series analysis or for the coastal ocean where solar angle combines with sea state to produce surface glint that can obscure the signal. Furthermore, the primary flight control imperative to minimize tracking error should compromise with the requirement to minimize aircraft motion artifacts in the spatial measurement distribution. A second example involves mapping of natural resources in the Earth's crust using precision magnetometry. In this case the vehicle flight path must be oriented to optimize magnetic flux gradients over a spatial domain having continually emerging features, while optimizing the efficiency of the spatial mapping task. These requirements were highlighted in recent Earth Science missions including the OCEANIA mission directed at improving the capability for spectral and radiometric reflectance measurements in the coastal ocean, and the Surprise Valley Mission directed at mapping sub-surface mineral composition and faults, using high-sensitivity magnetometry. This paper reports the development of specific aircraft control approaches to incorporate the unusual and demanding requirements to manage solar angle, aircraft attitude and flight path orientation, and efficient (directly geo-rectified) surface and sub-surface mapping, including the near-time optimization of these sometimes competing requirements.

Respiratory syncytial virus increases lung cellular bioenergetics in neonatal C57BL/6 mice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alsuwaidi, Ahmed R., E-mail: alsuwaidia@uaeu.ac.ae; Albawardi, Alia, E-mail: alia.albawardi@uaeu.ac.ae; Almarzooqi, Saeeda, E-mail: saeeda.almarzooqi@uaeu.ac.ae

2014-04-15

We have previously reported that lung cellular bioenergetics (cellular respiration and ATP) increased in 4–10 week-old BALB/c mice infected with respiratory syncytial virus (RSV). This study examined the kinetics and changes in cellular bioenergetics in ≤2-week-old C57BL/6 mice following RSV infection. Mice (5–14 days old) were inoculated intranasally with RSV and the lungs were examined on days 1–10 post-infection. Histopathology and electron microscopy revealed preserved pneumocyte architectures and organelles. Increased lung cellular bioenergetics was noted from days 1–10 post-infection. Cellular GSH remained unchanged. These results indicate that the increased lung cellular respiration (measured by mitochondrial O{sub 2} consumption) and ATPmore » following RSV infection is independent of either age or genetic background of the host. - Highlights: • RSV infection increases lung cellular respiration and ATP in neonatal C57BL/6 mice. • Increased lung cellular bioenergetics is a biomarker of RSV infection. • Lung cellular glutathione remains unchanged in RSV infection.« less

Prospective Elementary Science Teachers' Understanding of Photosynthesis and Cellular Respiration in the Context of Multiple Biological Levels as Nested Systems

ERIC Educational Resources Information Center

Akçay, Süleyman

2017-01-01

In this study, Turkish prospective elementary science teachers' understanding of photosynthesis and cellular respiration has been analysed within the contexts of ecosystem knowledge, organism knowledge and interconnection knowledge (IK). In the analysis, concept maps developed by 74 prospective teachers were used. The study was carried out with…

Radiological Operations Support Specialist (ROSS) Pilot Course Summary and Recommendations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alai, M.; Askin, A.; Buddemeier, B.

In support of the Department of Homeland Security / Science and Technology Directorate’s (DHS/S&T) creation of a new position called the Radiological Operations Support Specialist (ROSS), Lawrence Livermore National Laboratory (LLNL) in Sub-task 1.1 and 1.2 has assisted in the development of the ROSS skills, knowledge, and abilities (SKAs); identified potentially relevant training; cross-mapped the training to the SKAs; and identified gaps in the training related to the SKAs, as well as their respective level of training knowledge - current versus desired. In the follow on task, Sub-task 1.3, a 5 day ROSS Pilot Training course was developed to fillmore » the priority gaps identified in Sub-Task 1.2. Additionally, in Sub-Task 1.5, LLNL has performed a gap analysis of electronic tools, handbooks, and job-aides currently available to the ROSS and developed recommendations for additional and next generation tools to ensure the operational effectiveness of the ROSS position. This document summarizes the feedback received from the instructors and pilot course observers on what worked in the course and what could be improved as well as an assessment of the Pre- and Post-Test administered to the students.« less

Predicting multicellular function through multi-layer tissue networks

PubMed Central

Zitnik, Marinka; Leskovec, Jure

2017-01-01

Abstract Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here, we present OhmNet, a hierarchy-aware unsupervised node feature learning approach for multi-layer networks. We build a multi-layer network, where each layer represents molecular interactions in a different human tissue. OhmNet then automatically learns a mapping of proteins, represented as nodes, to a neural embedding-based low-dimensional space of features. OhmNet encourages sharing of similar features among proteins with similar network neighborhoods and among proteins activated in similar tissues. The algorithm generalizes prior work, which generally ignores relationships between tissues, by modeling tissue organization with a rich multiscale tissue hierarchy. We use OhmNet to study multicellular function in a multi-layer protein interaction network of 107 human tissues. In 48 tissues with known tissue-specific cellular functions, OhmNet provides more accurate predictions of cellular function than alternative approaches, and also generates more accurate hypotheses about tissue-specific protein actions. We show that taking into account the tissue hierarchy leads to improved predictive power. Remarkably, we also demonstrate that it is possible to leverage the tissue hierarchy in order to effectively transfer cellular functions to a functionally uncharacterized tissue. Overall, OhmNet moves from flat networks to multiscale models able to predict a range of phenotypes spanning cellular subsystems. Availability and implementation: Source code and datasets are available at http://snap.stanford.edu/ohmnet. Contact: jure@cs.stanford.edu PMID:28881986

Deep neural mapping support vector machines.

PubMed

Li, Yujian; Zhang, Ting

2017-09-01

The choice of kernel has an important effect on the performance of a support vector machine (SVM). The effect could be reduced by NEUROSVM, an architecture using multilayer perceptron for feature extraction and SVM for classification. In binary classification, a general linear kernel NEUROSVM can be theoretically simplified as an input layer, many hidden layers, and an SVM output layer. As a feature extractor, the sub-network composed of the input and hidden layers is first trained together with a virtual ordinary output layer by backpropagation, then with the output of its last hidden layer taken as input of the SVM classifier for further training separately. By taking the sub-network as a kernel mapping from the original input space into a feature space, we present a novel model, called deep neural mapping support vector machine (DNMSVM), from the viewpoint of deep learning. This model is also a new and general kernel learning method, where the kernel mapping is indeed an explicit function expressed as a sub-network, different from an implicit function induced by a kernel function traditionally. Moreover, we exploit a two-stage procedure of contrastive divergence learning and gradient descent for DNMSVM to jointly training an adaptive kernel mapping instead of a kernel function, without requirement of kernel tricks. As a whole of the sub-network and the SVM classifier, the joint training of DNMSVM is done by using gradient descent to optimize the objective function with the sub-network layer-wise pre-trained via contrastive divergence learning of restricted Boltzmann machines. Compared to the separate training of NEUROSVM, the joint training is a new algorithm for DNMSVM to have advantages over NEUROSVM. Experimental results show that DNMSVM can outperform NEUROSVM and RBFSVM (i.e., SVM with the kernel of radial basis function), demonstrating its effectiveness. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sub-cellular distribution and translocation of TRP channels.

PubMed

Toro, Carlos A; Arias, Luis A; Brauchi, Sebastian

2011-01-01

Cellular electrical activity is the result of a highly complex processes that involve the activation of ion channel proteins. Ion channels make pores on cell membranes that rapidly transit between conductive and non-conductive states, allowing different ions to flow down their electrochemical gradients across cell membranes. In the case of neuronal cells, ion channel activity orchestrates action potentials traveling through axons, enabling electrical communication between cells in distant parts of the body. Somatic sensation -our ability to feel touch, temperature and noxious stimuli- require ion channels able to sense and respond to our peripheral environment. Sensory integration involves the summing of various environmental cues and their conversion into electrical signals. Members of the Transient Receptor Potential (TRP) family of ion channels have emerged as important mediators of both cellular sensing and sensory integration. The regulation of the spatial and temporal distribution of membrane receptors is recognized as an important mechanism for controlling the magnitude of the cellular response and the time scale on which cellular signaling occurs. Several studies have shown that this mechanism is also used by TRP channels to modulate cellular response and ultimately fulfill their physiological function as sensors. However, the inner-working of this mode of control for TRP channels remains poorly understood. The question of whether TRPs intrinsically regulate their own vesicular trafficking or weather the dynamic regulation of TRP channel residence on the cell surface is caused by extrinsic changes in the rates of vesicle insertion or retrieval remain open. This review will examine the evidence that sub-cellular redistribution of TRP channels plays an important role in regulating their activity and explore the mechanisms that control the trafficking of vesicles containing TRP channels.

Geometric accuracy of LANDSAT-4 MSS image data

NASA Technical Reports Server (NTRS)

Welch, R.; Usery, E. L.

1983-01-01

Analyses of the LANDSAT-4 MSS image data of North Georgia provided by the EDC in CCT-p formats reveal that errors of approximately + or - 30 m in the raw data can be reduced to about + or - 55 m based on rectification procedures involving the use of 20 to 30 well-distributed GCPs and 2nd or 3rd degree polynomial equations. Higher order polynomials do not appear to improve the rectification accuracy. A subscene area of 256 x 256 pixels was rectified with a 1st degree polynomial to yield an RMSE sub xy value of + or - 40 m, indicating that USGS 1:24,000 scale quadrangle-sized areas of LANDSAT-4 data can be fitted to a map base with relatively few control points and simple equations. The errors in the rectification process are caused by the spatial resolution of the MSS data, by errors in the maps and GCP digitizing process, and by displacements caused by terrain relief. Overall, due to the improved pointing and attitude control of the spacecraft, the geometric quality of the LANDSAT-4 MSS data appears much improved over that of LANDSATS -1, -2 and -3.

A novel 3D micron-scale DPTV (Defocused Particle Tracking Velocimetry) and its applications in microfluidic devices

NASA Astrophysics Data System (ADS)

Roberts, John

2005-11-01

The rapid advancements in micro/nano biotechnology demand quantitative tools for characterizing microfluidic flows in lab-on-a-chip applications, validation of computational results for fully 3D flows in complex micro-devices, and efficient observation of cellular dynamics in 3D. We present a novel 3D micron-scale DPTV (defocused particle tracking velocimetry) that is capable of mapping out 3D Lagrangian, as well as 3D Eulerian velocity flow fields at sub-micron resolution and with one camera. The main part of the imaging system is an epi-fluorescent microscope (Olympus IX 51), and the seeding particles are fluorescent particles with diameter range 300nm - 10um. A software package has been developed for identifying (x,y,z,t) coordinates of the particles using the defocused images. Using the imaging system, we successfully mapped the pressure driven flow fields in microfluidic channels. In particular, we measured the Laglangian flow fields in a microfluidic channel with a herring bone pattern at the bottom, the later is used to enhance fluid mixing in lateral directions. The 3D particle tracks revealed the flow structure that has only been seen in numerical computation. This work is supported by the National Science Foundation (CTS - 0514443), the Nanobiotechnology Center at Cornell, and The New York State Center for Life Science Enterprise.

Evaluation and optimization of the extended information process unit (E-IPU) validation module integrating the sysmex flag systems and the recommendations of the French-speaking cellular hematology group (GFHC).

PubMed

Cornet, Edouard; Mullier, François; Despas, Noemie; Jacqmin, Hugues; Geara, Carole; Boubaya, Marouane; Chatelain, Bernard; Troussard, Xavier

2016-10-01

The French-Speaking Cellular Haematology Group (GFHC) recently published criteria for microscopic analysis of a blood smears when a hemogram is requested. In order to evaluate and improve these recommendations using an XN (Sysmex) analyzer, we assessed 31,836 samples categorized into two sub-groups of patients either receiving or not receiving care in the clinical hematology/oncology departments of two university hospitals. By combining the manufacturer's recommendations and the GFHC recommendations, 21.3% of samples had a positive review flag in phase 1 of our study (17,991 samples). In phase 2 (13,845 samples), increasing the immature granulocytes (IG) percentage from 5-10% as a review trigger threshold, and ignoring slides with isolated flags 'PLT HIGH' (thrombocytosis) or 'MCV LOW' (microcytosis) or 'Blast/Abn Lymph and Atypical Lymph' (blast cells/abnormal lymphocytes and atypical lymphocytes) (in the absence of abnormal cells on a previous blood smear within 72 h), enabled us to significantly reduce the number of slides reviewed from 21.3-15.0% (p < 0.0001), without loss of clinical value. This decrease occurred in both sub-groups (hematology 48.7-38.0%, non-hematology 18.3-11.7%, p < 0.0001). In conclusion, the application of the GFHC criteria adapted to XN analyzers has enabled us to optimize the hematology laboratory processes, and thus reduce the production costs and the turnaround time of hemogram results.

Biophotonics for imaging and cell manipulation: quo vadis?

NASA Astrophysics Data System (ADS)

Serafetinides, Alexandros A.; Makropoulou, Mirsini; Kotsifaki, Domna G.; Tsigaridas, Giorgos

2016-01-01

As one of the major health problems for mankind is cancer, any development for the early detection and effective treatment of cancer is crucial to saving lives. Worldwide, the dream for the anti-cancer procedure of attack is the development of a safe and efficient early diagnosis technique, the so called "optical biopsy". As early diagnosis of cancer is associated with improved prognosis, several laser based optical diagnostic methods were developed to enable earlier, non-invasive detection of human cancer, as Laser Induced Fluorescence spectroscopy (LIFs), Diffuse Reflectance spectroscopy (DRs), confocal microscopy, and Optical Coherence Tomography (OCT). Among them, Optical Coherence Tomography (OCT) imaging is considered to be a useful tool to differentiate healthy from malignant (e.g. basal cell carcinoma, squamous cell carcinoma) skin tissue. If the demand is to perform imaging in sub-tissular or even sub-cellular level, optical tweezers and atomic force microscopy have enabled the visualization of molecular events underlying cellular processes in live cells, as well as the manipulation and characterization of microscale or even nanoscale biostructures. In this work, we will present the latest advances in the field of laser imaging and manipulation techniques, discussing some representative experimental data focusing on the 21th century biophotonics roadmap of novel diagnostic and therapeutical approaches. As an example of a recently discussed health and environmental problem, we studied both experimentally and theoretically the optical trapping forces exerted on yeast cells and modified with estrogen-like acting compounds yeast cells, suspended in various buffer media.

Anticancer Activity of Chloroform Extract and Sub-fractions of Nepeta deflersiana on Human Breast and Lung Cancer Cells: An In vitro Cytotoxicity Assessment.

PubMed

Al-Oqail, Mai M; Al-Sheddi, Ebtesam S; Siddiqui, Maqsood A; Musarrat, Javed; Al-Khedhairy, Abdulaziz A; Farshori, Nida N

2015-10-01

Cancer is one of the major causes of death worldwide. The plant-derived natural products have received considerable attention in recent years due to their diverse pharmacological properties including anticancer effects. Nepeta deflersiana (ND) is used in the folk medicine as antiseptic, carminative, antimicrobial, antioxidant, and for treating rheumatic disorders. However, the anticancer activity of ND chloroform extract has not been explored so far. The present study was aimed to investigate the anticancer activities of chloroform Nepeta deflersiana extract and various sub-fractions (ND-1-ND-15) of ND against human breast cancer cells (MCF-7) and human lung cancer cells (A-549). The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide and neutral red uptake assays, and cellular morphological alterations using phase contrast light microscope were studied. Cells were exposed with 10-1000 μg/ml of sub-fractions of ND for 24 h. Results showed that selected sub-fractions of the chloroform extract significantly reduced the cell viability of MCF-7 and A-549 cells, and altered the cellular morphology in a concentration-dependent manner. Among the sub-fractions, ND-10 fraction showed relatively higher cytotoxicity compared to other fractions whereas, ND-1 did not cause any cytotoxicity even at higher concentrations. The A-549 cells were found to be more sensitive to growth inhibition by all the extracts as compared to the MCF-7 cells. The present study provides preliminary screening of anticancer activities of chloroform extract and sub-fractions of ND, which can be further used for the development of a potential therapeutic anticancer agent. Nepeta deflersiana extract exhibit cytotoxicity and altered the cellular morphology. Sub-fractions of the chloroform extract of Nepeta deflersiana reduced the cell viability of MCF-7 and A-549 cells. Among the sub-fractions, ND-10 fraction showed relatively higher cytotoxicity. The A-549 cells were found to be more sensitive as compared to the MCF-7 cells. Abbreviations used: MTT: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide; NRU: Neutral red uptake; DMEM: Dulbecco's modified eagle medium; FBS: Fetal bovine serum; PBS: Phosphate buffer saline; DMSO: Dimethyl sulfoxide.

Land cover mapping at sub-pixel scales

NASA Astrophysics Data System (ADS)

Makido, Yasuyo Kato

One of the biggest drawbacks of land cover mapping from remotely sensed images relates to spatial resolution, which determines the level of spatial details depicted in an image. Fine spatial resolution images from satellite sensors such as IKONOS and QuickBird are now available. However, these images are not suitable for large-area studies, since a single image is very small and therefore it is costly for large area studies. Much research has focused on attempting to extract land cover types at sub-pixel scale, and little research has been conducted concerning the spatial allocation of land cover types within a pixel. This study is devoted to the development of new algorithms for predicting land cover distribution using remote sensory imagery at sub-pixel level. The "pixel-swapping" optimization algorithm, which was proposed by Atkinson for predicting sub-pixel land cover distribution, is investigated in this study. Two limitations of this method, the arbitrary spatial range value and the arbitrary exponential model of spatial autocorrelation, are assessed. Various weighting functions, as alternatives to the exponential model, are evaluated in order to derive the optimum weighting function. Two different simulation models were employed to develop spatially autocorrelated binary class maps. In all tested models, Gaussian, Exponential, and IDW, the pixel swapping method improved classification accuracy compared with the initial random allocation of sub-pixels. However the results suggested that equal weight could be used to increase accuracy and sub-pixel spatial autocorrelation instead of using these more complex models of spatial structure. New algorithms for modeling the spatial distribution of multiple land cover classes at sub-pixel scales are developed and evaluated. Three methods are examined: sequential categorical swapping, simultaneous categorical swapping, and simulated annealing. These three methods are applied to classified Landsat ETM+ data that has been resampled to 210 meters. The result suggested that the simultaneous method can be considered as the optimum method in terms of accuracy performance and computation time. The case study employs remote sensing imagery at the following sites: tropical forests in Brazil and temperate multiple land mosaic in East China. Sub-areas for both sites are used to examine how the characteristics of the landscape affect the ability of the optimum technique. Three types of measurement: Moran's I, mean patch size (MPS), and patch size standard deviation (STDEV), are used to characterize the landscape. All results suggested that this technique could increase the classification accuracy more than traditional hard classification. The methods developed in this study can benefit researchers who employ coarse remote sensing imagery but are interested in detailed landscape information. In many cases, the satellite sensor that provides large spatial coverage has insufficient spatial detail to identify landscape patterns. Application of the super-resolution technique described in this dissertation could potentially solve this problem by providing detailed land cover predictions from the coarse resolution satellite sensor imagery.

Earlier Detection of Tumor Treatment Response Using Magnetic Resonance Diffusion Imaging with Oscillating Gradients

PubMed Central

Colvin, Daniel C.; Loveless, Mary E.; Does, Mark D.; Yue, Zou; Yankeelov, Thomas E.; Gore, John C.

2011-01-01

An improved method for detecting early changes in tumors in response to treatment, based on a modification of diffusion-weighted magnetic resonance imaging, has been demonstrated in an animal model. Early detection of therapeutic response in tumors is important both clinically and in pre-clinical assessments of novel treatments. Non-invasive imaging methods that can detect and assess tumor response early in the course of treatment, and before frank changes in tumor morphology are evident, are of considerable interest as potential biomarkers of treatment efficacy. Diffusion-weighted magnetic resonance imaging is sensitive to changes in water diffusion rates in tissues that result from structural variations in the local cellular environment, but conventional methods mainly reflect changes in tissue cellularity and do not convey information specific to micro-structural variations at sub-cellular scales. We implemented a modified imaging technique using oscillating gradients of the magnetic field for evaluating water diffusion rates over very short spatial scales that are more specific for detecting changes in intracellular structure that may precede changes in cellularity. Results from a study of orthotopic 9L gliomas in rat brains indicate that this method can detect changes as early as 24 hours following treatment with 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU), when conventional approaches do not find significant effects. These studies suggest that diffusion imaging using oscillating gradients may be used to obtain an earlier indication of treatment efficacy than previous magnetic resonance imaging methods. PMID:21190804

Photoelectron velocity-map imaging and theoretical studies of heteronuclear metal carbonyls MNi(CO){sub 3}{sup −} (M = Mg, Ca, Al)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Hua, E-mail: ljiang@dicp.ac.cn, E-mail: xiehua@dicp.ac.cn, E-mail: zctang@dicp.ac.cn; Zou, Jinghan; Yuan, Qinqin

2016-03-28

The heteronuclear metal carbonyl anions MNi(CO){sub 3}{sup −} (M = Mg, Ca, Al) have been investigated using photoelectron velocity-map imaging spectroscopy. Electron affinities of neutral MNi(CO){sub 3} (M = Mg, Ca, Al) are measured from the photoelectron spectra to be 1.064 ± 0.063, 1.050 ± 0.064, and 1.541 ± 0.040 eV, respectively. The C–O stretching mode in these three clusters is observed and the vibrational frequency is determined to be 2049, 2000, and 2041 cm{sup −1} for MgNi(CO){sub 3}, CaNi(CO){sub 3}, and AlNi(CO){sub 3}, respectively. Density functional theory calculations are carried out to elucidate the geometric and electronic structures and to aid the experimental assignments. Itmore » has been found that three terminal carbonyls are preferentially bonded to the nickel atom in these heterobinuclear nickel carbonyls MNi(CO){sub 3}{sup −1/0}, resulting in the formation of the Ni(CO){sub 3} motif. Ni remains the 18-electron configuration for MgNi(CO){sub 3} and CaNi(CO){sub 3} neutrals, but not for AlNi(CO){sub 3}. This is different from the homobinuclear nickel carbonyl Ni–Ni(CO){sub 3} with the involvement of three bridging ligands. Present findings would be helpful for understanding CO adsorption on alloy surfaces.« less

Mapping Ad Hoc Communications Network of a Large Number Fixed-Wing UAV Swarm

DTIC Science & Technology

2017-03-01

partitioned sub-swarms. The work covered in this thesis is to build a model of the NPS swarm’s communication network in ns-3 simulation software and use...partitioned sub- swarms. The work covered in this thesis is to build a model of the NPS swarm’s communication network in ns-3 simulation software and...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS MAPPING AD HOC COMMUNICATIONS NETWORK OF A LARGE NUMBER FIXED-WING UAV SWARM by Alexis

Confocal Endomicroscopy: Instrumentation and Medical Applications

PubMed Central

Jabbour, Joey M.; Saldua, Meagan A.; Bixler, Joel N.; Maitland, Kristen C.

