Sample records for interaction doi information

  1. Pulse shape discrimination and classification methods for continuous depth of interaction encoding PET detectors.

    PubMed

    Roncali, Emilie; Phipps, Jennifer E; Marcu, Laura; Cherry, Simon R

    2012-10-21

    In previous work we demonstrated the potential of positron emission tomography (PET) detectors with depth-of-interaction (DOI) encoding capability based on phosphor-coated crystals. A DOI resolution of 8 mm full-width at half-maximum was obtained for 20 mm long scintillator crystals using a delayed charge integration linear regression method (DCI-LR). Phosphor-coated crystals modify the pulse shape to allow continuous DOI information determination, but the relationship between pulse shape and DOI is complex. We are therefore interested in developing a sensitive and robust method to estimate the DOI. Here, linear discriminant analysis (LDA) was implemented to classify the events based on information extracted from the pulse shape. Pulses were acquired with 2×2×20 mm(3) phosphor-coated crystals at five irradiation depths and characterized by their DCI values or Laguerre coefficients. These coefficients were obtained by expanding the pulses on a Laguerre basis set and constituted a unique signature for each pulse. The DOI of individual events was predicted using LDA based on Laguerre coefficients (Laguerre-LDA) or DCI values (DCI-LDA) as discriminant features. Predicted DOIs were compared to true irradiation depths. Laguerre-LDA showed higher sensitivity and accuracy than DCI-LDA and DCI-LR and was also more robust to predict the DOI of pulses with higher statistical noise due to low light levels (interaction depths further from the photodetector face). This indicates that Laguerre-LDA may be more suitable to DOI estimation in smaller crystals where lower collected light levels are expected. This novel approach is promising for calculating DOI using pulse shape discrimination in single-ended readout depth-encoding PET detectors.

  2. Pulse Shape Discrimination and Classification Methods for Continuous Depth of Interaction Encoding PET Detectors

    PubMed Central

    Roncali, Emilie; Phipps, Jennifer E.; Marcu, Laura; Cherry, Simon R.

    2012-01-01

    In previous work we demonstrated the potential of positron emission tomography (PET) detectors with depth-of-interaction (DOI) encoding capability based on phosphor-coated crystals. A DOI resolution of 8 mm full-width at half-maximum was obtained for 20 mm long scintillator crystals using a delayed charge integration linear regression method (DCI-LR). Phosphor-coated crystals modify the pulse shape to allow continuous DOI information determination, but the relationship between pulse shape and DOI is complex. We are therefore interested in developing a sensitive and robust method to estimate the DOI. Here, linear discriminant analysis (LDA) was implemented to classify the events based on information extracted from the pulse shape. Pulses were acquired with 2 × 2 × 20 mm3 phosphor-coated crystals at five irradiation depths and characterized by their DCI values or Laguerre coefficients. These coefficients were obtained by expanding the pulses on a Laguerre basis set and constituted a unique signature for each pulse. The DOI of individual events was predicted using LDA based on Laguerre coefficients (Laguerre-LDA) or DCI values (DCI-LDA) as discriminant features. Predicted DOIs were compared to true irradiation depths. Laguerre-LDA showed higher sensitivity and accuracy than DCI-LDA and DCI-LR and was also more robust to predict the DOI of pulses with higher statistical noise due to low light levels (interaction depths further from the photodetector face). This indicates that Laguerre-LDA may be more suitable to DOI estimation in smaller crystals where lower collected light levels are expected. This novel approach is promising for calculating DOI using pulse shape discrimination in single-ended readout depth-encoding PET detectors. PMID:23010690

  3. Evolving a NASA Digital Object Identifiers System with Community Engagement

    NASA Technical Reports Server (NTRS)

    Wanchoo, Lalit; James, Nathan

    2016-01-01

    To demonstrate how the ESDIS (Earth Science Data and Information System) DOI (Digital Object Identifier) system and its processes have evolved over these years based on the recommendations provided by the user community (whether the community members create and manage DOI information or use DOIs in the data citations). The user community is comprised of people with common interests and needs for data identifiers who are actively involved in the creation and usage process. Engagement describes the interactive context wherein the community provides information, evaluates the proposed processes, and provides guidance in the area of identifiers.

  4. Depth of interaction decoding of a continuous crystal detector module.

    PubMed

    Ling, T; Lewellen, T K; Miyaoka, R S

    2007-04-21

    We present a clustering method to extract the depth of interaction (DOI) information from an 8 mm thick crystal version of our continuous miniature crystal element (cMiCE) small animal PET detector. This clustering method, based on the maximum-likelihood (ML) method, can effectively build look-up tables (LUT) for different DOI regions. Combined with our statistics-based positioning (SBP) method, which uses a LUT searching algorithm based on the ML method and two-dimensional mean-variance LUTs of light responses from each photomultiplier channel with respect to different gamma ray interaction positions, the position of interaction and DOI can be estimated simultaneously. Data simulated using DETECT2000 were used to help validate our approach. An experiment using our cMiCE detector was designed to evaluate the performance. Two and four DOI region clustering were applied to the simulated data. Two DOI regions were used for the experimental data. The misclassification rate for simulated data is about 3.5% for two DOI regions and 10.2% for four DOI regions. For the experimental data, the rate is estimated to be approximately 25%. By using multi-DOI LUTs, we also observed improvement of the detector spatial resolution, especially for the corner region of the crystal. These results show that our ML clustering method is a consistent and reliable way to characterize DOI in a continuous crystal detector without requiring any modifications to the crystal or detector front end electronics. The ability to characterize the depth-dependent light response function from measured data is a major step forward in developing practical detectors with DOI positioning capability.

  5. A flood map based DOI decoding method for block detector: a GATE simulation study.

    PubMed

    Shi, Han; Du, Dong; Su, Zhihong; Peng, Qiyu

    2014-01-01

    Positron Emission Tomography (PET) systems using detectors with Depth of Interaction (DOI) capabilities could achieve higher spatial resolution and better image quality than those without DOI. Up till now, most DOI methods developed are not cost-efficient for a whole body PET system. In this paper, we present a DOI decoding method based on flood map for low-cost conventional block detector with four-PMT readout. Using this method, the DOI information can be directly extracted from the DOI-related crystal spot deformation in the flood map. GATE simulations are then carried out to validate the method, confirming a DOI sorting accuracy of 85.27%. Therefore, we conclude that this method has the potential to be applied in conventional detectors to achieve a reasonable DOI measurement without dramatically increasing their complexity and cost of an entire PET system.

  6. Continuous depth-of-interaction encoding using phosphor-coated scintillators.

    PubMed

    Du, Huini; Yang, Yongfeng; Glodo, Jarek; Wu, Yibao; Shah, Kanai; Cherry, Simon R

    2009-03-21

    We investigate a novel detector using a lutetium oxyorthosilicate (LSO) scintillator and YGG (yttrium-aluminum-gallium oxide:cerium, Y(3)(Al,Ga)(5)O(12):Ce) phosphor to construct a detector with continuous depth-of-interaction (DOI) information. The far end of the LSO scintillator is coated with a thin layer of YGG phosphor powder which absorbs some fraction of the LSO scintillation light and emits wavelength-shifted photons with a characteristic decay time of approximately 50 ns. The near end of the LSO scintillator is directly coupled to a photodetector. The photodetector detects a mixture of the LSO light and the light emitted by YGG. With appropriate placement of the coating, the ratio of the light converted from the YGG coating with respect to the unconverted LSO light can be made to depend on the interaction depth. DOI information can then be estimated by inspecting the overall light pulse decay time. Experiments were conducted to optimize the coating method. 19 ns decay time differences across the length of the detector were achieved experimentally when reading out a 1.5 x 1.5 x 20 mm(3) LSO crystal with unpolished surfaces and half-coated with YGG phosphor. The same coating scheme was applied to a 4 x 4 LSO array. Pulse shape discrimination (PSD) methods were studied to extract DOI information from the pulse shape changes. The DOI full-width-half-maximum (FWHM) resolution was found to be approximately 8 mm for this 2 cm thick array.

  7. Continuous Depth-of-Interaction Encoding Using Phosphor-Coated Scintillators

    PubMed Central

    Du, Huini; Yang, Yongfeng; Glodo, Jarek; Wu, Yibao; Shah, Kanai; Cherry, Simon R.

    2009-01-01

    We investigate a novel detector using lutetium oxyorthosilicate (LSO) scintillator and YGG (yttrium aluminum gallium oxide:cerium, Y3(Al,Ga)5O12:Ce) phosphor to construct a detector with continuous depth-of-interaction (DOI) information. The far end of the LSO scintillator is coated with a thin layer of YGG phosphor powder which absorbs some fraction of the LSO scintillation light and emits wavelength-shifted photons with a characteristic decay time of ∼ 50 ns. The near end of the LSO scintillator is directly coupled to a photodetector. The photodetector detects a mixture of the LSO light and the light emitted by YGG. With appropriate placement of the coating, the ratio of the light converted from the YGG coating with respect to the unconverted LSO light can be made to depend on the interaction depth. DOI information can then be estimated by inspecting the overall light pulse decay time. Experiments were conducted to optimize the coating method. 19 ns decay time differences across the length of the detector were achieved experimentally when reading out a 1.5×1.5×20 mm3 LSO crystal with unpolished surfaces and half-coated with YGG phosphor. The same coating scheme was applied to a 4 by 4 LSO array. Pulse shape discrimination (PSD) methods were studied to extract DOI information from the pulse shape changes. The DOI full-width-half-maximum (FWHM) resolution was found to be ∼8 mm for this 2 cm thick array. PMID:19258685

  8. Sensitivity booster for DOI-PET scanner by utilizing Compton scattering events between detector blocks

    NASA Astrophysics Data System (ADS)

    Yoshida, Eiji; Tashima, Hideaki; Yamaya, Taiga

    2014-11-01

    In a conventional PET scanner, coincidence events are measured with a limited energy window for detection of photoelectric events in order to reject Compton scatter events that occur in a patient, but Compton scatter events caused in detector crystals are also rejected. Scatter events within the patient causes scatter coincidences, but inter crystal scattering (ICS) events have useful information for determining an activity distribution. Some researchers have reported the feasibility of PET scanners based on a Compton camera for tracing ICS into the detector. However, these scanners require expensive semiconductor detectors for high-energy resolution. In the Anger-type block detector, single photons interacting with multiple detectors can be obtained for each interacting position and complete information can be gotten just as for photoelectric events in the single detector. ICS events in the single detector have been used to get coincidence, but single photons interacting with multiple detectors have not been used to get coincidence. In this work, we evaluated effect of sensitivity improvement using Compton kinetics in several types of DOI-PET scanners. The proposed method promises to improve the sensitivity using coincidence events of single photons interacting with multiple detectors, which are identified as the first interaction (FI). FI estimation accuracy can be improved to determine FI validity from the correlation between Compton scatter angles calculated on the coincidence line-of-response. We simulated an animal PET scanner consisting of 42 detectors. Each detector block consists of three types of scintillator crystals (LSO, GSO and GAGG). After the simulation, coincidence events are added as information for several depth-of-interaction (DOI) resolutions. From the simulation results, we concluded the proposed method promises to improve the sensitivity considerably when effective atomic number of a scintillator is low. Also, we showed that FI estimate accuracy is improved, as DOI resolution is high.

  9. WE-C-217BCD-10: Development of High Performance PET for Animal Imaging and Therapy Applications.

    PubMed

    Shao, Y; Sun, X; Lan, K; Bircher, C

    2012-06-01

    A prototype small animal PET is developed with several novel technologies to measure 3D gamma-interaction positions and to substantially improve imaging performance. Each new detector has an 8×8 array of 1.95×1.95×30 mm̂3 LYSO scintillators, with each end optically connected to a solid-state photo multiplier (SSPM) array through a light guide. This dual-ended-readout enables the depth-of-interaction (DOI) measurement. Each SSPM array has 16 SSPMs arranged in a 4×4 matrix. Each SSPM has active area about 3×3 mm̂2, with its output read by an ASIC electronics that directly converts analog signals to digital timing pulses which encode the interaction information for energy, timing, crystal of interaction, and DOI calculations. These digital pulses are transferred to and decoded by FPGA-based TDC for coincident event selection and data acquisition. This independent readout of each SSPM and parallel signal process significantly improve signal-to-noise ratio and permit applying flexible data processing algorithms. The current prototype system consists of two rotating detector panels on a portable gantry, with 4 detectors linearly packed together in each panel to provide ∼16 mm axial and variable trans- axial FOV with adjustable panel-to-panel distance. List-mode OSEM-based image reconstruction with resolution modeling was implemented. Both Na- 22 point source and phantom were used to evaluate the system performance. The measured energy, timing, spatial and DOI resolutions for each crystal were around 16%, 2.6 ns, 2.0 mm and 5.0 mm, respectively. The measured spatial resolutions with DOI were ∼1.7 mm across the entire FOV in all direction, while those without DOI were much worse and non-uniform across the FOV, in the range predominately around 3.0 to 4.0 mm. In addition, images from a F-18 hot-rod phantom with DOI show significantly improved quality compared to those without DOI. DOI- measurable PET shows substantially improved image performance for a compact system. National Institute of Health. University of Texas MD Anderson Cancer Center. © 2012 American Association of Physicists in Medicine.

  10. A combined time-of-flight and depth-of-interaction detector for total-body positron emission tomography.

    PubMed

    Berg, Eric; Roncali, Emilie; Kapusta, Maciej; Du, Junwei; Cherry, Simon R

    2016-02-01

    In support of a project to build a total-body PET scanner with an axial field-of-view of 2 m, the authors are developing simple, cost-effective block detectors with combined time-of-flight (TOF) and depth-of-interaction (DOI) capabilities. This work focuses on investigating the potential of phosphor-coated crystals with conventional PMT-based block detector readout to provide DOI information while preserving timing resolution. The authors explored a variety of phosphor-coating configurations with single crystals and crystal arrays. Several pulse shape discrimination techniques were investigated, including decay time, delayed charge integration (DCI), and average signal shapes. Pulse shape discrimination based on DCI provided the lowest DOI positioning error: 2 mm DOI positioning error was obtained with single phosphor-coated crystals while 3-3.5 mm DOI error was measured with the block detector module. Minimal timing resolution degradation was observed with single phosphor-coated crystals compared to uncoated crystals, and a timing resolution of 442 ps was obtained with phosphor-coated crystals in the block detector compared to 404 ps without phosphor coating. Flood maps showed a slight degradation in crystal resolvability with phosphor-coated crystals; however, all crystals could be resolved. Energy resolution was degraded by 3%-7% with phosphor-coated crystals compared to uncoated crystals. These results demonstrate the feasibility of obtaining TOF-DOI capabilities with simple block detector readout using phosphor-coated crystals.

  11. Depth of interaction determination in monolithic scintillator with double side SiPM readout.

    PubMed

    Morrocchi, Matteo; Ambrosi, Giovanni; Bisogni, Maria Giuseppina; Bosi, Filippo; Boretto, Marco; Cerello, Piergiorgio; Ionica, Maria; Liu, Ben; Pennazio, Francesco; Piliero, Maria Antonietta; Pirrone, Giovanni; Postolache, Vasile; Wheadon, Richard; Del Guerra, Alberto

    2017-12-01

    Monolithic scintillators read out by arrays of photodetectors represent a promising solution to obtain high spatial resolution and the depth of interaction (DOI) of the annihilation photon. We have recently investigated a detector geometry composed of a monolithic scintillator readout on two sides by silicon photomultiplier (SiPM) arrays, and we have proposed two parameters for the DOI determination: the difference in the number of triggered SiPMs on the two sides of the detector and the difference in the maximum collected signal on a single SiPM on each side. This work is focused on the DOI calibration and on the determination of the capability of our detector. For the DOI calibration, we studied a method which can be implemented also in detectors mounted in a full PET scanner. We used a PET detector module composed of a monolithic 20 × 20 × 10 mm 3 LYSO scintillator crystal coupled on two opposite faces to two arrays of SiPMs. On each side, the scintillator was coupled to 6 × 6 SiPMs. In this paper, the two parameters previously proposed for the DOI determination were calibrated with two different methods. The first used a lateral scan of the detector with a collimated 511 keV pencil beam at steps of 0.5 mm to study the detector DOI capability, while the second used the background radiation of the 176 Lu in the scintillator. The DOI determination capability was tested on different regions of the detector using each parameter and the combination of the two. With both parameters for the DOI determination, in the lateral scan, the bias between the mean reconstructed DOI and the real beam position was lower than 0.3 mm, and the DOI distribution had a standard deviation of about 1.5 mm. When using the calibration with the radioactivity of the LYSO, the mean bias increased of about 0.2 mm but with no degradation of the standard deviation of the DOI distribution. The two parameters allow to achieve a DOI resolution comparable with the state of the art, giving a continuous information about the three-dimensional interaction position of the scintillation. These results were obtained by using simple estimators and a detector scalable to a whole PET system. The DOI calibration obtained using lutetium natural radioactivity gives results comparable to the other standard method but appears more readily applicable to detectors mounted in a full PET scanner.

  12. Prototype pre-clinical PET scanner with depth-of-interaction measurements using single-layer crystal array and single-ended readout

    NASA Astrophysics Data System (ADS)

    Lee, Min Sun; Kim, Kyeong Yun; Ko, Guen Bae; Lee, Jae Sung

    2017-05-01

    In this study, we developed a proof-of-concept prototype PET system using a pair of depth-of-interaction (DOI) PET detectors based on the proposed DOI-encoding method and digital silicon photomultiplier (dSiPM). Our novel cost-effective DOI measurement method is based on a triangular-shaped reflector that requires only a single-layer pixelated crystal and single-ended signal readout. The DOI detector consisted of an 18  ×  18 array of unpolished LYSO crystal (1.47  ×  1.47  ×  15 mm3) wrapped with triangular-shaped reflectors. The DOI information was encoded by depth-dependent light distribution tailored by the reflector geometry and DOI correction was performed using four-step depth calibration data and maximum-likelihood (ML) estimation. The detector pair and the object were placed on two motorized rotation stages to demonstrate 12-block ring PET geometry with 11.15 cm diameter. Spatial resolution was measured and phantom and animal imaging studies were performed to investigate imaging performance. All images were reconstructed with and without the DOI correction to examine the impact of our DOI measurement. The pair of dSiPM-based DOI PET detectors showed good physical performances respectively: 2.82 and 3.09 peak-to-valley ratios, 14.30% and 18.95% energy resolution, and 4.28 and 4.24 mm DOI resolution averaged over all crystals and all depths. A sub-millimeter spatial resolution was achieved at the center of the field of view (FOV). After applying ML-based DOI correction, maximum 36.92% improvement was achieved in the radial spatial resolution and a uniform resolution was observed within 5 cm of transverse PET FOV. We successfully acquired phantom and animal images with improved spatial resolution and contrast by using the DOI measurement. The proposed DOI-encoding method was successfully demonstrated in the system level and exhibited good performance, showing its feasibility for animal PET applications with high spatial resolution and sensitivity.

  13. Effects of Detector Thickness on Geometric Sensitivity and Event Positioning Errors in the Rectangular PET/X Scanner

    NASA Astrophysics Data System (ADS)

    MacDonald, Lawrence R.; Hunter, William C. J.; Kinahan, Paul E.; Miyaoka, Robert S.

    2013-10-01

    We used simulations to investigate the relationship between sensitivity and spatial resolution as a function of crystal thickness in a rectangular PET scanner intended for quantitative assessment of breast cancers. The system had two 20 × 15-cm2 and two 10 × 15-cm2 flat detectors forming a box, with the larger detectors separated by 4 or 8 cm. Depth-of-interaction (DOI) resolution was modeled as a function of crystal thickness based on prior measurements. Spatial resolution was evaluated independent of image reconstruction by deriving and validating a surrogate metric from list-mode data ( dFWHM). When increasing crystal thickness from 5 to 40 mm, and without using DOI information, the dFWHM for a centered point source increased from 0.72 to 1.6 mm. Including DOI information improved dFWHM by 12% and 27% for 5- and 40-mm-thick crystals, respectively. For a point source in the corner of the FOV, use of DOI information improved dFWHM by 20% (5-mm crystal) and 44% (40-mm crystal). Sensitivity was 7.7% for 10-mm-thick crystals (8-cm object). Increasing crystal thickness on the smaller side detectors from 10 to 20 mm (keeping 10-mm crystals on the larger detectors) boosted sensitivity by 24% (relative) and degraded dFWHM by only 3%/8% with/without DOI information. The benefits of measuring DOI must be evaluated in terms of the intended clinical task of assessing tracer uptake in small lesions. Increasing crystal thickness on the smaller side detectors provides substantial sensitivity increase with minimal accompanying loss in resolution.

  14. Sequence co-evolution gives 3D contacts and structures of protein complexes

    PubMed Central

    Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

    2014-01-01

    Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

  15. Side readout of long scintillation crystal elements with digital SiPM for TOF-DOI PET.

    PubMed

    Yeom, Jung Yeol; Vinke, Ruud; Levin, Craig S

    2014-12-01

    Side readout of scintillation light from crystal elements in positron emission tomography (PET) is an alternative to conventional end-readout configurations, with the benefit of being able to provide accurate depth-of-interaction (DOI) information and good energy resolution while achieving excellent timing resolution required for time-of-flight PET. This paper explores different readout geometries of scintillation crystal elements with the goal of achieving a detector that simultaneously achieves excellent timing resolution, energy resolution, spatial resolution, and photon sensitivity. The performance of discrete LYSO scintillation elements of different lengths read out from the end/side with digital silicon photomultipliers (dSiPMs) has been assessed. Compared to 3 × 3 × 20 mm(3) LYSO crystals read out from their ends with a coincidence resolving time (CRT) of 162 ± 6 ps FWHM and saturated energy spectra, a side-readout configuration achieved an excellent CRT of 144 ± 2 ps FWHM after correcting for timing skews within the dSiPM and an energy resolution of 11.8% ± 0.2% without requiring energy saturation correction. Using a maximum likelihood estimation method on individual dSiPM pixel response that corresponds to different 511 keV photon interaction positions, the DOI resolution of this 3 × 3 × 20 mm(3) crystal side-readout configuration was computed to be 0.8 mm FWHM with negligible artifacts at the crystal ends. On the other hand, with smaller 3 × 3 × 5 mm(3) LYSO crystals that can also be tiled/stacked to provide DOI information, a timing resolution of 134 ± 6 ps was attained but produced highly saturated energy spectra. The energy, timing, and DOI resolution information extracted from the side of long scintillation crystal elements coupled to dSiPM have been acquired for the first time. The authors conclude in this proof of concept study that such detector configuration has the potential to enable outstanding detector performance in terms of timing, energy, and DOI resolution.

  16. Side readout of long scintillation crystal elements with digital SiPM for TOF-DOI PET

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

    Yeom, Jung Yeol, E-mail: yeomjy@kumoh.ac.kr, E-mail: cslevin@stanford.edu; Vinke, Ruud; Levin, Craig S., E-mail: yeomjy@kumoh.ac.kr, E-mail: cslevin@stanford.edu

    Purpose: Side readout of scintillation light from crystal elements in positron emission tomography (PET) is an alternative to conventional end-readout configurations, with the benefit of being able to provide accurate depth-of-interaction (DOI) information and good energy resolution while achieving excellent timing resolution required for time-of-flight PET. This paper explores different readout geometries of scintillation crystal elements with the goal of achieving a detector that simultaneously achieves excellent timing resolution, energy resolution, spatial resolution, and photon sensitivity. Methods: The performance of discrete LYSO scintillation elements of different lengths read out from the end/side with digital silicon photomultipliers (dSiPMs) has been assessed.more » Results: Compared to 3 × 3 × 20 mm{sup 3} LYSO crystals read out from their ends with a coincidence resolving time (CRT) of 162 ± 6 ps FWHM and saturated energy spectra, a side-readout configuration achieved an excellent CRT of 144 ± 2 ps FWHM after correcting for timing skews within the dSiPM and an energy resolution of 11.8% ± 0.2% without requiring energy saturation correction. Using a maximum likelihood estimation method on individual dSiPM pixel response that corresponds to different 511 keV photon interaction positions, the DOI resolution of this 3 × 3 × 20 mm{sup 3} crystal side-readout configuration was computed to be 0.8 mm FWHM with negligible artifacts at the crystal ends. On the other hand, with smaller 3 × 3 × 5 mm{sup 3} LYSO crystals that can also be tiled/stacked to provide DOI information, a timing resolution of 134 ± 6 ps was attained but produced highly saturated energy spectra. Conclusions: The energy, timing, and DOI resolution information extracted from the side of long scintillation crystal elements coupled to dSiPM have been acquired for the first time. The authors conclude in this proof of concept study that such detector configuration has the potential to enable outstanding detector performance in terms of timing, energy, and DOI resolution.« less

  17. A depth-of-interaction PET detector using a stair-shaped reflector arrangement and a single-ended scintillation light readout.

    PubMed

    Son, Jeong-Whan; Lee, Min Sun; Lee, Jae Sung

    2017-01-21

    Positron emission tomography (PET) detectors with the ability to encode depth-of-interaction (DOI) information allow us to simultaneously improve the spatial resolution and sensitivity of PET scanners. In this study, we propose a DOI PET detector based on a stair-pattern reflector arrangement inserted between pixelated crystals and a single-ended scintillation light readout. The main advantage of the proposed method is its simplicity; DOI information is decoded from a flood map and the data can be simply acquired by using a single-ended readout system. Another potential advantage is that the two-step DOI detectors can provide the largest peak position distance in a flood map because two-dimensional peak positions can be evenly distributed. We conducted a Monte Carlo simulation and obtained flood maps. Then, we conducted experimental studies using two-step DOI arrays of 5  ×  5 Lu 1.9 Y 0.1 SiO 5 :Ce crystals with a cross-section of 1.7  ×  1.7 mm 2 and different detector configurations: an unpolished single-layer ( U S) array, a polished single-layer ( P S) array and a polished stacked two-layer ( P T) array. For each detector configuration, both air gaps and room-temperature vulcanization (RTV) silicone gaps were tested. Detectors U S and P T showed good peak separation in each scintillator with an average peak-to-valley ratio (PVR) and distance-to-width ratio (DWR) of 2.09 and 1.53, respectively. Detector P S RTV showed lower PVR and DWR (1.65 and 1.34, respectively). The configuration of detector P T Air is preferable for the construction of time-of-flight-DOI detectors because timing resolution was degraded by only about 40 ps compared with that of a non-DOI detector. The performance of detectors U S Air and P S RTV was lower than that of a non-DOI detector, and thus these designs are favorable when the manufacturing cost is more important than timing performance. The results demonstrate that the proposed DOI-encoding method is a promising candidate for PET scanners that require high resolution and sensitivity and operate with conventional acquisition systems.

  18. A combined time-of-flight and depth-of-interaction detector for total-body positron emission tomography

    PubMed Central

    Berg, Eric; Roncali, Emilie; Kapusta, Maciej; Du, Junwei; Cherry, Simon R.

    2016-01-01

    Purpose: In support of a project to build a total-body PET scanner with an axial field-of-view of 2 m, the authors are developing simple, cost-effective block detectors with combined time-of-flight (TOF) and depth-of-interaction (DOI) capabilities. Methods: This work focuses on investigating the potential of phosphor-coated crystals with conventional PMT-based block detector readout to provide DOI information while preserving timing resolution. The authors explored a variety of phosphor-coating configurations with single crystals and crystal arrays. Several pulse shape discrimination techniques were investigated, including decay time, delayed charge integration (DCI), and average signal shapes. Results: Pulse shape discrimination based on DCI provided the lowest DOI positioning error: 2 mm DOI positioning error was obtained with single phosphor-coated crystals while 3–3.5 mm DOI error was measured with the block detector module. Minimal timing resolution degradation was observed with single phosphor-coated crystals compared to uncoated crystals, and a timing resolution of 442 ps was obtained with phosphor-coated crystals in the block detector compared to 404 ps without phosphor coating. Flood maps showed a slight degradation in crystal resolvability with phosphor-coated crystals; however, all crystals could be resolved. Energy resolution was degraded by 3%–7% with phosphor-coated crystals compared to uncoated crystals. Conclusions: These results demonstrate the feasibility of obtaining TOF–DOI capabilities with simple block detector readout using phosphor-coated crystals. PMID:26843254

  19. A combined time-of-flight and depth-of-interaction detector for total-body positron emission tomography

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

    Berg, Eric, E-mail: eberg@ucdavis.edu; Roncali, Emilie; Du, Junwei

    Purpose: In support of a project to build a total-body PET scanner with an axial field-of-view of 2 m, the authors are developing simple, cost-effective block detectors with combined time-of-flight (TOF) and depth-of-interaction (DOI) capabilities. Methods: This work focuses on investigating the potential of phosphor-coated crystals with conventional PMT-based block detector readout to provide DOI information while preserving timing resolution. The authors explored a variety of phosphor-coating configurations with single crystals and crystal arrays. Several pulse shape discrimination techniques were investigated, including decay time, delayed charge integration (DCI), and average signal shapes. Results: Pulse shape discrimination based on DCI providedmore » the lowest DOI positioning error: 2 mm DOI positioning error was obtained with single phosphor-coated crystals while 3–3.5 mm DOI error was measured with the block detector module. Minimal timing resolution degradation was observed with single phosphor-coated crystals compared to uncoated crystals, and a timing resolution of 442 ps was obtained with phosphor-coated crystals in the block detector compared to 404 ps without phosphor coating. Flood maps showed a slight degradation in crystal resolvability with phosphor-coated crystals; however, all crystals could be resolved. Energy resolution was degraded by 3%–7% with phosphor-coated crystals compared to uncoated crystals. Conclusions: These results demonstrate the feasibility of obtaining TOF–DOI capabilities with simple block detector readout using phosphor-coated crystals.« less

  20. The molecular mechanism of nuclear transport revealed by atomic-scale measurements

    PubMed Central

    Hough, Loren E; Dutta, Kaushik; Sparks, Samuel; Temel, Deniz B; Kamal, Alia; Tetenbaum-Novatt, Jaclyn; Rout, Michael P; Cowburn, David

    2015-01-01

    Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the passage of other macromolecules. Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats line the pore and interact with TFs. However, the reason that transport can be both fast and specific remains undetermined, through lack of atomic-scale information on the behavior of FGs and their interaction with TFs. We used nuclear magnetic resonance spectroscopy to address these issues. We show that FG repeats are highly dynamic IDPs, stabilized by the cellular environment. Fast transport of TFs is supported because the rapid motion of FG motifs allows them to exchange on and off TFs extremely quickly through transient interactions. Because TFs uniquely carry multiple pockets for FG repeats, only they can form the many frequent interactions needed for specific passage between FG repeats to cross the NPC. DOI: http://dx.doi.org/10.7554/eLife.10027.001 PMID:26371551

  1. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

    PubMed Central

    Clark, Natalie M; Hinde, Elizabeth; Winter, Cara M; Fisher, Adam P; Crosti, Giuseppe; Blilou, Ikram; Gratton, Enrico; Benfey, Philip N; Sozzani, Rosangela

    2016-01-01

    To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric state, and association with SCR using a combination of Fluorescent Correlation Spectroscopy (FCS) techniques. We then incorporate these parameters into a mathematical model of SHR and SCR, which shows that SHR reaches a steady state in minutes, while SCR and the SHR-SCR complex reach a steady-state between 18 and 24 hr. Our model reveals the timing of SHR and SCR dynamics and allows us to understand how protein movement and protein-protein stoichiometry contribute to development. DOI: http://dx.doi.org/10.7554/eLife.14770.001 PMID:27288545

  2. A novel method to calibrate DOI function of a PET detector with a dual-ended-scintillator readout.

    PubMed

    Shao, Yiping; Yao, Rutao; Ma, Tianyu

    2008-12-01

    The detection of depth-of-interaction (DOI) is a critical detector capability to improve the PET spatial resolution uniformity across the field-of-view and will significantly enhance, in particular, small bore system performance for brain, breast, and small animal imaging. One promising technique of DOI detection is to use dual-ended-scintillator readout that uses two photon sensors to detect scintillation light from both ends of a scintillator array and estimate DOI based on the ratio of signals (similar to Anger logic). This approach needs a careful DOI function calibration to establish accurate relationship between DOI and signal ratios, and to recalibrate if the detection condition is shifted due to the drift of sensor gain, bias variations, or degraded optical coupling, etc. However, the current calibration method that uses coincident events to locate interaction positions inside a single scintillator crystal has severe drawbacks, such as complicated setup, long and repetitive measurements, and being prone to errors from various possible misalignments among the source and detector components. This method is also not practically suitable to calibrate multiple DOI functions of a crystal array. To solve these problems, a new method has been developed that requires only a uniform flood source to irradiate a crystal array without the need to locate the interaction positions, and calculates DOI functions based solely on the uniform probability distribution of interactions over DOI positions without knowledge or assumption of detector responses. Simulation and experiment have been studied to validate the new method, and the results show that the new method, with a simple setup and one single measurement, can provide consistent and accurate DOI functions for the entire array of multiple scintillator crystals. This will enable an accurate, simple, and practical DOI function calibration for the PET detectors based on the design of dual-ended-scintillator readout. In addition, the new method can be generally applied to calibrating other types of detectors that use the similar dual-ended readout to acquire the radiation interaction position.

  3. A novel method to calibrate DOI function of a PET detector with a dual-ended-scintillator readout

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

    Shao Yiping; Yao Rutao; Ma Tianyu

    The detection of depth-of-interaction (DOI) is a critical detector capability to improve the PET spatial resolution uniformity across the field-of-view and will significantly enhance, in particular, small bore system performance for brain, breast, and small animal imaging. One promising technique of DOI detection is to use dual-ended-scintillator readout that uses two photon sensors to detect scintillation light from both ends of a scintillator array and estimate DOI based on the ratio of signals (similar to Anger logic). This approach needs a careful DOI function calibration to establish accurate relationship between DOI and signal ratios, and to recalibrate if the detectionmore » condition is shifted due to the drift of sensor gain, bias variations, or degraded optical coupling, etc. However, the current calibration method that uses coincident events to locate interaction positions inside a single scintillator crystal has severe drawbacks, such as complicated setup, long and repetitive measurements, and being prone to errors from various possible misalignments among the source and detector components. This method is also not practically suitable to calibrate multiple DOI functions of a crystal array. To solve these problems, a new method has been developed that requires only a uniform flood source to irradiate a crystal array without the need to locate the interaction positions, and calculates DOI functions based solely on the uniform probability distribution of interactions over DOI positions without knowledge or assumption of detector responses. Simulation and experiment have been studied to validate the new method, and the results show that the new method, with a simple setup and one single measurement, can provide consistent and accurate DOI functions for the entire array of multiple scintillator crystals. This will enable an accurate, simple, and practical DOI function calibration for the PET detectors based on the design of dual-ended-scintillator readout. In addition, the new method can be generally applied to calibrating other types of detectors that use the similar dual-ended readout to acquire the radiation interaction position.« less

  4. Choice of crystal surface finishing for a dual-ended readout depth-of-interaction (DOI) detector.

    PubMed

    Fan, Peng; Ma, Tianyu; Wei, Qingyang; Yao, Rutao; Liu, Yaqiang; Wang, Shi

    2016-02-07

    The objective of this study was to choose the crystal surface finishing for a dual-ended readout (DER) DOI detector. Through Monte Carlo simulations and experimental studies, we evaluated 4 crystal surface finishing options as combinations of crystal surface polishing (diffuse or specular) and reflector (diffuse or specular) options on a DER detector. We also tested one linear and one logarithm DOI calculation algorithm. The figures of merit used were DOI resolution, DOI positioning error, and energy resolution. Both the simulation and experimental results show that (1) choosing a diffuse type in either surface polishing or reflector would improve DOI resolution but degrade energy resolution; (2) crystal surface finishing with a diffuse polishing combined with a specular reflector appears a favorable candidate with a good balance of DOI and energy resolution; and (3) the linear and logarithm DOI calculation algorithms show overall comparable DOI error, and the linear algorithm was better for photon interactions near the ends of the crystal while the logarithm algorithm was better near the center. These results provide useful guidance in DER DOI detector design in choosing the crystal surface finishing and DOI calculation methods.

  5. 43 CFR Appendix B to Part 2 - Internet Addresses

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Page: http://www.doi.gov 2. DOI FOIA Home Page: http://www.doi.gov/foia/ 3. DOI Reference Guide for Obtaining Information: http://www.doi.gov/foia/foitabl.htm 4. List of DOI Public Affairs Offices: http://www.doi.gov/foia/list.html 5. DOI FOIA Contacts: http://www.doi.gov/foia/contacts.html 6. DOI FOIA...

  6. 43 CFR Appendix B to Part 2 - Internet Addresses

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Page: http://www.doi.gov 2. DOI FOIA Home Page: http://www.doi.gov/foia/ 3. DOI Reference Guide for Obtaining Information: http://www.doi.gov/foia/foitabl.htm 4. List of DOI Public Affairs Offices: http://www.doi.gov/foia/list.html 5. DOI FOIA Contacts: http://www.doi.gov/foia/contacts.html 6. DOI FOIA...

  7. A Novel Method for gamma - text{photons} Depth-of-Interaction Detection in Monolithic Scintillation Crystals

    NASA Astrophysics Data System (ADS)

    Pani, Roberto; Bettiol, Marco; Preziosi, Enrico; Borrazzo, Cristian; Pellegrini, Rosanna; González, Antonio J.; Conde, Pablo; Cinti, Maria Nerina; Fabbri, Andrea; Di Castro, Elisabetta; Majewski, Stan

    2016-10-01

    Achieved spatial resolution of the PET systems is often limited by the parallax error due to the lack of information about the Depth of Interaction (DoI) inside the crystal of the incoming 511 keV annihilation photons. The smaller the diameter of the PET ring and the thicker the scintillator are, the more this error affects imaging performance. In this work, a DoI calculator suitable for monolithic scintillation crystals and based on the shape of the scintillation light distribution at the photodetector surface has been proposed. To test the estimator performance, a test PET module with a 50 × 50 × 20 mm monolithic LYSO crystal coupled to a 12 × 12 SiPM array has been employed. In addition, for calibration and validation of the method, Geant4 simulations have been also used. The key result of the application of the proposed DoI estimator is obtaining a continuous DoI estimation with an average DoI resolution of about 5 mm in the 20 mm-thick crystal. Benefiting from the DoI estimation capabilities of the method, it has been also possible to achieve additional important goals, first of all reducing the parallax error. First, because the scintillation light collection varies as a function of the 3D position of the interaction of the annihilation photon inside the crystal, a method to correct this response variation via a proper 3D look-up-table is proposed. This has led to an improvement of about 35% in energy resolution. Moreover, a DoI-dependent position algorithm has been proposed, allowing an improvement of both planar (X-Y) position linearity and planar spatial resolution. This algorithm is specifically developed for the rows/columns multi-channel readout logic, that reduces the number of independent channels from N × N to N + N, where N is the number of SiPM photodetection elements (12 in our case) in each row and column. This development was performed in the framework of the MindView PET/MilI brain imaging project.

  8. Predicting the timing properties of phosphor-coated scintillators using Monte Carlo light transport simulation

    PubMed Central

    Roncali, Emilie; Schmall, Jeffrey P.; Viswanath, Varsha; Berg, Eric; Cherry, Simon R.

    2014-01-01

    Current developments in positron emission tomography (PET) focus on improving timing performance for scanners with time-of-flight (TOF) capability, and incorporating depth-of-interaction (DOI) information. Recent studies have shown that incorporating DOI correction in TOF detectors can improve timing resolution, and that DOI also becomes more important in long axial field-of-view scanners. We have previously reported the development of DOI-encoding detectors using phosphor-coated scintillation crystals; here we study the timing properties of those crystals to assess the feasibility of providing some level of DOI information without significantly degrading the timing performance. We used Monte Carlo simulations to provide a detailed understanding of light transport in phosphor-coated crystals which cannot be fully characterized experimentally. Our simulations used a custom reflectance model based on 3D crystal surface measurements. Lutetium oxyorthosilicate (LSO) crystals were simulated with a phosphor coating in contact with the scintillator surfaces and an external diffuse reflector (teflon). Light output, energy resolution, and pulse shape showed excellent agreement with experimental data obtained on 3 × 3 × 10 mm3 crystals coupled to a photomultiplier tube (PMT). Scintillator intrinsic timing resolution was simulated with head-on and side-on configurations, confirming the trends observed experimentally. These results indicate that the model may be used to predict timing properties in phosphor-coated crystals and guide the coating for optimal DOI resolution/timing performance trade-off for a given crystal geometry. Simulation data suggested that a time stamp generated from early photoelectrons minimizes degradation of the timing resolution, thus making this method potentially more useful for TOF-DOI detectors than our initial experiments suggested. Finally, this approach could easily be extended to the study of timing properties in other scintillation crystals, with a range of treatments and materials attached to the surface. PMID:24694727

  9. 43 CFR 17.323 - Information collection requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... of Doi Recipients § 17.323 Information collection requirements. Each recipient shall: (a) Keep records in a form and containing information which DOI determines may be necessary to ascertain whether the recipient is complying with the Act and these regulations. (b) Provide to DOI, upon request...

  10. 43 CFR 17.323 - Information collection requirements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... of Doi Recipients § 17.323 Information collection requirements. Each recipient shall: (a) Keep records in a form and containing information which DOI determines may be necessary to ascertain whether the recipient is complying with the Act and these regulations. (b) Provide to DOI, upon request...

  11. A fitness trade-off between seasons causes multigenerational cycles in phenotype and population size

    PubMed Central

    Betini, Gustavo S; McAdam, Andrew G; Griswold, Cortland K; Norris, D Ryan

    2017-01-01

    Although seasonality is widespread and can cause fluctuations in the intensity and direction of natural selection, we have little information about the consequences of seasonal fitness trade-offs for population dynamics. Here we exposed populations of Drosophila melanogaster to repeated seasonal changes in resources across 58 generations and used experimental and mathematical approaches to investigate how viability selection on body size in the non-breeding season could affect demography. We show that opposing seasonal episodes of natural selection on body size interacted with both direct and delayed density dependence to cause populations to undergo predictable multigenerational density cycles. Our results provide evidence that seasonality can set the conditions for life-history trade-offs and density dependence, which can, in turn, interact to cause multigenerational population cycles. DOI: http://dx.doi.org/10.7554/eLife.18770.001 PMID:28164780

  12. Publications - DDS 1 | Alaska Division of Geological & Geophysical Surveys

    Science.gov Websites

    Surveys Digital Data Series 1, http://doi.org/10.14509/agdi. http://doi.org/10.14509/24504 Publication Products Interactive Interactive Map Alaska Geologic Data Index (AGDI) Digital Geospatial Data Digital

  13. 41 CFR 102-75.635 - What information must the Department of the Interior (DOI) furnish eligible public agencies?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What information must the Department of the Interior (DOI) furnish eligible public agencies? 102-75.635 Section 102-75.635... the Interior (DOI) furnish eligible public agencies? Upon request, DOI must furnish eligible public...

  14. 41 CFR 102-75.635 - What information must the Department of the Interior (DOI) furnish eligible public agencies?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false What information must the Department of the Interior (DOI) furnish eligible public agencies? 102-75.635 Section 102-75.635... the Interior (DOI) furnish eligible public agencies? Upon request, DOI must furnish eligible public...

  15. Determining rotational dynamics of the guanidino group of arginine side chains in proteins by carbon-detected NMR† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7cc04821a

    PubMed Central

    Gerecht, Karola; Figueiredo, Angelo Miguel

    2017-01-01

    Arginine residues are imperative for many active sites and protein-interaction interfaces. A new NMR-based method is presented to determine the rotational dynamics around the Nε–Cζ bond of arginine side chains. An application to a 19 kDa protein shows that the strengths of interactions involving arginine side chains can be characterised. PMID:28840203

  16. Developing Data Citations from Digital Object Identifier Metadata

    NASA Technical Reports Server (NTRS)

    James, Nathan; Wanchoo, Lalit

    2015-01-01

    NASA's Earth Science Data and Information System (ESDIS) Project has been processing information for the registration of Digital Object Identifiers (DOI) for the last five years of which an automated system has been in operation for the last two years. The ESDIS DOI registration system has registered over 2000 DOIs with over 1000 DOIs held in reserve until all required information has been collected. By working towards the goal of assigning DOIs to the 8000+ data collections under its management, ESDIS has taken the first step towards facilitating the use of data citations with those products. Jeanne Behnke, ESDIS Deputy Project Manager has reviewed and approved the poster.

  17. Japan Link Center (JaLC): link management and DOI assignment for Japanese electronic scholarly contents

    NASA Astrophysics Data System (ADS)

    Kato, Takafumi; Tsuchiya, Eri; Kubota, Soichi; Miyagawa, Yoshiyuki

    JST, cooperated with several national institutes, is currently developing “Japan Link Center”, which manages Japanese electronic scholarly contents (journal articles, books, dissertations etc.) in an integrated fashion using Digital Object Identifier (DOI). Japan Link Center will manage metadata and whereabouts information of the contents in the digital environment and provide domestic and international linking information, cite/cited information to activate dissemination of S&T information, furthermore, to strengthen transmission of S&T information from Japan. Japan Link Center is expected to be appointed as the 9th DOI registration agency (RA) in the world by the International DOI Foundation (IDF) this spring.

  18. Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states

    PubMed Central

    Tan, Dan; Li, Qiang; Zhang, Mei-Jun; Liu, Chao; Ma, Chengying; Zhang, Pan; Ding, Yue-He; Fan, Sheng-Bo; Tao, Li; Yang, Bing; Li, Xiangke; Ma, Shoucai; Liu, Junjie; Feng, Boya; Liu, Xiaohui; Wang, Hong-Wei; He, Si-Min; Gao, Ning; Ye, Keqiong; Dong, Meng-Qiu; Lei, Xiaoguang

    2016-01-01

    To improve chemical cross-linking of proteins coupled with mass spectrometry (CXMS), we developed a lysine-targeted enrichable cross-linker containing a biotin tag for affinity purification, a chemical cleavage site to separate cross-linked peptides away from biotin after enrichment, and a spacer arm that can be labeled with stable isotopes for quantitation. By locating the flexible proteins on the surface of 70S ribosome, we show that this trifunctional cross-linker is effective at attaining structural information not easily attainable by crystallography and electron microscopy. From a crude Rrp46 immunoprecipitate, it helped identify two direct binding partners of Rrp46 and 15 protein-protein interactions (PPIs) among the co-immunoprecipitated exosome subunits. Applying it to E. coli and C. elegans lysates, we identified 3130 and 893 inter-linked lysine pairs, representing 677 and 121 PPIs. Using a quantitative CXMS workflow we demonstrate that it can reveal changes in the reactivity of lysine residues due to protein-nucleic acid interaction. DOI: http://dx.doi.org/10.7554/eLife.12509.001 PMID:26952210

  19. Experimental evaluation of depth-of-interaction correction in a small-animal positron emission tomography scanner.

    PubMed

    Green, Michael V; Ostrow, Harold G; Seidel, Jurgen; Pomper, Martin G

    2010-12-01

    Human and small-animal positron emission tomography (PET) scanners with cylindrical geometry and conventional detectors exhibit a progressive reduction in radial spatial resolution with increasing radial distance from the geometric axis of the scanner. This "depth-of-interaction" (DOI) effect is sufficiently deleterious that many laboratories have devised novel schemes to reduce the magnitude of this effect and thereby yield PET images of greater quantitative accuracy. Here we examine experimentally the effects of a particular DOI correction method (dual-scintillator phoswich detectors with pulse shape discrimination) implemented in a small-animal PET scanner by comparing the same phantom and same mouse images with and without DOI correction. The results suggest that even this relatively coarse, two-level estimate of radial gamma ray interaction position significantly reduces the DOI parallax error. This study also confirms two less appreciated advantages of DOI correction: a reduction in radial distortion and radial source displacement as a source is moved toward the edge of the field of view and a resolution improvement detectable in the central field of view likely owing to improved spatial sampling.

  20. A machine learning method for fast and accurate characterization of depth-of-interaction gamma cameras

    NASA Astrophysics Data System (ADS)

    Pedemonte, Stefano; Pierce, Larry; Van Leemput, Koen

    2017-11-01

    Measuring the depth-of-interaction (DOI) of gamma photons enables increasing the resolution of emission imaging systems. Several design variants of DOI-sensitive detectors have been recently introduced to improve the performance of scanners for positron emission tomography (PET). However, the accurate characterization of the response of DOI detectors, necessary to accurately measure the DOI, remains an unsolved problem. Numerical simulations are, at the state of the art, imprecise, while measuring directly the characteristics of DOI detectors experimentally is hindered by the impossibility to impose the depth-of-interaction in an experimental set-up. In this article we introduce a machine learning approach for extracting accurate forward models of gamma imaging devices from simple pencil-beam measurements, using a nonlinear dimensionality reduction technique in combination with a finite mixture model. The method is purely data-driven, not requiring simulations, and is applicable to a wide range of detector types. The proposed method was evaluated both in a simulation study and with data acquired using a monolithic gamma camera designed for PET (the cMiCE detector), demonstrating the accurate recovery of the DOI characteristics. The combination of the proposed calibration technique with maximum- a posteriori estimation of the coordinates of interaction provided a depth resolution of  ≈1.14 mm for the simulated PET detector and  ≈1.74 mm for the cMiCE detector. The software and experimental data are made available at http://occiput.mgh.harvard.edu/depthembedding/.

  1. 43 CFR 17.333 - Investigation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., Conciliation, and Enforcement Procedures § 17.333 Investigation. (a) Informal investigation. (1) DOI will... mediation agreement. (2) As part of the initial investigation, DOI will use informal fact finding methods... possible, settle the complaint on terms that are mutually agreeable to the parties. DOI may seek the...

  2. 43 CFR 17.333 - Investigation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., Conciliation, and Enforcement Procedures § 17.333 Investigation. (a) Informal investigation. (1) DOI will... mediation agreement. (2) As part of the initial investigation, DOI will use informal fact finding methods... possible, settle the complaint on terms that are mutually agreeable to the parties. DOI may seek the...

  3. Amae as metalanguage: a critique of Doi's theory of amae.

    PubMed

    Taketomo, Y

    1986-10-01

    For many years Doi's ideas on the links between amae and the satisfaction of dependency needs have influenced discussions of the so-called Japanese character. In reviewing Doi's theory, however, major problems emerge. Beginning with the very definition of amae, one finds that Doi has chosen to stress only one aspect of amae. When one returns to his lexical sources, one discovers that the common denominator in the various definitions of amae does not lie in a single, monolithic motivation, as Doi proposes. Instead, it is suggested, amae should be viewed as a metalanguage. To understand the metacommunicational significance of amae, one must consider the rules that govern the behavior of the interactants in amae. Three different situations of amae are delineated. In the childhood interaction, the child playfully mimicks the infant's attachment behavior. With the adult coquetry situation, one observes the female playfully behaving as if she were the child mimicking the infant-mother prototype. Finally, in the third context subset of amae, there is a "trespassing on" or "taking advantage of" another person, with the beneficent approval of the second interactant. The common factor thus appears to be a mutually agreed-upon suspension of certain ordinary restraints on behavior. A metalanguage theory of amae, as an alternative to Doi's proposal, places emphasis on the culture-specific message of the interaction itself rather than on a single, monolithic motivation or an object-language interpretation. Indeed, various motivations are suggested, depending on the specific context of amae as well as the individual case. In this way, it is hoped, a metacommunicational approach to the understanding of amae may broaden the consideration of motivational issues, extending far beyond Doi's insistence on dependency and the search for passive love.

  4. Evolution of DOI Usage and Registration

    NASA Astrophysics Data System (ADS)

    James, N.; Wanchoo, L.

    2017-12-01

    NASA's Earth Science Data and Information System (ESDIS) Project has implemented an automated system for assigning Digital Object Identifiers (DOIs) to Earth Science data products being managed by its network of 12 distributed active archive centers (DAACs). Using the ESDIS DOI system, over 3000 DOIs have been assigned, registered, and made publicly accessible while over 1000 assigned DOIs are being held in reserve until ready for public use. The goal is to assign a DOI to each of the 8000+ data collections under ESDIS management. DOIs make it easier for researchers to discover and use earth science data and they enable users to provide valid citations for the data they use in research. Also for the researcher wishing to reproduce the results presented in science publications, the DOI can be used to locate the exact data or data products being cited. ESDIS DOIs also provide data "Provenance" which is information about the creation and history of the data in question. This would include when the data was collected, which instrument was used to collect the data, and the version of the product at the time the DOI was assigned. Over the past few years, requests for DOIs have increased significantly as DAACs assign DOIs to both legacy data from earlier missions and new data products from in-orbit missions. This study will evaluate the evolution of DOI registration and its usage over those years comparing data products as they are organized by mission, science discipline and data product level. It is hoped that the study results will help NASA determine how to prioritize future products for DOI assignment and inform future studies that would identify trends over time of increased use of data citations resulting in increased discovery and distribution of NASA Earth science data products.

  5. Performance and field tests of a handheld Compton camera using 3-D position-sensitive scintillators coupled to multi-pixel photon counter arrays

    NASA Astrophysics Data System (ADS)

    Kishimoto, A.; Kataoka, J.; Nishiyama, T.; Fujita, T.; Takeuchi, K.; Okochi, H.; Ogata, H.; Kuroshima, H.; Ohsuka, S.; Nakamura, S.; Hirayanagi, M.; Adachi, S.; Uchiyama, T.; Suzuki, H.

    2014-11-01

    After the nuclear disaster in Fukushima, radiation decontamination has become particularly urgent. To help identify radiation hotspots and ensure effective decontamination operation, we have developed a novel Compton camera based on Ce-doped Gd3Al2Ga3O12 scintillators and multi-pixel photon counter (MPPC) arrays. Even though its sensitivity is several times better than that of other cameras being tested in Fukushima, we introduce a depth-of-interaction (DOI) method to further improve the angular resolution. For gamma rays, the DOI information, in addition to 2-D position, is obtained by measuring the pulse-height ratio of the MPPC arrays coupled to ends of the scintillator. We present the detailed performance and results of various field tests conducted in Fukushima with the prototype 2-D and DOI Compton cameras. Moreover, we demonstrate stereo measurement of gamma rays that enables measurement of not only direction but also approximate distance to radioactive hotspots.

  6. Performance study of a PET scanner based on monolithic scintillators for different DoI-dependent methods

    NASA Astrophysics Data System (ADS)

    Preziosi, E.; Sánchez, S.; González, A. J.; Pani, R.; Borrazzo, C.; Bettiol, M.; Rodriguez-Alvarez, M. J.; González-Montoro, A.; Moliner, L.; Benlloch, J. M.

    2016-12-01

    One of the technical objectives of the MindView project is developing a brain-dedicated PET insert based on monolithic scintillation crystals. It will be inserted in MRI systems with the purpose to obtain simultaneous PET and MRI brain images. High sensitivity, high image quality performance and accurate detection of the Depth-of-Interaction (DoI) of the 511keV photons are required. We have developed a DoI estimation method, dedicated to monolithic scintillators, allowing continuous DoI estimation and a DoI-dependent algorithm for the estimation of the photon planar impact position, able to improve the single module imaging capabilities. In this work, through experimental measurements, the proposed methods have been used for the estimation of the impact positions within the monolithic crystal block. We have evaluated the PET system performance following the NEMA NU 4-2008 protocol by reconstructing the images using the STIR 3D platform. The results obtained with two different methods, providing discrete and continuous DoI information, are compared with those obtained from an algorithm without DoI capabilities and with the ideal response of the detector. The proposed DoI-dependent imaging methods show clear improvements in the spatial resolution (FWHM) of reconstructed images, allowing to obtain values from 2mm (at the center FoV) to 3mm (at the FoV edges).

  7. Domain–domain interactions determine the gating, permeation, pharmacology, and subunit modulation of the IKs ion channel

    PubMed Central

    Zaydman, Mark A; Kasimova, Marina A; McFarland, Kelli; Beller, Zachary; Hou, Panpan; Kinser, Holly E; Liang, Hongwu; Zhang, Guohui; Shi, Jingyi; Tarek, Mounir; Cui, Jianmin

    2014-01-01

    Voltage-gated ion channels generate electrical currents that control muscle contraction, encode neuronal information, and trigger hormonal release. Tissue-specific expression of accessory (β) subunits causes these channels to generate currents with distinct properties. In the heart, KCNQ1 voltage-gated potassium channels coassemble with KCNE1 β-subunits to generate the IKs current (Barhanin et al., 1996; Sanguinetti et al., 1996), an important current for maintenance of stable heart rhythms. KCNE1 significantly modulates the gating, permeation, and pharmacology of KCNQ1 (Wrobel et al., 2012; Sun et al., 2012; Abbott, 2014). These changes are essential for the physiological role of IKs (Silva and Rudy, 2005); however, after 18 years of study, no coherent mechanism explaining how KCNE1 affects KCNQ1 has emerged. Here we provide evidence of such a mechanism, whereby, KCNE1 alters the state-dependent interactions that functionally couple the voltage-sensing domains (VSDs) to the pore. DOI: http://dx.doi.org/10.7554/eLife.03606.001 PMID:25535795

  8. Molecular insights into the origin of the Hox-TALE patterning system

    PubMed Central

    Hudry, Bruno; Thomas-Chollier, Morgane; Volovik, Yael; Duffraisse, Marilyne; Dard, Amélie; Frank, Dale; Technau, Ulrich; Merabet, Samir

    2014-01-01

    Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox–TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI: http://dx.doi.org/10.7554/eLife.01939.001 PMID:24642410

  9. Molecular insights into the origin of the Hox-TALE patterning system.

    PubMed

    Hudry, Bruno; Thomas-Chollier, Morgane; Volovik, Yael; Duffraisse, Marilyne; Dard, Amélie; Frank, Dale; Technau, Ulrich; Merabet, Samir

    2014-03-18

    Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior-posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox-TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI: http://dx.doi.org/10.7554/eLife.01939.001.

  10. Reward modulates the effect of visual cortical microstimulation on perceptual decisions

    PubMed Central

    Cicmil, Nela; Cumming, Bruce G; Parker, Andrew J; Krug, Kristine

    2015-01-01

    Effective perceptual decisions rely upon combining sensory information with knowledge of the rewards available for different choices. However, it is not known where reward signals interact with the multiple stages of the perceptual decision-making pathway and by what mechanisms this may occur. We combined electrical microstimulation of functionally specific groups of neurons in visual area V5/MT with performance-contingent reward manipulation, while monkeys performed a visual discrimination task. Microstimulation was less effective in shifting perceptual choices towards the stimulus preferences of the stimulated neurons when available reward was larger. Psychophysical control experiments showed this result was not explained by a selective change in response strategy on microstimulated trials. A bounded accumulation decision model, applied to analyse behavioural performance, revealed that the interaction of expected reward with microstimulation can be explained if expected reward modulates a sensory representation stage of perceptual decision-making, in addition to the better-known effects at the integration stage. DOI: http://dx.doi.org/10.7554/eLife.07832.001 PMID:26402458

  11. Influence of depth of interaction upon the performance of scintillator detectors.

    PubMed

    Brown, Mark S; Gundacker, Stefan; Taylor, Alaric; Tummeltshammer, Clemens; Auffray, Etiennette; Lecoq, Paul; Papakonstantinou, Ioannis

    2014-01-01

    The uncertainty in time of particle detection within a scintillator detector, characterised by the coincidence time resolution (CTR), is explored with respect to the interaction position within the scintillator crystal itself. Electronic collimation between two scintillator detectors is utilised to determine the CTR with depth of interaction (DOI) for different materials, geometries and wrappings. Significantly, no relationship between the CTR and DOI is observed within experimental error. Confinement of the interaction position is seen to degrade the CTR in long scintillator crystals by 10%.

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

    Virador, Patrick R.G.

    The author performs image reconstruction for a novel Positron Emission Tomography camera that is optimized for breast cancer imaging. This work addresses for the first time, the problem of fully-3D, tomographic reconstruction using a septa-less, stationary, (i.e. no rotation or linear motion), and rectangular camera whose Field of View (FOV) encompasses the entire volume enclosed by detector modules capable of measuring Depth of Interaction (DOI) information. The camera is rectangular in shape in order to accommodate breasts of varying sizes while allowing for soft compression of the breast during the scan. This non-standard geometry of the camera exacerbates two problems:more » (a) radial elongation due to crystal penetration and (b) reconstructing images from irregularly sampled data. Packing considerations also give rise to regions in projection space that are not sampled which lead to missing information. The author presents new Fourier Methods based image reconstruction algorithms that incorporate DOI information and accommodate the irregular sampling of the camera in a consistent manner by defining lines of responses (LORs) between the measured interaction points instead of rebinning the events into predefined crystal face LORs which is the only other method to handle DOI information proposed thus far. The new procedures maximize the use of the increased sampling provided by the DOI while minimizing interpolation in the data. The new algorithms use fixed-width evenly spaced radial bins in order to take advantage of the speed of the Fast Fourier Transform (FFT), which necessitates the use of irregular angular sampling in order to minimize the number of unnormalizable Zero-Efficiency Bins (ZEBs). In order to address the persisting ZEBs and the issue of missing information originating from packing considerations, the algorithms (a) perform nearest neighbor smoothing in 2D in the radial bins (b) employ a semi-iterative procedure in order to estimate the unsampled data and (c) mash the in plane projections, i.e. 2D data, with the projection data from the first oblique angles, which are then used to reconstruct the preliminary image in the 3D Reprojection Projection algorithm. The author presents reconstructed images of point sources and extended sources in both 2D and 3D. The images show that the camera is anticipated to eliminate radial elongation and produce artifact free and essentially spatially isotropic images throughout the entire FOV. It has a resolution of 1.50 ± 0.75 mm FWHM near the center, 2.25 ±0.75 mm FWHM in the bulk of the FOV, and 3.00 ± 0.75 mm FWHM near the edge and corners of the FOV.« less

  13. Application of Digital Object Identifiers to data sets at the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC)

    NASA Astrophysics Data System (ADS)

    Vollmer, B.; Ostrenga, D.; Johnson, J. E.; Savtchenko, A. K.; Shen, S.; Teng, W. L.; Wei, J. C.

    2013-12-01

    Digital Object Identifiers (DOIs) are applied to selected data sets at the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC). The DOI system provides an Internet resolution service for unique and persistent identifiers of digital objects. Products assigned DOIs include data from the NASA MEaSUREs Program, the Earth Observing System (EOS) Aqua Atmospheric Infrared Sounder (AIRS) and EOS Aura High Resolution Dynamics Limb Sounder (HIRDLS). DOIs are acquired and registered through EZID, California Digital Library and DataCite. GES DISC hosts a data set landing page associated with each DOI containing information on and access to the data including a recommended data citation when using the product in research or applications. This work includes participation with the earth science community (e.g., Earth Science Information Partners (ESIP) Federation) and the NASA Earth Science Data and Information System (ESDIS) Project to identify, establish and implement best practices for assigning DOIs and managing supporting information, including metadata, for earth science data sets. Future work includes (1) coordination with NASA mission Science Teams and other data providers on the assignment of DOIs for other GES DISC data holdings, particularly for future missions such as Orbiting Carbon Observatory -2 and -3 (OCO-2, OCO-3) and projects (MEaSUREs 2012), (2) construction of landing pages that are both human and machine readable, and (3) pursuing the linking of data and publications with tools such as the Thomson Reuters Data Citation Index.

  14. A novel depth-of-interaction block detector for positron emission tomography using a dichotomous orthogonal symmetry decoding concept.

    PubMed

    Zhang, Yuxuan; Yan, Han; Baghaei, Hossain; Wong, Wai-Hoi

    2016-02-21

    Conventionally, a dual-end depth-of-interaction (DOI) block detector readout requires two two-dimensional silicon photomultiplier (SiPM) arrays, one on top and one on the bottom, to define the XYZ positions. However, because both the top and bottom SiPM arrays are reading the same pixels, this creates information redundancy. We propose a dichotomous orthogonal symmetric (DOS) dual-end readout block detector design, which removes this redundancy by reducing the number of SiPMs and still achieves XY and DOI (Z) decoding for positron emission tomography (PET) block detector. Reflecting films are used within the block detector to channel photons going to the top of the block to go only in the X direction, and photons going to the bottom are channeled along the Y direction. Despite the unidirectional channeling on each end, the top readout provides both X and Y information using two one-dimensional SiPM arrays instead of a two-dimensional SiPM array; similarly, the bottom readout also provides both X and Y information with just two one-dimensional SiPM arrays. Thus, a total of four one-dimensional SiPM arrays (4  ×  N SiPMs) are used to decode the XYZ positions of the firing pixels instead of two two-dimensional SiPM arrays (2  ×  N  ×  N SiPMs), reducing the number of SiPM arrays per block from 2N(2) to 4 N for PET/MR or PET/CT systems. Moreover, the SiPM arrays on one end can be replaced by two regular photomultiplier tubes (PMTs), so that a block needs only 2 N SiPMs  +  2 half-PMTs; this hybrid-DOS DOI block detector can be used in PET/CT systems. Monte Carlo simulations were carried out to study the performance of our DOS DOI block detector design, including the XY-decoding quality, energy resolution, and DOI resolution. Both BGO and LSO scintillators were studied. We found that 4 mm pixels were well decoded for 5  ×  5 BGO and 9  ×  9 LSO arrays with 4 to 5 mm DOI resolution and 16-20% energy resolution. By adding light-channel decoding, we modified the DOS design to a high-resolution design, which resolved scintillator pixels smaller than the SiPM dimensions. Detector pixels of 2.4 mm were decoded for 8  ×  8 BGO and 15  ×  15 LSO arrays with 5 mm DOI resolution and 20-23% energy resolution. Time performance was also studied for the 8  ×  8 BGO and 15  ×  15 LSO HR-DOS arrays. The timing resolution for the corner and central crystals is 986  ±  122 ps and 1.89  ±  0.17 μs respectively with BGO, 137  ±  42 ps and 458  ±  67 ps respectively with LSO. Monte Carlo simulations with GATE/Geant4 demonstrated the feasibility of our DOS DOI block detector design. In conclusion, our novel design achieved good performance except the time performance while using fewer SiPMs and supporting electronic channels than the current non-DOI PET detectors. This novel design can significantly reduce the cost, heat, and readout complexity of DOI block detectors for PET/MR/CT systems that don't require the time-of-flight capability.

  15. 43 CFR 2.2 - What is DOI's policy regarding release of records under the FOIA?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false What is DOI's policy regarding release of... RECORDS AND TESTIMONY; FREEDOM OF INFORMATION ACT General Information § 2.2 What is DOI's policy regarding... public consistent with the spirit of the FOIA and the Privacy Act. ...

  16. Design and simulation of a novel method for determining depth-of-interaction in a PET scintillation crystal array using a single-ended readout by a multi-anode PMT

    NASA Astrophysics Data System (ADS)

    Ito, Mikiko; Lee, Jae Sung; Park, Min-Jae; Sim, Kwang-Souk; Jong Hong, Seong

    2010-07-01

    PET detectors with depth-of-interaction (DOI) encoding capability allow high spatial resolution and high sensitivity to be achieved simultaneously. To obtain DOI information from a mono-layer array of scintillation crystals using a single-ended readout, the authors devised a method based on light spreading within a crystal array and performed Monte Carlo simulations with individual scintillation photon tracking to prove the concept. A scintillation crystal array model was constructed using a grid method. Conventional grids are constructed using comb-shaped reflector strips with rectangular teeth to isolate scintillation crystals optically. However, the authors propose the use of triangularly shaped teeth, such that scintillation photons spread only in the x-direction in the upper halves of crystals and in the y-direction in lower halves. DOI positions can be estimated by considering the extent of two-dimensional light dispersion, which can be determined from the multiple anode outputs of a position-sensitive PMT placed under the crystal array. In the main simulation, a crystal block consisting of a 29 × 29 array of 1.5 mm × 1.5 mm × 20 mm crystals and a multi-anode PMT with 16 × 16 pixels were used. The effects of crystal size and non-uniform PMT output gain were also explored by simulation. The DOI resolution estimated for 1.5 × 1.5 × 20 mm3 crystals was 2.16 mm on average. Although the flood map was depth dependent, each crystal was well identified at all depths when a corner of the crystal array was irradiated with 511 keV gamma rays (peak-to-valley ratio ~9:1). DOI resolution was better than 3 mm up to a crystal length of 28 mm with a 1.5 × 1.5 mm2 or 2.0 × 2.0 mm2 crystal surface area. The devised light-sharing method allowed excellent DOI resolutions to be obtained without the use of dual-ended readout or multiple crystal arrays.

  17. 44 CFR 206.348 - Consultation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... designated representative of the Department of the Interior (DOI) at the regional level before approving any.... (a) The consultation shall be by written memorandum to the DOI representative and shall contain the... understanding with DOI, the DOI representative will provide technical information and an opinion whether or not...

  18. 44 CFR 206.348 - Consultation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... designated representative of the Department of the Interior (DOI) at the regional level before approving any.... (a) The consultation shall be by written memorandum to the DOI representative and shall contain the... understanding with DOI, the DOI representative will provide technical information and an opinion whether or not...