2013-01-01

Advances in fiber optic technology and miniaturized optics and mechanics have propelled confocal endomicroscopy into the clinical realm. This high resolution, non-invasive imaging technology provides the ability to microscopically evaluate cellular and sub-cellular features in tissue in vivo by optical sectioning. Because many cancers originate in epithelial tissues accessible by endoscopes, confocal endomicroscopy has been explored to detect regions of possible neoplasia at an earlier stage by imaging morphological features in vivo that are significant in histopathologic evaluation. This technique allows real-time assessment of tissue which may improve diagnostic yield by guiding biopsy. Research and development continues to reduce the overall size of the imaging probe, increase the image acquisition speed, and improve resolution and field of view of confocal endomicroscopes. Technical advances will continue to enable application to less accessible organs and more complex systems in the body. Lateral and axial resolutions down to 0.5 μm and 3 μm, respectively, field of view as large as 800×450 μm, and objective lens and total probe outer diameters down to 350 μm and 1.25 mm, respectively, have been achieved. We provide a review of the historical developments of confocal imaging in vivo, the evolution of endomicroscope instrumentation, and the medical applications of confocal endomicroscopy. PMID:21994069

Evaluating Cellular Instrumentation on Rural Handpumps to Improve Service Delivery-A Longitudinal Study in Rural Rwanda.

PubMed

Nagel, Corey; Beach, Jack; Iribagiza, Chantal; Thomas, Evan A

2015-12-15

In rural sub-Saharan Africa, where handpumps are common, 10-67% are nonfunctional at any one time, and many never get repaired. Increased reliability requires improved monitoring and responsiveness of maintenance providers. In 2014, 181 cellular enabled water pump use sensors were installed in three provinces of Rwanda. In three arms, the nominal maintenance model was compared against a "best practice" circuit rider model, and an "ambulance" service model. In only the ambulance model was the sensor data available to the implementer, and used to dispatch technicians. The study ran for seven months in 2014-2015. In the study period, the nominal maintenance group had a median time to successful repair of approximately 152 days, with a mean per-pump functionality of about 68%. In the circuit rider group, the median time to successful repair was nearly 57 days, with a per-pump functionality mean of nearly 73%. In the ambulance service group, the successful repair interval was nearly 21 days with a functionality mean of nearly 91%. An indicative cost analysis suggests that the cost per functional pump per year is approximately similar between the three models. However, the benefits of reliable water service may justify greater focus on servicing models over installation models.

Analyzing spatial clustering and the spatiotemporal nature and trends of HIV/AIDS prevalence using GIS: the case of Malawi, 1994-2010.

PubMed

Zulu, Leo C; Kalipeni, Ezekiel; Johannes, Eliza

2014-05-23

Although local spatiotemporal analysis can improve understanding of geographic variation of the HIV epidemic, its drivers, and the search for targeted interventions, it is limited in sub-Saharan Africa. Despite recent declines, Malawi's estimated 10.0% HIV prevalence (2011) remained among the highest globally. Using data on pregnant women in Malawi, this study 1) examines spatiotemporal trends in HIV prevalence 1994-2010, and 2) for 2010, identifies and maps the spatial variation/clustering of factors associated with HIV prevalence at district level. Inverse distance weighting was used within ArcGIS Geographic Information Systems (GIS) software to generate continuous surfaces of HIV prevalence from point data (1994, 1996, 1999, 2001, 2003, 2005, 2007, and 2010) obtained from surveillance antenatal clinics. From the surfaces prevalence estimates were extracted at district level and the results mapped nationally. Spatial dependency (autocorrelation) and clustering of HIV prevalence were also analyzed. Correlation and multiple regression analyses were used to identify factors associated with HIV prevalence for 2010 and their spatial variation/clustering mapped and compared to HIV clustering. Analysis revealed wide spatial variation in HIV prevalence at regional, urban/rural, district and sub-district levels. However, prevalence was spatially leveling out within and across 'sub-epidemics' while declining significantly after 1999. Prevalence exhibited statistically significant spatial dependence nationally following initial (1995-1999) localized, patchy low/high patterns as the epidemic spread rapidly. Locally, HIV "hotspots" clustered among eleven southern districts/cities while a "coldspot" captured configurations of six central region districts. Preliminary multiple regression of 2010 HIV prevalence produced a model with four significant explanatory factors (adjusted R2 = 0.688): mean distance to main roads, mean travel time to nearest transport, percentage that had taken an HIV test ever, and percentage attaining a senior primary education. Spatial clustering linked some factors to particular subsets of high HIV-prevalence districts. Spatial analysis enhanced understanding of local spatiotemporal variation in HIV prevalence, possible underlying factors, and potential for differentiated spatial targeting of interventions. Findings suggest that intervention strategies should also emphasize improved access to health/HIV services, basic education, and syphilis management, particularly in rural hotspot districts, as further research is done on drivers at finer scale.

Analyzing spatial clustering and the spatiotemporal nature and trends of HIV/AIDS prevalence using GIS: the case of Malawi, 1994-2010

PubMed Central

2014-01-01

Background Although local spatiotemporal analysis can improve understanding of geographic variation of the HIV epidemic, its drivers, and the search for targeted interventions, it is limited in sub-Saharan Africa. Despite recent declines, Malawi’s estimated 10.0% HIV prevalence (2011) remained among the highest globally. Using data on pregnant women in Malawi, this study 1) examines spatiotemporal trends in HIV prevalence 1994-2010, and 2) for 2010, identifies and maps the spatial variation/clustering of factors associated with HIV prevalence at district level. Methods Inverse distance weighting was used within ArcGIS Geographic Information Systems (GIS) software to generate continuous surfaces of HIV prevalence from point data (1994, 1996, 1999, 2001, 2003, 2005, 2007, and 2010) obtained from surveillance antenatal clinics. From the surfaces prevalence estimates were extracted at district level and the results mapped nationally. Spatial dependency (autocorrelation) and clustering of HIV prevalence were also analyzed. Correlation and multiple regression analyses were used to identify factors associated with HIV prevalence for 2010 and their spatial variation/clustering mapped and compared to HIV clustering. Results Analysis revealed wide spatial variation in HIV prevalence at regional, urban/rural, district and sub-district levels. However, prevalence was spatially leveling out within and across ‘sub-epidemics’ while declining significantly after 1999. Prevalence exhibited statistically significant spatial dependence nationally following initial (1995-1999) localized, patchy low/high patterns as the epidemic spread rapidly. Locally, HIV “hotspots” clustered among eleven southern districts/cities while a “coldspot” captured configurations of six central region districts. Preliminary multiple regression of 2010 HIV prevalence produced a model with four significant explanatory factors (adjusted R2 = 0.688): mean distance to main roads, mean travel time to nearest transport, percentage that had taken an HIV test ever, and percentage attaining a senior primary education. Spatial clustering linked some factors to particular subsets of high HIV-prevalence districts. Conclusions Spatial analysis enhanced understanding of local spatiotemporal variation in HIV prevalence, possible underlying factors, and potential for differentiated spatial targeting of interventions. Findings suggest that intervention strategies should also emphasize improved access to health/HIV services, basic education, and syphilis management, particularly in rural hotspot districts, as further research is done on drivers at finer scale. PMID:24886573

Mapping of the gene for the Mel{sub 1a}-melatonin receptor to human chromosome 4 (MTNR1A) and mouse chromosome 8 (Mtnr1a)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slaugenhaupt, S.A.; Liebert, C.B.; Altherr, M.R.

The pineal hormone melatonin elicits potent circadian and reproductive effects in mammals. The authors report the chromosomal location of the gene for the Mel{sub 1a}-melatonin receptor that likely mediates these circadian and reproductive actions. PCR analysis of human-rodent somatic cell hybrids showed that the receptor gene (MTNR1A) maps to human chromosome 4q35.1. An interspecific backcross analysis revealed that the mouse gene (Mtnr1a) maps to the proximal portion of chromosome 8. These loci may be involved in genetically based circadian and neuroendocrine disorders. 14 refs., 1 fig.

The 700-1500 cm{sup −1} region of the S{sub 1} (A{sup ~1}B{sub 2}) state of toluene studied with resonance-enhanced multiphoton ionization (REMPI), zero-kinetic-energy (ZEKE) spectroscopy, and time-resolved slow-electron velocity-map imaging (tr-SEVI) spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, Adrian M.; Green, Alistair M.; Tamé-Reyes, Victor M.

We report (nanosecond) resonance-enhanced multiphoton ionization (REMPI), (nanosecond) zero-kinetic-energy (ZEKE) and (picosecond) time-resolved slow-electron velocity map imaging (tr-SEVI) spectra of fully hydrogenated toluene (Tol-h{sub 8}) and the deuterated-methyl group isotopologue (α{sub 3}-Tol-d{sub 3}). Vibrational assignments are made making use of the activity observed in the ZEKE and tr-SEVI spectra, together with the results from quantum chemical and previous experimental results. Here, we examine the 700–1500 cm{sup −1} region of the REMPI spectrum, extending our previous work on the region ≤700 cm{sup −1}. We provide assignments for the majority of the S{sub 1} and cation bands observed, and in particular wemore » gain insight regarding a number of regions where vibrations are coupled via Fermi resonance. We also gain insight into intramolecular vibrational redistribution in this molecule.« less

Non-Gaussian microwave background fluctuations from nonlinear gravitational effects

NASA Technical Reports Server (NTRS)

Salopek, D. S.; Kunstatter, G. (Editor)

1991-01-01

Whether the statistics of primordial fluctuations for structure formation are Gaussian or otherwise may be determined if the Cosmic Background Explorer (COBE) Satellite makes a detection of the cosmic microwave-background temperature anisotropy delta T(sub CMB)/T(sub CMB). Non-Gaussian fluctuations may be generated in the chaotic inflationary model if two scalar fields interact nonlinearly with gravity. Theoretical contour maps are calculated for the resulting Sachs-Wolfe temperature fluctuations at large angular scales (greater than 3 degrees). In the long-wavelength approximation, one can confidently determine the nonlinear evolution of quantum noise with gravity during the inflationary epoch because: (1) different spatial points are no longer in causal contact; and (2) quantum gravity corrections are typically small-- it is sufficient to model the system using classical random fields. If the potential for two scalar fields V(phi sub 1, phi sub 2) possesses a sharp feature, then non-Gaussian fluctuations may arise. An explicit model is given where cold spots in delta T(sub CMB)/T(sub CMB) maps are suppressed as compared to the Gaussian case. The fluctuations are essentially scale-invariant.

Blockade of Drp1 rescues oxidative stress-induced osteoblast dysfunction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gan, Xueqi; Huang, Shengbin; Yu, Qing

Osteoblast dysfunction, induced by oxidative stress, plays a critical role in the pathophysiology of osteoporosis. However, the underlying mechanisms remain unclarified. Imbalance of mitochondrial dynamics has been closely linked to oxidative stress. Here, we reveal an unexplored role of dynamic related protein 1(Drp1), the major regulator in mitochondrial fission, in the oxidative stress-induced osteoblast injury model. We demonstrate that levels of phosphorylation and expression of Drp1 significantly increased under oxidative stress. Blockade of Drp1, through pharmaceutical inhibitor or gene knockdown, significantly protected against H{sub 2}O{sub 2}-induced osteoblast dysfunction, as shown by increased cell viability, improved cellular alkaline phosphatase (ALP) activitymore » and mineralization and restored mitochondrial function. The protective effects of blocking Drp1 in H{sub 2}O{sub 2}-induced osteoblast dysfunction were evidenced by increased mitochondrial function and suppressed production of reactive oxygen species (ROS). These findings provide new insights into the role of the Drp1-dependent mitochondrial pathway in the pathology of osteoporosis, indicating that the Drp1 pathway may be targetable for the development of new therapeutic approaches in the prevention and the treatment of osteoporosis. - Highlights: • Oxidative stress is an early pathological event in osteoporosis. • Imbalance of mitochondrial dynamics are linked to oxidative stress in osteoporosis. • The role of the Drp1-dependent mitochondrial pathway in osteoporosis.« less

Controlled synthesis of bright and compatible lanthanide-doped upconverting nanocrystals

DOEpatents

Cohen, Bruce E.; Ostrowski, Alexis D.; Chan, Emory M.; Gargas, Daniel J.; Katz, Elan M.; Schuck, P. James; Milliron, Delia J.

2017-01-31

Certain nanocrystals possess exceptional optical properties that may make them valuable probes for biological imaging, but rendering these nanoparticles biocompatible requires that they be small enough not to perturb cellular systems. This invention describes a phosphorescent upconverting sub-10 nm nanoparticle comprising a lanthanide-doped hexagonal .beta.-phase NaYF.sub.4 nanocrystal and methods for making the same.

Mapping the subcellular localization of Fe3O4@TiO2 nanoparticles by X-ray Fluorescence Microscopy.

PubMed

Yuan, Y; Chen, S; Gleber, S C; Lai, B; Brister, K; Flachenecker, C; Wanzer, B; Paunesku, T; Vogt, S; Woloschak, G E

The targeted delivery of Fe 3 O 4 @TiO2 nanoparticles to cancer cells is an important step in their development as nanomedicines. We have synthesized nanoparticles that can bind the Epidermal Growth Factor Receptor, a cell surface protein that is overexpressed in many epithelial type cancers. In order to study the subcellular distribution of these nanoparticles, we have utilized the sub-micron resolution of X-ray Fluorescence Microscopy to map the locationof Fe 3 O4@TiO 2 NPs and other trace metal elements within HeLa cervical cancer cells. Here we demonstrate how the higher resolution of the newly installed Bionanoprobe at the Advanced Photon Source at Argonne National Laboratory can greatly improve our ability to distinguish intracellular nanoparticles and their spatial relationship with subcellular compartments.

Sub-pixel mineral mapping using EO-1 Hyperion hyperspectral data

NASA Astrophysics Data System (ADS)

Kumar, C.; Shetty, A.; Raval, S.; Champatiray, P. K.; Sharma, R.

2014-11-01

This study describes the utility of Earth Observation (EO)-1 Hyperion data for sub-pixel mineral investigation using Mixture Tuned Target Constrained Interference Minimized Filter (MTTCIMF) algorithm in hostile mountainous terrain of Rajsamand district of Rajasthan, which hosts economic mineralization such as lead, zinc, and copper etc. The study encompasses pre-processing, data reduction, Pixel Purity Index (PPI) and endmember extraction from reflectance image of surface minerals such as illite, montmorillonite, phlogopite, dolomite and chlorite. These endmembers were then assessed with USGS mineral spectral library and lab spectra of rock samples collected from field for spectral inspection. Subsequently, MTTCIMF algorithm was implemented on processed image to obtain mineral distribution map of each detected mineral. A virtual verification method has been adopted to evaluate the classified image, which uses directly image information to evaluate the result and confirm the overall accuracy and kappa coefficient of 68 % and 0.6 respectively. The sub-pixel level mineral information with reasonable accuracy could be a valuable guide to geological and exploration community for expensive ground and/or lab experiments to discover economic deposits. Thus, the study demonstrates the feasibility of Hyperion data for sub-pixel mineral mapping using MTTCIMF algorithm with cost and time effective approach.

Discrete quantum dot like emitters in monolayer MoSe{sub 2}: Spatial mapping, magneto-optics, and charge tuning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Branny, Artur; Kumar, Santosh; Gerardot, Brian D., E-mail: b.d.gerardot@hw.ac.uk

Transition metal dichalcogenide monolayers such as MoSe{sub 2}, MoS{sub 2}, and WSe{sub 2} are direct bandgap semiconductors with original optoelectronic and spin-valley properties. Here we report on spectrally sharp, spatially localized emission in monolayer MoSe{sub 2}. We find this quantum dot-like emission in samples exfoliated onto gold substrates and also suspended flakes. Spatial mapping shows a correlation between the location of emitters and the existence of wrinkles (strained regions) in the flake. We tune the emission properties in magnetic and electric fields applied perpendicular to the monolayer plane. We extract an exciton g-factor of the discrete emitters close to −4,more » as for 2D excitons in this material. In a charge tunable sample, we record discrete jumps on the meV scale as charges are added to the emitter when changing the applied voltage.« less

Pathogenesis, Molecular Genetics, and Genomics of Mycobacterium avium subsp. paratuberculosis, the Etiologic Agent of Johne’s Disease

PubMed Central

Rathnaiah, Govardhan; Zinniel, Denise K.; Bannantine, John P.; Stabel, Judith R.; Gröhn, Yrjö T.; Collins, Michael T.; Barletta, Raúl G.

2017-01-01

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne’s disease in ruminants causing chronic diarrhea, malnutrition, and muscular wasting. Neonates and young animals are infected primarily by the fecal–oral route. MAP attaches to, translocates via the intestinal mucosa, and is phagocytosed by macrophages. The ensuing host cellular immune response leads to granulomatous enteritis characterized by a thick and corrugated intestinal wall. We review various tissue culture systems, ileal loops, and mice, goats, and cattle used to study MAP pathogenesis. MAP can be detected in clinical samples by microscopy, culturing, PCR, and an enzyme-linked immunosorbent assay. There are commercial vaccines that reduce clinical disease and shedding, unfortunately, their efficacies are limited and may not engender long-term protective immunity. Moreover, the potential linkage with Crohn’s disease and other human diseases makes MAP a concern as a zoonotic pathogen. Potential therapies with anti-mycobacterial agents are also discussed. The completion of the MAP K-10 genome sequence has greatly improved our understanding of MAP pathogenesis. The analysis of this sequence has identified a wide range of gene functions involved in virulence, lipid metabolism, transcriptional regulation, and main metabolic pathways. We also review the transposons utilized to generate random transposon mutant libraries and the recent advances in the post-genomic era. This includes the generation and characterization of allelic exchange mutants, transcriptomic analysis, transposon mutant banks analysis, new efforts to generate comprehensive mutant libraries, and the application of transposon site hybridization mutagenesis and transposon sequencing for global analysis of the MAP genome. Further analysis of candidate vaccine strains development is also provided with critical discussions on their benefits and shortcomings, and strategies to develop a highly efficacious live-attenuated vaccine capable of differentiating infected from vaccinated animals. PMID:29164142

Genomic Tools in Cowpea Breeding Programs: Status and Perspectives

PubMed Central

Boukar, Ousmane; Fatokun, Christian A.; Huynh, Bao-Lam; Roberts, Philip A.; Close, Timothy J.

2016-01-01

Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved varieties available to farmers, thereby boosting cowpea production and productivity in SSA. PMID:27375632

Helpful self-management strategies to cope with enduring depression from the patients' point of view: a concept map study.

PubMed

van Grieken, Rosa A; Kirkenier, Anneloes C E; Koeter, Maarten W J; Schene, Aart H

2014-12-13

Despite the development of various self-management programmes that attempt to ameliorate symptoms of patients with chronic major depressive disorder (MDD), little is known about what these patients perceive as helpful in their struggle during daily live. The present study aims to explore what patients believe they can do themselves to cope with enduring MDD besides professional treatment, and which self-management strategies patients perceive as being most helpful to cope with their MDD. We used concept mapping, a method specifically designed for the conceptualisation of a specific subject, in this case patients' point of view (n = 25) on helpful self-management strategies in their coping with enduring MDD. A purposive sample of participants was invited at the Academic Medical Center and through requests on several MDD-patient websites in the Netherlands. Participants generated strategies in focus group discussions which were successively clustered on a two-dimensional concept map by hierarchical cluster analysis. Fifty strategies were perceived as helpful. They were combined into three meta-clusters each comprising two clusters: A focus on the depression (sub clusters: Being aware that my depression needs active coping and Active coping with professional treatment); An active lifestyle (sub clusters: Active self-care, structure and planning and Free time activities) and Participation in everyday social life (sub clusters: Social engagement and Work-related activities). MDD patients believe they can use various strategies to cope with enduring MDD in daily life. Although current developments in e-health occur, patients emphasise on face-to-face treatments and long-term relations, being engaged in social and working life, and involving their family, friends, colleagues and clinicians in their disease management. Our findings may help clinicians to improve their knowledge about what patients consider beneficial to cope with enduring MDD and to incorporate these suggested self-management strategies in their treatments.

A novel chaotic based image encryption using a hybrid model of deoxyribonucleic acid and cellular automata

NASA Astrophysics Data System (ADS)

Enayatifar, Rasul; Sadaei, Hossein Javedani; Abdullah, Abdul Hanan; Lee, Malrey; Isnin, Ismail Fauzi

2015-08-01

Currently, there are many studies have conducted on developing security of the digital image in order to protect such data while they are sending on the internet. This work aims to propose a new approach based on a hybrid model of the Tinkerbell chaotic map, deoxyribonucleic acid (DNA) and cellular automata (CA). DNA rules, DNA sequence XOR operator and CA rules are used simultaneously to encrypt the plain-image pixels. To determine rule number in DNA sequence and also CA, a 2-dimension Tinkerbell chaotic map is employed. Experimental results and computer simulations, both confirm that the proposed scheme not only demonstrates outstanding encryption, but also resists various typical attacks.

A relationship between three-dimensional surface hydration structures and force distribution measured by atomic force microscopy.

PubMed

Miyazawa, Keisuke; Kobayashi, Naritaka; Watkins, Matthew; Shluger, Alexander L; Amano, Ken-ichi; Fukuma, Takeshi

2016-04-07

Hydration plays important roles in various solid-liquid interfacial phenomena. Very recently, three-dimensional scanning force microscopy (3D-SFM) has been proposed as a tool to visualise solvated surfaces and their hydration structures with lateral and vertical (sub) molecular resolution. However, the relationship between the 3D force map obtained and the equilibrium water density, ρ(r), distribution above the surface remains an open question. Here, we investigate this relationship at an interface of an inorganic mineral, fluorite, and water. The force maps measured in pure water are directly compared to force maps generated using the solvent tip approximation (STA) model and from explicit molecular dynamics simulations. The results show that the simulated STA force map describes the major features of the experimentally obtained force image. The agreement between the STA data and the experiment establishes the correspondence between the water density used as an input to the STA model and the experimental hydration structure and thus provides a tool to bridge the experimental force data and atomistic solvation structures. Further applications of this method should improve the accuracy and reliability of both interpretation of 3D-SFM force maps and atomistic simulations in a wide range of solid-liquid interfacial phenomena.

Phosphatidylinositol 5-phosphate 4-kinase type II beta is required for vitamin D receptor-dependent E-cadherin expression in SW480 cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kouchi, Zen, E-mail: zkouchi@toyaku.ac.jp; Fujiwara, Yuki; Yamaguchi, Hideki

2011-05-20

Highlights: {yields} We analyzed Phosphatidylinositol 5-phosphate kinase II{beta} (PIPKII{beta}) function in cancer. {yields} PIPKII{beta} is required for vitamin D receptor-mediated E-cadherin upregulation in SW480. {yields} PIPKII{beta} suppresses cellular motility through E-cadherin induction in SW480 cells. {yields} Nuclear PIP{sub 2} but not plasma membrane-localized PIP{sub 2} mediates E-cadherin upregulation. -- Abstract: Numerous epidemiological data indicate that vitamin D receptor (VDR) signaling induced by its ligand or active metabolite 1{alpha},25-dihydroxyvitamin D{sub 3} (1{alpha},25(OH){sub 2}D{sub 3}) has anti-cancer activity in several colon cancers. 1{alpha},25(OH){sub 2}D{sub 3} induces the epithelial differentiation of SW480 colon cancer cells expressing VDR (SW480-ADH) by upregulating E-cadherin expression; however,more » its precise mechanism remains unknown. We found that phosphatidylinositol-5-phosphate 4-kinase type II beta (PIPKII{beta}) but not PIPKII{alpha} is required for VDR-mediated E-cadherin induction in SW480-ADH cells. The syntenin-2 postsynaptic density protein/disc large/zona occludens (PDZ) domain and pleckstrin homology domain of phospholipase C-delta1 (PLC{delta}1 PHD) possess high affinity for phosphatidylinositol-4,5-bisphosphate (PI(4,5)P{sub 2}) mainly localized to the nucleus and plasma membrane, respectively. The expression of syntenin-2 PDZ but not PLC{delta}1 PHD inhibited 1{alpha},25(OH){sub 2}D{sub 3}-induced E-cadherin upregulation, suggesting that nuclear PI(4,5)P{sub 2} production mediates E-cadherin expression through PIPKII{beta} in a VDR-dependent manner. PIPKII{beta} is also involved in the suppression of the cell motility induced by 1{alpha},25(OH){sub 2}D{sub 3}. These results indicate that PIPKII{beta}-mediated PI(4,5)P{sub 2} signaling is important for E-cadherin upregulation and inhibition of cellular motility induced by VDR activation.« less

Characteristics of the uridine uptake system in normal and polyoma transformed hamster embryo cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lemkin, J.A.