  19. Sex-specific processing of social cues in the medial amygdala

    PubMed Central

    Bergan, Joseph F; Ben-Shaul, Yoram; Dulac, Catherine

    2014-01-01

    Animal–animal recognition within, and across species, is essential for predator avoidance and social interactions. Despite its essential role in orchestrating responses to animal cues, basic principles of information processing by the vomeronasal system are still unknown. The medial amygdala (MeA) occupies a central position in the vomeronasal pathway, upstream of hypothalamic centers dedicated to defensive and social responses. We have characterized sensory responses in the mouse MeA and uncovered emergent properties that shed new light onto the transformation of vomeronasal information into sex- and species-specific responses. In particular, we show that the MeA displays a degree of stimulus selectivity and a striking sexually dimorphic sensory representation that are not observed in the upstream relay of the accessory olfactory bulb (AOB). Furthermore, our results demonstrate that the development of sexually dimorphic circuits in the MeA requires steroid signaling near the time of puberty to organize the functional representation of sensory stimuli. DOI: http://dx.doi.org/10.7554/eLife.02743.001 PMID:24894465

  20. Integrated action of pheromone signals in promoting courtship behavior in male mice

    PubMed Central

    Haga-Yamanaka, Sachiko; Ma, Limei; He, Jie; Qiu, Qiang; Lavis, Luke D; Looger, Loren L; Yu, C Ron

    2014-01-01

    The mammalian vomeronasal organ encodes pheromone information about gender, reproductive status, genetic background and individual differences. It remains unknown how pheromone information interacts to trigger innate behaviors. In this study, we identify vomeronasal receptors responsible for detecting female pheromones. A sub-group of V1re clade members recognizes gender-identifying cues in female urine. Multiple members of the V1rj clade are cognate receptors for urinary estrus signals, as well as for sulfated estrogen (SE) compounds. In both cases, the same cue activates multiple homologous receptors, suggesting redundancy in encoding female pheromone cues. Neither gender-specific cues nor SEs alone are sufficient to promote courtship behavior in male mice, whereas robust courtship behavior can be induced when the two cues are applied together. Thus, integrated action of different female cues is required in pheromone-triggered mating behavior. These results suggest a gating mechanism in the vomeronasal circuit in promoting specific innate behavior. DOI: http://dx.doi.org/10.7554/eLife.03025.001 PMID:25073926

  1. Cortical network architecture for context processing in primate brain

    PubMed Central

    Chao, Zenas C; Nagasaka, Yasuo; Fujii, Naotaka

    2015-01-01

    Context is information linked to a situation that can guide behavior. In the brain, context is encoded by sensory processing and can later be retrieved from memory. How context is communicated within the cortical network in sensory and mnemonic forms is unknown due to the lack of methods for high-resolution, brain-wide neuronal recording and analysis. Here, we report the comprehensive architecture of a cortical network for context processing. Using hemisphere-wide, high-density electrocorticography, we measured large-scale neuronal activity from monkeys observing videos of agents interacting in situations with different contexts. We extracted five context-related network structures including a bottom-up network during encoding and, seconds later, cue-dependent retrieval of the same network with the opposite top-down connectivity. These findings show that context is represented in the cortical network as distributed communication structures with dynamic information flows. This study provides a general methodology for recording and analyzing cortical network neuronal communication during cognition. DOI: http://dx.doi.org/10.7554/eLife.06121.001 PMID:26416139

  2. Synchronous beta rhythms of frontoparietal networks support only behaviorally relevant representations

    PubMed Central

    Antzoulatos, Evan G; Miller, Earl K

    2016-01-01

    Categorization has been associated with distributed networks of the primate brain, including the prefrontal cortex (PFC) and posterior parietal cortex (PPC). Although category-selective spiking in PFC and PPC has been established, the frequency-dependent dynamic interactions of frontoparietal networks are largely unexplored. We trained monkeys to perform a delayed-match-to-spatial-category task while recording spikes and local field potentials from the PFC and PPC with multiple electrodes. We found category-selective beta- and delta-band synchrony between and within the areas. However, in addition to the categories, delta synchrony and spiking activity also reflected irrelevant stimulus dimensions. By contrast, beta synchrony only conveyed information about the task-relevant categories. Further, category-selective PFC neurons were synchronized with PPC beta oscillations, while neurons that carried irrelevant information were not. These results suggest that long-range beta-band synchrony could act as a filter that only supports neural representations of the variables relevant to the task at hand. DOI: http://dx.doi.org/10.7554/eLife.17822.001 PMID:27841747

  3. Influence of Depth of Interaction upon the Performance of Scintillator Detectors

    PubMed Central

    Brown, Mark S.; Gundacker, Stefan; Taylor, Alaric; Tummeltshammer, Clemens; Auffray, Etiennette; Lecoq, Paul; Papakonstantinou, Ioannis

    2014-01-01

    The uncertainty in time of particle detection within a scintillator detector, characterised by the coinci- dence time resolution (CTR), is explored with respect to the interaction position within the scintillator crystal itself. Electronic collimation between two scintillator detectors is utilised to determine the CTR with depth of interaction (DOI) for different materials, geometries and wrappings. Significantly, no rela- tionship between the CTR and DOI is observed within experimental error. Confinement of the interaction position is seen to degrade the CTR in long scintillator crystals by 10%. PMID:24875832

  4. 43 CFR 2.2 - What is DOI's policy regarding release of records under the FOIA?

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true What is DOI's policy regarding release of records under the FOIA? 2.2 Section 2.2 Public Lands: Interior Office of the Secretary of the Interior RECORDS AND TESTIMONY; FREEDOM OF INFORMATION ACT General Information § 2.2 What is DOI's policy regarding...

  5. 43 CFR 2.2 - What is DOI's policy regarding release of records under the FOIA?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false What is DOI's policy regarding release of records under the FOIA? 2.2 Section 2.2 Public Lands: Interior Office of the Secretary of the Interior RECORDS AND TESTIMONY; FREEDOM OF INFORMATION ACT General Information § 2.2 What is DOI's policy regarding...

  6. 75 FR 10810 - Notice of Proposed Renewal of Information Collection: OMB Control Number 1035-0004, Trust Funds...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-09

    ..., the Office of the Special Trustee for American Indians, Department of the Interior (DOI), announces... Street, NE., Albuquerque, New Mexico 87109, or via e-mail to [email protected]doi.gov . Individuals... also e-mail requests for further information to him at [email protected]doi.gov or call (505) 816-1096...

  7. 43 CFR 17.320 - General responsibilities.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... ASSISTED PROGRAMS OF THE DEPARTMENT OF THE INTERIOR Nondiscrimination on the Basis of Age Duties of Doi Recipients § 17.320 General responsibilities. Each DOI recipient has primary responsibility to ensure that... information, and to afford DOI access to its records to the extent DOI finds necessary to determine whether...

  8. 43 CFR 17.320 - General responsibilities.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... ASSISTED PROGRAMS OF THE DEPARTMENT OF THE INTERIOR Nondiscrimination on the Basis of Age Duties of Doi Recipients § 17.320 General responsibilities. Each DOI recipient has primary responsibility to ensure that... information, and to afford DOI access to its records to the extent DOI finds necessary to determine whether...

  9. Intramolecular interactions in the polar headgroup of sphingosine: serinol† †Electronic supplementary information (ESI) available: Ab initio parameters for serinol conformers within 1000 cm–1, measured transition frequencies, typical a-type transition for conformer aa1, interconversion barriers and possible tunnelling pathways. See DOI: 10.1039/c5cc09423b Click here for additional data file.

    PubMed Central

    Loru, Donatella; Peña, Isabel; Alonso, José L.

    2016-01-01

    The intramolecular interactions in the lipid sphingosine have been elucidated through the investigation of the amino alcohol serinol which mimics its polar headgroup. Intricate networks of intramolecular hydrogen bonds involving the hydroxyl groups and the amino group contribute to the stabilisation of five different conformations observed in the broadband rotational spectrum. PMID:26727395

  10. A single-molecule force spectroscopy study of the interactions between lectins and carbohydrates on cancer and normal cells

    NASA Astrophysics Data System (ADS)

    Zhao, Weidong; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

    2013-03-01

    The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells.The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells. Electronic supplementary information (ESI) available: Experimental details. See DOI: 10.1039/c3nr00553d

  11. Process Architecture for Managing Digital Object Identifiers

    NASA Astrophysics Data System (ADS)

    Wanchoo, L.; James, N.; Stolte, E.

    2014-12-01

    In 2010, NASA's Earth Science Data and Information System (ESDIS) Project implemented a process for registering Digital Object Identifiers (DOIs) for data products distributed by Earth Observing System Data and Information System (EOSDIS). For the first 3 years, ESDIS evolved the process involving the data provider community in the development of processes for creating and assigning DOIs, and guidelines for the landing page. To accomplish this, ESDIS established two DOI User Working Groups: one for reviewing the DOI process whose recommendations were submitted to ESDIS in February 2014; and the other recently tasked to review and further develop DOI landing page guidelines for ESDIS approval by end of 2014. ESDIS has recently upgraded the DOI system from a manually-driven system to one that largely automates the DOI process. The new automated feature include: a) reviewing the DOI metadata, b) assigning of opaque DOI name if data provider chooses, and c) reserving, registering, and updating the DOIs. The flexibility of reserving the DOI allows data providers to embed and test the DOI in the data product metadata before formally registering with EZID. The DOI update process allows the changing of any DOI metadata except the DOI name unless the name has not been registered. Currently, ESDIS has processed a total of 557 DOIs of which 379 DOIs are registered with EZID and 178 are reserved with ESDIS. The DOI incorporates several metadata elements that effectively identify the data product and the source of availability. Of these elements, the Uniform Resource Locator (URL) attribute has the very important function of identifying the landing page which describes the data product. ESDIS in consultation with data providers in the Earth Science community is currently developing landing page guidelines that specify the key data product descriptive elements to be included on each data product's landing page. This poster will describe in detail the unique automated process and underlying system implemented by ESDIS for registering DOIs, as well as some of the lessons learned from the development of the process. In addition, this paper will summarize the recommendations made by the DOI Process and DOI Landing Page User Working Groups, and the procedures developed for implementing those recommendations.

  12. 43 CFR 2.5 - Does DOI maintain an index of its reading room materials?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Does DOI maintain an index of its reading room materials? 2.5 Section 2.5 Public Lands: Interior Office of the Secretary of the Interior RECORDS AND TESTIMONY; FREEDOM OF INFORMATION ACT Information Routinely Available to the Public without Filing a FOIA Request § 2.5 Does DOI maintain an...

  13. 43 CFR 2.5 - Does DOI maintain an index of its reading room materials?

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true Does DOI maintain an index of its reading room materials? 2.5 Section 2.5 Public Lands: Interior Office of the Secretary of the Interior RECORDS AND TESTIMONY; FREEDOM OF INFORMATION ACT Information Routinely Available to the Public without Filing a FOIA Request § 2.5 Does DOI maintain an...

  14. Experimental Evaluation of Depth-of-Interaction Correction in a Small-Animal Positron Emission Tomography Scanner

    PubMed Central

    Green, Michael V.; Ostrow, Harold G.; Seidel, Jurgen; Pomper, Martin G.

    2013-01-01

    Human and small-animal positron emission tomography (PET) scanners with cylindrical geometry and conventional detectors exhibit a progressive reduction in radial spatial resolution with increasing radial distance from the geometric axis of the scanner. This “depth-of-interaction” (DOI) effect is sufficiently deleterious that many laboratories have devised novel schemes to reduce the magnitude of this effect and thereby yield PET images of greater quantitative accuracy. Here we examine experimentally the effects of a particular DOI correction method (dual-scintillator phoswich detectors with pulse shape discrimination) implemented in a small-animal PET scanner by comparing the same phantom and same mouse images with and without DOI correction. The results suggest that even this relatively coarse, two-level estimate of radial gamma ray interaction position significantly reduces the DOI parallax error. This study also confirms two less appreciated advantages of DOI correction: a reduction in radial distortion and radial source displacement as a source is moved toward the edge of the field of view and a resolution improvement detectable in the central field of view likely owing to improved spatial sampling. PMID:21084028

  15. Depth-of-interaction estimates in pixelated scintillator sensors using Monte Carlo techniques

    NASA Astrophysics Data System (ADS)

    Sharma, Diksha; Sze, Christina; Bhandari, Harish; Nagarkar, Vivek; Badano, Aldo

    2017-01-01

    Image quality in thick scintillator detectors can be improved by minimizing parallax errors through depth-of-interaction (DOI) estimation. A novel sensor for low-energy single photon imaging having a thick, transparent, crystalline pixelated micro-columnar CsI:Tl scintillator structure has been described, with possible future application in small-animal single photon emission computed tomography (SPECT) imaging when using thicker structures under development. In order to understand the fundamental limits of this new structure, we introduce cartesianDETECT2, an open-source optical transport package that uses Monte Carlo methods to obtain estimates of DOI for improving spatial resolution of nuclear imaging applications. Optical photon paths are calculated as a function of varying simulation parameters such as columnar surface roughness, bulk, and top-surface absorption. We use scanning electron microscope images to estimate appropriate surface roughness coefficients. Simulation results are analyzed to model and establish patterns between DOI and photon scattering. The effect of varying starting locations of optical photons on the spatial response is studied. Bulk and top-surface absorption fractions were varied to investigate their effect on spatial response as a function of DOI. We investigated the accuracy of our DOI estimation model for a particular screen with various training and testing sets, and for all cases the percent error between the estimated and actual DOI over the majority of the detector thickness was ±5% with a maximum error of up to ±10% at deeper DOIs. In addition, we found that cartesianDETECT2 is computationally five times more efficient than MANTIS. Findings indicate that DOI estimates can be extracted from a double-Gaussian model of the detector response. We observed that our model predicts DOI in pixelated scintillator detectors reasonably well.

  16. When is Information Sufficient for Action Search with Unreliable Yet Informative Intelligence

    DTIC Science & Technology

    2016-03-30

    information: http://pubsonline.informs.org When Is Information Sufficient for Action? Search with Unreliable yet Informative Intelligence Michael Atkinson... Search with Unreliable yet Informative Intelligence. Operations Research Published online in Articles in Advance 30 Mar 2016 . http://dx.doi.org/10.1287...print) � ISSN 1526-5463 (online) http://dx.doi.org/10.1287/opre.2016.1488 © 2016 INFORMS When Is Information Sufficient for Action? Search with

  17. 43 CFR 2.31 - How will DOI respond to my appeal?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false How will DOI respond to my appeal? 2.31... OF INFORMATION ACT FOIA Appeals § 2.31 How will DOI respond to my appeal? (a) Appeals will be decided... will state the basis for DOI's decision as follows: (1) Decision to release or withhold records. (i) If...

  18. 43 CFR 2.31 - How will DOI respond to my appeal?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false How will DOI respond to my appeal? 2.31... OF INFORMATION ACT FOIA Appeals § 2.31 How will DOI respond to my appeal? (a) Appeals will be decided... will state the basis for DOI's decision as follows: (1) Decision to release or withhold records. (i) If...

  19. Towards monolithic scintillator based TOF-PET systems: practical methods for detector calibration and operation.

    PubMed

    Borghi, Giacomo; Tabacchini, Valerio; Schaart, Dennis R

    2016-07-07

    Gamma-ray detectors based on thick monolithic scintillator crystals can achieve spatial resolutions  <2 mm full-width-at-half-maximum (FWHM) and coincidence resolving times (CRTs) better than 200 ps FWHM. Moreover, they provide high sensitivity and depth-of-interaction (DOI) information. While these are excellent characteristics for clinical time-of-flight (TOF) positron emission tomography (PET), the application of monolithic scintillators has so far been hampered by the lengthy and complex procedures needed for position- and time-of-interaction estimation. Here, the algorithms previously developed in our group are revised to make the calibration and operation of a large number of monolithic scintillator detectors in a TOF-PET system practical. In particular, the k-nearest neighbor (k-NN) classification method for x,y-position estimation is accelerated with an algorithm that quickly preselects only the most useful reference events, reducing the computation time for position estimation by a factor of ~200 compared to the previously published k-NN 1D method. Also, the procedures for estimating the DOI and time of interaction are revised to enable full detector calibration by means of fan-beam or flood irradiations only. Moreover, a new technique is presented to allow the use of events in which some of the photosensor pixel values and/or timestamps are missing (e.g. due to dead time), so as to further increase system sensitivity. The accelerated methods were tested on a monolithic scintillator detector specifically developed for clinical PET applications, consisting of a 32 mm  ×  32 mm  ×  22 mm LYSO : Ce crystal coupled to a digital photon counter (DPC) array. This resulted in a spatial resolution of 1.7 mm FWHM, an average DOI resolution of 3.7 mm FWHM, and a CRT of 214 ps. Moreover, the possibility of using events missing the information of up to 16 out of 64 photosensor pixels is shown. This results in only a small deterioration of the detector performance.

  20. Improving Depth, Energy and Timing Estimation in PET Detectors with Deconvolution and Maximum Likelihood Pulse Shape Discrimination

    PubMed Central

    Berg, Eric; Roncali, Emilie; Hutchcroft, Will; Qi, Jinyi; Cherry, Simon R.

    2016-01-01

    In a scintillation detector, the light generated in the scintillator by a gamma interaction is converted to photoelectrons by a photodetector and produces a time-dependent waveform, the shape of which depends on the scintillator properties and the photodetector response. Several depth-of-interaction (DOI) encoding strategies have been developed that manipulate the scintillator’s temporal response along the crystal length and therefore require pulse shape discrimination techniques to differentiate waveform shapes. In this work, we demonstrate how maximum likelihood (ML) estimation methods can be applied to pulse shape discrimination to better estimate deposited energy, DOI and interaction time (for time-of-flight (TOF) PET) of a gamma ray in a scintillation detector. We developed likelihood models based on either the estimated detection times of individual photoelectrons or the number of photoelectrons in discrete time bins, and applied to two phosphor-coated crystals (LFS and LYSO) used in a previously developed TOF-DOI detector concept. Compared with conventional analytical methods, ML pulse shape discrimination improved DOI encoding by 27% for both crystals. Using the ML DOI estimate, we were able to counter depth-dependent changes in light collection inherent to long scintillator crystals and recover the energy resolution measured with fixed depth irradiation (~11.5% for both crystals). Lastly, we demonstrated how the Richardson-Lucy algorithm, an iterative, ML-based deconvolution technique, can be applied to the digitized waveforms to deconvolve the photodetector’s single photoelectron response and produce waveforms with a faster rising edge. After deconvolution and applying DOI and time-walk corrections, we demonstrated a 13% improvement in coincidence timing resolution (from 290 to 254 ps) with the LFS crystal and an 8% improvement (323 to 297 ps) with the LYSO crystal. PMID:27295658

  1. Improving Depth, Energy and Timing Estimation in PET Detectors with Deconvolution and Maximum Likelihood Pulse Shape Discrimination.

    PubMed

    Berg, Eric; Roncali, Emilie; Hutchcroft, Will; Qi, Jinyi; Cherry, Simon R

    2016-11-01

    In a scintillation detector, the light generated in the scintillator by a gamma interaction is converted to photoelectrons by a photodetector and produces a time-dependent waveform, the shape of which depends on the scintillator properties and the photodetector response. Several depth-of-interaction (DOI) encoding strategies have been developed that manipulate the scintillator's temporal response along the crystal length and therefore require pulse shape discrimination techniques to differentiate waveform shapes. In this work, we demonstrate how maximum likelihood (ML) estimation methods can be applied to pulse shape discrimination to better estimate deposited energy, DOI and interaction time (for time-of-flight (TOF) PET) of a gamma ray in a scintillation detector. We developed likelihood models based on either the estimated detection times of individual photoelectrons or the number of photoelectrons in discrete time bins, and applied to two phosphor-coated crystals (LFS and LYSO) used in a previously developed TOF-DOI detector concept. Compared with conventional analytical methods, ML pulse shape discrimination improved DOI encoding by 27% for both crystals. Using the ML DOI estimate, we were able to counter depth-dependent changes in light collection inherent to long scintillator crystals and recover the energy resolution measured with fixed depth irradiation (~11.5% for both crystals). Lastly, we demonstrated how the Richardson-Lucy algorithm, an iterative, ML-based deconvolution technique, can be applied to the digitized waveforms to deconvolve the photodetector's single photoelectron response and produce waveforms with a faster rising edge. After deconvolution and applying DOI and time-walk corrections, we demonstrated a 13% improvement in coincidence timing resolution (from 290 to 254 ps) with the LFS crystal and an 8% improvement (323 to 297 ps) with the LYSO crystal.

  2. Evolution of NASA's Earth Science Digital Object Identifier Registration System

    NASA Technical Reports Server (NTRS)

    Wanchoo, Lalit; James, Nathan

    2017-01-01

    NASA's Earth Science Data and Information System (ESDIS) Project has implemented a fully automated system for assigning Digital Object Identifiers (DOIs) to Earth Science data products being managed by its network of 12 distributed active archive centers (DAACs). A key factor in the successful evolution of the DOI registration system over last 7 years has been the incorporation of community input from three focus groups under the NASA's Earth Science Data System Working Group (ESDSWG). These groups were largely composed of DOI submitters and data curators from the 12 data centers serving the user communities of various science disciplines. The suggestions from these groups were formulated into recommendations for ESDIS consideration and implementation. The ESDIS DOI registration system has evolved to be fully functional with over 5,000 publicly accessible DOIs and over 200 DOIs being held in reserve status until the information required for registration is obtained. The goal is to assign DOIs to the entire 8000+ data collections under ESDIS management via its network of discipline-oriented data centers. DOIs make it easier for researchers to discover and use earth science data and they enable users to provide valid citations for the data they use in research. Also for the researcher wishing to reproduce the results presented in science publications, the DOI can be used to locate the exact data or data products being cited.

  3. A depth-of-interaction PET detector using mutual gain-equalized silicon photomultiplier

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

    W. Xi, A.G, Weisenberger, H. Dong, Brian Kross, S. Lee, J. McKisson, Carl Zorn

    We developed a prototype high resolution, high efficiency depth-encoding detector for PET applications based on dual-ended readout of LYSO array with two silicon photomultipliers (SiPMs). Flood images, energy resolution, and depth-of-interaction (DOI) resolution were measured for a LYSO array - 0.7 mm in crystal pitch and 10 mm in thickness - with four unpolished parallel sides. Flood images were obtained such that individual crystal element in the array is resolved. The energy resolution of the entire array was measured to be 33%, while individual crystal pixel elements utilizing the signal from both sides ranged from 23.3% to 27%. By applyingmore » a mutual-gain equalization method, a DOI resolution of 2 mm for the crystal array was obtained in the experiments while simulations indicate {approx}1 mm DOI resolution could possibly be achieved. The experimental DOI resolution can be further improved by obtaining revised detector supporting electronics with better energy resolutions. This study provides a detailed detector calibration and DOI response characterization of the dual-ended readout SiPM-based PET detectors, which will be important in the design and calibration of a PET scanner in the future.« less

  4. Investigation of depth-of-interaction (DOI) effects in single- and dual-layer block detectors by the use of light sharing in scintillators.

    PubMed

    Yamamoto, Seiichi

    2012-01-01

    In block detectors for PET scanners that use different lengths of slits in scintillators to share light among photomultiplier tubes (PMTs), a position histogram is distorted when the depth of interaction (DOI) of the gamma photons is near the PMTs (DOI effect). However, it remains unclear whether a DOI effect is observed for block detectors that use light sharing in scintillators. To investigate the effect, I tested the effect for single- and dual-layer block detectors. In the single-layer block detector, Ce doped Gd₂SiO₅ (GSO) crystals of 1.9 × 1.9 × 15 mm³ (0.5 mol% Ce) were used. In the dual-layer block detector, GSO crystals of a 1.9 × 1.9 × 6 mm³ (1.5 mol% Ce) were used for the front layer and GSO crystals of 1.9 × 1.9 × 9 mm³ (0.5 mol% Ce) for the back layer. These scintillators were arranged to form an 8 × 8 matrix with multi-layer optical film inserted partly between the scintillators for obtaining an optimized position response with use of two dual-PMTs. Position histograms and energy responses were measured for these block detectors at three different DOI positions, and the flood histograms were obtained. The results indicated that DOI effects are observed in both block detectors, but the dual-layer block showed more severe distortion in the position histogram as well as larger energy variations. We conclude that, in the block detectors that use light sharing in the scintillators, the DOI effect is an important factor for the performance of the detectors, especially for DOI block detectors.

  5. Tapered whiskers are required for active tactile sensation.

    PubMed

    Hires, Samuel Andrew; Pammer, Lorenz; Svoboda, Karel; Golomb, David

    2013-11-19

    Many mammals forage and burrow in dark constrained spaces. Touch through facial whiskers is important during these activities, but the close quarters makes whisker deployment challenging. The diverse shapes of facial whiskers reflect distinct ecological niches. Rodent whiskers are conical, often with a remarkably linear taper. Here we use theoretical and experimental methods to analyze interactions of mouse whiskers with objects. When pushed into objects, conical whiskers suddenly slip at a critical angle. In contrast, cylindrical whiskers do not slip for biologically plausible movements. Conical whiskers sweep across objects and textures in characteristic sequences of brief sticks and slips, which provide information about the tactile world. In contrast, cylindrical whiskers stick and remain stuck, even when sweeping across fine textures. Thus the conical whisker structure is adaptive for sensor mobility in constrained environments and in feature extraction during active haptic exploration of objects and surfaces. DOI: http://dx.doi.org/10.7554/eLife.01350.001.

  6. 43 CFR 2.34 - Where can I get a copy of DOI's FOIA annual report?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Where can I get a copy of DOI's FOIA... AND TESTIMONY; FREEDOM OF INFORMATION ACT FOIA Annual Report § 2.34 Where can I get a copy of DOI's FOIA annual report? Under 5 U.S.C. 552(e), DOI is required to prepare an annual report regarding its...

  7. 76 FR 77244 - Renewal of Information Collection; OMB Control Number 1040-0001, DOI Programmatic Clearance for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-12

    ... Number 1040-0001, DOI Programmatic Clearance for Customer Satisfaction Surveys AGENCY: Department of [email protected] . Reference ``DOI Programmatic Clearance for Customer Satisfaction Surveys'' in your email... public accountability by promoting a new focus on results, service quality, and customer satisfaction...

  8. Erratum.

    PubMed

    2015-04-01

    In issue 21.1 three of the DOIs were printed incorrectly, please see below for the correct information. Andrea Giorgianni, et al. Flow-diverter stenting of post-traumatic bilateral anterior cerebral artery pseudoaneurysm: A case report. Doi: 10.15274/INR-2014-10059 Correct: Doi: 10.1177/1591019915575441 Lee-Anne Slater, et al. Effect of flow diversion with silk on aneurysm size: A single center experience. Doi: 10.15274/INR-2014-10062 Correct DOI: 10.1177/1591019915576433 Robert J McDonald, et al. Periprocedural safety of Pipeline therapy for unruptured cerebral aneurysms: Analysis of 279 Patients in a multihospital database. Doi: 10.15274/INR-2014-10074 Correct DOI: 10.1177/1591019915576289. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  9. 77 FR 17493 - Agency Information Collection Activities: Proposed Collection; Comment Request; DOI Generic...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-26

    ... Don Bieniewicz at DOI via email at [email protected]ios.doi.gov or via facsimile (202) 208-4867. FOR... yield quantitative results that can be generalized to the population of study. This feedback will... operations might improve delivery of products or services. These collections will allow for ongoing...

  10. 77 FR 22799 - Tribal Consultation Sessions-Administrative Organizational Assessment Draft Report...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-17

    ...) and the Department of the Interior (DOI) to improve American Indian and Alaska Native education. The... proposed MOU between DOI and ED received by close of business on June 15, 2012. ADDRESSES: See the..., Washington, DC 20240. FOR FURTHER INFORMATION CONTACT: For the proposed MOU between ED and DOI, contact...

  11. 43 CFR 2.34 - Where can I get a copy of DOI's FOIA annual report?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Where can I get a copy of DOI's FOIA annual report? 2.34 Section 2.34 Public Lands: Interior Office of the Secretary of the Interior RECORDS AND TESTIMONY; FREEDOM OF INFORMATION ACT FOIA Annual Report § 2.34 Where can I get a copy of DOI's FOIA annual report? Under 5 U.S.C. 552(e), DOI is...

  12. Evolving a NASA Digital Object Identifiers System with Community Engagement

    NASA Astrophysics Data System (ADS)

    Wanchoo, L.; James, N.

    2016-12-01

    In 2010, NASA's Earth Science Data and Information System (ESDIS) Project began investigating the assignment of unique identifiers to its suite of data products being stewarded at data centers distributed across the country. This process led to the use of Digital Object Identifiers (DOIs) and the development of an automated system for the registration of these DOIs. Since that time, the ESDIS DOI registration system has evolved to be fully functional with over 3000 publicly accessible DOIs and over 1000 being held in reserve status until the information required for registration is obtained. The goal is to assign DOIs to the entire 7000+ data collections under ESDIS management via its network of discipline-oriented data centers. A key factor in the successful evolution of the DOI registration system has been the incorporation of community input. Over the last 3 years, ESDIS has solicited community input for making the DOI registration process more efficient through three focus groups under NASA's Earth Science Data System Working Group (ESDSWG). These groups were largely composed of DOI submitters and data curators from the 12 data centers serving user communities of various science disciplines. The suggestions from these groups were formulated into recommendations for ESDIS consideration and implementation. This poster will describe the process and the activities of each focus group, their recommendations, and how these recommendations were implemented.

  13. 43 CFR 2.27 - How will a bureau handle a request for information that is contained in a Privacy Act system of...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false How will a bureau handle a request for information that is contained in a Privacy Act system of records? (See DOI's Privacy Act regulations (Subpart... system of records? (See DOI's Privacy Act regulations (Subpart G of this part) for additional information...

  14. Current directions in behavioral medicine research on genetic testing for disease susceptibility: introduction to the special section.

    PubMed

    Sherman, Kerry A; Cameron, Linda D

    2015-10-01

    The aim of this special section is to showcase research contributing to our understanding of factors influencing decisions to undergo genetic testing and the impact of the genetic testing process on health-related behaviors of tested individuals. The first two articles report studies investigating factors associated with interest in genetic testing and acceptance of test results (Sherman et al. in J Behav Med doi: 10.1007/s10865-015-9630-9 , 2015; Taber et al. in J Behav Med doi: 10.1007/s10865-015-9642-5 , 2015b). The next two papers address the unique contribution of genetic risk information to understanding risk beyond genetic counseling alone (Heiniger et al. in J Behav Med doi 10.1007/s10865-015-9632-7 , 2015; Taber et al. in J Behav Med doi: 10.1007/s10865-015-9648-z , 2015a). The final three articles investigate the effects of genetic risk information on beliefs about disease control and prevention (Aspinwall et al. in J Behav Med doi: 10.1007/s10865-015-9631-8 , 2015; Kelly et al. in J Behav Med doi 10.1007/s10865-014-9613-2 , 2014; Myers et al. in J Behav Med doi: 10.1007/s10865-015-9626-5 , 2015). Collectively, the special section of papers highlights the diverse ways in which behavioural medicine contributes to our understanding of genetic testing for disease risk, and points to the value of further research to better understand ways in which individuals perceive, interpret and respond to genetic risk information.

  15. Departures from Axisymmetric Balance Dynamics during Secondary Eyewall Formation

    DTIC Science & Technology

    2014-10-01

    tensification of Hurricane Opal as diagnosed from a GFDL model forecast. Mon. Wea. Rev., 130, 1866–1881, doi:10.1175/ 1520-0493(2002)130,1866:BCTTIO...2002: Environ- mental interactions in the GFDL hurricane model for Hurri- cane Opal . Mon. Wea. Rev., 130, 298–317, doi:10.1175/ 1520-0493(2002

  16. Impulsive behaviour in rats induced by intracortical DOI infusions is antagonized by co-administration of an mGlu2/3 receptor agonist.

    PubMed

    Wischhof, Lena; Hollensteiner, Karl J; Koch, Michael

    2011-12-01

    The orbitofrontal cortex (OFC) and the medial prefrontal cortex (mPFC) modulate impulsive behaviours. Serotonin [5-hydroxytryptamine (5-HT)] 2A receptors have also been implicated in impulsivity and govern antagonistic interactions with metabotropic glutamate (mGlu)2/3 receptors. This study examined the interactions between 5-HT2A and mGlu2/3 receptors in the OFC and mPFC with relevance to impulsive choice and impulsive action. Impulsive choice was assessed in Lister Hooded rats, trained in a delay-discounting T-maze task, after bilateral intra-OFC infusions of the 5-HT2A/C receptor agonist DOI [(+/-)-1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropan hydrochloride; 5 μg/0.5 μl] and the mGlu2/3 receptor agonist LY379268 (1 μg/0.5 μl). Impulsive action was assessed in a second group of rats trained in a five-choice serial reaction time task (5-CSRTT) and receiving bilateral intra-mPFC infusions of DOI (5 μg/0.5 μl) and LY379268 (1 μg/0.5 μl). Intra-OFC DOI increased impulsive choice, which was not seen when DOI was co-administered with LY379268. LY379268 itself had no effect on choice behaviour. Intra-mPFC DOI caused impulsive over-responding in the 5-CSRTT that was attenuated when DOI and LY379268 were co-injected. Local mPFC-infusions of LY379268 had no effect on 5-CSRTT performance. This study suggests a differential involvement of OFC and mPFC 5-HT2A receptors in impulsive choice and impulsive action. Moreover, compounds acting at mGlu2/3 receptors might have the potential to improve impulsivity-related impairments.

  17. Intrinsic Information Processing and Energy Dissipation in Stochastic Input-Output Dynamical Systems

    DTIC Science & Technology

    2015-07-09

    Crutchfield. Information Anatomy of Stochastic Equilibria, Entropy , (08 2014): 0. doi: 10.3390/e16094713 Virgil Griffith, Edwin Chong, Ryan James...Christopher Ellison, James Crutchfield. Intersection Information Based on Common Randomness, Entropy , (04 2014): 0. doi: 10.3390/e16041985 TOTAL: 5 Number...Learning Group Seminar, Complexity Sciences Center, UC Davis. Korana Burke and Greg Wimsatt (UCD), reviewed PRL “Measurement of Stochastic Entropy

  18. DOI Determination by Rise Time Discrimination in Single-Ended Readout for TOF PET Imaging

    PubMed Central

    Wiener, R.I.; Surti, S.; Karp, J.S.

    2013-01-01

    Clinical TOF PET systems achieve detection efficiency using thick crystals, typically of thickness 2–3cm. The resulting dispersion in interaction depths degrades spatial resolution for increasing radial positions due to parallax error. Furthermore, interaction depth dispersion results in time pickoff dispersion and thus in degraded timing resolution, and is therefore of added concern in TOF scanners. Using fast signal digitization, we characterize the timing performance, pulse shape and light output of LaBr3:Ce, CeBr3 and LYSO. Coincidence timing resolution is shown to degrade by ~50ps/cm for scintillator pixels of constant cross section and increasing length. By controlling irradiation depth in a scintillator pixel, we show that DOI-dependence of time pickoff is a significant factor in the loss of timing performance in thick detectors. Using the correlated DOI-dependence of time pickoff and charge collection, we apply a charge-based correction to the time pickoff, obtaining improved coincidence timing resolution of <200ps for a uniform 4×4×30mm3 LaBr3 pixel. In order to obtain both DOI identification and improved timing resolution, we design a two layer LaBr3[5%Ce]/LaBr3[30%Ce] detector of total size 4×4×30mm3, exploiting the dependence of scintillator rise time on [Ce] in LaBr3:Ce. Using signal rise time to determine interaction layer, excellent interaction layer discrimination is achieved, while maintaining coincidence timing resolution of <250ps and energy resolution <7% using a R4998 PMT. Excellent layer separation and timing performance is measured with several other commercially-available TOF photodetectors, demonstrating the practicality of this design. These results indicate the feasibility of rise time discrimination as a technique for measuring event DOI while maintaining sensitivity, timing and energy performance, in a well-known detector architecture. PMID:24403611

  19. DOI Determination by Rise Time Discrimination in Single-Ended Readout for TOF PET Imaging.

    PubMed

    Wiener, R I; Surti, S; Karp, J S

    2013-06-01

    Clinical TOF PET systems achieve detection efficiency using thick crystals, typically of thickness 2-3cm. The resulting dispersion in interaction depths degrades spatial resolution for increasing radial positions due to parallax error. Furthermore, interaction depth dispersion results in time pickoff dispersion and thus in degraded timing resolution, and is therefore of added concern in TOF scanners. Using fast signal digitization, we characterize the timing performance, pulse shape and light output of LaBr 3 :Ce, CeBr 3 and LYSO. Coincidence timing resolution is shown to degrade by ~50ps/cm for scintillator pixels of constant cross section and increasing length. By controlling irradiation depth in a scintillator pixel, we show that DOI-dependence of time pickoff is a significant factor in the loss of timing performance in thick detectors. Using the correlated DOI-dependence of time pickoff and charge collection, we apply a charge-based correction to the time pickoff, obtaining improved coincidence timing resolution of <200ps for a uniform 4×4×30mm 3 LaBr 3 pixel. In order to obtain both DOI identification and improved timing resolution, we design a two layer LaBr 3 [5%Ce]/LaBr 3 [30%Ce] detector of total size 4×4×30mm 3 , exploiting the dependence of scintillator rise time on [Ce] in LaBr 3 :Ce. Using signal rise time to determine interaction layer, excellent interaction layer discrimination is achieved, while maintaining coincidence timing resolution of <250ps and energy resolution <7% using a R4998 PMT. Excellent layer separation and timing performance is measured with several other commercially-available TOF photodetectors, demonstrating the practicality of this design. These results indicate the feasibility of rise time discrimination as a technique for measuring event DOI while maintaining sensitivity, timing and energy performance, in a well-known detector architecture.

  20. panMetaDocs, eSciDoc, and DOIDB - an infrastructure for the curation and publication of file-based datasets for 'GFZ Data Services'

    NASA Astrophysics Data System (ADS)

    Ulbricht, Damian; Elger, Kirsten; Bertelmann, Roland; Klump, Jens

    2016-04-01

    With the foundation of DataCite in 2009 and the technical infrastructure installed in the last six years it has become very easy to create citable dataset DOIs. Nowadays, dataset DOIs are increasingly accepted and required by journals in reference lists of manuscripts. In addition, DataCite provides usage statistics [1] of assigned DOIs and offers a public search API to make research data count. By linking related information to the data, they become more useful for future generations of scientists. For this purpose, several identifier systems, as ISBN for books, ISSN for journals, DOI for articles or related data, Orcid for authors, and IGSN for physical samples can be attached to DOIs using the DataCite metadata schema [2]. While these are good preconditions to publish data, free and open solutions that help with the curation of data, the publication of research data, and the assignment of DOIs in one software seem to be rare. At GFZ Potsdam we built a modular software stack that is made of several free and open software solutions and we established 'GFZ Data Services'. 'GFZ Data Services' provides storage, a metadata editor for publication and a facility to moderate minted DOIs. All software solutions are connected through web APIs, which makes it possible to reuse and integrate established software. Core component of 'GFZ Data Services' is an eSciDoc [3] middleware that is used as central storage, and has been designed along the OAIS reference model for digital preservation. Thus, data are stored in self-contained packages that are made of binary file-based data and XML-based metadata. The eSciDoc infrastructure provides access control to data and it is able to handle half-open datasets, which is useful in embargo situations when a subset of the research data are released after an adequate period. The data exchange platform panMetaDocs [4] makes use of eSciDoc's REST API to upload file-based data into eSciDoc and uses a metadata editor [5] to annotate the files with metadata. The metadata editor has a user-friendly interface with nominal lists, extensive explanations, and an interactive mapping tool to provide assistance to scientists describing the data. It is possible to deposit metadata templates to fill certain fields with default values. The metadata editor generates metadata in the schemas ISO19139, NASA GCMD DIF, and DataCite and could be extended for other schemas. panMetaDocs is able to mint dataset DOIs through DOIDB, which is our component to moderate dataset DOIs issued through 'GFZ Data Services'. DOIDB accepts metadata in the schemas ISO19139, DIF, and DataCite. In addition, DOIDB provides an OAI-PMH interface to disseminate all deposited metadata to data portals. The presentation of datasets on DOI landing pages is done though XSLT stylesheet transformation of the XML-based metadata. The landing pages have been designed to meet needs of scientists. We are able to render the metadata to different layouts. Furthermore, additional information about datasets and publications is assembled into the webpage by querying public databases on the internet. The work presented here will focus on technical details of the software stack. [1] http://stats.datacite.org [2] http://www.dlib.org/dlib/january11/starr/01starr.html [3] http://www.escidoc.org [4] http://panmetadocs.sf.net [5] http://github.com/ulbricht

  1. Use of the PIXEL method to investigate gas adsorption in metal–organic frameworks† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6ce00555a Click here for additional data file. Click here for additional data file. Click here for additional data file.

    PubMed Central

    Maloney, Andrew G. P.; Wood, Peter A.

    2016-01-01

    PIXEL has been used to perform calculations of adsorbate-adsorbent interaction energies between a range of metal–organic frameworks (MOFs) and simple guest molecules. Interactions have been calculated for adsorption between MOF-5 and Ar, H2, and N2; Zn2(BDC)2(TED) (BDC = 1,4-benzenedicarboxylic acid, TED = triethylenediamine) and H2; and HKUST-1 and CO2. The locations of the adsorption sites and the calculated energies, which show differences in the Coulombic or dispersion characteristic of the interaction, compare favourably to experimental data and literature energy values calculated using density functional theory. PMID:28496380

  2. A genome-wide resource for the analysis of protein localisation in Drosophila

    PubMed Central

    Sarov, Mihail; Barz, Christiane; Jambor, Helena; Hein, Marco Y; Schmied, Christopher; Suchold, Dana; Stender, Bettina; Janosch, Stephan; KJ, Vinay Vikas; Krishnan, RT; Krishnamoorthy, Aishwarya; Ferreira, Irene RS; Ejsmont, Radoslaw K; Finkl, Katja; Hasse, Susanne; Kämpfer, Philipp; Plewka, Nicole; Vinis, Elisabeth; Schloissnig, Siegfried; Knust, Elisabeth; Hartenstein, Volker; Mann, Matthias; Ramaswami, Mani; VijayRaghavan, K; Tomancak, Pavel; Schnorrer, Frank

    2016-01-01

    The Drosophila genome contains >13000 protein-coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here, we present a genome-wide fosmid library of 10000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins, we created transgenic lines, and for a total of 207 lines, we assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we visualised many proteins at endogenous expression levels and found a large fraction of them localising to subcellular compartments. By applying genetic complementation tests, we estimate that about two-thirds of the tagged proteins are functional. Moreover, these tagged proteins enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will boost systematic analysis of protein expression and localisation in various cellular and developmental contexts. DOI: http://dx.doi.org/10.7554/eLife.12068.001 PMID:26896675

  3. Task-dependent recurrent dynamics in visual cortex

    PubMed Central

    Tajima, Satohiro; Koida, Kowa; Tajima, Chihiro I; Suzuki, Hideyuki; Aihara, Kazuyuki; Komatsu, Hidehiko

    2017-01-01

    The capacity for flexible sensory-action association in animals has been related to context-dependent attractor dynamics outside the sensory cortices. Here, we report a line of evidence that flexibly modulated attractor dynamics during task switching are already present in the higher visual cortex in macaque monkeys. With a nonlinear decoding approach, we can extract the particular aspect of the neural population response that reflects the task-induced emergence of bistable attractor dynamics in a neural population, which could be obscured by standard unsupervised dimensionality reductions such as PCA. The dynamical modulation selectively increases the information relevant to task demands, indicating that such modulation is beneficial for perceptual decisions. A computational model that features nonlinear recurrent interaction among neurons with a task-dependent background input replicates the key properties observed in the experimental data. These results suggest that the context-dependent attractor dynamics involving the sensory cortex can underlie flexible perceptual abilities. DOI: http://dx.doi.org/10.7554/eLife.26868.001 PMID:28737487

  4. Sequential selection of economic good and action in medial frontal cortex of macaques during value-based decisions

    PubMed Central

    Chen, Xiaomo; Stuphorn, Veit

    2015-01-01

    Value-based decisions could rely either on the selection of desired economic goods or on the selection of the actions that will obtain the goods. We investigated this question by recording from the supplementary eye field (SEF) of monkeys during a gambling task that allowed us to distinguish chosen good from chosen action signals. Analysis of the individual neuron activity, as well as of the population state-space dynamic, showed that SEF encodes first the chosen gamble option (the desired economic good) and only ~100 ms later the saccade that will obtain it (the chosen action). The action selection is likely driven by inhibitory interactions between different SEF neurons. Our results suggest that during value-based decisions, the selection of economic goods precedes and guides the selection of actions. The two selection steps serve different functions and can therefore not compensate for each other, even when information guiding both processes is given simultaneously. DOI: http://dx.doi.org/10.7554/eLife.09418.001 PMID:26613409

  5. A neural basis for the spatial suppression of visual motion perception

    PubMed Central

    Liu, Liu D; Haefner, Ralf M; Pack, Christopher C

    2016-01-01

    In theory, sensory perception should be more accurate when more neurons contribute to the representation of a stimulus. However, psychophysical experiments that use larger stimuli to activate larger pools of neurons sometimes report impoverished perceptual performance. To determine the neural mechanisms underlying these paradoxical findings, we trained monkeys to discriminate the direction of motion of visual stimuli that varied in size across trials, while simultaneously recording from populations of motion-sensitive neurons in cortical area MT. We used the resulting data to constrain a computational model that explained the behavioral data as an interaction of three main mechanisms: noise correlations, which prevented stimulus information from growing with stimulus size; neural surround suppression, which decreased sensitivity for large stimuli; and a read-out strategy that emphasized neurons with receptive fields near the stimulus center. These results suggest that paradoxical percepts reflect tradeoffs between sensitivity and noise in neuronal populations. DOI: http://dx.doi.org/10.7554/eLife.16167.001 PMID:27228283

  6. Externally induced frontoparietal synchronization modulates network dynamics and enhances working memory performance

    PubMed Central

    Violante, Ines R; Li, Lucia M; Carmichael, David W; Lorenz, Romy; Leech, Robert; Hampshire, Adam; Rothwell, John C; Sharp, David J

    2017-01-01

    Cognitive functions such as working memory (WM) are emergent properties of large-scale network interactions. Synchronisation of oscillatory activity might contribute to WM by enabling the coordination of long-range processes. However, causal evidence for the way oscillatory activity shapes network dynamics and behavior in humans is limited. Here we applied transcranial alternating current stimulation (tACS) to exogenously modulate oscillatory activity in a right frontoparietal network that supports WM. Externally induced synchronization improved performance when cognitive demands were high. Simultaneously collected fMRI data reveals tACS effects dependent on the relative phase of the stimulation and the internal cognitive processing state. Specifically, synchronous tACS during the verbal WM task increased parietal activity, which correlated with behavioral performance. Furthermore, functional connectivity results indicate that the relative phase of frontoparietal stimulation influences information flow within the WM network. Overall, our findings demonstrate a link between behavioral performance in a demanding WM task and large-scale brain synchronization. DOI: http://dx.doi.org/10.7554/eLife.22001.001 PMID:28288700

  7. Functional mapping of yeast genomes by saturated transposition

    PubMed Central

    Michel, Agnès H; Hatakeyama, Riko; Kimmig, Philipp; Arter, Meret; Peter, Matthias; Matos, Joao; De Virgilio, Claudio; Kornmann, Benoît

    2017-01-01

    Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Thus, SATAY allows to easily explore the yeast genome at unprecedented resolution and throughput. DOI: http://dx.doi.org/10.7554/eLife.23570.001 PMID:28481201

  8. 43 CFR 2.32 - How long does DOI have to respond to my appeal?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false How long does DOI have to respond to my appeal? 2.32 Section 2.32 Public Lands: Interior Office of the Secretary of the Interior RECORDS AND TESTIMONY; FREEDOM OF INFORMATION ACT FOIA Appeals § 2.32 How long does DOI have to respond to my appeal? (a...

  9. 43 CFR 2.32 - How long does DOI have to respond to my appeal?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false How long does DOI have to respond to my appeal? 2.32 Section 2.32 Public Lands: Interior Office of the Secretary of the Interior RECORDS AND TESTIMONY; FREEDOM OF INFORMATION ACT FOIA Appeals § 2.32 How long does DOI have to respond to my appeal? (a...

  10. Overview of Performance Based Practical Design

    DOT National Transportation Integrated Search

    2018-03-01

    DOI: https://doi.org/10.13023/KTC.RR.2018.03 State transportation agencies (STAs) have increasingly turned to practical design and performance based practical design(PBPD) to inform project development and implementation and to reduce project cos...

  11. Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1

    PubMed Central

    Butryn, Agata; Schuller, Jan M; Stoehr, Gabriele; Runge-Wollmann, Petra; Förster, Friedrich; Auble, David T; Hopfner, Karl-Peter

    2015-01-01

    Swi2/Snf2 ATPases remodel substrates such as nucleosomes and transcription complexes to control a wide range of DNA-associated processes, but detailed structural information on the ATP-dependent remodeling reactions is largely absent. The single subunit remodeler Mot1 (modifier of transcription 1) dissociates TATA box-binding protein (TBP):DNA complexes, offering a useful system to address the structural mechanisms of Swi2/Snf2 ATPases. Here, we report the crystal structure of the N-terminal domain of Mot1 in complex with TBP, DNA, and the transcription regulator negative cofactor 2 (NC2). Our data show that Mot1 reduces DNA:NC2 interactions and unbends DNA as compared to the TBP:DNA:NC2 state, suggesting that Mot1 primes TBP:NC2 displacement in an ATP-independent manner. Electron microscopy and cross-linking data suggest that the Swi2/Snf2 domain of Mot1 associates with the upstream DNA and the histone fold of NC2, thereby revealing parallels to some nucleosome remodelers. This study provides a structural framework for how a Swi2/Snf2 ATPase interacts with its substrate DNA:protein complex. DOI: http://dx.doi.org/10.7554/eLife.07432.001 PMID:26258880

  12. Concept for Future Data Services at the Long-Term Archive of WDCC combining DOIs with common PIDs

    NASA Astrophysics Data System (ADS)

    Stockhause, Martina; Weigel, Tobias; Toussaint, Frank; Höck, Heinke; Thiemann, Hannes; Lautenschlager, Michael

    2013-04-01

    The World Data Center for Climate (WDCC) hosted at the German Climate Computing Center (DKRZ) maintains a long-term archive (LTA) of climate model data as well as observational data. WDCC distinguishes between two types of LTA data: Structured data: Data output of an instrument or of a climate model run consists of numerous, highly structured individual datasets in a uniform format. Part of these data is also published on an ESGF (Earth System Grid Federation) data node. Detailed metadata is available allowing for fine-grained user-defined data access. Unstructured data: LTA data of finished scientific projects are in general unstructured and consist of datasets of different formats, different sizes, and different contents. For these data compact metadata is available as content information. The structured data is suitable for WDCC's DataCite DOI process, the project data only in exceptional cases. The DOI process includes a thorough quality control process of technical as well as scientific aspects by the publication agent and the data creator. DOIs are assigned to data collections appropriate to be cited in scientific publications, like a simulation run. The data collection is defined in agreement with the data creator. At the moment there is no possibility to identify and cite individual datasets within this DOI data collection analogous to the citation of chapters in a book. Also missing is a compact citation regulation for a user-specified collection of data. WDCC therefore complements its existing LTA/DOI concept by Persistent Identifier (PID) assignment to datasets using Handles. In addition to data identification for internal and external use, the concept of PIDs allows to define relations among PIDs. Such structural information is stored as key-value pair directly in the handles. Thus, relations provide basic provenance or lineage information, even if part of the data like intermediate results are lost. WDCC intends to use additional PIDs on metadata entities with a relation to the data PID(s). These add background information on the data creation process (e.g. descriptions of experiment, model, model set-up, and platform for the model run etc.) to the data. These pieces of additional information increase the re-usability of the archived model data, significantly. Other valuable additional information for scientific collaboration could be added by the same mechanism, like quality information and annotations. Apart from relations among data and metadata entities, PIDs on collections are advantageous for model data: Collections allow for persistent references to single datasets or subsets of data assigned a DOI, Data objects and additional information objects can be consistently connected via relations (provenance, creation, quality information for data),

  13. Color sensitive silicon photomultiplers with micro-cell level encoding for DOI PET detectors

    NASA Astrophysics Data System (ADS)

    Shimazoe, Kenji; Koyama, Akihiro; Takahashi, Hiroyuki; Ganka, Thomas; Iskra, Peter; Marquez Seco, Alicia; Schneider, Florian; Wiest, Florian

    2017-11-01

    There have been many studies on Depth Of Interaction (DOI) identification for high resolution Positron Emission Tomography (PET) systems, including those on phoswich detectors, double-sided readout, light sharing methods, and wavelength discrimination. The wavelength discrimination method utilizes the difference in wavelength of stacked scintillators and requires a color sensitive photodetector. Here, a new silicon photomultiplier (SiPM) coupled to a color filter (colorSiPM) was designed and fabricated for DOI detection. The fabricated colorSiPM has two anode readouts that are sensitive to blue and green color. The colorSiPM's response and DOI identification capability for stacked GAGG and LYSO crystals are characterized. The fabricated colorSiPM is sensitive enough to detect a peak of 662 keV from a 137 Cs source.

  14. Delineating interpersonal communication networks: a study of the diffusion of an intervention among female entertainment workers in Shanghai, China.

    PubMed

    Chen, Yiyun; Latkin, Carl; Celentano, David D; Yang, Xiushi; Li, Xiaoming; Xia, Guomei; Miao, Jia; Surkan, Pamela J

    2012-10-01

    Diffusion of innovation (DOI) is widely cited in the HIV behavior change literature; however there is a dearth of research on the application of DOI in interventions for sex workers. Following a randomized-controlled trial of HIV risk reduction among female entertainment workers (FEWs) in Shanghai, China, we used qualitative approaches to delineate potential interpersonal communication networks and contributing factors that promote diffusion of information in entertainment venues. Results showed that top-down communication networks from the venue owners to the FEWs were efficient for diffusion of information. Mammies/madams, who act as intermediaries between FEWs and clients form an essential part of FEWs' social networks but do not function as information disseminators due to a conflict of interest between safer sex and maximizing profits. Diffusion of information in large venues tended to rely more on aspects of the physical environment to create intimacy and on pressure from managers to stimulate communication. In small venues, communication and conversations occurred more spontaneously among FEWs. Information about safer sex appeared to be more easily disseminated when the message and the approach used to convey information could be tailored to people working at different levels in the venues. Results suggest that safer sex messages should be provided consistently following an intervention to further promote intervention diffusion, and health-related employer liability systems in entertainment venues should be established, in which employers are responsible for the health of their employees. Our study suggests that existing personal networks can be used to disseminate information in entertainment venues and one should be mindful about the context-specific interactions between FEWs and others in their social networks to better achieve diffusion of interventions.

  15. Delineating Interpersonal Communication Networks: A Study of the Diffusion of an Intervention Among Female Entertainment Workers in Shanghai, China

    PubMed Central

    Latkin, Carl; Celentano, David D.; Yang, Xiushi; Li, Xiaoming; Xia, Guomei; Miao, Jia; Surkan, Pamela J.

    2013-01-01

    Diffusion of innovation (DOI) is widely cited in the HIV behavior change literature; however there is a dearth of research on the application of DOI in interventions for sex workers. Following a randomized-controlled trial of HIV risk reduction among female entertainment workers (FEWs) in Shanghai, China, we used qualitative approaches to delineate potential interpersonal communication networks and contributing factors that promote diffusion of information in entertainment venues. Results showed that top-down communication networks from the venue owners to the FEWs were efficient for diffusion of information. Mammies/madams, who act as intermediaries between FEWs and clients form an essential part of FEWs’ social networks but do not function as information disseminators due to a conflict of interest between safer sex and maximizing profits. Diffusion of information in large venues tended to rely more on aspects of the physical environment to create intimacy and on pressure from managers to stimulate communication. In small venues, communication and conversations occurred more spontaneously among FEWs. Information about safer sex appeared to be more easily disseminated when the message and the approach used to convey information could be tailored to people working at different levels in the venues. Results suggest that safer sex messages should be provided consistently following an intervention to further promote intervention diffusion, and health-related employer liability systems in entertainment venues should be established, in which employers are responsible for the health of their employees. Our study suggests that existing personal networks can be used to disseminate information in entertainment venues and one should be mindful about the context-specific interactions between FEWs and others in their social networks to better achieve diffusion of interventions. PMID:22638867

  16. Evolution of Evaluation and Assessment in Diverse Audiences in the Digital Age

    NASA Astrophysics Data System (ADS)

    Eriksson, S. C.

    2015-12-01

    Over the past decades, researchers have learned more about how people think and act and about the social and political aspects of teaching and learning. This understanding has brought changes in researchers' and practitioners' interactions with diverse groups and individuals. This paper addresses evaluation, a process that measures the degree to which learning and project goals are met and factors contributing to or hindering outcomes. Parallels are drawn to learning assessment. The concepts of inclusion, participation, and constructivism (Mertens, 1999; Mertens and Hopson, 2006) now drive best evaluation practices for projects with persons with disabilities (AEA, 2011). This is also true in cases of other people who have been marginalized in STEM fields, e.g. women and underrepresented groups. Inclusion of these stakeholders has important implications for the validity of an evaluation, including the accuracy of results (Jacobson et al, 2012; Gill, 1999; Lee, 1999). The American Indian Higher Education Consortium's framework for indigenous groups incorporates their values and goals into evaluation design and implementation. It is feasible to include participant input in designing the questions and methods of obtaining data, ensuring that issues of access, opportunity, and power (Shuffelbeam, 2001) are taken into consideration. Geoscience projects with u-learning and m-learning provide opportunities to test these theoretical models in innovative programs such as: field work for students with physical disability; underrepresented minority, secondary students using mobile devices in contextualized learning in informal settings; and graduate students using digital maps to enhance traditional field work. This study compares program evaluation methodology of tradition learning with that of programs for diverse groups of students using digital technology. Ref: Mertens doi:10.1177/109821409902000102; Mertens and Hopson DOI: 10.1002/ev.177; AEA http://www.eval.org/p/cm/ld/fid=92; Jacobson et al DOI 10.1177/1098214012461558; Gill DOI:10.1016/S1098-2140(99)00018-1; Lee DOI: 10.1177/109821409902000210; Shuffelbeam ISBN: 978-0-7879-5755-1

  17. Emergence and evolution of an interaction between intrinsically disordered proteins

    PubMed Central

    Hultqvist, Greta; Åberg, Emma; Camilloni, Carlo; Sundell, Gustav N; Andersson, Eva; Dogan, Jakob; Chi, Celestine N; Vendruscolo, Michele; Jemth, Per

    2017-01-01

    Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. However, it is not clear how such interactions emerge and evolve on a molecular level. We performed phylogenetic reconstruction, resurrection and biophysical characterization of two interacting disordered protein domains, CID and NCBD. CID appeared after the divergence of protostomes and deuterostomes 450–600 million years ago, while NCBD was present in the protostome/deuterostome ancestor. The most ancient CID/NCBD formed a relatively weak complex (Kd∼5 µM). At the time of the first vertebrate-specific whole genome duplication, the affinity had increased (Kd∼200 nM) and was maintained in further speciation. Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations. DOI: http://dx.doi.org/10.7554/eLife.16059.001 PMID:28398197

  18. Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

    PubMed Central

    Momeni, Babak; Xie, Li; Shou, Wenying

    2017-01-01

    Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

  19. Space Particle Hazard Measurement and Modeling

    DTIC Science & Technology

    2016-09-01

    understand the interactions of the physical processes driving, then specify and ultimately predict the state of the energetic particle populations...Hudson, and B. T. Kress (2013), Direct observation of the CRAND proton radiation belt source, J. Geophys. Res. Space Physics , 118, doi:10.1002...anticritical temperature for spacecraft charging, J. Geophys Res.: Space Physics , 113, 2156-2202, doi: 10.1029/2008JA013161 2010 – Tested basic

  20. Spatial resolution recovery utilizing multi-ray tracing and graphic processing unit in PET image reconstruction.

    PubMed

    Liang, Yicheng; Peng, Hao

    2015-02-07

    Depth-of-interaction (DOI) poses a major challenge for a PET system to achieve uniform spatial resolution across the field-of-view, particularly for small animal and organ-dedicated PET systems. In this work, we implemented an analytical method to model system matrix for resolution recovery, which was then incorporated in PET image reconstruction on a graphical processing unit platform, due to its parallel processing capacity. The method utilizes the concepts of virtual DOI layers and multi-ray tracing to calculate the coincidence detection response function for a given line-of-response. The accuracy of the proposed method was validated for a small-bore PET insert to be used for simultaneous PET/MR breast imaging. In addition, the performance comparisons were studied among the following three cases: 1) no physical DOI and no resolution modeling; 2) two physical DOI layers and no resolution modeling; and 3) no physical DOI design but with a different number of virtual DOI layers. The image quality was quantitatively evaluated in terms of spatial resolution (full-width-half-maximum and position offset), contrast recovery coefficient and noise. The results indicate that the proposed method has the potential to be used as an alternative to other physical DOI designs and achieve comparable imaging performances, while reducing detector/system design cost and complexity.

  1. X-ray computed microtomography of sea ice - comment on "A review of air-ice chemical and physical interactions (AICI): liquids, quasi-liquids, and solids in snow" by Bartels-Rausch et al. (2014)

    NASA Astrophysics Data System (ADS)

    Obbard, R. W.

    2015-07-01

    This comment addresses a statement made in "A review of air-ice chemical and physical interactions (AICI): liquids, quasi-liquids, and solids in snow" by Bartels-Rausch et al. (Atmos. Chem. Phys., 14, 1587-1633, doi:10.5194/acp-14-1587-2014, 2014). Here we rebut the assertion that X-ray computed microtomography of sea ice fails to reveal liquid brine inclusions by discussing the phases present at the analysis temperature.

  2. Female mice ultrasonically interact with males during courtship displays

    PubMed Central

    Neunuebel, Joshua P; Taylor, Adam L; Arthur, Ben J; Egnor, SE Roian

    2015-01-01

    During courtship males attract females with elaborate behaviors. In mice, these displays include ultrasonic vocalizations. Ultrasonic courtship vocalizations were previously attributed to the courting male, despite evidence that both sexes produce virtually indistinguishable vocalizations. Because of this similarity, and the difficulty of assigning vocalizations to individuals, the vocal contribution of each individual during courtship is unknown. To address this question, we developed a microphone array system to localize vocalizations from socially interacting, individual adult mice. With this system, we show that female mice vocally interact with males during courtship. Males and females jointly increased their vocalization rates during chases. Furthermore, a female's participation in these vocal interactions may function as a signal that indicates a state of increased receptivity. Our results reveal a novel form of vocal communication during mouse courtship, and lay the groundwork for a mechanistic dissection of communication during social behavior. DOI: http://dx.doi.org/10.7554/eLife.06203.001 PMID:26020291

  3. Decoupling global biases and local interactions between cell biological variables

    PubMed Central

    Zaritsky, Assaf; Obolski, Uri; Gan, Zhuo; Reis, Carlos R; Kadlecova, Zuzana; Du, Yi; Schmid, Sandra L; Danuser, Gaudenz

    2017-01-01

    Analysis of coupled variables is a core concept of cell biological inference, with co-localization of two molecules as a proxy for protein interaction being a ubiquitous example. However, external effectors may influence the observed co-localization independently from the local interaction of two proteins. Such global bias, although biologically meaningful, is often neglected when interpreting co-localization. Here, we describe DeBias, a computational method to quantify and decouple global bias from local interactions between variables by modeling the observed co-localization as the cumulative contribution of a global and a local component. We showcase four applications of DeBias in different areas of cell biology, and demonstrate that the global bias encapsulates fundamental mechanistic insight into cellular behavior. The DeBias software package is freely accessible online via a web-server at https://debias.biohpc.swmed.edu. DOI: http://dx.doi.org/10.7554/eLife.22323.001 PMID:28287393

  4. Unmanned Aircraft Systems for Monitoring Department of the Interior Lands

    NASA Astrophysics Data System (ADS)

    Hutt, M. E.; Quirk, B.

    2013-12-01

    Unmanned Aircraft Systems (UAS) technology is quickly evolving and will have a significant impact on Earth science research. The U.S. Geological Survey (USGS) is conducting an operational test and evaluation of UAS to see how this technology supports the mission of the Department of the Interior (DOI). Over the last 4 years, the USGS, working with many partners, has been actively conducting proof of concept UAS operations, which are designed to evaluate the potential of UAS technology to support the mandated DOI scientific, resource and land management missions. UAS technology is being made available to monitor environmental conditions, analyze the impacts of climate change, respond to natural hazards, understand landscape change rates and consequences, conduct wildlife inventories and support related land management and law enforcement missions. Using small UAS (sUAS), the USGS is able to tailor solutions to meet project requirements by obtaining very high resolution video data, acquiring thermal imagery, detecting chemical plumes, and generating digital terrain models at a fraction of the cost of conventional surveying methods. UAS technology is providing a mechanism to collect timely remote sensing data at a low cost and at low risk over DOI lands that can be difficult to monitor and consequently enhances our ability to provide unbiased scientific information to better enable decision makers to make informed decisions. This presentation describes the UAS technology and infrastructure being employed, the application projects already accomplished, lessons learned and future of UAS within the DOI. We fully expect that by 2020 UAS will emerge as a primary platform for all DOI remote sensing applications. Much like the use of Internet technology, Geographic Information Systems (GIS) and Global Positioning Systems (GPS), UAS have the potential of enabling the DOI to be better stewards of the land.

  5. Erratum to: Adsorption energies of H and H2: a quantum-chemical study. Eur. Phys. J. D 71: 45 (2017), DOI: 10.1140/epjd/e2017-70610-4

    NASA Astrophysics Data System (ADS)

    Sil, Milan; Gorai, Prasanta; Das, Ankan; Sahu, Dipen; Chakrabarti, Sandip K.

    2017-12-01

    Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic and B. Sivaraman.The online version of the original article can be found at http://https://doi.org/10.1140/epjd/e2017-70610-4.

  6. Reply to Comment by Nishimura Et Al.

    NASA Astrophysics Data System (ADS)

    Mozer, F. S.; Hull, A.; Lejosne, S.; Vasko, I. Y.

    2018-03-01

    Nishimura et al. (2010, https://doi.org/10.1126/science.1193186, 2011, https://doi.org/10.1029/2011JA016876, 2013, https://doi.org/10.1029/2012JA018242, and in their comment, hereafter called N18) have suggested that chorus waves interact with equatorial electrons to produce pulsating auroras. We agree that chorus can scatter electrons >10 keV, as do Time Domain Structures (TDSs). Lower-energy electrons occurring in pulsating auroras cannot be produced by chorus, but such electrons are scattered and accelerated by TDS. TDSs often occur with chorus and have power in their spectra at chorus frequencies. Thus, the absence of power at low frequencies is not evidence that TDSs are absent, as an example shows. Through examination of equatorial electric field waveforms and electron pitch angle distributions measured on the Time History of Events and Macroscale Interactions during Substorms satellites (in place of examining field and particle spectra, as done by Nishimura et al.), we show that chorus cannot produce the field-aligned electrons associated with pulsating auroras in the Nishimura et al. (2010, https://doi.org/10.1126/science.1193186) events, but TDSs can. Equatorial field-aligned electron distributions associated with pulsating auroras and created by TDS in the absence of chorus or any other wave at the equator are also shown.

  7. Temperature data acquired from the DOI/GTN-P Deep Borehole Array on the Arctic Slope of Alaska, 1973-2013

    USGS Publications Warehouse

    Clow, Gary D.

    2014-01-01

    System (GTOS). The data will also be useful for refining our basic understanding of the physical conditions in permafrost in Arctic Alaska, as well as providing important information for validating predictive models used for climate impact assessments. The processed data are available from the Advanced Cooperative Arctic Data and Information Service (ACADIS) repository at doi:10.5065/D6N014HK.

  8. Proceedings of the U.S. Geological Survey 2004 Mercury Workshop - Mercury research and its relation to Department of the Interior resource management

    USGS Publications Warehouse

    Colman, John A.

    2007-01-01

    IntroductionAs part of the Department of the Interior (DOI) program Science on the DOI Landscape Initiative, the U.S. Geological Survey (USGS), Eastern Region, held a workshop during August 17–18, 2004, in Reston, VA, on mercury in the environment as it relates to DOI resource management. DOI bureaus manage millions of acres of land and offshore resources subject to mercury deposition and to the effects of mercury on ecosystems and human health. The goals of the workshop were to (1) summarize information on mercury sources and cycling on DOI lands in the eastern United States, (2) learn the perspectives of the DOI bureaus regarding mercury on DOI lands, (3) provide information to DOI land managers about monitoring mercury and minimizing mercury accumulation in wildlife and humans, and (4) consider future directions for mercury monitoring and research on DOI lands. The workshop focused on mercury research as it relates to DOI resource-management issues primarily in the eastern part of the United States (east of the Mississippi River). Topics included the influence of ecosystem setting on mercury biogeochemical transformation, land- and air-management practices as they affect mercury in the environment, mercury source issues, and effects of mercury on humans and wildlife. Mercury research topics were addressed by 24 invited oral presentations and 30 contributed posters. The perspectives of the DOI bureaus and land managers were addressed through a panel of scientists from the DOI resource-management bureaus and a Chippewa Indian Tribe of Minnesota. Discussion at the conclusion of the workshop was directed toward goals and long-term strategies for mercury research that will benefit DOI resource management. The panel, presentations, and discussions were videotaped and are available at the following URL, along with the slides presented: http://www.usgs.gov/mercury/2004workshop/ Abstracts from the presentations and posters are included in this report, together with summaries of each presentation session. The abstracts in this volume that were written by U.S. Geological Survey authors were reviewed and approved for publication by the Survey. Abstracts submitted by researchers from academia and from state and other federal agencies are published as part of these proceedings, but do not necessarily reflect the Survey’s policies and views. The use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

  9. A multiplexed TOF and DOI capable PET detector using a binary position sensitive network.

    PubMed

    Bieniosek, M F; Cates, J W; Levin, C S

    2016-11-07

    Time of flight (TOF) and depth of interaction (DOI) capabilities can significantly enhance the quality and uniformity of positron emission tomography (PET) images. Many proposed TOF/DOI PET detectors require complex readout systems using additional photosensors, active cooling, or waveform sampling. This work describes a high performance, low complexity, room temperature TOF/DOI PET module. The module uses multiplexed timing channels to significantly reduce the electronic readout complexity of the PET detector while maintaining excellent timing, energy, and position resolution. DOI was determined using a two layer light sharing scintillation crystal array with a novel binary position sensitive network. A 20 mm effective thickness LYSO crystal array with four 3 mm  ×  3 mm silicon photomultipliers (SiPM) read out by a single timing channel, one energy channel and two position channels achieved a full width half maximum (FWHM) coincidence time resolution of 180  ±  2 ps with 10 mm of DOI resolution and 11% energy resolution. With sixteen 3 mm  ×  3 mm SiPMs read out by a single timing channel, one energy channel and four position channels a coincidence time resolution 204  ±  1 ps was achieved with 10 mm of DOI resolution and 15% energy resolution. The methods presented here could significantly simplify the construction of high performance TOF/DOI PET detectors.

  10. Data always getting bigger -- A scalable DOI architecture for big and expanding scientific data

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

    Prakash, Giri; Shrestha, Biva; Younkin, Katarina

    The Atmospheric Radiation Measurement (ARM) Data Archive established a data citation strategy based on Digital Object Identifiers (DOIs) for the ARM datasets in order to facilitate citing continuous and diverse ARM datasets in articles and other papers. This strategy eases the tracking of data provided as supplements to articles and papers. Additionally, it allows future data users and the ARM Climate Research Facility to easily locate the exact data used in various articles. Traditionally, DOIs are assigned to individual digital objects (a report or a data table), but for ARM datasets, these DOIs are assigned to an ARM data product.more » This eliminates the need for creating DOIs for numerous components of the ARM data product, in turn making it easier for users to manage and cite the ARM data with fewer DOIs. In addition, the ARM data infrastructure team, with input from scientific users, developed a citation format and an online data citation generation tool for continuous data streams. As a result, this citation format includes DOIs along with additional details such as spatial and temporal information.« less

  11. Data always getting bigger -- A scalable DOI architecture for big and expanding scientific data

    DOE PAGES

    Prakash, Giri; Shrestha, Biva; Younkin, Katarina; ...