1973-01-01

The lability of the uridine uptake system in the normal and polyoma transformed hamster embryo fibroblast was studied. The major areas investigated were: the kinetic parameters of uridine transport, a comparison of changes in cellular ATP content by factors which modulate uridine uptake, and a comparison of the qualitative and quantitative effects of the same modulating agent on uridine transport, cell growth, and cellular ATP content. Uridine uptake into cells in vitro was examined using tritiated uridine as a tracer to measure the amount of uridine incorporated into the acid soluble and acid-insoluble fractions of the cells studied. The ATPmore » content of the cells was determined by the firefly bioluminescence method. It was found that the K/sub t/ for uridine uptake into the normal hamster embryo cell and two polyoma transformed hamster embryo cell lines was identical. However, the V/sub max/ for uridine transport was higher in both polyoma transformed cell lines. Furthermore, the K/sub t/ in both the normal and transformed cell cultured in serum-less or serum-containing media was identical, although the V/sub max/ was higher in the serum-stimulated cell in both the normal and transformed cell. Stimulation of the normal cell with adenosine produced a different K/sub t/ for uridine transport. Preliminary investigations have demonstrated that treatment of the polyoma transformed with adenosine also induces a different K/sub t/ (not shown). The K/sub i/ for phloretin inhibition in serum-less and serum-stimulated normal and polyoma transformed cells was found to be identical in each case.« less

Modeling Land Use/Cover Changes in an African Rural Landscape

NASA Astrophysics Data System (ADS)

Kamusoko, C.; Aniya, M.

2006-12-01

Land use/cover changes are analyzed in the Bindura district of Zimbabwe, Africa through the integration of data from a time series of Landsat imagery (1973, 1989 and 2000), a household survey and GIS coverages. We employed a hybrid supervised/unsupervised classification approach to generate land use/cover maps from which landscape metrics were calculated. Population and other household variables were derived from a sample of surveyed villages, while road accessibility and slope were obtained from topographic maps and digital elevation model, respectively. Markov-cellular automata modeling approach that incorporates Markov chain analysis, cellular automata and multi-criteria evaluation (MCE) / multi-objective allocation (MOLA) procedures was used to simulate land use/cover changes. A GIS-based MCE technique computed transition potential maps, whereas transition areas were derived from the 1973-2000 land use/cover maps using the Markov chain analysis. A 5 x 5 cellular automata filter was used to develop a spatially explicit contiguity- weighting factor to change the cells based on its previous state and those of its neighbors, while MOLA resolved land use/cover class allocation conflicts. The kappa index of agreement was used for model validation. Observed trends in land use/cover changes indicate that deforestation and the encroachment of cultivation in woodland areas is a continuous trend in the study area. This suggests that economic activities driven by agricultural expansion were the main causes of landscape fragmentation, leading to landscape degradation. Rigorous calibration of transition potential maps done by a MCE algorithm and Markovian transition probabilities produced accurate inputs for the simulation of land use/cover changes. Overall standard kappa index of agreement ranged from 0.73 to 0.83, which is sufficient for simulating land use/cover changes in the study area. Land use/cover simulations under the 1989 and 2000 scenario indicated further landscape degradation in the rural areas of the Bindura district. Keywords: Zimbabwe, land use/cover changes, landscape fragmentation, GIS, land use/cover change modeling, multi-criteria evaluation/multi-objective allocation procedures, Markov-cellular automata

The binding of platinum hexahalides (Cl, Br and I) to hen egg-white lysozyme and the chemical transformation of the PtI{sub 6} octahedral complex to a PtI{sub 3} moiety bound to His15

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tanley, Simon W. M.; Starkey, Laurina-Victoria; Lamplough, Lucinda

The platinum hexahalides have an octahedral arrangement of six halogen atoms bound to a Pt centre, thus having an octahedral shape that could prove to be useful in interpreting poor electron-density maps. In a detailed characterization, PtI{sub 6} chemically transformed to a square-planar PtI{sub 3} complex bound to the N{sup δ} atom of His15 of HEWL was also observed, which was not observed for PtBr{sub 6} or PtCl{sub 6}. This study examines the binding and chemical stability of the platinum hexahalides K{sub 2}PtCl{sub 6}, K{sub 2}PtBr{sub 6} and K{sub 2}PtI{sub 6} when soaked into pre-grown hen egg-white lysozyme (HEWL) crystalsmore » as the protein host. Direct comparison of the iodo complex with the chloro and bromo complexes shows that the iodo complex is partly chemically transformed to a square-planar PtI{sub 3} complex bound to the N{sup δ} atom of His15, a chemical behaviour that is not exhibited by the chloro or bromo complexes. Each complex does, however, bind to HEWL in its octahedral form either at one site (PtI{sub 6}) or at two sites (PtBr{sub 6} and PtCl{sub 6}). As heavy-atom derivatives of a protein, the octahedral shape of the hexahalides could be helpful in cases of difficult-to-interpret electron-density maps as they would be recognisable ‘objects’.« less

Correlations Between the Cosmic X-Ray and Microwave Backgrounds: Constraints on a Cosmological Constant

NASA Technical Reports Server (NTRS)

Boughn, S. P.; Crittenden, R. G.; Turok, N. G.

1998-01-01

In universes with significant curvature or cosmological constant, cosmic microwave background (CMB) anisotropies are created very recently via the Rees-Sciama or integrated Sachs-Wolfe effects. This causes the CMB anisotropies to become partially correlated with the local matter density (z less than 4). We examine the prospects of using the hard (2- 10 keV) X-ray background as a probe of the local density and the measured correlation between the HEAO1 A2 X-ray survey and the 4-year COBE-DMR map to obtain a constraint on the cosmological constant. The 95% confidence level upper limit on the cosmological constant is OMega(sub Lambda) less than or equal to 0.5, assuming that the observed fluctuations in the X-ray map result entirely from large scale structure. (This would also imply that the X-rays trace matter with a bias factor of b(sub x) approx. = 5.6 Omega(sub m, sup 0.53)). This bound is weakened considerably if a large portion of the X-ray fluctuations arise from Poisson noise from unresolved sources. For example, if one assumes that the X-ray bias is b(sub x) = 2, then the 95% confidence level upper limit is weaker, Omega(sub Lambda) less than or equal to 0.7. More stringent limits should be attainable with data from the next generation of CMB and X-ray background maps.

Method for Enhancing a Three Dimensional Image from a Plurality of Frames of Flash LIDAR Data

NASA Technical Reports Server (NTRS)

Bulyshev, Alexander (Inventor); Vanek, Michael D. (Inventor); Amzajerdian, Farzin (Inventor)

2013-01-01

A method for enhancing a three dimensional image from frames of flash LIDAR data includes generating a first distance R(sub i) from a first detector i to a first point on a surface S(sub i). After defining a map with a mesh theta having cells k, a first array S(k), a second array M(k), and a third array D(k) are initialized. The first array corresponds to the surface, the second array corresponds to the elevation map, and the third array D(k) receives an output for the DEM. The surface is projected onto the mesh theta, so that a second distance R(sub k) from a second point on the mesh theta to the detector can be found. From this, a height may be calculated, which permits the generation of a digital elevation map. Also, using sequential frames of flash LIDAR data, vehicle control is possible using an offset between successive frames.

Troponin T3 regulates nuclear localization of the calcium channel Ca{sub v}β{sub 1a} subunit in skeletal muscle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Tan; Taylor, Jackson; Jiang, Yang

The voltage-gated calcium channel (Ca{sub v}) β{sub 1a} subunit (Ca{sub v}β{sub 1a}) plays an important role in excitation–contraction coupling (ECC), a process in the myoplasm that leads to muscle-force generation. Recently, we discovered that the Ca{sub v}β{sub 1a} subunit travels to the nucleus of skeletal muscle cells where it helps to regulate gene transcription. To determine how it travels to the nucleus, we performed a yeast two-hybrid screening of the mouse fast skeletal muscle cDNA library and identified an interaction with troponin T3 (TnT3), which we subsequently confirmed by co-immunoprecipitation and co-localization assays in mouse skeletal muscle in vivo andmore » in cultured C2C12 muscle cells. Interacting domains were mapped to the leucine zipper domain in TnT3 COOH-terminus (160–244 aa) and Ca{sub v}β{sub 1a} NH{sub 2}-terminus (1–99 aa), respectively. The double fluorescence assay in C2C12 cells co-expressing TnT3/DsRed and Ca{sub v}β{sub 1a}/YFP shows that TnT3 facilitates Ca{sub v}β{sub 1a} nuclear recruitment, suggesting that the two proteins play a heretofore unknown role during early muscle differentiation in addition to their classical role in ECC regulation. - Highlights: • Previously, we demonstrated that Ca{sub v}β{sub 1a} is a gene transcription regulator. • Here, we show that TnT3 interacts with Ca{sub v}β{sub 1a}. • We mapped TnT3 and Ca{sub v}β{sub 1a} interaction domain. • TnT3 facilitates Ca{sub v}β{sub 1a} nuclear enrichment. • The two proteins play a heretofore unknown role during early muscle differentiation.« less

Improved AFM Mapping of ICF Target Surfaces

NASA Astrophysics Data System (ADS)

Olson, D. K.; Drake, T.; Frey, D.; Huang, H.; Stephens, R. B.

2003-10-01

Targets for Inertial Confinement Fusion (ICF) research are made from spherical shells with very strict requirements on surface smoothness. Hydrodynamic instabilities are amplified by the presence of surface defects, greatly reducing the gain of ICF targets. Sub-micron variations in the surface can be examined using an Atomic Force Microscope. The current sphere mapping assembly at General Atomics is designed to trace near the equator of a rotating sphere under the AFM head. Spheres are traced on three mutually orthogonal planes. The ˜10 mm piezo-electric actuator range limits how far off the equator we can scan spheres of millimeter diameter. Because only a small fraction of the target's surface can be covered, localized high-mode defects are difficult to detect. In order to meet the needs of ICF research, we need to scan more surface area of the sphere with the AFM. By integrating an additional stepping motor to the sphere mapping assembly, we will be able to recenter the piezo driver of the AFM while mapping. This additional ability allows us to increase the amount of the sphere's surface we are able to scan with the AFM by extending the range of the AFM from the sphere's equator.

A molecular genetic linkage map identifying the St and H sub-genomes of Elymus wheatgrass (Poaceae: Triticeae)

USDA-ARS?s Scientific Manuscript database

Elymus L. is the largest and most complex genus in the Triticeae with approximately 150 polyploid perennial grass species occurring worldwide. We report here the first genetic linkage map for Elymus. Backcross mapping populations were created by crossing caespitose Elymus wawawaiensis (EW) (Snake ...

Hypoxia-induced pulmonary arterial hypertension augments lung injury and airway reactivity caused by ozone exposure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zychowski, Katherine E.; Lucas, Selita N.; Sanchez

Ozone (O{sub 3})-related cardiorespiratory effects are a growing public health concern. Ground level O{sub 3} can exacerbate pre-existing respiratory conditions; however, research regarding therapeutic interventions to reduce O{sub 3}-induced lung injury is limited. In patients with chronic obstructive pulmonary disease, hypoxia-associated pulmonary hypertension (HPH) is a frequent comorbidity that is difficult to treat clinically, yet associated with increased mortality and frequency of exacerbations. In this study, we hypothesized that established HPH would confer vulnerability to acute O{sub 3} pulmonary toxicity. Additionally, we tested whether improvement of pulmonary endothelial barrier integrity via rho-kinase inhibition could mitigate pulmonary inflammation and injury. Tomore » determine if O{sub 3} exacerbated HPH, male C57BL/6 mice were subject to either 3 weeks continuous normoxia (20.9% O{sub 2}) or hypoxia (10.0% O{sub 2}), followed by a 4-h exposure to either 1 ppm O{sub 3} or filtered air (FA). As an additional experimental intervention fasudil (20 mg/kg) was administered intraperitoneally prior to and after O{sub 3} exposures. As expected, hypoxia significantly increased right ventricular pressure and hypertrophy. O{sub 3} exposure in normoxic mice caused lung inflammation but not injury, as indicated by increased cellularity and edema in the lung. However, in hypoxic mice, O{sub 3} exposure led to increased inflammation and edema, along with a profound increase in airway hyperresponsiveness to methacholine. Fasudil administration resulted in reduced O{sub 3}-induced lung injury via the enhancement of pulmonary endothelial barrier integrity. These results indicate that increased pulmonary vascular pressure may enhance lung injury, inflammation and edema when exposed to pollutants, and that enhancement of pulmonary endothelial barrier integrity may alleviate such vulnerability. - Highlights: • Environmental exposures can exacerbate chronic obstructive pulmonary disease (COPD). • It is unknown if comorbid pulmonary hypertension may influence such effects in COPD patients. • Pulmonary hypertension in a mouse model significantly exacerbated ozone-induced lung injury. • Adverse ozone outcomes were largely attenuated by a rho kinase inhibitor, fasudil. • Therapeutic benefit from rho kinase inhibition may be related to endothelial barrier integrity.« less

Brain refractive index measured in vivo with high-NA defocus-corrected full-field OCT and consequences for two-photon microscopy.

PubMed

Binding, Jonas; Ben Arous, Juliette; Léger, Jean-François; Gigan, Sylvain; Boccara, Claude; Bourdieu, Laurent

2011-03-14

Two-photon laser scanning microscopy (2PLSM) is an important tool for in vivo tissue imaging with sub-cellular resolution, but the penetration depth of current systems is potentially limited by sample-induced optical aberrations. To quantify these, we measured the refractive index n' in the somatosensory cortex of 7 rats in vivo using defocus optimization in full-field optical coherence tomography (ff-OCT). We found n' to be independent of imaging depth or rat age. From these measurements, we calculated that two-photon imaging beyond 200 µm into the cortex is limited by spherical aberration, indicating that adaptive optics will improve imaging depth.

Systematic evaluation of four-dimensional hybrid depth scanning for carbon-ion lung therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mori, Shinichiro; Furukawa, Takuji; Inaniwa, Taku

2013-03-15

Purpose: Irradiation of a moving target with a scanning beam requires a comprehensive understanding of organ motion as well as a robust dose error mitigation technique. The authors studied the effects of intrafractional respiratory motion for carbon-ion pencil beam scanning with phase-controlled rescanning on dose distributions for lung tumors. To address density variations, they used 4DCT data. Methods: Dose distributions for various rescanning methods, such as simple layer rescanning (LR), volumetric rescanning, and phase-controlled rescanning (PCR), were calculated for a lung phantom and a lung patient studies. To ensure realism, they set the scanning parameters such as scanning velocity andmore » energy variation time to be similar to those used at our institution. Evaluation metrics were determined with regard to clinical relevance, and consisted of (i) phase-controlled rescanning, (ii) sweep direction, (iii) target motion (direction and amplitude), (iv) respiratory cycle, and (v) prescribed dose. Spot weight maps were calculated by using a beam field-specific target volume, which takes account of range variations for respective respiratory phases. To emphasize the impact of intrafractional motion on the dose distribution, respiratory gating was not used. The accumulated dose was calculated by applying a B-spline-based deformable image registration, and the results for phase-controlled layered rescanning (PCR{sub L}) and phase-controlled volumetric rescanning (PCR{sub V}) were compared. Results: For the phantom study, simple LR was unable to improve the dose distributions for an increased number of rescannings. The phase-controlled technique without rescanning (1 Multiplication-Sign PCR{sub L} and 1 Multiplication-Sign PCR{sub V}) degraded dose conformity significantly due to a reduced scan velocity. In contrast, 4 Multiplication-Sign PCR{sub L} or more significantly and consistently improved dose distribution. PCR{sub V} showed interference effects, but in general also improved dose homogeneity with higher numbers of rescannings. Dose distributions with single PCR{sub L}/PCR{sub V} with a sweep direction perpendicular to motion direction showed large hot/cold spots; however, this effect vanished with higher numbers of rescannings for both methods. Similar observations were obtained for the other dose metrics, such as target motion (SI/AP), amplitude (6-22 mm peak-to-peak) and respiratory period (3.0-5.0 s). For four or more rescannings, both methods showed significantly better results, albeit that volumetric PCR was more affected by interference effects, which lead to severe degradation of a few dose distributions. The clinical example showed the same tendencies as the phantom study. Dose assessment metrics (D95, Dmax/Dmin, homogeneity index) were improved with an increasing number of PCR{sub L}/PCR{sub V}, but with PCR{sub L} being more robust. Conclusions: PCR{sub L} requires a longer treatment time than PCR{sub V} for high numbers of rescannings in the NIRS scanning system but is more robust. Although four or more rescans provided good dose homogeneity and conformity, the authors prefer to use more rescannings for clinical cases to further minimize dose degradation effects due to organ motion.« less

Using concept maps to describe undergraduate students’ mental model in microbiology course

NASA Astrophysics Data System (ADS)

Hamdiyati, Y.; Sudargo, F.; Redjeki, S.; Fitriani, A.

2018-05-01

The purpose of this research was to describe students’ mental model in a mental model based-microbiology course using concept map as assessment tool. Respondents were 5th semester of undergraduate students of Biology Education of Universitas Pendidikan Indonesia. The mental modelling instrument used was concept maps. Data were taken on Bacteria sub subject. A concept map rubric was subsequently developed with a maximum score of 4. Quantitative data was converted into a qualitative one to determine mental model level, namely: emergent = score 1, transitional = score 2, close to extended = score 3, and extended = score 4. The results showed that mental model level on bacteria sub subject before the implementation of mental model based-microbiology course was at the transitional level. After implementation of mental model based-microbiology course, mental model was at transitional level, close to extended, and extended. This indicated an increase in the level of students’ mental model after the implementation of mental model based-microbiology course using concept map as assessment tool.

Identification of microbes from the surfaces of food-processing lines based on the flow cytometric evaluation of cellular metabolic activity combined with cell sorting.

PubMed

Juzwa, W; Duber, A; Myszka, K; Białas, W; Czaczyk, K

2016-09-01

In this study the design of a flow cytometry-based procedure to facilitate the detection of adherent bacteria from food-processing surfaces was evaluated. The measurement of the cellular redox potential (CRP) of microbial cells was combined with cell sorting for the identification of microorganisms. The procedure enhanced live/dead cell discrimination owing to the measurement of the cell physiology. The microbial contamination of the surface of a stainless steel conveyor used to process button mushrooms was evaluated in three independent experiments. The flow cytometry procedure provided a step towards monitoring of contamination and enabled the assessment of microbial food safety hazards by the discrimination of active, mid-active and non-active bacterial sub-populations based on determination of their cellular vitality and subsequently single cell sorting to isolate microbial strains from discriminated sub-populations. There was a significant correlation (r = 0.97; p < 0.05) between the bacterial cell count estimated by the pour plate method and flow cytometry, despite there being differences in the absolute number of cells detected. The combined approach of flow cytometric CRP measurement and cell sorting allowed an in situ analysis of microbial cell vitality and the identification of species from defined sub-populations, although the identified microbes were limited to culturable cells.

Imaging live cells at high spatiotemporal resolution for lab-on-a-chip applications.

PubMed

Chin, Lip Ket; Lee, Chau-Hwang; Chen, Bi-Chang

2016-05-24

Conventional optical imaging techniques are limited by the diffraction limit and difficult-to-image biomolecular and sub-cellular processes in living specimens. Novel optical imaging techniques are constantly evolving with the desire to innovate an imaging tool that is capable of seeing sub-cellular processes in a biological system, especially in three dimensions (3D) over time, i.e. 4D imaging. For fluorescence imaging on live cells, the trade-offs among imaging depth, spatial resolution, temporal resolution and photo-damage are constrained based on the limited photons of the emitters. The fundamental solution to solve this dilemma is to enlarge the photon bank such as the development of photostable and bright fluorophores, leading to the innovation in optical imaging techniques such as super-resolution microscopy and light sheet microscopy. With the synergy of microfluidic technology that is capable of manipulating biological cells and controlling their microenvironments to mimic in vivo physiological environments, studies of sub-cellular processes in various biological systems can be simplified and investigated systematically. In this review, we provide an overview of current state-of-the-art super-resolution and 3D live cell imaging techniques and their lab-on-a-chip applications, and finally discuss future research trends in new and breakthrough research areas of live specimen 4D imaging in controlled 3D microenvironments.

The in vitro sub-cellular localization and in vivo efficacy of novel chitosan/GMO nanostructures containing paclitaxel.

PubMed

Trickler, W J; Nagvekar, A A; Dash, A K

2009-08-01

To determine the in vitro sub-cellular localization and in vivo efficacy of chitosan/GMO nanostructures containing paclitaxel (PTX) compared to a conventional PTX treatment (Taxol). The sub-cellular localization of coumarin-6 labeled chitosan/GMO nanostructures was determined by confocal microscopy in MDA-MB-231 cells. The antitumor efficacy was evaluated in two separate studies using FOX-Chase (CB17) SCID Female-Mice MDA-MB-231 xenograph model. Treatments consisted of intravenous Taxol or chitosan/GMO nanostructures with or without PTX, local intra-tumor bolus of Taxol or chitosan/GMO nanostructures with or without PTX. The tumor diameter and animal weight was monitored at various intervals. Histopathological changes were evaluated in end-point tumors. The tumor diameter increased at a constant rate for all the groups between days 7-14. After a single intratumoral bolus dose of chitosan/GMO containing PTX showed significant reduction in tumor diameter on day 15 when compared to control, placebo and intravenous PTX administration. The tumor diameter reached a maximal decrease (4-fold) by day 18, and the difference was reduced to approximately 2-fold by day 21. Qualitatively similar results were observed in a separate study containing PTX when administered intravenously. Chitosan/GMO nanostructures containing PTX are safe and effective administered locally or intravenously. Partially supported by DOD Award BC045664.

Focus on the emerging new fields of network physiology and network medicine

NASA Astrophysics Data System (ADS)

Ivanov, Plamen Ch; Liu, Kang K. L.; Bartsch, Ronny P.

2016-10-01

Despite the vast progress and achievements in systems biology and integrative physiology in the last decades, there is still a significant gap in understanding the mechanisms through which (i) genomic, proteomic and metabolic factors and signaling pathways impact vertical processes across cells, tissues and organs leading to the expression of different disease phenotypes and influence the functional and clinical associations between diseases, and (ii) how diverse physiological systems and organs coordinate their functions over a broad range of space and time scales and horizontally integrate to generate distinct physiologic states at the organism level. Two emerging fields, network medicine and network physiology, aim to address these fundamental questions. Novel concepts and approaches derived from recent advances in network theory, coupled dynamical systems, statistical and computational physics show promise to provide new insights into the complexity of physiological structure and function in health and disease, bridging the genetic and sub-cellular level with inter-cellular interactions and communications among integrated organ systems and sub-systems. These advances form first building blocks in the methodological formalism and theoretical framework necessary to address fundamental problems and challenges in physiology and medicine. This ‘focus on’ issue contains 26 articles representing state-of-the-art contributions covering diverse systems from the sub-cellular to the organism level where physicists have key role in laying the foundations of these new fields.