    2016-08-31

    The Atmospheric Radiation Measurement (ARM) Data Archive established a data citation strategy based on Digital Object Identifiers (DOIs) for the ARM datasets in order to facilitate citing continuous and diverse ARM datasets in articles and other papers. This strategy eases the tracking of data provided as supplements to articles and papers. Additionally, it allows future data users and the ARM Climate Research Facility to easily locate the exact data used in various articles. Traditionally, DOIs are assigned to individual digital objects (a report or a data table), but for ARM datasets, these DOIs are assigned to an ARM data product.more » This eliminates the need for creating DOIs for numerous components of the ARM data product, in turn making it easier for users to manage and cite the ARM data with fewer DOIs. In addition, the ARM data infrastructure team, with input from scientific users, developed a citation format and an online data citation generation tool for continuous data streams. As a result, this citation format includes DOIs along with additional details such as spatial and temporal information.« less

  12. MO-F-CAMPUS-J-03: Development of a Human Brain PET for On-Line Proton Beam-Range Verification

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

    Shao, Yiping

    Purpose: To develop a prototype PET for verifying proton beam-range before each fractionated therapy that will enable on-line re-planning proton therapy. Methods: Latest “edge-less” silicon photomultiplier arrays and customized ASIC readout electronics were used to develop PET detectors with depth-of-interaction (DOI) measurement capability. Each detector consists of one LYSO array with each end coupled to a SiPM array. Multiple detectors can be seamlessly tiled together to form a large detector panel. Detectors with 1.5×1.5 and 2.0×2.0 mm crystals at 20 or 30 mm lengths were studied. Readout of individual SiPM or signal multiplexing was used to transfer 3D interaction position-codedmore » analog signals through flexible-print-circuit cables or PCB board to dedicated ASIC front-end electronics to output digital timing pulses that encode interaction information. These digital pulses can be transferred to, through standard LVDS cables, and decoded by a FPGA-based data acquisition of coincidence events and data transfer. The modular detector and scalable electronics/data acquisition will enable flexible PET system configuration for different imaging geometry. Results: Initial detector performance measurement shows excellent crystal identification even with 30 mm long crystals, ∼18% and 2.8 ns energy and timing resolutions, and around 2–3 mm DOI resolution. A small prototype PET scanner with one detector ring has been built and evaluated, validating the technology and design. A large size detector panel has been fabricated by scaling up from modular detectors. Different designs of resistor and capacitor based signal multiplexing boards were tested and selected based on optimal crystal identification and timing performance. Stackable readout electronics boards and FPGA-based data acquisition boards were developed and tested. A brain PET is under construction. Conclusion: Technology of large-size DOI detector based on SiPM array and advanced readout has been developed. PET imaging performance and initial phantom studies of on-line proton beam-range measurement will be conducted and reported. NIH grant R21CA187717; Cancer Prevention and Research Institute of Texas grant RP120326.« less

  13. Tsunami mitigation - redistribution of energy

    NASA Astrophysics Data System (ADS)

    Kadri, Usama

    2017-04-01

    Tsunamis are water waves caused by the displacement of a large volume of water, in the deep ocean or a large lake, following an earthquake, landslide, underwater explosion, meteorite impacts, or other violent geological events. On the coastline, the resulting waves evolve from unnoticeable to devastating, reaching heights of tens of meters and causing destruction of property and loss of life. Over 225,000 people were killed in the 2004 Indian Ocean tsunami alone. For many decades, scientists have been studying tsunami, and progress has been widely reported in connection with the causes (1), forecasting (2), and recovery (3). However, none of the studies ratifies the approach of a direct mitigation of tsunamis, with the exception of mitigation using submarine barriers (e.g. see Ref. (4)). In an attempt to open a discussion on direct mitigation, I examine the feasibility of redistributing the total energy of a very long surface ocean (gravity) wave over a larger space through nonlinear resonant interaction with two finely tuned acoustic-gravity waves (see Refs. (5-8)). Theoretically, while the energy input in the acoustic-gravity waves required for an effective interaction is comparable to that in a tsunami (i.e. impractically large), employing the proposed mitigation technique the initial tsunami amplitude could be reduced substantially resulting in a much milder impact at the coastline. Moreover, such a technique would allow for the harnessing of the tsunami's own energy. Practically, this mitigation technique requires the design of highly accurate acoustic-gravity wave frequency transmitters or modulators, which is a rather challenging ongoing engineering problem. References 1. E. Bryant, 2014. Tsunami: the underrated hazard. Springer, doi:10.1007/978-3-319- 06133-7. 2. V. V. Titov, F. I. Gonza`lez, E. N. Bernard, M. C. Eble, H. O. Mofjeld, J. C. Newman, A. J. Venturato, 2005. Real-Time Tsunami Forecasting: Challenges and Solutions. Nat. Hazards 35:41-58, doi:10.1007/1-4020-3607-8 3 3. E. Check, 2005. Natural disasters: Roots of recovery. Nature 438, 910-911, doi:10.1038/438910a. 4. A. M. Fridman, L. S. Alperovich, L. Shemer, L. Pustil'nik, D. Shtivelman, A. G. Marchuk, D. Liberzon, 2010. Tsunami wave suppression using submarine barriers. Phys. Usp. 53 809-816, doi:10.3367/UFNe.0180.201008d.0843. 5. U. Kadri, M. Stiassnie, 2013. Generation of an acoustic-gravity wave by two gravity waves, and their mutual interaction. J. Fluid Mech. 735, R6, doi:10.1017/jfm.2013.539. 6. U. Kadri, 2015. Wave motion in a heavy compressible fluid: revisited. European Journal of Mechanics - B/Fluids, 49(A), 50-57, doi:10.1016/j.euromechflu.2014.07.008 7. U. Kadri, T.R. Akylas, 2016. On resonant triad interactions of acoustic-gravity waves. J. Fluid Mech., 788, R1(12 pages), doi:10.1017/jfm.2015.721. 8. U. Kadri, 2016. Triad resonance between a surface-gravity wave and two high frequency hydro-acoustic waves. Eur. J. Mech. B/Fluid, 55(1), 157-161, doi:10.1016/j.euromechflu.2015.09.008.

  14. Reaching 200-ps timing resolution in a time-of-flight and depth-of-interaction positron emission tomography detector using phosphor-coated crystals and high-density silicon photomultipliers

    PubMed Central

    Kwon, Sun Il; Ferri, Alessandro; Gola, Alberto; Berg, Eric; Piemonte, Claudio; Cherry, Simon R.; Roncali, Emilie

    2016-01-01

    Abstract. Current research in the field of positron emission tomography (PET) focuses on improving the sensitivity of the scanner with thicker detectors, extended axial field-of-view, and time-of-flight (TOF) capability. These create the need for depth-of-interaction (DOI) encoding to correct parallax errors. We have proposed a method to encode DOI using phosphor-coated crystals. Our initial work using photomultiplier tubes (PMTs) demonstrated the possibilities of the proposed method, however, a major limitation of PMTs for this application is poor quantum efficiency in yellow light, corresponding to the wavelengths of the converted light by the phosphor coating. In contrast, the red-green-blue-high-density (RGB-HD) silicon photomultipliers (SiPMs) have a high photon detection efficiency across the visible spectrum. Excellent coincidence resolving time (CRT; <210  ps) was obtained by coupling RGB-HD SiPMs and  3 × 3 × 20  mm3 lutetium fine silicate crystals coated on a third of one of their lateral sides. Events were classified in three DOI bins (∼6.7-mm width) with an average sensitivity of 83.1%. A CRT of ∼200  ps combined with robust DOI encoding is a marked improvement in the phosphor-coated approach that we pioneered. For the first time, we read out these crystals with SiPMs and clearly demonstrated the potential of the RGB-HD SiPMs for this TOF-DOI PET detector. PMID:27921069

  15. Promiscuous binding by Hsp70 results in conformational heterogeneity and fuzzy chaperone-substrate ensembles

    PubMed Central

    Rosenzweig, Rina; Sekhar, Ashok; Nagesh, Jayashree; Kay, Lewis E

    2017-01-01

    The Hsp70 chaperone system is integrated into a myriad of biochemical processes that are critical for cellular proteostasis. Although detailed pictures of Hsp70 bound with peptides have emerged, correspondingly detailed structural information on complexes with folding-competent substrates remains lacking. Here we report a methyl-TROSY based solution NMR study showing that the Escherichia coli version of Hsp70, DnaK, binds to as many as four distinct sites on a small 53-residue client protein, hTRF1. A fraction of hTRF1 chains are also bound to two DnaK molecules simultaneously, resulting in a mixture of DnaK-substrate sub-ensembles that are structurally heterogeneous. The interactions of Hsp70 with a client protein at different sites results in a fuzzy chaperone-substrate ensemble and suggests a mechanism for Hsp70 function whereby the structural heterogeneity of released substrate molecules enables them to circumvent kinetic traps in their conformational free energy landscape and fold efficiently to the native state. DOI: http://dx.doi.org/10.7554/eLife.28030.001 PMID:28708484

  16. Time-resolved studies define the nature of toxic IAPP intermediates, providing insight for anti-amyloidosis therapeutics

    PubMed Central

    Abedini, Andisheh; Plesner, Annette; Cao, Ping; Ridgway, Zachary; Zhang, Jinghua; Tu, Ling-Hsien; Middleton, Chris T; Chao, Brian; Sartori, Daniel J; Meng, Fanling; Wang, Hui; Wong, Amy G; Zanni, Martin T; Verchere, C Bruce; Raleigh, Daniel P; Schmidt, Ann Marie

    2016-01-01

    Islet amyloidosis by IAPP contributes to pancreatic β-cell death in diabetes, but the nature of toxic IAPP species remains elusive. Using concurrent time-resolved biophysical and biological measurements, we define the toxic species produced during IAPP amyloid formation and link their properties to induction of rat INS-1 β-cell and murine islet toxicity. These globally flexible, low order oligomers upregulate pro-inflammatory markers and induce reactive oxygen species. They do not bind 1-anilnonaphthalene-8-sulphonic acid and lack extensive β-sheet structure. Aromatic interactions modulate, but are not required for toxicity. Not all IAPP oligomers are toxic; toxicity depends on their partially structured conformational states. Some anti-amyloid agents paradoxically prolong cytotoxicity by prolonging the lifetime of the toxic species. The data highlight the distinguishing properties of toxic IAPP oligomers and the common features that they share with toxic species reported for other amyloidogenic polypeptides, providing information for rational drug design to treat IAPP induced β-cell death. DOI: http://dx.doi.org/10.7554/eLife.12977.001 PMID:27213520

  17. Activation-triggered subunit exchange between CaMKII holoenzymes facilitates the spread of kinase activity

    PubMed Central

    Stratton, Margaret; Lee, Il-Hyung; Bhattacharyya, Moitrayee; Christensen, Sune M; Chao, Luke H; Schulman, Howard; Groves, Jay T; Kuriyan, John

    2014-01-01

    The activation of the dodecameric Ca2+/calmodulin dependent kinase II (CaMKII) holoenzyme is critical for memory formation. We now report that CaMKII has a remarkable property, which is that activation of the holoenzyme triggers the exchange of subunits between holoenzymes, including unactivated ones, enabling the calcium-independent phosphorylation of new subunits. We show, using a single-molecule TIRF microscopy technique, that the exchange process is triggered by the activation of CaMKII, and that exchange is modulated by phosphorylation of two residues in the calmodulin-binding segment, Thr 305 and Thr 306. Based on these results, and on the analysis of molecular dynamics simulations, we suggest that the phosphorylated regulatory segment of CaMKII interacts with the central hub of the holoenzyme and weakens its integrity, thereby promoting exchange. Our results have implications for an earlier idea that subunit exchange in CaMKII may have relevance for information storage resulting from brief coincident stimuli during neuronal signaling. DOI: http://dx.doi.org/10.7554/eLife.01610.001 PMID:24473075

  18. Basic Performance Test of a Prototype PET Scanner Using CdTe Semiconductor Detectors

    NASA Astrophysics Data System (ADS)

    Ueno, Y.; Morimoto, Y.; Tsuchiya, K.; Yanagita, N.; Kojima, S.; Ishitsu, T.; Kitaguchi, H.; Kubo, N.; Zhao, S.; Tamaki, N.; Amemiya, K.

    2009-02-01

    A prototype positron emission tomography (PET) scanner using CdTe semiconductor detectors was developed, and its initial evaluation was conducted. The scanner was configured to form a single detector ring with six separated detector units, each having 96 detectors arranged in three detector layers. The field of view (FOV) size was 82 mm in diameter. Basic physical performance indicators of the scanner were measured through phantom studies and confirmed by rat imaging. The system-averaged energy resolution and timing resolution were 5.4% and 6.0 ns (each in FWHM) respectively. Spatial resolution measured at FOV center was 2.6 mm FWHM. Scatter fraction was measured and calculated in a National Electrical Manufacturers Association (NEMA)-fashioned manner using a 3-mm diameter hot capillary in a water-filled 80-mm diameter acrylic cylinder. The calculated result was 3.6%. Effect of depth of interaction (DOI) measurement was demonstrated by comparing hot-rod phantom images reconstructed with and without DOI information. Finally, images of a rat myocardium and an implanted tumor were visually assessed, and the imaging performance was confirmed.

  19. The homo-oligomerisation of both Sas-6 and Ana2 is required for efficient centriole assembly in flies

    PubMed Central

    Cottee, Matthew A; Muschalik, Nadine; Johnson, Steven; Leveson, Joanna; Raff, Jordan W; Lea, Susan M

    2015-01-01

    Sas-6 and Ana2/STIL proteins are required for centriole duplication and the homo-oligomerisation properties of Sas-6 help establish the ninefold symmetry of the central cartwheel that initiates centriole assembly. Ana2/STIL proteins are poorly conserved, but they all contain a predicted Central Coiled-Coil Domain (CCCD). Here we show that the Drosophila Ana2 CCCD forms a tetramer, and we solve its structure to 0.8 Å, revealing that it adopts an unusual parallel-coil topology. We also solve the structure of the Drosophila Sas-6 N-terminal domain to 2.9 Å revealing that it forms higher-order oligomers through canonical interactions. Point mutations that perturb Sas-6 or Ana2 homo-oligomerisation in vitro strongly perturb centriole assembly in vivo. Thus, efficient centriole duplication in flies requires the homo-oligomerisation of both Sas-6 and Ana2, and the Ana2 CCCD tetramer structure provides important information on how these proteins might cooperate to form a cartwheel structure. DOI: http://dx.doi.org/10.7554/eLife.07236.001 PMID:26002084

  20. Dual interaction of scaffold protein Tim44 of mitochondrial import motor with channel-forming translocase subunit Tim23

    PubMed Central

    Ting, See-Yeun; Yan, Nicholas L; Schilke, Brenda A; Craig, Elizabeth A

    2017-01-01

    Proteins destined for the mitochondrial matrix are targeted to the inner membrane Tim17/23 translocon by their presequences. Inward movement is driven by the matrix-localized, Hsp70-based motor. The scaffold Tim44, interacting with the matrix face of the translocon, recruits other motor subunits and binds incoming presequence. The basis of these interactions and their functional relationships remains unclear. Using site-specific in vivo crosslinking and genetic approaches in Saccharomyces cerevisiae, we found that both domains of Tim44 interact with the major matrix-exposed loop of Tim23, with the C-terminal domain (CTD) binding Tim17 as well. Results of in vitro experiments showed that the N-terminal domain (NTD) is intrinsically disordered and binds presequence near a region important for interaction with Hsp70 and Tim23. Our data suggest a model in which the CTD serves primarily to anchor Tim44 to the translocon, whereas the NTD is a dynamic arm, interacting with multiple components to drive efficient translocation. DOI: http://dx.doi.org/10.7554/eLife.23609.001 PMID:28440746

  1. Viruses are a dominant driver of protein adaptation in mammals

    PubMed Central

    Enard, David; Cai, Le; Gwennap, Carina; Petrov, Dmitri A

    2016-01-01

    Viruses interact with hundreds to thousands of proteins in mammals, yet adaptation against viruses has only been studied in a few proteins specialized in antiviral defense. Whether adaptation to viruses typically involves only specialized antiviral proteins or affects a broad array of virus-interacting proteins is unknown. Here, we analyze adaptation in ~1300 virus-interacting proteins manually curated from a set of 9900 proteins conserved in all sequenced mammalian genomes. We show that viruses (i) use the more evolutionarily constrained proteins within the cellular functions they interact with and that (ii) despite this high constraint, virus-interacting proteins account for a high proportion of all protein adaptation in humans and other mammals. Adaptation is elevated in virus-interacting proteins across all functional categories, including both immune and non-immune functions. We conservatively estimate that viruses have driven close to 30% of all adaptive amino acid changes in the part of the human proteome conserved within mammals. Our results suggest that viruses are one of the most dominant drivers of evolutionary change across mammalian and human proteomes. DOI: http://dx.doi.org/10.7554/eLife.12469.001 PMID:27187613

  2. Characterization of stacked-crystal PET detector designs for measurement of both TOF and DOI.

    PubMed

    Schmall, Jeffrey P; Surti, Suleman; Karp, Joel S

    2015-05-07

    A PET detector with good timing resolution and two-level depth-of-interaction (DOI) discrimination can be constructed using a single-ended readout of scintillator stacks of Lanthanum Bromide (LaBr3), with various Cerium dopant concentrations, including pure Cerium Bromide (CeBr3). The stacked crystal geometry creates a unique signal shape for interactions occurring in each layer, which can be used to identify the DOI, while retaining the inherently good timing properties of LaBr3 and CeBr3. In this work, single pixel elements are used to optimize the choice of scintillator, coupling of layers, and type of photodetector, evaluating the performance using a fast, single-channel photomultiplier tube (PMT) and a single 4 × 4 mm(2) silicon photomultiplier (SiPM). We also introduce a method to quantify and evaluate the DOI discrimination accuracy. From signal shape measurements using fast waveform sampling, we found that in addition to differences in signal rise times, between crystal layers, there were also differences in the signal fall times. A DOI accuracy of 98% was achieved using our classification method for a stacked crystal pair, consisting of a 15 mm long LaBr3(Ce:20%) crystal on top of a 15 mm long CeBr3 crystal, readout using a PMT. A DOI accuracy of 95% was measured with a stack of two, identical, 12 mm long, CeBr3 crystals. The DOI accuracy of this crystal pair was reduced to 91% when using a SiPM for readout. For the stack of two, 12 mm long, CeBr3 crystals, a coincidence timing resolution (average of timing results from the top and bottom layer) of 199 ps was measured using a PMT, and this was improved to 153 ps when using a SiPM. These results show that with stacked LaBr3/CeBr3 scintillators and fast waveform sampling nearly perfect DOI accuracy can be achieved with excellent timing resolution-timing resolution that is only minimally degraded compared to results from a single CeBr3 crystal of comparable length to the stacked crystals. The interface in the stacked crystal geometry itself plays a major role in creating the differences in signal shape and this can be used to construct stacked DOI detectors using the same scintillator type, thereby simplifying and broadening the application of this technique.

  3. Characterization of stacked-crystal PET detector designs for measurement of both TOF and DOI

    PubMed Central

    Schmall, Jeffrey P; Surti, Suleman; Karp, Joel S

    2015-01-01

    A PET detector with good timing resolution and two-level depth-of-interaction (DOI) discrimination can be constructed using a single-ended readout of scintillator stacks of Lanthanum Bromide (LaBr3), with various Cerium dopant concentrations, including pure Cerium Bromide (CeBr3). The stacked crystal geometry creates a unique signal shape for interactions occurring in each layer, which can be used to identify the DOI, while retaining the inherently good timing properties of LaBr3 and CeBr3. In this work, single pixel elements are used to optimize the choice of scintillator, coupling of layers, and type of photodetector, evaluating the performance using a fast, single-channel photomultiplier tube (PMT) and a single 4×4 mm2 silicon photomultiplier (SiPM). We also introduce a method to quantify and evaluate the DOI discrimination accuracy. From signal shape measurements using fast waveform sampling, we found that in addition to differences in signal rise times, between crystal layers, there were also differences in the signal fall times. A DOI accuracy of 98% was achieved using our classification method for a stacked crystal pair, consisting of a 15-mm long LaBr3(Ce:20%) crystal on top of a 15-mm long CeBr3 crystal, readout using a PMT. A DOI accuracy of 95% was measured with a stack of two, identical, 12-mm long, CeBr3 crystals. The DOI accuracy of this crystal pair was reduced to 91% when using a SiPM for readout. For the stack of two, 12-mm long, CeBr3 crystals, a coincidence timing resolution (average of timing results from the top and bottom layer) of 199 ps was measured using a PMT, and this was improved to 153 ps when using a SiPM. These results show that with stacked LaBr3/CeBr3 scintillators and fast waveform sampling nearly perfect DOI accuracy can be achieved with excellent timing resolution—timing resolution that is only minimally degraded compared to results from a single CeBr3 crystal of comparable length to the stacked crystals. The interface in the stacked crystal geometry itself plays a major role in creating the differences in signal shape and this can be used to construct stacked DOI detectors using the same scintillator type, thereby simplifying and broadening the application of this technique. PMID:25860172

  4. Digital Object Identifiers (DOI's) usage and adoption in U.S Geological Survey (USGS)

    NASA Astrophysics Data System (ADS)

    Frame, M. T.; Palanisamy, G.

    2013-12-01

    Addressing grand environmental science challenges requires unprecedented access to easily understood data that cross the breadth of temporal, spatial, and thematic scales. From a scientist's perspective, the big challenges lie in discovering the relevant data, dealing with extreme data heterogeneity, large data volumes, and converting data to information and knowledge. Historical linkages between derived products, i.e. Publications, and associated datasets has not existed in the earth science community. The USGS Core Science Analytics and Synthesis, in collaboration with DOE's Oak Ridge National Laboratory (ORNL) Mercury Consortium (funded by NASA, USGS and DOE), established a Digital Object Identifier (DOI) service for USGS data, metadata, and other media. This service is offered in partnership through the University of California Digital Library EZID service. USGS scientists, data managers, and other professionals can generate globally unique, persistent and resolvable identifiers for any kind of digital objects. Additional efforts to assign DOIs to historical data and publications have also been underway. These DOI identifiers are being used to cite data in journal articles, web-accessible datasets, and other media for distribution, integration, and in support of improved data management practices. The session will discuss the current DOI efforts within USGS, including a discussion on adoption, challenges, and future efforts necessary to improve access, reuse, sharing, and discoverability of USGS data and information.

  5. Use of internal scintillator radioactivity to calibrate DOI function of a PET detector with a dual-ended-scintillator readout

    PubMed Central

    Bircher, Chad; Shao, Yiping

    2012-01-01

    Purpose: Positron emission tomography (PET) detectors that use a dual-ended-scintillator readout to measure depth-of-interaction (DOI) must have an accurate DOI function to provide the relationship between DOI and signal ratios to be used for detector calibration and recalibration. In a previous study, the authors used a novel and simple method to accurately and quickly measure DOI function by irradiating the detector with an external uniform flood source; however, as a practical concern, implementing external uniform flood sources in an assembled PET system is technically challenging and expensive. In the current study, therefore, the authors investigated whether the same method could be used to acquire DOI function from scintillator-generated (i.e., internal) radiation. The authors also developed a method for calibrating the energy scale necessary to select the events within the desired energy window. Methods: The authors measured the DOI function of a PET detector with lutetium yttrium orthosilicate (LYSO) scintillators. Radiation events originating from the scintillators’ internal Lu-176 beta decay were used to measure DOI functions which were then compared with those measured from both an external uniform flood source and an electronically collimated external point source. The authors conducted these studies with several scintillators of differing geometries (1.5 × 1.5 and 2.0 × 2.0 mm2 cross-section area and 20, 30, and 40 mm length) and various surface finishes (mirror-finishing, saw-cut rough, and other finishes in between), and in a prototype array. Results: All measured results using internal and external radiation sources showed excellent agreement in DOI function measurement. The mean difference among DOI values for all scintillators measured from internal and external radiation sources was less than 1.0 mm for different scintillator geometries and various surface finishes. Conclusions: The internal radioactivity of LYSO scintillators can be used to accurately measure DOI function in PET detectors, regardless of scintillator geometry or surface finish. Because an external radiation source is not needed, this method of DOI function measurement can be practically applied to individual PET detectors as well as assembled systems. PMID:22320787

  6. Use of internal scintillator radioactivity to calibrate DOI function of a PET detector with a dual-ended-scintillator readout.

    PubMed

    Bircher, Chad; Shao, Yiping

    2012-02-01

    Positron emission tomography (PET) detectors that use a dual-ended-scintillator readout to measure depth-of-interaction (DOI) must have an accurate DOI function to provide the relationship between DOI and signal ratios to be used for detector calibration and recalibration. In a previous study, the authors used a novel and simple method to accurately and quickly measure DOI function by irradiating the detector with an external uniform flood source; however, as a practical concern, implementing external uniform flood sources in an assembled PET system is technically challenging and expensive. In the current study, therefore, the authors investigated whether the same method could be used to acquire DOI function from scintillator-generated (i.e., internal) radiation. The authors also developed a method for calibrating the energy scale necessary to select the events within the desired energy window. The authors measured the DOI function of a PET detector with lutetium yttrium orthosilicate (LYSO) scintillators. Radiation events originating from the scintillators' internal Lu-176 beta decay were used to measure DOI functions which were then compared with those measured from both an external uniform flood source and an electronically collimated external point source. The authors conducted these studies with several scintillators of differing geometries (1.5 × 1.5 and 2.0 × 2.0 mm(2) cross-section area and 20, 30, and 40 mm length) and various surface finishes (mirror-finishing, saw-cut rough, and other finishes in between), and in a prototype array. All measured results using internal and external radiation sources showed excellent agreement in DOI function measurement. The mean difference among DOI values for all scintillators measured from internal and external radiation sources was less than 1.0 mm for different scintillator geometries and various surface finishes. The internal radioactivity of LYSO scintillators can be used to accurately measure DOI function in PET detectors, regardless of scintillator geometry or surface finish. Because an external radiation source is not needed, this method of DOI function measurement can be practically applied to individual PET detectors as well as assembled systems.

  7. Use of internal scintillator radioactivity to calibrate DOI function of a PET detector with a dual-ended-scintillator readout

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

    Bircher, Chad; Shao Yiping

    Purpose: Positron emission tomography (PET) detectors that use a dual-ended-scintillator readout to measure depth-of-interaction (DOI) must have an accurate DOI function to provide the relationship between DOI and signal ratios to be used for detector calibration and recalibration. In a previous study, the authors used a novel and simple method to accurately and quickly measure DOI function by irradiating the detector with an external uniform flood source; however, as a practical concern, implementing external uniform flood sources in an assembled PET system is technically challenging and expensive. In the current study, therefore, the authors investigated whether the same method couldmore » be used to acquire DOI function from scintillator-generated (i.e., internal) radiation. The authors also developed a method for calibrating the energy scale necessary to select the events within the desired energy window. Methods: The authors measured the DOI function of a PET detector with lutetium yttrium orthosilicate (LYSO) scintillators. Radiation events originating from the scintillators' internal Lu-176 beta decay were used to measure DOI functions which were then compared with those measured from both an external uniform flood source and an electronically collimated external point source. The authors conducted these studies with several scintillators of differing geometries (1.5 x 1.5 and 2.0 x 2.0 mm{sup 2} cross-section area and 20, 30, and 40 mm length) and various surface finishes (mirror-finishing, saw-cut rough, and other finishes in between), and in a prototype array. Results: All measured results using internal and external radiation sources showed excellent agreement in DOI function measurement. The mean difference among DOI values for all scintillators measured from internal and external radiation sources was less than 1.0 mm for different scintillator geometries and various surface finishes. Conclusions: The internal radioactivity of LYSO scintillators can be used to accurately measure DOI function in PET detectors, regardless of scintillator geometry or surface finish. Because an external radiation source is not needed, this method of DOI function measurement can be practically applied to individual PET detectors as well as assembled systems.« less

  8. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

    PubMed Central

    Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

    2016-01-01

    Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

  9. A hierarchy of timescales explains distinct effects of local inhibition of primary visual cortex and frontal eye fields

    PubMed Central

    Cocchi, Luca; Sale, Martin V; L Gollo, Leonardo; Bell, Peter T; Nguyen, Vinh T; Zalesky, Andrew; Breakspear, Michael; Mattingley, Jason B

    2016-01-01

    Within the primate visual system, areas at lower levels of the cortical hierarchy process basic visual features, whereas those at higher levels, such as the frontal eye fields (FEF), are thought to modulate sensory processes via feedback connections. Despite these functional exchanges during perception, there is little shared activity between early and late visual regions at rest. How interactions emerge between regions encompassing distinct levels of the visual hierarchy remains unknown. Here we combined neuroimaging, non-invasive cortical stimulation and computational modelling to characterize changes in functional interactions across widespread neural networks before and after local inhibition of primary visual cortex or FEF. We found that stimulation of early visual cortex selectively increased feedforward interactions with FEF and extrastriate visual areas, whereas identical stimulation of the FEF decreased feedback interactions with early visual areas. Computational modelling suggests that these opposing effects reflect a fast-slow timescale hierarchy from sensory to association areas. DOI: http://dx.doi.org/10.7554/eLife.15252.001 PMID:27596931

  10. Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity

    PubMed Central

    Bhattacharyya, Sanchari; Bershtein, Shimon; Yan, Jin; Argun, Tijda; Gilson, Amy I; Trauger, Sunia A; Shakhnovich, Eugene I

    2016-01-01

    Gene dosage toxicity (GDT) is an important factor that determines optimal levels of protein abundances, yet its molecular underpinnings remain unknown. Here, we demonstrate that overexpression of DHFR in E. coli causes a toxic metabolic imbalance triggered by interactions with several functionally related enzymes. Though deleterious in the overexpression regime, surprisingly, these interactions are beneficial at physiological concentrations, implying their functional significance in vivo. Moreover, we found that overexpression of orthologous DHFR proteins had minimal effect on all levels of cellular organization – molecular, systems, and phenotypic, in sharp contrast to E. coli DHFR. Dramatic difference of GDT between ‘E. coli’s self’ and ‘foreign’ proteins suggests the crucial role of evolutionary selection in shaping protein-protein interaction (PPI) networks at the whole proteome level. This study shows how protein overexpression perturbs a dynamic metabolon of weak yet potentially functional PPI, with consequences for the metabolic state of cells and their fitness. DOI: http://dx.doi.org/10.7554/eLife.20309.001 PMID:27938662

  11. Meiosis I chromosome segregation is established through regulation of microtubule–kinetochore interactions

    PubMed Central

    Miller, Matthew P; Ünal, Elçin; Brar, Gloria A; Amon, Angelika

    2012-01-01

    During meiosis, a single round of DNA replication is followed by two consecutive rounds of nuclear divisions called meiosis I and meiosis II. In meiosis I, homologous chromosomes segregate, while sister chromatids remain together. Determining how this unusual chromosome segregation behavior is established is central to understanding germ cell development. Here we show that preventing microtubule–kinetochore interactions during premeiotic S phase and prophase I is essential for establishing the meiosis I chromosome segregation pattern. Premature interactions of kinetochores with microtubules transform meiosis I into a mitosis-like division by disrupting two key meiosis I events: coorientation of sister kinetochores and protection of centromeric cohesin removal from chromosomes. Furthermore we find that restricting outer kinetochore assembly contributes to preventing premature engagement of microtubules with kinetochores. We propose that inhibition of microtubule–kinetochore interactions during premeiotic S phase and prophase I is central to establishing the unique meiosis I chromosome segregation pattern. DOI: http://dx.doi.org/10.7554/eLife.00117.001 PMID:23275833

  12. An internal thioester in a pathogen surface protein mediates covalent host binding

    PubMed Central

    Walden, Miriam; Edwards, John M; Dziewulska, Aleksandra M; Bergmann, Rene; Saalbach, Gerhard; Kan, Su-Yin; Miller, Ona K; Weckener, Miriam; Jackson, Rosemary J; Shirran, Sally L; Botting, Catherine H; Florence, Gordon J; Rohde, Manfred; Banfield, Mark J; Schwarz-Linek, Ulrich

    2015-01-01

    To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a ‘chemical harpoon’. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. DOI: http://dx.doi.org/10.7554/eLife.06638.001 PMID:26032562

  13. 77 FR 19307 - Renewal of Information Collection; OMB Control Number 1040-0001, DOI Programmatic Clearance for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-30

    ... Number 1040-0001, DOI Programmatic Clearance for Customer Satisfaction Surveys AGENCY: Department of the... Customer Satisfaction Surveys'' in your email subject line. Include your name and return address in your... accountability by promoting a new focus on results, service quality, and customer satisfaction.'' In order to...

  14. Streptomyces exploration is triggered by fungal interactions and volatile signals

    PubMed Central

    Jones, Stephanie E; Ho, Louis; Rees, Christiaan A; Hill, Jane E; Nodwell, Justin R; Elliot, Marie A

    2017-01-01

    It has long been thought that the life cycle of Streptomyces bacteria encompasses three developmental stages: vegetative hyphae, aerial hyphae and spores. Here, we show interactions between Streptomyces and fungi trigger a previously unobserved mode of Streptomyces development. We term these Streptomyces cells ‘explorers’, for their ability to adopt a non-branching vegetative hyphal conformation and rapidly transverse solid surfaces. Fungi trigger Streptomyces exploratory growth in part by altering the composition of the growth medium, and Streptomyces explorer cells can communicate this exploratory behaviour to other physically separated streptomycetes using an airborne volatile organic compound (VOC). These results reveal that interkingdom interactions can trigger novel developmental behaviours in bacteria, here, causing Streptomyces to deviate from its classically-defined life cycle. Furthermore, this work provides evidence that VOCs can act as long-range communication signals capable of propagating microbial morphological switches. DOI: http://dx.doi.org/10.7554/eLife.21738.001 PMID:28044982

  15. The hallucinogen DOI reduces low-frequency oscillations in rat prefrontal cortex: reversal by antipsychotic drugs.

    PubMed

    Celada, Pau; Puig, M Victoria; Díaz-Mataix, Llorenç; Artigas, Francesc

    2008-09-01

    Perceptual and psychic alterations and thought disorder are fundamental elements of schizophrenia symptoms, a pathology associated with an abnormal macro- and microcircuitry of several brain areas including the prefrontal cortex (PFC). Alterations in information processing in PFC may partly underlie schizophrenia symptoms. The 5-HT(2A/2C) agonist DOI and antipsychotic drugs were administered to anesthetized rats. Single unit and local field potential (LFP) extracellular recordings were made in medial PFC (mPFC). Electrolytic lesions were performed in the thalamic nuclei. DOI markedly disrupts cellular and network activity in rat PFC. DOI altered pyramidal discharge in mPFC (39% excited, 27% inhibited, 34% unaffected; n = 51). In all instances, DOI concurrently reduced low-frequency oscillations (.3-4 Hz; power spectrum: .25 +/- .02 and .14 +/- .01 microV(2) in basal conditions and after 50-300 microg/kg intravenous (i.v.) DOI, respectively; n = 51). Moreover, DOI disrupted the temporal association between the active phase of LFP and pyramidal discharge. Both effects were reversed by M100907 (5-HT(2A) receptor antagonist) and were not attenuated by thalamic lesions, supporting an intracortical origin of the effects of DOI. The reduction in low-frequency oscillations induced by DOI was significantly reversed by the antipsychotic drugs haloperidol (.1-.2 mg/kg i.v.) and clozapine (1 mg/kg i.v.). DOI disorganizes network activity in PFC, reducing low-frequency oscillations and desynchronizing pyramidal discharge from active phases of LFP. These effects may underlie DOI's psychotomimetic action. The reversal by clozapine and haloperidol indicates that antipsychotic drugs may reduce psychotic symptoms by normalizing an altered PFC function.

  16. Host-guest interaction induced supramolecular amphiphilic star architecture and uniform nanovesicle formation for anticancer drug delivery

    NASA Astrophysics Data System (ADS)

    Zhu, Jing-Ling; Liu, Kerh Li; Wen, Yuting; Song, Xia; Li, Jun

    2016-01-01

    A star polymer of poly[(R,S)-3-hydroxybutyrate] (PHB) with adamantyl end-terminals extended from an α-cyclodextrin (α-CD) core is designed. It subsequently self-assembles to form controllable and uniform nanovesicles induced by host-guest interactions between heptakis(2,6-di-O-methyl)-β-CD and the adamantyl ends. The nanovesicles are suitable for loading and intracellular delivery of the anticancer drug doxorubicin.A star polymer of poly[(R,S)-3-hydroxybutyrate] (PHB) with adamantyl end-terminals extended from an α-cyclodextrin (α-CD) core is designed. It subsequently self-assembles to form controllable and uniform nanovesicles induced by host-guest interactions between heptakis(2,6-di-O-methyl)-β-CD and the adamantyl ends. The nanovesicles are suitable for loading and intracellular delivery of the anticancer drug doxorubicin. Electronic supplementary information (ESI) available: Polymer synthesis, characterization, preparation of drug-loaded nanovesicles, intracellular drug release and cytotoxicity assays, TEM and DLS measurements. See DOI: 10.1039/c5nr06744h

  17. Interaction of nanoparticles with lipid membranes: a multiscale perspective

    NASA Astrophysics Data System (ADS)

    Montis, Costanza; Maiolo, Daniele; Alessandri, Ivano; Bergese, Paolo; Berti, Debora

    2014-05-01

    Freestanding lipid bilayers were challenged with 15 nm Au nanospheres either coated by a citrate layer or passivated by a protein corona. The effect of Au nanospheres on the bilayer morphology, permeability and fluidity presents strong differences or similarities, depending on the observation length scale, from the colloidal to the molecular domains. These findings suggest that the interaction between nanoparticles and lipid membranes should be conveniently treated as a multiscale phenomenon.Freestanding lipid bilayers were challenged with 15 nm Au nanospheres either coated by a citrate layer or passivated by a protein corona. The effect of Au nanospheres on the bilayer morphology, permeability and fluidity presents strong differences or similarities, depending on the observation length scale, from the colloidal to the molecular domains. These findings suggest that the interaction between nanoparticles and lipid membranes should be conveniently treated as a multiscale phenomenon. Electronic supplementary information (ESI) available: All the experimental details, figures and tables. See DOI: 10.1039/c4nr00838c

  18. Societal Interactions in Ovarian Cancer Metastases: A Quorum Sensing Hypothesis

    DTIC Science & Technology

    2007-11-01

    subsequent studies we found that the density of the cells in culture at the time of harvest for injection did have a significant effect on their...VJ (2003) From motility to virulence: sensing and responding to environmental signals in Vibrio chol- erae. Curr Opin Microbiol 6:186–190. doi:10.1016...of luminescence in Vibrio har- veyi: sequence and function of genes encoding a second sensory pathway. Mol Microbiol 13:273–286. doi:10.1111/j.1365

  19. Basic performance evaluation of a Si-PM array-based LGSO phoswich DOI block detector for a high-resolution small animal PET system.

    PubMed

    Yamamoto, Seiichi

    2013-07-01

    The silicon photomultiplier (Si-PM) is a promising photodetector for PET. However, it remains unclear whether Si-PM can be used for a depth-of-interaction (DOI) detector based on the decay time differences of the scintillator where pulse shape analysis is used. For clarification, we tested the Hamamatsu 4 × 4 Si-PM array (S11065-025P) combined with scintillators that used different decay times to develop DOI block detectors using the pulse shape analysis. First, Ce-doped Gd(2)SiO(5) (GSO) scintillators of 0.5 mol% Ce were arranged in a 4 × 4 matrix and were optically coupled to the center of each pixel of the Si-PM array for measurement of the energy resolution as well as its gain variations according to the temperature. Then two types of Ce-doped Lu(1.9)Gd(0.1)Si0(5) (LGSO) scintillators, 0.025 mol% Ce (decay time: ~31 ns) and 0.75 mol% Ce (decay time: ~46 ns), were optically coupled in the DOI direction, arranged in a 11 × 7 matrix, and optically coupled to a Si-PM array for testing of the possibility of a high-resolution DOI detector. The energy resolution of the Si-PM array-based GSO block detector was 18 ± 4.4 % FWHM for a Cs-137 gamma source (662 keV). Less than 1 mm crystals were clearly resolved in the position map of the LGSO DOI block detector. The peak-to-valley ratio (P/V) derived from the pulse shape spectra of the LGSO DOI block detector was 2.2. These results confirmed that Si-PM array-based DOI block detectors are promising for high-resolution small animal PET systems.

  20. Data publication and dissemination of interactive keys under the open access model

    USDA-ARS?s Scientific Manuscript database

    The concepts of publication, citation and dissemination of interactive keys and other online keys are discussed and illustrated by a sample paper published in the present issue (doi: 10.3897/zookeys.21.271). The present model is based on previous experience with several existing examples of publishi...

  1. Publications - DDS 8 | Alaska Division of Geological & Geophysical Surveys

    Science.gov Websites

    DGGS DDS 8 Publication Details Title: Alaska Volcano Observatory geochemical database Authors: Cameron ., Snedigar, S.F., and Nye, C.J., 2014, Alaska Volcano Observatory geochemical database: Alaska Division of ://doi.org/10.14509/29120 Publication Products Interactive Interactive Database Alaska Volcano Observatory

  2. Molecular interactions between single layered MoS2 and biological molecules† †Electronic supplementary information (ESI) available: SFG data analysis methods, spectral fitting parameters, additional spectra, CD spectrum, and details about MD simulation methods. See DOI: 10.1039/c7sc04884j

    PubMed Central

    Xiao, Minyu; Wei, Shuai; Li, Yaoxin; Jasensky, Joshua; Chen, Junjie; Brooks, Charles L.

    2017-01-01

    Two-dimensional (2D) materials such as graphene, molybdenum disulfide (MoS2), tungsten diselenide (WSe2), and black phosphorous are being developed for sensing applications with excellent selectivity and high sensitivity. In such applications, 2D materials extensively interact with various analytes including biological molecules. Understanding the interfacial molecular interactions of 2D materials with various targets becomes increasingly important for the progression of better-performing 2D-material based sensors. In this research, molecular interactions between several de novo designed alpha-helical peptides and monolayer MoS2 have been studied. Molecular dynamics simulations were used to validate experimental data. The results suggest that, in contrast to peptide–graphene interactions, peptide aromatic residues do not interact strongly with the MoS2 surface. It is also found that charged amino acids are important for ensuring a standing-up pose for peptides interacting with MoS2. By performing site-specific mutations on the peptide, we could mediate the peptide–MoS2 interactions to control the peptide orientation on MoS2. PMID:29675220

  3. Wikipedia as a gateway to biomedical research: The relative distribution and use of citations in the English Wikipedia.

    PubMed

    Maggio, Lauren A; Willinsky, John M; Steinberg, Ryan M; Mietchen, Daniel; Wass, Joseph L; Dong, Ting

    2017-01-01

    Wikipedia is a gateway to knowledge. However, the extent to which this gateway ends at Wikipedia or continues via supporting citations is unknown. Wikipedia's gateway functionality has implications for information design and education, notably in medicine. This study aims to establish benchmarks for the relative distribution and referral (click) rate of citations-as indicated by presence of a Digital Object Identifier (DOI)-from Wikipedia, with a focus on medical citations. DOIs referred from the English Wikipedia in August 2016 were obtained from Crossref.org. Next, based on a DOI's presence on a WikiProject Medicine page, all DOIs in Wikipedia were categorized as medical (WP:MED) or non-medical (non-WP:MED). Using this categorization, referred DOIs were classified as WP:MED, non-WP:MED, or BOTH, meaning the DOI may have been referred from either category. Data were analyzed using descriptive and inferential statistics. Out of 5.2 million Wikipedia pages, 4.42% (n = 229,857) included at least one DOI. 68,870 were identified as WP:MED, with 22.14% (n = 15,250) featuring one or more DOIs. WP:MED pages featured on average 8.88 DOI citations per page, whereas non-WP:MED pages had on average 4.28 DOI citations. For DOIs only on WP:MED pages, a DOI was referred every 2,283 pageviews and for non-WP:MED pages every 2,467 pageviews. DOIs from BOTH pages accounted for 12% (n = 58,475). The referral of DOI citations found in BOTH could not be assigned to WP:MED or non-WP:MED, as the page from which the referral was made was not provided with the data. While these results cannot provide evidence of greater citation referral from WP:MED than non-WP:MED, they do provide benchmarks to assess strategies for changing referral patterns. These changes might include editors adopting new methods for designing and presenting citations or the introduction of teaching strategies that address the value of consulting citations as a tool for extending learning.

  4. Digital Object Identifiers for NASA's Earth Observing System Products

    NASA Astrophysics Data System (ADS)

    Moses, J. F.; James, N.

    2012-12-01

    The science community has long recognized the importance of citing data in published literature to encourage replication of experiments and verification of results. Authors that try to cite their data often find that publishers will not accept Internet addresses because they are viewed as transient references, frequently changed by the data provider after the paper is published. Digital Object Identifiers (DOIs) and the DOI® System were created to avoid this problem by providing a unique and persistent identifier scheme and an online resolution service. DOIs and the Internet service provided by the DOI System have emerged as the most acceptable scheme for publishers. NASA's Earth Science Data and Information System (ESDIS) Project, in cooperation with several Earth Observing System (EOS) instrument teams and data providers, has developed methods for assigning DOIs to EOS products. By assigning DOIs we are enabling authors and publishers to find it easier and more compelling to cite EOS data products. DOIs are unique alphanumeric strings that consist of a prefix and suffix. The prefix is assigned by a registration agency for the DOI System. The suffix must be unique, but is otherwise free to be constructed by the publisher, in this case NASA ESDIS Project. A strategy was needed for constructing DOI suffix names that corresponds to each EOS product. Since the onset of the DOI System, publishers have developed conventions to suit their own purposes. These range from random generation to complex, formally controlled vocabularies. An overarching ESDIS goal has been for the DOI names to be attractive for researchers to use in publication applications. Keeping them short and simple is paramount. When adding meaning to the string, it is also important that the name only refer to the data and not to the publisher, so that the DOI can be accepted as persistent even if the data is moved to a new publisher. Most users download EOS product files to their local facilities when they want to use the data for analysis or applications. By imbedding DOIs in the file metadata, users have access to the DOI value long after the product has left the source data center. This enables users to find documentation about the product in the future - long after it has left the contextual environment of the data provider. Existing HDF and netCDF metadata structures have been adapted to accommodate the addition of DOIs. In addition, associated EOSDIS core metadata will also contain a product specific attribute for DOIs. Advances in computer science and Internet brought about a host of data identification schemes designed to solve problems inherent in developing advanced provenance models. Lessons from trying to use early satellite observations in climate studies today point to the importance of providing links in data archives to documentation and publications about the data. Data system engineers link data records to standard product documentation prepared at the time of the mission and archive with the data, but will need to add links to the whole range of information needed to support future research and long-term climate studies. DOIs can serve this need if referenced by developers when preparing technical data and reports, as well as when publishing research results.

  5. "Where did my data layer come from?" The semantics of data release

    NASA Astrophysics Data System (ADS)

    Leadbetter, Adam; Buck, Justin

    2015-04-01

    In his lecture, "Theory of Creative Fitting" (Margullis, Corner & Holt, 2006), Ian McHarg introduced his vision for cross-disciplinary data and information sharing networks with the end goal of producing detailed overlay maps for the purposes of ecological architectural planning. Within McHarg's networks, experts in various fields, such as hydrology or surface geology, would provide data layers to the final overlay map with full provenance, such that the users of the overlay maps would know the originator of the data, the "value systems" by which the data were created and could place their trust in the outcomes. In the light of McHarg's statements and in order to allow the encoding of value systems in a cyber-GIS, analyses of: data quality (Giarlo, 2013); data publication networks (Reinsfelder, 2012); trust in collaborative research networks (Leadbetter, 2015); and the metaphors of data publication, data release and data ecosystems (Parsons & Fox, 2013) have been synthesised into a logical model of the data release lifecycle. This model concerns the actors in the data release process; the data-information-knowledge ecosystem through the various stages of the data release process and the impact of data release on perceptions of trust through the data release lifecycle. The data-information-knowledge ecosystem described how the collection of data can be presented in new ways to form information products, and how these information products can inform conversations amongst information-consumers who integrate the information into new knowledge. The actors concerned in the process comprise: researchers data publishers academic publishers & academic administrators Finally, the lifecycle of data release involves the initial release of a data-layer, possibly with a Persistent Identifier (PID) more generic than a Digital Object Identifier (DOI). A data description paper can be written about the dataset, which then necessitates the assignment of a DOI to the datasets; the DOI can be seen as an indicator of trust through "benevolence". A technical document citing the dataset may then be informed by the dataset release or the dataset description paper. These citations may show the "competence" (in terms of a trust model) of the original datasets, and the dataset description papers or other technical articles show the integrity of the dataset. The synthesised logical model has been represented in freely available ontologies, such that data layers can be annotated with metadata about their provenance and stage within the data release lifecycle before incorporation into a cyber-GIS, in which distributed data providers provide for a collaborative research environment. References Giarlo, M. (2013). Academic libraries as data quality hubs. Journal of Librarianship and Scholarly Communication 1(3): eP1059. doi: 10.7710/2162-3309.1059 Leadbetter, A. (2015). Examining trust in collaborative research networks. In P. Diviacco, P. Fox, C. Pshenichny, and A. Leadbetter (Eds.) Collaborative Knowledge in Scientific Research Networks, Hershey, PA: IGI Global. doi: 10.4018/978-1-4666-6567-5.ch002 Margulis, L., Corner, J. and Hawthorne, B. (Editors), 2006. Ian McHarg: conversations with students. Dwelling with nature. New York, NY: Princeton Architectural Press. Parsons, M., and Fox, P. (2013). Is data publication the right metaphor? Data Science Journal 12, 32-46. doi:10.2481/dsj.WDS-042 Reinsfelder, T. (2012). Open access publishing practices in a complex environment: conditions, barriers and bases of power. Journal of Librarianship and Scholarly Communication 1(1): eP1029. doi: 10.7710/2162-3309.1029

  6. Validation of the EORTC QLQ-INFO 25 questionnaire in Lebanese cancer patients: Is ignorance a Bliss?

    PubMed

    Tabchi, Samer; El Rassy, Elie; Khazaka, Aline; El Karak, Fadi; Kourie, Hampig Raphael; Chebib, Ralph; Assi, Tarek; Ghor, Maya; Naamani, Lara; Richa, Sami; Ghosn, Marwan; Kattan, Joseph

    2016-06-01

    Despite worldwide trends toward optimizing full disclosure of information (DOI), the prevailing belief that cancer diagnosis should be concealed from patients, for their own good, has endured for a substantial period of time in Middle Eastern communities. This study would assess the reliability of the Arabic translated version of the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-INFO 25). The study was also designed to quantify DOI to Lebanese cancer patients and determine patient satisfaction with this DOI. Moreover, we compared the differences in the level of information among groups based on clinical and biographical variables. A sample of patients, being treated for a variety of malignancies, was prospectively evaluated. A physician interviewed patients using the Arabic version of the EORTC QLQ-INFO 25, on the day of hospitalization for chemotherapy, before treatment was administered. In total 201 patients were interviewed. The translated version of the EORTC QLQ-INFO 25 showed high reliability when assessed using Cronbach's alpha coefficients for internal consistency with values scoring higher than 0.7 for all scales and the full questionnaire. There was a considerable lack of information provided to the participants with 38.8 % being unaware of their diagnosis and more than half being uninformed about the extent of their disease. Paradoxically, 86.5 % of patients expressed their satisfaction about the amount of information they received and 89.5 % believe the information provided was helpful. Further analysis showed no significant association between gender, marital status, cancer site and stage and the amount of information received. However, age and level of education were associated with DOI such as younger and more educated patients received more information. Older patients were also found to be the most satisfied with the information they received, despite having less access to information. Although a high proportion of patients were not properly informed about their diagnosis, the overwhelming majority were satisfied with the amount of information they received and believed it was useful, reflecting the complexity of Middle Eastern cultural influences on cancer patients' perspectives.

  7. Functionalized graphene nanomaterials: new insight into direct exfoliation of graphite with supramolecular polymers

    NASA Astrophysics Data System (ADS)

    Cheng, Chih-Chia; Chang, Feng-Chih; Wang, Jui-Hsu; Chen, Jem-Kun; Yen, Ying-Chieh; Lee, Duu-Jong

    2015-12-01

    A novel urea-cytosine end-capped polypropylene glycol (UrCy-PPG) can self-assemble into a long-range ordered lamellar microstructure on the surface of graphene, due to the strong specific interactions between UrCy-PPG and graphene. In addition, the graphene composite produced exhibits a high conductivity (~1093 S m-1) with a dramatic thermo-responsive ON/OFF resistance-switching behavior (10 consecutive cycles).A novel urea-cytosine end-capped polypropylene glycol (UrCy-PPG) can self-assemble into a long-range ordered lamellar microstructure on the surface of graphene, due to the strong specific interactions between UrCy-PPG and graphene. In addition, the graphene composite produced exhibits a high conductivity (~1093 S m-1) with a dramatic thermo-responsive ON/OFF resistance-switching behavior (10 consecutive cycles). Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr07076g

  8. A new compilation of stomach content data for commercially-important pelagic fish species in the Northeast Atlantic

    NASA Astrophysics Data System (ADS)

    Pinnegar, J. K.; Goñi, N.; Trenkel, V. M.; Arrizabalaga, H.; Melle, W.; Keating, J.; Óskarsson, G.

    2014-04-01

    There is increasing demand for information on predator-prey interactions in the ocean as a result of legislative commitments aimed at achieving sustainable exploitation. However, comprehensive datasets are lacking for many fish species and this has hampered development of multispecies fisheries models and the formulation of effective food-web indicators. This work describes a new compilation of stomach content data for five pelagic fish species (herring, blue whiting, mackerel, albacore and bluefin tuna) sampled across the northeast Atlantic and submitted to the PANGAEA open-access data portal (www.pangaea.de). We provide detailed descriptions of sample origin and of the corresponding database structures. We describe the main results in terms of diet composition and predator-prey relationships. The feeding preferences of small pelagic fish (herring, blue whiting, mackerel) were sampled over a very broad geographic area within the North Atlantic basin, from Greenland in the west, to the Lofoten Islands in the east and from the Bay of Biscay northwards to the Arctic. This analysis revealed significant differences in the prey items selected in different parts of the region at different times of year. Tunas (albacore and bluefin) were sampled in the Bay of Biscay and Celtic Sea. Dominant prey items for these species varied by location, year and season. This data compilation exercise represents one of the largest and most wide-ranging ever attempted for pelagic fish in the north Atlantic. The earliest data included in the database were collected in 1864, whereas the most recent were collected in 2012.Datasets are available at doi:10.1594/PANGAEA.820041 and doi:10.1594/PANGAEA.826992.

  9. A new compilation of stomach content data for commercially important pelagic fish species in the northeast Atlantic

    NASA Astrophysics Data System (ADS)

    Pinnegar, J. K.; Goñi, N.; Trenkel, V. M.; Arrizabalaga, H.; Melle, W.; Keating, J.; Óskarsson, G.

    2015-02-01

    There is increasing demand for information on predator-prey interactions in the ocean as a result of legislative commitments aimed at achieving sustainable exploitation. However, comprehensive data sets are lacking for many fish species and this has hampered development of multispecies fisheries models and the formulation of effective food-web indicators. This work describes a new compilation of stomach content data for five pelagic fish species (herring, blue whiting, mackerel, albacore and bluefin tuna) sampled across the northeast Atlantic and submitted to the PANGAEA open-access data portal (www.pangaea.de). We provide detailed descriptions of sample origin and of the corresponding database structures. We describe the main results in terms of diet composition and predator-prey relationships. The feeding preferences of small pelagic fish (herring, blue whiting, mackerel) were sampled over a very broad geographic area within the North Atlantic basin, from Greenland in the west, to the Lofoten Islands in the east and from the Bay of Biscay northwards to the Arctic. This analysis revealed significant differences in the prey items selected in different parts of the region at different times of year. Tunas (albacore and bluefin) were sampled in the Bay of Biscay and Celtic Sea. Dominant prey items for these species varied by location, year and season. This data compilation exercise represents one of the largest and most wide-ranging ever attempted for pelagic fish in the North Atlantic. The earliest data included in the database were collected in 1864, whereas the most recent were collected in 2012. Data sets are available at doi:10.1594/PANGAEA.820041 and doi:10.1594/PANGAEA.826992.

  10. Highly improved operation of monolithic BGO-PET blocks

    NASA Astrophysics Data System (ADS)

    Gonzalez-Montoro, A.; Sanchez, F.; Majewski, S.; Zanettini, S.; Benlloch, J. M.; Gonzalez, A. J.

    2017-11-01

    In PET scanners both scintillation crystals and photosensors are key components defining the system's performance and cost. Original PET systems used BGO or NaI(Tl) scintillators but achieved limited performance due to its slow decay and relatively low light output. Moreover, NaI(Tl) has low stopping power for 511 keV annihilation photons. In this study we report the possibility to reintroduce BGO crystals, and in particular in the form of monolithic blocks, especially suitable for low-dose large-size PET scanners, offering significantly improved sensitivity at a highly reduced cost compared to LYSO type fast scintillators. We have studied the performance of a monolithic BGO block as large as 50 × 50 × 15 mm3 with black-painted lateral walls to reduce lights spread, enabling accurate photon depth of interaction (DOI) measurements. A directional optical layer, called retro-reflector, was coupled to the entrance face bouncing back the scintillation light in the direction of the emission source and, therefore, adding to the light signal while preserving the narrow light cone distribution. Four configurations namely 12 × 12 and 16 × 16 SiPM arrays (3 mm × 3 mm each) as photosensors, with or without a nanopattern treatment at the crystal exit face, have been studied. This structure consisted of a thin layer of a specific high refractive index material shaped with a periodic nanopattern, increasing the scintillation light extraction. The readout returned information for each SiPM row and column, characterizing the X-Y light distribution projections. We have studied the detector spatial resolution using collimated 22Na sources at normal incidence. The DOI resolution was evaluated using collimated gamma beams with lateral incidence. The overall best detector performance was obtained for the 16× 16 SiPM array offering higher readout granularity. We have determined the spatial resolution for 3 separated DOI layers, obtaining the best results for the DOI region near to the photosensor.

  11. Pharmacological modulation of abnormal involuntary DOI-induced head twitch response in male DBA/2J mice: I. Effects of D2/D3 and D2 dopamine receptor selective compounds.

    PubMed

    Rangel-Barajas, Claudia; Malik, Maninder; Vangveravong, Suwanna; Mach, Robert H; Luedtke, Robert R

    2014-08-01

    Because of the complexity and heterogeneity of human neuropsychiatric disorders, it has been difficult to identify animal models that mimic the symptoms of these neuropathologies and can be used to screen for antipsychotic agents. For this study we selected the murine 5HT2A/2C receptor agonist-induced head twitch response (HTR) induced by the administration of 1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane (DOI), which has been proposed as an animal model of symptoms associated with a variety of behavioral and psychiatric conditions. We investigated the DOI-induced HTR in male DBA/2J mice using a panel of D2-like (D2, D3 and D4) and D2 dopamine receptor selective compounds. When DBA/2J mice were administered a daily dose of DOI (5 mg/kg), tolerance to the DOI occurs. However, administrations of the same dose of DOI every other day (48 h) or on a weekly basis did not lead to tolerance and the ability to induce tolerance after daily administration of DOI remains intact after repeated weekly administration of DOI. Subsequently, a panel of D2-like dopamine receptor antagonists was found to effectively inhibit the DOI-induced HTR in DBA/2J mice. However, the benzamide eticlopride, which is a high affinity D2-like antagonist, was a notable exception. SV 293, SV-III-130s and N-methylbenperidol, which exhibit a high affinity for D2 versus the D3 dopamine receptor subtypes (60- to 100-fold binding selectivity), were also found to inhibit the HTR in DBA/2J mice. This observation suggests a functional interaction between dopaminergic and serotonergic systems through D2 dopamine receptors and the 5-HT2A serotonin receptors in vivo. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. An FPGA-Based Real-Time Maximum Likelihood 3D Position Estimation for a Continuous Crystal PET Detector

    NASA Astrophysics Data System (ADS)

    Wang, Yonggang; Xiao, Yong; Cheng, Xinyi; Li, Deng; Wang, Liwei

    2016-02-01

    For the continuous crystal-based positron emission tomography (PET) detector built in our lab, a maximum likelihood algorithm adapted for implementation on a field programmable gate array (FPGA) is proposed to estimate the three-dimensional (3D) coordinate of interaction position with the single-end detected scintillation light response. The row-sum and column-sum readout scheme organizes the 64 channels of photomultiplier (PMT) into eight row signals and eight column signals to be readout for X- and Y-coordinates estimation independently. By the reference events irradiated in a known oblique angle, the probability density function (PDF) for each depth-of-interaction (DOI) segment is generated, by which the reference events in perpendicular irradiation are assigned to DOI segments for generating the PDFs for X and Y estimation in each DOI layer. Evaluated by the experimental data, the algorithm achieves an average X resolution of 1.69 mm along the central X-axis, and DOI resolution of 3.70 mm over the whole thickness (0-10 mm) of crystal. The performance improvements from 2D estimation to the 3D algorithm are also presented. Benefiting from abundant resources of FPGA and a hierarchical storage arrangement, the whole algorithm can be implemented into a middle-scale FPGA. By a parallel structure in pipelines, the 3D position estimator on the FPGA can achieve a processing throughput of 15 M events/s, which is sufficient for the requirement of real-time PET imaging.

  13. ARC: An open-source library for calculating properties of alkali Rydberg atoms

    NASA Astrophysics Data System (ADS)

    Šibalić, N.; Pritchard, J. D.; Adams, C. S.; Weatherill, K. J.

    2017-11-01

    We present an object-oriented Python library for the computation of properties of highly-excited Rydberg states of alkali atoms. These include single-body effects such as dipole matrix elements, excited-state lifetimes (radiative and black-body limited) and Stark maps of atoms in external electric fields, as well as two-atom interaction potentials accounting for dipole and quadrupole coupling effects valid at both long and short range for arbitrary placement of the atomic dipoles. The package is cross-referenced to precise measurements of atomic energy levels and features extensive documentation to facilitate rapid upgrade or expansion by users. This library has direct application in the field of quantum information and quantum optics which exploit the strong Rydberg dipolar interactions for two-qubit gates, robust atom-light interfaces and simulating quantum many-body physics, as well as the field of metrology using Rydberg atoms as precise microwave electrometers. Program Files doi:http://dx.doi.org/10.17632/hm5n8w628c.1 Licensing provisions: BSD-3-Clause Programming language: Python 2.7 or 3.5, with C extension External Routines: NumPy [1], SciPy [1], Matplotlib [2] Nature of problem: Calculating atomic properties of alkali atoms including lifetimes, energies, Stark shifts and dipole-dipole interaction strengths using matrix elements evaluated from radial wavefunctions. Solution method: Numerical integration of radial Schrödinger equation to obtain atomic wavefunctions, which are then used to evaluate dipole matrix elements. Properties are calculated using second order perturbation theory or exact diagonalisation of the interaction Hamiltonian, yielding results valid even at large external fields or small interatomic separation. Restrictions: External electric field fixed to be parallel to quantisation axis. Supplementary material: Detailed documentation (.html), and Jupyter notebook with examples and benchmarking runs (.html and .ipynb). [1] T.E. Oliphant, Comput. Sci. Eng. 9, 10 (2007). http://www.scipy.org/. [2] J.D. Hunter, Comput. Sci. Eng. 9, 90 (2007). http://matplotlib.org/.

  14. Wikipedia as a gateway to biomedical research: The relative distribution and use of citations in the English Wikipedia

    PubMed Central

    Willinsky, John M.; Steinberg, Ryan M.; Mietchen, Daniel; Wass, Joseph L.; Dong, Ting

    2017-01-01

    Wikipedia is a gateway to knowledge. However, the extent to which this gateway ends at Wikipedia or continues via supporting citations is unknown. Wikipedia’s gateway functionality has implications for information design and education, notably in medicine. This study aims to establish benchmarks for the relative distribution and referral (click) rate of citations—as indicated by presence of a Digital Object Identifier (DOI)—from Wikipedia, with a focus on medical citations. DOIs referred from the English Wikipedia in August 2016 were obtained from Crossref.org. Next, based on a DOI’s presence on a WikiProject Medicine page, all DOIs in Wikipedia were categorized as medical (WP:MED) or non-medical (non-WP:MED). Using this categorization, referred DOIs were classified as WP:MED, non-WP:MED, or BOTH, meaning the DOI may have been referred from either category. Data were analyzed using descriptive and inferential statistics. Out of 5.2 million Wikipedia pages, 4.42% (n = 229,857) included at least one DOI. 68,870 were identified as WP:MED, with 22.14% (n = 15,250) featuring one or more DOIs. WP:MED pages featured on average 8.88 DOI citations per page, whereas non-WP:MED pages had on average 4.28 DOI citations. For DOIs only on WP:MED pages, a DOI was referred every 2,283 pageviews and for non-WP:MED pages every 2,467 pageviews. DOIs from BOTH pages accounted for 12% (n = 58,475). The referral of DOI citations found in BOTH could not be assigned to WP:MED or non-WP:MED, as the page from which the referral was made was not provided with the data. While these results cannot provide evidence of greater citation referral from WP:MED than non-WP:MED, they do provide benchmarks to assess strategies for changing referral patterns. These changes might include editors adopting new methods for designing and presenting citations or the introduction of teaching strategies that address the value of consulting citations as a tool for extending learning. PMID:29267345

  15. A model of mechanical interactions between heart and lungs.

    PubMed

    Fontecave Jallon, Julie; Abdulhay, Enas; Calabrese, Pascale; Baconnier, Pierre; Gumery, Pierre-Yves

    2009-12-13

    To study the mechanical interactions between heart, lungs and thorax, we propose a mathematical model combining a ventilatory neuromuscular model and a model of the cardiovascular system, as described by Smith et al. (Smith, Chase, Nokes, Shaw & Wake 2004 Med. Eng. Phys.26, 131-139. (doi:10.1016/j.medengphy.2003.10.001)). The respiratory model has been adapted from Thibault et al. (Thibault, Heyer, Benchetrit & Baconnier 2002 Acta Biotheor. 50, 269-279. (doi:10.1023/A:1022616701863)); using a Liénard oscillator, it allows the activity of the respiratory centres, the respiratory muscles and rib cage internal mechanics to be simulated. The minimal haemodynamic system model of Smith includes the heart, as well as the pulmonary and systemic circulation systems. These two modules interact mechanically by means of the pleural pressure, calculated in the mechanical respiratory system, and the intrathoracic blood volume, calculated in the cardiovascular model. The simulation by the proposed model provides results, first, close to experimental data, second, in agreement with the literature results and, finally, highlighting the presence of mechanical cardiorespiratory interactions.

  16. Angiopoietin-like proteins stimulate HSPC development through interaction with notch receptor signaling

    PubMed Central

    Lin, Michelle I; Price, Emily N; Boatman, Sonja; Hagedorn, Elliott J; Trompouki, Eirini; Satishchandran, Sruthi; Carspecken, Charles W; Uong, Audrey; DiBiase, Anthony; Yang, Song; Canver, Matthew C; Dahlberg, Ann; Lu, Zhigang; Zhang, Cheng Cheng; Orkin, Stuart H; Bernstein, Irwin D; Aster, Jon C; White, Richard M; Zon, Leonard I

    2015-01-01

    Angiopoietin-like proteins (angptls) are capable of ex vivo expansion of mouse and human hematopoietic stem and progenitor cells (HSPCs). Despite this intriguing ability, their mechanism is unknown. In this study, we show that angptl2 overexpression is sufficient to expand definitive HSPCs in zebrafish embryos. Angptl1/2 are required for definitive hematopoiesis and vascular specification of the hemogenic endothelium. The loss-of-function phenotype is reminiscent of the notch mutant mindbomb (mib), and a strong genetic interaction occurs between angptls and notch. Overexpressing angptl2 rescues mib while overexpressing notch rescues angptl1/2 morphants. Gene expression studies in ANGPTL2-stimulated CD34+ cells showed a strong MYC activation signature and myc overexpression in angptl1/2 morphants or mib restored HSPCs formation. ANGPTL2 can increase NOTCH activation in cultured cells and ANGPTL receptor interacted with NOTCH to regulate NOTCH cleavage. Together our data provide insight to the angptl-mediated notch activation through receptor interaction and subsequent activation of myc targets. DOI: http://dx.doi.org/10.7554/eLife.05544.001 PMID:25714926

  17. Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice

    PubMed Central

    Overman, Jeroen; Fontaine, Frank; Moustaqil, Mehdi; Mittal, Deepak; Sierecki, Emma; Sacilotto, Natalia; Zuegg, Johannes; Robertson, Avril AB; Holmes, Kelly; Salim, Angela A; Mamidyala, Sreeman; Butler, Mark S; Robinson, Ashley S; Lesieur, Emmanuelle; Johnston, Wayne; Alexandrov, Kirill; Black, Brian L; Hogan, Benjamin M; De Val, Sarah; Capon, Robert J; Carroll, Jason S; Bailey, Timothy L; Koopman, Peter; Jauch, Ralf; Smyth, Mark J; Cooper, Matthew A; Gambin, Yann; Francois, Mathias

    2017-01-01

    Pharmacological targeting of transcription factors holds great promise for the development of new therapeutics, but strategies based on blockade of DNA binding, nuclear shuttling, or individual protein partner recruitment have yielded limited success to date. Transcription factors typically engage in complex interaction networks, likely masking the effects of specifically inhibiting single protein-protein interactions. Here, we used a combination of genomic, proteomic and biophysical methods to discover a suite of protein-protein interactions involving the SOX18 transcription factor, a known regulator of vascular development and disease. We describe a small-molecule that is able to disrupt a discrete subset of SOX18-dependent interactions. This compound selectively suppressed SOX18 transcriptional outputs in vitro and interfered with vascular development in zebrafish larvae. In a mouse pre-clinical model of breast cancer, treatment with this inhibitor significantly improved survival by reducing tumour vascular density and metastatic spread. Our studies validate an interactome-based molecular strategy to interfere with transcription factor activity, for the development of novel disease therapeutics. DOI: http://dx.doi.org/10.7554/eLife.21221.001 PMID:28137359

  18. Estrogen receptor coregulator binding modulators (ERXs) effectively target estrogen receptor positive human breast cancers

    PubMed Central

    Raj, Ganesh V; Sareddy, Gangadhara Reddy; Ma, Shihong; Lee, Tae-Kyung; Viswanadhapalli, Suryavathi; Li, Rui; Liu, Xihui; Murakami, Shino; Chen, Chien-Cheng; Lee, Wan-Ru; Mann, Monica; Krishnan, Samaya Rajeshwari; Manandhar, Bikash; Gonugunta, Vijay K; Strand, Douglas; Tekmal, Rajeshwar Rao; Ahn, Jung-Mo; Vadlamudi, Ratna K

    2017-01-01

    The majority of human breast cancer is estrogen receptor alpha (ER) positive. While anti-estrogens/aromatase inhibitors are initially effective, resistance to these drugs commonly develops. Therapy-resistant tumors often retain ER signaling, via interaction with critical oncogenic coregulator proteins. To address these mechanisms of resistance, we have developed a novel ER coregulator binding modulator, ERX-11. ERX-11 interacts directly with ER and blocks the interaction between a subset of coregulators with both native and mutant forms of ER. ERX-11 effectively blocks ER-mediated oncogenic signaling and has potent anti-proliferative activity against therapy-sensitive and therapy-resistant human breast cancer cells. ERX-11 is orally bioavailable, with no overt signs of toxicity and potent activity in both murine xenograft and patient-derived breast tumor explant models. This first-in-class agent, with its novel mechanism of action of disrupting critical protein-protein interactions, overcomes the limitations of current therapies and may be clinically translatable for patients with therapy-sensitive and therapy-resistant breast cancers. DOI: http://dx.doi.org/10.7554/eLife.26857.001 PMID:28786813

  19. Dna2 nuclease-helicase structure, mechanism and regulation by Rpa

    PubMed Central

    Zhou, Chun; Pourmal, Sergei; Pavletich, Nikola P

    2015-01-01

    The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5’ end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5’ but not 3’ end, explaining how Rpa regulates cleavage polarity. DOI: http://dx.doi.org/10.7554/eLife.09832.001 PMID:26491943

  20. Effects of myosin variants on interacting-heads motif explain distinct hypertrophic and dilated cardiomyopathy phenotypes

    PubMed Central

    Alamo, Lorenzo; Ware, James S; Pinto, Antonio; Gillilan, Richard E; Seidman, Jonathan G; Seidman, Christine E; Padrón, Raúl

    2017-01-01

    Cardiac β-myosin variants cause hypertrophic (HCM) or dilated (DCM) cardiomyopathy by disrupting sarcomere contraction and relaxation. The locations of variants on isolated myosin head structures predict contractility effects but not the prominent relaxation and energetic deficits that characterize HCM. During relaxation, pairs of myosins form interacting-heads motif (IHM) structures that with other sarcomere proteins establish an energy-saving, super-relaxed (SRX) state. Using a human β-cardiac myosin IHM quasi-atomic model, we defined interactions sites between adjacent myosin heads and associated protein partners, and then analyzed rare variants from 6112 HCM and 1315 DCM patients and 33,370 ExAC controls. HCM variants, 72% that changed electrostatic charges, disproportionately altered IHM interaction residues (expected 23%; HCM 54%, p=2.6×10−19; DCM 26%, p=0.66; controls 20%, p=0.23). HCM variant locations predict impaired IHM formation and stability, and attenuation of the SRX state - accounting for altered contractility, reduced diastolic relaxation, and increased energy consumption, that fully characterizes HCM pathogenesis. DOI: http://dx.doi.org/10.7554/eLife.24634.001 PMID:28606303

  1. Optimization, evaluation and calibration of a cross-strip DOI detector

    NASA Astrophysics Data System (ADS)

    Schmidt, F. P.; Kolb, A.; Pichler, B. J.

    2018-02-01

    This study depicts the evaluation of a SiPM detector with depth of interaction (DOI) capability via a dual-sided readout that is suitable for high-resolution positron emission tomography and magnetic resonance (PET/MR) imaging. Two different 12  ×  12 pixelated LSO scintillator arrays with a crystal pitch of 1.60 mm are examined. One array is 20 mm-long with a crystal separation by the specular reflector Vikuiti enhanced specular reflector (ESR), and the other one is 18 mm-long and separated by the diffuse reflector Lumirror E60 (E60). An improvement in energy resolution from 22.6% to 15.5% for the scintillator array with the E60 reflector is achieved by taking a nonlinear light collection correction into account. The results are FWHM energy resolutions of 14.0% and 15.5%, average FWHM DOI resolutions of 2.96 mm and 1.83 mm, and FWHM coincidence resolving times of 1.09 ns and 1.48 ns for the scintillator array with the ESR and that with the E60 reflector, respectively. The measured DOI signal ratios need to be assigned to an interaction depth inside the scintillator crystal. A linear and a nonlinear method, using the intrinsic scintillator radiation from lutetium, are implemented for an easy to apply calibration and are compared to the conventional method, which exploits a setup with an externally collimated radiation beam. The deviation between the DOI functions of the linear or nonlinear method and the conventional method is determined. The resulting average of differences in DOI positions is 0.67 mm and 0.45 mm for the nonlinear calibration method for the scintillator array with the ESR and with the E60 reflector, respectively; Whereas the linear calibration method results in 0.51 mm and 0.32 mm for the scintillator array with the ESR and the E60 reflector, respectively; and is, due to its simplicity, also applicable in assembled detector systems.

  2. Optimization, evaluation and calibration of a cross-strip DOI detector.

    PubMed

    Schmidt, F P; Kolb, A; Pichler, B J

    2018-02-20

    This study depicts the evaluation of a SiPM detector with depth of interaction (DOI) capability via a dual-sided readout that is suitable for high-resolution positron emission tomography and magnetic resonance (PET/MR) imaging. Two different 12  ×  12 pixelated LSO scintillator arrays with a crystal pitch of 1.60 mm are examined. One array is 20 mm-long with a crystal separation by the specular reflector Vikuiti enhanced specular reflector (ESR), and the other one is 18 mm-long and separated by the diffuse reflector Lumirror E60 (E60). An improvement in energy resolution from 22.6% to 15.5% for the scintillator array with the E60 reflector is achieved by taking a nonlinear light collection correction into account. The results are FWHM energy resolutions of 14.0% and 15.5%, average FWHM DOI resolutions of 2.96 mm and 1.83 mm, and FWHM coincidence resolving times of 1.09 ns and 1.48 ns for the scintillator array with the ESR and that with the E60 reflector, respectively. The measured DOI signal ratios need to be assigned to an interaction depth inside the scintillator crystal. A linear and a nonlinear method, using the intrinsic scintillator radiation from lutetium, are implemented for an easy to apply calibration and are compared to the conventional method, which exploits a setup with an externally collimated radiation beam. The deviation between the DOI functions of the linear or nonlinear method and the conventional method is determined. The resulting average of differences in DOI positions is 0.67 mm and 0.45 mm for the nonlinear calibration method for the scintillator array with the ESR and with the E60 reflector, respectively; Whereas the linear calibration method results in 0.51 mm and 0.32 mm for the scintillator array with the ESR and the E60 reflector, respectively; and is, due to its simplicity, also applicable in assembled detector systems.

  3. Timing properties of phosphor-coated polished LSO crystals.

    PubMed

    Schmall, Jeffrey P; Roncali, Emilie; Berg, Eric; Viswanath, Varsha; Du, Junwei; Cherry, Simon R

    2014-08-07

    This study investigates a time-of-flight (TOF)-depth-of-interaction (DOI) detector design for positron emission tomography (PET), based on phosphor-coated lutetium oxyorthosilicate (LSO) scintillator crystals coupled to fast single channel photomultiplier tubes. Interaction of the scintillation light with the phosphor coating changes the pulse shape in a depth-dependent manner. 3 × 3 × 10 mm(3) LSO scintillation crystals with polished surfaces were characterized, with and without phosphor coating, to assess DOI capability and timing properties. Two different phosphor coating geometries were studied: coating of the top surface of the crystal, and the top plus half of the crystal sides. There was negligible depth dependency in the decay time when coating only the top surface, however there was a ∼10 ns difference in end-to-end decay time when coating the top plus half of the crystal sides, sufficient to support the use of three DOI bins (3.3 mm DOI bin width). The rise time of the half-coated phosphor crystal was slightly faster at all depths, compared to uncoated crystals, however the signal amplitude was lower. Phosphor coating resulted in depth-dependent photopeak positions with an energy resolution of 13.7%, at a depth of 1 mm, and 15.3%, at a depth of 9 mm, for the half-coated crystal. Uncoated LSO crystals showed no change in photopeak position as a function of depth, with an energy resolution of 10.4%. The head-on coincidence timing resolution (CTR) of two uncoated LSO crystals was 287 ps using constant fraction discrimination for time pick-off. With phosphor coating, the CTR of the top-coated crystal was 314 ps, compared to 384 ps for the half-coated crystal. We demonstrate that the trade-off between timing resolution and DOI resolution can be controlled by the phosphor coating geometry. Here we present preliminary results demonstrating that good DOI resolution can be achieved with only a modest 26% degradation in CTR.

  4. Patterns of call communication between group-housed zebra finches change during the breeding cycle

    PubMed Central

    Gill, Lisa F; Goymann, Wolfgang; Ter Maat, Andries; Gahr, Manfred

    2015-01-01

    Vocal signals such as calls play a crucial role for survival and successful reproduction, especially in group-living animals. However, call interactions and call dynamics within groups remain largely unexplored because their relation to relevant contexts or life-history stages could not be studied with individual-level resolution. Using on-bird microphone transmitters, we recorded the vocalisations of individual zebra finches (Taeniopygia guttata) behaving freely in social groups, while females and males previously unknown to each other passed through different stages of the breeding cycle. As birds formed pairs and shifted their reproductive status, their call repertoire composition changed. The recordings revealed that calls occurred non-randomly in fine-tuned vocal interactions and decreased within groups while pair-specific patterns emerged. Call-type combinations of vocal interactions changed within pairs and were associated with successful egg-laying, highlighting a potential fitness relevance of calling dynamics in communication systems. DOI: http://dx.doi.org/10.7554/eLife.07770.001 PMID:26441403

  5. A bacteriophage endolysin that eliminates intracellular streptococci

    PubMed Central

    Shen, Yang; Barros, Marilia; Vennemann, Tarek; Gallagher, D Travis; Yin, Yizhou; Linden, Sara B; Heselpoth, Ryan D; Spencer, Dennis J; Donovan, David M; Moult, John; Fischetti, Vincent A; Heinrich, Frank; Lösche, Mathias; Nelson, Daniel C

    2016-01-01

    PlyC, a bacteriophage-encoded endolysin, lyses Streptococcus pyogenes (Spy) on contact. Here, we demonstrate that PlyC is a potent agent for controlling intracellular Spy that often underlies refractory infections. We show that the PlyC holoenzyme, mediated by its PlyCB subunit, crosses epithelial cell membranes and clears intracellular Spy in a dose-dependent manner. Quantitative studies using model membranes establish that PlyCB interacts strongly with phosphatidylserine (PS), whereas its interaction with other lipids is weak, suggesting specificity for PS as its cellular receptor. Neutron reflection further substantiates that PlyC penetrates bilayers above a PS threshold concentration. Crystallography and docking studies identify key residues that mediate PlyCB–PS interactions, which are validated by site-directed mutagenesis. This is the first report that a native endolysin can traverse epithelial membranes, thus substantiating the potential of PlyC as an antimicrobial for Spy in the extracellular and intracellular milieu and as a scaffold for engineering other functionalities. DOI: http://dx.doi.org/10.7554/eLife.13152.001 PMID:26978792

  6. Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

    PubMed Central

    Freire-Pritchett, Paula; Schoenfelder, Stefan; Várnai, Csilla; Wingett, Steven W; Cairns, Jonathan; Collier, Amanda J; García-Vílchez, Raquel; Furlan-Magaril, Mayra; Osborne, Cameron S; Fraser, Peter; Rugg-Gunn, Peter J; Spivakov, Mikhail

    2017-01-01

    Long-range cis-regulatory elements such as enhancers coordinate cell-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. Deciphering the interplay between the promoter connectivity and activity of cis-regulatory elements during lineage commitment is crucial for understanding developmental transcriptional control. Here, we use Promoter Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements. We reveal extensive dynamics of cis-regulatory contacts upon lineage commitment, including the acquisition and loss of promoter interactions. This spatial rewiring occurs preferentially with predicted changes in the activity of cis-regulatory elements and is associated with changes in target gene expression. Our results provide a global and integrated view of promoter interactome dynamics during lineage commitment of human pluripotent cells. DOI: http://dx.doi.org/10.7554/eLife.21926.001 PMID:28332981

  7. Bidirectional interactions between indomethacin and the murine intestinal microbiota

    PubMed Central

    Liang, Xue; Bittinger, Kyle; Li, Xuanwen; Abernethy, Darrell R; Bushman, Frederic D; FitzGerald, Garret A

    2015-01-01

    The vertebrate gut microbiota have been implicated in the metabolism of xenobiotic compounds, motivating studies of microbe-driven metabolism of clinically important drugs. Here, we studied interactions between the microbiota and indomethacin, a nonsteroidal anti-inflammatory drug (NSAID) that inhibits cyclooxygenases (COX) -1 and -2. Indomethacin was tested in both acute and chronic exposure models in mice at clinically relevant doses, which suppressed production of COX-1- and COX-2-derived prostaglandins and caused small intestinal (SI) damage. Deep sequencing analysis showed that indomethacin exposure was associated with alterations in the structure of the intestinal microbiota in both dosing models. Perturbation of the intestinal microbiome by antibiotic treatment altered indomethacin pharmacokinetics and pharmacodynamics, which is probably the result of reduced bacterial β-glucuronidase activity. Humans show considerable inter-individual differences in their microbiota and their responses to indomethacin — thus, the drug-microbe interactions described here provide candidate mediators of individualized drug responses. DOI: http://dx.doi.org/10.7554/eLife.08973.001 PMID:26701907

  8. Attention operates uniformly throughout the classical receptive field and the surround

    PubMed Central

    Verhoef, Bram-Ernst; Maunsell, John HR

    2016-01-01

    Shifting attention among visual stimuli at different locations modulates neuronal responses in heterogeneous ways, depending on where those stimuli lie within the receptive fields of neurons. Yet how attention interacts with the receptive-field structure of cortical neurons remains unclear. We measured neuronal responses in area V4 while monkeys shifted their attention among stimuli placed in different locations within and around neuronal receptive fields. We found that attention interacts uniformly with the spatially-varying excitation and suppression associated with the receptive field. This interaction explained the large variability in attention modulation across neurons, and a non-additive relationship among stimulus selectivity, stimulus-induced suppression and attention modulation that has not been previously described. A spatially-tuned normalization model precisely accounted for all observed attention modulations and for the spatial summation properties of neurons. These results provide a unified account of spatial summation and attention-related modulation across both the classical receptive field and the surround. DOI: http://dx.doi.org/10.7554/eLife.17256.001 PMID:27547989

  9. Spatial signals link exit from mitosis to spindle position

    PubMed Central

    Falk, Jill Elaine; Tsuchiya, Dai; Verdaasdonk, Jolien; Lacefield, Soni; Bloom, Kerry; Amon, Angelika

    2016-01-01

    In budding yeast, if the spindle becomes mispositioned, cells prevent exit from mitosis by inhibiting the mitotic exit network (MEN). The MEN is a signaling cascade that localizes to spindle pole bodies (SPBs) and activates the phosphatase Cdc14. There are two competing models that explain MEN regulation by spindle position. In the 'zone model', exit from mitosis occurs when a MEN-bearing SPB enters the bud. The 'cMT-bud neck model' posits that cytoplasmic microtubule (cMT)-bud neck interactions prevent MEN activity. Here we find that 1) eliminating cMT– bud neck interactions does not trigger exit from mitosis and 2) loss of these interactions does not precede Cdc14 activation. Furthermore, using binucleate cells, we show that exit from mitosis occurs when one SPB enters the bud despite the presence of a mispositioned spindle. We conclude that exit from mitosis is triggered by a correctly positioned spindle rather than inhibited by improper spindle position. DOI: http://dx.doi.org/10.7554/eLife.14036.001 PMID:27166637

  10. A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem

    PubMed Central

    Rabe, Franziska; Bosch, Jason; Stirnberg, Alexandra; Guse, Tilo; Bauer, Lisa; Seitner, Denise; Rabanal, Fernando A; Czedik-Eysenberg, Angelika; Uhse, Simon; Bindics, Janos; Genenncher, Bianca; Navarrete, Fernando; Kellner, Ronny; Ekker, Heinz; Kumlehn, Jochen; Vogel, John P; Gordon, Sean P; Marcel, Thierry C; Münsterkötter, Martin; Walter, Mathias C; Sieber, Christian MK; Mannhaupt, Gertrud; Güldener, Ulrich; Kahmann, Regine; Djamei, Armin

    2016-01-01

    Due to their economic relevance, the study of plant pathogen interactions is of importance. However, elucidating these interactions and their underlying molecular mechanisms remains challenging since both host and pathogen need to be fully genetically accessible organisms. Here we present milestones in the establishment of a new biotrophic model pathosystem: Ustilago bromivora and Brachypodium sp. We provide a complete toolset, including an annotated fungal genome and methods for genetic manipulation of the fungus and its host plant. This toolset will enable researchers to easily study biotrophic interactions at the molecular level on both the pathogen and the host side. Moreover, our research on the fungal life cycle revealed a mating type bias phenomenon. U. bromivora harbors a haplo-lethal allele that is linked to one mating type region. As a result, the identified mating type bias strongly promotes inbreeding, which we consider to be a potential speciation driver. DOI: http://dx.doi.org/10.7554/eLife.20522.001 PMID:27835569

  11. Light-Sharing Interface for dMiCE Detectors Using Sub-Surface Laser Engraving

    PubMed Central

    Hunter, William C. J.; Miyaoka, Robert S.; MacDonald, Lawrence; McDougald, Wendy; Lewellen, Thomas K.

    2015-01-01

    We have previously reported on dMiCE, a method of resolving depth or interaction (DOI) in a pair of discrete crystals by encoding light sharing properties as a function of depth in the interface of a crystal-element pair. A challenge for this method is the cost and repeatability of interface treatment for each crystal pair. In this work, we report our preliminary results on using sub-surface laser engraving (SSLE) as a means of forming this depth-dependent interface in a dMiCE detector. A surplus first-generation SSLE system was used to create a partially reflective layer 100-microns thick at the boundary between two halves of a 1.4-by-2.9-by-20 mm3 LYSO crystal. The boundary of these paired crystal elements was positioned between two 3-mm wide Silicon photomultiplier arrays. The responses of these two photodetectors were acquired for an ensemble of 511-keV photons collimated to interact at a fixed depth in just one crystal element. Interaction position was then varied to measure detector response as a function of depth, which was then used to maximum-likelihood positions. Despite use of sub-optimal SSLE processing we found an average DOI resolution of 3.4 mm for front-sided readout and 3.9 mm for back-sided readout while obtaining energy resolutions on the order of 10%. We expect DOI resolution can be improved significantly by optimizing the SSLE process and pattern. PMID:25914421

  12. Light-Sharing Interface for dMiCE Detectors using Sub-Surface Laser Engraving.

    PubMed

    Hunter, William C J; Miyaoka, Robert S; MacDonald, Lawrence; McDougald, Wendy; Lewellen, Thomas K

    2013-10-01

    We have previously reported on dMiCE, a method of resolving depth or interaction (DOI) in a pair of discrete crystals by encoding light sharing properties as a function of depth in the interface of this crystal-element pair. A challenge for this method is the cost and repeatability of interface treatment for a crystal pair. In this work, we report our preliminary results on using sub-surface laser engraving (SSLE) as a means of forming this depth-dependent interface in a dMiCE detector. A surplus first-generation SSLE system was used to create a partially reflective layer 100-microns thick at the boundary between two halves of a 1.4-by-2.9-by-20 mmˆ3 LYSO crystal. The boundary of these paired crystal elements was positioned between two 3-mm wide Geiger-Müller avalanche photodiodes from Hamamatsu. The responses of these two photodetectors were acquired for an ensemble of 511-keV photons collimated to interact at a fixed depth in just one crystal element. Interaction position was then varied to measure detector response as a function of depth, which was then used to maximum-likelihood positions events. Despite use of sub-optimal SSLE processing we found an average DOI resolution of 3.4 mm for front-sided readout and 3.9 mm for back-sided readout. We expect DOI resolution can be improved significantly by optimizing the SSLE process and pattern.

  13. Light-Sharing Interface for dMiCE Detectors using Sub-Surface Laser Engraving

    PubMed Central

    Hunter, William C.J.; Miyaoka, Robert S.; MacDonald, Lawrence; McDougald, Wendy; Lewellen, Thomas K.

    2014-01-01

    We have previously reported on dMiCE, a method of resolving depth or interaction (DOI) in a pair of discrete crystals by encoding light sharing properties as a function of depth in the interface of this crystal-element pair. A challenge for this method is the cost and repeatability of interface treatment for a crystal pair. In this work, we report our preliminary results on using sub-surface laser engraving (SSLE) as a means of forming this depth-dependent interface in a dMiCE detector. A surplus first-generation SSLE system was used to create a partially reflective layer 100-microns thick at the boundary between two halves of a 1.4-by-2.9-by-20 mmˆ3 LYSO crystal. The boundary of these paired crystal elements was positioned between two 3-mm wide Geiger-Müller avalanche photodiodes from Hamamatsu. The responses of these two photodetectors were acquired for an ensemble of 511-keV photons collimated to interact at a fixed depth in just one crystal element. Interaction position was then varied to measure detector response as a function of depth, which was then used to maximum-likelihood positions events. Despite use of sub-optimal SSLE processing we found an average DOI resolution of 3.4 mm for front-sided readout and 3.9 mm for back-sided readout. We expect DOI resolution can be improved significantly by optimizing the SSLE process and pattern. PMID:25506194

  14. Light-Sharing Interface for dMiCE Detectors Using Sub-Surface Laser Engraving.

    PubMed

    Hunter, William C J; Miyaoka, Robert S; MacDonald, Lawrence; McDougald, Wendy; Lewellen, Thomas K

    2015-02-06

    We have previously reported on dMiCE, a method of resolving depth or interaction (DOI) in a pair of discrete crystals by encoding light sharing properties as a function of depth in the interface of a crystal-element pair. A challenge for this method is the cost and repeatability of interface treatment for each crystal pair. In this work, we report our preliminary results on using sub-surface laser engraving (SSLE) as a means of forming this depth-dependent interface in a dMiCE detector. A surplus first-generation SSLE system was used to create a partially reflective layer 100-microns thick at the boundary between two halves of a 1.4-by-2.9-by-20 mm 3 LYSO crystal. The boundary of these paired crystal elements was positioned between two 3-mm wide Silicon photomultiplier arrays. The responses of these two photodetectors were acquired for an ensemble of 511-keV photons collimated to interact at a fixed depth in just one crystal element. Interaction position was then varied to measure detector response as a function of depth, which was then used to maximum-likelihood positions. Despite use of sub-optimal SSLE processing we found an average DOI resolution of 3.4 mm for front-sided readout and 3.9 mm for back-sided readout while obtaining energy resolutions on the order of 10%. We expect DOI resolution can be improved significantly by optimizing the SSLE process and pattern.

  15. Determining the Depth of Injury in Bioengineered Tissue Models of Cornea and Conjunctiva for the Prediction of All Three Ocular GHS Categories

    PubMed Central

    Zorn-Kruppa, Michaela; Houdek, Pia; Wladykowski, Ewa; Engelke, Maria; Bartok, Melinda; Mewes, Karsten R.; Moll, Ingrid; Brandner, Johanna M.

    2014-01-01

    The depth of injury (DOI) is a mechanistic correlate to the ocular irritation response. Attempts to quantitatively determine the DOI in alternative tests have been limited to ex vivo animal eyes by fluorescent staining for biomarkers of cell death and viability in histological cross sections. It was the purpose of this study to assess whether DOI could also be measured by means of cell viability detected by the MTT assay using 3-dimensional (3D) reconstructed models of cornea and conjunctiva. The formazan-free area of metabolically inactive cells in the tissue after topical substance application is used as the visible correlate of the DOI. Areas of metabolically active or inactive cells are quantitatively analyzed on cryosection images with ImageJ software analysis tools. By incorporating the total tissue thickness, the relative MTT-DOI (rMTT-DOI) was calculated. Using the rMTT-DOI and human reconstructed cornea equivalents, we developed a prediction model based on suitable viability cut-off values. We tested 25 chemicals that cover the whole range of eye irritation potential based on the globally harmonized system of classification and labelling of chemicals (GHS). Principally, the MTT-DOI test method allows distinguishing between the cytotoxic effects of the different chemicals in accordance with all 3 GHS categories for eye irritation. Although the prediction model is slightly over-predictive with respect to non-irritants, it promises to be highly valuable to discriminate between severe irritants (Cat. 1), and mild to moderate irritants (Cat. 2). We also tested 3D conjunctiva models with the aim to specifically address conjunctiva-damaging substances. Using the MTT-DOI method in this model delivers comparable results as the cornea model, but does not add additional information. However, the MTT-DOI method using reconstructed cornea models already provided good predictability that was superior to the already existing established in vitro/ex vivo methods. PMID:25494045

  16. Investigation of the Hydantoin Monomer and its Interaction with Water Molecules

    NASA Astrophysics Data System (ADS)

    Gruet, Sébastien; Perez, Cristobal; Schnell, Melanie

    2017-06-01

    Hydantoin (Imidazolidine-2,4-dione, C_3H_4N_2O_2) is a five-membered heterocyclic compound of astrobiological interest. This molecule has been detected in carbonaceous chondrites [1], and its formation can rise from the presence of glycolic acid and urea, two prebiotic molecules [2]. The hydrolysis of hydantoin under acidic conditions can also produce glycine [3], an amino acid actively searched for in the interstellar medium. Spectroscopic data of hydantoin is very limited and mostly dedicated to the solid phase. The high resolution study in gas phase is restricted to the work recently published by Ozeki et al. reporting the pure rotational spectra of the ground state and two vibrational states of the molecule in the millimeter-wave region (90-370 GHz)[4]. Using chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy, we recorded the jet-cooled rotational spectra of hydantoin with water between 2 to 8 GHz. We observed the ground state of hydantoin monomer and several water complexes with one or two water molecules. All the observed species exhibit a hyperfine structure due to the two nitrogen atoms present in the molecule, which were fully resolved and analyzed. Additional experiments with a ^{18}O enriched water sample were realized to determine the oxygen-atom positions of the water monomers. These experiments yielded accurate structural information on the preferred water binding sites. The observed complexes and the interactions that hold them together, mainly strong directional hydrogen bonds, will be presented and discussed. [1] Shimoyama, A. and Ogasawara, R., Orig. Life Evol. Biosph., 32, 165-179, 2002. DOI:10.1023/A:1016015319112. [2] Menor-Salván, C. and Marín-Yaseli, M.R., Chem. Soc. Rev., 41(16), 5404-5415, 2012. DOI:10.1039/c2cs35060b. [3] De Marcellus P., Bertrand M., Nuevo M., Westall F. and Le Sergeant d'Hendecourt L., Astrobiology. 11(9), 847-854, 2011. DOI:10.1089/ast.2011.0677. [4] Ozeki, H., Miyahara R., Ihara H., Todaka S., Kobayashi K., and Ohishi M., Astron. Astrophys., Forthcoming article (

  17. Biophysical landscape interactions: Bridging disciplines and scale with connectivity

    NASA Astrophysics Data System (ADS)

    van der Ploeg, Martine; Baartman, Jantiene; Robinson, David

    2017-04-01

    The combination of climate change, population growth and soil threats, such as carbon loss, biodiversity decline or erosion amongst others , increasingly confront the global community [1]. One of the major challenges in studying processes involved in soil threats, landscape resilience, ecosystem stability, sustainable land management and the economic consequences, is that it is an interdisciplinary field [2], that needs less stringent scientific disciplinary boundaries [3]. As a result of disciplinary focus, ambiguity may arise on the understanding of landscape interactions, and this is especially true in the interaction between a landscape's physical and biological processes [4]. Another important aspect in biophysical landscape interactions are the differences in scale related to the various processes that play a role in these systems. While scaling of environmental processes is possible, as long as the phenomena at hand can be described by the same set of differential equations [5], biophysical landscape interactions pose problems for scaling approaches. Landscape position and land use impact the coupled processes in soil and vegetation. Differences in micro-behavior, driven by the interplay of heterogeneous soil and vegetation dynamics, impact emergent characteristics across a landscape. A complicating factor is the response of vegetation to changing environmental conditions, including a possible and often unknown time-lag. By altering soil conditions, plants may leave an imprint in the landscape that remains even after vegetation has disappeared due to e.g. drought, wildfire or overgrazing. Plants also respond biochemically to their environment, while the models used for hydrology are often based on physical interactions. Gene-expression and genotype adaptation may further complicate our modelling efforts in for example climate change impacts. What are we missing by not having more connectivity in our thinking, and what we can solve? We think that integrated concepts of biophysical landscape interactions are needed to evaluate soil water availability in relation to the stability of natural vegetation, especially in the perspective of soil threats, population growth, climate change, and global water scarcity. An integrated concept can only be established by bridging the gap between several disciplines, but needs to be appealing to those disciplines at the same time. As evidence suggests interdisciplinary work is more challenging to get funded [6]. The key aspect of the connectivity concept is that it can create pathways for feedbacks which are so often missing in soil and water models. Connectivity could thus play an important role in bridging disciplines and scales. [1] Schwilch G, Bernet L. Fleskens L, Giannakis E, Leventon J, Marañón T, Mills J, Short C, Stolte J, van Delden H, Verzandvoort S. 2016. Operationalizing ecosystem services for the mitigation of soil threats: A proposed framework. Ecological Indicators 67: 586-597,doi:10.1016/j.ecolind.2016.03.016 [2] Pelletier JD, DeLong SB, Orem CA, Becerra P, Compton K, Gressett K, Lyons-Baral J, McGuire LA, Molaro JL, Spinler JCCF. 2012. How do vegetation bands form in dry lands? Insights from numerical modeling and field studies in southern Nevada, USA. Journal of Geophysical Research: Earth Surface 117: F04026,doi:10.1029/2012JF002465 [3] Liu J, Dietz T, Carpenter SR, Alberti M, Folke C, Moran E, ..., Ostrom E. 2007. Complexity of coupled human and natural systems. Science 317.5844: 1513-1516,doi:10.1126/science.1144004 [4] Cook BJ, Hauer FR. 2007. Effects of hydrologic connectivity on water chemistry, soils, and vegetation structure and function in an intermontane depressional wetland landscape. Wetlands 27.3: 719-738,doi:10.1672/0277-5212(2007)27 [5] Roth K. 2008. Scaling of water flow through porous media and soils. European journal of soil science, 59(1), 125-130, doi: 10.1111/j.1365-2389.2007.00986.x [6] Bromham, L, Dinnage R, Hua X. 2016. Interdisciplinary research has consistently lower funding success. Nature 534: 684-687,doi:10.1038/nature18315

  18. Discrepancies and Known Issues

    Atmospheric Science Data Center

    2018-06-15

    ... No data received for this mission SEAC4RS information available at  ... No data received for this mission TOLNET information available at  https://www-air.larc.nasa.gov/missions/TOLNet/ ... DOI registered incorrectly POLAR WINDS II data and information available at  ...

  19. Modulation of electrostatic interactions to reveal a reaction network unifying the aggregation behaviour of the Aβ42 peptide and its variants† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00215g Click here for additional data file.

    PubMed Central

    Meisl, Georg; Yang, Xiaoting

    2017-01-01

    The aggregation of the amyloid β peptide (Aβ42), which is linked to Alzheimer's disease, can be altered significantly by modulations of the peptide's intermolecular electrostatic interactions. Variations in sequence and solution conditions have been found to lead to highly variable aggregation behaviour. Here we modulate systematically the electrostatic interactions governing the aggregation kinetics by varying the ionic strength of the solution. We find that changes in the solution ionic strength induce a switch in the reaction pathway, altering the dominant mechanisms of aggregate multiplication. This strategy thereby allows us to continuously sample a large space of different reaction mechanisms and develop a minimal reaction network that unifies the experimental kinetics under a wide range of different conditions. More generally, this universal reaction network connects previously separate systems, such as charge mutants of the Aβ42 peptide, on a continuous mechanistic landscape, providing a unified picture of the aggregation mechanism of Aβ42. PMID:28979758

  20. Trading Freshness for Performance in Distributed Systems

    DTIC Science & Technology

    2014-12-01

    Systems (IOPADS ’99), May 1999. 3.6 Charles Babcock. Data, data, everywhere. Information Week, January 2006. 3.2 Peter Bailis, Shivaram Venkataraman ... Venkataraman , Michael J. Franklin, Joseph M. Hellerstein, and Ion Stoica. Pbs at work: Advancing data management with consistency metrics. In Proceedings of...5. doi: 10.1145/2463676.2465260. URL http://doi.acm.org/10. 1145/2463676.2465260. 2.4 Peter Bailis, Shivaram Venkataraman , Michael J. Franklin, Joseph

  1. Reply to Comment by W. R. Peltier, D. F. Argus, and R. Drummond on "An Assessment of the ICE6G_C (VM5a) Glacial Isostatic Adjustment Model"

    NASA Astrophysics Data System (ADS)

    Purcell, A.; Tregoning, P.; Dehecq, A.

    2018-02-01

    The empirical approximation of Purcell et al. (2011, https://doi.org/10.1029/2011GL048624) has been validated by Peltier et al. (2018, https://doi.org/10.1002/2016JB013844). In their Comment they introduced new results derived from the same ice/rheology models of ICE6G_C (VM5a) but using a different model for Antarctic bathymetry. This has greatly reduced the differences in predicted Antarctic uplift rates relative to those of Purcell et al. (2016, https://doi.org/10.1002/2015JB012742). In fact, with a ˜50% reduction in uplift rate in the Weddell Sea, the results of Peltier et al. (2018, https://doi.org/10.1002/2016JB013844) now agree more closely with the predictions of Purcell et al. (2016, https://doi.org/10.1002/2015JB012742) than with the original ICE6G_C values. Peltier et al. (2018, https://doi.org/10.1002/2016JB013844) state that the high power in their high-frequency spherical harmonic coefficients remains in their new calculations. They also claim that Purcell et al. (2016, https://doi.org/10.1002/2015JB012742) used an inaccurate loading history in deriving their velocity field. In fact, the ice load history was unchanged; to remove any ambiguity, the ice and water load histories used in the CALSEA calculations are provided in the supporting information.

  2. Leadership emergence in a data-driven model of zebrafish shoals with speed modulation

    NASA Astrophysics Data System (ADS)

    Zienkiewicz, A.; Barton, D. A. W.; Porfiri, M.; Di Bernardo, M.

    2015-11-01

    Models of collective animal motion can greatly aid in the design and interpretation of behavioural experiments that seek to unravel, isolate, and manipulate the determinants of leader-follower relationships. Here, we develop an initial model of zebrafish social behaviour, which accounts for both speed and angular velocity regulatory interactions among conspecifics. Using this model, we analyse the macroscopic observables of small shoals influenced by an "informed" agent, showing that leaders which actively modulate their speed with respect to their neighbours can entrain and stabilise collective dynamics of the naïve shoal. Supplementary material in the form of two mp4 files available from the Journal web page at http://dx.doi.org/10.1140/epjst/e2015-50093-5

  3. Proteomics profiling of interactome dynamics by colocalisation analysis (COLA)† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6mb00701e Click here for additional data file. Click here for additional data file.

    PubMed Central

    Sailem, Heba Z.; Kümper, Sandra; Tape, Christopher J.; McCully, Ryan R.; Paul, Angela; Anjomani-Virmouni, Sara; Jørgensen, Claus; Poulogiannis, George; Marshall, Christopher J.

    2017-01-01

    Localisation and protein function are intimately linked in eukaryotes, as proteins are localised to specific compartments where they come into proximity of other functionally relevant proteins. Significant co-localisation of two proteins can therefore be indicative of their functional association. We here present COLA, a proteomics based strategy coupled with a bioinformatics framework to detect protein–protein co-localisations on a global scale. COLA reveals functional interactions by matching proteins with significant similarity in their subcellular localisation signatures. The rapid nature of COLA allows mapping of interactome dynamics across different conditions or treatments with high precision. PMID:27824369

  4. Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions

    PubMed Central

    Turner, Leslie M; Harr, Bettina

    2014-01-01

    Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone. DOI: http://dx.doi.org/10.7554/eLife.02504.001 PMID:25487987

  5. Radar measurements of surface deformation in the sub mm-range

    NASA Astrophysics Data System (ADS)

    Peters, Gerhard; Hort, Matthias; Gerst, Alexander; Scharff, Lea

    2016-04-01

    A portable low power Doppler radar at 24 GHz is used for volcano eruption observations since more than a decade (e.g. Hort and Seyfried, 1998, doi: 10.1029/97GL03482; Seyfried and Hort, 1999, doi: 10.1007/s004450050256; Vöge et al., 2005, doi: 10.1029/2005 EO510001, Vöge and Hort, 2009, doi: 10.1109/TGRS. 2008.2002693, Gerst et al., 2013, doi: 10.1002/jgrb.50234; Scharff et al, 2015, doi: 10.1130/G36705.1) The typical radar products are range resolved Doppler spectra containing information on the reflectivity, radial velocity and its distribution of ejected particles. Here we present the analysis of the phase of radar signals for the detection of comparably slow and small deformations of the solid surface which may occur for example prior to an eruption [Hort et al., 2010, AGU Fall meeting, Abstract V32B-03]. While the phase analysis of weather radar echoes from ground targets is established for estimating the atmospheric refractivity [Besson and du Châtelet, 2013, http://dx.doi.org/ 10.1175/ JTECH-D-12-00167.1], we consider here the variability of the atmosphere as a source of uncertainty. We describe the implementation of this technique in a dedicated compact low power FMCW system. Observations at Stromboli suggest an expansion of the vent prior to the eruption on the order of millimeter which is on the same oder as reported by [Noferini et al., 2009, doi: 10.1109/IGARSS. 2009. 5416901] and in case of Santiaguito volcano we were able to observe the post eruptive subsidence of the volcanic dome. We suggest further to resolve the range/refractivity ambiguity by using a dual frequency radar with sufficient frequency separation for utilizing the frequency dependence of refractivity.

  6. Revealing the synergetic effects in Ni nanoparticle-carbon nanotube hybrids by scanning transmission X-ray microscopy and their application in the hydrolysis of ammonia borane

    NASA Astrophysics Data System (ADS)

    Zhao, Guanqi; Zhong, Jun; Wang, Jian; Sham, Tsun-Kong; Sun, Xuhui; Lee, Shuit-Tong

    2015-05-01

    The hybrids of carbon nanotubes (CNTs) and the supported Ni nanoparticles (NPs) have been studied by scanning transmission X-ray microscopy (STXM) and tested by the hydrolysis reaction of ammonia borane (AB, NH3BH3). Data clearly showed the existence of a strong interaction between Ni NPs and thin CNTs (C-O-Ni bonds), which favored the tunable (buffer) electronic structure of Ni NPs facilitating the catalytic process. The hydrolysis process of AB confirmed the hypothesis that the hybrids with a strong interfacial interaction would show superior catalytic performance, while the hybrids with a weak interfacial interaction show poor performance. Our results provide a wealth of detailed information regarding the electronic structure of the NP-CNT hybrids and provide guidance towards the rational design of high-performance catalysts for energy applications.The hybrids of carbon nanotubes (CNTs) and the supported Ni nanoparticles (NPs) have been studied by scanning transmission X-ray microscopy (STXM) and tested by the hydrolysis reaction of ammonia borane (AB, NH3BH3). Data clearly showed the existence of a strong interaction between Ni NPs and thin CNTs (C-O-Ni bonds), which favored the tunable (buffer) electronic structure of Ni NPs facilitating the catalytic process. The hydrolysis process of AB confirmed the hypothesis that the hybrids with a strong interfacial interaction would show superior catalytic performance, while the hybrids with a weak interfacial interaction show poor performance. Our results provide a wealth of detailed information regarding the electronic structure of the NP-CNT hybrids and provide guidance towards the rational design of high-performance catalysts for energy applications. Electronic supplementary information (ESI) available: Magnified TEM images, high resolution TEM images and the particle size distributions of the samples, the STXM results of a thick tube at different positions, XPS results, stability test. See DOI: 10.1039/c5nr01168j

  7. Experimental Evidence of Dipolar Interaction in Bilayer Nanocomposite Magnets

    DTIC Science & Technology

    2010-11-25

    corporated to improve experimental systems. However, re- ported bulk nanocomposite magnets exhibit (BH)max val- ues that are far below the...Appl Phys A DOI 10.1007/s00339-010-6073-6 Experimental evidence of dipolar interaction in bilayer nanocomposite magnets A.J. Zambano · H. Oguchi · I...Abstract We use magnetic thin film hard/non/soft-mag- netic trilayer systems to probe the nature of the hard–soft phase interaction and the role

  8. A novel single-ended readout depth-of-interaction PET detector fabricated using sub-surface laser engraving.

    PubMed

    Uchida, H; Sakai, T; Yamauchi, H; Hakamata, K; Shimizu, K; Yamashita, T

    2016-09-21

    We propose a novel scintillation detector design for positron emission tomography (PET), which has depth of interaction (DOI) capability and uses a single-ended readout scheme. The DOI detector contains a pair of crystal bars segmented using sub-surface laser engraving (SSLE). The two crystal bars are optically coupled to each other at their top segments and are coupled to two photo-sensors at their bottom segments. Initially, we evaluated the performance of different designs of single crystal bars coupled to photomultiplier tubes at both ends. We found that segmentation by SSLE results in superior performance compared to the conventional method. As the next step, we constructed a crystal unit composed of a 3  ×  3  ×  20 mm 3 crystal bar pair, with each bar containing four layers segmented using the SSLE. We measured the DOI performance by changing the optical conditions for the crystal unit. Based on the experimental results, we then assessed the detector performance in terms of the DOI capability by evaluating the position error, energy resolution, and light collection efficiency for various crystal unit designs with different bar sizes and a different number of layers (four to seven layers). DOI encoding with small position error was achieved for crystal units composed of a 3  ×  3  ×  20 mm 3 LYSO bar pair having up to seven layers, and with those composed of a 2  ×  2  ×  20 mm 3 LYSO bar pair having up to six layers. The energy resolution of the segment in the seven-layer 3  ×  3  ×  20 mm 3 crystal bar pair was 9.3%-15.5% for 662 keV gamma-rays, where the segments closer to the photo-sensors provided better energy resolution. SSLE provides high geometrical accuracy at low production cost due to the simplicity of the crystal assembly. Therefore, the proposed DOI detector is expected to be an attractive choice for practical small-bore PET systems dedicated to imaging of the brain, breast, and small animals.

  9. Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior

    PubMed Central

    Fischer, Caleb N; Trautman, Eric P; Crawford, Jason M; Stabb, Eric V; Handelsman, Jo; Broderick, Nichole A

    2017-01-01

    Animals host multi-species microbial communities (microbiomes) whose properties may result from inter-species interactions; however, current understanding of host-microbiome interactions derives mostly from studies in which elucidation of microbe-microbe interactions is difficult. In exploring how Drosophila melanogaster acquires its microbiome, we found that a microbial community influences Drosophila olfactory and egg-laying behaviors differently than individual members. Drosophila prefers a Saccharomyces-Acetobacter co-culture to the same microorganisms grown individually and then mixed, a response mainly due to the conserved olfactory receptor, Or42b. Acetobacter metabolism of Saccharomyces-derived ethanol was necessary, and acetate and its metabolic derivatives were sufficient, for co-culture preference. Preference correlated with three emergent co-culture properties: ethanol catabolism, a distinct volatile profile, and yeast population decline. Egg-laying preference provided a context-dependent fitness benefit to larvae. We describe a molecular mechanism by which a microbial community affects animal behavior. Our results support a model whereby emergent metabolites signal a beneficial multispecies microbiome. DOI: http://dx.doi.org/10.7554/eLife.18855.001 PMID:28068220

  10. SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells

    PubMed Central

    Myers, Samuel A; Peddada, Sailaja; Chatterjee, Nilanjana; Friedrich, Tara; Tomoda, Kiichrio; Krings, Gregor; Thomas, Sean; Maynard, Jason; Broeker, Michael; Thomson, Matthew; Pollard, Katherine; Yamanaka, Shinya; Burlingame, Alma L; Panning, Barbara

    2016-01-01

    The transcription factor SOX2 is central in establishing and maintaining pluripotency. The processes that modulate SOX2 activity to promote pluripotency are not well understood. Here, we show SOX2 is O-GlcNAc modified in its transactivation domain during reprogramming and in mouse embryonic stem cells (mESCs). Upon induction of differentiation SOX2 O-GlcNAcylation at serine 248 is decreased. Replacing wild type with an O-GlcNAc-deficient SOX2 (S248A) increases reprogramming efficiency. ESCs with O-GlcNAc-deficient SOX2 exhibit alterations in gene expression. This change correlates with altered protein-protein interactions and genomic occupancy of the O-GlcNAc-deficient SOX2 compared to wild type. In addition, SOX2 O-GlcNAcylation impairs the SOX2-PARP1 interaction, which has been shown to regulate ESC self-renewal. These findings show that SOX2 activity is modulated by O-GlcNAc, and provide a novel regulatory mechanism for this crucial pluripotency transcription factor. DOI: http://dx.doi.org/10.7554/eLife.10647.001 PMID:26949256

  11. Cyclophilin A-regulated ubiquitination is critical for RIG-I-mediated antiviral immune responses

    PubMed Central

    Liu, Wei; Li, Jing; Zheng, Weinan; Shang, Yingli; Zhao, Zhendong; Wang, Shanshan; Bi, Yuhai; Zhang, Shuang; Xu, Chongfeng; Duan, Ziyuan; Zhang, Lianfeng; Wang, Yue L; Jiang, Zhengfan; Liu, Wenjun; Sun, Lei

    2017-01-01

    RIG-I is a key cytosolic pattern recognition receptor that interacts with MAVS to induce type I interferons (IFNs) against RNA virus infection. In this study, we found that cyclophilin A (CypA), a peptidyl-prolyl cis/trans isomerase, functioned as a critical positive regulator of RIG-I-mediated antiviral immune responses. Deficiency of CypA impaired RIG-I-mediated type I IFN production and promoted viral replication in human cells and mice. Upon Sendai virus infection, CypA increased the interaction between RIG-I and its E3 ubiquitin ligase TRIM25, leading to enhanced TRIM25-mediated K63-linked ubiquitination of RIG-I that facilitated recruitment of RIG-I to MAVS. In addition, CypA and TRIM25 competitively interacted with MAVS, thereby inhibiting TRIM25-induced K48-linked ubiquitination of MAVS. Taken together, our findings reveal an essential role of CypA in boosting RIG-I-mediated antiviral immune responses by controlling the ubiquitination of RIG-I and MAVS. DOI: http://dx.doi.org/10.7554/eLife.24425.001 PMID:28594325

  12. Dynamic metabolic exchange governs a marine algal-bacterial interaction

    PubMed Central

    Segev, Einat; Wyche, Thomas P; Kim, Ki Hyun; Petersen, Jörn; Ellebrandt, Claire; Vlamakis, Hera; Barteneva, Natasha; Paulson, Joseph N; Chai, Liraz; Clardy, Jon; Kolter, Roberto

    2016-01-01

    Emiliania huxleyi is a model coccolithophore micro-alga that generates vast blooms in the ocean. Bacteria are not considered among the major factors influencing coccolithophore physiology. Here we show through a laboratory model system that the bacterium Phaeobacter inhibens, a well-studied member of the Roseobacter group, intimately interacts with E. huxleyi. While attached to the algal cell, bacteria initially promote algal growth but ultimately kill their algal host. Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic acid. Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased by tryptophan, which is exuded from the algal cell. Algal death triggered by bacteria involves activation of pathways unique to oxidative stress response and programmed cell death. Our observations suggest that bacteria greatly influence the physiology and metabolism of E. huxleyi. Coccolithophore-bacteria interactions should be further studied in the environment to determine whether they impact micro-algal population dynamics on a global scale. DOI: http://dx.doi.org/10.7554/eLife.17473.001 PMID:27855786

  13. The E3 ligase Ubr3 regulates Usher syndrome and MYH9 disorder proteins in the auditory organs of Drosophila and mammals

    PubMed Central

    Li, Tongchao; Giagtzoglou, Nikolaos; Eberl, Daniel F; Jaiswal, Sonal Nagarkar; Cai, Tiantian; Godt, Dorothea; Groves, Andrew K; Bellen, Hugo J

    2016-01-01

    Myosins play essential roles in the development and function of auditory organs and multiple myosin genes are associated with hereditary forms of deafness. Using a forward genetic screen in Drosophila, we identified an E3 ligase, Ubr3, as an essential gene for auditory organ development. Ubr3 negatively regulates the mono-ubiquitination of non-muscle Myosin II, a protein associated with hearing loss in humans. The mono-ubiquitination of Myosin II promotes its physical interaction with Myosin VIIa, a protein responsible for Usher syndrome type IB. We show that ubr3 mutants phenocopy pathogenic variants of Myosin II and that Ubr3 interacts genetically and physically with three Usher syndrome proteins. The interactions between Myosin VIIa and Myosin IIa are conserved in the mammalian cochlea and in human retinal pigment epithelium cells. Our work reveals a novel mechanism that regulates protein complexes affected in two forms of syndromic deafness and suggests a molecular function for Myosin IIa in auditory organs. DOI: http://dx.doi.org/10.7554/eLife.15258.001 PMID:27331610

  14. Sgol2 provides a regulatory platform that coordinates essential cell cycle processes during meiosis I in oocytes

    PubMed Central

    Rattani, Ahmed; Wolna, Magda; Ploquin, Mickael; Helmhart, Wolfgang; Morrone, Seamus; Mayer, Bernd; Godwin, Jonathan; Xu, Wenqing; Stemmann, Olaf; Pendas, Alberto; Nasmyth, Kim

    2013-01-01

    Accurate chromosome segregation depends on coordination between cohesion resolution and kinetochore-microtubule interactions (K-fibers), a process regulated by the spindle assembly checkpoint (SAC). How these diverse processes are coordinated remains unclear. We show that in mammalian oocytes Shugoshin-like protein 2 (Sgol2) in addition to protecting cohesin, plays an important role in turning off the SAC, in promoting the congression and bi-orientation of bivalents on meiosis I spindles, in facilitating formation of K-fibers and in limiting bivalent stretching. Sgol2’s ability to protect cohesin depends on its interaction with PP2A, as is its ability to silence the SAC, with the latter being mediated by direct binding to Mad2. In contrast, its effect on bivalent stretching and K-fiber formation is independent of PP2A and mediated by recruitment of MCAK and inhibition of Aurora C kinase activity respectively. By virtue of its multiple interactions, Sgol2 links many of the processes essential for faithful chromosome segregation. DOI: http://dx.doi.org/10.7554/eLife.01133.001 PMID:24192037

  15. Integration of Tmc1/2 into the mechanotransduction complex in zebrafish hair cells is regulated by Transmembrane O-methyltransferase (Tomt)

    PubMed Central

    Erickson, Timothy; Morgan, Clive P; Olt, Jennifer; Hardy, Katherine; Busch-Nentwich, Elisabeth; Maeda, Reo; Clemens, Rachel; Krey, Jocelyn F; Nechiporuk, Alex; Barr-Gillespie, Peter G; Marcotti, Walter; Nicolson, Teresa

    2017-01-01

    Transmembrane O-methyltransferase (TOMT/LRTOMT) is responsible for non-syndromic deafness DFNB63. However, the specific defects that lead to hearing loss have not been described. Using a zebrafish model of DFNB63, we show that the auditory and vestibular phenotypes are due to a lack of mechanotransduction (MET) in Tomt-deficient hair cells. GFP-tagged Tomt is enriched in the Golgi of hair cells, suggesting that Tomt might regulate the trafficking of other MET components to the hair bundle. We found that Tmc1/2 proteins are specifically excluded from the hair bundle in tomt mutants, whereas other MET complex proteins can still localize to the bundle. Furthermore, mouse TOMT and TMC1 can directly interact in HEK 293 cells, and this interaction is modulated by His183 in TOMT. Thus, we propose a model of MET complex assembly where Tomt and the Tmcs interact within the secretory pathway to traffic Tmc proteins to the hair bundle. DOI: http://dx.doi.org/10.7554/eLife.28474.001 PMID:28534737

  16. Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex

    PubMed Central

    Kang, Jin Young; Olinares, Paul Dominic B; Chen, James; Campbell, Elizabeth A; Mustaev, Arkady; Chait, Brian T; Gottesman, Max E; Darst, Seth A

    2017-01-01

    Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λ DNA. To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP β and β’ subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions. The nature of Nun interactions inside the RNAP active site cleft suggests that RNAP clamp opening is required for Nun to establish its interactions, explaining why Nun acts on paused TECs. DOI: http://dx.doi.org/10.7554/eLife.25478.001 PMID:28318486

  17. Dynamic NF-κB and E2F interactions control the priority and timing of inflammatory signalling and cell proliferation

    PubMed Central

    Ankers, John M; Awais, Raheela; Jones, Nicholas A; Boyd, James; Ryan, Sheila; Adamson, Antony D; Harper, Claire V; Bridge, Lloyd; Spiller, David G; Jackson, Dean A; Paszek, Pawel; Sée, Violaine; White, Michael RH

    2016-01-01

    Dynamic cellular systems reprogram gene expression to ensure appropriate cellular fate responses to specific extracellular cues. Here we demonstrate that the dynamics of Nuclear Factor kappa B (NF-κB) signalling and the cell cycle are prioritised differently depending on the timing of an inflammatory signal. Using iterative experimental and computational analyses, we show physical and functional interactions between NF-κB and the E2 Factor 1 (E2F-1) and E2 Factor 4 (E2F-4) cell cycle regulators. These interactions modulate the NF-κB response. In S-phase, the NF-κB response was delayed or repressed, while cell cycle progression was unimpeded. By contrast, activation of NF-κB at the G1/S boundary resulted in a longer cell cycle and more synchronous initial NF-κB responses between cells. These data identify new mechanisms by which the cellular response to stress is differentially controlled at different stages of the cell cycle. DOI: http://dx.doi.org/10.7554/eLife.10473.001 PMID:27185527

  18. Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

    PubMed Central

    Manna, Moutusi; Niemelä, Miia; Tynkkynen, Joona; Javanainen, Matti; Kulig, Waldemar; Müller, Daniel J; Rog, Tomasz; Vattulainen, Ilpo

    2016-01-01

    There is evidence that lipids can be allosteric regulators of membrane protein structure and activation. However, there are no data showing how exactly the regulation emerges from specific lipid-protein interactions. Here we show in atomistic detail how the human β2-adrenergic receptor (β2AR) – a prototypical G protein-coupled receptor – is modulated by cholesterol in an allosteric fashion. Extensive atomistic simulations show that cholesterol regulates β2AR by limiting its conformational variability. The mechanism of action is based on the binding of cholesterol at specific high-affinity sites located near the transmembrane helices 5–7 of the receptor. The alternative mechanism, where the β2AR conformation would be modulated by membrane-mediated interactions, plays only a minor role. Cholesterol analogues also bind to cholesterol binding sites and impede the structural flexibility of β2AR, however cholesterol generates the strongest effect. The results highlight the capacity of lipids to regulate the conformation of membrane receptors through specific interactions. DOI: http://dx.doi.org/10.7554/eLife.18432.001 PMID:27897972

  19. Development of high resolution phoswich depth-of-interaction block detectors utilizing Mg co-doped new scintillators

    NASA Astrophysics Data System (ADS)

    Kobayashi, Takahiro; Yamamoto, Seiichi; Yeom, Jung-Yeol; Kamada, Kei; Yoshikawa, Akira

    2017-12-01

    To correct for parallax error in positron emission tomography (PET), phoswich depth-of-interaction (DOI) detector using multiple scintillators with different decay times is a practical approach. However not many scintillator combinations suitable for phoswich DOI detector have been reported. Ce doped Gd3Ga3Al2O12 (GFAG) is a newly developed promising scintillator for PET detector, which has high density, high light output, appropriate light emission wavelength for silicon-photomultiplier (Si-PM) and faster decay time than that of Ce doped Gd3Al2Ga3O12 (GAGG). In this study, we developed a Si-PM based phoswich DOI block detector of GFAG with GAGG crystal arrays and evaluated its performance. We assembled a GFAG block and a GAGG block and they were optically coupled in depth direction to form a phoswich detector block. The phoswich block was optically coupled to a Si-PM array with a 1 mm thick light guide. The sizes of the GFAG and GAGG pixels were 0.9 mm x 0.9 mm x 7.5 mm and they were arranged into 24 x 24 matrix with 0.1 mm thick BaSO4 as reflector. We conducted the performance evaluation for two types of configurations; GFAG block arranged in upper layer (GFAG/GAGG) and GAGG arranged in upper layer (GAGG/GFAG). The measured two dimensional position histograms of these block detectors showed good separation and pulse shape spectra produced two distinct peaks for both configurations although some difference in energy spectra were observed. These results indicate phoswich block detectors composed of GFAG and GAGG are promising for high resolution DOI PET systems.

  20. Selective and directional actuation of elastomer films using chained magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Mishra, Sumeet R.; Dickey, Michael D.; Velev, Orlin D.; Tracy, Joseph B.

    2016-01-01

    We report selective and directional actuation of elastomer films utilizing magnetic anisotropy introduced by chains of Fe3O4 magnetic nanoparticles (MNPs). Under uniform magnetic fields or field gradients, dipolar interactions between the MNPs favor magnetization along the chain direction and cause selective lifting. This mechanism is described using a simple model.We report selective and directional actuation of elastomer films utilizing magnetic anisotropy introduced by chains of Fe3O4 magnetic nanoparticles (MNPs). Under uniform magnetic fields or field gradients, dipolar interactions between the MNPs favor magnetization along the chain direction and cause selective lifting. This mechanism is described using a simple model. Electronic supplementary information (ESI) available: Two videos for actuation while rotating the sample, experimental details of nanoparticle synthesis, polymer composite preparation, and alignment and bending studies, details of the theoretical model of actuation, and supplemental figures for understanding the behavior of rotating samples and results from modelling. See DOI: 10.1039/c5nr07410j

  1. Non-covalent S···O interactions control conformation in a scaffold that disrupts islet amyloid polypeptide fibrillation† †Electronic supplementary information (ESI) available: Experimental procedures; 1H, 13C and NOESY spectra; HRMS, and IR values. CCDC 1453550 (24), ThT assay data, computation, electron microscopy. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc00756b Click here for additional data file.

    PubMed Central

    Peacock, Hayden; Luo, Jinghui; Yamashita, Tohru; Luccarelli, James

    2016-01-01

    Conformationally-constrained molecules that selectively recognise the surfaces of proteins have the potential to direct the path of protein folding. Such molecules are of therapeutic interest because the misfolding of proteins, especially that which results in fibrillation and aggregation, is strongly correlated with numerous diseases. Here we report the novel use of S···O interactions as a conformational control element in a new class of non-peptidic scaffold that mimics key elements of protein surfaces. These molecules disrupt the fibrillation of islet amyloid polypeptide (IAPP), a process that is implicated in the pathology of type II diabetes. PMID:28451100

  2. High-speed AFM for scanning the architecture of living cells

    NASA Astrophysics Data System (ADS)

    Li, Jing; Deng, Zhifeng; Chen, Daixie; Ao, Zhuo; Sun, Quanmei; Feng, Jiantao; Yin, Bohua; Han, Li; Han, Dong

    2013-08-01

    We address the modelling of tip-cell membrane interactions under high speed atomic force microscopy. Using a home-made device with a scanning area of 100 × 100 μm2, in situ imaging of living cells is successfully performed under loading rates from 1 to 50 Hz, intending to enable detailed descriptions of physiological processes in living samples.We address the modelling of tip-cell membrane interactions under high speed atomic force microscopy. Using a home-made device with a scanning area of 100 × 100 μm2, in situ imaging of living cells is successfully performed under loading rates from 1 to 50 Hz, intending to enable detailed descriptions of physiological processes in living samples. Electronic supplementary information (ESI) available: Movie of the real-time change of inner surface within fresh blood vessel. The movie was captured at a speed of 30 Hz in the range of 80 μm × 80 μm. See DOI: 10.1039/c3nr01464a

  3. Meteorological and snow distribution data in the Izas Experimental Catchment (Spanish Pyrenees) from 2011 to 2017

    NASA Astrophysics Data System (ADS)

    Revuelto, Jesús; Azorin-Molina, Cesar; Alonso-González, Esteban; Sanmiguel-Vallelado, Alba; Navarro-Serrano, Francisco; Rico, Ibai; López-Moreno, Juan Ignacio

    2017-12-01

    This work describes the snow and meteorological data set available for the Izas Experimental Catchment in the Central Spanish Pyrenees, from the 2011 to 2017 snow seasons. The experimental site is located on the southern side of the Pyrenees between 2000 and 2300 m above sea level, covering an area of 55 ha. The site is a good example of a subalpine environment in which the evolution of snow accumulation and melt are of major importance in many mountain processes. The climatic data set consists of (i) continuous meteorological variables acquired from an automatic weather station (AWS), (ii) detailed information on snow depth distribution collected with a terrestrial laser scanner (TLS, lidar technology) for certain dates across the snow season (between three and six TLS surveys per snow season) and (iii) time-lapse images showing the evolution of the snow-covered area (SCA). The meteorological variables acquired at the AWS are precipitation, air temperature, incoming and reflected solar radiation, infrared surface temperature, relative humidity, wind speed and direction, atmospheric air pressure, surface temperature (snow or soil surface), and soil temperature; all were taken at 10 min intervals. Snow depth distribution was measured during 23 field campaigns using a TLS, and daily information on the SCA was also retrieved from time-lapse photography. The data set (https://doi.org/10.5281/zenodo.848277) is valuable since it provides high-spatial-resolution information on the snow depth and snow cover, which is particularly useful when combined with meteorological variables to simulate snow energy and mass balance. This information has already been analyzed in various scientific studies on snow pack dynamics and its interaction with the local climatology or topographical characteristics. However, the database generated has great potential for understanding other environmental processes from a hydrometeorological or ecological perspective in which snow dynamics play a determinant role.

  4. Blood Smear: MedlinePlus Lab Test Information

    MedlinePlus

    ... Test Information → Blood Smear URL of this page: https://medlineplus.gov/labtests/bloodsmear.html Blood Smear To ... May 26]; 353(5): 498–507. Available from: http://www.nejm.org/doi/full/10.1056/NEJMra043442 ...

  5. The modulation of savouring by prediction error and its effects on choice

    PubMed Central

    Iigaya, Kiyohito; Story, Giles W; Kurth-Nelson, Zeb; Dolan, Raymond J; Dayan, Peter

    2016-01-01

    When people anticipate uncertain future outcomes, they often prefer to know their fate in advance. Inspired by an idea in behavioral economics that the anticipation of rewards is itself attractive, we hypothesized that this preference of advance information arises because reward prediction errors carried by such information can boost the level of anticipation. We designed new empirical behavioral studies to test this proposal, and confirmed that subjects preferred advance reward information more strongly when they had to wait for rewards for a longer time. We formulated our proposal in a reinforcement-learning model, and we showed that our model could account for a wide range of existing neuronal and behavioral data, without appealing to ambiguous notions such as an explicit value for information. We suggest that such boosted anticipation significantly drives risk-seeking behaviors, most pertinently in gambling. DOI: http://dx.doi.org/10.7554/eLife.13747.001 PMID:27101365

  6. Coevolutionary modeling of protein sequences: Predicting structure, function, and mutational landscapes

    NASA Astrophysics Data System (ADS)

    Weigt, Martin

    Over the last years, biological research has been revolutionized by experimental high-throughput techniques, in particular by next-generation sequencing technology. Unprecedented amounts of data are accumulating, and there is a growing request for computational methods unveiling the information hidden in raw data, thereby increasing our understanding of complex biological systems. Statistical-physics models based on the maximum-entropy principle have, in the last few years, played an important role in this context. To give a specific example, proteins and many non-coding RNA show a remarkable degree of structural and functional conservation in the course of evolution, despite a large variability in amino acid sequences. We have developed a statistical-mechanics inspired inference approach - called Direct-Coupling Analysis - to link this sequence variability (easy to observe in sequence alignments, which are available in public sequence databases) to bio-molecular structure and function. In my presentation I will show, how this methodology can be used (i) to infer contacts between residues and thus to guide tertiary and quaternary protein structure prediction and RNA structure prediction, (ii) to discriminate interacting from non-interacting protein families, and thus to infer conserved protein-protein interaction networks, and (iii) to reconstruct mutational landscapes and thus to predict the phenotypic effect of mutations. References [1] M. Figliuzzi, H. Jacquier, A. Schug, O. Tenaillon and M. Weigt ''Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1'', Mol. Biol. Evol. (2015), doi: 10.1093/molbev/msv211 [2] E. De Leonardis, B. Lutz, S. Ratz, S. Cocco, R. Monasson, A. Schug, M. Weigt ''Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction'', Nucleic Acids Research (2015), doi: 10.1093/nar/gkv932 [3] F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. Marks, C. Sander, R. Zecchina, J.N. Onuchic, T. Hwa, M. Weigt, ''Direct-coupling analysis of residue co-evolution captures native contacts across many protein families'', Proc. Natl. Acad. Sci. 108, E1293-E1301 (2011).

  7. DOI Climate Science Centers--Regional science to address management priorities

    USGS Publications Warehouse

    O'Malley, Robin

    2012-01-01

    Our Nation's lands, waters, and ecosystems and the living and cultural resources they contain face myriad challenges from invasive species, the effects of changing land and water use, habitat fragmentation and degradation, and other influences. These challenges are compounded by increasing influences from a changing climate—higher temperatures, increasing droughts, floods, and wildfires, and overall increasing variability in weather and climate. The Department of the Interior (DOI) has established eight regional Climate Science Centers (CSC) (fig. 1) that will provide scientific information and tools to natural and cultural resource managers as they plan for conserving these resources in a changing world. The U.S. Geological Survey (USGS) National Climate Change and Wildlife Science Center (NCCWSC) is managing the CSCs on behalf of the DOI.

  8. Emission Data For Climate-Chemistry Interactions

    NASA Astrophysics Data System (ADS)

    Smith, S. J.

    2012-12-01

    Data on anthropogenic and natural emissions of reactive species are a critical input for studies of atmospheric chemistry and climate. The availability and characteristics of anthropogenic emissions data that can be used for such studies are reviewed and pathways for future work discuss Global and regional datasets for historical and future emissions are available, but their characteristics and applicability for specific studies differ. For the first time, a coordinated set of historical emissions (Lamarque et al 2010) and the future projections (van Vuurren et al. 2011) have been developed for use in the CMIP5 and ACCMIP long-term simulation comparison projects. These data have decadal resolution and were designed for long-term, global simulations. These data, however, lack finer-scale spatial and temporal detail that might be needed for some studies. Robust and timely updates of emissions data is generally lacking, although recent updates will be presented. While historical emission data is often treated as known, emissions are uncertain, even though this uncertainty is rarely quantified. Uncertainty varies by species and location. Inverse modeling is starting to indicate where emission data may be uncertain, which opens the way to improving these data overall. Further interaction between the chemistry modeling and inventory development communities are needed. Future projections are intrinsically uncertain, and while institutions and processes are in place to develop and review long-term century-scale scenarios, a need has remained for a wider range in shorter-term (e.g., several decade) projections. Emissions and scenario development communities have been working to fill this need. Communication across disciplines of the assumptions embedded in emissions projections remains a challenge. Atmospheric chemistry models are a central tool needed for studying chemistry-climate interactions. Simpler models, however, are also needed in order to examine interactions between different physical systems and also between the physical and human systems. Statistical models of system responses are particularly needed both to parameterize interactions in models that cannot simulate particular processes directly, and also to represent uncertainty. Coordinated model experiments are necessary to provide the information needed to develop these representations (i.e. Wild et al 2011). Lamarque, J. F, et al. (2010) Historical (1850-2000) gridded anthropogenic and biomass burning emissions of reactive gases and aerosols: methodology and application. Atmospheric Chemistry and Physics 10 pp. 7017-7039. doi:10.5194/acp-10-7017-2010 Van Vuuren, D, JA Edmonds, M Kainuma, K Riahi, AM Thomson, KA Hibbard, G Hurtt, T Kram, V Krey, JF Lamarque, matsui, M Meinhausen, N Nakicenovic, SJ Smith, and SK Rose. 2011. "The Representative Concentration Pathways: An Overview." Climatic Change 109 (1-2) 5-31. doi: 10.1007/s10584-011-0148-z. Wild, O., et al. (2012) Modelling future changes in surface ozone: A parameterized approach. Atmos. Chem. Phys., 12, 2037-2054, doi:10.5194/acp-12-2037-2012.

  9. Information Transfer Ion Wireless Networks

    DTIC Science & Technology

    2010-07-01

    conferences with proceed- ings to be made available online in the IEEE Xplore database, namely IFIP Wireless Days (WD 2008) at Dubai, UAE, and the...Poland, May 2008, pp. 61-64, IEEE Xplore , DOI = 10.1109/INFTECH. 2008.4621591. 2. J. Konorski, IEEE 802.11 LAN Capacity: Incentives and Incentive...2008, Dubai, UAE, Nov. 2008, IEEE Xplore DOI = 10.1109/WD.2008.4812857. 4. J. Konorski, QoS Provision in an Ad Hoc IEEE 802.11 WLAN: A Bayesian War

  10. Information Transfer in Wireless Networks

    DTIC Science & Technology

    2010-07-01

    conferences with proceed- ings to be made available online in the IEEE Xplore database, namely IFIP Wireless Days (WD 2008) at Dubai, UAE, and the...Poland, May 2008, pp. 61-64, IEEE Xplore , DOI = 10.1109/INFTECH. 2008.4621591. 2. J. Konorski, IEEE 802.11 LAN Capacity: Incentives and Incentive...2008, Dubai, UAE, Nov. 2008, IEEE Xplore DOI = 10.1109/WD.2008.4812857. 4. J. Konorski, QoS Provision in an Ad Hoc IEEE 802.11 WLAN: A Bayesian War

  11. Quantum Dot-Photonic Crystal Cavity QED Based Quantum Information Processing

    DTIC Science & Technology

    2012-08-14

    Majumdar, A. Faraon, M . Toishi, N. Stolz, P. Petroff, J. Vuckovic. Resonant Excitation of a Quantum Dot Strongly Coupled to a Photonic Crystal...11 J. O’Brien, A. Furusawa , J. Vuckovic. Photonic Quantum Technologies, Nature Photonics, (12 2009): . doi: 2010/08/30 15:11:17 10 D. Englund, A...devices via micron-scale electrical heaters, Applied Physics Letters, ( 2009): . doi: 2009/08/19 13:18:36 7 M . Toishi, D. Englund, A. Faraon, J

  12. Label-free biomolecular characterization of human breast cancer tissue with stimulated Raman scattering (SRS) spectral imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Lu, Fa-Ke F.; Calligaris, David; Suo, Yuanzhen; Santagata, Sandro; Golby, Alexandra J.; Xie, X. Sunney; Mallory, Melissa A.; Golshan, Mehra; Dillon, Deborah A.; Agar, Nathalie Y. R.