Valproate inhibits MAP kinase signalling and cell cycle progression in S. cerevisiae.

PubMed

Desfossés-Baron, Kristelle; Hammond-Martel, Ian; Simoneau, Antoine; Sellam, Adnane; Roberts, Stephen; Wurtele, Hugo

2016-10-26

The mechanism of action of valproate (VPA), a widely prescribed short chain fatty acid with anticonvulsant and anticancer properties, remains poorly understood. Here, the yeast Saccharomyces cerevisiae was used as model to investigate the biological consequences of VPA exposure. We found that low pH strongly potentiates VPA-induced growth inhibition. Transcriptional profiling revealed that under these conditions, VPA modulates the expression of genes involved in diverse cellular processes including protein folding, cell wall organisation, sexual reproduction, and cell cycle progression. We further investigated the impact of VPA on selected processes and found that this drug: i) activates markers of the unfolded protein stress response such as Hac1 mRNA splicing; ii) modulates the cell wall integrity pathway by inhibiting the activation of the Slt2 MAP kinase, and synergizes with cell wall stressors such as micafungin and calcofluor white in preventing yeast growth; iii) prevents activation of the Kss1 and Fus3 MAP kinases of the mating pheromone pathway, which in turn abolishes cellular responses to alpha factor; and iv) blocks cell cycle progression and DNA replication. Overall, our data identify heretofore unknown biological responses to VPA in budding yeast, and highlight the broad spectrum of cellular pathways influenced by this chemical in eukaryotes.

High Sensitivity Detection of Broadband Acoustic Vibration Using Optical Demodulation Method

NASA Astrophysics Data System (ADS)

Zhang, Zhen

Measuring the high frequency acoustic vibrations represents the fundamental interest in revealing the intrinsic dynamic characteristic of board range of systems, such as the growth of the fetus, blood flow in human palms, and vibrations of carbon nanotube. However, the acoustic wave detection capability is limited by the detection bandwidth and sensitivity of the commonly used piezoelectric based ultrasound detectors. To overcome these limitations, this thesis focuses on exploring the optical demodulation method for highly sensitive detection of broadband acoustic vibration. First, a transparent optical ultrasonic detector has been developed using micro-ring resonator (MRR) made of soft polymeric materials. It outperforms the traditional piezoelectric detectors with broader detection bandwidth, miniaturized size and wide angular sensitivity. Its ease of integration into photoacoustic microscopy system has resulted in the great improvement of the imaging resolution. A theoretic framework has been developed to establish the quantitative understanding of its unique distance and angular dependent detection characteristics and was subsequently validated experimentally. The developed theoretic framework provides a guideline to fully accounts for the trade-offs between axial and lateral resolution, working distance, and the field of view in developing optimal imaging performance for a wide range of biological and clinical applications. MRR-based ultrasonic detector is further integrated into confocal fluorescence microscopy to realize the simultaneous imaging of fluorescence and optical absorption of retinal pigment epithelium, achieving multi-contrast imaging at sub-cellular level. The needs to resolve the fine details of the biological specimen with the resolution beyond the diffraction limit further motivate the development of optical demodulated ultrasonic detection method based on near-field scanning optical microscopy (NSOM). The nano-focusing probe was developed for adiabatic focusing of surface plasmon polaritons to the probe apex with high energy efficiency and the suppression of the background noise was accomplished through the implementation of the harmonic demodulation technique. Collectively, this system is capable of delivering intense near-field illumination source while effectively suppressing the background signal due to the far-field scattering and thus, allows for quantitative mapping of local evanescent field with enhanced contrast and improved resolutions. The performance of the developed NSOM system has been validated through the experimental measurements of the surface plasmon polariton mode. This new NSOM system enables optical demodulated ultrasound detection at nanoscale spatial resolution. Using it to detect the ultrasound signal within the acoustic near-field has led to the successful experimental demonstration of the sub-surface photoacoustic imaging of buried objects with sub-diffraction-limited resolution and high sensitivity. Such a new ultrasound detection method holds promising potential for super-resolution ultrasound imaging.

Distinct Redox Regulation in Sub-Cellular Compartments in Response to Various Stress Conditions in Saccharomyces cerevisiae

PubMed Central

Ayer, Anita; Sanwald, Julia; Pillay, Bethany A.; Meyer, Andreas J.; Perrone, Gabriel G.; Dawes, Ian W.

2013-01-01

Responses to many growth and stress conditions are assumed to act via changes to the cellular redox status. However, direct measurement of pH-adjusted redox state during growth and stress has never been carried out. Organellar redox state (E GSH) was measured using the fluorescent probes roGFP2 and pHluorin in Saccharomyces cerevisiae. In particular, we investigated changes in organellar redox state in response to various growth and stress conditions to better understand the relationship between redox-, oxidative- and environmental stress response systems. E GSH values of the cytosol, mitochondrial matrix and peroxisome were determined in exponential and stationary phase in various media. These values (−340 to −350 mV) were more reducing than previously reported. Interestingly, sub-cellular redox state remained unchanged when cells were challenged with stresses previously reported to affect redox homeostasis. Only hydrogen peroxide and heat stress significantly altered organellar redox state. Hydrogen peroxide stress altered the redox state of the glutathione disulfide/glutathione couple (GSSG, 2H+/2GSH) and pH. Recovery from moderate hydrogen peroxide stress was most rapid in the cytosol, followed by the mitochondrial matrix, with the peroxisome the least able to recover. Conversely, the bulk of the redox shift observed during heat stress resulted from alterations in pH and not the GSSG, 2H+/2GSH couple. This study presents the first direct measurement of pH-adjusted redox state in sub-cellular compartments during growth and stress conditions. Redox state is distinctly regulated in organelles and data presented challenge the notion that perturbation of redox state is central in the response to many stress conditions. PMID:23762325

Signal transduction pathways and transcription factors triggered by arsenic trioxide in leukemia cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sumi, Daigo, E-mail: sdaigo@ph.bunri-u.ac.j; Shinkai, Yasuhiro; Kumagai, Yoshito

2010-05-01

Arsenic trioxide (As{sub 2}O{sub 3}) is widely used to treat acute promyelocytic leukemia (APL). Several lines of evidence have indicated that As{sub 2}O{sub 3} affects signal transduction and transactivation of transcription factors, resulting in the stimulation of apoptosis in leukemia cells, because some transcription factors are reported to associate with the redox condition of the cells, and arsenicals cause oxidative stress. Thus, the disturbance and activation of the cellular signaling pathway and transcription factors due to reactive oxygen species (ROS) generation during arsenic exposure may explain the ability of As{sub 2}O{sub 3} to induce a complete remission in relapsed APLmore » patients. In this report, we review recent findings on ROS generation and alterations in signal transduction and in transactivation of transcription factors during As{sub 2}O{sub 3} exposure in leukemia cells.« less

A neural-network based estimator to search for primordial non-Gaussianity in Planck CMB maps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novaes, C.P.; Bernui, A.; Ferreira, I.S.

2015-09-01

We present an upgraded combined estimator, based on Minkowski Functionals and Neural Networks, with excellent performance in detecting primordial non-Gaussianity in simulated maps that also contain a weighted mixture of Galactic contaminations, besides real pixel's noise from Planck cosmic microwave background radiation data. We rigorously test the efficiency of our estimator considering several plausible scenarios for residual non-Gaussianities in the foreground-cleaned Planck maps, with the intuition to optimize the training procedure of the Neural Network to discriminate between contaminations with primordial and secondary non-Gaussian signatures. We look for constraints of primordial local non-Gaussianity at large angular scales in the foreground-cleanedmore » Planck maps. For the SMICA map we found f{sub NL} = 33 ± 23, at 1σ confidence level, in excellent agreement with the WMAP-9yr and Planck results. In addition, for the other three Planck maps we obtain similar constraints with values in the interval f{sub NL}  element of  [33, 41], concomitant with the fact that these maps manifest distinct features in reported analyses, like having different pixel's noise intensities.« less

Model-independent curvature determination with 21 cm intensity mapping experiments

NASA Astrophysics Data System (ADS)

Witzemann, Amadeus; Bull, Philip; Clarkson, Chris; Santos, Mario G.; Spinelli, Marta; Weltman, Amanda

2018-06-01

Measurements of the spatial curvature of the Universe have improved significantly in recent years, but still tend to require strong assumptions to be made about the equation of state of dark energy (DE) in order to reach sub-percent precision. When these assumptions are relaxed, strong degeneracies arise that make it hard to disentangle DE and curvature, degrading the constraints. We show that forthcoming 21 cm intensity mapping experiments such as Hydrogen Intensity and Real-time Analysis eXperiment (HIRAX) are ideally designed to carry out model-independent curvature measurements, as they can measure the clustering signal at high redshift with sufficient precision to break many of the degeneracies. We consider two different model-independent methods, based on `avoiding' the DE-dominated regime and non-parametric modelling of the DE equation of state, respectively. Our forecasts show that HIRAX will be able to improve upon current model-independent constraints by around an order of magnitude, reaching percent-level accuracy even when an arbitrary DE equation of state is assumed. In the same model-independent analysis, the sample variance limit for a similar survey is another order of magnitude better.

A fast feedback method to design easy-molding freeform optical system with uniform illuminance and high light control efficiency.

PubMed

Hongtao, Li; Shichao, Chen; Yanjun, Han; Yi, Luo

2013-01-14

A feedback method combined with fitting technique based on variable separation mapping is proposed to design freeform optical systems for an extended LED source with prescribed illumination patterns, especially with uniform illuminance distribution. Feedback process performs well with extended sources, while fitting technique contributes not only to the decrease of pieces of sub-surfaces in discontinuous freeform lenses which may cause loss in manufacture, but also the reduction in the number of feedback iterations. It is proved that light control efficiency can be improved by 5%, while keeping a high uniformity of 82%, with only two feedback iterations and one fitting operation can improve. Furthermore, the polar angle θ and azimuthal angle φ is used to specify the light direction from the light source, and the (θ,φ)-(x,y) based mapping and feedback strategy makes sure that even few discontinuous sections along the equi-φ plane exist in the system, they are perpendicular to the base plane, making it eligible for manufacturing the surfaces using injection molding.

Model-independent curvature determination with 21cm intensity mapping experiments

NASA Astrophysics Data System (ADS)

Witzemann, Amadeus; Bull, Philip; Clarkson, Chris; Santos, Mario G.; Spinelli, Marta; Weltman, Amanda

2018-04-01

Measurements of the spatial curvature of the Universe have improved significantly in recent years, but still tend to require strong assumptions to be made about the equation of state of dark energy (DE) in order to reach sub-percent precision. When these assumptions are relaxed, strong degeneracies arise that make it hard to disentangle DE and curvature, degrading the constraints. We show that forthcoming 21cm intensity mapping experiments such as HIRAX are ideally designed to carry out model-independent curvature measurements, as they can measure the clustering signal at high redshift with sufficient precision to break many of the degeneracies. We consider two different model-independent methods, based on `avoiding' the DE-dominated regime and non-parametric modelling of the DE equation of state respectively. Our forecasts show that HIRAX will be able to improve upon current model-independent constraints by around an order of magnitude, reaching percent-level accuracy even when an arbitrary DE equation of state is assumed. In the same model-independent analysis, the sample variance limit for a similar survey is another order of magnitude better.

SEVEN-YEAR WILKINSON MICROWAVE ANISOTROPY PROBE (WMAP ) OBSERVATIONS: POWER SPECTRA AND WMAP-DERIVED PARAMETERS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, D.; Bennett, C. L.; Gold, B.

2011-02-01

The WMAP mission has produced sky maps from seven years of observations at L2. We present the angular power spectra derived from the seven-year maps and discuss the cosmological conclusions that can be inferred from WMAP data alone. With the seven-year data, the temperature (TT) spectrum measurement has a signal-to-noise ratio per multipole that exceeds unity for l < 919; and in band powers of width {Delta}l = 10, the signal-to-noise ratio exceeds unity up to l = 1060. The third acoustic peak in the TT spectrum is now well measured by WMAP. In the context of a flat {Lambda}CDMmore » model, this improvement allows us to place tighter constraints on the matter density from WMAP data alone, {Omega}{sub m} h {sup 2} = 0.1334{sup +0.0056}{sub -0.0055}, and on the epoch of matter-radiation equality, z{sub eq} = 3196{sup +134}{sub -133}. The temperature-polarization (TE) spectrum is detected in the seven-year data with a significance of 20{sigma}, compared to 13{sigma} with the five-year data. We now detect the second dip in the TE spectrum near l {approx} 450 with high confidence. The TB and EB spectra remain consistent with zero, thus demonstrating low systematic errors and foreground residuals in the data. The low-l EE spectrum, a measure of the optical depth due to reionization, is detected at 5.5{sigma} significance when averaged over l = 2-7: l(l + 1)C {sup EE}{sub l}/(2{pi}) = 0.074{sup +0.034}{sub -0.025} {mu}K{sup 2} (68% CL). We now detect the high-l, 24 {<=} l {<=} 800, EE spectrum at over 8{sigma}. The BB spectrum, an important probe of gravitational waves from inflation, remains consistent with zero; when averaged over l = 2-7, l(l + 1)C {sup BB}{sub l}/(2{pi}) < 0.055 {mu}K{sup 2} (95% CL). The upper limit on tensor modes from polarization data alone is a factor of two lower with the seven-year data than it was using the five-year data. The data remain consistent with the simple {Lambda}CDM model: the best-fit TT spectrum has an effective {chi}{sup 2} of 1227 for 1170 degrees of freedom, with a probability to exceed of 9.6%. The allowable volume in the six-dimensional space of {Lambda}CDM parameters has been reduced by a factor of 1.5 relative to the five-year volume, while the {Lambda}CDM model that allows for tensor modes and a running scalar spectral index has a factor of three lower volume when fit to the seven-year data. We test the parameter recovery process for bias and find that the scalar spectral index, n{sub s} , is biased high, but only by 0.09{sigma}, while the remaining parameters are biased by <0.15{sigma}. The improvement in the third peak measurement leads to tighter lower limits from WMAP on the number of relativistic degrees of freedom (e.g., neutrinos) in the early universe: N{sub eff}>2.7(95%CL). Also, using WMAP data alone, the primordial helium mass fraction is found to be Y{sub He} = 0.28{sup +0.14}{sub -0.15}, and with data from higher-resolution cosmic microwave background experiments included, we now establish the existence of pre-stellar helium at >3{sigma}. These new WMAP measurements provide important tests of big bang cosmology.« less

Autofluorescence-based diagnostic UV imaging of tissues and cells

NASA Astrophysics Data System (ADS)

Renkoski, Timothy E.

Cancer is the second leading cause of death in the United States, and its early diagnosis is critical to improving treatment options and patient outcomes. In autofluorescence (AF) imaging, light of controlled wavelengths is projected onto tissue, absorbed by specific molecules, and re-emitted at longer wavelengths. Images of re-emitted light are used together with spectral information to infer tissue functional information and diagnosis. This dissertation describes AF imaging studies of three different organs using data collected from fresh human surgical specimens. In the ovary study, illumination was at 365 nm, and images were captured at 8 emission wavelengths. Measurements from a multispectral imaging system and fiber optic probe were used to map tissue diagnosis at every image pixel. For the colon and pancreas studies, instrumentation was developed extending AF imaging capability to sub-300 nm excitation. Images excited in the deep UV revealed tryptophan and protein content which are believed to change with disease state. Several excitation wavelength bands from 280 nm to 440 nm were investigated. Microscopic AF images collected in the pancreas study included both cultured and primary cells. Several findings are reported. A method of transforming fiber optic probe spectra for direct comparison with imager spectra was devised. Normalization of AF data by green reflectance data was found useful in correcting hemoglobin absorption. Ratio images, both AF and reflectance, were formulated to highlight growths in the colon. Novel tryptophan AF images were found less useful for colon diagnostics than the new ratio techniques. Microscopic tryptophan AF images produce useful visualization of cellular protein content, but their diagnostic value requires further study.

Uncertainty indication in soil function maps - transparent and easy-to-use information to support sustainable use of soil resources

NASA Astrophysics Data System (ADS)

Greiner, Lucie; Nussbaum, Madlene; Papritz, Andreas; Zimmermann, Stephan; Gubler, Andreas; Grêt-Regamey, Adrienne; Keller, Armin

2018-05-01

Spatial information on soil function fulfillment (SFF) is increasingly being used to inform decision-making in spatial planning programs to support sustainable use of soil resources. Soil function maps visualize soils abilities to fulfill their functions, e.g., regulating water and nutrient flows, providing habitats, and supporting biomass production based on soil properties. Such information must be reliable for informed and transparent decision-making in spatial planning programs. In this study, we add to the transparency of soil function maps by (1) indicating uncertainties arising from the prediction of soil properties generated by digital soil mapping (DSM) that are used for soil function assessment (SFA) and (2) showing the response of different SFA methods to the propagation of uncertainties through the assessment. For a study area of 170 km2 in the Swiss Plateau, we map 10 static soil sub-functions for agricultural soils for a spatial resolution of 20 × 20 m together with their uncertainties. Mapping the 10 soil sub-functions using simple ordinal assessment scales reveals pronounced spatial patterns with a high variability of SFF scores across the region, linked to the inherent properties of the soils and terrain attributes and climate conditions. Uncertainties in soil properties propagated through SFA methods generally lead to substantial uncertainty in the mapped soil sub-functions. We propose two types of uncertainty maps that can be readily understood by stakeholders. Cumulative distribution functions of SFF scores indicate that SFA methods respond differently to the propagated uncertainty of soil properties. Even where methods are comparable on the level of complexity and assessment scale, their comparability in view of uncertainty propagation might be different. We conclude that comparable uncertainty indications in soil function maps are relevant to enable informed and transparent decisions on the sustainable use of soil resources.

Differential contribution of key metabolic substrates and cellular oxygen in HIF signalling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhdanov, Alexander V., E-mail: a.zhdanov@ucc.ie; Waters, Alicia H.C.; Golubeva, Anna V.

2015-01-01

Changes in availability and utilisation of O{sub 2} and metabolic substrates are common in ischemia and cancer. We examined effects of substrate deprivation on HIF signalling in PC12 cells exposed to different atmospheric O{sub 2}. Upon 2–4 h moderate hypoxia, HIF-α protein levels were dictated by the availability of glutamine and glucose, essential for deep cell deoxygenation and glycolytic ATP flux. Nuclear accumulation of HIF-1α dramatically decreased upon inhibition of glutaminolysis or glutamine deprivation. Elevation of HIF-2α levels was transcription-independent and associated with the activation of Akt and Erk1/2. Upon 2 h anoxia, HIF-2α levels strongly correlated with cellular ATP,more » produced exclusively via glycolysis. Without glucose, HIF signalling was suppressed, giving way to other regulators of cell adaptation to energy crisis, e.g. AMPK. Consequently, viability of cells deprived of O{sub 2} and glucose decreased upon inhibition of AMPK with dorsomorphin. The capacity of cells to accumulate HIF-2α decreased after 24 h glucose deprivation. This effect, associated with increased AMPKα phosphorylation, was sensitive to dorsomorphin. In chronically hypoxic cells, glutamine played no major role in HIF-2α accumulation, which became mainly glucose-dependent. Overall, the availability of O{sub 2} and metabolic substrates intricately regulates HIF signalling by affecting cell oxygenation, ATP levels and pathways involved in production of HIF-α. - Highlights: • Gln and Glc regulate HIF levels in hypoxic cells by maintaining low O{sub 2} and high ATP. • HIF-α levels under anoxia correlate with cellular ATP and critically depend on Glc. • Gln and Glc modulate activity of Akt, Erk and AMPK, regulating HIF production. • HIF signalling is differentially inhibited by prolonged Glc and Gln deprivation. • Unlike Glc, Gln plays no major role in HIF signalling in chronically hypoxic cells.« less

Genome-wide chromatin state transitions associated with developmental and environmental cues.

PubMed

Zhu, Jiang; Adli, Mazhar; Zou, James Y; Verstappen, Griet; Coyne, Michael; Zhang, Xiaolan; Durham, Timothy; Miri, Mohammad; Deshpande, Vikram; De Jager, Philip L; Bennett, David A; Houmard, Joseph A; Muoio, Deborah M; Onder, Tamer T; Camahort, Ray; Cowan, Chad A; Meissner, Alexander; Epstein, Charles B; Shoresh, Noam; Bernstein, Bradley E

2013-01-31

Differences in chromatin organization are key to the multiplicity of cell states that arise from a single genetic background, yet the landscapes of in vivo tissues remain largely uncharted. Here, we mapped chromatin genome-wide in a large and diverse collection of human tissues and stem cells. The maps yield unprecedented annotations of functional genomic elements and their regulation across developmental stages, lineages, and cellular environments. They also reveal global features of the epigenome, related to nuclear architecture, that also vary across cellular phenotypes. Specifically, developmental specification is accompanied by progressive chromatin restriction as the default state transitions from dynamic remodeling to generalized compaction. Exposure to serum in vitro triggers a distinct transition that involves de novo establishment of domains with features of constitutive heterochromatin. We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming. Copyright © 2013 Elsevier Inc. All rights reserved.

Harnessing cell-to-cell variations to probe bacterial structure and biophysics

NASA Astrophysics Data System (ADS)

Cass, Julie A.

Advances in microscopy and biotechnology have given us novel insights into cellular biology and physics. While bacteria were long considered to be relatively unstructured, the development of fluorescence microscopy techniques, and spatially and temporally resolved high-throughput quantitative studies, have uncovered that the bacterial cell is highly organized, and its structure rigorously maintained. In this thesis I will describe our gateTool software, designed to harness cell-to-cell variations to probe bacterial structure, and discuss two exciting aspects of structure that we have employed gateTool to investigate: (i) chromosome organization and the cellular mechanisms for controlling DNA dynamics, and (ii) the study of cell wall synthesis, and how the genes in the synthesis pathway impact cellular shape. In the first project, we develop a spatial and temporal mapping of cell-cycle-dependent chromosomal organization, and use this quantitative map to discover that chromosomal loci segregate from midcell with universal dynamics. In the second project, I describe preliminary time- lapse and snapshot imaging analysis suggesting phentoypical coherence across peptidoglycan synthesis pathways.

A Liver-Centric Multiscale Modeling Framework for Xenobiotics.

PubMed

Sluka, James P; Fu, Xiao; Swat, Maciej; Belmonte, Julio M; Cosmanescu, Alin; Clendenon, Sherry G; Wambaugh, John F; Glazier, James A

2016-01-01

We describe a multi-scale, liver-centric in silico modeling framework for acetaminophen pharmacology and metabolism. We focus on a computational model to characterize whole body uptake and clearance, liver transport and phase I and phase II metabolism. We do this by incorporating sub-models that span three scales; Physiologically Based Pharmacokinetic (PBPK) modeling of acetaminophen uptake and distribution at the whole body level, cell and blood flow modeling at the tissue/organ level and metabolism at the sub-cellular level. We have used standard modeling modalities at each of the three scales. In particular, we have used the Systems Biology Markup Language (SBML) to create both the whole-body and sub-cellular scales. Our modeling approach allows us to run the individual sub-models separately and allows us to easily exchange models at a particular scale without the need to extensively rework the sub-models at other scales. In addition, the use of SBML greatly facilitates the inclusion of biological annotations directly in the model code. The model was calibrated using human in vivo data for acetaminophen and its sulfate and glucuronate metabolites. We then carried out extensive parameter sensitivity studies including the pairwise interaction of parameters. We also simulated population variation of exposure and sensitivity to acetaminophen. Our modeling framework can be extended to the prediction of liver toxicity following acetaminophen overdose, or used as a general purpose pharmacokinetic model for xenobiotics.