    2017-02-01

    Stimulated Raman scattering (SRS) microscopy has been used for rapid label-free imaging of various biomolecules and drugs in living cells and tissues (Science, doi:10.1126/science.aaa8870). Our recent work has demonstrated that lipid and protein mapping of cancer tissue renders pathology-like images, providing essential histopathological information with subcellular resolution of the entire specimen (Cancer Research, doi: 10.1158/0008-5472.CAN-16-027). We have also established the first SRS imaging Atlas of human brain tumors (Harvard Dataverse, doi: (doi:10.7910/DVN/EZW4EK). SRS imaging of tissue could provide invaluable information for cancer diagnosis and surgical guidance in two aspects: rapid surgical pathology and quantitative biomolecular characterization. In this work, we present the use of SRS microscopy for characterization of a few essential biomolecules in breast cancer. Human breast cancer tissue specimens at the tumor core, tumor margin and normal area (5 cm away from the tumor) from surgical cases will be imaged with SRS at multiple Raman shifts, including the peaks for lipid, protein, blood (absorption), collagen, microcalcification (calcium phosphates and calcium oxalate) and carotenoids. Most of these Raman shifts have relatively strong Raman cross sections, which ensures high-quality and fast imaging. This proof-of-principle study is sought to demonstrate the feasibility and potential of SRS imaging for ambient diagnosis and surgical guidance of breast cancer.

  13. Retraction Statement: "High-Volumetric Performance Aligned Nano-Porous Microwave Exfoliated Graphite Oxide-based Electrochemical Capacitors" and "Aligned Nano-Porous Microwave Exfoliated Graphite Oxide Ionic Actuators with High Strain and Elastic Energy Density".

    PubMed

    2016-11-01

    These articles first published on 15 August 2013 and 21 August 2013 on the Wiley Online Library have been retracted at the request of the Research Integrity Officer (RIO) of The Pennsylvania State University, in agreement with the corresponding authors, the journal's Editor-in-Chief, and Wiley-VCH Verlag GmbH & Co. KGaA, because portions of the reported results cannot be considered reliable or reproducible. Following an investigation by the RIO of The Pennsylvania State University, it was found that the data in Figure 2a,b and Figure S1a,b (Supporting Information) of the article with DOI: 10.1002/adma.201301243, and Figure S3 (Supporting Information) of the article with DOI: 10.1002/adma.201301370 were falsified. Data regarding the carbon electrode material, A-aMEGO, reported to have a density of 1.15 g cm -3 , in the article with DOI: 10.1002/adma.201301243, were falsified. The RIO of The Pennsylvania State University confirms that the investigation found that the mentioned data were falsified by the first author. No findings of research misconduct were made against the co-authors of these publications. [1] M. Ghaffari, Y. Zhou, H. Xu, M. Lin, T. Y. Kim, R. S. Ruoff, Q. M. Zhang, Adv. Mater. 25: 2013, 4879. doi:10.1002/adma.201301243 [2] M. Ghaffari, W. Kinsman, Y. Zhou, S. Murali, Q. Burlingame, M. Lin, R. S. Ruoff, Q. M. Zhang, Adv. Mater. 25: 2013, 6277. doi:10.1002/adma.201301370. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Ecological landscape elements: long-term monitoring in Great Britain, the Countryside Survey 1978-2007 and beyond

    NASA Astrophysics Data System (ADS)

    Wood, Claire M.; Bunce, Robert G. H.; Norton, Lisa R.; Maskell, Lindsay C.; Smart, Simon M.; Scott, W. Andrew; Henrys, Peter A.; Howard, David C.; Wright, Simon M.; Brown, Michael J.; Scott, Rod J.; Stuart, Rick C.; Watkins, John W.

    2018-04-01

    The Countryside Survey (CS) of Great Britain (GB) provides a unique and statistically robust series of datasets, consisting of an extensive set of repeated ecological measurements at a national scale, covering a time span of 29 years. CS was first undertaken in 1978 to provide a baseline for ecological and land use change monitoring in the rural environment of GB, following a stratified random design, based on 1 km squares. Originally, eight random 1 km squares were drawn from each of 32 environmental classes, thus comprising 256 sample squares in the 1978 survey. The number of these sites increased to 382 in 1984, 506 in 1990, 569 in 1998 and 591 in 2007. Detailed information regarding vegetation types and land use was mapped in all five surveys, allowing reporting by defined standard habitat classifications. Additionally, point and linear landscape features (such as trees and hedgerows) are available from all surveys after 1978. From these stratified, randomly located sample squares, information can be converted into national estimates, with associated error terms. Other data, relating to soils, freshwater and vegetation, were also sampled on analogous dates. However, the present paper describes only the surveys of landscape features and habitats. The resulting datasets provide a unique, comprehensive, quantitative ecological coverage of extent and change in these features in GB. Basic results are presented and their implications discussed. However, much opportunity for further analyses remains. Data from each of the survey years are available via the following DOIs: Landscape area data 1978: https://doi.org/10.5285/86c017ba-dc62-46f0-ad13-c862bf31740e, 1984: https://doi.org/10.5285/b656bb43-448d-4b2c-aade-7993aa243ea3, 1990: https://doi.org/10.5285/94f664e5-10f2-4655-bfe6-44d745f5dca7, 1998: https://doi.org/10.5285/1e050028-5c55-42f4-a0ea-c895d827b824, and 2007: https://doi.org/10.5285/bf189c57-61eb-4339-a7b3-d2e81fdde28d; Landscape linear feature data 1984: https://doi.org/10.5285/a3f5665c-94b2-4c46-909e-a98be97857e5, 1990: https://doi.org/10.5285/311daad4-bc8c-485a-bc8a-e0d054889219, 1998: https://doi.org/10.5285/8aaf6f8c-c245-46bb-8a2a-f0db012b2643 and 2007: https://doi.org/10.5285/e1d31245-4c0a-4dee-b36c-b23f1a697f88, Landscape point feature data 1984: https://doi.org/10.5285/124b872e-036e-4dd3-8316-476b5f42c16e, 1990: https://doi.org/10.5285/1481bc63-80d7-4d18-bcba-8804aa0a9e1b, 1998: https://doi.org/10.5285/ed10944f-40c8-4913-b3f5-13c8e844e153 and 2007: https://doi.org/10.5285/55dc5fd7-d3f7-4440-b8a7-7187f8b0550b.

  15. A depth-encoding PET detector that uses light sharing and single-ended readout with silicon photomultipliers

    NASA Astrophysics Data System (ADS)

    Kuang, Zhonghua; Yang, Qian; Wang, Xiaohui; Fu, Xin; Ren, Ning; Sang, Ziru; Wu, San; Zheng, Yunfei; Zhang, Xianming; Hu, Zhanli; Du, Junwei; Liang, Dong; Liu, Xin; Zheng, Hairong; Yang, Yongfeng

    2018-02-01

    Detectors with depth-encoding capability and good timing resolution are required to develop high-performance whole-body or total-body PET scanners. In this work, depth-encoding PET detectors that use light sharing between two discrete crystals and single-ended readout with silicon photomultipliers (SiPMs) were manufactured and evaluated. The detectors consisted of two unpolished 3  ×  3  ×  20 mm3 LYSO crystals with different coupling materials between them and were read out by Hamamatsu 3  ×  3 mm2 SiPMs with one-to-one coupling. The ratio of the energy of one SiPM to the total energy of two SiPMs was used to measure the depth of interaction (DOI). Detectors with different coupling materials in-between the crystals were measured in the singles mode in an effort to obtain detectors that can provide good DOI resolution. The DOI resolution and energy resolution of three types of detector were measured and the timing resolution was measured for the detector with the best DOI and energy resolution. The optimum detector, with 5 mm optical glue, a 9 mm triangular ESR and a 6 mm rectangular ESR in-between the unpolished crystals, provides a DOI resolution of 2.65 mm, an energy resolution of 10.0% and a timing resolution of 427 ps for events of E  >  400 keV. The detectors simultaneously provide good DOI and timing resolution, and show great promise for the development of high-performance whole-body and total-body PET scanners.

  16. 78 FR 3447 - Information Collection: Southern Alaska Sharing Network and Subsistence Study; Submitted for OMB...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-16

    ... address. FOR FURTHER INFORMATION CONTACT: Arlene Bajusz, Office of Policy, Regulations, and Analysis at... meeting of DOI/BOEM information needs on subsistence food harvest and sharing activities in various... gas development on subsistence food harvest and sharing activities. It investigates the resilience of...

  17. Structural characterization of framework–gas interactions in the metal–organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction† †Electronic supplementary information (ESI) available: Supplementary figures, crystallographic information, adsorption isotherms and fits, CCDC 1530119–1530126. For ESI and crystallographic data in CIF or other electronic format. See DOI: 10.1039/c7sc00449d Click here for additional data file. Click here for additional data file.

    PubMed Central

    Gonzalez, Miguel I.; Mason, Jarad A.; Bloch, Eric D.; Teat, Simon J.; Gagnon, Kevin J.; Morrison, Gregory Y.; Queen, Wendy L.

    2017-01-01

    The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH4, N2, O2, Ar, and P4 adsorption in Co2(dobdc) (dobdc4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(ii) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(ii) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH4 and Co–Ar interactions observed in Co2(dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(ii) sites in Co2(dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol–1 (for Ar). Moreover, the structures of Co2(dobdc)·3.8N2, Co2(dobdc)·5.9O2, and Co2(dobdc)·2.0Ar reveal the location of secondary (N2, O2, and Ar) and tertiary (O2) binding sites in Co2(dobdc), while high-pressure CO2, CO, CH4, N2, and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures. PMID:28966783

  18. Humans reclaimed lands in NorthEastern Italy and artificial drainage networks: effects of 30 years of Agricultural Surface Water Management

    NASA Astrophysics Data System (ADS)

    Sofia, Giulia; Pizzulli, Federica; Tarolli, Paolo

    2017-04-01

    Agriculture and land-use management has changed drastically in Italy since the end of the Second World War, driven by local but also European agricultural policies. As a result of these changes in farming practices and land use, many drainage networks have changed producing a greater exposure to flooding with a broad range of impacts on society, also because of climate inputs coupling with the human drivers. This study focuses on two main points: which kind of land use and farming changes have been observed in the most recent years ( 30 years)? How do these changes interact with climate and soil conditions? An open challenge to understand how these changes influence the watershed response, is, in fact, to understand if rainfall characteristics and climate have a synergistic effect, if their interaction matters, or to understand what element has the greatest influence on the watershed response connected to agricultural changes. The work is based on a simple model of water infiltration due to soil properties, and a connected evaluation of the distributed surface water storage offered by artificial drainage networks in a study area in Veneto (north-eastern Italy). The analysis shows that economic changes control the development of agro-industrial landscapes, with effects on the hydrological response. However, these changes deeply interact with antecedent soil conditions and climate characteristics. Intense and irregular rainfall events and events with a high recurrence should be expected to be the most critical. The presented outcomes highlight the importance of understanding how agricultural practices can be the driver of or can be used to avoid, or at least mitigate, flooding. The proposed methods can be valuable tools in evaluating the costs and benefits of the management of water in agriculture to inform better policy decision-making. References Sofia G, Tarolli P. 2017. Hydrological Response to 30 years of Agricultural Surface Water Management. Land 6 (1): 3 DOI: 10.3390/land6010003 Sofia G, Roder G, Dalla Fontana G, Tarolli P. 2017. Flood dynamics in urbanised landscapes: 100 years of climate and humans' interaction. Scientific Reports 7, 40527 DOI: 10.1038/srep40527

  19. A locally-blazed ant trail achieves efficient collective navigation despite limited information

    PubMed Central

    Fonio, Ehud; Heyman, Yael; Boczkowski, Lucas; Gelblum, Aviram; Kosowski, Adrian; Korman, Amos; Feinerman, Ofer

    2016-01-01

    Any organism faces sensory and cognitive limitations which may result in maladaptive decisions. Such limitations are prominent in the context of groups where the relevant information at the individual level may not coincide with collective requirements. Here, we study the navigational decisions exhibited by Paratrechina longicornis ants as they cooperatively transport a large food item. These decisions hinge on the perception of individuals which often restricts them from providing the group with reliable directional information. We find that, to achieve efficient navigation despite partial and even misleading information, these ants employ a locally-blazed trail. This trail significantly deviates from the classical notion of an ant trail: First, instead of systematically marking the full path, ants mark short segments originating at the load. Second, the carrying team constantly loses the guiding trail. We experimentally and theoretically show that the locally-blazed trail optimally and robustly exploits useful knowledge while avoiding the pitfalls of misleading information. DOI: http://dx.doi.org/10.7554/eLife.20185.001 PMID:27815944

  20. Social Media, Education and Data Sharing

    NASA Astrophysics Data System (ADS)

    King, T. A.; Walker, R. J.; Masters, A.

    2011-12-01

    Social media is a blending of technology and social interactions which allows for the creation and exchange of user-generated content. Social media started as conversations between groups of people, now companies are using social media to communicate with customers and politicians use it to communicate with their constituents. Social media is now finding uses in the science communities. This adoption is driven by the expectation of students that technology will be an integral part of their research and that it will match the technology they use in their social lifes. Students are using social media to keep informed and collaborate with others. They have also replaced notepads with smart mobile devices. We have been introducing social media components into Virtual Observatories as a way to quickly access and exchange information with a tap or a click. We discuss the use of Quick Response (QR) codes, Digital Object Identifiers (DOIs), unique identifiers, Twitter, Facebook and tiny URL redirects as ways to enable easier sharing of data and information. We also discuss what services and features are needed in a Virtual Observatory to make data sharing with social media possible.

  1. Summarizing components of U.S. Department of the Interior vulnerability assessments to focus climate adaptation planning

    USGS Publications Warehouse

    Thompson, Laura M.; Staudinger, Michelle D.; Carter, Shawn L.

    2015-09-29

    A secretarial order identified climate adaptation as a critical performance objective for future management of U.S. Department of the Interior (DOI) lands and resources in response to global change. Vulnerability assessments can inform climate adaptation planning by providing insight into what natural resources are most at risk and why. Three components of vulnerability—exposure, sensitivity, and adaptive capacity—were defined by the Intergovernmental Panel on Climate Change (IPCC) as necessary for identifying climate adaptation strategies and actions. In 2011, the DOI requested all internal bureaus report ongoing or completed vulnerability assessments about a defined range of assessment targets or climate-related threats. Assessment targets were defined as freshwater resources, landscapes and wildlife habitat, native and cultural resources, and ocean health. Climate-related threats were defined as invasive species, wildfire risk, sea-level rise, and melting ice and permafrost. Four hundred and three projects were reported, but the original DOI survey did not specify that information be provided on exposure, sensitivity, and adaptive capacity collectively as part of the request, and it was unclear which projects adhered to the framework recommended by the IPCC. Therefore, the U.S. Geological Survey National Climate Change and Wildlife Science Center conducted a supplemental survey to determine how frequently each of the three vulnerability components was assessed. Information was categorized for 124 of the 403 reported projects (30.8 percent) based on the three vulnerability components, and it was discovered that exposure was the most common component assessed (87.9 percent), followed by sensitivity (68.5 percent) and adaptive capacity (33.1 percent). The majority of projects did not fully assess vulnerability; projects focused on landscapes/wildlife habitats and sea-level rise were among the minority that simultaneously addressed all three vulnerability components. To maintain consistency with the IPCC definition of vulnerability, DOI may want to focus initial climate adaptation planning only on the outcomes of studies that comprehensively address vulnerability as inclusive of exposure, sensitivity, and adaptive capacity. Although the present study results are preliminary and used an unstructured survey design, they illustrate the importance of a comprehensive and consistent vulnerability definition and of using information on vulnerability components in DOI surveys to ensure relevant data are used to identify adaptation options.

  2. Understanding Protein-Protein Interactions: Essential Players in (Patho)physiology (Part 1).

    PubMed

    Wilson, Andrew J; Gunning, Patrick T

    2016-04-15

    This is the first of a two-part Editorial by the Guest Editors of the ChemBioChem and ChemMedChem joint Special Issue on Protein-Protein Interactions. Part 2 can be accessed via http://dx.doi.org/10.1002/cmdc.201600158; the complete issue can be viewed here: bit.ly/cbcVIppi. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Multiresolution Algorithms for Processing Giga-Models: Real-time Visualization, Reasoning, and Interaction

    DTIC Science & Technology

    2012-04-23

    Interactive Virtual Hair Salon , Presence, (05 2007): 237. doi: 2012/04/17 12:55:26 31 Theodore Kim, Jason Sewall, Avneesh Sud, Ming Lin. Fast...in Games , Utrecht, Netherlands, Nov. 2009. Keynote Speaker, IADIS International Conference on Computer Graphics and Visualization, Portugal, June 2009...Keynote Speaker, ACM Symposium on Virtual Reality Software and Technology, Bordeaux, France, October 2008. Invited Speaker, Motion in Games , Utrecht

  4. Efficient system modeling for a small animal PET scanner with tapered DOI detectors.

    PubMed

    Zhang, Mengxi; Zhou, Jian; Yang, Yongfeng; Rodríguez-Villafuerte, Mercedes; Qi, Jinyi

    2016-01-21

    A prototype small animal positron emission tomography (PET) scanner for mouse brain imaging has been developed at UC Davis. The new scanner uses tapered detector arrays with depth of interaction (DOI) measurement. In this paper, we present an efficient system model for the tapered PET scanner using matrix factorization and a virtual scanner geometry. The factored system matrix mainly consists of two components: a sinogram blurring matrix and a geometrical matrix. The geometric matrix is based on a virtual scanner geometry. The sinogram blurring matrix is estimated by matrix factorization. We investigate the performance of different virtual scanner geometries. Both simulation study and real data experiments are performed in the fully 3D mode to study the image quality under different system models. The results indicate that the proposed matrix factorization can maintain image quality while substantially reduce the image reconstruction time and system matrix storage cost. The proposed method can be also applied to other PET scanners with DOI measurement.

  5. CERTAIN: City Environment Range Testing for Autonomous Integrated Navigation

    NASA Technical Reports Server (NTRS)

    Brown, Jill

    2016-01-01

    This is a presentation to the DOI UAS Interagency group that is informational in nature; just sharing publicly available and previously released information on UAS regulations and some of the UAS operations Langley Center has, to create awareness with other government agencies.

  6. Interior's Climate Science Centers: Focus or Fail

    NASA Astrophysics Data System (ADS)

    Udall, B.

    2012-12-01

    After a whirlwind two years of impressive and critical infrastructure building, the Department of Interior's Climate Science Centers are now in a position to either succeed or fail. The CSCs have a number of difficult structural problems including too many constituencies relative to the available resources, an uneasy relationship among many of the constituencies including the DOI agencies themselves, a need to do science in a new, difficult and non-traditional way, and a short timeframe to produce useful products. The CSCs have built a broad and impressive network of scientists and stakeholders. These entities include science providers of the universities and the USGS, and decision makers from the states, tribes, DOI land managers and other federal agencies and NGOs. Rather than try to support all of these constituencies the CSCs would be better served by refocusing on a core mission of supporting DOI climate related decision making. The CSCs were designed to service the climate science needs of DOI agencies, many of which lost their scientific capabilities in the 1990s due to a well-intentioned but ultimately harmful re-organization at DOI involving the now defunct National Biological Survey. Many of these agencies would like to have their own scientists, have an uneasy relationship with the nominal DOI science provider, the USGS, and don't communicate effectively among themselves. The CSCs must not succumb to pursuing science in either the traditional mode of the USGS or in the traditional mode of the universities, or worse, both of them. These scientific partners will need to be flexible, learn how to collaborate and should expect to see fewer resources. Useful CSC processes and outputs should start with the recommendations of the 2009 NRC Report Informing Decisions in a Changing Climate: (1) begin with users' needs; (2) give priority to process over products; (3) link information producers and users; (4) build connections across disciplines and organizations; (5) seek institutional stability; and (6) design processes for learning. In addition, CSC outputs should help decision makers to embrace and focus on uncertainty rather than on attempts to reduce uncertainty. Model building can be a useful exercise if used as a broad intellectual exercise to understand systems instead of narrow projection-based efforts. In some cases DOI agencies may want very simple products including scientific syntheses. Social science work including but not limited to economics and policy should be considered when appropriate to decision maker needs. One method for allocating CSC resources would involve a limited number of small scoping meetings with climate sensitive regional DOI agencies. In the Southwest, for example, regional entities would include at least the Landscape Conservation Cooperatives, National Park Service, Fish and Wildlife Service, Bureau of Land Management, Reclamation and the US Forest Service, a critically important land manager with a well-funded and well-structured climate program. Given DOI's trust responsibility to the tribes, at least one project should be focused on meeting those needs in this region. The goal of these meetings would be to identify a small number of projects each with adequate funding for interdisciplinary teams of university and USGS scientists and DOI decision makers. Done correctly, the CSCs should be able to leverage resources with these DOI partners.

  7. The National Climate Change and Wildlife Science Center annual report for 2012

    USGS Publications Warehouse

    Varela-Acevedo, Elda; O'Malley, Robin

    2013-01-01

    Welcome to the inaugural edition of the U.S. Geological Survey (USGS) National Climate Change and Wildlife Science Center (NCCWSC) and the Department of the Interior (DOI) Climate Science Centers (CSCs) annual report. In 2008, Congress created the National Climate Change and Wildlife Science Center (NCCWSC) within the U.S. Geological Survey (USGS). The center was formed to respond to the demands of natural resource managers for rigorous scientific information and effective tools for assessing and responding to climate change. Located at the USGS National Headquarters in Reston, Va., the NCCWSC has invested more than $70 million in cutting-edge climate change research and, in response to Secretarial Order No. 3289,established and is managing eight regional Department of Interior (DOI) Climate Science Centers (CSCs). The mission of the NCCWSC is to provide natural resource managers with the tools and information they need to develop and execute management strategies that address the impacts of climate and other ongoing global changes on fish and wildlife and their habitats. The DOI CSCs are joint Federal-university partnerships that focus their scientific work on regional priorities identified by DOI Landscape Conservation Cooperatives (LCCs) as well as Federal, State, Tribal, and other resource managers. The CSCs provide access to a wide range of scientific capabilities through their network of university partners along with the USGS and other Federal agency scientists. The focus of the NCCWSC on multiregion and national priorities complements the regionally focused agendas of the CSCs.

  8. Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

    PubMed Central

    Bokulich, Nicholas A; Bergsveinson, Jordyn; Ziola, Barry; Mills, David A

    2015-01-01

    Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments. DOI: http://dx.doi.org/10.7554/eLife.04634.001 PMID:25756611

  9. Diabetes regulates fructose absorption through thioredoxin-interacting protein

    PubMed Central

    Dotimas, James R; Lee, Austin W; Schmider, Angela B; Carroll, Shannon H; Shah, Anu; Bilen, Julide; Elliott, Kayla R; Myers, Ronald B; Soberman, Roy J; Yoshioka, Jun; Lee, Richard T

    2016-01-01

    Metabolic studies suggest that the absorptive capacity of the small intestine for fructose is limited, though the molecular mechanisms controlling this process remain unknown. Here we demonstrate that thioredoxin-interacting protein (Txnip), which regulates glucose homeostasis in mammals, binds to fructose transporters and promotes fructose absorption by the small intestine. Deletion of Txnip in mice reduced fructose transport into the peripheral bloodstream and liver, as well as the severity of adverse metabolic outcomes resulting from long-term fructose consumption. We also demonstrate that fructose consumption induces expression of Txnip in the small intestine. Diabetic mice had increased expression of Txnip in the small intestine as well as enhanced fructose uptake and transport into the hepatic portal circulation. The deletion of Txnip in mice abolished the diabetes-induced increase in fructose absorption. Our results indicate that Txnip is a critical regulator of fructose metabolism and suggest that a diabetic state can promote fructose uptake. DOI: http://dx.doi.org/10.7554/eLife.18313.001 PMID:27725089

  10. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

    PubMed Central

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. DOI: http://dx.doi.org/10.7554/eLife.06181.001 PMID:25902402

  11. Protein translocation channel of mitochondrial inner membrane and matrix-exposed import motor communicate via two-domain coupling protein

    PubMed Central

    Banerjee, Rupa; Gladkova, Christina; Mapa, Koyeli; Witte, Gregor; Mokranjac, Dejana

    2015-01-01

    The majority of mitochondrial proteins are targeted to mitochondria by N-terminal presequences and use the TIM23 complex for their translocation across the mitochondrial inner membrane. During import, translocation through the channel in the inner membrane is coupled to the ATP-dependent action of an Hsp70-based import motor at the matrix face. How these two processes are coordinated remained unclear. We show here that the two domain structure of Tim44 plays a central role in this process. The N-terminal domain of Tim44 interacts with the components of the import motor, whereas its C-terminal domain interacts with the translocation channel and is in contact with translocating proteins. Our data suggest that the translocation channel and the import motor of the TIM23 complex communicate through rearrangements of the two domains of Tim44 that are stimulated by translocating proteins. DOI: http://dx.doi.org/10.7554/eLife.11897.001 PMID:26714107

  12. Coordination of planar cell polarity pathways through Spiny-legs

    PubMed Central

    Ambegaonkar, Abhijit A; Irvine, Kenneth D

    2015-01-01

    Morphogenesis and physiology of tissues and organs requires planar cell polarity (PCP) systems that orient and coordinate cells and their behaviors, but the relationship between PCP systems has been controversial. We have characterized how the Frizzled and Dachsous-Fat PCP systems are connected through the Spiny-legs isoform of the Prickle-Spiny-legs locus. Two different components of the Dachsous-Fat system, Dachsous and Dachs, can each independently interact with Spiny-legs and direct its localization in vivo. Through characterization of the contributions of Prickle, Spiny-legs, Dachsous, Fat, and Dachs to PCP in the Drosophila wing, eye, and abdomen, we define where Dachs-Spiny-legs and Dachsous-Spiny-legs interactions contribute to PCP, and provide a new understanding of the orientation of polarity and the basis of PCP phenotypes. Our results support the direct linkage of PCP systems through Sple in specific locales, while emphasizing that cells can be subject to and must ultimately resolve distinct, competing PCP signals. DOI: http://dx.doi.org/10.7554/eLife.09946.001 PMID:26505959

  13. Spatial self-organization favors heterotypic cooperation over cheating.

    PubMed

    Momeni, Babak; Waite, Adam James; Shou, Wenying

    2013-11-12

    Heterotypic cooperation-two populations exchanging distinct benefits that are costly to produce-is widespread. Cheaters, exploiting benefits while evading contribution, can undermine cooperation. Two mechanisms can stabilize heterotypic cooperation. In 'partner choice', cooperators recognize and choose cooperating over cheating partners; in 'partner fidelity feedback', fitness-feedback from repeated interactions ensures that aiding your partner helps yourself. How might a spatial environment, which facilitates repeated interactions, promote fitness-feedback? We examined this process through mathematical models and engineered Saccharomyces cerevisiae strains incapable of recognition. Here, cooperators and their heterotypic cooperative partners (partners) exchanged distinct essential metabolites. Cheaters exploited partner-produced metabolites without reciprocating, and were competitively superior to cooperators. Despite initially random spatial distributions, cooperators gained more partner neighbors than cheaters did. The less a cheater contributed, the more it was excluded and disfavored. This self-organization, driven by asymmetric fitness effects of cooperators and cheaters on partners during cell growth into open space, achieves assortment. DOI: http://dx.doi.org/10.7554/eLife.00960.001.

  14. Spatial self-organization favors heterotypic cooperation over cheating

    PubMed Central

    Momeni, Babak; Waite, Adam James; Shou, Wenying

    2013-01-01

    Heterotypic cooperation—two populations exchanging distinct benefits that are costly to produce—is widespread. Cheaters, exploiting benefits while evading contribution, can undermine cooperation. Two mechanisms can stabilize heterotypic cooperation. In ‘partner choice’, cooperators recognize and choose cooperating over cheating partners; in ‘partner fidelity feedback’, fitness-feedback from repeated interactions ensures that aiding your partner helps yourself. How might a spatial environment, which facilitates repeated interactions, promote fitness-feedback? We examined this process through mathematical models and engineered Saccharomyces cerevisiae strains incapable of recognition. Here, cooperators and their heterotypic cooperative partners (partners) exchanged distinct essential metabolites. Cheaters exploited partner-produced metabolites without reciprocating, and were competitively superior to cooperators. Despite initially random spatial distributions, cooperators gained more partner neighbors than cheaters did. The less a cheater contributed, the more it was excluded and disfavored. This self-organization, driven by asymmetric fitness effects of cooperators and cheaters on partners during cell growth into open space, achieves assortment. DOI: http://dx.doi.org/10.7554/eLife.00960.001 PMID:24220506

  15. A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies

    PubMed Central

    Zahn, Raphael; Osmanović, Dino; Ehret, Severin; Araya Callis, Carolina; Frey, Steffen; Stewart, Murray; You, Changjiang; Görlich, Dirk; Hoogenboom, Bart W; Richter, Ralf P

    2016-01-01

    The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior – a key element for the transport selectivity of the NPC – was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface. DOI: http://dx.doi.org/10.7554/eLife.14119.001 PMID:27058170

  16. Real-time imaging of Huntingtin aggregates diverting target search and gene transcription

    PubMed Central

    Li, Li; Liu, Hui; Dong, Peng; Li, Dong; Legant, Wesley R; Grimm, Jonathan B; Lavis, Luke D; Betzig, Eric; Tjian, Robert; Liu, Zhe

    2016-01-01

    The presumptive altered dynamics of transient molecular interactions in vivo contributing to neurodegenerative diseases have remained elusive. Here, using single-molecule localization microscopy, we show that disease-inducing Huntingtin (mHtt) protein fragments display three distinct dynamic states in living cells – 1) fast diffusion, 2) dynamic clustering and 3) stable aggregation. Large, stable aggregates of mHtt exclude chromatin and form 'sticky' decoy traps that impede target search processes of key regulators involved in neurological disorders. Functional domain mapping based on super-resolution imaging reveals an unexpected role of aromatic amino acids in promoting protein-mHtt aggregate interactions. Genome-wide expression analysis and numerical simulation experiments suggest mHtt aggregates reduce transcription factor target site sampling frequency and impair critical gene expression programs in striatal neurons. Together, our results provide insights into how mHtt dynamically forms aggregates and disrupts the finely-balanced gene control mechanisms in neuronal cells. DOI: http://dx.doi.org/10.7554/eLife.17056.001 PMID:27484239

  17. Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes

    PubMed Central

    Liepe, Juliane; Holzhütter, Hermann-Georg; Bellavista, Elena; Kloetzel, Peter M; Stumpf, Michael PH; Mishto, Michele

    2015-01-01

    Proteasomal protein degradation is a key determinant of protein half-life and hence of cellular processes ranging from basic metabolism to a host of immunological processes. Despite its importance the mechanisms regulating proteasome activity are only incompletely understood. Here we use an iterative and tightly integrated experimental and modelling approach to develop, explore and validate mechanistic models of proteasomal peptide-hydrolysis dynamics. The 20S proteasome is a dynamic enzyme and its activity varies over time because of interactions between substrates and products and the proteolytic and regulatory sites; the locations of these sites and the interactions between them are predicted by the model, and experimentally supported. The analysis suggests that the rate-limiting step of hydrolysis is the transport of the substrates into the proteasome. The transport efficiency varies between human standard- and immuno-proteasomes thereby impinging upon total degradation rate and substrate cleavage-site usage. DOI: http://dx.doi.org/10.7554/eLife.07545.001 PMID:26393687

  18. Homeostatic reinforcement learning for integrating reward collection and physiological stability

    PubMed Central

    Keramati, Mehdi; Gutkin, Boris

    2014-01-01

    Efficient regulation of internal homeostasis and defending it against perturbations requires adaptive behavioral strategies. However, the computational principles mediating the interaction between homeostatic and associative learning processes remain undefined. Here we use a definition of primary rewards, as outcomes fulfilling physiological needs, to build a normative theory showing how learning motivated behaviors may be modulated by internal states. Within this framework, we mathematically prove that seeking rewards is equivalent to the fundamental objective of physiological stability, defining the notion of physiological rationality of behavior. We further suggest a formal basis for temporal discounting of rewards by showing that discounting motivates animals to follow the shortest path in the space of physiological variables toward the desired setpoint. We also explain how animals learn to act predictively to preclude prospective homeostatic challenges, and several other behavioral patterns. Finally, we suggest a computational role for interaction between hypothalamus and the brain reward system. DOI: http://dx.doi.org/10.7554/eLife.04811.001 PMID:25457346

  19. Unfair competition governs the interaction of pCPI-17 with myosin phosphatase (PP1-MYPT1)

    PubMed Central

    Filter, Joshua J; Williams, Byron C; Eto, Masumi; Shalloway, David; Goldberg, Michael L

    2017-01-01

    The small phosphoprotein pCPI-17 inhibits myosin light-chain phosphatase (MLCP). Current models postulate that during muscle relaxation, phosphatases other than MLCP dephosphorylate and inactivate pCPI-17 to restore MLCP activity. We show here that such hypotheses are insufficient to account for the observed rapidity of pCPI-17 inactivation in mammalian smooth muscles. Instead, MLCP itself is the critical enzyme for pCPI-17 dephosphorylation. We call the mutual sequestration mechanism through which pCPI-17 and MLCP interact inhibition by unfair competition: MLCP protects pCPI-17 from other phosphatases, while pCPI-17 blocks other substrates from MLCP’s active site. MLCP dephosphorylates pCPI-17 at a slow rate that is, nonetheless, both sufficient and necessary to explain the speed of pCPI-17 dephosphorylation and the consequent MLCP activation during muscle relaxation. DOI: http://dx.doi.org/10.7554/eLife.24665.001 PMID:28387646

  20. Acknowledging selection at sub-organismal levels resolves controversy on pro-cooperation mechanisms

    PubMed Central

    Shou, Wenying

    2015-01-01

    Cooperators who pay a cost to produce publically-available benefits can be exploited by cheaters who do not contribute fairly. How might cooperation persist against cheaters? Two classes of mechanisms are known to promote cooperation: 'partner choice', where a cooperator preferentially interacts with cooperative over cheating partners; and 'partner fidelity feedback', where repeated interactions between individuals ensure that cheaters suffer as their cooperative partners languish (see, for example, Momeni et al., 2013). However when both mechanisms can act, differentiating them has generated controversy. Here, I resolve this controversy by noting that selection can operate on organismal and sub-organismal 'entities' such that partner fidelity feedback at sub-organismal level can appear as partner choice at organismal level. I also show that cooperation between multicellular eukaryotes and mitochondria is promoted by partner fidelity feedback and partner choice between sub-organismal entities, in addition to being promoted by partner fidelity feedback between hosts and symbionts, as was previously known. DOI: http://dx.doi.org/10.7554/eLife.10106.001 PMID:26714105

  1. Development of a novel depth of interaction PET detector using highly multiplexed G-APD cross-strip encoding

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

    Kolb, A., E-mail: armin.kolb@med.uni-tuebingen.de; Parl, C.; Liu, C. C.

    Purpose: The aim of this study was to develop a prototype PET detector module for a combined small animal positron emission tomography and magnetic resonance imaging (PET/MRI) system. The most important factor for small animal imaging applications is the detection sensitivity of the PET camera, which can be optimized by utilizing longer scintillation crystals. At the same time, small animal PET systems must yield a high spatial resolution. The measured object is very close to the PET detector because the bore diameter of a high field animal MR scanner is limited. When used in combination with long scintillation crystals, thesemore » small-bore PET systems generate parallax errors that ultimately lead to a decreased spatial resolution. Thus, we developed a depth of interaction (DoI) encoding PET detector module that has a uniform spatial resolution across the whole field of view (FOV), high detection sensitivity, compactness, and insensitivity to magnetic fields. Methods: The approach was based on Geiger mode avalanche photodiode (G-APD) detectors with cross-strip encoding. The number of readout channels was reduced by a factor of 36 for the chosen block elements. Two 12 × 2 G-APD strip arrays (25μm cells) were placed perpendicular on each face of a 12 × 12 lutetium oxyorthosilicate crystal block with a crystal size of 1.55 × 1.55 × 20 mm. The strip arrays were multiplexed into two channels and used to calculate the x, y coordinates for each array and the deposited energy. The DoI was measured in step sizes of 1.8 mm by a collimated {sup 18}F source. The coincident resolved time (CRT) was analyzed at all DoI positions by acquiring the waveform for each event and applying a digital leading edge discriminator. Results: All 144 crystals were well resolved in the crystal flood map. The average full width half maximum (FWHM) energy resolution of the detector was 12.8% ± 1.5% with a FWHM CRT of 1.14 ± 0.02 ns. The average FWHM DoI resolution over 12 crystals was 2.90 ± 0.15 mm. Conclusions: The novel DoI PET detector, which is based on strip G-APD arrays, yielded a DoI resolution of 2.9 mm and excellent timing and energy resolution. Its high multiplexing factor reduces the number of electronic channels. Thus, this cross-strip approach enables low-cost, high-performance PET detectors for dedicated small animal PET and PET/MRI and potentially clinical PET/MRI systems.« less

  2. Soil erosion measurements by means of experimental plots to determine best land management strategies in vineyards and olive orchards

    NASA Astrophysics Data System (ADS)

    Cerdà, Artemi; Keesstra, Saskia; Jordan, Antonio; Brevik, Erik; Nova, Agata; Prosdocimi, Massimo; Azorín-Molina, César; Yazdanpanah, Najme; Mahmoodabadi, Majid; Pereira, Paulo; Burguet, María

    2016-04-01

    In order to design sustainable land management there is a need to have accurate information on the impact this land management strategies have on water and sediment dynamics. This is especially important when a proper management is designed to reduce the soil losses due to the complex interaction of mechanisms that interact within the soil erosion process. Soil erosion is an non-linear process, both spatially and temporally, and as a consequence of that only well-monitored and accurate measurements can give insights in the processes and how these processes can be influenced by management to reduce soil losses (Cerdà, 2007; Ligonja and Shrestha, 2015; Nanko et al., 2015; Seutloali and Beckedahl, 2015). This is necessary at different scales: pedon, slope, and watershed because the governing processes differ at different scale (Keesstra, 2007; Jordán and Martínez Zavala, 2008; Borrelli et al., 2015). Soil erosion plots can give information about the temporal and spatial variability of soil losses. We present here a strategy developed by the Soil Erosion and Degradation Research Group from the University of Valencia to assess the soil erosion rates in Eastern Spain. In 2002 the Soil Erosion Experimental Station in El Teularet-Sierra de Enguera was installed, to assess soil losses in rainfed agriculture orchards, and 73 plots of 1, 2, 4, 16 and 48 m2 were installed. In 2005 6 plots of 300 m2 were installed in the nearby Montesa soil erosion station to assess soil losses in citrus orchards. In 2011 16 plots of 2 m2 where installed in Les Alcusses to determine soil losses in olive orchards, and in 2015 8 plots in Celler del Roure vineyard to assess the impact of land management in vineyards and 8 plots in the El Teularet to study the impact of straw mulch on soil erosion rates. All erosion stations are located in several kilometres distance from each other. This research which we developed since 2002 is complementary to previous research where we used rainfall simulation experiments to assess soil properties under different management (Cerdà, 1997; Cerdà, 1998a; Cerdà 1998b; Cerdà, 2001). The results from the soil erosion plots monitoring demonstrate the positive impact of vegetation to reduce soil loss. In addition, we proved that the use of straw, chipped pruned branches and rock fragments as surface cover reduces soil losses (Cerdà et al., 2015, Pereira et al., 2015; Prosdocimi et al., 2016). Acknowledgements The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 603498 (RECARE project) and by the Spanish Government with the research Project CGL2013- 47862-C2-1-R. References Borrelli, P., Märker, M., Schütt, B. 2015. Modelling Post-Tree-Harvesting soil erosion and sediment deposition potential in the turano river basin (Italian central apennine. Land Degradation and Development, 26, 356-366. DOI: 10.1002/ldr.2214 Cerdà, A. 1997.The effect of patchy distribution of Stipa tenacissima L. on runoff and erosion. Journal of Arid Environments, 36 (1), pp. 37-51.DOI: 10.1006/jare.1995.0198 Cerdà, A. 1998a. Changes in overland flow and infiltration after a rangeland fire in a Mediterranean scrubland. Hydrological Processes, 12 (7), pp. 1031-1042. Cerdà, A. 1998b Soil aggregate stability under different Mediterranean vegetation types. Catena, 32 (2), pp. 73-86. DOI: 10.1016/S0341-8162(98)00041-1 Cerdà, A. 2001. Effects of rock fragment cover on soil infiltration, interrill runoff and erosion. European Journal of Soil Science, 52 (1), pp. 59-68. DOI: 10.1046/j.1365-2389.2001.00354.x Cerdà, A. 2007. Soil water erosion on road embankments in eastern Spain. Science of the Total Environment, 378 (1-2), 151-155. DOI: 10.1016/j.scitotenv.2007.01.041 Cerdà, A., González-Pelayo, O., Giménez-Morera, A., Jordán, A., Pereira, P., Novara, A., Brevik, E.C., Prosdocimi, M., Mahmoodabadi, M., Keesstra, S., García Orenes, F., Ritsema, C., 2015. The use of barley straw residues to avoid high erosion and runoff rates on persimmon plantations in Eastern Spain under low frequency - high magnitude simulated rainfall events. Soil Res. (In press) Jordán, A., & Martínez-Zavala, L. 2008. Soil loss and runoff rates on unpaved forest roads in southern Spain after simulated rainfall. Forest Ecology and Management, 255(3), 913-919. Keesstra, S.D. 2007. Impact of natural reforestation on floodplain sedimentation in the Dragonja basin, SW Slovenia. Earth Surface Processes and Landforms, 32(1): 49-65. DOI: 10.1002/esp.1360 Ligonja, P.J., Shrestha, R.P. 2015. Soil erosion assessment in kondoa eroded area in Tanzania using universal soil loss equation, geographic information systems and socioeconomic approach (2015) Land Degradation and Development, 26 (4), pp. 367-379. DOI: 10.1002/ldr.2215 Nanko, K., Giambelluca, T.W., Sutherland, R.A., Mudd, R.G., Nullet, M.A., Ziegler, A.D. 2015.Erosion potential under miconia calvescens stands on the island of hawai'i. Land Degradation and Development, 26 (3), pp. 218-226. DOI: 10.1002/ldr.2200 Pereira, P., Giménez-Morera, A., Novara, A., Keesstra, S., Jordán, A., Masto, R. E., Brevik, E., Azorin-Molina, C. Cerdà, A. 2015. The impact of road and railway embankments on runoff and soil erosion in eastern Spain. Hydrology and Earth System Sciences Discussions, 12, 12947-12985. Prosdocimi,M., Jordán, A., Tarolli, P., Keesstra, S., Novara, A., Cerdà, A. 2016. The immediate effectiveness of barley straw mulch in reducing soil erodibility and surface runoff generation in Mediterranean vineyards. Science of The Total Environment, 547, 15 ,323-330, doi:10.1016/j.scitotenv.2015.12.076 Seutloali, K.E., Beckedahl, H.R. 2015. Understanding the factors influencing rill erosion on roadcuts in the south eastern region of South Africa. Solid Earth, 6 (2) 633-641. DOI: 10.5194/se-6-633-2015

  3. Centriolar satellites assemble centrosomal microcephaly proteins to recruit CDK2 and promote centriole duplication

    PubMed Central

    Kodani, Andrew; Yu, Timothy W; Johnson, Jeffrey R; Jayaraman, Divya; Johnson, Tasha L; Al-Gazali, Lihadh; Sztriha, Lāszló; Partlow, Jennifer N; Kim, Hanjun; Krup, Alexis L; Dammermann, Alexander; Krogan, Nevan J; Walsh, Christopher A; Reiter, Jeremy F

    2015-01-01

    Primary microcephaly (MCPH) associated proteins CDK5RAP2, CEP152, WDR62 and CEP63 colocalize at the centrosome. We found that they interact to promote centriole duplication and form a hierarchy in which each is required to localize another to the centrosome, with CDK5RAP2 at the apex, and CEP152, WDR62 and CEP63 at sequentially lower positions. MCPH proteins interact with distinct centriolar satellite proteins; CDK5RAP2 interacts with SPAG5 and CEP72, CEP152 with CEP131, WDR62 with MOONRAKER, and CEP63 with CEP90 and CCDC14. These satellite proteins localize their cognate MCPH interactors to centrosomes and also promote centriole duplication. Consistent with a role for satellites in microcephaly, homozygous mutations in one satellite gene, CEP90, may cause MCPH. The satellite proteins, with the exception of CCDC14, and MCPH proteins promote centriole duplication by recruiting CDK2 to the centrosome. Thus, centriolar satellites build a MCPH complex critical for human neurodevelopment that promotes CDK2 centrosomal localization and centriole duplication. DOI: http://dx.doi.org/10.7554/eLife.07519.001 PMID:26297806

  4. PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3

    PubMed Central

    Chung, Ho-Ryun; Xu, Chao; Fuchs, Alisa; Mund, Andreas; Lange, Martin; Staege, Hannah; Schubert, Tobias; Bian, Chuanbing; Dunkel, Ilona; Eberharter, Anton; Regnard, Catherine; Klinker, Henrike; Meierhofer, David; Cozzuto, Luca; Winterpacht, Andreas; Di Croce, Luciano; Min, Jinrong; Will, Hans; Kinkley, Sarah

    2016-01-01

    PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes. DOI: http://dx.doi.org/10.7554/eLife.10607.001 PMID:27223324

  5. Performance studies towards a TOF-PET sensor using Compton scattering at plastic scintillators

    NASA Astrophysics Data System (ADS)

    Kuramoto, M.; Nakamori, T.; Gunji, S.; Kamada, K.; Shoji, Y.; Yoshikawa, A.; Aoki, T.

    2018-01-01

    We have developed a sensor head for a time-of-flight (TOF) PET scanner using plastic scintillators that have a very fast timing property. Given the very small cross section of photoelectric absorption in plastic scintillators at 511 keV, we use Compton scattering in order to compensate for detection efficiency. The detector will consist of two layers of scatterers and absorbers which are made of plastic and inorganic scintillators such as GAGG:Ce, respectively. Signals are read by monolithic Multi Pixel Photon Counters, and with energy deposits and interaction time stamps are being acquired. The scintillators are built to be capable of resolving interaction position in three dimensions, so that our system has also a function of depth-of-interaction (DOI) PET scanners. TOF resolution of ~ 200 ps (FWHM) is achieved in both cases of using the leading-edge discriminator and time-walk correction and using a configuration sensitive to DOI. Both the position resolution and spectroscopy are demonstrated using the prototype data acquisition system, with Compton scattering events subsequently being obtained. We also demonstrated that the background rejection technique using the Compton cone constraint could be valid with our system.

  6. Distinct lateral inhibitory circuits drive parallel processing of sensory information in the mammalian olfactory bulb

    PubMed Central

    Geramita, Matthew A; Burton, Shawn D; Urban, Nathan N

    2016-01-01

    Splitting sensory information into parallel pathways is a common strategy in sensory systems. Yet, how circuits in these parallel pathways are composed to maintain or even enhance the encoding of specific stimulus features is poorly understood. Here, we have investigated the parallel pathways formed by mitral and tufted cells of the olfactory system in mice and characterized the emergence of feature selectivity in these cell types via distinct lateral inhibitory circuits. We find differences in activity-dependent lateral inhibition between mitral and tufted cells that likely reflect newly described differences in the activation of deep and superficial granule cells. Simulations show that these circuit-level differences allow mitral and tufted cells to best discriminate odors in separate concentration ranges, indicating that segregating information about different ranges of stimulus intensity may be an important function of these parallel sensory pathways. DOI: http://dx.doi.org/10.7554/eLife.16039.001 PMID:27351103

  7. Near-Local Interstellar Medium (LISM): What we know from the Voyagers and ENA and what an Interstellar Probe (ISP) can do

    NASA Astrophysics Data System (ADS)

    Krimigis, S. M.

    2017-12-01

    In situ measurements by the two Voyagers over the past 13 years have revealed the presence of the long-predicted termination shock (TS) and heliopause (HP), albeit not where theory had placed them. Further, the advent of energetic neutral atom (ENA) imaging by Cassini/INCA since 2003 and IBEX since 2009 have provided images of the global heliosphere that have challenged our long-held views of its shape and the processes that are dominant in its formation (Krimigis et al, and McComas et al, 2009; Dialynas et al, 2017). In addition, continuing measurements from Voyager 1 beyond the HP, now at 140 AU (1 AU=1.5x108 km, the Sun-Earth distance), have shown that the influence of the Sun extends well beyond the HP (at 122 AU). This influence is manifested through the occasional appearance of anisotropies in the galactic cosmic rays (GCR) where none were predicted, that last as long as a year and are accompanied by electron plasma oscillations in the vicinity of the spacecraft. Thus, an ISP mission with a fast ( 15 AU per year compared to Voyager's 3.6) trajectory would traverse a dynamic region near and beyond the TS and HP, and enable imaging the shape of the heliosphere from beyond its boundaries through ENA. In situ measurements should include the ISM magnetic field (ISMF), plasma density and distribution function, plasma waves, and neutral atom density and composition, as a minimum. All of these measurements would be new information with modern instrumentation that would place the very limited Voyager measurements into the proper context. References: Krimigis, S. M., D. G. Mitchell, E. C. Roelof, K. C. Hsieh and D. J. McComas, Imaging the Interaction of the Heliosphere with the Interstellar Medium from Saturn with Cassini, Science, 326, 5955, p. 971, doi: 10.1126/science.1181079, 2009 McComas, D. J., et al, Global Observations of the Interstellar Interaction from the Interstellar Boundary Explorer (IBEX), Science, 326, 5955, pp. 959, doi: 10.1126/science.1180906, 2009. Dialynas, K., S. M. Krimigis, D. G. Mitchell, R. B. Decker, and E. C. Roelof, Voyager and Cassini measurements suggest a "bubble-like" shape of the global heliosphere, Nature Astronomy, 1, 0115 (2017) | DOI: 10.1038/s41550-017-0115

  8. Persistent neural activity in auditory cortex is related to auditory working memory in humans and nonhuman primates

    PubMed Central

    Huang, Ying; Matysiak, Artur; Heil, Peter; König, Reinhard; Brosch, Michael

    2016-01-01

    Working memory is the cognitive capacity of short-term storage of information for goal-directed behaviors. Where and how this capacity is implemented in the brain are unresolved questions. We show that auditory cortex stores information by persistent changes of neural activity. We separated activity related to working memory from activity related to other mental processes by having humans and monkeys perform different tasks with varying working memory demands on the same sound sequences. Working memory was reflected in the spiking activity of individual neurons in auditory cortex and in the activity of neuronal populations, that is, in local field potentials and magnetic fields. Our results provide direct support for the idea that temporary storage of information recruits the same brain areas that also process the information. Because similar activity was observed in the two species, the cellular bases of some auditory working memory processes in humans can be studied in monkeys. DOI: http://dx.doi.org/10.7554/eLife.15441.001 PMID:27438411

  9. Active sensing in the categorization of visual patterns

    PubMed Central

    Yang, Scott Cheng-Hsin; Lengyel, Máté; Wolpert, Daniel M

    2016-01-01

    Interpreting visual scenes typically requires us to accumulate information from multiple locations in a scene. Using a novel gaze-contingent paradigm in a visual categorization task, we show that participants' scan paths follow an active sensing strategy that incorporates information already acquired about the scene and knowledge of the statistical structure of patterns. Intriguingly, categorization performance was markedly improved when locations were revealed to participants by an optimal Bayesian active sensor algorithm. By using a combination of a Bayesian ideal observer and the active sensor algorithm, we estimate that a major portion of this apparent suboptimality of fixation locations arises from prior biases, perceptual noise and inaccuracies in eye movements, and the central process of selecting fixation locations is around 70% efficient in our task. Our results suggest that participants select eye movements with the goal of maximizing information about abstract categories that require the integration of information from multiple locations. DOI: http://dx.doi.org/10.7554/eLife.12215.001 PMID:26880546

  10. PPI layouts: BioJS components for the display of Protein-Protein Interactions.

    PubMed

    Salazar, Gustavo A; Meintjes, Ayton; Mulder, Nicola

    2014-01-01

    We present two web-based components for the display of Protein-Protein Interaction networks using different self-organizing layout methods: force-directed and circular. These components conform to the BioJS standard and can be rendered in an HTML5-compliant browser without the need for third-party plugins. We provide examples of interaction networks and how the components can be used to visualize them, and refer to a more complex tool that uses these components. http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7753.

  11. Collimator Design for a Brain SPECT/MRI Insert

    NASA Astrophysics Data System (ADS)

    Salvado, Debora; Erlandsson, Kjell; Bousse, Alexandre; Occhipinti, Michele; Busca, Paolo; Fiorini, Carlo; Hutton, Brian F.

    2015-08-01

    This project's goal is to design a SPECT insert for a clinical MRI system for simultaneous brain SPECT/MR imaging, with a high-sensitivity collimator and high-resolution detectors. We have compared eight collimator designs, four multi-pinhole and four multi-slit slit-slat configurations. The collimation was designed for a system with 2 rings of 25 5 × 5 cm detectors. We introduce the concept of 1/2-pinhole and 1/2-slit, which are transaxially shared between two adjacent detectors. Analytical geometric efficiency was calculated for an activity distribution corresponding to a human brain and a range of intrinsic detector resolutions Ri and target resolutions Rt at the centre of the FOV. Noise-free data were simulated with and without depth-of-interaction (DOI) information, 0.8 mm Ri and 10 mm Rt FWHM, and reconstructed for uniform, Defrise, Derenzo, and Zubal brain phantoms. Comparing the multi-pinhole and multi-slit slit-slat collimators, the former gives better reconstructed uniformity and transaxial resolution, while the latter gives better axial resolution. Although the 2 ×2-pinhole and 2-slit designs give the highest sensitivities, they result in a sub-optimal utilisation of the detector FOV. The best options are therefore the 5+ 2 1/2-pinhole and the 1 + 2 1/2-slit systems, with sensitivities of 1.8 ×10-4 and 3.2 ×10-4, respectively. Noiseless brain phantom reconstructions with the multi-pinhole collimator are slightly superior as compared to slit-slat, in terms of symmetry and accuracy of the activity distribution, but the same is not true when noise is included. DOI information reduces artefacts and improves uniformity in geometric phantoms. Further evaluation is needed with prototype collimators.

  12. DataCite - Making data sets citable

    NASA Astrophysics Data System (ADS)

    Brase, J.

    2013-12-01

    The scientific and information communities have largely mastered the presentation of, and linkages between, text-based electronic information by assigning persistent identifiers to give scientific literature unique identities and accessibility. Knowledge, as published through scientific literature, is however often the last step in a process originating from scientific research data. Today scientists are using simulation, observational, and experimentation techniques that yield massive quantities of research data. These data are analysed, synthesised, interpreted, and the outcome of this process is generally published as a scientific article. Access to the original data as the foundation of knowledge has become an important issue throughout the world and different projects have started to find solutions. Global collaboration and scientific advances could be accelerated through broader access to scientific research data. In other words, data access could be revolutionized through the same technologies used to make textual literature accessible. The most obvious opportunity to broaden visibility of and access to research data is to integrate its access into the medium where it is most often cited: electronic textual information. Besides this opportunity, it is important, irrespective of where they are cited, for research data to have an internet identity. Since 2005, the German National Library of Science and Technology (TIB) has offered a successful Digital Object Identifier (DOI) registration service for persistent identification of research data. Since 2010 these services are offered by the global consortium DataCite, carried by 17 member organisations from 12 different countries: The German National Library of Science and Technology (TIB), the German National Library of Medicine (ZB MED), the German National Library of Economics (ZBW) and the German GESIS - Leibniz Institute for the Social Sciences. Additional European members are: The Library of the ETH Zürich in Switzerland, the Library of TU Delft, from the Netherlands, the L'Institut de l'Information Scientifique et Technique (INIST) from France, The technical Information Center of Denmark, The British Library, the Sedish National Data Service (SND), the Conferenza dei Rettori delle Università Italiane (CRUI) from Italy. North America is represented through: the California Digital Library, the Office of Scientific and Technical Information (OSTI), the Purdue University and the Canada Institute for Scientific and Technical Information (CISTI). Furthermore the Australian National Data Service (ANDS) and the National Research Council of Thailand (NRCT) are members. DataCite offers through its members DOI registration for data centers, currently over 2 million objects have been registered with a DOI name and are available through a central search portal at http://search.datacite.org . Based on the DOI registration DataCite offers a variety of services such as a detailed statistic portal of the number of DOI names registered and resolved (http://stats.datacite.org). In June 2012 DataCite and the STM association (http://www.stm-assoc.org) signed a joint statement to encourage publishers and data centers to link articles and underlying data (http://www.datacite.org/node/65 )

  13. Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article

    PubMed Central

    Shotton, David; Portwin, Katie; Klyne, Graham; Miles, Alistair

    2009-01-01

    Scientific innovation depends on finding, integrating, and re-using the products of previous research. Here we explore how recent developments in Web technology, particularly those related to the publication of data and metadata, might assist that process by providing semantic enhancements to journal articles within the mainstream process of scholarly journal publishing. We exemplify this by describing semantic enhancements we have made to a recent biomedical research article taken from PLoS Neglected Tropical Diseases, providing enrichment to its content and increased access to datasets within it. These semantic enhancements include provision of live DOIs and hyperlinks; semantic markup of textual terms, with links to relevant third-party information resources; interactive figures; a re-orderable reference list; a document summary containing a study summary, a tag cloud, and a citation analysis; and two novel types of semantic enrichment: the first, a Supporting Claims Tooltip to permit “Citations in Context”, and the second, Tag Trees that bring together semantically related terms. In addition, we have published downloadable spreadsheets containing data from within tables and figures, have enriched these with provenance information, and have demonstrated various types of data fusion (mashups) with results from other research articles and with Google Maps. We have also published machine-readable RDF metadata both about the article and about the references it cites, for which we developed a Citation Typing Ontology, CiTO (http://purl.org/net/cito/). The enhanced article, which is available at http://dx.doi.org/10.1371/journal.pntd.0000228.x001, presents a compelling existence proof of the possibilities of semantic publication. We hope the showcase of examples and ideas it contains, described in this paper, will excite the imaginations of researchers and publishers, stimulating them to explore the possibilities of semantic publishing for their own research articles, and thereby break down present barriers to the discovery and re-use of information within traditional modes of scholarly communication. PMID:19381256

  14. Performance evaluation for 120 four-layer DOI block detectors of the jPET-D4.

    PubMed

    Inadama, Naoko; Murayama, Hideo; Ono, Yusuke; Tsuda, Tomoaki; Hamamoto, Manabu; Yamaya, Taiga; Yoshida, Eiji; Shibuya, Kengo; Nishikido, Fumihiko; Takahashi, Kei; Kawai, Hideyuki

    2008-01-01

    The jPET-D4 is a brain positron emission tomography (PET) scanner that we have developed to meet user demands for high sensitivity and high spatial resolution. For this scanner, we developed a four-layer depth-of-interaction (DOI) detector. The four-layer DOI detector is a key component for the jPET-D4, its performance has great influence on the overall system performance. Previously, we reported the original technique for encoding four-layer DOI. Here, we introduce the final design of the jPET-D4 detector and present the results of an investigation on uniformity in performance of the detector. The performance evaluation was done over the 120 DOI crystal blocks for the detectors, which are to be assembled into the jPET-D4 scanner. We also introduce the crystal assembly method, which is simple enough, even though each DOI crystal block is composed of 1,024 crystal elements. The jPET-D4 detector consists of four layers of 16 x 16 Gd(2)SiO(5) (GSO) crystals and a 256-channel flat-panel position-sensitive photomultiplier tube (256ch FP-PMT). To identify scintillated crystals in the four-layer DOI detector, we use pulse shape discrimination and position discrimination on the two-dimensional (2D) position histogram. For pulse shape discrimination, two kinds of GSO crystals that show different scintillation decay time constants are used in the upper two and lower two layers, respectively. Proper reflector arrangement in the crystal block then allows the scintillated crystals to be identified in these two-layer groupings with two 2D position histograms. We produced the 120 DOI crystal blocks for the jPET-D4 system, and measured their characteristics such as the accuracy of pulse shape discrimination, energy resolution, and the pulse height of the full energy peak. The results show a satisfactory and uniform performance of the four-layer DOI crystal blocks; for example, misidentification rate in each GSO layer is <5% based on pulse shape discrimination, the averaged energy resolutions for the central four crystals of the first (farthest from the FP-PMT), second, third, and 4th layers are 15.7 +/- 1.0, 15.8 +/- 0.6, 17.7 +/- 1.2, and 17.3 +/- 1.4%, respectively, and variation in pulse height of the full energy peak among the four layers is <5% on average.

  15. Length-scale dependent transport properties of colloidal and protein solutions for prediction of crystal nucleation rates

    NASA Astrophysics Data System (ADS)

    Kalwarczyk, Tomasz; Sozanski, Krzysztof; Jakiela, Slawomir; Wisniewska, Agnieszka; Kalwarczyk, Ewelina; Kryszczuk, Katarzyna; Hou, Sen; Holyst, Robert

    2014-08-01

    We propose a scaling equation describing transport properties (diffusion and viscosity) in the solutions of colloidal particles. We apply the equation to 23 different systems including colloids and proteins differing in size (range of diameters: 4 nm to 1 μm), and volume fractions (10-3-0.56). In solutions under study colloids/proteins interact via steric, hydrodynamic, van der Waals and/or electrostatic interactions. We implement contribution of those interactions into the scaling law. Finally we use our scaling law together with the literature values of the barrier for nucleation to predict crystal nucleation rates of hard-sphere like colloids. The resulting crystal nucleation rates agree with existing experimental data.We propose a scaling equation describing transport properties (diffusion and viscosity) in the solutions of colloidal particles. We apply the equation to 23 different systems including colloids and proteins differing in size (range of diameters: 4 nm to 1 μm), and volume fractions (10-3-0.56). In solutions under study colloids/proteins interact via steric, hydrodynamic, van der Waals and/or electrostatic interactions. We implement contribution of those interactions into the scaling law. Finally we use our scaling law together with the literature values of the barrier for nucleation to predict crystal nucleation rates of hard-sphere like colloids. The resulting crystal nucleation rates agree with existing experimental data. Electronic supplementary information (ESI) available: Experimental and some analysis details. See DOI: 10.1039/c4nr00647j

  16. Advancing biology through a deeper understanding of zebrafish ecology and evolution

    PubMed Central

    Parichy, David M

    2015-01-01

    Over the last two decades, the zebrafish has joined the ranks of premier model organisms for biomedical research, with a full suite of tools and genomic resources. Yet we still know comparatively little about its natural history. Here I review what is known about the natural history of the zebrafish, where significant gaps in our knowledge remain, and how a fuller appreciation of this organism's ecology and behavior, population genetics, and phylogeny can inform a variety of research endeavors. DOI: http://dx.doi.org/10.7554/eLife.05635.001 PMID:25807087

  17. Radiation Belt Transport Driven by Solar Wind Dynamic Pressure Fluctuations

    NASA Astrophysics Data System (ADS)

    Kress, B. T.; Hudson, M. K.; Ukhorskiy, A. Y.; Mueller, H.

    2012-12-01

    The creation of the Earth's outer zone radiation belts is attributed to earthward transport and adiabatic acceleration of electrons by drift-resonant interactions with electromagnetic fluctuations in the magnetosphere. Three types of radial transport driven by solar wind dynamic pressure fluctuations that have been identified are: (1) radial diffusion [Falthammer, 1965], (2) significant changes in the phase space density radial profile due to a single or few ULF drift-resonant interactions [Ukhorskiy et al., 2006; Degeling et al., 2008], and (3) shock associated injections of radiation belt electrons occurring in less than a drift period [Li et al., 1993]. A progress report will be given on work to fully characterize different forms of radial transport and their effect on the Earth's radiation belts. The work is being carried out by computing test-particle trajectories in electric and magnetic fields from a simple analytic ULF field model and from global MHD simulations of the magnetosphere. Degeling, A. W., L. G. Ozeke, R. Rankin, I. R. Mann, and K. Kabin (2008), Drift resonant generation of peaked relativistic electron distributions by Pc 5 ULF waves, textit{J. Geophys. Res., 113}, A02208, doi:10.1029/2007JA012411. Fälthammar, C.-G. (1965), Effects of Time-Dependent Electric Fields on Geomagnetically Trapped Radiation, J. Geophys. Res., 70(11), 2503-2516, doi:10.1029/JZ070i011p02503. Li, X., I. Roth, M. Temerin, J. R. Wygant, M. K. Hudson, and J. B. Blake (1993), Simulation of the prompt energization and transport of radiation belt particles during the March 24, 1991 SSC, textit{Geophys. Res. Lett., 20}(22), 2423-2426, doi:10.1029/93GL02701. Ukhorskiy, A. Y., B. J. Anderson, K. Takahashi, and N. A. Tsyganenko (2006), Impact of ULF oscillations in solar wind dynamic pressure on the outer radiation belt electrons, textit{Geophys. Res. Lett., 33}(6), L06111, doi:10.1029/2005GL024380.

  18. MMS observation of energy conversion and collisionless plasma dissipation channels in the turbulent magnetosheath

    NASA Astrophysics Data System (ADS)

    Parashar, T.; Yang, Y.; Chasapis, A.; Matthaeus, W. H.

    2017-12-01

    High resolution Magnetospheric Multiscale (MMS) plasma and magnetic field data obtained in the inhomogeneous turbulent magnetosheath directly reveals the exchanges of energy between electromagnetic, flow and random kinetic energy. The parameters that quantify these exchanges are based on standard manipulations of the collisionless Vlasov model of plasma dynamics [1], without appeal to viscous or other closures. No analysis of heat transport or heat conduction is carried out. Several intervals of burst mode data in the magnetosheath are considered. Time series of the work done by the electromagnetic field, and the pressure-stress interaction enable description of the pathways to dissipation in this low collisionality plasma. Using these examples we demonstrate that the pressure-stress interaction provides important information not readily revealed in other diagnostics concerning the physical processes that are observed. This method does not require any specific mechanism for its application such as reconnection or a selected mode, although with increased experience it will be useful in distinguishing among proposed possibilities. [1] Y. Yang et al, Phys. Plasmas 24, 072306 (2017); doi: 10.1063/1.4990421.

  19. Cellular uptake and trafficking of polydiacetylene micelles

    NASA Astrophysics Data System (ADS)

    Gravel, Edmond; Thézé, Benoit; Jacques, Isabelle; Anilkumar, Parambath; Gombert, Karine; Ducongé, Frédéric; Doris, Eric

    2013-02-01

    Polydiacetylene (PDA) micelles coated with either carboxylate-, ammonium-, or methoxy-polyethyleneglycol (PEG) chains were assembled and loaded with a fluorescent dye (DiO). Their interaction with MCF-7 human breast tumor cells was investigated by epi-fluorescence microscopy and fluorescence-activated cell sorting (FACS) to determine their internalization pathway and intracellular fate. It was found that the ionic character of the micelles influenced their internalization kinetics through a caveolae-mediated pathway and that all micelle types behaved somewhat similarly inside cells.Polydiacetylene (PDA) micelles coated with either carboxylate-, ammonium-, or methoxy-polyethyleneglycol (PEG) chains were assembled and loaded with a fluorescent dye (DiO). Their interaction with MCF-7 human breast tumor cells was investigated by epi-fluorescence microscopy and fluorescence-activated cell sorting (FACS) to determine their internalization pathway and intracellular fate. It was found that the ionic character of the micelles influenced their internalization kinetics through a caveolae-mediated pathway and that all micelle types behaved somewhat similarly inside cells. Electronic supplementary information (ESI) available: Detailed synthetic procedures and supplementary figures. See DOI: 10.1039/c2nr34149b

  20. A New In Vitro Model of Breast Cancer Metastasis to Bone

    DTIC Science & Technology

    2009-04-01

    videomicroscopy [11, 12] have revealed that early stage, pre-angiogenic interactions between the cancer cells and the bone environment are crucial regulators of...1995) Steps in tumor metastasis: new concepts from intravital videomicroscopy . Cancer Metastasis Rev 14:279–301. doi:10.1007/BF00690599 12. Chambers AF

  1. Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α-synuclein assemblies by mass spectrometry

    PubMed Central

    Shrivastava, Amulya Nidhi; Redeker, Virginie; Fritz, Nicolas; Pieri, Laura; Almeida, Leandro G.; Spolidoro, Maria; Liebmann, Thomas; Bousset, Luc; Renner, Marianne; Léna, Clément; Aperia, Anita; Melki, Ronald; Triller, Antoine

    2016-01-01

    α-Synuclein (α-syn) is the principal component of Lewy bodies, the pathophysiological hallmark of individuals affected by Parkinson disease (PD). This neuropathologic form of α-syn contributes to PD progression and propagation of α-syn assemblies between neurons. The data we present here support the proteomic analysis used to identify neuronal proteins that specifically interact with extracellularly applied oligomeric or fibrillar α-syn assemblies (conditions 1 and 2, respectively) (doi: 10.15252/embj.201591397[1]). α-syn assemblies and their cellular partner proteins were pulled down from neuronal cell lysed shortly after exposure to exogenous α-syn assemblies and the associated proteins were identified by mass spectrometry using a shotgun proteomic-based approach. We also performed experiments on pure cultures of astrocytes to identify astrocyte-specific proteins interacting with oligomeric or fibrillar α-syn (conditions 3 and 4, respectively). For each condition, proteins interacting selectively with α-syn assemblies were identified by comparison to proteins pulled-down from untreated cells used as controls. The mass spectrometry data, the database search and the peak lists have been deposited to the ProteomeXchange Consortium database via the PRIDE partner repository with the dataset identifiers PRIDE: PXD002256 to PRIDE: PXD002263 and doi: 10.6019/PXD002256 to 10.6019/PXD002263. PMID:26958642

  2. Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α-synuclein assemblies by mass spectrometry.

    PubMed

    Shrivastava, Amulya Nidhi; Redeker, Virginie; Fritz, Nicolas; Pieri, Laura; Almeida, Leandro G; Spolidoro, Maria; Liebmann, Thomas; Bousset, Luc; Renner, Marianne; Léna, Clément; Aperia, Anita; Melki, Ronald; Triller, Antoine

    2016-06-01

    α-Synuclein (α-syn) is the principal component of Lewy bodies, the pathophysiological hallmark of individuals affected by Parkinson disease (PD). This neuropathologic form of α-syn contributes to PD progression and propagation of α-syn assemblies between neurons. The data we present here support the proteomic analysis used to identify neuronal proteins that specifically interact with extracellularly applied oligomeric or fibrillar α-syn assemblies (conditions 1 and 2, respectively) (doi: 10.15252/embj.201591397[1]). α-syn assemblies and their cellular partner proteins were pulled down from neuronal cell lysed shortly after exposure to exogenous α-syn assemblies and the associated proteins were identified by mass spectrometry using a shotgun proteomic-based approach. We also performed experiments on pure cultures of astrocytes to identify astrocyte-specific proteins interacting with oligomeric or fibrillar α-syn (conditions 3 and 4, respectively). For each condition, proteins interacting selectively with α-syn assemblies were identified by comparison to proteins pulled-down from untreated cells used as controls. The mass spectrometry data, the database search and the peak lists have been deposited to the ProteomeXchange Consortium database via the PRIDE partner repository with the dataset identifiers PRIDE: PXD002256 to PRIDE: PXD002263 and doi: 10.6019/PXD002256 to 10.6019/PXD002263.

  3. 77 FR 36568 - Proposed Renewal of Information Collection: Payments in Lieu of Taxes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-19

    ... DEPARTMENT OF THE INTERIOR Office of the Secretary Proposed Renewal of Information Collection: Payments in Lieu of Taxes AGENCY: Office of Budget, Interior. ACTION: Notice and Request for Comments... Budget, Office of the Secretary, Department of the Interior (DOI), announces the proposed extension of a...

  4. Observing terrestrial water storage and land-atmosphere dynamics from space: Implications for forecasting and climate projections

    NASA Astrophysics Data System (ADS)

    Seneviratne, S. I.; Humphrey, V.; Nicolai-Shaw, N.; Gudmundsson, L.; Guillod, B.; Hirschi, M.; Michel, D.; Orth, R.; Zscheischler, J.

    2016-12-01

    In recent years, several new satellite products have been derived which allow an unprecendented assessment of terrestrial water storage and land-atmosphere dynamics. This presentation will review some of these new developments, with a focus on drought dynamics, plant-water interactions, and soil moisture-atmosphere feedbacks. Results derived based on the Gravity Recovery and Climate Experiment (GRACE, Humphrey et al. 2016) and the European Space Agency Climate Change Initiative (ESA CCI) Soil Moisture dataset (Nicolai-Shaw et al. 2015, 2016; Hirschi et al. 2014) will be highlighted, as well as assessments using satellite-based estimates of evapotranspiration (Mueller and Seneviratne 2014, Michel et al. 2016), vegetation activity (Zscheischler et al. 2015), and combined soil moisture and precipitation analyses (Guillod et al. 2015). These findings provide new insights on the development of prediction capabilities for droughts, precipitation events, and heat waves, and the reduction of uncertainties in climate model projections. References: Guillod, B.P., B. Orlowsky, D.G. Miralles, A.J. Teuling, and S.I. Seneviratne, 2015. Nature Communications, 6:6443, DOI: 10.1038/ncomms7443 Hirschi, M., B. Mueller, W. Dorigo, and S.I. Seneviratne, 2014. Remote Sensing of Environment, 154, 246-252. Humphrey, V., L. Gudmundsson, and S.I. Seneviratne, 2016. Surv. Geophysics, 37, 357-395, DOI 10.1007/s10712-016-9367-1. Michel, D., et al. 2016. Hydrol. Earth Syst. Sci. 20, 803-822, doi:10.5194/hess-20-803-2016. Mueller, M., and S.I. Seneviratne, 2014. Geophys. Res. Lett., 41, 1-7, doi:10.1002/2013GL058055. Nicolai-Shaw, N., L. Gudmundsson, M. Hirschi, and S.I. Seneviratne, 2016. Geophys. Res. Lett., in review. Nicolai-Shaw, N., M. Hirschi, H. Mittelbach, and S.I. Seneviratne, 2015. Journal of Geophysical Research, 120, doi:10.1002/2015JD023305. Zscheischler, J., R. Orth, and S.I. Seneviratne, 2015. Geophys. Res. Lett., 42, 9816-9824, doi:10.1002/2015GL066563.

  5. Impact location of objects hitting the water surface

    NASA Astrophysics Data System (ADS)

    Kadri, Usama

    2017-04-01

    Analysis of data, recorded on March 8th 2014 at the Comprehensive Test ban Treaty Organisation's hydroacoustic station off Cape Leeuwin Western Australia, reveal pressure signatures of objects impacting at the sea surface which could be associated with falling meteorites as well as the missing Malaysian MH370 airplane. The location of the sources are identified analytically by an inverse solution based on acoustic-gravity wave theory (e.g. see references below) which have been developed and validated experimentally. Apart from the direct contribution to the search efforts after the missing airplane, the method we describe here is very efficient for identifying the location of sources that result in a sudden change in the water pressure in general. References 1. T.Yamamoto,1982.Gravity waves and acoustic waves generated by submarine earthquakes, Soil Dyn. Earthquake Eng., 1, 75-82. 2. M. Stiassnie, 2010. Tsunamis and acoustic-gravity waves from underwater earthquakes, J. Eng. Math., 67, 23-32, doi:10.1007/s10665-009-9323-x. 3. U. Kadri and M. Staissnie, 2012. Acoustic-gravity waves interacting with the shelf break. J. Geophys. Res., 117, C03035, doi: 10.1029/2011JC007674. 4. E. Eyov, A. Klar, U. Kadri and M. Stiassnie, 2013. Progressive waves in a compressible ocean with elastic bottom, Wave Motion 50, 929-939. doi: 10.1016/j.wavemoti.2013.03.003 5. G. Hendin and M. Stiassnie, 2013. Tsunami and acoustic-gravity waves in water of constant depth, Phys. Fluids 25, 086103, doi: 10.1063/1.481799. 6. U. Kadri, 2016. Acoustic-gravity waves from an oscillating ice-block in arctic zones. Advances in Acoustics and Vibration, 8076108, http://dx.doi.org/10.1155/2016/8076108 7. T.C.A. Oliveira, U. Kadri, 2016. Acoustic-gravity waves from the 2004 Indian Ocean earthquake and tsunami. Journal of Geophysical Research: Oceans. doi: 10.1002/2016JC011742

  6. Development of 1.45-mm resolution four-layer DOI-PET detector for simultaneous measurement in 3T MRI.

    PubMed

    Nishikido, Fumihiko; Tachibana, Atsushi; Obata, Takayuki; Inadama, Naoko; Yoshida, Eiji; Suga, Mikio; Murayama, Hideo; Yamaya, Taiga

    2015-01-01

    Recently, various types of PET-MRI systems have been developed by a number of research groups. However, almost all of the PET detectors used in these PET-MRI systems have no depth-of-interaction (DOI) capability. The DOI detector can reduce the parallax error and lead to improvement of the performance. We are developing a new PET-MRI system which consists of four-layer DOI detectors positioned close to the measured object to achieve high spatial resolution and high scanner sensitivity. As a first step, we are investigating influences the PET detector and the MRI system have on each other using a prototype four-layer DOI-PET detector. This prototype detector consists of a lutetium yttrium orthosilicate crystal block and a 4 × 4 multi-pixel photon counter array. The size of each crystal element is 1.45 mm × 1.45 mm × 4.5 mm, and the crystals are arranged in 6 × 6 elements × 4 layers with reflectors. The detector and some electric components are packaged in an aluminum shielding box. Experiments were carried out with 3.0 T MRI (GE, Signa HDx) and a birdcage-type RF coil. We demonstrated that the DOI-PET detector was normally operated in simultaneous measurements with no influence of the MRI measurement. A slight influence of the PET detector on the static magnetic field of the MRI was observed near the PET detector. The signal-to-noise ratio was decreased by presence of the PET detector due to environmental noise entering the MRI room through the cables, even though the PET detector was not powered up. On the other hand, no influence of electric noise from the PET detector in the simultaneous measurement on the MRI images was observed, even though the PET detector was positioned near the RF coil.

  7. Vortex, ULF wave and Aurora Observation after Solar Wind Dynamic Pressure Change

    NASA Astrophysics Data System (ADS)

    Shi, Q.

    2017-12-01

    Here we will summarize our recent study and show some new results on the Magnetosphere and Ionosphere Response to Dynamic Pressure Change/disturbances in the Solar Wind and foreshock regions. We study the step function type solar wind dynamic pressure change (increase/decrease) interaction with the magnetosphere using THEMIS satellites at both dayside and nightside in different geocentric distances. Vortices generated by the dynamic pressure change passing along the magnetopause are found and compared with model predictions. ULF waves and vortices are excited in the dayside and nightside plasma sheet when dynamic pressure change hit the magnetotail. The related ionospheric responses, such as aurora and TCVs, are also investigated. We compare Global MHD simulations with the observations. We will also show some new results that dayside magnetospheric FLRs might be caused by foreshock structures.Shi, Q. Q. et al. (2013), THEMIS observations of ULF wave excitation in the nightside plasma sheet during sudden impulse events, J. Geophys. Res. Space Physics, 118, doi:10.1029/2012JA017984. Shi, Q. Q. et al. (2014), Solar wind pressure pulse-driven magnetospheric vortices and their global consequences, J. Geophys. Res. Space Physics, 119, doi:10.1002/2013JA019551. Tian, A.M. et al.(2016), Dayside magnetospheric and ionospheric responses to solar wind pressure increase: Multispacecraft and ground observations, J. Geophys. Res., 121, doi:10.1002/2016JA022459. Shen, X.C. et al.(2015), Magnetospheric ULF waves with increasing amplitude related to solar wind dynamic pressure changes: THEMIS observations, J. Geophys. Res., 120, doi:10.1002/2014JA020913Zhao, H. Y. et al. (2016), Magnetospheric vortices and their global effect after a solar wind dynamic pressure decrease, J. Geophys. Res. Space Physics, 121, doi:10.1002/2015JA021646. Shen, X. C., et al. (2017), Dayside magnetospheric ULF wave frequency modulated by a solar wind dynamic pressure negative impulse, J. Geophys. Res., 122, doi:10.1002/2016JA023351.

  8. Designing a compact high performance brain PET scanner—simulation study

    NASA Astrophysics Data System (ADS)

    Gong, Kuang; Majewski, Stan; Kinahan, Paul E.; Harrison, Robert L.; Elston, Brian F.; Manjeshwar, Ravindra; Dolinsky, Sergei; Stolin, Alexander V.; Brefczynski-Lewis, Julie A.; Qi, Jinyi

    2016-05-01

    The desire to understand normal and disordered human brain function of upright, moving persons in natural environments motivates the development of the ambulatory micro-dose brain PET imager (AMPET). An ideal system would be light weight but with high sensitivity and spatial resolution, although these requirements are often in conflict with each other. One potential approach to meet the design goals is a compact brain-only imaging device with a head-sized aperture. However, a compact geometry increases parallax error in peripheral lines of response, which increases bias and variance in region of interest (ROI) quantification. Therefore, we performed simulation studies to search for the optimal system configuration and to evaluate the potential improvement in quantification performance over existing scanners. We used the Cramér-Rao variance bound to compare the performance for ROI quantification using different scanner geometries. The results show that while a smaller ring diameter can increase photon detection sensitivity and hence reduce the variance at the center of the field of view, it can also result in higher variance in peripheral regions when the length of detector crystal is 15 mm or more. This variance can be substantially reduced by adding depth-of-interaction (DOI) measurement capability to the detector modules. Our simulation study also shows that the relative performance depends on the size of the ROI, and a large ROI favors a compact geometry even without DOI information. Based on these results, we propose a compact ‘helmet’ design using detectors with DOI capability. Monte Carlo simulations show the helmet design can achieve four-fold higher sensitivity and resolve smaller features than existing cylindrical brain PET scanners. The simulations also suggest that improving TOF timing resolution from 400 ps to 200 ps also results in noticeable improvement in image quality, indicating better timing resolution is desirable for brain imaging.

  9. Designing a compact high performance brain PET scanner—simulation study

    PubMed Central

    Gong, Kuang; Majewski, Stan; Kinahan, Paul E; Harrison, Robert L; Elston, Brian F; Manjeshwar, Ravindra; Dolinsky, Sergei; Stolin, Alexander V; Brefczynski-Lewis, Julie A; Qi, Jinyi

    2016-01-01

    The desire to understand normal and disordered human brain function of upright, moving persons in natural environments motivates the development of the ambulatory micro-dose brain PET imager (AMPET). An ideal system would be light weight but with high sensitivity and spatial resolution, although these requirements are often in conflict with each other. One potential approach to meet the design goals is a compact brain-only imaging device with a head-sized aperture. However, a compact geometry increases parallax error in peripheral lines of response, which increases bias and variance in region of interest (ROI) quantification. Therefore, we performed simulation studies to search for the optimal system configuration and to evaluate the potential improvement in quantification performance over existing scanners. We used the Cramér–Rao variance bound to compare the performance for ROI quantification using different scanner geometries. The results show that while a smaller ring diameter can increase photon detection sensitivity and hence reduce the variance at the center of the field of view, it can also result in higher variance in peripheral regions when the length of detector crystal is 15 mm or more. This variance can be substantially reduced by adding depth-of- interaction (DOI) measurement capability to the detector modules. Our simulation study also shows that the relative performance depends on the size of the ROI, and a large ROI favors a compact geometry even without DOI information. Based on these results, we propose a compact ‘helmet’ design using detectors with DOI capability. Monte Carlo simulations show the helmet design can achieve four-fold higher sensitivity and resolve smaller features than existing cylindrical brain PET scanners. The simulations also suggest that improving TOF timing resolution from 400 ps to 200 ps also results in noticeable improvement in image quality, indicating better timing resolution is desirable for brain imaging. PMID:27081753

  10. Cherenkov radiation-based three-dimensional position-sensitive PET detector: A Monte Carlo study.

    PubMed

    Ota, Ryosuke; Yamada, Ryoko; Moriya, Takahiro; Hasegawa, Tomoyuki

    2018-05-01

    Cherenkov radiation has recently received attention due to its prompt emission phenomenon, which has the potential to improve the timing performance of radiation detectors dedicated to positron emission tomography (PET). In this study, a Cherenkov-based three-dimensional (3D) position-sensitive radiation detector was proposed, which is composed of a monolithic lead fluoride (PbF 2 ) crystal and a photodetector array of which the signals can be readout independently. Monte Carlo simulations were performed to estimate the performance of the proposed detector. The position- and time resolution were evaluated under various practical conditions. The radiator size and various properties of the photodetector, e.g., readout pitch and single photon timing resolution (SPTR), were parameterized. The single photon time response of the photodetector was assumed to be a single Gaussian for the simplification. The photo detection efficiency of the photodetector was ideally 100% for all wavelengths. Compton scattering was included in simulations, but partly analyzed. To estimate the position at which a γ-ray interacted in the Cherenkov radiator, the center-of-gravity (COG) method was employed. In addition, to estimate the depth-of-interaction (DOI) principal component analysis (PCA), which is a multivariate analysis method and has been used to identify the patterns in data, was employed. The time-space distribution of Cherenkov photons was quantified to perform PCA. To evaluate coincidence time resolution (CTR), the time difference of two independent γ-ray events was calculated. The detection time was defined as the first photon time after the SPTR of the photodetector was taken into account. The position resolution on the photodetector plane could be estimated with high accuracy, by using a small number of Cherenkov photons. Moreover, PCA showed an ability to estimate the DOI. The position resolution heavily depends on the pitch of the photodetector array and the radiator thickness. If the readout pitch were ideally 0 and practically 3 mm, a full-width at half-maximum (FWHM) of 0.348 and 1.92 mm was achievable with a 10-mm-thick PbF 2 crystal, respectively. Furthermore, first-order correlation could be observed between the primary principal component and the true DOI. To obtain a coincidence timing resolution better than 100-ps FWHM with a 20-mm-thick PbF 2 crystal, a photodetector with SPTR of better than σ = 30 ps was necessary. From these results, the improvement of SPTR allows us to achieve CTR better than 100-ps FWHM, even in the case where a 20-mm-thick radiator is used. Our proposed detector has the potential to estimate the 3D interaction position of γ-rays in the radiator, using only time and space information of Cherenkov photons. © 2018 American Association of Physicists in Medicine.

  11. Variation Process of Radiation Belt Electron Fluxes due to Interaction With Chorus and EMIC Rising-tone Emissions Localized in Longitude

    NASA Astrophysics Data System (ADS)

    Kubota, Y.; Omura, Y.

    2017-12-01

    Using results of test particle simulations of a large number of electrons interacting with a pair of chorus emissions, we create Green's functions to model the electron distribution function after all of the possible interactions with the waves [Omura et al., 2015]. Assuming that the waves are generated in a localized range of longitudes in the dawn side, we repeat taking the convolution integral of the Green's function with the distribution function of the electrons injected into the generation region of the localized waves. From numerical and theoretical analyses, we find that electron acceleration process only takes place efficiently below 4 MeV. Because extremely relativistic electrons go through the wave generation region rapidly due to grad-B0 and curvature drift, they don't have enough interaction time to be accelerated. In setting up the electrons after all interaction with chorus emissions as initial electron distribution function, we also compute the loss process of radiation belt electron fluxes due to interaction with EMIC rising-tone emissions generated in a localized range of longitudes in the dusk side [Kubota and Omura,2017]. References: (1) Omura, Y., Y. Miyashita, M. Yoshikawa, D. Summers, M. Hikishima, Y. Ebihara, and Y. Kubota (2015), Formation process of relativistic electron flux through interaction with chorus emissions in the Earth's inner magnetosphere, J. Geophys. Res. Space Physics, 120, 9545-9562, doi:10.1002/2015JA021563. (2) Kubota, Y., and Y. Omura (2017), Rapid precipitation of radiation belt electrons induced by EMIC rising tone emissions localized in longitude inside and outside the plasmapause, J. Geophys. Res. Space Physics, 122, 293-309, doi:10.1002/2016JA023267.

  12. PPI layouts: BioJS components for the display of Protein-Protein Interactions

    PubMed Central

    Salazar, Gustavo A.; Meintjes, Ayton; Mulder, Nicola

    2014-01-01

    Summary: We present two web-based components for the display of Protein-Protein Interaction networks using different self-organizing layout methods: force-directed and circular. These components conform to the BioJS standard and can be rendered in an HTML5-compliant browser without the need for third-party plugins. We provide examples of interaction networks and how the components can be used to visualize them, and refer to a more complex tool that uses these components. Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7753 PMID:25075288

  13. Metabotropic glutamate mGlu2 receptor is necessary for the pharmacological and behavioral effects induced by hallucinogenic 5-HT2A receptor agonists.

    PubMed

    Moreno, José L; Holloway, Terrell; Albizu, Laura; Sealfon, Stuart C; González-Maeso, Javier

    2011-04-15

    Hallucinogenic drugs, including mescaline, psilocybin and lysergic acid diethylamide (LSD), act at serotonin 5-HT2A receptors (5-HT2ARs). Metabotropic glutamate receptor 2/3 (mGluR2/3) ligands show efficacy in modulating the responses induced by activation of 5-HT2ARs. The formation of a 5-HT2AR-mGluR2 complex suggests a functional interaction that affects the hallucinogen-regulated cellular signaling pathways. Here, we tested the cellular and behavioral effects of hallucinogenic 5-HT2AR agonists in mGluR2 knockout (mGluR2-KO) mice. Mice were intraperitoneally injected with the hallucinogens DOI (2 mg/kg) and LSD (0.24 mg/kg), or vehicle. Head-twitch behavioral response, expression of c-fos, which is induced by all 5-HT2AR agonists, and expression of egr-2, which is hallucinogen-specific, were determined in wild type and mGluR2-KO mice. [(3)H]Ketanserin binding displacement curves by DOI were performed in mouse frontal cortex membrane preparations. Head twitch behavior was abolished in mGluR2-KO mice. The high-affinity binding site of DOI was undetected in mGluR2-KO mice. The hallucinogen DOI induced c-fos in both wild type and mGluR2-KO mice. However, the induction of egr-2 by DOI was eliminated in mGlu2-KO mice. These findings suggest that the 5-HT2AR-mGluR2 complex is necessary for the neuropsychological responses induced by hallucinogens. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  14. Metabotropic glutamate mGlu2 receptor is necessary for the pharmacological and behavioral effects induced by hallucinogenic 5-HT2A receptor agonists

    PubMed Central

    Moreno, José L.; Holloway, Terrell; Albizu, Laura; Sealfon, Stuart C.; González-Maeso, Javier

    2011-01-01

    Hallucinogenic drugs, including mescaline, psilocybin and lysergic acid diethylamide (LSD), act at serotonin 5-HT2A receptors (5-HT2ARs). Metabotropic glutamate receptor 2/3 (mGluR2/3) ligands show efficacy in modulating the responses induced by activation of 5-HT2ARs. The formation of a 5-HT2AR-mGluR2 complex suggests a functional interaction that affects the hallucinogen-regulated cellular signaling pathways. Here, we tested the cellular and behavioral effects of hallucinogenic 5-HT2AR agonists in mGluR2 knockout (mGluR2-KO) mice. Mice were intraperitoneally injected with the hallucinogens DOI (2 mg/kg) and LSD (0.24 mg/kg), or vehicle. Head-twitch behavioral response, expression of c-fos, which is induced by all 5-HT2AR agonists, and expression of egr-2, which is hallucinogen-specific, were determined in wild type and mGluR2-KO mice. [3H]Ketanserin binding displacement curves by DOI were performed in mouse frontal cortex membrane preparations. Head twitch behavior was abolished in mGluR2-KO mice. The high-affinity binding site of DOI was undetected in mGluR2-KO mice. The hallucinogen DOI induced c-fos in both wild type and mGluR2-KO mice. However, the induction of egr-2 by DOI was eliminated in mGlu2-KO mice. These findings suggest that the 5-HT2AR-mGluR2 complex is necessary for the neuropsychological responses induced by hallucinogens. PMID:21276828

  15. Time-over-threshold for pulse shape discrimination in a time-of-flight phoswich PET detector.

    PubMed

    Chang, Chen-Ming; Cates, Joshua W; Levin, Craig S

    2017-01-07

    It is well known that a PET detector capable of measuring both photon time-of-flight (TOF) and depth-of-interaction (DOI) improves the image quality and accuracy. Phoswich designs have been realized in PET detectors to measure DOI for more than a decade. However, PET detectors based on phoswich designs put great demand on the readout circuits, which have to differentiate the pulse shape produced by different crystal layers. A simple pulse shape discrimination approach is required to realize the phoswich designs in a clinical PET scanner, which consists of thousands of scintillation crystal elements. In this work, we studied time-over-threshold (ToT) as a pulse shape parameter for DOI. The energy, timing and DOI performance were evaluated for a phoswich detector design comprising [Formula: see text] mm LYSO:Ce crystal optically coupled to [Formula: see text] mm calcium co-doped LSO:Ce,Ca(0.4%) crystal read out by a silicon photomultiplier (SiPM). A DOI accuracy of 97.2% has been achieved for photopeak events using the proposed time-over-threshold (ToT) processing. The energy resolution without correction for SiPM non-linearity was [Formula: see text]% and [Formula: see text]% FWHM at 511 keV for LYSO and LSO crystal layers, respectively. The coincidence time resolution for photopeak events ranges from 164.6 ps to 183.1 ps FWHM, depending on the layer combinations. The coincidence time resolution for inter-crystal scatter events ranges from 214.6 ps to 418.3 ps FWHM, depending on the energy windows applied. These results show great promises of using ToT for pulse shape discrimination in a TOF phoswich detector since a ToT measurement can be easily implemented in readout electronics.

  16. SU-C-206-01: Impact of Charge Sharing Effect On Sub-Pitch Resolution for CZT-Based Photon Counting CT Systems

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

    Zheng, X; Cheng, Z; Deen, J

    Purposes: Photon counting CT is a new imaging technology that can provide tissue composition information such as calcium/iodine content quantification. Cadmium zinc telluride CZT is considered a good candidate the photon counting CT due to its relatively high atomic number and band gap. One potential challenge is the degradation of both spatial and energy resolution as the fine electrode pitch is deployed (<50 µm). We investigated the extent of charge sharing effect as functions of gap width, bias voltage and depth-of-interaction (DOI). Methods: The initial electron cloud size and diffusion process were modeled analytically. The valid range of charge sharingmore » effect refers to the range over which both signals of adjacent electrodes are above the triggering threshold (10% of the amplitude of 60keV X-ray photons). The intensity ratios of output in three regions (I1/I2/I3: left pixel, gap area and right pixel) were calculated. With Gaussian white noises modeled (a SNR of 5 based upon the preliminary experiments), the sub-pitch resolution as a function of the spatial position in-between two pixels was studied. Results: The valid range of charge sharing increases linearly with depth-of-interaction (DOI) but decreases with gap width and bias voltage. For a 1.5mm thickness CZT detector (pitch: 50µm, bias: 400 V), the range increase from ∼90µm up to ∼110µm. Such an increase can be attributed to a longer travel distance and the associated electron cloud broadening. The achievable sub-pitch resolution is in the range of ∼10–30µm. Conclusion: The preliminary results demonstrate that sub-pixel spatial resolution can be achieved using the ratio of amplitudes of two neighboring pixels. Such ratio may also be used to correct charge loss and help improve energy resolution of a CZT detector. The impact of characteristic X-rays hitting adjacent pixels (i.e., multiple interaction) on charge sharing is currently being investigated.« less

  17. The integrated water balance and soil data set of the Rollesbroich hydrological observatory

    NASA Astrophysics Data System (ADS)

    Qu, Wei; Bogena, Heye R.; Huisman, Johan A.; Schmidt, Marius; Kunkel, Ralf; Weuthen, Ansgar; Schiedung, Henning; Schilling, Bernd; Sorg, Jürgen; Vereecken, Harry

    2016-10-01

    The Rollesbroich headwater catchment located in western Germany is a densely instrumented hydrological observatory and part of the TERENO (Terrestrial Environmental Observatories) initiative. The measurements acquired in this observatory present a comprehensive data set that contains key hydrological fluxes in addition to important hydrological states and properties. Meteorological data (i.e., precipitation, air temperature, air humidity, radiation components, and wind speed) are continuously recorded and actual evapotranspiration is measured using the eddy covariance technique. Runoff is measured at the catchment outlet with a gauging station. In addition, spatiotemporal variations in soil water content and temperature are measured at high resolution with a wireless sensor network (SoilNet). Soil physical properties were determined using standard laboratory procedures from samples taken at a large number of locations in the catchment. This comprehensive data set can be used to validate remote sensing retrievals and hydrological models, to improve the understanding of spatial temporal dynamics of soil water content, to optimize data assimilation and inverse techniques for hydrological models, and to develop upscaling and downscaling procedures of soil water content information. The complete data set is freely available online (http://www.tereno.net, doi:10.5880/TERENO.2016.001, doi:10.5880/TERENO.2016.004, doi:10.5880/TERENO.2016.003) and additionally referenced by three persistent identifiers securing the long-term data and metadata availability.

  18. Controlling the Electronic Structure of Graphene Using Surface-adsorbate Interactions

    DTIC Science & Technology

    2015-07-21

    substrate via n doping, with or without intercalation, suggests that the graphene-to-substrate interaction could be controlled dynamically. DOI : 10.1103...which form a Dirac cone and are degenerate at the Fermi level [1]. These states change in response to atoms adsorbed on top of graphene (doping) or when...coupling to the substrate is strong. In the case of graphene on metals, the energy of the Dirac cone can change as a result of interfacial doping, or

  19. Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy

    PubMed Central

    Jobst, Markus A; Milles, Lukas F; Schoeler, Constantin; Ott, Wolfgang; Fried, Daniel B; Bayer, Edward A; Gaub, Hermann E; Nash, Michael A

    2015-01-01

    Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicteddual binding modes across multiple bacterial species, our approach opens up newpossibilities for understanding assembly and catalytic properties of a broadrange of multi-enzyme complexes. DOI: http://dx.doi.org/10.7554/eLife.10319.001 PMID:26519733

  20. Multiscale modeling and simulation of microtubule-motor-protein assemblies

    NASA Astrophysics Data System (ADS)

    Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; Betterton, M. D.; Shelley, Michael J.

    2015-12-01

    Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation.

  1. Multiscale modeling and simulation of microtubule-motor-protein assemblies.

    PubMed

    Gao, Tong; Blackwell, Robert; Glaser, Matthew A; Betterton, M D; Shelley, Michael J

    2015-01-01

    Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation.

  2. NuMA-microtubule interactions are critical for spindle orientation and the morphogenesis of diverse epidermal structures

    PubMed Central

    Seldin, Lindsey; Muroyama, Andrew; Lechler, Terry

    2016-01-01

    Mitotic spindle orientation is used to generate cell fate diversity and drive proper tissue morphogenesis. A complex of NuMA and dynein/dynactin is required for robust spindle orientation in a number of cell types. Previous research proposed that cortical dynein/dynactin was sufficient to generate forces on astral microtubules (MTs) to orient the spindle, with NuMA acting as a passive tether. In this study, we demonstrate that dynein/dynactin is insufficient for spindle orientation establishment in keratinocytes and that NuMA’s MT-binding domain, which targets MT tips, is also required. Loss of NuMA-MT interactions in skin caused defects in spindle orientation and epidermal differentiation, leading to neonatal lethality. In addition, we show that NuMA-MT interactions are also required in adult mice for hair follicle morphogenesis and spindle orientation within the transit-amplifying cells of the matrix. Loss of spindle orientation in matrix cells results in defective differentiation of matrix-derived lineages. Our results reveal an additional and direct function of NuMA during mitotic spindle positioning, as well as a reiterative use of spindle orientation in the skin to build diverse structures. DOI: http://dx.doi.org/10.7554/eLife.12504.001 PMID:26765568

  3. Interaction of serotonin and cholecystokinin in the lateral parabrachial nucleus to control sodium intake.

    PubMed

    Fratucci De Gobbi, J I; De Luca, L A; Johnson, A K; Menani, J V

    2001-05-01

    Serotonin [5-hydroxytryptamine (5-HT)] and CCK injected into the lateral parabrachial nucleus (LPBN) inhibit NaCl and water intake. In this study, we investigated interactions between 5-HT and CCK into the LPBN to control water and NaCl intake. Male Holtzman rats with cannulas implanted bilaterally in the LPBN were treated with furosemide + captopril to induce water and NaCl intake. Bilateral LPBN injections of high doses of the 5-HT antagonist methysergide (4 microg) or the CCK antagonist proglumide (50 microg), alone or combined, produced similar increases in water and 1.8% NaCl intake. Low doses of methysergide (0.5 microg) + proglumide (20 microg) produced greater increases in NaCl intake than when they were injected alone. The 5-HT(2a/2c) agonist 2,5-dimetoxy-4-iodoamphetamine hydrobromide (DOI; 5 microg) into the LPBN reduced water and NaCl intake. After proglumide (50 microg) + DOI treatment, the intake was not different from vehicle treatment. CCK-8 (1 microg) alone produced no effect. CCK-8 combined with methysergide (4 microg) reduced the effect of methysergide on NaCl intake. The data suggest that functional interactions between 5-HT and CCK in the LPBN may be important for exerting inhibitory control of NaCl intake.

  4. Multiscale modeling and simulation of microtubule–motor-protein assemblies

    PubMed Central

    Gao, Tong; Blackwell, Robert; Glaser, Matthew A.; Betterton, M. D.; Shelley, Michael J.

    2016-01-01

    Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate–consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation. PMID:26764729

  5. Studying post-etching silicon crystal defects on 300mm wafer by automatic defect review AFM

    NASA Astrophysics Data System (ADS)

    Zandiatashbar, Ardavan; Taylor, Patrick A.; Kim, Byong; Yoo, Young-kook; Lee, Keibock; Jo, Ahjin; Lee, Ju Suk; Cho, Sang-Joon; Park, Sang-il

    2016-03-01

    Single crystal silicon wafers are the fundamental elements of semiconductor manufacturing industry. The wafers produced by Czochralski (CZ) process are very high quality single crystalline materials with known defects that are formed during the crystal growth or modified by further processing. While defects can be unfavorable for yield for some manufactured electrical devices, a group of defects like oxide precipitates can have both positive and negative impacts on the final device. The spatial distribution of these defects may be found by scattering techniques. However, due to limitations of scattering (i.e. light wavelength), many crystal defects are either poorly classified or not detected. Therefore a high throughput and accurate characterization of their shape and dimension is essential for reviewing the defects and proper classification. While scanning electron microscopy (SEM) can provide high resolution twodimensional images, atomic force microscopy (AFM) is essential for obtaining three-dimensional information of the defects of interest (DOI) as it is known to provide the highest vertical resolution among all techniques [1]. However AFM's low throughput, limited tip life, and laborious efforts for locating the DOI have been the limitations of this technique for defect review for 300 mm wafers. To address these limitations of AFM, automatic defect review AFM has been introduced recently [2], and is utilized in this work for studying DOI on 300 mm silicon wafer. In this work, we carefully etched a 300 mm silicon wafer with a gaseous acid in a reducing atmosphere at a temperature and for a sufficient duration to decorate and grow the crystal defects to a size capable of being detected as light scattering defects [3]. The etched defects form a shallow structure and their distribution and relative size are inspected by laser light scattering (LLS). However, several groups of defects couldn't be properly sized by the LLS due to the very shallow depth and low light scattering. Likewise, SEM cannot be used effectively for post-inspection defect review and classification of these very shallow types of defects. To verify and obtain accurate shape and three-dimensional information of those defects, automatic defect review AFM (ADR AFM) is utilized for accurate locating and imaging of DOI. In ADR AFM, non-contact mode imaging is used for non-destructive characterization and preserving tip sharpness for data repeatability and reproducibility. Locating DOI and imaging are performed automatically with a throughput of many defects per hour. Topography images of DOI has been collected and compared with SEM images. The ADR AFM has been shown as a non-destructive metrology tool for defect review and obtaining three-dimensional topography information.

  6. 77 FR 50712 - Information Collection: Southern Alaska Sharing Network and Subsistence Study; Proposed...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-22

    ... Analysis at (703) 787-1025. You may also request a free copy of the study description. [[Page 50713... meeting of DOI/BOEM information needs on subsistence food harvest and sharing activities in various... southern Alaska as to the potential effects of offshore oil and gas development on subsistence food harvest...

  7. Exploring the role of ionic liquids to tune the polymorphic outcome of organic compounds† †Electronic supplementary information (ESI) available: CCDC 1577981. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04353h

    PubMed Central

    Zeng, Qingying; Mukherjee, Arijit; Müller, Peter; Rogers, Robin D.

    2017-01-01

    While molecular solvents are commonly used in the screening of polymorphs, the choices are often restricted. Ionic liquids (ILs) – also referred as designer solvents – have immense possibility in this regard because of their wide flexibility of tunability. More importantly, the interactions among the IL components are completely unique compared to those present in the molecular solvents. In this context, we have chosen tetrolic acid (TA) and isonicotinamide (INA), which showed solution-structure link in molecular solvents in the past, as probes to investigate the role of imidazolium based ionic liquids in the polymorphism of these two systems and whether the different solute–solvent interactions in ILs affect the polymorphic outcome. It is observed that the selected imidazolium-based ILs, with varying anion basicity have influenced the crystallization outcome by the interaction between ILs and model compounds. Later, we have utilized the concept of double salt ionic liquids (DSIL) for INA, a penta-morphic system, to investigate the variation in the polymorphic outcome. This approach helped to obtain the forms that were otherwise inaccessible in ILs. PMID:29675194

  8. Cover Image, Volume 119, Number 1, January 2018.

    PubMed

    Rubio-Infante, Nestor; Ilhuicatzi-Alvarado, Damaris; Torres-Martínez, Marilu; Reyes-Grajeda, Juan Pablo; Nava-Acosta, Raúl; González-González, Edith; Moreno-Fierros, Leticia

    2018-01-01

    Cover: The cover image, by Nestor Rubio-Infante et al., is based on the Article The Macrophage Activation Induced by Bacillus thuringiensis Cry1Ac Protoxin Involves ERK1/2 and p38 Pathways and the Interaction with Cell-Surface-HSP70, DOI: 10.1002/jcb.26216. © 2017 Wiley Periodicals, Inc.

  9. A thesaurus for a neural population code

    PubMed Central

    Ganmor, Elad; Segev, Ronen; Schneidman, Elad

    2015-01-01

    Information is carried in the brain by the joint spiking patterns of large groups of noisy, unreliable neurons. This noise limits the capacity of the neural code and determines how information can be transmitted and read-out. To accurately decode, the brain must overcome this noise and identify which patterns are semantically similar. We use models of network encoding noise to learn a thesaurus for populations of neurons in the vertebrate retina responding to artificial and natural videos, measuring the similarity between population responses to visual stimuli based on the information they carry. This thesaurus reveals that the code is organized in clusters of synonymous activity patterns that are similar in meaning but may differ considerably in their structure. This organization is highly reminiscent of the design of engineered codes. We suggest that the brain may use this structure and show how it allows accurate decoding of novel stimuli from novel spiking patterns. DOI: http://dx.doi.org/10.7554/eLife.06134.001 PMID:26347983

  10. Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

    PubMed Central

    Mitrea, Diana M; Cika, Jaclyn A; Guy, Clifford S; Ban, David; Banerjee, Priya R; Stanley, Christopher B; Nourse, Amanda; Deniz, Ashok A; Kriwacki, Richard W

    2016-01-01

    The nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that nucleophosmin (NPM1) integrates within the nucleolus via a multi-modal mechanism involving multivalent interactions with proteins containing arginine-rich linear motifs (R-motifs) and ribosomal RNA (rRNA). Importantly, these R-motifs are found in canonical nucleolar localization signals. Based on a novel combination of biophysical approaches, we propose a model for the molecular organization within liquid-like droplets formed by the N-terminal domain of NPM1 and R-motif peptides, thus providing insights into the structural organization of the nucleolus. We identify multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, as structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli. We propose that one mechanism of nucleolar localization involves phase separation of proteins within the nucleolus. DOI: http://dx.doi.org/10.7554/eLife.13571.001 PMID:26836305

  11. Protein arginine methylation facilitates KCNQ channel-PIP2 interaction leading to seizure suppression

    PubMed Central

    Kim, Hyun-Ji; Jeong, Myong-Ho; Kim, Kyung-Ran; Jung, Chang-Yun; Lee, Seul-Yi; Kim, Hanna; Koh, Jewoo; Vuong, Tuan Anh; Jung, Seungmoon; Yang, Hyunwoo; Park, Su-Kyung; Choi, Dahee; Kim, Sung Hun; Kang, KyeongJin; Sohn, Jong-Woo; Park, Joo Min; Jeon, Daejong; Koo, Seung-Hoi; Ho, Won-Kyung; Kang, Jong-Sun; Kim, Seong-Tae; Cho, Hana

    2016-01-01

    KCNQ channels are critical determinants of neuronal excitability, thus emerging as a novel target of anti-epileptic drugs. To date, the mechanisms of KCNQ channel modulation have been mostly characterized to be inhibitory via Gq-coupled receptors, Ca2+/CaM, and protein kinase C. Here we demonstrate that methylation of KCNQ by protein arginine methyltransferase 1 (Prmt1) positively regulates KCNQ channel activity, thereby preventing neuronal hyperexcitability. Prmt1+/- mice exhibit epileptic seizures. Methylation of KCNQ2 channels at 4 arginine residues by Prmt1 enhances PIP2 binding, and Prmt1 depletion lowers PIP2 affinity of KCNQ2 channels and thereby the channel activities. Consistently, exogenous PIP2 addition to Prmt1+/- neurons restores KCNQ currents and neuronal excitability to the WT level. Collectively, we propose that Prmt1-dependent facilitation of KCNQ-PIP2 interaction underlies the positive regulation of KCNQ activity by arginine methylation, which may serve as a key target for prevention of neuronal hyperexcitability and seizures. DOI: http://dx.doi.org/10.7554/eLife.17159.001 PMID:27466704

  12. Response of radiation belt simulations to different radial diffusion coefficients for relativistic and ultra-relativistic electrons

    NASA Astrophysics Data System (ADS)

    Drozdov, Alexander; Mann, Ian; Baker, Daniel N.; Subbotin, Dmitriy; Ozeke, Louis; Shprits, Yuri; Kellerman, Adam

    Two parameterizations of the resonant wave-particle interactions of electrons with ULF waves in the magnetosphere by Brautigam and Albert [2000] and Ozeke et al. [2012] are evaluated using the Versatile Electron Radiation Belt (VERB) diffusion code to estimate the effect of changing a diffusion coefficient on the radiation belt simulation. The period of investigation includes geomagnetically quiet and active time. The simulations take into account wave-particle interactions represented by radial diffusion transport, local acceleration, losses due to pitch-angle diffusion, and mixed diffusion. 1. Brautigam, D. H., and J. M. Albert (2000), Radial diffusion analysis of outer radiation belt electrons during the October 9, 1990, magnetic storm, J. Geophys. Res., 105(A1), 291-309, doi:10.1029/1999JA900344 2. Ozeke, L. G., I. R. Mann, K. R. Murphy, I. J. Rae, D. K. Milling, S. R. Elkington, A. A. Chan, and H. J. Singer (2012), ULF wave derived radiation belt radial diffusion coefficients, J. Geophys. Res., 117, A04222, doi:10.1029/2011JA017463.

  13. The Ndc80 complex bridges two Dam1 complex rings

    PubMed Central

    Kim, Jae ook; Zelter, Alex; Umbreit, Neil T; Bollozos, Athena; Riffle, Michael; Johnson, Richard; MacCoss, Michael J; Asbury, Charles L; Davis, Trisha N

    2017-01-01

    Strong kinetochore-microtubule attachments are essential for faithful segregation of sister chromatids during mitosis. The Dam1 and Ndc80 complexes are the main microtubule binding components of the Saccharomyces cerevisiae kinetochore. Cooperation between these two complexes enhances kinetochore-microtubule coupling and is regulated by Aurora B kinase. We show that the Ndc80 complex can simultaneously bind and bridge across two Dam1 complex rings through a tripartite interaction, each component of which is regulated by Aurora B kinase. Mutations in any one of the Ndc80p interaction regions abrogates the Ndc80 complex’s ability to bind two Dam1 rings in vitro, and results in kinetochore biorientation and microtubule attachment defects in vivo. We also show that an extra-long Ndc80 complex, engineered to space the two Dam1 rings further apart, does not support growth. Taken together, our work suggests that each kinetochore in vivo contains two Dam1 rings and that proper spacing between the rings is vital. DOI: http://dx.doi.org/10.7554/eLife.21069.001 PMID:28191870

  14. Na+/K+ pump interacts with the h-current to control bursting activity in central pattern generator neurons of leeches

    PubMed Central

    Kueh, Daniel; Barnett, William H; Cymbalyuk, Gennady S; Calabrese, Ronald L

    2016-01-01

    The dynamics of different ionic currents shape the bursting activity of neurons and networks that control motor output. Despite being ubiquitous in all animal cells, the contribution of the Na+/K+ pump current to such bursting activity has not been well studied. We used monensin, a Na+/H+ antiporter, to examine the role of the pump on the bursting activity of oscillator heart interneurons in leeches. When we stimulated the pump with monensin, the period of these neurons decreased significantly, an effect that was prevented or reversed when the h-current was blocked by Cs+. The decreased period could also occur if the pump was inhibited with strophanthidin or K+-free saline. Our monensin results were reproduced in model, which explains the pump’s contributions to bursting activity based on Na+ dynamics. Our results indicate that a dynamically oscillating pump current that interacts with the h-current can regulate the bursting activity of neurons and networks. DOI: http://dx.doi.org/10.7554/eLife.19322.001 PMID:27588351

  15. A FYVE zinc finger domain protein specifically links mRNA transport to endosome trafficking

    PubMed Central

    Pohlmann, Thomas; Baumann, Sebastian; Haag, Carl; Albrecht, Mario; Feldbrügge, Michael

    2015-01-01

    An emerging theme in cellular logistics is the close connection between mRNA and membrane trafficking. A prominent example is the microtubule-dependent transport of mRNAs and associated ribosomes on endosomes. This coordinated process is crucial for correct septin filamentation and efficient growth of polarised cells, such as fungal hyphae. Despite detailed knowledge on the key RNA-binding protein and the molecular motors involved, it is unclear how mRNAs are connected to membranes during transport. Here, we identify a novel factor containing a FYVE zinc finger domain for interaction with endosomal lipids and a new PAM2-like domain required for interaction with the MLLE domain of the key RNA-binding protein. Consistently, loss of this FYVE domain protein leads to specific defects in mRNA, ribosome, and septin transport without affecting general functions of endosomes or their movement. Hence, this is the first endosomal component specific for mRNP trafficking uncovering a new mechanism to couple mRNPs to endosomes. DOI: http://dx.doi.org/10.7554/eLife.06041.001 PMID:25985087

  16. Assembling the Tat protein translocase

    PubMed Central

    Alcock, Felicity; Stansfeld, Phillip J; Basit, Hajra; Habersetzer, Johann; Baker, Matthew AB; Palmer, Tracy; Wallace, Mark I; Berks, Ben C

    2016-01-01

    The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues. Unexpectedly, we find that TatA also associates with TatC at the polar cluster site. Our data provide a structural model for assembly of the active Tat translocase in which substrate binding triggers replacement of TatB by TatA at the polar cluster site. Our work demonstrates the power of co-evolution analysis to predict protein interfaces in multi-subunit complexes. DOI: http://dx.doi.org/10.7554/eLife.20718.001 PMID:27914200

  17. Monochromatic multicomponent fluorescence sedimentation velocity for the study of high-affinity protein interactions

    PubMed Central

    Zhao, Huaying; Fu, Yan; Glasser, Carla; Andrade Alba, Eric J; Mayer, Mark L; Patterson, George; Schuck, Peter

    2016-01-01

    The dynamic assembly of multi-protein complexes underlies fundamental processes in cell biology. A mechanistic understanding of assemblies requires accurate measurement of their stoichiometry, affinity and cooperativity, and frequently consideration of multiple co-existing complexes. Sedimentation velocity analytical ultracentrifugation equipped with fluorescence detection (FDS-SV) allows the characterization of protein complexes free in solution with high size resolution, at concentrations in the nanomolar and picomolar range. Here, we extend the capabilities of FDS-SV with a single excitation wavelength from single-component to multi-component detection using photoswitchable fluorescent proteins (psFPs). We exploit their characteristic quantum yield of photo-switching to imprint spatio-temporal modulations onto the sedimentation signal that reveal different psFP-tagged protein components in the mixture. This novel approach facilitates studies of heterogeneous multi-protein complexes at orders of magnitude lower concentrations and for higher-affinity systems than previously possible. Using this technique we studied high-affinity interactions between the amino-terminal domains of GluA2 and GluA3 AMPA receptors. DOI: http://dx.doi.org/10.7554/eLife.17812.001 PMID:27436096

  18. Multi-functional roles for the polypeptide transport associated domains of Toc75 in chloroplast protein import

    PubMed Central

    Paila, Yamuna D; Richardson, Lynn GL; Inoue, Hitoshi; Parks, Elizabeth S; McMahon, James; Inoue, Kentaro; Schnell, Danny J

    2016-01-01

    Toc75 plays a central role in chloroplast biogenesis in plants as the membrane channel of the protein import translocon at the outer envelope of chloroplasts (TOC). Toc75 is a member of the Omp85 family of bacterial and organellar membrane insertases, characterized by N-terminal POTRA (polypeptide-transport associated) domains and C-terminal membrane-integrated β-barrels. We demonstrate that the Toc75 POTRA domains are essential for protein import and contribute to interactions with TOC receptors, thereby coupling preprotein recognition at the chloroplast surface with membrane translocation. The POTRA domains also interact with preproteins and mediate the recruitment of molecular chaperones in the intermembrane space to facilitate membrane transport. Our studies are consistent with the multi-functional roles of POTRA domains observed in other Omp85 family members and demonstrate that the domains of Toc75 have evolved unique properties specific to the acquisition of protein import during endosymbiotic evolution of the TOC system in plastids. DOI: http://dx.doi.org/10.7554/eLife.12631.001 PMID:26999824

  19. A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress

    PubMed Central

    McMurchy, Alicia N; Stempor, Przemyslaw; Gaarenstroom, Tessa; Wysolmerski, Brian; Dong, Yan; Aussianikava, Darya; Appert, Alex; Huang, Ni; Kolasinska-Zwierz, Paulina; Sapetschnig, Alexandra; Miska, Eric A; Ahringer, Julie

    2017-01-01

    Repetitive sequences derived from transposons make up a large fraction of eukaryotic genomes and must be silenced to protect genome integrity. Repetitive elements are often found in heterochromatin; however, the roles and interactions of heterochromatin proteins in repeat regulation are poorly understood. Here we show that a diverse set of C. elegans heterochromatin proteins act together with the piRNA and nuclear RNAi pathways to silence repetitive elements and prevent genotoxic stress in the germ line. Mutants in genes encoding HPL-2/HP1, LIN-13, LIN-61, LET-418/Mi-2, and H3K9me2 histone methyltransferase MET-2/SETDB1 also show functionally redundant sterility, increased germline apoptosis, DNA repair defects, and interactions with small RNA pathways. Remarkably, fertility of heterochromatin mutants could be partially restored by inhibiting cep-1/p53, endogenous meiotic double strand breaks, or the expression of MIRAGE1 DNA transposons. Functional redundancy among factors and pathways underlies the importance of safeguarding the genome through multiple means. DOI: http://dx.doi.org/10.7554/eLife.21666.001 PMID:28294943

  20. Axon tension regulates fasciculation/defasciculation through the control of axon shaft zippering

    PubMed Central

    Šmít, Daniel; Fouquet, Coralie; Pincet, Frédéric; Zapotocky, Martin; Trembleau, Alain

    2017-01-01

    While axon fasciculation plays a key role in the development of neural networks, very little is known about its dynamics and the underlying biophysical mechanisms. In a model system composed of neurons grown ex vivo from explants of embryonic mouse olfactory epithelia, we observed that axons dynamically interact with each other through their shafts, leading to zippering and unzippering behavior that regulates their fasciculation. Taking advantage of this new preparation suitable for studying such interactions, we carried out a detailed biophysical analysis of zippering, occurring either spontaneously or induced by micromanipulations and pharmacological treatments. We show that zippering arises from the competition of axon-axon adhesion and mechanical tension in the axons, and provide the first quantification of the force of axon-axon adhesion. Furthermore, we introduce a biophysical model of the zippering dynamics, and we quantitatively relate the individual zipper properties to global characteristics of the developing axon network. Our study uncovers a new role of mechanical tension in neural development: the regulation of axon fasciculation. DOI: http://dx.doi.org/10.7554/eLife.19907.001 PMID:28422009

  1. Autophagy functions as an antiviral mechanism against geminiviruses in plants

    PubMed Central

    Haxim, Yakupjan; Ismayil, Asigul; Jia, Qi; Wang, Yan; Zheng, Xiyin; Chen, Tianyuan; Qian, Lichao; Liu, Na; Wang, Yunjing; Han, Shaojie; Cheng, Jiaxuan; Qi, Yijun; Hong, Yiguo; Liu, Yule

    2017-01-01

    Autophagy is an evolutionarily conserved process that recycles damaged or unwanted cellular components, and has been linked to plant immunity. However, how autophagy contributes to plant immunity is unknown. Here we reported that the plant autophagic machinery targets the virulence factor βC1 of Cotton leaf curl Multan virus (CLCuMuV) for degradation through its interaction with the key autophagy protein ATG8. A V32A mutation in βC1 abolished its interaction with NbATG8f, and virus carrying βC1V32A showed increased symptoms and viral DNA accumulation in plants. Furthermore, silencing of autophagy-related genes ATG5 and ATG7 reduced plant resistance to the DNA viruses CLCuMuV, Tomato yellow leaf curl virus, and Tomato yellow leaf curl China virus, whereas activating autophagy by silencing GAPC genes enhanced plant resistance to viral infection. Thus, autophagy represents a novel anti-pathogenic mechanism that plays an important role in antiviral immunity in plants. DOI: http://dx.doi.org/10.7554/eLife.23897.001 PMID:28244873

  2. The dimerization equilibrium of a ClC Cl−/H+ antiporter in lipid bilayers

    PubMed Central

    Chadda, Rahul; Krishnamani, Venkatramanan; Mersch, Kacey; Wong, Jason; Brimberry, Marley; Chadda, Ankita; Kolmakova-Partensky, Ludmila; Friedman, Larry J; Gelles, Jeff; Robertson, Janice L

    2016-01-01

    Interactions between membrane protein interfaces in lipid bilayers play an important role in membrane protein folding but quantification of the strength of these interactions has been challenging. Studying dimerization of ClC-type transporters offers a new approach to the problem, as individual subunits adopt a stable and functionally verifiable fold that constrains the system to two states – monomer or dimer. Here, we use single-molecule photobleaching analysis to measure the probability of ClC-ec1 subunit capture into liposomes during extrusion of large, multilamellar membranes. The capture statistics describe a monomer to dimer transition that is dependent on the subunit/lipid mole fraction density and follows an equilibrium dimerization isotherm. This allows for the measurement of the free energy of ClC-ec1 dimerization in lipid bilayers, revealing that it is one of the strongest membrane protein complexes measured so far, and introduces it as new type of dimerization model to investigate the physical forces that drive membrane protein association in membranes. DOI: http://dx.doi.org/10.7554/eLife.17438.001 PMID:27484630

  3. Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules

    PubMed Central

    Kroschwald, Sonja; Maharana, Shovamayee; Mateju, Daniel; Malinovska, Liliana; Nüske, Elisabeth; Poser, Ina; Richter, Doris; Alberti, Simon

    2015-01-01

    RNA-protein (RNP) granules have been proposed to assemble by forming solid RNA/protein aggregates or through phase separation into a liquid RNA/protein phase. Which model describes RNP granules in living cells is still unclear. In this study, we analyze P bodies in budding yeast and find that they have liquid-like properties. Surprisingly, yeast stress granules adopt a different material state, which is reminiscent of solid protein aggregates and controlled by protein disaggregases. By using an assay to ectopically nucleate RNP granules, we further establish that RNP granule formation does not depend on amyloid-like aggregation but rather involves many promiscuous interactions. Finally, we show that stress granules have different properties in mammalian cells, where they show liquid-like behavior. Thus, we propose that the material state of RNP granules is flexible and that the solid state of yeast stress granules is an adaptation to extreme environments, made possible by the presence of a powerful disaggregation machine. DOI: http://dx.doi.org/10.7554/eLife.06807.001 PMID:26238190

  4. Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

    PubMed Central

    Roux, Simon; Hallam, Steven J; Woyke, Tanja; Sullivan, Matthew B

    2015-01-01

    The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes. DOI: http://dx.doi.org/10.7554/eLife.08490.001 PMID:26200428

  5. Impaired retrograde transport of axonal autophagosomes contributes to autophagic stress in Alzheimer’s disease neurons

    PubMed Central

    Tammineni, Prasad; Ye, Xuan; Feng, Tuancheng; Aikal, Daniyal; Cai, Qian

    2017-01-01

    Neurons face unique challenges of transporting nascent autophagic vacuoles (AVs) from distal axons toward the soma, where mature lysosomes are mainly located. Autophagy defects have been linked to Alzheimer’s disease (AD). However, the mechanisms underlying altered autophagy remain unknown. Here, we demonstrate that defective retrograde transport contributes to autophagic stress in AD axons. Amphisomes predominantly accumulate at axonal terminals of mutant hAPP mice and AD patient brains. Amyloid-β (Aβ) oligomers associate with AVs in AD axons and interact with dynein motors. This interaction impairs dynein recruitment to amphisomes through competitive interruption of dynein-Snapin motor-adaptor coupling, thus immobilizing them in distal axons. Consistently, deletion of Snapin in mice causes AD-like axonal autophagic stress, whereas overexpressing Snapin in hAPP neurons reduces autophagic accumulation at presynaptic terminals by enhancing AV retrograde transport. Altogether, our study provides new mechanistic insight into AD-associated autophagic stress, thus establishing a foundation for ameliorating axonal pathology in AD. DOI: http://dx.doi.org/10.7554/eLife.21776.001 PMID:28085665

  6. Long-range population dynamics of anatomically defined neocortical networks

    PubMed Central

    Chen, Jerry L; Voigt, Fabian F; Javadzadeh, Mitra; Krueppel, Roland; Helmchen, Fritjof

    2016-01-01

    The coordination of activity across neocortical areas is essential for mammalian brain function. Understanding this process requires simultaneous functional measurements across the cortex. In order to dissociate direct cortico-cortical interactions from other sources of neuronal correlations, it is furthermore desirable to target cross-areal recordings to neuronal subpopulations that anatomically project between areas. Here, we combined anatomical tracers with a novel multi-area two-photon microscope to perform simultaneous calcium imaging across mouse primary (S1) and secondary (S2) somatosensory whisker cortex during texture discrimination behavior, specifically identifying feedforward and feedback neurons. We find that coordination of S1-S2 activity increases during motor behaviors such as goal-directed whisking and licking. This effect was not specific to identified feedforward and feedback neurons. However, these mutually projecting neurons especially participated in inter-areal coordination when motor behavior was paired with whisker-texture touches, suggesting that direct S1-S2 interactions are sensory-dependent. Our results demonstrate specific functional coordination of anatomically-identified projection neurons across sensory cortices. DOI: http://dx.doi.org/10.7554/eLife.14679.001 PMID:27218452

  7. Gap junctions composed of connexins 41.8 and 39.4 are essential for colour pattern formation in zebrafish

    PubMed Central

    Irion, Uwe; Frohnhöfer, Hans Georg; Krauss, Jana; Çolak Champollion, Tuǧba; Maischein, Hans-Martin; Geiger-Rudolph, Silke; Weiler, Christian; Nüsslein-Volhard, Christiane

    2014-01-01

    Interactions between all three pigment cell types are required to form the stripe pattern of adult zebrafish (Danio rerio), but their molecular nature is poorly understood. Mutations in leopard (leo), encoding Connexin 41.8 (Cx41.8), a gap junction subunit, cause a phenotypic series of spotted patterns. A new dominant allele, leotK3, leads to a complete loss of the pattern, suggesting a dominant negative impact on another component of gap junctions. In a genetic screen, we identified this component as Cx39.4 (luchs). Loss-of-function alleles demonstrate that luchs is required for stripe formation in zebrafish; however, the fins are almost not affected. Double mutants and chimeras, which show that leo and luchs are only required in xanthophores and melanophores, but not in iridophores, suggest that both connexins form heteromeric gap junctions. The phenotypes indicate that these promote homotypic interactions between melanophores and xanthophores, respectively, and those cells instruct the patterning of the iridophores. DOI: http://dx.doi.org/10.7554/eLife.05125.001 PMID:25535837

  8. The structure of SV40 large T hexameric helicase in complex with AT-rich origin DNA

    PubMed Central

    Gai, Dahai; Wang, Damian; Li, Shu-Xing; Chen, Xiaojiang S

    2016-01-01

    DNA replication is a fundamental biological process. The initial step in eukaryotic DNA replication is the assembly of the pre-initiation complex, including the formation of two head-to-head hexameric helicases around the replication origin. How these hexameric helicases interact with their origin dsDNA remains unknown. Here, we report the co-crystal structure of the SV40 Large-T Antigen (LT) hexameric helicase bound to its origin dsDNA. The structure shows that the six subunits form a near-planar ring that interacts with the origin, so that each subunit makes unique contacts with the DNA. The origin dsDNA inside the narrower AAA+ domain channel shows partial melting due to the compression of the two phosphate backbones, forcing Watson-Crick base-pairs within the duplex to flip outward. This structure provides the first snapshot of a hexameric helicase binding to origin dsDNA, and suggests a possible mechanism of origin melting by LT during SV40 replication in eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.18129.001 PMID:27921994

  9. Dopamine and opioid systems interact within the nucleus accumbens to maintain monogamous pair bonds

    PubMed Central

    Resendez, Shanna L; Keyes, Piper C; Day, Jeremy J; Hambro, Caely; Austin, Curtis J; Maina, Francis K; Eidson, Lori N; Porter-Stransky, Kirsten A; Nevárez, Natalie; McLean, J William; Kuhnmuench, Morgan A; Murphy, Anne Z; Mathews, Tiffany A; Aragona, Brandon J

    2016-01-01

    Prairie vole breeder pairs form monogamous pair bonds, which are maintained through the expression of selective aggression toward novel conspecifics. Here, we utilize behavioral and anatomical techniques to extend the current understanding of neural mechanisms that mediate pair bond maintenance. For both sexes, we show that pair bonding up-regulates mRNA expression for genes encoding D1-like dopamine (DA) receptors and dynorphin as well as enhances stimulated DA release within the nucleus accumbens (NAc). We next show that D1-like receptor regulation of selective aggression is mediated through downstream activation of kappa-opioid receptors (KORs) and that activation of these receptors mediates social avoidance. Finally, we also identified sex-specific alterations in KOR binding density within the NAc shell of paired males and demonstrate that this alteration contributes to the neuroprotective effect of pair bonding against drug reward. Together, these findings suggest motivational and valence processing systems interact to mediate the maintenance of social bonds. DOI: http://dx.doi.org/10.7554/eLife.15325.001 PMID:27371827

  10. A conserved MCM single-stranded DNA binding element is essential for replication initiation.

    PubMed

    Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

    2014-04-01

    The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001.

  11. A conserved MCM single-stranded DNA binding element is essential for replication initiation

    PubMed Central

    Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

    2014-01-01

    The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001 PMID:24692448

  12. Interaction of plasticity and circuit organization during the acquisition of cerebellum-dependent motor learning

    PubMed Central

    Yang, Yan; Lisberger, Stephen G

    2013-01-01

    Motor learning occurs through interactions between the cerebellar circuit and cellular plasticity at different sites. Previous work has established plasticity in brain slices and suggested plausible sites of behavioral learning. We now reveal what actually happens in the cerebellum during short-term learning. We monitor the expression of plasticity in the simple-spike firing of cerebellar Purkinje cells during trial-over-trial learning in smooth pursuit eye movements of monkeys. Our findings imply that: 1) a single complex-spike response driven by one instruction for learning causes short-term plasticity in a Purkinje cell’s mossy fiber/parallel-fiber input pathways; 2) complex-spike responses and simple-spike firing rate are correlated across the Purkinje cell population; and 3) simple-spike firing rate at the time of an instruction for learning modulates the probability of a complex-spike response, possibly through a disynaptic feedback pathway to the inferior olive. These mechanisms may participate in long-term motor learning. DOI: http://dx.doi.org/10.7554/eLife.01574.001 PMID:24381248

  13. MorphoGraphX: A platform for quantifying morphogenesis in 4D

    PubMed Central

    Barbier de Reuille, Pierre; Routier-Kierzkowska, Anne-Lise; Kierzkowski, Daniel; Bassel, George W; Schüpbach, Thierry; Tauriello, Gerardo; Bajpai, Namrata; Strauss, Sören; Weber, Alain; Kiss, Annamaria; Burian, Agata; Hofhuis, Hugo; Sapala, Aleksandra; Lipowczan, Marcin; Heimlicher, Maria B; Robinson, Sarah; Bayer, Emmanuelle M; Basler, Konrad; Koumoutsakos, Petros; Roeder, Adrienne HK; Aegerter-Wilmsen, Tinri; Nakayama, Naomi; Tsiantis, Miltos; Hay, Angela; Kwiatkowska, Dorota; Xenarios, Ioannis; Kuhlemeier, Cris; Smith, Richard S

    2015-01-01

    Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX (www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth. DOI: http://dx.doi.org/10.7554/eLife.05864.001 PMID:25946108

  14. Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1

    PubMed Central

    Iwig, Jeffrey S; Vercoulen, Yvonne; Das, Rahul; Barros, Tiago; Limnander, Andre; Che, Yan; Pelton, Jeffrey G; Wemmer, David E; Roose, Jeroen P; Kuriyan, John

    2013-01-01

    RasGRP1 and SOS are Ras-specific nucleotide exchange factors that have distinct roles in lymphocyte development. RasGRP1 is important in some cancers and autoimmune diseases but, in contrast to SOS, its regulatory mechanisms are poorly understood. Activating signals lead to the membrane recruitment of RasGRP1 and Ras engagement, but it is unclear how interactions between RasGRP1 and Ras are suppressed in the absence of such signals. We present a crystal structure of a fragment of RasGRP1 in which the Ras-binding site is blocked by an interdomain linker and the membrane-interaction surface of RasGRP1 is hidden within a dimerization interface that may be stabilized by the C-terminal oligomerization domain. NMR data demonstrate that calcium binding to the regulatory module generates substantial conformational changes that are incompatible with the inactive assembly. These features allow RasGRP1 to be maintained in an inactive state that is poised for activation by calcium and membrane-localization signals. DOI: http://dx.doi.org/10.7554/eLife.00813.001 PMID:23908768

  15. Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response

    PubMed Central

    Zhang, Xu; Chen, Xiaoli; Liu, Qiuying; Zhang, Shaojie; Hu, Wenqian

    2017-01-01

    Gene expression is precisely regulated during the inflammatory response to control infection and limit the detrimental effects of inflammation. Here, we profiled global mRNA translation dynamics in the mouse primary macrophage-mediated inflammatory response and identified hundreds of differentially translated mRNAs. These mRNAs’ 3’UTRs have enriched binding motifs for several RNA-binding proteins, which implies extensive translational regulatory networks. We characterized one such protein, Zfp36, as a translation repressor. Using primary macrophages from a Zfp36-V5 epitope tagged knock-in mouse generated by CRISPR/Cas9-mediated genome editing, we found that the endogenous Zfp36 directly interacts with the cytoplasmic poly(A)-binding protein. Importantly, this interaction is required for the translational repression of Zfp36’s target mRNAs in resolving inflammation. Altogether, these results uncovered critical roles of translational regulations in controlling appropriate gene expression during the inflammatory response and revealed a new biologically relevant molecular mechanism of translational repression via modulating the cytoplasmic poly(A)-binding protein. DOI: http://dx.doi.org/10.7554/eLife.27786.001 PMID:28635594

  16. Exploring the reversal of enantioselectivity on a zinc-dependent alcohol dehydrogenase† †Electronic supplementary information (ESI) available. See DOI: 10.1039/C7OB00482F Click here for additional data file.

    PubMed Central

    Maria-Solano, Miguel A.; Romero-Rivera, Adrian

    2017-01-01

    Alcohol Dehydrogenase (ADH) enzymes catalyse the reversible reduction of prochiral ketones to the corresponding alcohols. These enzymes present two differently shaped active site pockets, which dictate their substrate scope and selectivity. In this study, we computationally evaluate the effect of two commonly reported active site mutations (I86A, and W110T) on a secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) through Molecular Dynamics simulations. Our results indicate that the introduced mutations induce dramatic changes in the shape of the active site, but most importantly they impact the substrate–enzyme interactions. We demonstrate that the combination of Molecular Dynamics simulations with the tools POVME and NCIplot corresponds to a powerful strategy for rationalising and engineering the stereoselectivity of ADH variants. PMID:28436515

  17. Theoretical studies on a carbonaceous molecular bearing: association thermodynamics and dual-mode rolling dynamics† †Electronic supplementary information (ESI) available: Supplementary figures, tables and atomic coordinates of representative geometries. See DOI: 10.1039/c5sc00335k

    PubMed Central

    Nakamura, Kosuke; Hitosugi, Shunpei; Sato, Sota; Tokoyama, Hiroaki; Yamakado, Hideo; Ohno, Koichi

    2015-01-01

    The thermodynamics and dynamics of a carbonaceous molecular bearing comprising a belt-persistent tubular molecule and a fullerene molecule have been investigated using density functional theory (DFT). Among ten representative methods, two DFT methods afforded an association energy that reasonably reproduced the experimental enthalpy of –12.5 kcal mol–1 at the unique curved π-interface. The dynamics of the molecular bearing, which was assembled solely with van der Waals interactions, exhibited small energy barriers with maximum values of 2–3 kcal mol–1 for the rolling motions. The dynamic motions responded sensitively to the steric environment and resulted in two distinct motions, precession and spin, which explained the unique NMR observations that were not clarified in previous experimental studies. PMID:29142679

  18. Effects of reflector and crystal surface on the performance of a depth-encoding PET detector with dual-ended readout

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

    Ren, Silin; Yang, Yongfeng, E-mail: yfyang@ucdavis.edu; Cherry, Simon R.

    Purpose: Depth encoding detectors are required to improve the spatial resolution and spatial resolution uniformity of small animal positron emission tomography (PET) scanners, as well as dedicated breast and brain scanners. Depth of interaction (DOI) can be measured by using dual-ended readout of lutetium oxyorthosilicate (LSO) scintillator arrays with position-sensitive avalanche photodiodes. Inter-crystal reflectors and crystal surface treatments play important roles in determining the performance of dual-ended detectors. In this paper, the authors evaluated five LSO arrays made with three different intercrystal reflectors and with either polished or unpolished crystal surfaces. Methods: The crystal size in all arrays was 1.5more » mm, which is typical of the detector size used in small animal and dedicated breast scanners. The LSO arrays were measured with dual-ended readout and were compared in terms of flood histogram, energy resolution, and DOI resolution performance. Results: The four arrays using enhanced specular reflector (ESR) and Toray reflector provided similar quality flood histograms and the array using Crystal Wrap reflector gave the worst flood histogram. The two arrays using ESR reflector provided the best energy resolution and the array using Crystal Wrap reflector yielded the worst energy resolution. All arrays except the polished ESR array provided good DOI resolution ranging from 1.9 mm to 2.9 mm. DOI resolution improved as the gradient in light collection efficiency with depth (GLCED) increased. The geometric mean energies were also calculated for these dual-ended readout detectors as an alternative to the conventional summed total energy. It was shown that the geometric mean energy is advantageous in that it provides more uniform photopeak amplitude at different depths for arrays with high GLCED, and is beneficial in event selection by allowing a fixed energy window independent of depth. A new method of DOI calculation that improved the linearity of DOI ratio vs depth and simplifies the DOI calibration procedure also was developed and tested. Conclusions: The results of these studies provide useful guidance in selecting the proper reflectors and crystal surface treatments when LSO arrays are used for high-resolution PET applications in small animal scanners or dedicated breast and brain scanners.« less

  19. An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability

    PubMed Central

    Schütte, Judith; Wang, Huange; Antoniou, Stella; Jarratt, Andrew; Wilson, Nicola K; Riepsaame, Joey; Calero-Nieto, Fernando J; Moignard, Victoria; Basilico, Silvia; Kinston, Sarah J; Hannah, Rebecca L; Chan, Mun Chiang; Nürnberg, Sylvia T; Ouwehand, Willem H; Bonzanni, Nicola; de Bruijn, Marella FTR; Göttgens, Berthold

    2016-01-01

    Transcription factor (TF) networks determine cell-type identity by establishing and maintaining lineage-specific expression profiles, yet reconstruction of mammalian regulatory network models has been hampered by a lack of comprehensive functional validation of regulatory interactions. Here, we report comprehensive ChIP-Seq, transgenic and reporter gene experimental data that have allowed us to construct an experimentally validated regulatory network model for haematopoietic stem/progenitor cells (HSPCs). Model simulation coupled with subsequent experimental validation using single cell expression profiling revealed potential mechanisms for cell state stabilisation, and also how a leukaemogenic TF fusion protein perturbs key HSPC regulators. The approach presented here should help to improve our understanding of both normal physiological and disease processes. DOI: http://dx.doi.org/10.7554/eLife.11469.001 PMID:26901438

  20. Sleep deprivation suppresses aggression in Drosophila

    PubMed Central

    Kayser, Matthew S; Mainwaring, Benjamin; Yue, Zhifeng; Sehgal, Amita

    2015-01-01

    Sleep disturbances negatively impact numerous functions and have been linked to aggression and violence. However, a clear effect of sleep deprivation on aggressive behaviors remains unclear. We find that acute sleep deprivation profoundly suppresses aggressive behaviors in the fruit fly, while other social behaviors are unaffected. This suppression is recovered following post-deprivation sleep rebound, and occurs regardless of the approach to achieve sleep loss. Genetic and pharmacologic approaches suggest octopamine signaling transmits changes in aggression upon sleep deprivation, and reduced aggression places sleep-deprived flies at a competitive disadvantage for obtaining a reproductive partner. These findings demonstrate an interaction between two phylogenetically conserved behaviors, and suggest that previous sleep experiences strongly modulate aggression with consequences for reproductive fitness. DOI: http://dx.doi.org/10.7554/eLife.07643.001 PMID:26216041

  1. Cannabinoids: clearing the smoke on pain, inflammation and neurodegeneration.

    PubMed

    Downer, E J; Finn, D P

    2014-03-01

    This article is part of a themed section on Cannabinoids 2013. To view the other articles in this section, see Fagan and Campbell (2014) DOI: 10.1111/bph.12492, Ignatowska-Jankowska et al. (2014) DOI: 10.1111/bph.12298, Ligresti et al. (2014) DOI: 10.1111/bph.12410, Lopez-Rodriguez et al. (2014) DOI: 10.1111/bph.12519, Murataeva et al. (2014) DOI: 10.1111/bph.12411, Okine et al. (2014) DOI: 10.1111/bph.12540, Rodríguez-Cueto et al. (2014) DOI: 10.1111/bph.12283, Stanley and O'Sullivan (2014) DOI: 10.1111/bph.12560, Toguri et al. (2014) DOI: 10.1111/bph.12545, Wu et al. (2014) DOI: 10.1111/bph.12500. Linked articles are: Avraham et al. (2014) DOI: 10.1111/bph.12478, Machado et al. (2014) DOI: 10.1111/bph.12488, Ward et al. (2014) DOI: 10.1111/bph.12439. © 2014 The British Pharmacological Society.