A Liver-Centric Multiscale Modeling Framework for Xenobiotics

PubMed Central

Swat, Maciej; Cosmanescu, Alin; Clendenon, Sherry G.; Wambaugh, John F.; Glazier, James A.

2016-01-01

We describe a multi-scale, liver-centric in silico modeling framework for acetaminophen pharmacology and metabolism. We focus on a computational model to characterize whole body uptake and clearance, liver transport and phase I and phase II metabolism. We do this by incorporating sub-models that span three scales; Physiologically Based Pharmacokinetic (PBPK) modeling of acetaminophen uptake and distribution at the whole body level, cell and blood flow modeling at the tissue/organ level and metabolism at the sub-cellular level. We have used standard modeling modalities at each of the three scales. In particular, we have used the Systems Biology Markup Language (SBML) to create both the whole-body and sub-cellular scales. Our modeling approach allows us to run the individual sub-models separately and allows us to easily exchange models at a particular scale without the need to extensively rework the sub-models at other scales. In addition, the use of SBML greatly facilitates the inclusion of biological annotations directly in the model code. The model was calibrated using human in vivo data for acetaminophen and its sulfate and glucuronate metabolites. We then carried out extensive parameter sensitivity studies including the pairwise interaction of parameters. We also simulated population variation of exposure and sensitivity to acetaminophen. Our modeling framework can be extended to the prediction of liver toxicity following acetaminophen overdose, or used as a general purpose pharmacokinetic model for xenobiotics. PMID:27636091

Selective protection of cultured human cells from the toxic effects of ultraviolet light by proflavine pretreatment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, J.R.; Little, J.B.

1977-10-01

Pretreatment of LICH human cells by nontoxic doses (0.1 to 5.0 ..mu..g/ml) of proflavine protects them from inactivation by ultraviolet light. The protection is acquired rapidly after exposure of cells to proflavine, with 50 percent of maximum protection being afforded within 5 min and cells being maximally protected by 20 min. Loss of protection follows similar kinetics upon removal of proflavine from the culture medium. Protection is selective and cannot be explained on the basis of proflavine absorption of uv light. Cellular survival curves after ultraviolet light for cells protected by 1, 2, 3, 4, or 5 ..mu..g/ml of proflavinemore » show that protection alters only the slope of the survival curve, not altering the quasi-threshold dose, D/sub q/. The D/sub 0/ varies from 4.8 J/m/sup 2/ for untreated cells to 10.5 J/m/sup 2/ for cells pretreated with 5 ..mu..g/ml. These data suggest the D/sub 0/ and D/sub q/ do not represent parameters of a single underlying process, manifested in a random stochastic manner, but may reflect different cellular mechanisms or responses to different DNA damage. Proflavine is selective in mitigating only those which predominate at uv doses greater than the D/sub q/.« less

A Concept Mapping Study of Physicians' Perceptions of Factors Influencing Management and Control of Hypertension in Sub-Saharan Africa

PubMed Central

Iwelunmor, Juliet; Blackstone, Sarah; Gyamfi, Joyce; Airhihenbuwa, Collins; Plange-Rhule, Jacob; Tayo, Bamidele; Adanu, Richard; Ogedegbe, Gbenga

2015-01-01

Hypertension, once a rare problem in Sub-Saharan Africa (SSA), is predicted to be a major cause of death by 2020 with mortality rates as high as 75%. However, comprehensive knowledge of provider-level factors that influence optimal management is limited. The objective of the current study was to discover physicians' perceptions of factors influencing optimal management and control of hypertension in SSA. Twelve physicians attending the Cardiovascular Research Training (CaRT) Institute at the University of Ghana, College of Health Sciences, were invited to complete a concept mapping process that included brainstorming the factors influencing optimal management and control of hypertension in patients, sorting and organizing the factors into similar domains, and rating the importance and feasibility of efforts to address these factors. The highest ranked important and feasible factors include helping patients accept their condition and availability of adequate equipment to enable the provision of needed care. The findings suggest that patient self-efficacy and support, physician-related factors, policy factors, and economic factors are important aspects that must be addressed to achieve optimal hypertension management. Given the work demands identified by physicians, future research should investigate cost-effective strategies of shifting physician responsibilities to well-trained no-physician clinicians in order to improve hypertension management. PMID:26550488

DOE Office of Scientific and Technical Information (OSTI.GOV)

Litvinova, Larisa, E-mail: larisalitvinova@yandex.ru, E-mail: vshupletsova@mail.ru, E-mail: leitsin@mail.ru; Shupletsova, Valeria, E-mail: larisalitvinova@yandex.ru, E-mail: vshupletsova@mail.ru, E-mail: leitsin@mail.ru; Leitsin, Vladimir, E-mail: larisalitvinova@yandex.ru, E-mail: vshupletsova@mail.ru, E-mail: leitsin@mail.ru

The work studies ZrO{sub 2}(Me{sub x}O{sub y})-based porous ceramics produced from the powders consisting of hollow spherical particles. It was shown that the structure is represented by a cellular framework with bimodal porosity consisting of sphere-like large pores and pores that were not filled with the powder particles during the compaction. For such ceramics, the increase of pore volume is accompanied by the increased strain in an elastic area. It was also shown that the porous ZrO{sub 2} ceramics had no acute or chronic cytotoxicity. At the same time, ceramics possess the following osteoconductive properties: adhesion support, spreading, proliferation andmore » osteogenic differentiation of MSCs.« less

Spatiotemporal chaos near the onset of cellular growth during thin-film solidification of a binary alloy

NASA Technical Reports Server (NTRS)

Lee, J. T. C.; Tsiveriotis, K.; Brown, R. A.

1992-01-01

Thin-film solidification experiments with a succinonitrile-acetone alloy are used to observe the long time-scale dynamics of cellular crystal growth at growth rates only slightly above the critical value VC = Vc(lambda sub c) for the onset of morphological instability. Under these conditions only very small amplitude cells are observed with wavelengths near the value predicted by linear stability theory lambda = lambda sub c. At long times, microstructures with wavelengths significantly finer than lambda suc c form by nucleation at defects across the interface. These interfaces do not have a unique microstructure, but seem to exhibit spatiotemporal chaos on a long time scale caused by the continual birth and death of cells by tip splitting and cell annihilation in grooves.

Mapping evidence of interventions and strategies to bridge the gap in the implementation of the prevention of mother-to-child transmission of HIV programme policy in sub-Saharan countries: A scoping review

PubMed Central

Naidoo, Joanne R.

2017-01-01

Background Prevention of mother-to-child transmission (PMTCT) of HIV is a life-saving public health intervention. Sub-Saharan African (SSA) countries have made significant progress in the programme, but little is known about the strategies used by them to eliminate mother-to-child transmission of HIV. Aim To map evidence of strategies and interventions employed by SSA in bridging the implementation gap in the rapidly changing PMTCT of HIV programme policy. Methods Electronic search of the databases MEDLINE, PubMed and SABINET for articles published in English between 2001 and August 2016. Key words included ‘Sub-Saharan African countries’, ‘implementation strategies’, ‘interventions to bridge implementation gap’, ‘prevention of mother-to-child transmission of HIV’ and ‘closing implementation gap’. Results Of a total of 743 articles, 25 articles that met the inclusion criteria were included in the study. Manual content analysis resulted in the identification of three categories of strategies: (1) health system (referral systems, integration of services, supportive leadership, systematic quality-improvement approaches that vigorously monitors programme performance); (2) health service delivery (task shifting, networking, shared platform for learning, local capacity building, supportive supervision); as well as (3) community-level strategies (community health workers, technology use – mHealth, family-centred approaches, male involvement, culturally appropriate interventions). Conclusion There are strategies that exist in SSA countries. Future research should examine multifaceted scientific models to prioritise the highest impact and be evaluated for effectiveness and efficiency. PMID:28582993

Dissociation energies of Ag–RG (RG = Ar, Kr, Xe) and AgO molecules from velocity map imaging studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cooper, Graham A.; Gentleman, Alexander S.; Iskra, Andreas

2015-09-28

The near ultraviolet photodissociation dynamics of silver atom—rare gas dimers have been studied by velocity map imaging. Ag–RG (RG = Ar, Kr, Xe) species generated by laser ablation are excited in the region of the C ({sup 2}Σ{sup +})←X ({sup 2}Σ{sup +}) continuum leading to direct, near-threshold dissociation generating Ag* ({sup 2}P{sub 3/2}) + RG ({sup 1}S{sub 0}) products. Images recorded at excitation wavelengths throughout the C ({sup 2}Σ{sup +})←X ({sup 2}Σ{sup +}) continuum, coupled with known atomic energy levels, permit determination of the ground X ({sup 2}Σ{sup +}) state dissociation energies of 85.9 ± 23.4 cm{sup −1} (Ag–Ar), 149.3 ±more » 22.4 cm{sup −1} (Ag–Kr), and 256.3 ± 16.0 cm{sup −1} (Ag–Xe). Three additional photolysis processes, each yielding Ag atom photoproducts, are observed in the same spectral region. Two of these are markedly enhanced in intensity upon seeding the molecular beam with nitrous oxide, and are assigned to photodissociation of AgO at the two-photon level. These features yield an improved ground state dissociation energy for AgO of 15 965 ± 81 cm{sup −1}, which is in good agreement with high level calculations. The third process results in Ag atom fragments whose kinetic energy shows anomalously weak photon energy dependence and is assigned tentatively to dissociative ionization of the silver dimer Ag{sub 2}.« less

SNM Movement Detection/Radiation Sensors and Advanced Materials Portfolio Review, CdMnTe (CMT) Gamma Ray Detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolotnikov,A.

2009-06-02

The project goals are: (1) Develop CMT radiation detectors - Demonstrate feasibility (Phase 1 is complete) and Improve material properties and device performance; (2) This project will lead to novel radiation detectors - high detection efficiency, high energy-resolution, ambient-temperature operation, and low production cost; and (3) Such detectors are needed in areas of nonproliferation and national security for detection of SNM. Research highlights are: (1) We achieved our Phase-I goal - Demonstration of CMT detector performance approaching that of CZT detectors; (2) Demonstrated that In-doped CMT is much closer to its anticipated performance as radiation detectors than other alternative materials,more » TlBr and HgI{sub 2} - Large crystal volumes, 10{sup 10}{Omega}{center_dot}cm, 3 x 10{sup -3}cm{sup 2}/V, and stable response; and (3) Conducted material and device characterization experiments - Detectors: I-V, {mu}{sub e}, ({mu}{tau}){sub e}, internal E fields, energy spectra, and high-resolution x-ray response mapping data and Materials - DLTS, TCT, PL, EPDs, XRD, PCD and IR transmission.« less

Development of 3D woven cellular structures for adaptive composites based on thermoplastic hybrid yarns

NASA Astrophysics Data System (ADS)

Sennewald, C.; Vorhof, M.; Schegner, P.; Hoffmann, G.; Cherif, C.; Boblenz, J.; Sinapius, M.; Hühne, C.

2018-05-01

Flexible cellular 3D structures with structure-inherent compliance made of fiber-reinforced composites have repeatedly aroused the interest of international research groups. Such structures offer the possibility to meet the increasing demand for flexible and adaptive structures. The aim of this paper is the development of cellular 3D structures based on weaving technology. Considering the desired geometry of the 3D structure, algorithms are developed for the formation of geometry through tissue sub-areas. Subsequently, these sub-areas are unwound into the weaving level and appropriate weave patterns are developed. A particular challenge is the realization of compliant mechanisms in the woven fabric. This can be achieved either by combining different materials or, in particular, by implementing large stiffness gradients by means of varying the woven fabrics thickness, whereas differences in wall thickness have to be realized with a factor of 1:10. A manufacturing technology based on the weaving process is developed for the realization of the developed 3D cellular structures. To this end, solutions for the processing of hybrid thermoplastic materials (e.g. tapes), solutions for the integration of inlays in the weaving process (thickening of partial areas), and solutions for tissue retraction, as well as for the fabric pull-off (linear pull-off system) are being developed. In this way, woven cellular 3D structures with woven outer layers and woven joint areas (compliance) can be realized in a single process step and are subsequently characterized.

The ECM moves during primitive streak formation--computation of ECM versus cellular motion.

PubMed

Zamir, Evan A; Rongish, Brenda J; Little, Charles D

2008-10-14

Galileo described the concept of motion relativity--motion with respect to a reference frame--in 1632. He noted that a person below deck would be unable to discern whether the boat was moving. Embryologists, while recognizing that embryonic tissues undergo large-scale deformations, have failed to account for relative motion when analyzing cell motility data. A century of scientific articles has advanced the concept that embryonic cells move ("migrate") in an autonomous fashion such that, as time progresses, the cells and their progeny assemble an embryo. In sharp contrast, the motion of the surrounding extracellular matrix scaffold has been largely ignored/overlooked. We developed computational/optical methods that measure the extent embryonic cells move relative to the extracellular matrix. Our time-lapse data show that epiblastic cells largely move in concert with a sub-epiblastic extracellular matrix during stages 2 and 3 in primitive streak quail embryos. In other words, there is little cellular motion relative to the extracellular matrix scaffold--both components move together as a tissue. The extracellular matrix displacements exhibit bilateral vortical motion, convergence to the midline, and extension along the presumptive vertebral axis--all patterns previously attributed solely to cellular "migration." Our time-resolved data pose new challenges for understanding how extracellular chemical (morphogen) gradients, widely hypothesized to guide cellular trajectories at early gastrulation stages, are maintained in this dynamic extracellular environment. We conclude that models describing primitive streak cellular guidance mechanisms must be able to account for sub-epiblastic extracellular matrix displacements.

Semi-automated extraction of landslides in Taiwan based on SPOT imagery and DEMs

NASA Astrophysics Data System (ADS)

Eisank, Clemens; Hölbling, Daniel; Friedl, Barbara; Chen, Yi-Chin; Chang, Kang-Tsung

2014-05-01

The vast availability and improved quality of optical satellite data and digital elevation models (DEMs), as well as the need for complete and up-to-date landslide inventories at various spatial scales have fostered the development of semi-automated landslide recognition systems. Among the tested approaches for designing such systems, object-based image analysis (OBIA) stepped out to be a highly promising methodology. OBIA offers a flexible, spatially enabled framework for effective landslide mapping. Most object-based landslide mapping systems, however, have been tailored to specific, mainly small-scale study areas or even to single landslides only. Even though reported mapping accuracies tend to be higher than for pixel-based approaches, accuracy values are still relatively low and depend on the particular study. There is still room to improve the applicability and objectivity of object-based landslide mapping systems. The presented study aims at developing a knowledge-based landslide mapping system implemented in an OBIA environment, i.e. Trimble eCognition. In comparison to previous knowledge-based approaches, the classification of segmentation-derived multi-scale image objects relies on digital landslide signatures. These signatures hold the common operational knowledge on digital landslide mapping, as reported by 25 Taiwanese landslide experts during personal semi-structured interviews. Specifically, the signatures include information on commonly used data layers, spectral and spatial features, and feature thresholds. The signatures guide the selection and implementation of mapping rules that were finally encoded in Cognition Network Language (CNL). Multi-scale image segmentation is optimized by using the improved Estimation of Scale Parameter (ESP) tool. The approach described above is developed and tested for mapping landslides in a sub-region of the Baichi catchment in Northern Taiwan based on SPOT imagery and a high-resolution DEM. An object-based accuracy assessment is conducted by quantitatively comparing extracted landslide objects with landslide polygons that were visually interpreted by local experts. The applicability and transferability of the mapping system are evaluated by comparing initial accuracies with those achieved for the following two tests: first, usage of a SPOT image from the same year, but for a different area within the Baichi catchment; second, usage of SPOT images from multiple years for the same region. The integration of the common knowledge via digital landslide signatures is new in object-based landslide studies. In combination with strategies to optimize image segmentation this may lead to a more objective, transferable and stable knowledge-based system for the mapping of landslides from optical satellite data and DEMs.

CD4 T Cells From Intestinal Biopsies of Crohn's Disease Patients React to Mycobacterium avium subspecies paratuberculosis

USDA-ARS?s Scientific Manuscript database

The role of Mycobacterium avium subspecies paratuberculosis (MAP) in Crohn’s disease (CD) remains controversial. One issue that has been raised is the lack of data showing a cellular immune response to MAP. Earlier studies have mostly focused on responses in peripheral blood which have several limit...

Genes encoding a callose synthase and phytochrome A are adjacent to a MAP3Ka-like gene in Beta vulgaris USH20

USDA-ARS?s Scientific Manuscript database

MAP3Ka encodes a key conserved protein kinase responsible for orchestrating a rapid cascade of cellular events ultimately leading to localized cell death. Hypersensitive response, as it is termed, enables genetically-resistant plants to limit microbial invasion under the right environmental conditio...

Numerically exploring habitat fragmentation effects on populations using cell-based coupled map lattices

Treesearch

Michael Bevers; Curtis H. Flather

1999-01-01

We examine habitat size, shape, and arrangement effects on populations using a discrete reaction-diffusion model. Diffusion is modeled passively and applied to a cellular grid of territories forming a coupled map lattice. Dispersal mortality is proportional to the amount of nonhabitat and fully occupied habitat surrounding a given cell, with distance decay. After...

Motivation and Pleasure Scale-Self-Report (MAP-SR): Validation of the German version of a self-report measure for screening negative symptoms in schizophrenia.

PubMed

Engel, Maike; Lincoln, Tania Marie

2016-02-01

Validated self-report instruments could provide a time efficient screening method for negative symptoms in people with schizophrenia. The aim of this study was to examine the psychometric properties of a German version of the Motivation and Pleasure Scale-Self-Report (MAP-SR) which is based on the Clinical Assessment Interview for Negative Symptoms (CAINS). In- and outpatients (N=50) with schizophrenia or schizoaffective disorder were assessed with standardized interviews and questionnaires on negative and positive symptoms and general psychopathology in schizophrenia, depression, and global functioning. The German version of the MAP-SR showed high internal consistency. Convergent validity was supported by significant correlations between the MAP-SR with the experience sub-scale of the CAINS and the negative symptom sub-scale of the Positive and Negative Syndrome Scale. The MAP-SR also exhibited discriminant validity indicated by its non-significant correlations with positive symptoms and general psychopathology, which is in line with the findings for the original version of the MAP-SR. However, the MAP-SR correlated moderately with depression. The German MAP-SR appears to be a valid and suitable diagnostic tool for the identification of negative symptoms in schizophrenia. Copyright © 2015 Elsevier Inc. All rights reserved.

TH-CD-202-09: Free-Breathing Proton MRI Functional Lung Avoidance Maps to Guide Radiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Capaldi, D; Sheikh, K; Parraga, G

Purpose: Pulmonary functional MRI using inhaled gas contrast agents was previously investigated as a way to identify well-functioning lung in patients with NSCLC who are clinical candidates for radiotherapy. Hyperpolarized noble-gas ({sup 3}He and {sup 129}Xe) MRI has also been optimized to measure functional lung information, but for a number of reasons, the clinical translation of this approach to guide radiotherapy planning has been limited. As an alternative, free-breathing pulmonary 1H MRI using clinically available MRI systems and pulse sequences provides a non-contrast-enhanced method to generate both ventilation and perfusion maps. Free-breathing {sup 1}H MRI exploits non-rigid registration and Fouriermore » decomposition of MRI signal intensity differences (Bauman et al., MRM, 2009) that may be generated during normal tidal breathing. Here, our objective was to generate free-breathing {sup 1}H MRI ventilation and lung function avoidance maps in patients with NSCLC as a way to guide radiation therapy planning. Methods: Stage IIIA/IIIB NSCLC patients (n=8, 68±9yr) provided written informed consent to a randomized controlled clinical trial ( https://clinicaltrials.gov/ct2/show/NCT02002052 ) that aimed to compare outcomes related to image-guided versus conventional radiation therapy planning. Hyperpolarized {sup 3}He/{sup 129}Xe and dynamic free tidal-breathing {sup 1}H MRI were acquired as previously described (Capaldi et al., Acad Radiol, 2015). Non-rigid registration was performed using the modality-independent-neighbourhood-descriptor (MIND) deformable approach (Heinrich et al., Med Image Anal, 2012). Ventilation-defect-percent ({sup 3}He:VDP{sub He}, {sup 129}Xe:VDP{sub Xe}, Free-breathing-{sup 1}H:VDP{sub FB}) and the corresponding ventilation maps were compared using Pearson correlation coefficients (r) and the Dice similarity coefficient (DSC). Results: VDP{sub FB} was significantly related to VDP{sub He} (r=.71; p=.04) and VDP{sub Xe} (r=.80; p=.01) and there were also strong spatial relationships (DSC{sub He}/DSC{sub Xe}=89±3%/77±11%). Conclusion: In this proof of concept study in NSCLC patients, free-breathing {sup 1}H MRI ventilation defects were quantitatively and spatially related to inhaled-noble-gas MRI ventilation defects. Free-breathing {sup 1}H MRI measures lung function/ventilation that can be used to optimize radiotherapy planning in NSCLC patients.« less

Comparison of neural network applications for channel assignment in cellular TDMA networks and dynamically sectored PCS networks

NASA Astrophysics Data System (ADS)

Hortos, William S.

1997-04-01

The use of artificial neural networks (NNs) to address the channel assignment problem (CAP) for cellular time-division multiple access and code-division multiple access networks has previously been investigated by this author and many others. The investigations to date have been based on a hexagonal cell structure established by omnidirectional antennas at the base stations. No account was taken of the use of spatial isolation enabled by directional antennas to reduce interference between mobiles. Any reduction in interference translates into increased capacity and consequently alters the performance of the NNs. Previous studies have sought to improve the performance of Hopfield- Tank network algorithms and self-organizing feature map algorithms applied primarily to static channel assignment (SCA) for cellular networks that handle uniformly distributed, stationary traffic in each cell for a single type of service. The resulting algorithms minimize energy functions representing interference constraint and ad hoc conditions that promote convergence to optimal solutions. While the structures of the derived neural network algorithms (NNAs) offer the potential advantages of inherent parallelism and adaptability to changing system conditions, this potential has yet to be fulfilled the CAP for emerging mobile networks. The next-generation communication infrastructures must accommodate dynamic operating conditions. Macrocell topologies are being refined to microcells and picocells that can be dynamically sectored by adaptively controlled, directional antennas and programmable transceivers. These networks must support the time-varying demands for personal communication services (PCS) that simultaneously carry voice, data and video and, thus, require new dynamic channel assignment (DCA) algorithms. This paper examines the impact of dynamic cell sectoring and geometric conditioning on NNAs developed for SCA in omnicell networks with stationary traffic to improve the metrics of convergence rate and call blocking. Genetic algorithms (GAs) are also considered in PCS networks as a means to overcome the known weakness of Hopfield NNAs in determining global minima. The resulting GAs for DCA in PCS networks are compared to improved DCA algorithms based on Hopfield NNs for stationary cellular networks. Algorithm performance is compared on the basis of rate of convergence, blocking probability, analytic complexity, and parametric sensitivity to transient traffic demands and channel interference.