  2. New design and facilities for the International Database for Absolute Gravity Measurements (AGrav): A support for the Establishment of a new Global Absolute Gravity Reference System

    NASA Astrophysics Data System (ADS)

    Wziontek, Hartmut; Falk, Reinhard; Bonvalot, Sylvain; Rülke, Axel

    2017-04-01

    After about 10 years of successful joint operation by BGI and BKG, the International Database for Absolute Gravity Measurements "AGrav" (see references hereafter) was under a major revision. The outdated web interface was replaced by a responsive, high level web application framework based on Python and built on top of Pyramid. Functionality was added, like interactive time series plots or a report generator and the interactive map-based station overview was updated completely, comprising now clustering and the classification of stations. Furthermore, the database backend was migrated to PostgreSQL for better support of the application framework and long-term availability. As comparisons of absolute gravimeters (AG) become essential to realize a precise and uniform gravity standard, the database was extended to document the results on international and regional level, including those performed at monitoring stations equipped with SGs. By this it will be possible to link different AGs and to trace their equivalence back to the key comparisons under the auspices of International Committee for Weights and Measures (CIPM) as the best metrological realization of the absolute gravity standard. In this way the new AGrav database accommodates the demands of the new Global Absolute Gravity Reference System as recommended by the IAG Resolution No. 2 adopted in Prague 2015. The new database will be presented with focus on the new user interface and new functionality, calling all institutions involved in absolute gravimetry to participate and contribute with their information to built up a most complete picture of high precision absolute gravimetry and improve its visibility. A Digital Object Identifier (DOI) will be provided by BGI to contributors to give a better traceability and facilitate the referencing of their gravity surveys. Links and references: BGI mirror site : http://bgi.obs-mip.fr/data-products/Gravity-Databases/Absolute-Gravity-data/ BKG mirror site: http://agrav.bkg.bund.de/agrav-meta/ Wilmes, H., H. Wziontek, R. Falk, S. Bonvalot (2009). AGrav - the New Absolute Gravity Database and a Proposed Cooperation with the GGP Project. J. of Geodynamics, 48, pp. 305-309. doi:10.1016/j.jog.2009.09.035. Wziontek, H., H. Wilmes, S. Bonvalot (2011). AGrav: An international database for absolute gravity measurements. In Geodesy for Planet Earth (S. Kenyon at al. eds). IAG Symposia, 136, 1035-1040, Springer, Berlin. 2011. doi:10.1007/978-3-642-20338-1_130.

  3. Data DOIs - virtues and weak points from the perspective of the data journal ESSD

    NASA Astrophysics Data System (ADS)

    Pfeiffenberger, Hans; Carlson, David

    2016-04-01

    Fundamentally, data publication seeks to provide improved access, trust and utility for data users accompanied by improved recognition for data providers. The features of persistent identifier schemes used in this context and the policies of providers of their resolver systems can greatly contribute towards these aims! Unfortunately, we also recognize situations where identifier systems undermine some of our lofty data publication aims. From our 7 years of successful experience with the data journal ESSD, we will present our practical observations as well as future requirements on the DOI-system in particular, such as: * Most scientists contributing to or drawing benefit from ESSD seem to understand the notion of published data in the sense of a static, citable entity to build on, relying on its long term availability and integrity (as is the case with journal articles), secured by DOIs. * It is still true that many data providers - individuals or projects - can not find a repository for their (type of) data which would provide a DOI (or other persistent identifier) and that many data centers and databases holding valuable data have a hard time adding DOIs as a feature of their systems for conceptual, legacy or funding reasons. * The typical evolution of many important data collections or data products - such as the Global Carbon Budget - can adequately be tracked with yearly (or less frequent) issues of dataset and data article, each having a new DOI. However, issuing a new DOI for a dataset extended in time clashes with many producers' wish to amass all references to the developing dataset under one citation (and one DOI). * Current practises with DOIs and metadata associated with DOIs need to be clarified and amended so the identifier systems can and do express and track the relationships between versions of data, addressing extensions, corrections, modifications, revisions and retractions in an unambiguous (and machine readable) manner, while also removing extraneous information (dates, page numbers) from the identifier itself. * Similarly, we recognize a clear need to hold one or more copies of important data in different locations (continents), under different governance and technologies but to still be able to identify these copies as intellectually identical. Today, however, we observe identical datasets held in separate repositories with different metadata and DOIs without a process to easily identify the duplicates. * The dataset and data article - coupled with a research article citing both and drawing conclusions and perhaps with an additional article describing and publishing the software - offer a valid and vivid example of linking objects reliably across many players' (publishers') systems. Too often, however, establishing such linkages requires substantial human intervention to initiate and synchronize the necessary processes, in particular to ensure high-fidelity mutual citation among the individual items. As editors of a data journal we firmly embrace the notion of persistence and persistent identifiers, in particular DOIs. We see the need and applaud all efforts to enhance its features to serve the important needs of published and linked data.

  4. Publications - GMC 363 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    Division of Geological & Geophysical Surveys Comments: Excel files of grain size data and point count . http://doi.org/10.14509/20244 Publication Products Report Report Information gmc363.pdf (6.6 M) Excel

  5. Direct neural pathways convey distinct visual information to Drosophila mushroom bodies

    PubMed Central

    Vogt, Katrin; Aso, Yoshinori; Hige, Toshihide; Knapek, Stephan; Ichinose, Toshiharu; Friedrich, Anja B; Turner, Glenn C; Rubin, Gerald M; Tanimoto, Hiromu

    2016-01-01

    Previously, we demonstrated that visual and olfactory associative memories of Drosophila share mushroom body (MB) circuits (Vogt et al., 2014). Unlike for odor representation, the MB circuit for visual information has not been characterized. Here, we show that a small subset of MB Kenyon cells (KCs) selectively responds to visual but not olfactory stimulation. The dendrites of these atypical KCs form a ventral accessory calyx (vAC), distinct from the main calyx that receives olfactory input. We identified two types of visual projection neurons (VPNs) directly connecting the optic lobes and the vAC. Strikingly, these VPNs are differentially required for visual memories of color and brightness. The segregation of visual and olfactory domains in the MB allows independent processing of distinct sensory memories and may be a conserved form of sensory representations among insects. DOI: http://dx.doi.org/10.7554/eLife.14009.001 PMID:27083044

  6. The scale effect on soil erosion. A plot approach to understand connectivity on slopes under cultivation at variable plot sizes and under Mediterranean climatic conditions

    NASA Astrophysics Data System (ADS)

    Cerdà, Artemi; Bagarello, Vicenzo; Ferro, Vito; Iovino, Massimo; Borja, Manuel Estaban Lucas; Francisco Martínez Murillo, Juan; González Camarena, Rafael

    2017-04-01

    It is well known that soil erosion changes along time and seasons and attention was paid to this issue in the past (González Hidalgo et al., 2010; 2012). However, although the scientific community knows that soil erosion is also a time spatial scale-scale dependent process (Parsons et al., 1990; Cerdà et al., 2009; González Hidalgo et al., 2013; Sadeghi et al., 2015) very little is done on this topic. This is due to the fact that at different scales, different soil erosion mechanisms (splash, sheetflow, rill development) are active and their rates change with the scale of measurement (Wainwright et al., 2002; López-Vicente et al., 2015). This is making the research on soil erosion complex and difficult, and it is necessary to develop a conceptual framework but also measurements that will inform about the soil erosion behaviour. Connectivity is the key concept to understand how changes in the scale results in different rates of soil and water losses (Parsons et al., 1996; Parsons et al., 2015; Poeppl et al., 2016). Most of the research developed around the connectivity concept was applied in watershed or basin scales (Galdino et al., 2016; Martínez-Casasnovas et al., 2016; López Vicente et al., 2016; Marchamalo et al., 2015; Masselink et al., 2016), but very little is known about the connectivity issue at slope scale (Cerdà and Jurgensen, 2011). El Teularet (Eastern Iberian Peninsula) and Sparacia (Sicily) soil erosion experimental stations are being active for 15 years and data collected on different plots sizes can shed light into the effect of scale on runoff generation and soil losses at different scales and give information to understand how the transport of materials is determined by the connectivity between pedon to slope scale (Cerdà et al., 2014; Bagarello et al., 2015a; 2015b). The comparison of the results of the two research stations will shed light into the rates of soil erosion and mechanisms involved that act under different scales. Our research share information collected during the last 15 years in the Sparacia and El Teularet soil erosion experimental stations under the same management and research how the concept of connectivity can help us to have a better understanding of the soil erosion process, and the effect of scale. All the data will be treated to show the runoff and sediment eroded at different plot sizes to understand how the sediment is transported at event scale. The rainfall characteristics will be also analysed to understand the soil erosion processes at different scales. Acknowledgements The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n 603498 (RECARE project) and the CGL2013- 47862-C2-1-R and CGL2016-75178-C2-2-R national research projects. References Bagarello, V., Ferro, V., Pampalone, V. 2015b. A new version of the USLE-MM for predicting bare plot soil loss at the Sparacia (South Italy) experimental site. Hydrological Processes, 29(19), 4210-4219. Bagarello, V., Ferro, V., Giordano, G., Mannocchi, F., Pampalone, V., Todisco, F. 2015a. A modified applicative criterion of the physical model concept for evaluating plot soil erosion predictions. Catena, 126, 53-58. Cerdà, A. and M. F. Jurgensen. 2011. Ant Mounds as a Source of Sediment on Citrus Orchard Plantations in Eastern Spain. A Three-Scale Rainfall Simulation Approach. Catena 85 (3): 231-236. doi:10.1016/j.catena.2011.01.008. Cerdà, A., Giménez-Morera, A., Jordan, A., Pereira, P., Novara, A., Keesstra, S., Sinoga, J. D. R. 2015. Shrubland as a soil and water conservation agent in Mediterranean-type ecosystems: The Sierra de Enguera study site contribution. Monitoring and Modelling Dynamic Environments, 45. Cerdà, A., R. Brazier, M. Nearing, and J. de Vente. 2013. Scales and Erosion. Catena 102: 1-2. doi:10.1016/j.catena.2011.09.006. Galdino, S., E. E. Sano, R. G. Andrade, C. R. Grego, S. F. Nogueira, C. Bragantini, and A. H. G. Flosi. 2016. Large-Scale Modeling of Soil Erosion with RUSLE for Conservationist Planning of Degraded Cultivated Brazilian Pastures. Land Degradation and Development 27 (3): 773-784. doi:10.1002/ldr.2414. Gonzalez-Hidalgo, J. C., R. J. Batalla, A. Cerdá, and M. de Luis. 2010. Contribution of the Largest Events to Suspended Sediment Transport Across the USA. Land Degradation and Development 21 (2): 83-91. doi:10.1002/ldr.897. Gonzalez-Hidalgo, J. C., R. J. Batalla, A. Cerdà, and M. de Luis. 2012. A Regional Analysis of the Effects of Largest Events on Soil Erosion. Catena 95: 85-90. doi:10.1016/j.catena.2012.03.006. Gonzalez-Hidalgo, J. C., R. J. Batalla, and A. Cerdà. 2013. Catchment Size and Contribution of the Largest Daily Events to Suspended Sediment Load on a Continental Scale. Catena 102: 40-45. doi:10.1016/j.catena.2010.10.011. López-Vicente, M., E. Nadal-Romero, and E. L. H. Cammeraat. 2016. Hydrological Connectivity does Change Over 70 Years of Abandonment and Afforestation in the Spanish Pyrenees. Land Degradation and Development. doi:10.1002/ldr.2531. López-Vicente, M., L. Quijano, L. Palazón, L. Gaspar, and A. Navas. 2015. Assessment of Soil Redistribution at Catchment Scale by Coupling a Soil Erosion Model and a Sediment Connectivity Index (Central Spanish Pre-Pyrenees). Cuadernos De Investigacion Geografica 41 (1): 127-147. doi:10.18172/cig.2649. Marchamalo, M., J. M. Hooke, and P. J. Sandercock. 2016. Flow and Sediment Connectivity in Semi-Arid Landscapes in SE Spain: Patterns and Controls. Land Degradation and Development 27 (4): 1032-1044. doi:10.1002/ldr.2352. Martínez-Casasnovas, J. A., M. C. Ramos, and G. Benites. 2016. Soil and Water Assessment Tool Soil Loss Simulation at the Sub-Basin Scale in the Alt Penedès-Anoia Vineyard Region (Ne Spain) in the 2000s. Land Degradation and Development 27 (2): 160-170. doi:10.1002/ldr.2240. Masselink, R.J.H., S.D. Keesstra, A J.A.M. Temme, M. Seeger, R. Giménez, J. Casalí. 2016. Modelling Discharge and Sediment Yield at Catchment Scale using Connectivity Components. Land Degradation and Development 27 (4): 933-945. doi:10.1002/ldr.2512. Parsons, A.J., Abrahams, A.D., Luk, S.H. 1990. Hydraulics of interrill overland flow on a semi-arid hillslope, southern Arizona. Journal of Hydrology, 117(1), 255-273. Parsons, A.J., Abrahams, A. D., Wainwright, J. 1996. Responses of interrill runoff and erosion rates to vegetation change in southern Arizona. Geomorphology, 14(4), 311-317. Parsons A.J., Bracken L., Peoppl , R., Wainwright J., Keesstra, S.D., 2015. Editorial: Introduction to special issue on connectivity in water and sediment dynamics. In press in Earth Surface Processes and Landforms. DOI: 10.1002/esp.3714 Poeppl, R.,E. Maroulis, J., Keesstra, S.D., 2016. Geomorphology. A conceptual connectivity framework for understanding geomorphic change in human-impacted fluvial systems. http://dx.doi.org/10.1016/j.geomorph.2016.07.033 Sadeghi, S.H.R., Gholami, L., Sharifi, E., Khaledi Darvishan, A., Homaee, M. Scale effect on runoff and soil loss control using rice straw mulch under laboratory conditions. (2015) Solid Earth, 6 (1), pp. 1-8.. DOI: http://dx.doi.org/10.5194/se-6-1-2015 Wainwright, J., Parsons, A.J., Schlesinger, W.H., Abrahams, A.D. 2002. Hydrology-vegetation interactions in areas of discontinuous flow on a semi-arid bajada, southern New Mexico. Journal of Arid Environments, 51(3), 319-338.

  7. Hallucinogenic 5-HT2AR agonists LSD and DOI enhance dopamine D2R protomer recognition and signaling of D2-5-HT2A heteroreceptor complexes.

    PubMed

    Borroto-Escuela, Dasiel O; Romero-Fernandez, Wilber; Narvaez, Manuel; Oflijan, Julia; Agnati, Luigi F; Fuxe, Kjell

    2014-01-03

    Dopamine D2LR-serotonin 5-HT2AR heteromers were demonstrated in HEK293 cells after cotransfection of the two receptors and shown to have bidirectional receptor-receptor interactions. In the current study the existence of D2L-5-HT2A heteroreceptor complexes was demonstrated also in discrete regions of the ventral and dorsal striatum with in situ proximity ligation assays (PLA). The hallucinogenic 5-HT2AR agonists LSD and DOI but not the standard 5-HT2AR agonist TCB2 and 5-HT significantly increased the density of D2like antagonist (3)H-raclopride binding sites and significantly reduced the pKiH values of the high affinity D2R agonist binding sites in (3)H-raclopride/DA competition experiments. Similar results were obtained in HEK293 cells and in ventral striatum. The effects of the hallucinogenic 5-HT2AR agonists on D2R density and affinity were blocked by the 5-HT2A antagonist ketanserin. In a forskolin-induced CRE-luciferase reporter gene assay using cotransfected but not D2R singly transfected HEK293 cells DOI and LSD but not TCB2 significantly enhanced the D2LR agonist quinpirole induced inhibition of CRE-luciferase activity. Haloperidol blocked the effects of both quinpirole alone and the enhancing actions of DOI and LSD while ketanserin only blocked the enhancing actions of DOI and LSD. The mechanism for the allosteric enhancement of the D2R protomer recognition and signalling observed is likely mediated by a biased agonist action of the hallucinogenic 5-HT2AR agonists at the orthosteric site of the 5-HT2AR protomer. This mechanism may contribute to the psychotic actions of LSD and DOI and the D2-5-HT2A heteroreceptor complex may thus be a target for the psychotic actions of hallunicogenic 5-HT2A agonists. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Head-twitch response in rodents induced by the hallucinogen 2,5-dimethoxy-4-iodoamphetamine: a comprehensive history, a re-evaluation of mechanisms, and its utility as a model

    PubMed Central

    Canal, Clint E.; Morgan, Drake

    2013-01-01

    Two primary animal models persist for assessing hallucinogenic potential of novel compounds and for examining the pharmacological and neurobiological substrates underlying the actions of classical hallucinogens, the two-lever drug discrimination procedure and the drug-induced head-twitch response (HTR) in rodents. The substituted amphetamine hallucinogen, serotonin 2 (5-HT2) receptor agonist, 2,5-dimethoxy-4-iodoamphetamine (DOI) has emerged as the most popular pharmacological tool used in HTR studies of hallucinogens. Synthesizing classic, recent, and relatively overlooked findings, addressing ostensibly conflicting observations, and considering contemporary theories in receptor and behavioural pharmacology, this review provides an up-to-date and comprehensive synopsis of DOI and the HTR model, from neural mechanisms to utility for understanding psychiatric diseases. Also presented is support for the argument that, although both the two-lever drug discrimination and the HTR models in rodents are useful for uncovering receptors, interacting proteins, intracellular signalling pathways, and neurochemical processes affected by DOI and related classical hallucinogens, results from both models suggest they are not reporting hallucinogenic experiences in animals. PMID:22517680

  9. Influence of detector pixel size, TOF resolution and DOI on image quality in MR-compatible whole-body PET.

    PubMed

    Thoen, Hendrik; Keereman, Vincent; Mollet, Pieter; Van Holen, Roel; Vandenberghe, Stefaan

    2013-09-21

    The optimization of a whole-body PET system remains a challenging task, as the imaging performance is influenced by a complex interaction of different design parameters. However, it is not always clear which parameters have the largest impact on image quality and are most eligible for optimization. To determine this, we need to be able to assess their influence on image quality. We performed Monte-Carlo simulations of a whole-body PET scanner to predict the influence on image quality of three detector parameters: the TOF resolution, the transverse pixel size and depth-of-interaction (DOI)-correction. The inner diameter of the PET scanner was 65 cm, small enough to allow physical integration into a simultaneous PET-MR system. Point sources were used to evaluate the influence of transverse pixel size and DOI-correction on spatial resolution as function of radial distance. To evaluate the influence on contrast recovery and pixel noise a cylindrical phantom of 35 cm diameter was used, representing a large patient. The phantom contained multiple hot lesions with 5 mm diameter. These lesions were placed at radial distances of 50, 100 and 150 mm from the center of the field-of-view, to be able to study the effects at different radial positions. The non-prewhitening (NPW) observer was used for objective analysis of the detectability of the hot lesions in the cylindrical phantom. Based on this analysis the NPW-SNR was used to quantify the relative improvements in image quality due to changes of the variable detector parameters. The image quality of a whole-body PET scanner can be improved significantly by reducing the transverse pixel size from 4 to 2.6 mm and improving the TOF resolution from 600 to 400 ps and further from 400 to 200 ps. Compared to pixel size, the TOF resolution has the larger potential to increase image quality for the simulated phantom. The introduction of two layer DOI-correction only leads to a modest improvement for the spheres at radial distance of 150 mm from the center of the transaxial FOV.

  10. Publications - RDF 2007-1 | Alaska Division of Geological & Geophysical

    Science.gov Websites

    ://doi.org/10.14509/15759 Publication Products Report Report Information rdf2007_001.pdf (443.0 K) Digital Geospatial Data Digital Geospatial Data Fairbanks Mining District Geochemical Data Data File Format File Size

  11. Publications - RDF 2011-4 v. 2 | Alaska Division of Geological &

    Science.gov Websites

    ://doi.org/10.14509/23002 Publication Products Report Report Information rdf2011_004.pdf (519.0 K) Digital Geospatial Data Digital Geospatial Data Moran Geochemistry Data File Format File Size Info Download moran

  12. Cholesterol-directed nanoparticle assemblies based on single amino acid peptide mutations activate cellular uptake and decrease tumor volume† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc02616a Click here for additional data file.

    PubMed Central

    Li, Shang; Zou, Rongfeng; Tu, Yaoquan

    2017-01-01

    Peptide drugs have been difficult to translate into effective therapies due to their low in vivo stability. Here, we report a strategy to develop peptide-based therapeutic nanoparticles by screening a peptide library differing by single-site amino acid mutations of lysine-modified cholesterol. Certain cholesterol-modified peptides are found to promote and stabilize peptide α-helix formation, resulting in selectively cell-permeable peptides. One cholesterol-modified peptide self-assembles into stable nanoparticles with considerable α-helix propensity stabilized by intermolecular van der Waals interactions between inter-peptide cholesterol molecules, and shows 68.3% stability after incubation with serum for 16 h. The nanoparticles in turn interact with cell membrane cholesterols that are disproportionately present in cancer cell membranes, inducing lipid raft-mediated endocytosis and cancer cell death. Our results introduce a strategy to identify peptide nanoparticles that can effectively reduce tumor volumes when administered to in in vivo mice models. Our results also provide a simple platform for developing peptide-based anticancer drugs. PMID:29163910

  13. Data citation in climate sciences: Improvements in CMIP6 compared to CMIP5

    NASA Astrophysics Data System (ADS)

    Stockhause, M.; Lautenschlager, M.

    2017-12-01

    Within CMIP5 (Coupled Model Intercomparison Project Phase 5) the citation of the data was not possible prior its long-term archival in the IPCC Data Distribution Centre (DDC). The Reference Data Archive for AR5 (Assessment Report 5) was built up after the submission deadline for part 1 of the AR5. This was too late for many scientific articles. But even the AR5 data in the IPCC DDC is rarely cited in literature in spite of annual download volumes between one and three PBytes. On the other hand, the request for a citation possibility for the evolving CMIP6 data prior to long-term archival came from the CMIP6 data providers. The additional provision of data citations for the project input4MIPs (input data for CMIP6) could raise the scientists' awareness of the discrepancy between the readiness to cite data and the desire to be cited and get credit. The CMIP6 Citation Service is a pragmatic approach built on existing services and services under development, such as ESGF (Earth System Grid Federation) as data infrastructure component, DataCite as DOI registration agency, and Scholix services for tracking data usage information. Other principles followed to overcome barriers of data citation are: Collect data and literature references in the data citation metadata to enable data-data and data-literature interlinking. Visibility of data citation information in the ESGF data portals (low barrier to access data citation information) Provide data usage information in literature for the data providers, data node managers and their funders (requested by some ESGF data node managers) The CMIP6 Citation Service is an implementation only of the credit part of the RDA WGDC recommendation for the citation of dynamic data. The second part, the identification of the data subset underlying an article, is planned for CMIP7 as a data cart approach comprising multiple pre-defined CMIP6 DataCite DOIs. Additional policies on the long-term data availability are required. References: M. Stockhause and M. Lautenschlager (2017). CMIP6 Data Citation of Evolving Data. Data Science Journal. 16, p.30. doi:10.5334/dsj-2017-030. https://doi.org/10.5334/dsj-2017-030 . http://cmip6cite.wdc-climate.de

  14. 43 CFR 2.4 - How do I obtain information routinely available to the public?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 20240 (see appendix A to this part). The Library is open to the public for on-site reference use from 7...) Another source of information is DOI's Library, which contains over one million holdings dealing with a broad range of matters pertaining to the Department's mission. You may wish to visit the Library, which...

  15. 43 CFR 2.4 - How do I obtain information routinely available to the public?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 20240 (see appendix A to this part). The Library is open to the public for on-site reference use from 7...) Another source of information is DOI's Library, which contains over one million holdings dealing with a broad range of matters pertaining to the Department's mission. You may wish to visit the Library, which...

  16. 43 CFR 2.27 - How will a bureau handle a request for information that is contained in a Privacy Act system of...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false How will a bureau handle a request for information that is contained in a Privacy Act system of records? (See DOI's Privacy Act regulations (Subpart G of this part) for additional information.) 2.27 Section 2.27 Public Lands: Interior Office of the Secretary of the Interior RECORDS AND...

  17. Core Science Systems--Mission overview

    USGS Publications Warehouse

    Gallagher, Kevin T.

    2012-01-01

    CSS provides a foundation for all USGS Mission Areas, as well as for the mission of the Department of the Interior (DOI), in the following ways: 1) Conducts basic and applied science research and development 2) Fosters broad understanding and application of analyses and information 3) Provides a framework for data and information sharing 4) Creates new geospatially enabled data and information 5) Provides technical expertise in standards and methods 6) Builds and facilitates partnerships and innovation

  18. Biological versus Electronic Adaptive Coloration: How Can One Inform the Other?

    DTIC Science & Technology

    2012-01-01

    Hyperspectral imaging of cuttlefish camouflage indicates good color match in the eyes of fish predators. Proc. Natl Acad. Sci. USA 108, 9148–9153. (doi...Patrick B. Dennis, Rajesh R. Naik, Eric Forsythe and inform the other? Biological versus electronic adaptive coloration : how can one References...TYPE 3. DATES COVERED 00-00-2012 to 00-00-2012 4. TITLE AND SUBTITLE Biological versus electronic adaptive coloration : how can one inform the

  19. Carbon-free production of 2-deoxy-scyllo-inosose (DOI) in cyanobacterium Synechococcus elongatus PCC 7942.

    PubMed

    Watanabe, Satoru; Ozawa, Hiroaki; Kato, Hiroaki; Nimura-Matsune, Kaori; Hirayama, Toshifumi; Kudo, Fumitaka; Eguchi, Tadashi; Kakinuma, Katsumi; Yoshikawa, Hirofumi

    2018-01-01

    Owing to their photosynthetic capabilities, there is increasing interest in utilizing cyanobacteria to convert solar energy into biomass. 2-Deoxy-scyllo-inosose (DOI) is a valuable starting material for the benzene-free synthesis of catechol and other benzenoids. DOI synthase (DOIS) is responsible for the formation of DOI from d-glucose-6-phosphate (G6P) in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics such as neomycin and butirosin. DOI fermentation using a recombinant Escherichia coli strain has been reported, although a carbon source is necessary for high-yield DOI production. We constructed DOI-producing cyanobacteria toward carbon-free and sustainable DOI production. A DOIS gene derived from the butirosin producer strain Bacillus circulans (btrC) was introduced and expressed in the cyanobacterium Synechococcus elongatus PCC 7942. We ultimately succeeded in producing 400 mg/L of DOI in S. elongatus without using a carbon source. DOI production by cyanobacteria represents a novel and efficient approach for producing benzenoids from G6P synthesized by photosynthesis.

  20. Joint Applications Pilot of the National Climate Predictions and Projections Platform and the North Central Climate Science Center: Delivering climate projections on regional scales to support adaptation planning

    NASA Astrophysics Data System (ADS)

    Ray, A. J.; Ojima, D. S.; Morisette, J. T.

    2012-12-01

    The DOI North Central Climate Science Center (NC CSC) and the NOAA/NCAR National Climate Predictions and Projections (NCPP) Platform and have initiated a joint pilot study to collaboratively explore the "best available climate information" to support key land management questions and how to provide this information. NCPP's mission is to support state of the art approaches to develop and deliver comprehensive regional climate information and facilitate its use in decision making and adaptation planning. This presentation will describe the evolving joint pilot as a tangible, real-world demonstration of linkages between climate science, ecosystem science and resource management. Our joint pilot is developing a deliberate, ongoing interaction to prototype how NCPP will work with CSCs to develop and deliver needed climate information products, including translational information to support climate data understanding and use. This pilot also will build capacity in the North Central CSC by working with NCPP to use climate information used as input to ecological modeling. We will discuss lessons to date on developing and delivering needed climate information products based on this strategic partnership. Four projects have been funded to collaborate to incorporate climate information as part of an ecological modeling project, which in turn will address key DOI stakeholder priorities in the region: Riparian Corridors: Projecting climate change effects on cottonwood and willow seed dispersal phenology, flood timing, and seedling recruitment in western riparian forests. Sage Grouse & Habitats: Integrating climate and biological data into land management decision models to assess species and habitat vulnerability Grasslands & Forests: Projecting future effects of land management, natural disturbance, and CO2 on woody encroachment in the Northern Great Plains The value of climate information: Supporting management decisions in the Plains and Prairie Potholes LCC. NCCSC's role in these projects is to provide the connections between climate data and running ecological models, and prototype these for future work. NCPP will develop capacities to provide enhanced climate information at relevant spatial and temporal scales, both for historical climate and projections of future climate, and will work to link expert guidance and understanding of modeling processes and evaluation of modeling with the use of numerical climate data. Translational information thus is a suite of information that aids in translation of numerical climate information into usable knowledge for applications, e.g. ecological response models, hydrologic risk studies. This information includes technical and scientific aspects including, but not limited to: 1) results of objective, quantitative evaluation of climate models & downscaling techniques, 2) guidance on appropriate uses and interpretation, i.e., understanding the advantages and limitations of various downscaling techniques for specific user applications, 3) characterizing and interpreting uncertainty, 4) Descriptions meaningful to applications, e.g. narratives. NCPP believes that translational information is best co-developed between climate scientists and applications scientists, such as the NC-CSC pilot.

  1. The antipsychotic-like effects of positive allosteric modulators of metabotropic glutamate mGlu4 receptors in rodents

    PubMed Central

    Sławińska, Anna; Wierońska, Joanna M; Stachowicz, Katarzyna; Marciniak, Marcin; Łasoń-Tyburkiewicz, Magdalena; Gruca, Piotr; Papp, Mariusz; Kusek, Magdalena; Tokarski, Krzysztof; Doller, Darío; Pilc, Andrzej

    2013-01-01

    Background and Purpose Because agonists at metabotropic glutamate receptors exert beneficial effects in schizophrenia, we have assessed the actions of Lu AF21934 and Lu AF32615, two chemically distinct, selective and brain-penetrant positive allosteric modulators (PAMs) of the mGlu4 receptor, in several tests reflecting positive, negative and cognitive symptoms of schizophrenia in rodents. Experimental Approach Hyperactivity induced by MK-801 or amphetamine and head twitches induced by 2,5-dimethoxy-4-iodoamphetamine (DOI) in mice were used as models for positive symptoms. Disruption of social interaction and spatial delayed alternation tests induced by MK-801 in rats were used as models for negative and cognitive symptoms of schizophrenia, respectively. Key Results Lu AF21934 (0.1–5 mg·kg−1) and Lu AF32615 (2–10 mg·kg−1) dose-dependently inhibited hyperactivity induced by MK-801 or amphetamine. They also antagonized head twitches and increased frequency of spontaneous excitatory postsynaptic currents (EPSCs) in brain slices, induced by DOI. In mice lacking the mGlu4 receptor (mGlu4−/−) mice, Lu AF21934 did not antagonize DOI-induced head twitches. MK-801-induced disruption in the social interaction test was decreased by Lu AF21934 at 0.5 mg·kg−1 and by Lu AF32615 at 10 mg·kg−1. In the delayed spatial alternation test, Lu AF21934 was active at 1 and 2 mg·kg−1, while Lu AF32615 was active at 10 mg·kg−1. Conclusions and Implications We propose that activation by PAMs of the mGlu4 receptor is a promising approach to the discovery of novel antipsychotic drugs. PMID:23714045

  2. A scintillator geometry suitable for very small PET gantries

    NASA Astrophysics Data System (ADS)

    Gonzalez, A. J.; Gonzalez-Montoro, A.; Aguilar, A.; Cañizares, G.; Martí, R.; Iranzo, S.; Lamprou, E.; Sanchez, S.; Sanchez, F.; Benlloch, J. M.

    2017-12-01

    In this work we are describing a novel approach to the scintillator crystal configuration as used in nuclear medicine imaging. Our design is related to the coupling in one PET module of the two separate crystal configurations used so far there: monolithic and crystal arrays. The particular design we have studied is based on a two-layer scintillator approach (hybrid) composed of a monolithic LYSO crystal (5-6 mm thickness) and a LYSO crystal array with 4-5 mm height (0.8 and 1 mm pixels). We show here the detector block performance, in terms of spatial, energy and DOI information, to be used as a module in the design of PET scanners. The design we propose allows one to achieve accurate three-dimensional spatial resolution (including DOI information) while assuring high detection efficiency at reasonable cost. Moreover, the proposed design improves the spatial response uniformity across the whole detector module, and especially at the edge region. The crystal arrays are mounted in the front and were well resolved. The monolithic crystal inserted between crystal array and the photosensor, provided measured FWHM resolution as good as 1.5-1.7 mm including the 1 mm source size. The monolithic block achieved a DOI resolution (FWHM) nearing 3 mm. We compared these results with an approach in which we use a single monolithic block with total volume equals to the hybrid approach. In general, comparable performances were obtained.

  3. Webcam network and image database for studies of phenological changes of vegetation and snow cover in Finland, image time series from 2014 to 2016

    NASA Astrophysics Data System (ADS)

    Peltoniemi, Mikko; Aurela, Mika; Böttcher, Kristin; Kolari, Pasi; Loehr, John; Karhu, Jouni; Linkosalmi, Maiju; Melih Tanis, Cemal; Tuovinen, Juha-Pekka; Nadir Arslan, Ali

    2018-01-01

    In recent years, monitoring of the status of ecosystems using low-cost web (IP) or time lapse cameras has received wide interest. With broad spatial coverage and high temporal resolution, networked cameras can provide information about snow cover and vegetation status, serve as ground truths to Earth observations and be useful for gap-filling of cloudy areas in Earth observation time series. Networked cameras can also play an important role in supplementing laborious phenological field surveys and citizen science projects, which also suffer from observer-dependent observation bias. We established a network of digital surveillance cameras for automated monitoring of phenological activity of vegetation and snow cover in the boreal ecosystems of Finland. Cameras were mounted at 14 sites, each site having 1-3 cameras. Here, we document the network, basic camera information and access to images in the permanent data repository (http://www.zenodo.org/communities/phenology_camera/). Individual DOI-referenced image time series consist of half-hourly images collected between 2014 and 2016 (https://doi.org/10.5281/zenodo.1066862). Additionally, we present an example of a colour index time series derived from images from two contrasting sites.

  4. A diffusion of innovations model of physician order entry.

    PubMed

    Ash, J S; Lyman, J; Carpenter, J; Fournier, L

    2001-01-01

    To interpret the results of a cross-site study of physician order entry (POE) in hospitals using a diffusion of innovations theory framework. Qualitative study using observation, focus groups, and interviews. Data were analyzed by an interdisciplinary team of researchers using a grounded approach to identify themes. Themes were then interpreted using classical Diffusion of Innovations (DOI) theory as described by Rogers [1]. Four high level themes were identified: organizational issues; clinical and professional issues; technology implementation issues; and issues related to the organization of information and knowledge. Further analysis using the DOI framework indicated that POE is an especially complex information technology innovation when one considers communication, time, and social system issues in addition to attributes of the innovation itself. Implementation strategies for POE should be designed to account for its complex nature. The ideal would be a system that is both customizable and integrated with other parts of the information system, is implemented with maximum involvement of users and high levels of support, and is surrounded by an atmosphere of trust and collaboration.

  5. Two FGFRL-Wnt circuits organize the planarian anteroposterior axis

    PubMed Central

    Scimone, M Lucila; Cote, Lauren E; Rogers, Travis; Reddien, Peter W

    2016-01-01

    How positional information instructs adult tissue maintenance is poorly understood. Planarians undergo whole-body regeneration and tissue turnover, providing a model for adult positional information studies. Genes encoding secreted and transmembrane components of multiple developmental pathways are predominantly expressed in planarian muscle cells. Several of these genes regulate regional identity, consistent with muscle harboring positional information. Here, single-cell RNA-sequencing of 115 muscle cells from distinct anterior-posterior regions identified 44 regionally expressed genes, including multiple Wnt and ndk/FGF receptor-like (ndl/FGFRL) genes. Two distinct FGFRL-Wnt circuits, involving juxtaposed anterior FGFRL and posterior Wnt expression domains, controlled planarian head and trunk patterning. ndl-3 and wntP-2 inhibition expanded the trunk, forming ectopic mouths and secondary pharynges, which independently extended and ingested food. fz5/8-4 inhibition, like that of ndk and wntA, caused posterior brain expansion and ectopic eye formation. Our results suggest that FGFRL-Wnt circuits operate within a body-wide coordinate system to control adult axial positioning. DOI: http://dx.doi.org/10.7554/eLife.12845.001 PMID:27063937

  6. Molecular architecture of the yeast Mediator complex

    PubMed Central

    Robinson, Philip J; Trnka, Michael J; Pellarin, Riccardo; Greenberg, Charles H; Bushnell, David A; Davis, Ralph; Burlingame, Alma L; Sali, Andrej; Kornberg, Roger D

    2015-01-01

    The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI: http://dx.doi.org/10.7554/eLife.08719.001 PMID:26402457

  7. EZID: Long term identifiers made easy (Invited)

    NASA Astrophysics Data System (ADS)

    Starr, J.

    2013-12-01

    Scholarly research is producing ever increasing amounts of digital research data, and this data should be managed throughout the research life cycle both as part of good scientific practice, but also to comply with funder mandates, such as the 2013 OSTP Public Access Memo (http://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf). By assigning unique and persistent identifiers to data objects, data managers can gain control and flexibility over what can be a daunting task. This is due to the fact that the objects can be moved to new locations without disruption to links, as long as the identifier target is maintained. EZID is a tool that makes assigning and maintaining unique, persistent identifiers easy. It was designed and built by California Digital Library (CDL) and has both a user interface and a RESTful API. EZID currently offers services for two globally unique, persistent identifier schemes: Digital Object Identifiers (DOIs) and Archival Resource Keys (ARKs). DOIs are identifiers originating from the publishing world and are in widespread use for journal articles. CDL is able to offer DOIs because of being a founding member of DataCite (http://www.datacite.org/), an international consortium established to provide easier access to scientific research data on the Internet. ARKs are identifiers originating from the library, archive and museum community. Like DOIs, they become persistent when the objects and identifier forwarding information is maintained. DOIs and ARKs have a key role in data management and, therefore, in data management plans. DOIs are the recommended identifier for use in data citation, and ARKs provide the maximum flexibility needed for data documentation and management throughout the early phases of a project. The two identifier schemes are able to be used together, and EZID is made to work with both. EZID clients, coming from education, research, government, and the private sector, are utilizing the tool for these use cases and more.

  8. Coordination and Collective Decision Making

    DTIC Science & Technology

    2015-08-21

    Fisheries , (06 2014): 1. doi: 10.1111/faf.12084 L. Giuggioli, J. R. Potts, D. I. Rubenstein, S. A. Levin. Stigmergy, collective actions, and animal ...terrestrial and marine food webs, as well as enabling interspecies interactions such as reproduction. Eulerian models describe aggregations of animals in...achieved in decision-making. Animal groups frequently display highly coordinated movements, and provide an excellent vehicle by which to understand

  9. The structure of the core NuRD repression complex provides insights into its interaction with chromatin

    PubMed Central

    Millard, Christopher J; Varma, Niranjan; Saleh, Almutasem; Morris, Kyle; Watson, Peter J; Bottrill, Andrew R; Fairall, Louise; Smith, Corinne J; Schwabe, John WR

    2016-01-01

    The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin. DOI: http://dx.doi.org/10.7554/eLife.13941.001 PMID:27098840

  10. Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch

    PubMed Central

    Le, My-Tra; Kasprzak, Wojciech K; Kim, Taejin; Gao, Feng; Young, Megan YL; Yuan, Xuefeng; Shapiro, Bruce A; Seog, Joonil; Simon, Anne E

    2017-01-01

    Turnip crinkle virus contains a T-shaped, ribosome-binding, translation enhancer (TSS) in its 3’UTR that serves as a hub for interactions throughout the region. The viral RNA-dependent RNA polymerase (RdRp) causes the TSS/surrounding region to undergo a conformational shift postulated to inhibit translation. Using optical tweezers (OT) and steered molecular dynamic simulations (SMD), we found that the unusual stability of pseudoknotted element H4a/Ψ3 required five upstream adenylates, and H4a/Ψ3 was necessary for cooperative association of two other hairpins (H5/H4b) in Mg2+. SMD recapitulated the TSS unfolding order in the absence of Mg2+, showed dependence of the resistance to pulling on the 3D orientation and gave structural insights into the measured contour lengths of the TSS structure elements. Adenylate mutations eliminated one-site RdRp binding to the 3’UTR, suggesting that RdRp binding to the adenylates disrupts H4a/Ψ3, leading to loss of H5/H4b interaction and promoting a conformational switch interrupting translation and promoting replication. DOI: http://dx.doi.org/10.7554/eLife.22883.001 PMID:28186489

  11. Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins

    PubMed Central

    Yang, Aimin; Pantoom, Supansa; Wu, Yao-Wen

    2017-01-01

    Autophagy is a conserved cellular process involved in the elimination of proteins and organelles. It is also used to combat infection with pathogenic microbes. The intracellular pathogen Legionella pneumophila manipulates autophagy by delivering the effector protein RavZ to deconjugate Atg8/LC3 proteins coupled to phosphatidylethanolamine (PE) on autophagosomal membranes. To understand how RavZ recognizes and deconjugates LC3-PE, we prepared semisynthetic LC3 proteins and elucidated the structures of the RavZ:LC3 interaction. Semisynthetic LC3 proteins allowed the analysis of structure-function relationships. RavZ extracts LC3-PE from the membrane before deconjugation. RavZ initially recognizes the LC3 molecule on membranes via its N-terminal LC3-interacting region (LIR) motif. The RavZ α3 helix is involved in extraction of the PE moiety and docking of the acyl chains into the lipid-binding site of RavZ that is related in structure to that of the phospholipid transfer protein Sec14. Thus, Legionella has evolved a novel mechanism to specifically evade host autophagy. DOI: http://dx.doi.org/10.7554/eLife.23905.001 PMID:28395732

  12. Unipolar distributions of junctional Myosin II identify cell stripe boundaries that drive cell intercalation throughout Drosophila axis extension

    PubMed Central

    Tetley, Robert J; Blanchard, Guy B; Fletcher, Alexander G; Adams, Richard J; Sanson, Bénédicte

    2016-01-01

    Convergence and extension movements elongate tissues during development. Drosophila germ-band extension (GBE) is one example, which requires active cell rearrangements driven by Myosin II planar polarisation. Here, we develop novel computational methods to analyse the spatiotemporal dynamics of Myosin II during GBE, at the scale of the tissue. We show that initial Myosin II bipolar cell polarization gives way to unipolar enrichment at parasegmental boundaries and two further boundaries within each parasegment, concomitant with a doubling of cell number as the tissue elongates. These boundaries are the primary sites of cell intercalation, behaving as mechanical barriers and providing a mechanism for how cells remain ordered during GBE. Enrichment at parasegment boundaries during GBE is independent of Wingless signaling, suggesting pair-rule gene control. Our results are consistent with recent work showing that a combinatorial code of Toll-like receptors downstream of pair-rule genes contributes to Myosin II polarization via local cell-cell interactions. We propose an updated cell-cell interaction model for Myosin II polarization that we tested in a vertex-based simulation. DOI: http://dx.doi.org/10.7554/eLife.12094.001 PMID:27183005

  13. A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination

    PubMed Central

    Pornsiriwong, Wannarat; Estavillo, Gonzalo M; Chan, Kai Xun; Tee, Estee E; Ganguly, Diep; Crisp, Peter A; Phua, Su Yin; Zhao, Chenchen; Qiu, Jiaen; Park, Jiyoung; Yong, Miing Tiem; Nisar, Nazia; Yadav, Arun Kumar; Schwessinger, Benjamin; Rathjen, John; Cazzonelli, Christopher I; Wilson, Philippa B; Gilliham, Matthew; Chen, Zhong-Hua; Pogson, Barry J

    2017-01-01

    Organelle-nuclear retrograde signaling regulates gene expression, but its roles in specialized cells and integration with hormonal signaling remain enigmatic. Here we show that the SAL1-PAP (3′-phosphoadenosine 5′- phosphate) retrograde pathway interacts with abscisic acid (ABA) signaling to regulate stomatal closure and seed germination in Arabidopsis. Genetically or exogenously manipulating PAP bypasses the canonical signaling components ABA Insensitive 1 (ABI1) and Open Stomata 1 (OST1); priming an alternative pathway that restores ABA-responsive gene expression, ROS bursts, ion channel function, stomatal closure and drought tolerance in ost1-2. PAP also inhibits wild type and abi1-1 seed germination by enhancing ABA sensitivity. PAP-XRN signaling interacts with ABA, ROS and Ca2+; up-regulating multiple ABA signaling components, including lowly-expressed Calcium Dependent Protein Kinases (CDPKs) capable of activating the anion channel SLAC1. Thus, PAP exhibits many secondary messenger attributes and exemplifies how retrograde signals can have broader roles in hormone signaling, allowing chloroplasts to fine-tune physiological responses. DOI: http://dx.doi.org/10.7554/eLife.23361.001 PMID:28323614

  14. A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 Å resolution

    PubMed Central

    Zhang, Xing; Guo, Huatao; Jin, Lei; Czornyj, Elizabeth; Hodes, Asher; Hui, Wong H; Nieh, Angela W; Miller, Jeff F; Zhou, Z Hong

    2013-01-01

    Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like (‘Johnson’) for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering. DOI: http://dx.doi.org/10.7554/eLife.01299.001 PMID:24347545

  15. A host basal transcription factor is a key component for infection of rice by TALE-carrying bacteria

    PubMed Central

    Yuan, Meng; Ke, Yinggen; Huang, Renyan; Ma, Ling; Yang, Zeyu; Chu, Zhaohui; Xiao, Jinghua; Li, Xianghua; Wang, Shiping

    2016-01-01

    Transcription activator-like effectors (TALEs) are sequence-specific DNA binding proteins found in a range of plant pathogenic bacteria, where they play important roles in host-pathogen interactions. However, it has been unclear how TALEs, after they have been injected into the host cells, activate transcription of host genes required for infection success. Here, we show that the basal transcription factor IIA gamma subunit TFIIAγ5 from rice is a key component for infection by the TALE-carrying bacterium Xanthomonas oryzae pv. oryzae, the causal agent for bacterial blight. Direct interaction of several TALEs with TFIIAγ5 is required for activation of disease susceptibility genes. Conversely, reduced expression of the TFIIAγ5 host gene limits the induction of susceptibility genes and thus decreases bacterial blight symptoms. Suppression or mutation of TFIIAγ5 can also reduce bacterial streak, another devastating disease of rice caused by TALE-carrying X. oryzae pv. oryzicola. These results have important implications for formulating a widely applicable strategy with which to improve resistance of plants to TALE-carrying pathogens. DOI: http://dx.doi.org/10.7554/eLife.19605.001 PMID:27472897

  16. The RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage

    PubMed Central

    Kitevski-LeBlanc, Julianne; Fradet-Turcotte, Amélie; Portella, Guillem; Yuwen, Tairan; Panier, Stephanie; Duan, Shili; Canny, Marella D; van Ingen, Hugo; Arrowsmith, Cheryl H; Rubinstein, John L; Vendruscolo, Michele; Durocher, Daniel; Kay, Lewis E

    2017-01-01

    Site-specific histone ubiquitylation plays a central role in orchestrating the response to DNA double-strand breaks (DSBs). DSBs elicit a cascade of events controlled by the ubiquitin ligase RNF168, which promotes the accumulation of repair factors such as 53BP1 and BRCA1 on the chromatin flanking the break site. RNF168 also promotes its own accumulation, and that of its paralog RNF169, but how they recognize ubiquitylated chromatin is unknown. Using methyl-TROSY solution NMR spectroscopy and molecular dynamics simulations, we present an atomic resolution model of human RNF169 binding to a ubiquitylated nucleosome, and validate it by electron cryomicroscopy. We establish that RNF169 binds to ubiquitylated H2A-Lys13/Lys15 in a manner that involves its canonical ubiquitin-binding helix and a pair of arginine-rich motifs that interact with the nucleosome acidic patch. This three-pronged interaction mechanism is distinct from that by which 53BP1 binds to ubiquitylated H2A-Lys15 highlighting the diversity in site-specific recognition of ubiquitylated nucleosomes. DOI: http://dx.doi.org/10.7554/eLife.23872.001 PMID:28406400

  17. Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation

    PubMed Central

    Velazquez Camacho, Oscar; Galan, Carmen; Swist-Rosowska, Kalina; Ching, Reagan; Gamalinda, Michael; Karabiber, Fethullah; De La Rosa-Velazquez, Inti; Engist, Bettina; Koschorz, Birgit; Shukeir, Nicholas; Onishi-Seebacher, Megumi; van de Nobelen, Suzanne; Jenuwein, Thomas

    2017-01-01

    The Suv39h1 and Suv39h2 histone lysine methyltransferases are hallmark enzymes at mammalian heterochromatin. We show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity for major satellite repeat RNA. To analyze an RNA-dependent interaction with chromatin, we purified native nucleosomes from mouse ES cells and detect that Suv39h1 and Suv39h2 exclusively associate with poly-nucleosomes. This association was attenuated upon RNaseH incubation and entirely lost upon RNaseA digestion of native chromatin. Major satellite repeat transcripts remain chromatin-associated and have a secondary structure that favors RNA:DNA hybrid formation. Together, these data reveal an RNA-mediated mechanism for the stable chromatin interaction of the Suv39h KMT and suggest a function for major satellite non-coding RNA in the organization of an RNA-nucleosome scaffold as the underlying structure of mouse heterochromatin. DOI: http://dx.doi.org/10.7554/eLife.25293.001 PMID:28760199

  18. The E3 ubiquitin ligase ZNRF2 is a substrate of mTORC1 and regulates its activation by amino acids

    PubMed Central

    Hoxhaj, Gerta; Caddye, Edward; Najafov, Ayaz; Houde, Vanessa P; Johnson, Catherine; Dissanayake, Kumara; Toth, Rachel; Campbell, David G; Prescott, Alan R; MacKintosh, Carol

    2016-01-01

    The mechanistic Target of Rapamycin complex 1 (mTORC1) senses intracellular amino acid levels through an intricate machinery, which includes the Rag GTPases, Ragulator and vacuolar ATPase (V-ATPase). The membrane-associated E3 ubiquitin ligase ZNRF2 is released into the cytosol upon its phosphorylation by Akt. In this study, we show that ZNRF2 interacts with mTOR on membranes, promoting the amino acid-stimulated translocation of mTORC1 to lysosomes and its activation in human cells. ZNRF2 also interacts with the V-ATPase and preserves lysosomal acidity. Moreover, knockdown of ZNRF2 decreases cell size and cell proliferation. Upon growth factor and amino acid stimulation, mTORC1 phosphorylates ZNRF2 on Ser145, and this phosphosite is dephosphorylated by protein phosphatase 6. Ser145 phosphorylation stimulates vesicle-to-cytosol translocation of ZNRF2 and forms a novel negative feedback on mTORC1. Our findings uncover ZNRF2 as a component of the amino acid sensing machinery that acts upstream of Rag-GTPases and the V-ATPase to activate mTORC1. DOI: http://dx.doi.org/10.7554/eLife.12278.001 PMID:27244671

  19. TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway

    PubMed Central

    Neerincx, Andreas; Hermann, Clemens; Antrobus, Robin; van Hateren, Andy; Cao, Huan; Trautwein, Nico; Stevanović, Stefan; Elliott, Tim; Deane, Janet E; Boyle, Louise H

    2017-01-01

    Recently, we revealed that TAPBPR is a peptide exchange catalyst that is important for optimal peptide selection by MHC class I molecules. Here, we asked whether any other co-factors associate with TAPBPR, which would explain its effect on peptide selection. We identify an interaction between TAPBPR and UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1), a folding sensor in the calnexin/calreticulin quality control cycle that is known to regenerate the Glc1Man9GlcNAc2 moiety on glycoproteins. Our results suggest the formation of a multimeric complex, dependent on a conserved cysteine at position 94 in TAPBPR, in which TAPBPR promotes the association of UGT1 with peptide-receptive MHC class I molecules. We reveal that the interaction between TAPBPR and UGT1 facilities the reglucosylation of the glycan on MHC class I molecules, promoting their recognition by calreticulin. Our results suggest that in addition to being a peptide editor, TAPBPR improves peptide optimisation by promoting peptide-receptive MHC class I molecules to associate with the peptide-loading complex. DOI: http://dx.doi.org/10.7554/eLife.23049.001 PMID:28425917

  20. 48 CFR 1404.402 - General.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false General. 1404.402 Section 1404.402 Federal Acquisition Regulations System DEPARTMENT OF THE INTERIOR GENERAL ADMINISTRATIVE MATTERS Safeguarding Classified Information Within Industry 1404.402 General. (a) The DOI has entered into...

  1. 48 CFR 1404.402 - General.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false General. 1404.402 Section 1404.402 Federal Acquisition Regulations System DEPARTMENT OF THE INTERIOR GENERAL ADMINISTRATIVE MATTERS Safeguarding Classified Information Within Industry 1404.402 General. (a) The DOI has entered into...

  2. Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

    NASA Astrophysics Data System (ADS)

    Grace, J. M.; Verseux, C.; Gentry, D.; Moffet, A.; Thayabaran, R.; Wong, N.; Rothschild, L.

    2013-12-01

    The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates[Wielgoss et al., 2013]. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques[Wassmann et al., 2010]. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols[Alcántara-Díaz et al., 2004; Goldman and Travisano, 2011]. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the number or growth rate of surviving cells. We are on our second prototype iteration, with demonstrated functions of microbial growth monitoring and dynamic exposure to UV-C radiation and temperature. We plan to add functionality for general chemical presence or absence by Nov. 2013. By making the project low-cost and open-source, we hope to encourage others to use it as a basis for future development of a common microbial environmental adaptation testbed. References: Alcantara-Diaz, D. et al. (2004), Divergent adaptation of Escherichia coli to cyclic ultraviolet light exposures, Mutagenesis, 19(5), 349-354, doi:10.1093/mutage/geh039. Goldman, R. P., and Travisano, M. (2011), Experimental evolution of ultraviolet radiation resistance in Escherichia coli, Evolution, 65(12), 3486-3498, doi:10.1111/j.1558-5646.2011.01438.x. Wassmann, M. et al. (2010), Adaptation of Bacillus subtilis cells to Archean-like UV climate: relevant hints of microbial evolution to remarkably increased radiation resistance, Astrobiology, 10(6), 605-615, doi:10.1089/ast.2009.0455. Wielgoss, S. et al. (2013), Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load, Proc Natl Acad Sci USA, 110(1), 222-227, doi:10.1073/pnas.1219574110.

  3. Basic performance of Mg co-doped new scintillator used for TOF-DOI-PET systems

    NASA Astrophysics Data System (ADS)

    Kobayashi, Takahiro; Yamamoto, Seiichi; Okumura, Satoshi; Yeom, Jung Yeol; Kamada, Kei; Yoshikawa, Akira

    2017-01-01

    Phoswich depth-of-interaction (DOI) detectors utilizing multiple scintillators with different decay time are a useful device for developing a high spatial resolution, high sensitivity PET scanner. However, in order to apply pulse shape discrimination (PSD), there are not many combinations of scintillators for which phoswich technique can be implemented. Ce doped Gd3Ga3Al2O12 (GFAG) is a recently developed scintillator with a fast decay time. This scintillator is similar to Ce doped Gd3Al2Ga3O12 (GAGG), which is a promising scintillator for PET detector with high light yield. By stacking these scintillators, it may be possible to realize a high spatial resolution and high timing resolution phoswich DOI detector. Such phoswich DOI detector may be applied to time-of-flight (TOF) systems with high timing performance. Therefore, in this study, we tested the basic performance of the new scintillator -GFAG for use in a TOF phoswich detector. The measured decay time of a GFAG element of 2.9 mmx2.9 mmx10 mm in dimension, which was optically coupled to a photomultiplier tube (PMT), was faster (66 ns) than that of same sized GAGG (103 ns). The energy resolution of the GFAG element was 5.7% FWHM which was slightly worse than that of GAGG with 4.9% FWHM for 662 keV gamma photons without saturation correction. Then we assembled the GFAG and the GAGG crystals in the depth direction to form a 20 mm long phoswich element (GFAG/GAGG). By pulse shape analysis, the two types of scintillators were clearly resolved. Measured timing resolution of a pair of opposing GFAG/GAGG phoswich scintillator coupled to Silicon Photomultipliers (Si-PM) was good with coincidence resolving time of 466 ps FWHM. These results indicate that the GFAG combined with GAGG can be a candidate for TOF-DOI-PET systems.

  4. Time-over-threshold for pulse shape discrimination in a time-of-flight phoswich PET detector

    PubMed Central

    Chang, Chen-Ming; Cates, Joshua W.; Levin, Craig S.

    2016-01-01

    It is well known that a PET detector capable of measuring both photon time-of-flight (TOF) and depth-of-interaction (DOI) improves the image quality and accuracy. Phoswich designs have been realized in PET detectors to measure DOI for more than a decade. However, PET detectors based on phoswich designs put great demand on the readout circuits, which have to differentiate the pulse shape produced by different crystal layers. A simple pulse shape discrimination approach is required to realize the phoswich designs in a clinical PET scanner, which consists of thousands of scintillation crystal elements. In this work, we studied time-over-threshold (ToT) as a pulse shape parameter for DOI. The energy, timing and DOI performance were evaluated for a phoswich detector design comprising 3 mm × 3 mm × 10 mm LYSO:Ce crystal optically coupled to 3 mm × 3 mm × 10 mm calcium co-doped LSO:Ce,Ca(0.4%) crystal read out by a silicon photomultiplier (SiPM). A DOI accuracy of 97.2% has been achieved for photopeak events using the proposed time-over-threshold (ToT) processing. The energy resolution without correction for SiPM non-linearity was 9.7 ± 0.2% and 11.3 ± 0.2% FWHM at 511 keV for LYSO and LSO crystal layers, respectively. The coincidence time resolution for photopeak events ranges from 164.6 ps to 183.1 ps FWHM, depending on the layer combinations. The coincidence time resolution for inter-crystal scatter events ranges from 214.6 ps to 418.3 ps FWHM, depending on the energy windows applied. These results show great promises of using ToT for pulse shape discrimination in a TOF phoswich detector since a ToT measurement can be easily implemented in readout electronics. PMID:27991437

  5. In vitro dosimetry of agglomerates

    NASA Astrophysics Data System (ADS)

    Hirsch, V.; Kinnear, C.; Rodriguez-Lorenzo, L.; Monnier, C. A.; Rothen-Rutishauser, B.; Balog, S.; Petri-Fink, A.

    2014-06-01

    Agglomeration of nanoparticles in biological fluids is a pervasive phenomenon that leads to difficulty in the interpretation of results from in vitro exposure, primarily due to differing particokinetics of agglomerates to nanoparticles. Therefore, well-defined small agglomerates were designed that possessed different particokinetic profiles, and their cellular uptake was compared to a computational model of dosimetry. The approach used here paves the way for a better understanding of the impact of agglomeration on the nanoparticle-cell interaction.Agglomeration of nanoparticles in biological fluids is a pervasive phenomenon that leads to difficulty in the interpretation of results from in vitro exposure, primarily due to differing particokinetics of agglomerates to nanoparticles. Therefore, well-defined small agglomerates were designed that possessed different particokinetic profiles, and their cellular uptake was compared to a computational model of dosimetry. The approach used here paves the way for a better understanding of the impact of agglomeration on the nanoparticle-cell interaction. Electronic supplementary information (ESI) available: ITC data for tiopronin/Au-NP interactions, agglomeration kinetics at different pHs for tiopronin-coated Au-NPs, UV-Vis spectra in water, PBS and DMEM and temporal correlation functions for single Au-NPs and corresponding agglomerates, calculation of diffusion and sedimentation parameters, modelling of relative cell uptake based on the ISDD model and cytotoxicity of single Au-NPs and their agglomerates, and synthesis and cell uptake of large spherical Au-NPs. See DOI: 10.1039/c4nr00460d

  6. Environmental effects of ozone depletion and its interactions ...

    EPA Pesticide Factsheets

    When considering the effects of climate change, it has become clear that processes resulting in changes in stratospheric ozone are more complex than previously believed. As a result of this, human health and environmental issues will be longer-lasting and more regionally variable. Like the other Panels, the EEAP produces a detailed report every four years; the most recent was published as a series of seven papers in 2015 (Photochem. Photobiol. Sci., 2015, 14, 1-184). In the years in between, the EEAP produces less detailed and shorter Progress Reports of the relevant scientific findings. The most recent of these was for 2015 (Photochem. Photobiol. Sci., 2016, 15, 141-147). The present Progress Report for 2016 assesses some of the highlights and new insights with regard to the interactive nature of the direct and indirect effects of UV radiation, atmospheric processes, and climate change. The report is also published in (Photochem. Photobiol. Sci., 2017, DOI: 10.1039/c7pp90001e). The more detailed Quadrennial Assessment will be made available in 2018. The Parties to the Montreal Protocol are informed by three Panels of experts. One of these is the Environmental Effects Assessment Panel (EEAP), which deals with two focal issues. The first focus is the effects on increased UV radiation on human health, animals, plants, biogeochemistry, air quality, and materials. The second focus is on interactions between UV radiation and global climate change and how these may

  7. Novel indole-2-carboxamide compounds are potent broad-spectrum antivirals active against western equine encephalitis virus in vivo.

    PubMed

    Delekta, Phillip C; Dobry, Craig J; Sindac, Janice A; Barraza, Scott J; Blakely, Pennelope K; Xiang, Jianming; Kirchhoff, Paul D; Keep, Richard F; Irani, David N; Larsen, Scott D; Miller, David J

    2014-10-01

    Neurotropic alphaviruses, including western, eastern, and Venezuelan equine encephalitis viruses, cause serious and potentially fatal central nervous system infections in humans for which no currently approved therapies exist. We previously identified a series of thieno[3,2-b]pyrrole derivatives as novel inhibitors of neurotropic alphavirus replication, using a cell-based phenotypic assay (W. Peng et al., J. Infect. Dis. 199:950-957, 2009, doi:http://dx.doi.org/10.1086/597275), and subsequently developed second- and third-generation indole-2-carboxamide derivatives with improved potency, solubility, and metabolic stability (J. A. Sindac et al., J. Med. Chem. 55:3535-3545, 2012, doi:http://dx.doi.org/10.1021/jm300214e; J. A. Sindac et al., J. Med. Chem. 56:9222-9241, 2013, http://dx.doi.org/10.1021/jm401330r). In this report, we describe the antiviral activity of the most promising third-generation lead compound, CCG205432, and closely related analogs CCG206381 and CCG209023. These compounds have half-maximal inhibitory concentrations of ∼1 μM and selectivity indices of >100 in cell-based assays using western equine encephalitis virus replicons. Furthermore, CCG205432 retains similar potency against fully infectious virus in cultured human neuronal cells. These compounds show broad inhibitory activity against a range of RNA viruses in culture, including members of the Togaviridae, Bunyaviridae, Picornaviridae, and Paramyxoviridae families. Although their exact molecular target remains unknown, mechanism-of-action studies reveal that these novel indole-based compounds target a host factor that modulates cap-dependent translation. Finally, we demonstrate that both CCG205432 and CCG209023 dampen clinical disease severity and enhance survival of mice given a lethal western equine encephalitis virus challenge. These studies demonstrate that indole-2-carboxamide compounds are viable candidates for continued preclinical development as inhibitors of neurotropic alphaviruses and, potentially, of other RNA viruses. IMPORTANCE There are currently no approved drugs to treat infections with alphaviruses. We previously identified a novel series of compounds with activity against these potentially devastating pathogens (J. A. Sindac et al., J. Med. Chem. 55:3535-3545, 2012, doi:http://dx.doi.org/10.1021/jm300214e; W. Peng et al., J. Infect. Dis. 199:950-957, 2009, doi:http://dx.doi.org/10.1086/597275; J. A. Sindac et al., J. Med. Chem. 56:9222-9241, 2013, http://dx.doi.org/10.1021/jm401330r). We have now produced third-generation compounds with enhanced potency, and this manuscript provides detailed information on the antiviral activity of these advanced-generation compounds, including activity in an animal model. The results of this study represent a notable achievement in the continued development of this novel class of antiviral inhibitors. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  8. Novel Indole-2-Carboxamide Compounds Are Potent Broad-Spectrum Antivirals Active against Western Equine Encephalitis Virus In Vivo

    PubMed Central

    Delekta, Phillip C.; Dobry, Craig J.; Sindac, Janice A.; Barraza, Scott J.; Blakely, Pennelope K.; Xiang, Jianming; Kirchhoff, Paul D.; Keep, Richard F.; Irani, David N.; Larsen, Scott D.

    2014-01-01

    ABSTRACT Neurotropic alphaviruses, including western, eastern, and Venezuelan equine encephalitis viruses, cause serious and potentially fatal central nervous system infections in humans for which no currently approved therapies exist. We previously identified a series of thieno[3,2-b]pyrrole derivatives as novel inhibitors of neurotropic alphavirus replication, using a cell-based phenotypic assay (W. Peng et al., J. Infect. Dis. 199:950–957, 2009, doi:http://dx.doi.org/10.1086/597275), and subsequently developed second- and third-generation indole-2-carboxamide derivatives with improved potency, solubility, and metabolic stability (J. A. Sindac et al., J. Med. Chem. 55:3535–3545, 2012, doi:http://dx.doi.org/10.1021/jm300214e; J. A. Sindac et al., J. Med. Chem. 56:9222–9241, 2013, http://dx.doi.org/10.1021/jm401330r). In this report, we describe the antiviral activity of the most promising third-generation lead compound, CCG205432, and closely related analogs CCG206381 and CCG209023. These compounds have half-maximal inhibitory concentrations of ∼1 μM and selectivity indices of >100 in cell-based assays using western equine encephalitis virus replicons. Furthermore, CCG205432 retains similar potency against fully infectious virus in cultured human neuronal cells. These compounds show broad inhibitory activity against a range of RNA viruses in culture, including members of the Togaviridae, Bunyaviridae, Picornaviridae, and Paramyxoviridae families. Although their exact molecular target remains unknown, mechanism-of-action studies reveal that these novel indole-based compounds target a host factor that modulates cap-dependent translation. Finally, we demonstrate that both CCG205432 and CCG209023 dampen clinical disease severity and enhance survival of mice given a lethal western equine encephalitis virus challenge. These studies demonstrate that indole-2-carboxamide compounds are viable candidates for continued preclinical development as inhibitors of neurotropic alphaviruses and, potentially, of other RNA viruses. IMPORTANCE There are currently no approved drugs to treat infections with alphaviruses. We previously identified a novel series of compounds with activity against these potentially devastating pathogens (J. A. Sindac et al., J. Med. Chem. 55:3535–3545, 2012, doi:http://dx.doi.org/10.1021/jm300214e; W. Peng et al., J. Infect. Dis. 199:950–957, 2009, doi:http://dx.doi.org/10.1086/597275; J. A. Sindac et al., J. Med. Chem. 56:9222–9241, 2013, http://dx.doi.org/10.1021/jm401330r). We have now produced third-generation compounds with enhanced potency, and this manuscript provides detailed information on the antiviral activity of these advanced-generation compounds, including activity in an animal model. The results of this study represent a notable achievement in the continued development of this novel class of antiviral inhibitors. PMID:25031353

  9. Fort Collins Science Center- Policy Analysis and Science Assistance Branch : Integrating social, behavioral, economic and biological sciences

    USGS Publications Warehouse

    2010-01-01

    The Fort Collins Science Center's Policy Analysis and Science Assistance (PASA) Branch is a team of approximately 22 scientists, technicians, and graduate student researchers. PASA provides unique capabilities in the U.S. Geological Survey by leading projects that integrate social, behavioral, economic, and biological analyses in the context of human-natural resource interactions. Resource planners, managers, and policymakers in the U.S. Departments of the Interior (DOI) and Agriculture (USDA), State and local agencies, as well as international agencies use information from PASA studies to make informed natural resource management and policy decisions. PASA scientists' primary functions are to conduct both theoretical and applied social science research, provide technical assistance, and offer training to advance performance in policy relevant research areas. Management and research issues associated with human-resource interactions typically occur in a unique context, involve difficult to access populations, require knowledge of both natural/biological science in addition to social science, and require the skill to integrate multiple science disciplines. In response to these difficult contexts, PASA researchers apply traditional and state-of-the-art social science methods drawing from the fields of sociology, demography, economics, political science, communications, social-psychology, and applied industrial organization psychology. Social science methods work in concert with our rangeland/agricultural management, wildlife, ecology, and biology capabilities. The goal of PASA's research is to enhance natural resource management, agency functions, policies, and decision-making. Our research is organized into four broad areas of study.