THE VIRUS-P EXPLORATION OF NEARBY GALAXIES (VENGA): THE X {sub CO} GRADIENT IN NGC 628

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blanc, Guillermo A.; Schruba, Andreas; Evans, Neal J. II

2013-02-20

We measure the radial profile of the {sup 12}CO(1-0) to H{sub 2} conversion factor (X {sub CO}) in NGC 628. The H{alpha} emission from the VENGA integral field spectroscopy is used to map the star formation rate (SFR) surface density ({Sigma}{sub SFR}). We estimate the molecular gas surface density ({Sigma}{sub H2}) from {Sigma}{sub SFR} by inverting the molecular star formation law (SFL), and compare it to the CO intensity to measure X {sub CO}. We study the impact of systematic uncertainties by changing the slope of the SFL, using different SFR tracers (H{alpha} versus far-UV plus 24 {mu}m), and COmore » maps from different telescopes (single-dish and interferometers). The observed X {sub CO} profile is robust against these systematics, drops by a factor of two from R {approx} 7 kpc to the center of the galaxy, and is well fit by a gradient {Delta}log(X {sub CO}) = 0.06 {+-} 0.02 dex kpc{sup -1}. We study how changes in X {sub CO} follow changes in metallicity, gas density, and ionization parameter. Theoretical models show that the gradient in X {sub CO} can be explained by a combination of decreasing metallicity, and decreasing {Sigma}{sub H2} with radius. Photoelectric heating from the local UV radiation field appears to contribute to the decrease of X {sub CO} in higher density regions. Our results show that galactic environment plays an important role at setting the physical conditions in star-forming regions, in particular the chemistry of carbon in molecular complexes, and the radiative transfer of CO emission. We caution against adopting a single X {sub CO} value when large changes in gas surface density or metallicity are present.« less

Metabolomic mapping of cancer stem cells for reducing and exploiting tumor heterogeneity.

PubMed

Cuyàs, Elisabet; Verdura, Sara; Fernández-Arroyo, Salvador; Bosch-Barrera, Joaquim; Martin-Castillo, Begoña; Joven, Jorge; Menendez, Javier A

2017-11-21

Personalized cancer medicine based on the analysis of tumors en masse is limited by tumor heterogeneity, which has become a major obstacle to effective cancer treatment. Cancer stem cells (CSC) are emerging as key drivers of inter- and intratumoral heterogeneity. CSC have unique metabolic dependencies that are required not only for specific bioenergetic/biosynthetic demands but also for sustaining their operational epigenetic traits, i.e. self-renewal, tumor-initiation, and plasticity. Given that the metabolome is the final downstream product of all the -omic layers and, therefore, most representative of the biological phenotype, we here propose that a novel approach to better understand the complexity of tumor heterogeneity is by mapping and cataloging small numbers of CSC metabolomic phenotypes. The narrower metabolomic diversity of CSC states could be employed to reduce multidimensional tumor heterogeneity into dynamic models of fewer actionable sub-phenotypes. The identification of the driver nodes that are used differentially by CSC states to metabolically regulate self-renewal and tumor initation and escape chemotherapy might open new preventive and therapeutic avenues. The mapping of CSC metabolomic states could become a pioneering strategy to reduce the dimensionality of tumor heterogeneity and improve our ability to examine changes in tumor cell populations for cancer detection, prognosis, prediction/monitoring of therapy response, and detection of therapy resistance and recurrent disease. The identification of driver metabolites and metabolic nodes accounting for a large amount of variance within the CSC metabolomic sub-phenotypes might offer new unforeseen opportunities for reducing and exploiting tumor heterogeneity via metabolic targeting of CSC.

Cancer Diagnosis Epigenomics Scientific Workflow Scheduling in the Cloud Computing Environment Using an Improved PSO Algorithm

PubMed

N, Sadhasivam; R, Balamurugan; M, Pandi

2018-01-27

Objective: Epigenetic modifications involving DNA methylation and histone statud are responsible for the stable maintenance of cellular phenotypes. Abnormalities may be causally involved in cancer development and therefore could have diagnostic potential. The field of epigenomics refers to all epigenetic modifications implicated in control of gene expression, with a focus on better understanding of human biology in both normal and pathological states. Epigenomics scientific workflow is essentially a data processing pipeline to automate the execution of various genome sequencing operations or tasks. Cloud platform is a popular computing platform for deploying large scale epigenomics scientific workflow. Its dynamic environment provides various resources to scientific users on a pay-per-use billing model. Scheduling epigenomics scientific workflow tasks is a complicated problem in cloud platform. We here focused on application of an improved particle swam optimization (IPSO) algorithm for this purpose. Methods: The IPSO algorithm was applied to find suitable resources and allocate epigenomics tasks so that the total cost was minimized for detection of epigenetic abnormalities of potential application for cancer diagnosis. Result: The results showed that IPSO based task to resource mapping reduced total cost by 6.83 percent as compared to the traditional PSO algorithm. Conclusion: The results for various cancer diagnosis tasks showed that IPSO based task to resource mapping can achieve better costs when compared to PSO based mapping for epigenomics scientific application workflow. Creative Commons Attribution License

A Framework for Parallel Unstructured Grid Generation for Complex Aerodynamic Simulations

NASA Technical Reports Server (NTRS)

Zagaris, George; Pirzadeh, Shahyar Z.; Chrisochoides, Nikos

2009-01-01

A framework for parallel unstructured grid generation targeting both shared memory multi-processors and distributed memory architectures is presented. The two fundamental building-blocks of the framework consist of: (1) the Advancing-Partition (AP) method used for domain decomposition and (2) the Advancing Front (AF) method used for mesh generation. Starting from the surface mesh of the computational domain, the AP method is applied recursively to generate a set of sub-domains. Next, the sub-domains are meshed in parallel using the AF method. The recursive nature of domain decomposition naturally maps to a divide-and-conquer algorithm which exhibits inherent parallelism. For the parallel implementation, the Master/Worker pattern is employed to dynamically balance the varying workloads of each task on the set of available CPUs. Performance results by this approach are presented and discussed in detail as well as future work and improvements.

Genetically targeted 3D visualisation of Drosophila neurons under Electron Microscopy and X-Ray Microscopy using miniSOG

PubMed Central

Ng, Julian; Browning, Alyssa; Lechner, Lorenz; Terada, Masako; Howard, Gillian; Jefferis, Gregory S. X. E.

2016-01-01

Large dimension, high-resolution imaging is important for neural circuit visualisation as neurons have both long- and short-range patterns: from axons and dendrites to the numerous synapses at terminal endings. Electron Microscopy (EM) is the favoured approach for synaptic resolution imaging but how such structures can be segmented from high-density images within large volume datasets remains challenging. Fluorescent probes are widely used to localise synapses, identify cell-types and in tracing studies. The equivalent EM approach would benefit visualising such labelled structures from within sub-cellular, cellular, tissue and neuroanatomical contexts. Here we developed genetically-encoded, electron-dense markers using miniSOG. We demonstrate their ability in 1) labelling cellular sub-compartments of genetically-targeted neurons, 2) generating contrast under different EM modalities, and 3) segmenting labelled structures from EM volumes using computer-assisted strategies. We also tested non-destructive X-ray imaging on whole Drosophila brains to evaluate contrast staining. This enabled us to target specific regions for EM volume acquisition. PMID:27958322

Global Mapping of Traditional Chinese Medicine into Bioactivity Space and Pathways Annotation Improves Mechanistic Understanding and Discovers Relationships between Therapeutic Action (Sub)classes

PubMed Central

Mohamad Zobir, Siti Zuraidah; Mohd Fauzi, Fazlin; Liggi, Sonia; Drakakis, Georgios; Fu, Xianjun; Fan, Tai-Ping; Bender, Andreas

2016-01-01

Traditional Chinese medicine (TCM) still needs more scientific rationale to be proven for it to be accepted further in the West. We are now in the position to propose computational hypotheses for the mode-of-actions (MOAs) of 45 TCM therapeutic action (sub)classes from in silico target prediction algorithms, whose target was later annotated with Kyoto Encyclopedia of Genes and Genomes pathway, and to discover the relationship between them by generating a hierarchical clustering. The results of 10,749 TCM compounds showed 183 enriched targets and 99 enriched pathways from Estimation Score ≤ 0 and ≥ 5% of compounds/targets in a (sub)class. The MOA of a (sub)class was established from supporting literature. Overall, the most frequent top three enriched targets/pathways were immune-related targets such as tyrosine-protein phosphatase nonreceptor type 2 (PTPN2) and digestive system such as mineral absorption. We found two major protein families, G-protein coupled receptor (GPCR), and protein kinase family contributed to the diversity of the bioactivity space, while digestive system was consistently annotated pathway motif, which agreed with the important treatment principle of TCM, “the foundation of acquired constitution” that includes spleen and stomach. In short, the TCM (sub)classes, in many cases share similar targets/pathways despite having different indications. PMID:26989424

Environmental effects of dredging: Methods for the assessment of the genotoxic effects of environmental contaminants. Glossary and references. Technical notes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Honeycutt, M.E.; Jarvis, A.S.; McFarland, V.A.

1995-07-01

This technical note is the third in a series of three that outline and describe the principal methods that have been developed to test the potential of environmental contaminants to cause mutagenic, carcinogenic, and teratogenic effects. The first in this series (EEDP-04-24) describes methods used to discern genotoxic effects at the sub cellular level, while the second (EEDP-04-25) describes methods used to discern genotoxic effects at the cellular and organ/organism level. Recent literature citations for each topic referenced in this series of technical notes are provided in this technical note, in addition to a glossary of terms. The information inmore » these technical notes is intended to provide Corps of Engineers personnel with a working knowledge of the terminology and conceptual basis of genotoxicity testing. To develop an improved understanding of the concepts of genotoxicity, readers are encouraged to review A Primer in Genotoxicity (Jarvis, Reilly, and Lutz 1993), presented in Volume D-93-3 of the Environmental Effects of Dredging information exchange bulletin.« less

Minimally invasive multimode optical fiber microendoscope for deep brain fluorescence imaging

PubMed Central

Ohayon, Shay; Caravaca-Aguirre, Antonio; Piestun, Rafael; DiCarlo, James J.

2018-01-01

A major open challenge in neuroscience is the ability to measure and perturb neural activity in vivo from well defined neural sub-populations at cellular resolution anywhere in the brain. However, limitations posed by scattering and absorption prohibit non-invasive multi-photon approaches for deep (>2mm) structures, while gradient refractive index (GRIN) endoscopes are relatively thick and can cause significant damage upon insertion. Here, we present a novel micro-endoscope design to image neural activity at arbitrary depths via an ultra-thin multi-mode optical fiber (MMF) probe that has 5–10X thinner diameter than commercially available micro-endoscopes. We demonstrate micron-scale resolution, multi-spectral and volumetric imaging. In contrast to previous approaches, we show that this method has an improved acquisition speed that is sufficient to capture rapid neuronal dynamics in-vivo in rodents expressing a genetically encoded calcium indicator (GCaMP). Our results emphasize the potential of this technology in neuroscience applications and open up possibilities for cellular resolution imaging in previously unreachable brain regions. PMID:29675297

Computational Systems Biology in Cancer: Modeling Methods and Applications

PubMed Central

Materi, Wayne; Wishart, David S.

2007-01-01

In recent years it has become clear that carcinogenesis is a complex process, both at the molecular and cellular levels. Understanding the origins, growth and spread of cancer, therefore requires an integrated or system-wide approach. Computational systems biology is an emerging sub-discipline in systems biology that utilizes the wealth of data from genomic, proteomic and metabolomic studies to build computer simulations of intra and intercellular processes. Several useful descriptive and predictive models of the origin, growth and spread of cancers have been developed in an effort to better understand the disease and potential therapeutic approaches. In this review we describe and assess the practical and theoretical underpinnings of commonly-used modeling approaches, including ordinary and partial differential equations, petri nets, cellular automata, agent based models and hybrid systems. A number of computer-based formalisms have been implemented to improve the accessibility of the various approaches to researchers whose primary interest lies outside of model development. We discuss several of these and describe how they have led to novel insights into tumor genesis, growth, apoptosis, vascularization and therapy. PMID:19936081

Detection and signal amplification in zebrafish RNA FISH.

PubMed

Hauptmann, Giselbert; Lauter, Gilbert; Söll, Iris

2016-04-01

In situ hybridization (ISH) has become an invaluable tool for the detection of RNA in cells, tissues and organisms. Due to improvements in target and signal amplification and in probe design remarkable progress has been made concerning sensitivity, specificity and resolution of chromogenic and fluorescent ISH (FISH). These advancements allow for exquisite cellular and sub-cellular resolution and for detecting multiple RNA species at a time by multiplexing. In zebrafish (F)ISH non-enzymatic and enzymatic amplification systems have been employed to obtain enhanced signal intensities and signal-to-noise ratios. These amplification strategies include branched DNA-based RNAscope and in situ hybridization chain reaction (HCR) techniques, as well as alkaline phosphatase (AP)- and horseradish peroxidase (PO)-based immunoassays. For practical application, we provide proven multiplex FISH protocols for AP- and PO-based visualization of mRNAs at high resolution. The protocols take advantage of optimized tyramide signal amplification (TSA) conditions of the PO assay and long-lasting high signal-to-noise ratio of the AP reaction, thereby enabling detection of less abundant transcripts. Copyright © 2016 Elsevier Inc. All rights reserved.

Putting Pluto's Geology on the Map

NASA Image and Video Library

2016-02-11

This geological map covers a portion of Pluto's surface that measures 1,290 miles (2,070 kilometers) from top to bottom, and includes the vast nitrogen-ice plain informally named Sputnik Planum and surrounding terrain. The map is overlain with colors that represent different geological terrains. Each terrain, or unit, is defined by its texture and morphology -- smooth, pitted, craggy, hummocky or ridged, for example. How well a unit can be defined depends on the resolution of the images that cover it. All of the terrain in this map has been imaged at a resolution of approximately 1,050 feet (320 meters) per pixel or better, meaning scientists can map units with relative confidence. The various blue and greenish units that fill the center of the map represent different textures seen across Sputnik Planum, from the cellular terrain in the center and north, to the smooth and pitted plains in the south. The black lines represent the troughs that mark the boundaries of cellular regions in the nitrogen ice. The purple unit represents the chaotic, blocky mountain ranges that line Sputnik's western border, and the pink unit represents the scattered, floating hills at its eastern edge. The possible cryovolcanic feature informally named Wright Mons is mapped in red in the southern corner of the map. The rugged highlands of the informally named Cthulhu Regio is mapped in dark brown along the western edge, and is pockmarked by many large impact craters, mapped in yellow. The base map for this geologic map is a mosaic of 12 images obtained by the Long Range Reconnaissance Imager (LORRI) at a resolution of 1,280 feet (about 390 meters) per pixel. The mosaic was obtained at a range of approximately 48,000 miles (77,300 kilometers) from Pluto, about an hour and 40 minutes before New Horizons' closest approach on July 14, 2015. http://photojournal.jpl.nasa.gov/catalog/PIA20465

Quantification of rectifications for the Northwestern University Flexible Sub-Ischial Vacuum Socket.

PubMed

Fatone, Stefania; Johnson, William Brett; Tran, Lilly; Tucker, Kerice; Mowrer, Christofer; Caldwell, Ryan

2017-06-01

The fit and function of a prosthetic socket depend on the prosthetist's ability to design the socket's shape to distribute load comfortably over the residual limb. We recently developed a sub-ischial socket for persons with transfemoral amputation: the Northwestern University Flexible Sub-Ischial Vacuum Socket. This study aimed to quantify the rectifications required to fit the Northwestern University Flexible Sub-Ischial Vacuum Socket to teach the technique to prosthetists as well as provide a computer-aided design-computer-aided manufacturing option. Development project. A program was used to align scans of unrectified and rectified negative molds and calculate shape change as a result of rectification. Averaged rectifications were used to create a socket template, which was shared with a central fabrication facility engaged in provision of Northwestern University Flexible Sub-Ischial Vacuum Sockets to early clinical adopters. Feedback regarding quality of fitting was obtained. Rectification maps created from 30 cast pairs of successfully fit Northwestern University Flexible Sub-Ischial Vacuum Sockets confirmed that material was primarily removed from the positive mold in the proximal-lateral and posterior regions. The template was used to fabricate check sockets for 15 persons with transfemoral amputation. Feedback suggested that the template provided a reasonable initial fit with only minor adjustments. Rectification maps and template were used to facilitate teaching and central fabrication of the Northwestern University Flexible Sub-Ischial Vacuum Socket. Minor issues with quality of initial fit achieved with the template may be due to inability to adjust the template to patient characteristics (e.g. tissue type, limb shape) and/or the degree to which it represented a fully mature version of the technique. Clinical relevance Rectification maps help communicate an important step in the fabrication of the Northwestern University Flexible Sub-Ischial Vacuum Socket facilitating dissemination of the technique, while the average template provides an alternative fabrication option via computer-aided design-computer-aided manufacturing and central fabrication.

Comparison of Sub-pixel Classification Approaches for Crop-specific Mapping

EPA Science Inventory

The Moderate Resolution Imaging Spectroradiometer (MODIS) data has been increasingly used for crop mapping and other agricultural applications. Phenology-based classification approaches using the NDVI (Normalized Difference Vegetation Index) 16-day composite (250 m) data product...

4D-PET reconstruction using a spline-residue model with spatial and temporal roughness penalties

NASA Astrophysics Data System (ADS)

Ralli, George P.; Chappell, Michael A.; McGowan, Daniel R.; Sharma, Ricky A.; Higgins, Geoff S.; Fenwick, John D.

2018-05-01

4D reconstruction of dynamic positron emission tomography (dPET) data can improve the signal-to-noise ratio in reconstructed image sequences by fitting smooth temporal functions to the voxel time-activity-curves (TACs) during the reconstruction, though the optimal choice of function remains an open question. We propose a spline-residue model, which describes TACs as weighted sums of convolutions of the arterial input function with cubic B-spline basis functions. Convolution with the input function constrains the spline-residue model at early time-points, potentially enhancing noise suppression in early time-frames, while still allowing a wide range of TAC descriptions over the entire imaged time-course, thus limiting bias. Spline-residue based 4D-reconstruction is compared to that of a conventional (non-4D) maximum a posteriori (MAP) algorithm, and to 4D-reconstructions based on adaptive-knot cubic B-splines, the spectral model and an irreversible two-tissue compartment (‘2C3K’) model. 4D reconstructions were carried out using a nested-MAP algorithm including spatial and temporal roughness penalties. The algorithms were tested using Monte-Carlo simulated scanner data, generated for a digital thoracic phantom with uptake kinetics based on a dynamic [18F]-Fluromisonidazole scan of a non-small cell lung cancer patient. For every algorithm, parametric maps were calculated by fitting each voxel TAC within a sub-region of the reconstructed images with the 2C3K model. Compared to conventional MAP reconstruction, spline-residue-based 4D reconstruction achieved  >50% improvements for five of the eight combinations of the four kinetics parameters for which parametric maps were created with the bias and noise measures used to analyse them, and produced better results for 5/8 combinations than any of the other reconstruction algorithms studied, while spectral model-based 4D reconstruction produced the best results for 2/8. 2C3K model-based 4D reconstruction generated the most biased parametric maps. Inclusion of a temporal roughness penalty function improved the performance of 4D reconstruction based on the cubic B-spline, spectral and spline-residue models.

Addition of electrophilic lipids to actin alters filament structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gayarre, Javier; Sanchez, David; Sanchez-Gomez, Francisco J.

2006-11-03

Pathophysiological processes associated with oxidative stress lead to the generation of reactive lipid species. Among them, lipids bearing unsaturated aldehyde or ketone moieties can form covalent adducts with cysteine residues and modulate protein function. Through proteomic techniques we have identified actin as a target for the addition of biotinylated analogs of the cyclopentenone prostaglandins 15-deoxy-{delta}{sup 12,14}-PGJ{sub 2} (15d-PGJ{sub 2}) and PGA{sub 1} in NIH-3T3 fibroblasts. This modification could take place in vitro and mapped to the protein C-terminal end. Other electrophilic lipids, like the isoprostane 8-iso-PGA{sub 1} and 4-hydroxy-2-nonenal, also bound to actin. The C-terminal region of actin is importantmore » for monomer-monomer interactions and polymerization. Electron microscopy showed that actin treated with 15d-PGJ{sub 2} or 4-hydroxy-2-nonenal formed filaments which were less abundant and displayed shorter length and altered structure. Streptavidin-gold staining allowed mapping of biotinylated 15d-PGJ{sub 2} at sites of filament disruption. These results shed light on the structural implications of actin modification by lipid electrophiles.« less

Quantitative energy-filtered TEM imaging of interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bentley, J.; Kenik, E.A.; Siangchaew, K.

Quantitative elemental mapping by inner shell core-loss energy-filtered transmission electron microscopy (TEM) with a Gatan Imaging Filter (GIF) interfaced to a Philips CM30 TEM operated with a LaB{sub 6} filament at 300 kV has been applied to interfaces in a range of materials. In sensitized type 304L stainless steel aged 15 h at 600{degrees}C, grain-boundary Cr depletion occurs between Cr-rich intergranular M{sub 23}C{sub 6} particles. Images of net Cr L{sub 23} intensity show segregation profiles that agree quantitatively with focused-probe spectrum-line measurements recorded with a Gatan PEELS on a Philips EM400T/FEG (0.8 nA in 2-nm-diam probe) of the same regions.more » Rare-earth oxide additives that are used for the liquid-phase sintering of Si{sub 3}N{sub 4} generate second phases of complex composition at grain boundaries and edges. These grain boundary phases often control corrosion, crack growth and creep damage behavior. High resolution imaging has been widely and with focused probes can be compromised by beam damage, but elemental mapping by EFTEM appears not to cause appreciable beam damage.« less

Comparison and evaluation of satellite- and reanalysis-based precipitation products for water resources management in the Brahmaputra River basin

NASA Astrophysics Data System (ADS)

Saleh Khan, Abu; Sohel Masud, Md.; Abdulla Hel Kafi, Md.; Sultana, Tashrifa; Lopez Lopez, Patricia

2017-04-01

The Brahmaputra River, with a transboundary basin area of approx. 554,500 km2, has its origin on the northern slope of the Himalayas in China, from where it flows through India, Bhutan and finally Bangladesh. Brahmaputra basin's climatology is heavily conditioned by precipitation during the monsoon months, concentrating about the 85 % of the rainfall in this period and originating severe and frequent floods that impact specially the Bangladeshi population in the delta region. Recent campaigns to increase the quality and to share ground-based hydro-meteorological data, in particular precipitation, within the basin have provided limited results. Global rainfall data from satellite and reanalysis may improve the temporal and spatial availability of in-situ observations for advanced water resources management. This study aims to evaluate the applicability of several global precipitation products from satellite and reanalysis in comparison with in-situ data to quantify their added value for hydrological modeling at a basin and sub-basin scale for the Brahmaputra River. Precipitation products from CMORPH, TRMM-3B42, GsMAP, WFDEI, MSWEP and various combinations with ground-based data were evaluated at basin and sub-basin level at a daily and monthly temporal resolution. The Brahmaputra was delineated into 54 sub-basins for a more detailed evaluation of the precipitation products. The data were analysed and inter-compared for the time period from 2002 to 2010. Precipitation performance assessment was conducted including several indicators, such as probability of detection (POD), false alarm ratio (FAR), Pearson's correlation coefficient (r), bias and root mean square error (RMSE). Preliminary results indicate high correlation and low bias and RMSE values between WFDEI, TRMM-3B42 and CMORPH precipitation and in-situ observations at a monthly time scale. Lower correlations and higher bias and RMSE values were found between GsMAP and MSWEP and ground-observed precipitation. The best performance was achieved with TRMM-3B42 precipitation. Preliminary results also show that precipitation is better captured during monsoon season rather than in dry seasons with all the analysed precipitation products. Moreover, in the comparison at a sub-basin level, precipitation estimates are more accurate in those sub-basins located in the southern part of the Brahmaputra River basin. These results identify the added value of satellite-based and reanalysis derived precipitation products for improving available information and water resources management in the Brahmaputra River basin. Keywords: precipitation, earth observations, hydrological modeling, Brahmaputra River basin.

Tactile stimulations and wheel rotation responses: toward augmented lane departure warning systems

PubMed Central

Tandonnet, Christophe; Burle, Borís; Vidal, Franck; Hasbroucq, Thierry

2014-01-01

When an on-board system detects a drift of a vehicle to the left or to the right, in what way should the information be delivered to the driver? Car manufacturers have so far neglected relevant results from Experimental Psychology and Cognitive Neuroscience. Here we show that this situation possibly led to the sub-optimal design of a lane departure warning system (AFIL, PSA Peugeot Citroën) implemented in commercially available automobile vehicles. Twenty participants performed a two-choice reaction time task in which they were to respond by clockwise or counter-clockwise wheel-rotations to tactile stimulations of their left or right wrist. They performed poorer when responding counter-clockwise to the right vibration and clockwise to the left vibration (incompatible mapping) than when responding according to the reverse (compatible) mapping. This suggests that AFIL implements the worse (incompatible) mapping for the operators. This effect depended on initial practice with the interface. The present research illustrates how basic approaches in Cognitive Science may benefit to Human Factors Engineering and ultimately improve man-machine interfaces and show how initial learning can affect interference effects. PMID:25324791

A simulator for airborne laser swath mapping via photon counting

NASA Astrophysics Data System (ADS)

Slatton, K. C.; Carter, W. E.; Shrestha, R.

2005-06-01

Commercially marketed airborne laser swath mapping (ALSM) instruments currently use laser rangers with sufficient energy per pulse to work with return signals of thousands of photons per shot. The resulting high signal to noise level virtually eliminates spurious range values caused by noise, such as background solar radiation and sensor thermal noise. However, the high signal level approach requires laser repetition rates of hundreds of thousands of pulses per second to obtain contiguous coverage of the terrain at sub-meter spatial resolution, and with currently available technology, affords little scalability for significantly downsizing the hardware, or reducing the costs. A photon-counting ALSM sensor has been designed by the University of Florida and Sigma Space, Inc. for improved topographic mapping with lower power requirements and weight than traditional ALSM sensors. Major elements of the sensor design are presented along with preliminary simulation results. The simulator is being developed so that data phenomenology and target detection potential can be investigated before the system is completed. Early simulations suggest that precise estimates of terrain elevation and target detection will be possible with the sensor design.

Five-Year Wilkinson Microwave Anisotropy Probe (WMAP1) Observations: Galactic Foreground Emission

NASA Technical Reports Server (NTRS)

Gold, B.; Bennett, C.L.; Larson, D.; Hill, R.S.; Odegard, N.; Weiland, J.L.; Hinshaw, G.; Kogut, A.; Wollack, E.; Page, L.;

Geophysical Data Collected off the South Shore of Martha's Vineyard, Massachusetts

USGS Publications Warehouse

Denny, J.F.; Danforth, W.W.; Foster, D.S.; Sherwood, C.R.

2010-01-01

The U.S. Geological Survey Woods Hole Science Center conducted a nearshore geophysical survey offshore of the southern coast of Martha's Vineyard, in the vicinity of the Martha's Vineyard Coastal Observatory in 2007. This mapping program was part of a larger research effort supporting the Office of Naval Research Ripples Directed-Research Initiative studies at Martha's Vineyard Coastal Observatory designed to improve our understanding of coastal sediment-transport processes. The survey was conducted aboard the Megan T. Miller August 9-13, 2007. The study area covers 35 square kilometers from about 0.2 kilometers to 5 kilometers offshore of the south shore of Martha's Vineyard, and ranges in depth from ~6 to 24 meters. The geophysical mapping utilized the following suite of high-resolution instrumentation to map the surficial sediment distribution, bathymetry, and sub-surface geology: a dual-frequency 100/500 kilohertz sidescan-sonar system, 234 kilohertz interferometric sonar, and 500 hertz -12 kilohertz chirp subbottom profiler. These geophysical data will be used to provide initial conditions for wave and circulation modeling within the study area.

EELS Valence Mapping in Electron Beam Sensitive FeFx/C Nanocomposites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cosandey, F.; Al-Sharab, J.F.; Amatucci, Glenn G.

A new type of positive electrodes for Li-Ion batteries has been synthesized based on FeF{sub 2}/C and FeF3/C nanocomposites with particle size in the 8-12 nm range [1]. The measured high capacities rely on a complete reduction of Fe to its metallic state according to the following reaction: xLi{sup +}+xe{sup -} +Fe{sup x+}Fx = xLiF + Fe{sup 0}, where x=3 and x=2 for FeF3/C and FeF2/C respectively. This electrochemical reaction involves a change in valence state of Fe from 3+ or 2+ to 0 that can be determined uniquely by EELS from the peak energy of the L{sub 3} linemore » and from the L{sub 3}/L{sub 2} line intensity ratio. In this paper, we report EELS mapping results on the electrochemical conversion processes and in particular the mapping of the Fe valence state before and after discharge. This work was performed with a Hitachi HF2000 equipped with a Gatan PEELS and with a FEI CM200 FEG TEM equipped with a Gatan GIF. Both instruments were operated in STEM mode at 200kV with an EELS collection half angle of {beta}=5 mrad and spectrum imaging software.« less

Study of a MHEMT heterostructure with an In{sub 0.4}Ga{sub 0.6}As channel MBE-grown on a GaAs substrate using reciprocal space mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aleshin, A. N., E-mail: a.n.aleshin@mail.ru; Bugaev, A. S.; Ermakova, M. A.

2015-08-15

The crystallographic characteristics of the design elements of a metamorphic high-electron-mobility (MHEMT) heterostructure with an In{sub 0.4}Ga{sub 0.6}As channel are determined based on reciprocal space mapping. The heterostructure is grown by molecular beam epitaxy on the vicinal surface of a GaAs substrate with a deviation angle from the (001) plane of 2° and consists of a stepped metamorphic buffer containing six layers including an inverse step, a high-temperature buffer layer with constant composition, and active HEMT layers. The InAs content in the layers of the metamorphic buffer is varied from 0.1 to 0.48. Reciprocal space maps are constructed for themore » (004) symmetric reflection and (224)+ asymmetric reflection. It is found that the heterostructure layers are characterized both by a tilt angle relative to the plane of the (001) substrate and a rotation angle around the [001] axis. The tilt angle of the layer increases as the InAs concentration in the layer increases. It is shown that a high-temperature buffer layer of constant composition has the largest degree of relaxation compared with all other layers of the heterostructure.« less

Detection and Antigenic Profiling of Undeclared Peanut in Imported Garlic Using an xMAP Multiplex Immunoassay for Food Allergens.

PubMed

Pedersen, Ronnie O; Peters, Tim; Panda, Rakhi; Wehling, Paul; Garber, Eric A E

2017-07-01

A shipment of imported garlic powder was suspected of containing peanut. Samples (subs) collected from the shipment displayed considerable variability in peanut antigenicity when analyzed by enzyme-linked immunosorbent assay (ELISA). This raised questions regarding whether peanut was actually present, the amount present, and the basis for the variability in antigenic content. Analyses that used an xMAP multiplex assay for the detection of peanut and additional food allergens generated responses that were characteristic of peanut. Specifically, the relative intensities of two different peanut-specific antibodies coupled to beads (peanut-37 and -38) and the antigen profiles were identical to garlic controls spiked with peanut. In addition, the xMAP data did not indicate the presence of other allergens. Quantitative analyses indicated an approximately fivefold variation in peanut concentration among different subs. In contrast, within a sub, the apparent peanut concentration appeared constant. Particle size analyses of the garlic powder subs indicated a single distribution profile, with a peak at 380 μm. ELISA analysis of sieve-fractionated garlic powder from one of the subs indicated that slightly less than half of the detectable peanut was smaller than 212 μm, with the remainder almost evenly split between 212 and 300 μm and >300 μm. Modeling to predict possible oral exposure levels of peanut other than those directly measured requires additional research on the physicochemical properties of peanut and garlic, along with information on the production of the garlic powder.

Mapping evidence on the distribution of human papillomavirus-related cancers in sub-Saharan Africa: scoping review protocol.

PubMed

Lekoane, Bridget K M; Mashamba-Thompson, Tivani P; Ginindza, Themba G

2017-11-17

Despite the introduction of HPV vaccines, the incidence of HPV-related cancers (cervical, penile, anal, vulvar, vagina, head, and neck) in sub-Saharan Africa has been rising. The increasing incidence of these HPV-related cancers has been attributed to changes in lifestyle-related risk factors, most notably sexual behavior. The main objective of this study is to map evidence on the distribution of HIV-related cancers in sub-Saharan Africa (SSA). We will conduct a scoping review to explore, describe, and map literature on the distribution of HPV-related cancers in sub-Saharan Africa. The primary search will include peer-reviewed and review articles. The list of references from included studies will also be searched. The search will be performed using EBSCOhost platform by searching the following databases within the platform: Academic search complete, health source: nursing/academic edition, CINAHL with full text, PubMed, Science Direct, Google scholar and World Health Organization (WHO) library databases, and gray literature. The researcher will search the articles using keywords, from the included studies; abstract and full articles will be screened by two independent reviewers. The screening will be guided by the inclusion and exclusion criteria. A thematic content analysis will be used to present the narrative account of the reviews, using NVivo version 10. We anticipate finding relevant literature on the distribution of HPV-related cancers in sub-Saharan Africa. The study findings will help reveal research gaps to guide future research. PROSPERO CRD42017062403.

Quantitative assessment of desertification in south of Iran using MEDALUS method.

PubMed

Sepehr, A; Hassanli, A M; Ekhtesasi, M R; Jamali, J B

2007-11-01

The main aim of this study was the quantitative assessment of desertification process in the case study area of the Fidoye-Garmosht plain (Southern Iran). Based on the MEDALUS approach and the characteristics of study area a regional model developed using GIS. Six main factors or indicators of desertification including: soil, climate, erosion, plant cover, groundwater and management were considered for evaluation. Then several sub-indicators affecting the quality of each main indicator were identified. Based on the MEDALUS approach, each sub-indicator was quantified according to its quality and given a weighting of between 1.0 and 2.0. ArcGIS 9 was used to analyze and prepare the layers of quality maps using the geometric mean to integrate the individual sub-indicator maps. In turn the geometric mean of all six quality maps was used to generate a single desertification status map. Results showed that 12% of the area is classified as very severe, 81% as severe and 7% as moderately affected by desertification. In addition the plant cover and groundwater indicators were the most important factors affecting desertification process in the study area. The model developed may be used to assess desertification process and distinguish the areas sensitive to desertification in the study region and in regions with the similar characteristics.

Multiscale Auroral Emission Statistics as Evidence of Turbulent Reconnection in Earth's Midtail Plasma Sheet

NASA Technical Reports Server (NTRS)

Klimas, Alex; Uritsky, Vadim; Donovan, Eric

2010-01-01

We provide indirect evidence for turbulent reconnection in Earth's midtail plasma sheet by reexamining the statistical properties of bright, nightside auroral emission events as observed by the UVI experiment on the Polar spacecraft and discussed previously by Uritsky et al. The events are divided into two groups: (1) those that map to absolute value of (X(sub GSM)) < 12 R(sub E) in the magnetotail and do not show scale-free statistics and (2) those that map to absolute value of (X(sub GSM)) > 12 R(sub E) and do show scale-free statistics. The absolute value of (X(sub GSM)) dependence is shown to most effectively organize the events into these two groups. Power law exponents obtained for group 2 are shown to validate the conclusions of Uritsky et al. concerning the existence of critical dynamics in the auroral emissions. It is suggested that the auroral dynamics is a reflection of a critical state in the magnetotail that is based on the dynamics of turbulent reconnection in the midtail plasma sheet.

SNARE-mediated trafficking of {alpha}{sub 5}{beta}{sub 1} integrin is required for spreading in CHO cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Skalski, Michael; Coppolino, Marc G.

2005-10-07

In this study, the role of SNARE-mediated membrane traffic in regulating integrin localization was examined and the requirement for SNARE function in cellular spreading was quantitatively assessed. Membrane traffic was inhibited with the VAMP-specific catalytic light chain from tetanus toxin (TeTx-LC), a dominant-negative form (E329Q) of N-ethylmaleimide-sensitive fusion protein (NSF), and brefeldin A (BfA). Inhibition of membrane traffic with either E329Q-NSF or TeTx-LC, but not BfA, significantly inhibited spreading of CHO cells on fibronectin. Spreading was rescued in TeTx-LC-expressing cells by co-transfection with a TeTx-resistant cellubrevin/VAMP3. E329Q-NSF, a general inhibitor of SNARE function, was a more potent inhibitor of cellmore » spreading than TeTx-LC, suggesting that tetanus toxin-insensitive SNAREs contribute to adhesion. It was found that E329Q-NSF prevented trafficking of {alpha}{sub 5}{beta}{sub 1} integrins from a central Rab11-containing compartment to sites of protrusion during cell adhesion, while TeTx-LC delayed this trafficking. These results are consistent with a model of cellular adhesion that implicates SNARE function as an important component of integrin trafficking during the process of cell spreading.« less

Statistical parametric mapping of stimuli-evoked changes in quantitative blood flow using extended-focus optical coherence microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Marchand, Paul J.; Bouwens, Arno; Shamaei, Vincent; Nguyen, David; Extermann, Jerome; Bolmont, Tristan; Lasser, Theo

2016-03-01

Magnetic Resonance Imaging has revolutionised our understanding of brain function through its ability to image human cerebral structures non-invasively over the entire brain. By exploiting the different magnetic properties of oxygenated and deoxygenated blood, functional MRI can indirectly map areas undergoing neural activation. Alongside the development of fMRI, powerful statistical tools have been developed in an effort to shed light on the neural pathways involved in processing of sensory and cognitive information. In spite of the major improvements made in fMRI technology, the obtained spatial resolution of hundreds of microns prevents MRI in resolving and monitoring processes occurring at the cellular level. In this regard, Optical Coherence Microscopy is an ideal instrumentation as it can image at high spatio-temporal resolution. Moreover, by measuring the mean and the width of the Doppler spectra of light scattered by moving particles, OCM allows extracting the axial and lateral velocity components of red blood cells. The ability to assess quantitatively total blood velocity, as opposed to classical axial velocity Doppler OCM, is of paramount importance in brain imaging as a large proportion of cortical vascular is oriented perpendicularly to the optical axis. We combine here quantitative blood flow imaging with extended-focus Optical Coherence Microscopy and Statistical Parametric Mapping tools to generate maps of stimuli-evoked cortical hemodynamics at the capillary level.

First Year Wilkinson Microwave Anisotropy Probe (WMAP) Observations: Foreground Emission

NASA Technical Reports Server (NTRS)

Bennett, C. L.; Hill, R. S.; Hinshaw, G.; Nolta, M. R.; Odegard, N.; Page, L.; Spergel, D. N.; Weiland, J. L.; Wright, E. L.; Halpern, M.

2003-01-01

The WMAP mission has mapped the full sky to determine the geometry, content, and evolution of the universe. Full sky maps are made in five microwave frequency bands to separate the temperature anisotropy of the cosmic microwave background (CMB) from foreground emission, including diffuse Galactic emission and Galactic and extragalactic point sources. We define masks that excise regions of high foreground emission, so CMB analyses can became out with minimal foreground contamination. We also present maps and spectra of the individual emission components, leading to an improved understanding of Galactic astrophysical processes. The effectiveness of template fits to remove foreground emission from the WMAP data is also examined. These efforts result in a CMB map with minimal contamination and a demonstration that the WMAP CMB power spectrum is insensitive to residual foreground emission. We use a Maximum Entropy Method to construct a model of the Galactic emission components. The observed total Galactic emission matches the model to less than 1% and the individual model components are accurate to a few percent. We find that the Milky Way resembles other normal spiral galaxies between 408 MHz and 23 GHz, with a synchrotron spectral index that is flattest (beta(sub s) approx. -2.5) near star-forming regions, especially in the plane, and steepest (beta(sub s) approx. -3) in the halo. This is consistent with a picture of relativistic cosmic ray electron generation in star-forming regions and diffusion and convection within the plane. The significant synchrotron index steepening out of the plane suggests a diffusion process in which the halo electrons are trapped in the Galactic potential long enough to suffer synchrotron and inverse Compton energy losses and hence a spectral steepening. The synchrotron index is steeper in the WMAP bands than in lower frequency radio surveys, with a spectral break near 20 GHz to beta(sub s) less than -3. The modeled thermal dust spectral index is also steep in the WMAP bands, with beta(sub d) approx. = 2.2. Our model is driven to these conclusions by the low level of total foreground contamination at approx. 60 GHz. Microwave and Ha measurements of the ionized gas agree well with one another at about the expected levels. Spinning dust emission is limited to less than 5% of the Ka-band foreground emission. A catalog of 208 point sources is presented. The reliability of the catalog is 98%, i.e., we expect five of the 208 sources to be statistically spurious. The mean spectral index of the point sources is alpha approx. 0(beta approx. -2). Derived source counts suggest a contribution to the anisotropy power from unresolved sources of (15.0 +/- 1.4) x 10(exp -3)micro sq K sr at Q-band and negligible levels at V-band and W-band. The Sunyaev-Zeldovich effect is shown to be a negligible "contamination" to the maps.

Live-cell imaging of ER-PM contact architecture by a novel TIRFM approach reveals extension of junctions in response to store-operated Ca2+-entry.

PubMed

Poteser, Michael; Leitinger, Gerd; Pritz, Elisabeth; Platzer, Dieter; Frischauf, Irene; Romanin, Christoph; Groschner, Klaus

2016-10-19

Nanometer-spaced appositions between endoplasmic reticulum and plasma membrane (ER-PM junctions) stabilized by membrane-joining protein complexes are critically involved in cellular Ca 2+ -handling and lipid trafficking. ER-PM junctional architecture and plasticity associated with inter-membrane communication are as yet barely understood. Here, we introduce a method to precisely characterize ER-PM junction morphology and dynamics with high temporal resolution and minimal disturbance of junctional intermembrane communication. We show that expression of soluble cytosolic fluorophores in combination with TIRFM enables to delineate ER and PM distance in the range of 10-150 nm. Live-cell imaging of sub-plasmalemmal structures in RBL-2H3 mast cells by this method, designated as fluorescence density mapping (FDM), revealed profound dynamics of ER-PM contact sites in response to store-depletion. We report the existence of a Ca 2+ -dependent process that expands the junctional ER to enlarge its contact surface with the PM, thereby promoting and stabilizing STIM1-Orai1 competent ER-PM junctions.

Laser-induced Breakdown Spectroscopy: A New Approach for Nanoparticle's Mapping and Quantification in Organ Tissue

PubMed Central

Sancey, Lucie; Motto-Ros, Vincent; Kotb, Shady; Wang, Xiaochun; Lux, François; Panczer, Gérard; Yu, Jin; Tillement, Olivier

2014-01-01

Emission spectroscopy of laser-induced plasma was applied to elemental analysis of biological samples. Laser-induced breakdown spectroscopy (LIBS) performed on thin sections of rodent tissues: kidneys and tumor, allows the detection of inorganic elements such as (i) Na, Ca, Cu, Mg, P, and Fe, naturally present in the body and (ii) Si and Gd, detected after the injection of gadolinium-based nanoparticles. The animals were euthanized 1 to 24 hr after intravenous injection of particles. A two-dimensional scan of the sample, performed using a motorized micrometric 3D-stage, allowed the infrared laser beam exploring the surface with a lateral resolution less than 100 μm. Quantitative chemical images of Gd element inside the organ were obtained with sub-mM sensitivity. LIBS offers a simple and robust method to study the distribution of inorganic materials without any specific labeling. Moreover, the compatibility of the setup with standard optical microscopy emphasizes its potential to provide multiple images of the same biological tissue with different types of response: elemental, molecular, or cellular. PMID:24962015

Rewinding the process of mammalian extinction.

PubMed

Saragusty, Joseph; Diecke, Sebastian; Drukker, Micha; Durrant, Barbara; Friedrich Ben-Nun, Inbar; Galli, Cesare; Göritz, Frank; Hayashi, Katsuhiko; Hermes, Robert; Holtze, Susanne; Johnson, Stacey; Lazzari, Giovanna; Loi, Pasqualino; Loring, Jeanne F; Okita, Keisuke; Renfree, Marilyn B; Seet, Steven; Voracek, Thomas; Stejskal, Jan; Ryder, Oliver A; Hildebrandt, Thomas B

2016-07-01

With only three living individuals left on this planet, the northern white rhinoceros (Ceratotherium simum cottoni) could be considered doomed for extinction. It might still be possible, however, to rescue the (sub)species by combining novel stem cell and assisted reproductive technologies. To discuss the various practical options available to us, we convened a multidisciplinary meeting under the name "Conservation by Cellular Technologies." The outcome of this meeting and the proposed road map that, if successfully implemented, would ultimately lead to a self-sustaining population of an extremely endangered species are outlined here. The ideas discussed here, while centered on the northern white rhinoceros, are equally applicable, after proper adjustments, to other mammals on the brink of extinction. Through implementation of these ideas we hope to establish the foundation for reversal of some of the effects of what has been termed the sixth mass extinction event in the history of Earth, and the first anthropogenic one. Zoo Biol. 35:280-292, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.

Algorithm, applications and evaluation for protein comparison by Ramanujan Fourier transform.

PubMed

Zhao, Jian; Wang, Jiasong; Hua, Wei; Ouyang, Pingkai

2015-12-01

The amino acid sequence of a protein determines its chemical properties, chain conformation and biological functions. Protein sequence comparison is of great importance to identify similarities of protein structures and infer their functions. Many properties of a protein correspond to the low-frequency signals within the sequence. Low frequency modes in protein sequences are linked to the secondary structures, membrane protein types, and sub-cellular localizations of the proteins. In this paper, we present Ramanujan Fourier transform (RFT) with a fast algorithm to analyze the low-frequency signals of protein sequences. The RFT method is applied to similarity analysis of protein sequences with the Resonant Recognition Model (RRM). The results show that the proposed fast RFT method on protein comparison is more efficient than commonly used discrete Fourier transform (DFT). RFT can detect common frequencies as significant feature for specific protein families, and the RFT spectrum heat-map of protein sequences demonstrates the information conservation in the sequence comparison. The proposed method offers a new tool for pattern recognition, feature extraction and structural analysis on protein sequences. Copyright © 2015 Elsevier Ltd. All rights reserved.

Convergent evidence from systematic analysis of GWAS revealed genetic basis of esophageal cancer.

PubMed

Gao, Xue-Xin; Gao, Lei; Wang, Jiu-Qiang; Qu, Su-Su; Qu, Yue; Sun, Hong-Lei; Liu, Si-Dang; Shang, Ying-Li

2016-07-12

Recent genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with risk of esophageal cancer (EC). However, investigation of genetic basis from the perspective of systematic biology and integrative genomics remains scarce.In this study, we explored genetic basis of EC based on GWAS data and implemented a series of bioinformatics methods including functional annotation, expression quantitative trait loci (eQTL) analysis, pathway enrichment analysis and pathway grouped network analysis.Two hundred and thirteen risk SNPs were identified, in which 44 SNPs were found to have significantly differential gene expression in esophageal tissues by eQTL analysis. By pathway enrichment analysis, 170 risk genes mapped by risk SNPs were enriched into 38 significant GO terms and 17 significant KEGG pathways, which were significantly grouped into 9 sub-networks by pathway grouped network analysis. The 9 groups of interconnected pathways were mainly involved with muscle cell proliferation, cellular response to interleukin-6, cell adhesion molecules, and ethanol oxidation, which might participate in the development of EC.Our findings provide genetic evidence and new insight for exploring the molecular mechanisms of EC.

Visualizing protein partnerships in living cells and organisms.

PubMed

Lowder, Melissa A; Appelbaum, Jacob S; Hobert, Elissa M; Schepartz, Alanna

2011-12-01

In recent years, scientists have expanded their focus from cataloging genes to characterizing the multiple states of their translated products. One anticipated result is a dynamic map of the protein association networks and activities that occur within the cellular environment. While in vitro-derived network maps can illustrate which of a multitude of possible protein-protein associations could exist, they supply a falsely static picture lacking the subtleties of subcellular location (where) or cellular state (when). Generating protein association network maps that are informed by both subcellular location and cell state requires novel approaches that accurately characterize the state of protein associations in living cells and provide precise spatiotemporal resolution. In this review, we highlight recent advances in visualizing protein associations and networks under increasingly native conditions. These advances include second generation protein complementation assays (PCAs), chemical and photo-crosslinking techniques, and proximity-induced ligation approaches. The advances described focus on background reduction, signal optimization, rapid and reversible reporter assembly, decreased cytotoxicity, and minimal functional perturbation. Key breakthroughs have addressed many challenges and should expand the repertoire of tools useful for generating maps of protein interactions resolved in both time and space. Copyright © 2011 Elsevier Ltd. All rights reserved.

Phenotypic consequences of deletion of the {gamma}{sub 3}, {alpha}{sub 5}, or {beta}{sub 3} subunit of the type A {gamma}-aminobutyric acid receptor in mice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Culia, C.T.; Stubbs, L.J.; Montgomery, C.S.

1994-03-29

Three genes (Gabrg3, Gabra5, and Gabrb3) encoding the {gamma}{sub 3}, {alpha}{sub 5}, and {beta}{sub 3} subunits of the type A {gamma}-aminobutyric acid receptor, respectively, are known to map near the pink-eyed dilution (p) locus in mouse chromosome 7. This region shares homology with a segment of human chromosome 15 that is implicated in Angelman syndrome, an inherited neurobehavioral disorder. By mapping Gabrg3-Gabra5-Gabrb3-telomere. Like Gabrb3, neither the Gabra5 nor Gabrg3 gene is functionally imprinted in adult mouse brain. Mice deleted for all three subunits die at birth with a cleft palate, although there are rare survivors ({approximately} 5%) that do notmore » have a cleft palate but do exhibit a neurological abnormality characterized by tremor, jerky gait, and runtiness. The authors have previously suggested that deficiency of the {beta}{sub 3} subunit may be responsible for the clefting defect. Most notably, however, in this report they describe mice carrying two overlapping, complementing p deletions that fail to express the {gamma}{sub 3} transcript, as well as mice from another line that express neither the {gamma}{sub 3} nor {alpha}{sub 5} transcripts. Surprisingly, mice from both of these lines are phenotypically normal and do not exhibit any of the neurological symptoms characteristic of the rare survivors that are deleted for all three ({gamma}{sub 3}, {alpha}{sub 5}, and {beta}{sub 3}) subunits. These mice therefore provide a whole-organism type A {gamma}-aminobutyric-acid receptor background that is devoid of any receptor subtypes that normally contain the {gamma}{sub 3} and/or {alpha}{sub 5} subunits. The absence of an overt neurological phenotype in mice lacking the {gamma}{sub 3} and/or {alpha}{sub 5} subunits also suggests that mutations in these genes are unlikely to provide useful animal models for Angelman syndrome in humans.« less

In vivo microcirculation imaging of the sub surface fingertip using correlation mapping optical coherence tomography (cmOCT)

NASA Astrophysics Data System (ADS)

Dsouza, Roshan I.; Zam, Azhar; Subhash, Hrebesh M.; Larin, Kirill V.; Leahy, Martin

2013-02-01

We describe a novel application of correlation mapping optical coherence tomography (cmOCT) for sub-surface fingerprint biometric identification. Fingerprint biometrics including automated fingerprint identification systems, are commonly used to recognise the fingerprint, since they constitute simple, effective and valuable physical evidence. Spoofing of biometric fingerprint devices can be easily done because of the limited information obtained from the surface topography. In order to overcome this limitation a potentially more secure source of information is required for biometric identification applications. In this study, we retrieve the microcirculation map of the subsurface fingertip by use of the cmOCT technique. To increase probing depth of the sub surface microcirculation, an optical clearing agent composed of 75% glycerol in aqueous solution was applied topically and kept in contact for 15 min. OCT intensity images were acquired from commercial research grade swept source OCT system (model OCT1300SS, Thorlabs Inc. USA). A 3D OCT scan of the fingertip was acquired over an area of 5x5 mm using 1024x1024 A-scans in approximately 70 s. The resulting volume was then processed using the cmOCT technique with a 7x7 kernel to provide a microcirculation map. We believe these results will demonstrate an enhanced security level over artificial fingertips. To the best of our knowledge, this is the first demonstration of imaging microcirculation map of the subsurface fingertip.

Global rain-fed, irrigated, and paddy croplands: A new high resolution map derived from remote sensing, crop inventories and climate data

NASA Astrophysics Data System (ADS)

Salmon, J. Meghan; Friedl, Mark A.; Frolking, Steve; Wisser, Dominik; Douglas, Ellen M.

2015-06-01

Irrigation accounts for 70% of global water use by humans and 33-40% of global food production comes from irrigated croplands. Accurate and timely information related to global irrigation is therefore needed to manage increasingly scarce water resources and to improve food security in the face of yield gaps, climate change and extreme events such as droughts, floods, and heat waves. Unfortunately, this information is not available for many regions of the world. This study aims to improve characterization of global rain-fed, irrigated and paddy croplands by integrating information from national and sub-national surveys, remote sensing, and gridded climate data sets. To achieve this goal, we used supervised classification of remote sensing, climate, and agricultural inventory data to generate a global map of irrigated, rain-fed, and paddy croplands. We estimate that 314 million hectares (Mha) worldwide were irrigated circa 2005. This includes 66 Mha of irrigated paddy cropland and 249 Mha of irrigated non-paddy cropland. Additionally, we estimate that 1047 Mha of cropland are managed under rain-fed conditions, including 63 Mha of rain-fed paddy cropland and 985 Mha of rain-fed non-paddy cropland. More generally, our results show that global mapping of irrigated, rain-fed, and paddy croplands is possible by combining information from multiple data sources. However, regions with rapidly changing irrigation or complex mixtures of irrigated and non-irrigated crops present significant challenges and require more and better data to support high quality mapping of irrigation.

Identification of PM{sub 10} characteristics involved in cellular responses in human bronchial epithelial cells (Beas-2B)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Den Heuvel, Rosette, E-mail: rosette.vandenheuvel@vito.be; Den Hond, Elly, E-mail: elly.denhond@wiv-isp.be; Govarts, Eva, E-mail: eva.govarts@vito.be

Notwithstanding evidence is present that physicochemical characteristics of ambient particles attribute to adverse health effects, there is still some lack of understanding in this complex relationship. At this moment it is not clear which properties (such as particle size, chemical composition) or sources of the particles are most relevant for health effects. This study investigates the in vitro toxicity of PM{sub 10} in relation to PM chemical composition, black carbon (BC), endotoxin content and oxidative potential (OP). In 2013–2014 PM{sub 10} was sampled (24 h sampling, 108 sampling days) in ambient air at three sites in Flanders (Belgium) with differentmore » pollution characteristics: an urban traffic site (Borgerhout), an industrial area (Zelzate) and a rural background location (Houtem). To characterize the toxic potential of PM{sub 10}, airway epithelial cells (Beas-2B cells) have been exposed to particles in vitro. Different endpoints were studied including cell damage and death (cell viability) using the Neutral red Uptake assay, the production of pro-inflammatory molecules by interleukin 8 (IL-8) induction and DNA-damaging activity using the FPG-modified Comet assay. The endotoxin levels in the collected samples were analysed and the capacity of PM{sub 10} particles to produce reactive oxygen species (OP) was evaluated by electron paramagnetic resonance (EPR) spectroscopy. Chemical characteristics of PM{sub 10} (BC, As, Cd, Cr, Cu, Mn, Ni, Pb, Zn) and meteorological conditions were recorded on the sampling days. PM{sub 10} particles exhibited dose-dependent cytotoxicity in Beas-2B cells and were found to significantly induce the release of IL-8 in samples from the three locations. Oxidatively damaged DNA was observed in exposed Beas-2B cells. Endotoxin levels above the detection limit were detected in half of the samples. OP was measurable in all samples. Associations between PM{sub 10} characteristics and biological effects of PM{sub 10} were assessed by single and multiple regression analyses. The reduction in cell viability was significantly correlated with BC, Cd and Pb. The induction of IL-8 in Beas-2B cells was significantly associated with Cu, Ni and Zn and endotoxin. Endotoxin levels explained 33% of the variance in IL-8 induction. A significant interaction between ambient temperature and endotoxin on the pro-inflammatory activity was seen. No association was found between OP and the cellular responses. This study supports the hypothesis that, on an equal mass basis, PM{sub 10} induced biological effects differ due to differences in PM{sub 10} characteristics. Metals (Cd, Cu, Ni and Zn), BC, and endotoxin were among the main determinants for the observed biological responses. - Highlights: • On an equal mass basis, PM{sub 10} sampled at an urban, rural and industrial site induced different cellular effects in Beas-2B. • Endotoxin levels and oxidative potential (OP) were analysed in the PM{sub 10} samples. • Black carbon, cadmium and lead were correlated with decreased cell viability. • Endotoxin levels explained the majority of the variance in il-8 induction. • Oxidatively damaged DNA was observed in all the samples.« less

Developing a novel comprehensive framework for the investigation of cellular and whole heart electrophysiology in the in situ human heart: historical perspectives, current progress and future prospects.

PubMed

Taggart, Peter; Orini, Michele; Hanson, Ben; Hayward, Martin; Clayton, Richard; Dobrzynski, Halina; Yanni, Joseph; Boyett, Mark; Lambiase, Pier D

2014-08-01

Understanding the mechanisms of fatal ventricular arrhythmias is of great importance. In view of the many electrophysiological differences that exist between animal species and humans, the acquisition of basic electrophysiological data in the intact human heart is essential to drive and complement experimental work in animal and in-silico models. Over the years techniques have been developed to obtain basic electrophysiological signals directly from the patients by incorporating these measurements into routine clinical procedures which access the heart such as cardiac catheterisation and cardiac surgery. Early recordings with monophasic action potentials provided valuable information including normal values for the in vivo human heart, cycle length dependent properties, the effect of ischaemia, autonomic nervous system activity, and mechano-electric interaction. Transmural recordings addressed the controversial issue of the mid myocardial "M" cell. More recently, the technique of multielectrode mapping (256 electrodes) developed in animal models has been extended to humans, enabling mapping of activation and repolarisation on the entire left and right ventricular epicardium in patients during cardiac surgery. Studies have examined the issue of whether ventricular fibrillation was driven by a "mother" rotor with inhomogeneous and fragmented conduction as in some animal models, or by multiple wavelets as in other animal studies; results showed that both mechanisms are operative in humans. The simpler spatial organisation of human VF has important implications for treatment and prevention. To link in-vivo human electrophysiological mapping with cellular biophysics, multielectrode mapping is now being combined with myocardial biopsies. This technique enables region-specific electrophysiology changes to be related to underlying cellular biology, for example: APD alternans, which is a precursor of VF and sudden death. The mechanism is incompletely understood but related to calcium cycling and APD restitution. Multielectrode sock mapping during incremental pacing enables epicardial sites to be identified which exhibit marked APD alternans and sites where APD alternans is absent. Whole heart electrophysiology is assessed by activation repolarisation mapping and analysis is performed immediately on-site in order to guide biopsies to specific myocardial sites. Samples are analysed for ion channel expression, Ca(2+)-handling proteins, gap junctions and extracellular matrix. This new comprehensive approach to bridge cellular and whole heart electrophysiology allowed to identify 20 significant changes in mRNA for ion channels Ca(2+)-handling proteins, a gap junction channel, a Na(+)-K(+) pump subunit and receptors (particularly Kir 2.1) between the positive and negative alternans sites. Copyright © 2014 Elsevier Ltd. All rights reserved.

Cylinder stitching interferometry: with and without overlap regions

NASA Astrophysics Data System (ADS)

Peng, Junzheng; Chen, Dingfu; Yu, Yingjie

2017-06-01

Since the cylinder surface is closed and periodic in the azimuthal direction, existing stitching methods cannot be used to yield the 360° form map. To address this problem, this paper presents two methods for stitching interferometry of cylinder: one requires overlap regions, and the other does not need the overlap regions. For the former, we use the first order approximation of cylindrical coordinate transformation to build the stitching model. With it, the relative parameters between the adjacent sub-apertures can be calculated by the stitching model. For the latter, a set of orthogonal polynomials, termed Legendre Fourier (LF) polynomials, was developed. With these polynomials, individual sub-aperture data can be expanded as composition of inherent form of partial cylinder surface and additional misalignment parameters. Then the 360° form map can be acquired by simultaneously fitting all sub-aperture data with LF polynomials. Finally the two proposed methods are compared under various conditions. The merits and drawbacks of each stitching method are consequently revealed to provide suggestion in acquisition of 360° form map for a precision cylinder.

Photometric metallicity map of the Small Magellanic Cloud

NASA Astrophysics Data System (ADS)

Choudhury, S.; Subramaniam, A.; Cole, A. A.; Sohn, Y.-J.

2018-04-01

We have created an estimated metallicity map of the Small Magellanic Cloud (SMC) using the Magellanic Cloud Photometric Survey (MCPS) and Optical Gravitational Lensing Experiment (OGLE III) photometric data. This is a first of its kind map of metallicity up to a radius of ˜2.5°. We identify the Red Giant Branch (RGB) in the V, (V - I) colour-magnitude diagrams of small sub-regions of varying sizes in both data sets. We use the slope of the RGB as an indicator of the average metallicity of a sub-region and calibrate the RGB slope to metallicity using available spectroscopic data for selected sub-regions. The average metallicity of the SMC is found to be [Fe/H] = -0.94 dex (σ[Fe/H] = 0.09) from OGLE III and [Fe/H] = -0.95 dex (σ[Fe/H] = 0.08) from MCPS. We confirm a shallow but significant metallicity gradient within the inner SMC up to a radius of 2.5° (-0.045 ± 0.004 to -0.067 ± 0.006 dex deg-1).

Probing eukaryotic cell mechanics via mesoscopic simulations

PubMed Central

Shang, Menglin; Lim, Chwee Teck

2017-01-01

Cell mechanics has proven to be important in many biological processes. Although there is a number of experimental techniques which allow us to study mechanical properties of cell, there is still a lack of understanding of the role each sub-cellular component plays during cell deformations. We present a new mesoscopic particle-based eukaryotic cell model which explicitly describes cell membrane, nucleus and cytoskeleton. We employ Dissipative Particle Dynamics (DPD) method that provides us with the unified framework for modeling of a cell and its interactions in the flow. Data from micropipette aspiration experiments were used to define model parameters. The model was validated using data from microfluidic experiments. The validated model was then applied to study the impact of the sub-cellular components on the cell viscoelastic response in micropipette aspiration and microfluidic experiments. PMID:28922399

Influence of sub-lethal stresses on the survival of lactic acid bacteria after spray-drying in orange juice.

PubMed

Barbosa, J; Borges, S; Teixeira, P

2015-12-01

The demand for new functional non-dairy based products makes the production of a probiotic orange juice powder an encouraging challenge. However, during drying process and storage, loss of viability of the dried probiotic cultures can occur, since the cells are exposed to various stresses. The influence of sub-lethal conditions of temperature, acidic pH and hydrogen peroxide on the viability of Pediococcus acidilactici HA-6111-2 and Lactobacillus plantarum 299v during spray drying in orange juice and subsequent storage under different conditions was investigated. At the end of storage, the survival of both microorganisms through simulated gastro-intestinal tract (GIT) conditions was also determined. The viability of cells previously exposed to each stress was not affected by the drying process. However, during 180 days of storage at room temperature, unlike P. acidilactici HA-6111-2, survival of L. plantarum 299v was enhanced by prior exposure to sub-lethal conditions. Previous exposure to sub-lethal stresses of each microorganism did not improve their viability after passage through simulated GIT. Nevertheless, as cellular inactivation during 180 days of storage was low, both microorganisms were present in numbers of ca. 10(7) cfu/mL at the end of GIT. This is an indication that both bacteria are good candidates for use in the development of an orange juice powder with functional characteristics. Copyright © 2015 Elsevier Ltd. All rights reserved.

A First Comparison of Millimeter Continuum and Mg ii Ultraviolet Line Emission from the Solar Chromosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bastian, T. S.; Chintzoglou, G.; De Pontieu, B.

We present joint observations of the Sun by the Atacama Large Millimeter/submillimeter Array (ALMA) and the Interface Region Imaging Spectrograph ( IRIS ). Both millimeter/submillimeter- λ continuum emission and ultraviolet (UV) line emission originate from the solar chromosphere and both have the potential to serve as powerful and complementary diagnostics of physical conditions in this enigmatic region of the solar atmosphere. The observations were made of a solar active region on 2015 December 18 as part of the ALMA science verification effort. A map of the Sun’s continuum emission was obtained by ALMA at a wavelength of 1.25 mm (239more » GHz). A contemporaneous map was obtained by IRIS in the Mg ii h doublet line at 2803.5 Å. While a clear correlation between the 1.25 mm brightness temperature T{sub B} and the Mg ii h line radiation temperature T {sub rad} is observed, the slope is <1, perhaps as a result of the fact that these diagnostics are sensitive to different parts of the chromosphere and that the Mg ii h line source function includes a scattering component. There is a significant difference (35%) between the mean T{sub B} (1.25 mm) and mean T {sub rad} (Mg ii). Partitioning the maps into “sunspot,” “quiet areas,” and “plage regions” we find the relation between the IRIS Mg ii h line T {sub rad} and the ALMA T {sub B} region-dependent. We suggest this may be the result of regional dependences of the formation heights of the IRIS and ALMA diagnostics and/or the increased degree of coupling between the UV source function and the local gas temperature in the hotter, denser gas in plage regions.« less

The Life Science Exchange: a case study of a sectoral and sub-sectoral knowledge exchange programme.

PubMed

Perkins, Brian Lee; Garlick, Rob; Wren, Jodie; Smart, Jon; Kennedy, Julie; Stephens, Phil; Tudor, Gwyn; Bisson, Jonathan; Ford, David V

2016-04-27

Local and national governments have implemented sector-specific policies to support economic development through innovation, entrepreneurship and knowledge exchange. Supported by the Welsh Government through the European Regional Development Fund, The Life Science Exchange® project was created with the aim to increase interaction between stakeholders, to develop more effective knowledge exchange mechanisms, and to stimulate the formation and maintenance of long-term collaborative relationships within the Welsh life sciences ecosystem. The Life Science Exchange allowed participants to interact with other stakeholder communities (clinical, academic, business, governmental), exchange perspectives and discover new opportunities. Six sub-sector focus groups comprising over 200 senior stakeholders from academia, industry, the Welsh Government and National Health Service were established. Over 18 months, each focus group provided input to inform healthcare innovation policy and knowledge mapping exercises of their respective sub-sectors. Collaborative projects identified during the focus groups and stakeholder engagement were further developed through sandpit events and bespoke support. Each sub-sector focus group produced a report outlining the significant strengths and opportunities in their respective areas of focus, made recommendations to overcome any 'system failures', and identified the stakeholder groups which needed to take action. A second outcome was a stakeholder-driven knowledge mapping exercise for each area of focus. Finally, the sandpit events and bespoke support resulted in participants generating more than £1.66 million in grant funding and inward investment. This article outlines four separate outcomes from the Life Science Exchange programme. The Life Science Exchange process has resulted in a multitude of collaborations, projects, inward investment opportunities and special interest group formations, in addition to securing over ten times its own costs in funding for Wales. The Life Science Exchange model is a simple and straightforward mechanism for a regional or national government to adapt and implement in order to improve innovation, skills, networks and knowledge exchange.

Mapping stress in polycrystals with sub-10 nm spatial resolution.

PubMed

Polop, C; Vasco, E; Perrino, A P; Garcia, R

2017-09-28

From aircraft to electronic devices, and even in Formula One cars, stress is the main cause of degraded material performance and mechanical failure in applications incorporating thin films and coatings. Over the last two decades, the scientific community has searched for the mechanisms responsible for stress generation in films, with no consensus in sight. The main difficulty is that most current models of stress generation, while atomistic in nature, are based on macroscopic measurements. Here, we demonstrate a novel method for mapping the stress at the surface of polycrystals with sub-10 nm spatial resolution. This method consists of transforming elastic modulus maps measured by atomic force microscopy techniques into stress maps via the local stress-stiffening effect. The validity of this approach is supported by finite element modeling simulations. Our study reveals a strongly heterogeneous distribution of intrinsic stress in polycrystalline Au films, with gradients as high as 100 MPa nm -1 near the grain boundaries. Consequently, our study discloses the limited capacity of macroscopic stress assessments and standard tests to discriminate among models, and the great potential of nanometer-scale stress mapping.

Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity.

PubMed

Dalmasso, Giovanni; Marin Zapata, Paula Andrea; Brady, Nathan Ryan; Hamacher-Brady, Anne

2017-01-01

Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM) to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1) mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2) restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3) maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4) our model suggests sources of, and stress conditions amplifying, cell-to-cell variability of mitochondrial morphology and energetic stress states. Overall, our modeling approach integrates biochemical and imaging knowledge, and presents a novel open-modeling approach to investigate how spatial and temporal mitochondrial dynamics contribute to functional homeostasis, and how subcellular organelle heterogeneity contributes to the emergence of cell heterogeneity.

Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity

PubMed Central

Dalmasso, Giovanni; Marin Zapata, Paula Andrea; Brady, Nathan Ryan; Hamacher-Brady, Anne

2017-01-01

Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM) to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1) mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2) restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3) maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4) our model suggests sources of, and stress conditions amplifying, cell-to-cell variability of mitochondrial morphology and energetic stress states. Overall, our modeling approach integrates biochemical and imaging knowledge, and presents a novel open-modeling approach to investigate how spatial and temporal mitochondrial dynamics contribute to functional homeostasis, and how subcellular organelle heterogeneity contributes to the emergence of cell heterogeneity. PMID:28060865

Cellular Basis for Learning Impairment in Fragile X Syndrome

DTIC Science & Technology

2014-08-01

oxygen is restored. Induction of the heat shock proteins (HSPs) is one of the first lines of defense against physiological stress , shifting cellular...Haddad, 2001), and aid resistance to glutamate and hypoxic stress in mammals (Zhang et al., 2000). AMPA receptor currents, meanwhile, are also...level in anoxic turtle brain. These include increases in heat shock proteins, anti-apoptotic factors, the MAP kinases, antioxidants and modulation of