  10. Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB.

    PubMed

    Filippova, Ekaterina V; Zemaitaitis, Bozena; Aung, Theint; Wolfe, Alan J; Anderson, Wayne F

    2018-02-27

    RcsB is a highly conserved transcription regulator of the Rcs phosphorelay system, a complex two-component signal transduction system (N. Majdalani and S. Gottesman, Annu Rev Microbiol 59:379-405, 2005; A. J. Wolfe, Curr Opin Microbiol 13:204-209, 2010, https://doi.org/10.1016/j.mib.2010.01.002; D. J. Clarke, Future Microbiol 5:1173-1184, 2010, https://doi.org/10.2217/fmb.10.83). RcsB plays an important role in virulence and pathogenicity in human hosts by regulating biofilm formation. RcsB can regulate transcription alone or together with its auxiliary transcription regulators by forming heterodimers. This complexity allows RcsB to regulate transcription of more than 600 bacterial genes in response to different stresses (D. Wang et al., Mol Plant Microbe Interact 25:6-17, 2012, https://doi.org/10.1094/MPMI-08-11-0207). Despite increasing knowledge of RcsB importance, molecular mechanisms that drive the ability of RcsB to control transcription of a large number of genes remain unclear. Here, we present crystal structures of unphosphorylated RcsB in complex with the consensus DNA-binding sequence of 22-mer (DNA22) and 18-mer (DNA18) of the flhDC operon from Escherichia coli determined at 3.15- and 3.37-Å resolution, respectively. The results of our structural analysis combined with the results of in vitro binding assays provide valuable insights to the protein regulatory mechanism, demonstrate how RcsB recognizes target DNA sequences, and reveal a unique oligomeric state that allows RcsB to form homo- and heterodimers. This information will help us understand the complex mechanisms of transcriptional regulation by RcsB in bacteria. IMPORTANCE RcsB is a well-studied two-component response regulator of the Rcs phosphorelay system, conserved within the family Enterobacteriaceae , which includes many pathogens. It is a global regulator, controlling more than 5% of bacterial genes associated with capsule biosynthesis, flagellar biogenesis, cell wall biosynthesis, antibiotic resistance, biofilm formation, and virulence in pathogens. Knowledge of RcsB structure represents a unique opportunity to explore mechanisms that regulate the Rcs phosphorelay system and its role in the family Enterobacteriaceae . Copyright © 2018 Filippova et al.

  11. Impact of detector design on imaging performance of a long axial field-of-view, whole-body PET scanner

    NASA Astrophysics Data System (ADS)

    Surti, S.; Karp, J. S.

    2015-07-01

    Current generation of commercial time-of-flight (TOF) PET scanners utilize 20-25 mm thick LSO or LYSO crystals and have an axial FOV (AFOV) in the range of 16-22 mm. Longer AFOV scanners would provide increased intrinsic sensitivity and require fewer bed positions for whole-body imaging. Recent simulation work has investigated the sensitivity gains that can be achieved with these long AFOV scanners, and has motivated new areas of investigation such as imaging with a very low dose of injected activity as well as providing whole-body dynamic imaging capability in one bed position. In this simulation work we model a 72 cm long scanner and prioritize the detector design choices in terms of timing resolution, crystal size (spatial resolution), crystal thickness (detector sensitivity), and depth-of-interaction (DOI) measurement capability. The generated list data are reconstructed with a list-mode OSEM algorithm using a Gaussian TOF kernel that depends on the timing resolution and blob basis functions for regularization. We use lesion phantoms and clinically relevant metrics for lesion detectability and contrast measurement. The scan time was fixed at 10 min for imaging a 100 cm long object assuming a 50% overlap between adjacent bed positions. Results show that a 72 cm long scanner can provide a factor of ten reduction in injected activity compared to an identical 18 cm long scanner to get equivalent lesion detectability. While improved timing resolution leads to further gains, using 3 mm (as opposed to 4 mm) wide crystals does not show any significant benefits for lesion detectability. A detector providing 2-level DOI information with equal crystal thickness also does not show significant gains. Finally, a 15 mm thick crystal leads to lower lesion detectability than a 20 mm thick crystal when keeping all other detector parameters (crystal width, timing resolution, and DOI capability) the same. However, improved timing performance with 15 mm thick crystals can provide similar or better performance than that achieved by a detector using 20 mm thick crystals.

  12. Unmanned aircraft systems (UAS) activities at the Department of the Interior

    USGS Publications Warehouse

    Quirk, Bruce K.; Hutt, Michael E.

    2014-01-01

    The U.S. Department of the Interior (DOI) is responsible for protecting and managing the natural resources and heritage on almost 20% of the land in the United States. The DOI’s mission requires access to remotely sensed data over vast lands, including areas that are remote and potentially dangerous to access. Unmanned Aircraft Systems (UAS) technology has the potential to enable the DOI to be a better steward of the land by: (1) Improving natural hazard forecasting and the analysis of the impacts. (2) Improving the understanding of climate change to better plan for likely impacts. (3) Developing precipitation and evaporation forecasting to better manage water resources. (4) Monitoring Arctic ice change and its impacts on ecosystems, coasts, and transportation. (5) Increasing safety and effectiveness of wildland fire management. (6) Enhancing search and rescue capabilities. (7) Broadening the abilities to monitor environmental or landscape conditions and changes. (8) Better understanding and protecting the Nation’s ecosystems. The initial operational testing and evaluations performed by the DOI have proven that UAS technology can be used to support many of the Department’s activities. UAS technology provides scientists a way to look longer, closer and more frequently at some of Earth’s most remote areas—places that were previously too dangerous or expensive to monitor in detail. The flexibility of operations and relative low cost to purchase and operate Small Unmanned Aerial System (sUAS) enhances the ability to track long-term landscape and environmental change. The initial testing indicates the operational costs are approximately 10% of traditional manned aircraft. In addition, users can quickly assess landscape-altering events such as wildland fires, floods and volcanoes. UAS technology will allow the DOI to do more with less and in the process enhance the Department’s ability to provide unbiased scientific information to help stakeholders make informed decisions. It will also provide a digital baseline record that can be archived and used when monitoring future events or conditions. One possible future scenario has scientists carrying sUAS into the field allowing quick deployment and operation to observe the environment or for emergency response. This scenario could also include a persistent monitoring capability provided by a UAS that can stay airborne over a small geographic area for days or weeks, or possibly longer. While the DOI focus is on sUAS, the Department recognizes that larger UAS systems will also play a role in meeting its mission. The Department anticipates meeting long-duration or specialized acquisition commitments, such as state or national aerial photography, by collaboration with other agencies or through commercial contracts. Even though the DOI continues to evaluate UAS and sensor technology to meet the Department’s mission, some of its bureaus are already moving towards an operational capability. The authors fully anticipate that by 2020 UAS will emerge as one of the primary platforms for DOI remote sensing applications.

  13. Meteorological buoy measurements in the Iceland Sea, 2007-2009

    NASA Astrophysics Data System (ADS)

    Nína Petersen, Guðrún

    2017-10-01

    The Icelandic Meteorological Office (IMO) conducted meteorological buoy measurements in the central Iceland Sea in the time period 2007-2009, specifically in the northern Dreki area on the southern segment of the Jan Mayen Ridge. Due to difficulties in deployment and operations, in situ measurements in this region are sparse. Here the buoy, deployment and measurements are described with the aim of giving a future user of the data set information that is as comprehensive as possible. The data set has been quality-checked, suspect data removed and the data set made publicly available from PANGAEA Data Publisher (https://doi.org/10.1594/PANGAEA.876206).

  14. NVAP-M Data and Information

    Atmospheric Science Data Center

    2016-04-27

    ... Vonder Haar, Science and Technology Corp.   The NASA MEaSUREs program began in 2008 and has the goal of creating stable, ... observations."  Geophys. Res. Lett. ,  39 , L16802,  doi:10.1029/2012GL052094   The heritage NASA Water Vapor Project ...

  15. Demonstrating the value of publishing open data by linking DOI-based citations of source datasets to uses in research and policy

    NASA Astrophysics Data System (ADS)

    Copas, K.; Legind, J. K.; Hahn, A.; Braak, K.; Høftt, M.; Noesgaard, D.; Robertson, T.; Méndez Hernández, F.; Schigel, D.; Ko, C.

    2017-12-01

    GBIF—the Global Biodiversity Information Facility—has recently demonstrated a system that tracks publications back to individual datasets, giving data providers demonstrable evidence of the benefit and utility of sharing data to support an array of scholarly topics and practical applications. GBIF is an open-data network and research infrastructure funded by the world's governments. Its community consists of more than 90 formal participants and almost 1,000 data-publishing institutions, which currently make tens of thousands of datasets containing nearly 800 million species occurrence records freely and publicly available for discovery, use and reuse across a wide range of biodiversity-related research and policy investigations. Starting in 2015 with the help of DataONE, GBIF introduced DOIs as persistent identifiers for the datasets shared through its network. This enhancement soon extended to the assignment of DOIs to user downloads from GBIF.org, which typically filter the available records with a variety of taxonomic, geographic, temporal and other search terms. Despite the lack of widely accepted standards for citing data among researchers and publications, this technical infrastructure is beginning to take hold and support open, transparent, persistent and repeatable use and reuse of species occurrence data. These `download DOIs' provide canonical references for the search results researchers process and use in peer-reviewed articles—a practice GBIF encourages by confirming new DOIs with each download and offering guidelines on citation. GBIF has recently started linking these citation results back to dataset and publisher pages, offering more consistent, traceable evidence of the value of sharing data to support others' research. GBIF's experience may be a useful model for other repositories to follow.

  16. Assessing the future of diffuse optical imaging technologies for breast cancer management

    PubMed Central

    Tromberg, Bruce J.; Pogue, Brian W.; Paulsen, Keith D.; Yodh, Arjun G.; Boas, David A.; Cerussi, Albert E.

    2008-01-01

    Diffuse optical imaging (DOI) is a noninvasive optical technique that employs near-infrared (NIR) light to quantitatively characterize the optical properties of thick tissues. Although NIR methods were first applied to breast transillumination (also called diaphanography) nearly 80 years ago, quantitative DOI methods employing time- or frequency-domain photon migration technologies have only recently been used for breast imaging (i.e., since the mid-1990s). In this review, the state of the art in DOI for breast cancer is outlined and a multi-institutional Network for Translational Research in Optical Imaging (NTROI) is described, which has been formed by the National Cancer Institute to advance diffuse optical spectroscopy and imaging (DOSI) for the purpose of improving breast cancer detection and clinical management. DOSI employs broadband technology both in near-infrared spectral and temporal signal domains in order to separate absorption from scattering and quantify uptake of multiple molecular probes based on absorption or fluorescence contrast. Additional dimensionality in the data is provided by integrating and co-registering the functional information of DOSI with x-ray mammography and magnetic resonance imaging (MRI), which provide structural information or vascular flow information, respectively. Factors affecting DOSI performance, such as intrinsic and extrinsic contrast mechanisms, quantitation of biochemical components, image formation∕visualization, and multimodality co-registration are under investigation in the ongoing research NTROI sites. One of the goals is to develop standardized DOSI platforms that can be used as stand-alone devices or in conjunction with MRI, mammography, or ultrasound. This broad-based, multidisciplinary effort is expected to provide new insight regarding the origins of breast disease and practical approaches for addressing several key challenges in breast cancer, including: Detecting disease in mammographically dense tissue, distinguishing between malignant and benign lesions, and understanding the impact of neoadjuvant chemotherapies. PMID:18649477

  17. Spatial correlated games

    PubMed Central

    2017-01-01

    This article studies correlated two-person games constructed from games with independent players as proposed in Iqbal et al. (2016 R. Soc. open sci. 3, 150477. (doi:10.1098/rsos.150477)). The games are played in a collective manner, both in a two-dimensional lattice where the players interact with their neighbours, and with players interacting at random. Four game types are scrutinized in iterated games where the players are allowed to change their strategies, adopting that of their best paid mate neighbour. Particular attention is paid in the study to the effect of a variable degree of correlation on Nash equilibrium strategy pairs. PMID:29291120

  18. Next generation PET data acquisition architectures

    NASA Astrophysics Data System (ADS)

    Jones, W. F.; Reed, J. H.; Everman, J. L.; Young, J. W.; Seese, R. D.

    1997-06-01

    New architectures for higher performance data acquisition in PET are proposed. Improvements are demanded primarily by three areas of advancing PET state of the art. First, larger detector arrays such as the Hammersmith ECAT/sup (R/) EXACT HR/sup ++/ exceed the addressing capacity of 32 bit coincidence event words. Second, better scintillators (LSO) make depth-of interaction (DOI) and time-of-flight (TOF) operation more practical. Third, fully optimized single photon attenuation correction requires higher rates of data collection. New technologies which enable the proposed third generation Real Time Sorter (RTS III) include: (1) 80 Mbyte/sec Fibre Channel RAID disk systems, (2) PowerPC on both VMEbus and PCI Local bus, and (3) quadruple interleaved DRAM controller designs. Data acquisition flexibility is enhanced through a wider 64 bit coincidence event word. PET methodology support includes DOI (6 bits), TOF (6 bits), multiple energy windows (6 bits), 512/spl times/512 sinogram indexes (18 bits), and 256 crystal rings (16 bits). Throughput of 10 M events/sec is expected for list-mode data collection as well as both on-line and replay histogramming. Fully efficient list-mode storage for each PET application is provided by real-time bit packing of only the active event word bits. Real-time circuits provide DOI rebinning.

  19. NOAA tools to support CSC and LCC regional climate science priorities in the western Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Brown, D. P.; Marcy, D.; Robbins, K.; Shafer, M.; Stiller, H.

    2012-12-01

    The National Oceanic and Atmospheric Administration (NOAA) is an active regional partner with the Department of Interior (DOI) in supplying and supporting the delivery of climate science and services. A primary mechanism for NOAA-DOI coordination at the regional scale is the Landscape Conservation Cooperative (LCC) network, which is supported in part by DOI Climate Science Centers (CSC). Together, the CSCs and LCCs provide a framework to identify landscape-scale science and services priorities for conservation and management. As a key partner of the CSCs and an active member of many LCCs, NOAA is working to ensure its own regional product and service delivery efforts will help address these conservation and management challenges. Two examples of NOAA's regional efforts are highlighted here, with a focus on the coastal and interior geographies of the western Gulf of Mexico where NOAA partners with the South Central CSC and participates as a member of the Gulf Coast Prairie LCC. Along the Texas coastline, a sea level rise and coastal flooding impacts viewer, produced by NOAA's Coastal Services Center and available via its Digital Coast interface, allows constituents to visualize estimates of sea level rise, measures of uncertainty, flood frequencies, and environmental (e.g., marsh migration) and socioeconomic (e.g., tidal flooding of built environments) impacts. In the interior of Texas and Louisiana, NOAA's Southern Regional Climate Center is leading a consortium of partners in the development of a unified source of regional water reservoir information, including current conditions, a historical database, and web-based visualization tools to illustrate spatio-temporal variations in water availability to a broad array of hydrological, agricultural, and other customers. These two examples of NOAA products can, in their existing forms, support regional conservation and management priorities for CSCs and LCCs by informing vulnerability assessments and adaptation planning. Enhancements to these and other efforts can be achieved through a robust collaboration between NOAA and DOI that links regional science priorities to regional service delivery.

  20. X-ray Generation in Strongly Nonlinear Plasma Waves

    NASA Astrophysics Data System (ADS)

    Kiselev, S.; Pukhov, A.; Kostyukov, I.

    2004-09-01

    We show that a laser wake field in the “bubble” regime [

    A. Pukhov and J. Meyer-ter-Vehn Appl. Phys. BAPBOEM0946-2171 74, 355 (2002)10.1007/s003400200795
    ], works as a compact high-brightness source of x-rays. The self-trapped relativistic electrons make betatron oscillations in the transverse fields of the bubble and emit a bright broadband x-ray radiation with a maximum about 50 keV. The emission is confined to a small angle of about 0.1 rad. In addition, we make simulations of x-ray generation by an external 28.5 GeV electron bunch injected into the bubble. γ quanta with up to GeV energies are observed in the simulation in good agreement with analytical results. The energy conversion is efficient, leading to a significant stopping of the electron bunch over 5 mm interaction distance.

  1. Epsin deficiency impairs endocytosis by stalling the actin-dependent invagination of endocytic clathrin-coated pits

    PubMed Central

    Messa, Mirko; Fernández-Busnadiego, Rubén; Sun, Elizabeth Wen; Chen, Hong; Czapla, Heather; Wrasman, Kristie; Wu, Yumei; Ko, Genevieve; Ross, Theodora; Wendland, Beverly; De Camilli, Pietro

    2014-01-01

    Epsin is an evolutionarily conserved endocytic clathrin adaptor whose most critical function(s) in clathrin coat dynamics remain(s) elusive. To elucidate such function(s), we generated embryonic fibroblasts from conditional epsin triple KO mice. Triple KO cells displayed a dramatic cell division defect. Additionally, a robust impairment in clathrin-mediated endocytosis was observed, with an accumulation of early and U-shaped pits. This defect correlated with a perturbation of the coupling between the clathrin coat and the actin cytoskeleton, which we confirmed in a cell-free assay of endocytosis. Our results indicate that a key evolutionary conserved function of epsin, in addition to other roles that include, as we show here, a low affinity interaction with SNAREs, is to help generate the force that leads to invagination and then fission of clathrin-coated pits. DOI: http://dx.doi.org/10.7554/eLife.03311.001 PMID:25122462

  2. Preliminary evaluation of a monolithic detector module for integrated PET/MRI scanner with high spatial resolution

    NASA Astrophysics Data System (ADS)

    Pani, R.; Gonzalez, A. J.; Bettiol, M.; Fabbri, A.; Cinti, M. N.; Preziosi, E.; Borrazzo, C.; Conde, P.; Pellegrini, R.; Di Castro, E.; Majewski, S.

    2015-06-01

    The proposal of Mindview European Project concerns with the development of a very high resolution and high efficiency brain dedicated PET scanner simultaneously working with a Magnetic Resonance scanner, that expects to visualize neurotransmitter pathways and their disruptions in the quest to better diagnose schizophrenia. On behalf of this project, we propose a low cost PET module for the first prototype, based on monolithic crystals, suitable to be integrated with a head Radio Frequency (RF) coil. The aim of the suggested module is to achieve high performances in terms of efficiency, planar spatial resolution (expected about 1 mm) and discrimination of gamma Depth Of Interaction (DOI) in order to reduce the parallax error. Our preliminary results are very promising: a DOI resolution of about 3 mm, a spatial resolution ranging from about 1 to 1.5 mm and a good position linearity.

  3. Vocal development in a Waddington landscape

    PubMed Central

    Teramoto, Yayoi; Takahashi, Daniel Y; Holmes, Philip; Ghazanfar, Asif A

    2017-01-01

    Vocal development is the adaptive coordination of the vocal apparatus, muscles, the nervous system, and social interaction. Here, we use a quantitative framework based on optimal control theory and Waddington’s landscape metaphor to provide an integrated view of this process. With a biomechanical model of the marmoset monkey vocal apparatus and behavioral developmental data, we show that only the combination of the developing vocal tract, vocal apparatus muscles and nervous system can fully account for the patterns of vocal development. Together, these elements influence the shape of the monkeys’ vocal developmental landscape, tilting, rotating or shifting it in different ways. We can thus use this framework to make quantitative predictions regarding how interfering factors or experimental perturbations can change the landscape within a species, or to explain comparative differences in vocal development across species DOI: http://dx.doi.org/10.7554/eLife.20782.001 PMID:28092262

  4. Stacking the odds for Golgi cisternal maturation

    PubMed Central

    Mani, Somya; Thattai, Mukund

    2016-01-01

    What is the minimal set of cell-biological ingredients needed to generate a Golgi apparatus? The compositions of eukaryotic organelles arise through a process of molecular exchange via vesicle traffic. Here we statistically sample tens of thousands of homeostatic vesicle traffic networks generated by realistic molecular rules governing vesicle budding and fusion. Remarkably, the plurality of these networks contain chains of compartments that undergo creation, compositional maturation, and dissipation, coupled by molecular recycling along retrograde vesicles. This motif precisely matches the cisternal maturation model of the Golgi, which was developed to explain many observed aspects of the eukaryotic secretory pathway. In our analysis cisternal maturation is a robust consequence of vesicle traffic homeostasis, independent of the underlying details of molecular interactions or spatial stacking. This architecture may have been exapted rather than selected for its role in the secretion of large cargo. DOI: http://dx.doi.org/10.7554/eLife.16231.001 PMID:27542195

  5. Perception as a closed-loop convergence process

    PubMed Central

    Ahissar, Ehud; Assa, Eldad

    2016-01-01

    Perception of external objects involves sensory acquisition via the relevant sensory organs. A widely-accepted assumption is that the sensory organ is the first station in a serial chain of processing circuits leading to an internal circuit in which a percept emerges. This open-loop scheme, in which the interaction between the sensory organ and the environment is not affected by its concurrent downstream neuronal processing, is strongly challenged by behavioral and anatomical data. We present here a hypothesis in which the perception of external objects is a closed-loop dynamical process encompassing loops that integrate the organism and its environment and converging towards organism-environment steady-states. We discuss the consistency of closed-loop perception (CLP) with empirical data and show that it can be synthesized in a robotic setup. Testable predictions are proposed for empirical distinction between open and closed loop schemes of perception. DOI: http://dx.doi.org/10.7554/eLife.12830.001 PMID:27159238

  6. The structure of plant photosystem I super-complex at 2.8 Å resolution

    PubMed Central

    Mazor, Yuval; Borovikova, Anna; Nelson, Nathan

    2015-01-01

    Most life forms on Earth are supported by solar energy harnessed by oxygenic photosynthesis. In eukaryotes, photosynthesis is achieved by large membrane-embedded super-complexes, containing reaction centers and connected antennae. Here, we report the structure of the higher plant PSI-LHCI super-complex determined at 2.8 Å resolution. The structure includes 16 subunits and more than 200 prosthetic groups, which are mostly light harvesting pigments. The complete structures of the four LhcA subunits of LHCI include 52 chlorophyll a and 9 chlorophyll b molecules, as well as 10 carotenoids and 4 lipids. The structure of PSI-LHCI includes detailed protein pigments and pigment–pigment interactions, essential for the mechanism of excitation energy transfer and its modulation in one of nature's most efficient photochemical machines. DOI: http://dx.doi.org/10.7554/eLife.07433.001 PMID:26076232

  7. Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

    PubMed Central

    Berger, Stephanie; Procko, Erik; Margineantu, Daciana; Lee, Erinna F; Shen, Betty W; Zelter, Alex; Silva, Daniel-Adriano; Chawla, Kusum; Herold, Marco J; Garnier, Jean-Marc; Johnson, Richard; MacCoss, Michael J; Lessene, Guillaume; Davis, Trisha N; Stayton, Patrick S; Stoddard, Barry L; Fairlie, W Douglas; Hockenbery, David M; Baker, David

    2016-01-01

    Many cancers overexpress one or more of the six human pro-survival BCL2 family proteins to evade apoptosis. To determine which BCL2 protein or proteins block apoptosis in different cancers, we computationally designed three-helix bundle protein inhibitors specific for each BCL2 pro-survival protein. Following in vitro optimization, each inhibitor binds its target with high picomolar to low nanomolar affinity and at least 300-fold specificity. Expression of the designed inhibitors in human cancer cell lines revealed unique dependencies on BCL2 proteins for survival which could not be inferred from other BCL2 profiling methods. Our results show that designed inhibitors can be generated for each member of a closely-knit protein family to probe the importance of specific protein-protein interactions in complex biological processes. DOI: http://dx.doi.org/10.7554/eLife.20352.001 PMID:27805565

  8. Mapping the function of neuronal ion channels in model and experiment

    PubMed Central

    Podlaski, William F; Seeholzer, Alexander; Groschner, Lukas N; Miesenböck, Gero; Ranjan, Rajnish; Vogels, Tim P

    2017-01-01

    Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretation of simulations. However, the number of published models, and the lack of standardization, make the comparison of ion channel models with one another and with experimental data difficult. Here, we present a framework for the automated large-scale classification of ion channel models. Using annotated metadata and responses to a set of voltage-clamp protocols, we assigned 2378 models of voltage- and calcium-gated ion channels coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface provides an interactive resource for the categorization of new and existing models and experimental recordings. It enables quantitative comparisons of simulated and/or measured ion channel kinetics, and facilitates field-wide standardization of experimentally-constrained modeling. DOI: http://dx.doi.org/10.7554/eLife.22152.001 PMID:28267430

  9. Why developmental psychology is incomplete without comparative and cross-cultural perspectives.

    PubMed

    Nielsen, Mark; Haun, Daniel

    2016-01-19

    As a discipline, developmental psychology has a long history of relying on animal models and data collected among distinct cultural groups to enrich and inform theories of the ways social and cognitive processes unfold through the lifespan. However, approaches that draw together developmental, cross-cultural and comparative perspectives remain rare. The need for such an approach is reflected in the papers by Heyes (2015 Phil. Trans. R. Soc. B 371, 20150069. (doi:10.1098/rstb.2015.0069)), Schmelz & Call (2015 Phil. Trans. R. Soc. B 371, 20150067. (doi:10.1098/rstb.2015.0067)) and Keller (2015 Phil. Trans. R. Soc. B 371, 20150070. (doi:10.1098/rstb.2015.0070)) in this theme issue. Here, we incorporate these papers into a review of recent research endeavours covering a range of core aspects of social cognition, including social learning, cooperation and collaboration, prosociality, and theory of mind. In so doing, we aim to highlight how input from comparative and cross-cultural empiricism has altered our perspectives of human development and, in particular, led to a deeper understanding of the evolution of the human cultural mind. © 2015 The Author(s).

  10. Response to comment by Walker et al. on “From data to decisions: Processing information, biases, and beliefs for improved management of natural resources and environments”

    USGS Publications Warehouse

    Glynn, Pierre D.; Voinov, Alexey A.; Shapiro, Carl D.; White, Paul A.

    2018-01-01

    Our different kinds of minds and types of thinking affect the ways we decide, take action, and cooperate (or not). The comment by Walker et al. (2018, https://doi.org/10.1002/2017EF000750) illustrates several points made by Glynn et al. (2017, https://doi.org/10.1002/2016EF000487) and many other articles. Namely, biases and beliefs often drive scientific reasoning, and scientists, just like other humans, are intimately attached to their values and heuristics. Scientists, just like many other people, also tend to read and interpret text in ways that best match their individual perceptions of a problem or issue: in many cases paraphrasing and changing the meaning of what they read to better match their initial ideas. Walker et al. are doing interesting and important research on uncertainty. Nonetheless, they misinterpret the work, assumptions, and conclusions brought forth by Glynn et al. (2017, https://doi.org/10.1002/2016EF000487).

  11. Why developmental psychology is incomplete without comparative and cross-cultural perspectives

    PubMed Central

    Nielsen, Mark; Haun, Daniel

    2016-01-01

    As a discipline, developmental psychology has a long history of relying on animal models and data collected among distinct cultural groups to enrich and inform theories of the ways social and cognitive processes unfold through the lifespan. However, approaches that draw together developmental, cross-cultural and comparative perspectives remain rare. The need for such an approach is reflected in the papers by Heyes (2015 Phil. Trans. R. Soc. B 371, 20150069. (doi:10.1098/rstb.2015.0069)), Schmelz & Call (2015 Phil. Trans. R. Soc. B 371, 20150067. (doi:10.1098/rstb.2015.0067)) and Keller (2015 Phil. Trans. R. Soc. B 371, 20150070. (doi:10.1098/rstb.2015.0070)) in this theme issue. Here, we incorporate these papers into a review of recent research endeavours covering a range of core aspects of social cognition, including social learning, cooperation and collaboration, prosociality, and theory of mind. In so doing, we aim to highlight how input from comparative and cross-cultural empiricism has altered our perspectives of human development and, in particular, led to a deeper understanding of the evolution of the human cultural mind. PMID:26644590

  12. Amygdala neural activity reflects spatial attention towards stimuli promising reward or threatening punishment

    PubMed Central

    Peck, Christopher J; Salzman, C Daniel

    2014-01-01

    Humans and other animals routinely identify and attend to sensory stimuli so as to rapidly acquire rewards or avoid aversive experiences. Emotional arousal, a process mediated by the amygdala, can enhance attention to stimuli in a non-spatial manner. However, amygdala neural activity was recently shown to encode spatial information about reward-predictive stimuli, and to correlate with spatial attention allocation. If representing the motivational significance of sensory stimuli within a spatial framework reflects a general principle of amygdala function, then spatially selective neural responses should also be elicited by sensory stimuli threatening aversive events. Recordings from amygdala neurons were therefore obtained while monkeys directed spatial attention towards stimuli promising reward or threatening punishment. Neural responses encoded spatial information similarly for stimuli associated with both valences of reinforcement, and responses reflected spatial attention allocation. The amygdala therefore may act to enhance spatial attention to sensory stimuli associated with rewarding or aversive experiences. DOI: http://dx.doi.org/10.7554/eLife.04478.001 PMID:25358090

  13. Emergence of transformation-tolerant representations of visual objects in rat lateral extrastriate cortex

    PubMed Central

    Tafazoli, Sina; Safaai, Houman; De Franceschi, Gioia; Rosselli, Federica Bianca; Vanzella, Walter; Riggi, Margherita; Buffolo, Federica; Panzeri, Stefano; Zoccolan, Davide

    2017-01-01

    Rodents are emerging as increasingly popular models of visual functions. Yet, evidence that rodent visual cortex is capable of advanced visual processing, such as object recognition, is limited. Here we investigate how neurons located along the progression of extrastriate areas that, in the rat brain, run laterally to primary visual cortex, encode object information. We found a progressive functional specialization of neural responses along these areas, with: (1) a sharp reduction of the amount of low-level, energy-related visual information encoded by neuronal firing; and (2) a substantial increase in the ability of both single neurons and neuronal populations to support discrimination of visual objects under identity-preserving transformations (e.g., position and size changes). These findings strongly argue for the existence of a rat object-processing pathway, and point to the rodents as promising models to dissect the neuronal circuitry underlying transformation-tolerant recognition of visual objects. DOI: http://dx.doi.org/10.7554/eLife.22794.001 PMID:28395730

  14. Distinct cortical codes and temporal dynamics for conscious and unconscious percepts

    PubMed Central

    Salti, Moti; Monto, Simo; Charles, Lucie; King, Jean-Remi; Parkkonen, Lauri; Dehaene, Stanislas

    2015-01-01

    The neural correlates of consciousness are typically sought by comparing the overall brain responses to perceived and unperceived stimuli. However, this comparison may be contaminated by non-specific attention, alerting, performance, and reporting confounds. Here, we pursue a novel approach, tracking the neuronal coding of consciously and unconsciously perceived contents while keeping behavior identical (blindsight). EEG and MEG were recorded while participants reported the spatial location and visibility of a briefly presented target. Multivariate pattern analysis demonstrated that considerable information about spatial location traverses the cortex on blindsight trials, but that starting ≈270 ms post-onset, information unique to consciously perceived stimuli, emerges in superior parietal and superior frontal regions. Conscious access appears characterized by the entry of the perceived stimulus into a series of additional brain processes, each restricted in time, while the failure of conscious access results in the breaking of this chain and a subsequent slow decay of the lingering unconscious activity. DOI: http://dx.doi.org/10.7554/eLife.05652.001 PMID:25997100

  15. Decoupling kinematics and mechanics reveals coding properties of trigeminal ganglion neurons in the rat vibrissal system

    PubMed Central

    Bush, Nicholas E; Schroeder, Christopher L; Hobbs, Jennifer A; Yang, Anne ET; Huet, Lucie A; Solla, Sara A; Hartmann, Mitra JZ

    2016-01-01

    Tactile information available to the rat vibrissal system begins as external forces that cause whisker deformations, which in turn excite mechanoreceptors in the follicle. Despite the fundamental mechanical origin of tactile information, primary sensory neurons in the trigeminal ganglion (Vg) have often been described as encoding the kinematics (geometry) of object contact. Here we aimed to determine the extent to which Vg neurons encode the kinematics vs. mechanics of contact. We used models of whisker bending to quantify mechanical signals (forces and moments) at the whisker base while simultaneously monitoring whisker kinematics and recording single Vg units in both anesthetized rats and awake, body restrained rats. We employed a novel manual stimulation technique to deflect whiskers in a way that decouples kinematics from mechanics, and used Generalized Linear Models (GLMs) to show that Vg neurons more directly encode mechanical signals when the whisker is deflected in this decoupled stimulus space. DOI: http://dx.doi.org/10.7554/eLife.13969.001 PMID:27348221

  16. Global, quantitative and dynamic mapping of protein subcellular localization

    PubMed Central

    Itzhak, Daniel N; Tyanova, Stefka; Cox, Jürgen; Borner, Georg HH

    2016-01-01

    Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology. DOI: http://dx.doi.org/10.7554/eLife.16950.001 PMID:27278775

  17. The auditory representation of speech sounds in human motor cortex

    PubMed Central

    Cheung, Connie; Hamilton, Liberty S; Johnson, Keith; Chang, Edward F

    2016-01-01

    In humans, listening to speech evokes neural responses in the motor cortex. This has been controversially interpreted as evidence that speech sounds are processed as articulatory gestures. However, it is unclear what information is actually encoded by such neural activity. We used high-density direct human cortical recordings while participants spoke and listened to speech sounds. Motor cortex neural patterns during listening were substantially different than during articulation of the same sounds. During listening, we observed neural activity in the superior and inferior regions of ventral motor cortex. During speaking, responses were distributed throughout somatotopic representations of speech articulators in motor cortex. The structure of responses in motor cortex during listening was organized along acoustic features similar to auditory cortex, rather than along articulatory features as during speaking. Motor cortex does not contain articulatory representations of perceived actions in speech, but rather, represents auditory vocal information. DOI: http://dx.doi.org/10.7554/eLife.12577.001 PMID:26943778

  18. Convergence of pontine and proprioceptive streams onto multimodal cerebellar granule cells

    PubMed Central

    Huang, Cheng-Chiu; Sugino, Ken; Shima, Yasuyuki; Guo, Caiying; Bai, Suxia; Mensh, Brett D; Nelson, Sacha B; Hantman, Adam W

    2013-01-01

    Cerebellar granule cells constitute the majority of neurons in the brain and are the primary conveyors of sensory and motor-related mossy fiber information to Purkinje cells. The functional capability of the cerebellum hinges on whether individual granule cells receive mossy fiber inputs from multiple precerebellar nuclei or are instead unimodal; this distinction is unresolved. Using cell-type-specific projection mapping with synaptic resolution, we observed the convergence of separate sensory (upper body proprioceptive) and basilar pontine pathways onto individual granule cells and mapped this convergence across cerebellar cortex. These findings inform the long-standing debate about the multimodality of mammalian granule cells and substantiate their associative capacity predicted in the Marr-Albus theory of cerebellar function. We also provide evidence that the convergent basilar pontine pathways carry corollary discharges from upper body motor cortical areas. Such merging of related corollary and sensory streams is a critical component of circuit models of predictive motor control. DOI: http://dx.doi.org/10.7554/eLife.00400.001 PMID:23467508

  19. Differential inhibition onto developing and mature granule cells generates high-frequency filters with variable gain

    PubMed Central

    Pardi, María Belén; Ogando, Mora Belén; Schinder, Alejandro F; Marin-Burgin, Antonia

    2015-01-01

    Adult hippocampal neurogenesis provides the dentate gyrus with heterogeneous populations of granule cells (GC) originated at different times. The contribution of these cells to information encoding is under current investigation. Here, we show that incoming spike trains activate different populations of GC determined by the stimulation frequency and GC age. Immature GC respond to a wider range of stimulus frequencies, whereas mature GC are less responsive at high frequencies. This difference is dictated by feedforward inhibition, which restricts mature GC activation. Yet, the stronger inhibition of mature GC results in a higher temporal fidelity compared to that of immature GC. Thus, hippocampal inputs activate two populations of neurons with variable frequency filters: immature cells, with wide‐range responses, that are reliable transmitters of the incoming frequency, and mature neurons, with narrow frequency response, that are precise at informing the beginning of the stimulus, but with a sparse activity. DOI: http://dx.doi.org/10.7554/eLife.08764.001 PMID:26163657

  20. Widespread correlation patterns of fMRI signal across visual cortex reflect eccentricity organization

    PubMed Central

    Arcaro, Michael J; Honey, Christopher J; Mruczek, Ryan EB; Kastner, Sabine; Hasson, Uri

    2015-01-01

    The human visual system can be divided into over two-dozen distinct areas, each of which contains a topographic map of the visual field. A fundamental question in vision neuroscience is how the visual system integrates information from the environment across different areas. Using neuroimaging, we investigated the spatial pattern of correlated BOLD signal across eight visual areas on data collected during rest conditions and during naturalistic movie viewing. The correlation pattern between areas reflected the underlying receptive field organization with higher correlations between cortical sites containing overlapping representations of visual space. In addition, the correlation pattern reflected the underlying widespread eccentricity organization of visual cortex, in which the highest correlations were observed for cortical sites with iso-eccentricity representations including regions with non-overlapping representations of visual space. This eccentricity-based correlation pattern appears to be part of an intrinsic functional architecture that supports the integration of information across functionally specialized visual areas. DOI: http://dx.doi.org/10.7554/eLife.03952.001 PMID:25695154

  1. A nap to recap or how reward regulates hippocampal-prefrontal memory networks during daytime sleep in humans

    PubMed Central

    Igloi, Kinga; Gaggioni, Giulia; Sterpenich, Virginie; Schwartz, Sophie

    2015-01-01

    Sleep plays a crucial role in the consolidation of newly acquired memories. Yet, how our brain selects the noteworthy information that will be consolidated during sleep remains largely unknown. Here we show that post-learning sleep favors the selectivity of long-term consolidation: when tested three months after initial encoding, the most important (i.e., rewarded, strongly encoded) memories are better retained, and also remembered with higher subjective confidence. Our brain imaging data reveals that the functional interplay between dopaminergic reward regions, the prefrontal cortex and the hippocampus contributes to the integration of rewarded associative memories. We further show that sleep spindles strengthen memory representations based on reward values, suggesting a privileged replay of information yielding positive outcomes. These findings demonstrate that post-learning sleep determines the neural fate of motivationally-relevant memories and promotes a value-based stratification of long-term memory stores. DOI: http://dx.doi.org/10.7554/eLife.07903.001 PMID:26473618

  2. Data Publication: The Evolving Lifecyle

    NASA Astrophysics Data System (ADS)

    Studwell, S.; Elliott, J.; Anderson, A.

    2015-12-01

    Datasets are recognized as valuable information entities in their own right that, now and in the future, need to be available for citation, discovery, retrieval and reuse. The U.S. Department of Energy's Office of Scientific and Technical Information (OSTI) provides Digital Object Identifiers (DOIs) to DOE-funded data through partnership with DataCite. The Geothermal Data Repository (GDR) has been using OSTI's Data ID Service since summer, 2014 and is a success story for data publishing in several different ways. This presentation attributes the initial success to the insistence of DOE's Geothermal Technologies Office on detailed planning, robust data curation, and submitter participation. OSTI widely disseminates these data products across both U.S. and international platforms and continually enhances the Data ID Service to facilitate better linkage between published literature, supplementary data components, and the underlying datasets within the structure of the GDR repository. Issues of granularity in DOI assignment, the role of new federal government guidelines on public access to digital data, and the challenges still ahead will be addressed.

  3. Episodic-like memory trace in awake replay of hippocampal place cell activity sequences

    PubMed Central

    Takahashi, Susumu

    2015-01-01

    Episodic memory retrieval of events at a specific place and time is effective for future planning. Sequential reactivation of the hippocampal place cells along familiar paths while the animal pauses is well suited to such a memory retrieval process. It is, however, unknown whether this awake replay represents events occurring along the path. Using a subtask switching protocol in which the animal experienced three subtasks as ‘what’ information in a maze, I here show that the replay represents a trial type, consisting of path and subtask, in terms of neuronal firing timings and rates. The actual trial type to be rewarded could only be reliably predicted from replays that occurred at the decision point. This trial-type representation implies that not only ‘where and when’ but also ‘what’ information is contained in the replay. This result supports the view that awake replay is an episodic-like memory retrieval process. DOI: http://dx.doi.org/10.7554/eLife.08105.001 PMID:26481131

  4. Accurately Decoding Visual Information from fMRI Data Obtained in a Realistic Virtual Environment

    DTIC Science & Technology

    2015-06-09

    Center for Learning and Memory , The University of Texas at Austin, 100 E 24th Street, Stop C7000, Austin, TX 78712, USA afloren@utexas.edu Received: 18...information from fMRI data obtained in a realistic virtual environment. Front. Hum. Neurosci. 9:327. doi: 10.3389/fnhum.2015.00327 Accurately decoding...visual information from fMRI data obtained in a realistic virtual environment Andrew Floren 1*, Bruce Naylor 2, Risto Miikkulainen 3 and David Ress 4

  5. Using Open data in analyzing urban growth: urban density and change detection

    NASA Astrophysics Data System (ADS)

    murgante, Beniamino; Nolè, Gabriele; Lasaponara, Rosa; Lanorte, Antonio

    2013-04-01

    In recent years a great attention has been paid to the evolution and the use of spatial data. Internet technologies accelerated such a process, allowing more direct access to spatial information. It is estimated that more than 600 million people have been connected to the Internet at least once to display maps on the web. Consequently, there is an irreversible process which considers geographical dimension as a fundamental attribute for the management of information flows. Furthermore, the great activity produced by open data movement leads to an easier and clearer access to geospatial information. This trend concerns, in a less evident way, also satellite data, which are increasingly accessible through the web. Spatial planning, geography and other regional sciences find it difficult to build knowledge related to spatial transformation. These problems can be significantly reduced due to a large data availability, producing significant opportunities to capture knowledge useful for a better territorial governance. This study has been developed in a heavily anthropized area in southern Italy, Apulia region, using free spatial data and free multispectral and multitemporal satellite data (Apulia region was one of the first regions in Italy to adopt open data policies). The analysis concerns urban growth, which, in recent decades, showed a rapid increase. In a first step the evolution in time and change detection of urban areas has been analyzed paying particular attention to soil consumption. In the second step Kernel Density has been adopted in order to assess development pressures. KDE (Kernel Density Estimation) function is a technique that provides the density of a phenomenon based on point data. A mobile three dimensional surface has been produced from a set of points distributed over a region of space, which weighs the events within its sphere of influence, depending on their distance from the point from which intensity is estimated. It produces, considering as input point data (vector), a density continuous raster as an output. In this case, the intensity of phenomenon will be given by buildings volume. References • Bailey T. C., Gatrell A. C. (1995). Interactive spatial data analysis. Prentice Hall. • Danese M., Lazzari M., Murgante B. (2009). "Geostatistics in Historical Macroseismic Data Analysis" Transactions on Computational Sciences VI, LNCS Vol. 5730, pp. 324-341, Springer-Verlag, Berlin ISSN: 1611-3349, doi:10.1007/978-3-642-10649-1_19 • Nolè G., Danese M., Murgante B., Lasaponara R., Lanorte, A., (2012) "Using Spatial Autocorrelation Techniques and Multi-temporal Satellite Data for Analyzing Urban Sprawl" Lecture Notes in Computer Science vol. 7335, pp. 512-527. Springer-Verlag, Berlin. ISSN: 0302-9743, doi: 10.1007/978-3-642-31137-6_39 • Murgante, B., Las Casas, G., Danese, M., (2012), "Analyzing Neighbourhoods Suitable for Urban Renewal Programs with Autocorrelation Techniques" In Burian J. (Eds.) "Advances in Spatial Planning" InTech — Open Access DOI: 10.5772/33747 ISBN:978-953-51-0377-6 • Lanorte, A., Danese M., Lasaponara R., Murgante B. (2011) "Multiscale mapping of burn area and severity using multisensor satellite data and spatial autocorrelation analysis" International Journal of Applied Earth Observation and Geoinformation, Elsevier, doi:10.1016/j.jag.2011.09.005 • O'Sullivan D., Unwin D., (2002). Geographic Information Analysis. John Wiley & Sons • Yang, X., Lo, C. P.: Using a time series of satellite imagery to detect land use and land cover changes in the Atlanta, Georgia metropolitan area. Int. J. Rem. Sensing 23, pp. 1775--1798 (2002) • Yuan, F., Sawaya, K.,.Loeffelholz, B. C., Bauer, M. E.: Land cover classification and change analysis of the Twin Cities (Minnesota) Metropolitan Area by multitemporal Landsat remote sensing. Rem. Sensing Environ. 98, pp. 317--328 (2005)

  6. Spiked Models of Large Dimensional Random Matrices Applied to Wireless Communications and Array Signal Processing

    DTIC Science & Technology

    2013-12-14

    population covariance matrix with application to array signal processing; and 5) a sample covariance matrix for which a CLT is studied on linear...Applications , (01 2012): 1150004. doi: Walid Hachem, Malika Kharouf, Jamal Najim, Jack W. Silverstein. A CLT FOR INFORMATION- THEORETIC STATISTICS...for Multi-source Power Estimation, (04 2010) Malika Kharouf, Jamal Najim, Jack W. Silverstein, Walid Hachem. A CLT FOR INFORMATION- THEORETIC

  7. Erratum to: Circulating tumor markers: a guide to their appropriate clinical use | Comparative summary of recommendations from clinical practice guidelines (PART 1), (PART 2), (PART 3).

    PubMed

    2017-10-31

    Erratum To: Circulating tumor markers: a guide to their appropriate clinical use | Comparative summary of recommendations from clinical practice guidelines (PART 1) Gion M, Trevisiol C, Rutjes AW, Rainato G, Fabricio AS. Int J Biol Markers. 2016 Dec 23;31(4):e332-e367. doi: 10.5301/jbm.5000251. Circulating tumor markers: a guide to their appropriate clinical use | Comparative summary of recommendations from clinical practice guidelines (PART 2).Gion M, Trevisiol C, Rutjes AWS, Rainato G, Fabricio ASC. Int J Biol Markers. 2017 Mar 2;32(1):e1-e52. doi: 10.5301/ijbm.5000259. Circulating tumor markers: a guide to their appropriate clinical use | Comparative summary of recommendations from clinical practice guidelines (PART 3).Gion M, Trevisiol C, Rutjes AWS, Rainato G, Fabricio ASC. Int J Biol Markers. 2017 May 4;32(2):e147-e181. doi: 10.5301/ijbm.5000272. We report an amendment in the Detailed summary tables pages of the three parts of the guidelines above. The correct definition of detailed summary tables is reported below. Definition and target audience Detailed summary tables are tables prepared for every tumor type which report recommendations and supplementary information from different guidance documents with enough details to be useful for health care providers, policy makers (for potential adaptation to specific settings) and staff developing educational material informed by available evidence.

  8. Featured Image: A Galaxy Plunges Into a Cluster Core

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2015-10-01

    The galaxy that takes up most of the frame in this stunning image (click for the full view!) is NGC 1427A. This is a dwarf irregular galaxy (unlike the fortuitously-located background spiral galaxy in the lower right corner of the image), and its currently in the process of plunging into the center of the Fornax galaxy cluster. Marcelo Mora (Pontifical Catholic University of Chile) and collaborators have analyzed observations of this galaxy made by both the Very Large Telescope in Chile and the Hubble Advanced Camera for Surveys, which produced the image shown here as a color composite in three channels. The team worked to characterize the clusters of star formation within NGC 1427A identifiable in the image as bright knots within the galaxy and determine how the interactions of this galaxy with its cluster environment affect the star formation within it. For more information and the original image, see the paper below.Citation:Marcelo D. Mora et al 2015 AJ 150 93. doi:10.1088/0004-6256/150/3/93

  9. Catalysis of a 1,3-dipolar reaction by distorted DNA incorporating a heterobimetallic platinum(ii) and copper(ii) complex† †Electronic supplementary information (ESI) available: Experimental details, characterization of cycloadducts and intermediates, computational data. CCDC 1411372 and 1411373. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc02311a

    PubMed Central

    Rivilla, Iván; de Cózar, Abel; Schäfer, Thomas; Hernandez, Frank J.; Bittner, Alexander M.; Eleta-Lopez, Aitziber; Aboudzadeh, Ali; Santos, José I.; Miranda, José I.

    2017-01-01

    A novel catalytic system based on covalently modified DNA is described. This catalyst promotes 1,3-dipolar reactions between azomethine ylides and maleimides. The catalytic system is based on the distortion of the double helix of DNA by means of the formation of Pt(ii) adducts with guanine units. This distortion, similar to that generated in the interaction of DNA with platinum chemotherapeutic drugs, generates active sites that can accommodate N-metallated azomethine ylides. The proposed reaction mechanism, based on QM(DFT)/MM calculations, is compatible with thermally allowed concerted (but asynchronous) [π4s + π2s] mechanisms leading to the exclusive formation of racemic endo-cycloadducts. PMID:29147531

  10. Cation–π interactions in protein–ligand binding: theory and data-mining reveal different roles for lysine and arginine† †Electronic supplementary information (ESI) available: DLPNO-CCSD(T)/aug-cc-pVnZ benchmarks; PLIP geometric criteria; polycyclic aromatic ring visualizations; van der Waals surfaces of model complexes; absolute energies from DLPNO-CCSD(T)/aug-cc-pVTZ and SAPT2+3/aug-cc-pVDZ calculations; Cartesian coordinates; Table of PDB IDs and corresponding cation–π interactions identified (.xls). See DOI: 10.1039/c7sc04905f

    PubMed Central

    Kumar, Kiran; Woo, Shin M.; Siu, Thomas; Cortopassi, Wilian A.

    2018-01-01

    We have studied the cation–π interactions of neutral aromatic ligands with the cationic amino acid residues arginine, histidine and lysine using ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of all available Protein Data Bank (PDB) X-ray structures. Quantum chemical potential energy surfaces (PES) for these interactions were obtained at the DLPNO-CCSD(T) level of theory and compared against the empirical distribution of 2012 unique protein–ligand cation–π interactions found in X-ray crystal structures. We created a workflow to extract these structures from the PDB, filtering by interaction type and residue pKa. The gas phase cation–π interaction of lysine is the strongest by more than 10 kcal mol–1, but the empirical distribution of 582 X-ray structures lies away from the minimum on the interaction PES. In contrast, 1381 structures involving arginine match the underlying calculated PES with good agreement. SAPT analysis revealed that underlying differences in the balance of electrostatic and dispersion contributions are responsible for this behavior in the context of the protein environment. The lysine–arene interaction, dominated by electrostatics, is greatly weakened by a surrounding dielectric medium and causes it to become essentially negligible in strength and without a well-defined equilibrium separation. The arginine–arene interaction involves a near equal mix of dispersion and electrostatic attraction, which is weakened to a much smaller degree by the surrounding medium. Our results account for the paucity of cation–π interactions involving lysine, even though this is a more common residue than arginine. Aromatic ligands are most likely to interact with cationic arginine residues as this interaction is stronger than for lysine in higher polarity surroundings. PMID:29719674

  11. Stroke, tPA, and Physician Decision-Making

    MedlinePlus

    ... UIJT BSUJDMF JT QSPIJCJUFE Stroke, tPA, and physician decision-making Dominic Hovsepian and Steven Karceski Neurology 2013;81;e102-e105 DOI 10.1212/WNL.0b013e3182a94f3c This information is current as of September 23, 2013 Updated ...

  12. 75 FR 53325 - Proposed Scientific Integrity Policy of the Department of the Interior

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-31

    ... September 20, 2010. ADDRESSES: Send comments to: [email protected]ios.doi.gov . FOR FURTHER INFORMATION... scientific products, or on documents compiled and translated from scientific products, to ensure that agency... involving inventorying, monitoring, experimentation, study, research, modeling, and scientific assessment...

  13. Understanding the nanoscale local buckling behavior of vertically aligned MWCNT arrays with van der Waals interactions

    NASA Astrophysics Data System (ADS)

    Li, Yupeng; Kim, Hyung-Ick; Wei, Bingqing; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

    2015-08-01

    The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect.The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03581c

  14. Design study of a high-resolution breast-dedicated PET system built from cadmium zinc telluride detectors

    PubMed Central

    Peng, Hao; Levin, Craig S

    2013-01-01

    We studied the performance of a dual-panel positron emission tomography (PET) camera dedicated to breast cancer imaging using Monte Carlo simulation. The proposed system consists of two 4 cm thick 12 × 15 cm2 area cadmium zinc telluride (CZT) panels with adjustable separation, which can be put in close proximity to the breast and/or axillary nodes. Unique characteristics distinguishing the proposed system from previous efforts in breast-dedicated PET instrumentation are the deployment of CZT detectors with superior spatial and energy resolution, using a cross-strip electrode readout scheme to enable 3D positioning of individual photon interaction coordinates in the CZT, which includes directly measured photon depth-of-interaction (DOI), and arranging the detector slabs edge-on with respect to incoming 511 keV photons for high photon sensitivity. The simulation results show that the proposed CZT dual-panel PET system is able to achieve superior performance in terms of photon sensitivity, noise equivalent count rate, spatial resolution and lesion visualization. The proposed system is expected to achieve ~32% photon sensitivity for a point source at the center and a 4 cm panel separation. For a simplified breast phantom adjacent to heart and torso compartments, the peak noise equivalent count (NEC) rate is predicted to be ~94.2 kcts s−1 (breast volume: 720 cm3 and activity concentration: 3.7 kBq cm−3) for a ~10% energy window around 511 keV and ~8 ns coincidence time window. The system achieves 1 mm intrinsic spatial resolution anywhere between the two panels with a 4 cm panel separation if the detectors have DOI resolution less than 2 mm. For a 3 mm DOI resolution, the system exhibits excellent sphere resolution uniformity (σrms/mean) ≤ 10%) across a 4 cm width FOV. Simulation results indicate that the system exhibits superior hot sphere visualization and is expected to visualize 2 mm diameter spheres with a 5:1 activity concentration ratio within roughly 7 min imaging time. Furthermore, we observe that the degree of spatial resolution degradation along the direction orthogonal to the two panels that is typical of a limited angle tomography configuration is mitigated by having high-resolution DOI capabilities that enable more accurate positioning of oblique response lines. PMID:20400807

  15. Enhancing Geoscience Research Discovery Through the Semantic Web

    NASA Astrophysics Data System (ADS)

    Rowan, Linda R.; Gross, M. Benjamin; Mayernik, Matthew; Khan, Huda; Boler, Frances; Maull, Keith; Stott, Don; Williams, Steve; Corson-Rikert, Jon; Johns, Erica M.; Daniels, Michael; Krafft, Dean B.; Meertens, Charles

    2016-04-01

    UNAVCO, UCAR, and Cornell University are working together to leverage semantic web technologies to enable discovery of people, datasets, publications and other research products, as well as the connections between them. The EarthCollab project, a U.S. National Science Foundation EarthCube Building Block, is enhancing an existing open-source semantic web application, VIVO, to enhance connectivity across distributed networks of researchers and resources related to the following two geoscience-based communities: (1) the Bering Sea Project, an interdisciplinary field program whose data archive is hosted by NCAR's Earth Observing Laboratory (EOL), and (2) UNAVCO, a geodetic facility and consortium that supports diverse research projects informed by geodesy. People, publications, datasets and grant information have been mapped to an extended version of the VIVO-ISF ontology and ingested into VIVO's database. Much of the VIVO ontology was built for the life sciences, so we have added some components of existing geoscience-based ontologies and a few terms from a local ontology that we created. The UNAVCO VIVO instance, connect.unavco.org, utilizes persistent identifiers whenever possible; for example using ORCIDs for people, publication DOIs, data DOIs and unique NSF grant numbers. Data is ingested using a custom set of scripts that include the ability to perform basic automated and curated disambiguation. VIVO can display a page for every object ingested, including connections to other objects in the VIVO database. A dataset page, for example, includes the dataset type, time interval, DOI, related publications, and authors. The dataset type field provides a connection to all other datasets of the same type. The author's page shows, among other information, related datasets and co-authors. Information previously spread across several unconnected databases is now stored in a single location. In addition to VIVO's default display, the new database can be queried using SPARQL, a query language for semantic data. EarthCollab is extending the VIVO web application. One such extension is the ability to cross-link separate VIVO instances across institutions, allowing local display of externally curated information. For example, Cornell's VIVO faculty pages will display UNAVCO's dataset information and UNAVCO's VIVO will display Cornell faculty member contact and position information. About half of UNAVCO's membership is international and we hope to connect our data to institutions in other countries with a similar approach. Additional extensions, including enhanced geospatial capabilities, will be developed based on task-centered usability testing.

  16. An improved control mode for the ping-pong protocol operation in imperfect quantum channels

    NASA Astrophysics Data System (ADS)

    Zawadzki, Piotr

    2015-07-01

    Quantum direct communication (QDC) can bring confidentiality of sensitive information without any encryption. A ping-pong protocol, a well-known example of entanglement-based QDC, offers asymptotic security in a perfect quantum channel. However, it has been shown (Wójcik in Phys Rev Lett 90(15):157901, 2003. doi:10.1103/PhysRevLett.90.157901) that it is not secure in the presence of losses. Moreover, legitimate parities cannot rely on dense information coding due to possible undetectable eavesdropping even in the perfect setting (Pavičić in Phys Rev A 87(4):042326, 2013. doi:10.1103/PhysRevA.87.042326). We have identified the source of the above-mentioned weaknesses in the incomplete check of the EPR pair coherence. We propose an improved version of the control mode, and we discuss its relation to the already-known attacks that undermine the QDC security. It follows that the new control mode detects these attacks with high probability and independently on a quantum channel type. As a result, an asymptotic security of the QDC communication can be maintained for imperfect quantum channels, also in the regime of dense information coding.

  17. A trait database for marine copepods

    NASA Astrophysics Data System (ADS)

    Brun, Philipp; Payne, Mark R.; Kiørboe, Thomas

    2017-02-01

    The trait-based approach is gaining increasing popularity in marine plankton ecology but the field urgently needs more and easier accessible trait data to advance. We compiled trait information on marine pelagic copepods, a major group of zooplankton, from the published literature and from experts and organized the data into a structured database. We collected 9306 records for 14 functional traits. Particular attention was given to body size, feeding mode, egg size, spawning strategy, respiration rate, and myelination (presence of nerve sheathing). Most records were reported at the species level, but some phylogenetically conserved traits, such as myelination, were reported at higher taxonomic levels, allowing the entire diversity of around 10 800 recognized marine copepod species to be covered with a few records. Aside from myelination, data coverage was highest for spawning strategy and body size, while information was more limited for quantitative traits related to reproduction and physiology. The database may be used to investigate relationships between traits, to produce trait biogeographies, or to inform and validate trait-based marine ecosystem models. The data can be downloaded from PANGAEA, doi:10.1594/PANGAEA.862968.

  18. Toward Open Science at the European Scale: Geospatial Semantic Array Programming for Integrated Environmental Modelling

    NASA Astrophysics Data System (ADS)

    de Rigo, Daniele; Corti, Paolo; Caudullo, Giovanni; McInerney, Daniel; Di Leo, Margherita; San-Miguel-Ayanz, Jesús

    2013-04-01

    Interfacing science and policy raises challenging issues when large spatial-scale (regional, continental, global) environmental problems need transdisciplinary integration within a context of modelling complexity and multiple sources of uncertainty [1]. This is characteristic of science-based support for environmental policy at European scale [1], and key aspects have also long been investigated by European Commission transnational research [2-5]. Parameters ofthe neededdata- transformations ? = {?1????m} (a.5) Wide-scale transdisciplinary modelling for environment. Approaches (either of computational science or of policy-making) suitable at a given domain-specific scale may not be appropriate for wide-scale transdisciplinary modelling for environment (WSTMe) and corresponding policy-making [6-10]. In WSTMe, the characteristic heterogeneity of available spatial information (a) and complexity of the required data-transformation modelling (D- TM) appeal for a paradigm shift in how computational science supports such peculiarly extensive integration processes. In particular, emerging wide-scale integration requirements of typical currently available domain-specific modelling strategies may include increased robustness and scalability along with enhanced transparency and reproducibility [11-15]. This challenging shift toward open data [16] and reproducible research [11] (open science) is also strongly suggested by the potential - sometimes neglected - huge impact of cascading effects of errors [1,14,17-19] within the impressively growing interconnection among domain-specific computational models and frameworks. From a computational science perspective, transdisciplinary approaches to integrated natural resources modelling and management (INRMM) [20] can exploit advanced geospatial modelling techniques with an awesome battery of free scientific software [21,22] for generating new information and knowledge from the plethora of composite data [23-26]. From the perspective of the science-policy interface, INRMM should be able to provide citizens and policy-makers with a clear, accurate understanding of the implications of the technical apparatus on collective environmental decision-making [1]. Complexity of course should not be intended as an excuse for obscurity [27-29]. Geospatial Semantic Array Programming. Concise array-based mathematical formulation and implementation (with array programming tools, see (b) ) have proved helpful in supporting and mitigating the complexity of WSTMe [40-47] when complemented with generalized modularization and terse array-oriented semantic constraints. This defines the paradigm of Semantic Array Programming (SemAP) [35,36] where semantic transparency also implies free software use (although black-boxes [12] - e.g. legacy code - might easily be semantically interfaced). A new approach for WSTMe has emerged by formalizing unorganized best practices and experience-driven informal patterns. The approach introduces a lightweight (non-intrusive) integration of SemAP and geospatial tools (c) - called Geospatial Semantic Array Programming (GeoSemAP). GeoSemAP (d) exploits the joint semantics provided by SemAP and geospatial tools to split a complex D- TM into logical blocks which are easier to check by means of mathematical array-based and geospatial constraints. Those constraints take the form of precondition, invariant and postcondition semantic checks. This way, even complex WSTMe may be described as the composition of simpler GeoSemAP blocks, each of them structured as (d). GeoSemAP allows intermediate data and information layers to be more easily an formally semantically described so as to increase fault-tolerance [17], transparency and reproducibility of WSTMe. This might also help to better communicate part of the policy-relevant knowledge, often difficult to transfer from technical WSTMe to the science-policy interface [1,15]. References de Rigo, D., 2013. Behind the horizon of reproducible integrated environmental modelling at European scale: ethics and practice of scientific knowledge freedom. F1000 Research. To appear as discussion paper. Funtowicz, S. O., Ravetz, J. R., 1994. Uncertainty, complexity and post-normal science. Environmental Toxicology and Chemistry 13 (12), 1881-1885. http://dx.doi.org/10.1002/etc.5620131203 Funtowicz, S. O., Ravetz, J. R., 1994. The worth of a songbird: ecological economics as a post-normal science. Ecological Economics 10 (3), 197-207. http://dx.doi.org/10.1016/0921-8009(94)90108-2 Funtowicz, S. O., Ravetz, J. R., 2003. Funtowicz, S., Ravetz, J. (2003). Post-normal science. International Society for Ecological Economics, Internet Encyclopaedia of Ecological Economics Ravetz, J., 2004. The post-normal science of precaution. Futures 36 (3), 347-357. http://dx.doi.org/10.1016/S0016-3287(03)00160-5 van der Sluijs, J. P., 2012. Uncertainty and dissent in climate risk assessment: A Post-Normal perspective. Nature and Culture 7 (2), 174-195. http://dx.doi.org/10.3167/nc.2012.070204 Ulieru, M., Doursat, R., 2011. Emergent engineering: a radical paradigm shift. International Journal of Autonomous and Adaptive Communications Systems 4 (1), 39-60. http://dx.doi.org/10.1504/IJAACS.2011.037748 Turner, M. G., Dale, V. H., Gardner, R. H., Dec. 1989. Predicting across scales: Theory development and testing. Landscape Ecology 3 (3), 245-252. http://dx.doi.org/10.1007/BF00131542 Zhang, X., Drake, N. A., Wainwright, J., 2004. Scaling issues in environmental modelling. In: Wainwright, J., Mulligan, M. (Eds.), Environmental modelling : finding simplicity in complexity. Wiley. ISBN: 9780471496182 Bankes, S. C., 2002. Tools and techniques for developing policies for complex and uncertain systems. Proceedings of the National Academy of Sciences of the United States of America 99 (Suppl 3), 7263-7266. http://dx.doi.org/10.1073/pnas.092081399 Peng, R. D., 2011. Reproducible research in computational science. Science 334 (6060), 1226-1227. http://dx.doi.org/10.1126/science.1213847 Morin, A., Urban, J., Adams, P. D., Foster, I., Sali, A., Baker, D., Sliz, P., 2012. Shining light into black boxes. Science 336 (6078), 159-160. http://dx.doi.org/10.1126/science.1218263 Nature, 2011. Devil in the details. Nature 470 (7334), 305-306. http://dx.doi.org/10.1038/470305b Stodden, V., 2012. Reproducible research: Tools and strategies for scientific computing. Computing in Science and Engineering 14, 11-12. http://dx.doi.org/10.1109/MCSE.2012.82 de Rigo, D., Corti, P., Caudullo, G., McInerney, D., Di Leo, M., San-Miguel-Ayanz, J., (exp. 2013). Supporting Environmental Modelling and Science-Policy Interface at European Scale with Geospatial Semantic Array Programming. In prep. Molloy, J. C., 2011. The open knowledge foundation: Open data means better science. PLoS Biology 9 (12), e1001195+. http://dx.doi.org/10.1371/journal.pbio.1001195 de Rigo, D., 2013. Software Uncertainty in Integrated Environmental Modelling: the role of Semantics and Open Science. Geophysical Research Abstracts 15, EGU General Assembly 2013. Cerf, V. G., 2012. Where is the science in computer science? Commun. ACM 55 (10), 5. http://dx.doi.org/10.1145/2347736.2347737 Wilson, G., 2006. Where's the real bottleneck in scientific computing? American Scientist 94 (1), 5+. http://dx.doi.org/10.1511/2006.1.5 de Rigo, D. 2012. Integrated Natural Resources Modelling and Management: minimal redefinition of a known challenge for environmental modelling. Excerpt from the Call for a shared research agenda toward scientific knowledge freedom, Maieutike Research Initiative. http://www.citeulike.org/groupfunc/15400/home Stallman, R. M., 2005. Free community science and the free development of science. PLoS Med 2 (2), e47+. http://dx.doi.org/10.1371/journal.pmed.0020047 Stallman, R. M., 2009. Viewpoint: Why "open source" misses the point of free software. Communications of the ACM 52 (6), 31-33. http://dx.doi.org/10.1145/1516046.1516058 (free access version: http://www.gnu.org/philosophy/open-source-misses-the-point.html ) Rodriguez Aseretto, D., Di Leo, M., de Rigo, D., Corti, P., McInerney, D., Camia, A., San Miguel-Ayanz, J., 2013. Free and Open Source Software underpinning the European Forest Data Centre. Geophysical Research Abstracts 15, EGU General Assembly 2013. Giovando, C., Whitmore, C., Camia, A., San-Miguel-Ayanz, J., 2010. Enhancing the European Forest Fire Information System (EFFIS) with open source software. In: FOSS4G 2010. http://2010.foss4g.org/presentations_show.php?id=3693 Corti, P., San-Miguel-Ayanz, J., Camia, A., McInerney, D., Boca, R., Di Leo, M., 2012. Fire news management in the context of the European Forest Fire Information System (EFFIS). In: proceedings of "Quinta conferenza italiana sul software geografico e sui dati geografici liberi" (GFOSS DAY 2012). http://files.figshare.com/229492/Fire_news_management_in_the_context_of_EFFIS.pdf McInerney, D., Bastin, L., Diaz, L., Figueiredo, C., Barredo, J. I., San-Miguel-Ayanz, J., 2012. Developing a forest data portal to support Multi-Scale decision making. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 5 (6), 1-8. http://dx.doi.org/10.1109/JSTARS.2012.2194136 Morin, A., Urban, J., Adams, P. D., Foster, I., Sali, A., Baker, D., Sliz, P., (2012). Shining light into black boxes. Science 336 (6078), 159-160. http://dx.doi.org/10.1126/science.1218263 Stodden, V., 2011. Trust your science? Open your data and code. Amstat News July 2011, 21-22. http://www.stanford.edu/ vcs/papers/TrustYourScience-STODDEN.pdf van der Sluijs, J., 2005. Uncertainty as a monster in the science-policy interface: four coping strategies. Water Science & Technology 52 (6), 87-92. http://www.iwaponline.com/wst/05206/wst052060087.htm Iverson, K. E., 1980. Notation as a tool of thought. Communications of the ACM 23 (8), 444-465. http://awards.acm.org/images/awards/140/articles/9147499.pdf Eaton, J. W., Bateman, D., Hauberg, S., 2008. GNU Octave: a high-level interactive language for numerical computations. Network Theory. ISBN: 9780954612061 Eaton, J. W., 2012. GNU octave and reproducible research. Journal of Process Control 22 (8), 1433-1438. http://dx.doi.org/10.1016/j.jprocont.2012.04.006 R Development Core Team, 2011. The R reference manual. Network Theory Ltd. Vol. 1, ISBN: 978-1-906966-09-6. Vol. 2, ISBN: 978-1-906966-10-2. Vol. 3, ISBN: 978-1-906966-11-9. Vol. 4, ISBN: 978-1-906966-12-6. Ramey, C., Fox, B., 2006. Bash reference manual : reference documentation for Bash edition 2.5b, for Bash version 2.05b. Network Theory Limited. ISBN: 978-0-9541617-7-4. de Rigo, D., 2012. Semantic array programming for environmental modelling: Application of the mastrave library. In: Seppelt, R., Voinov, A. A., Lange, S., Bankamp, D. (Eds.), International Environmental Modelling and Software Society (iEMSs) 2012 International Congress on Environmental Modelling and Software. Managing Resources of a Limited Planet: Pathways and Visions under Uncertainty, Sixth Biennial Meeting. pp. 1167-1176. http://www.iemss.org/iemss2012/proceedings/D3_1_0715_deRigo.pdf de Rigo, D., 2012. Semantic Array Programming with Mastrave - Introduction to Semantic Computational Modelling. http://mastrave.org/doc/MTV-1.012-1.htm Van Rossum, G., Drake, F.J., 2011. Python Language Ref. Manual, Network Theory Ltd. ISBN: 0954161785. http://www.network-theory.co.uk/docs/pylang/ The Scipy community, 2012. NumPy Reference Guide. SciPy.org. http://docs.scipy.org/doc/numpy/reference/ The Scipy community, 2012. SciPy Reference Guide. SciPy.org. http://docs.scipy.org/doc/scipy/reference/ de Rigo, D., Castelletti, A., Rizzoli, A. E., Soncini-Sessa, R., Weber, E., Jul. 2005. A selective improvement technique for fastening neuro-dynamic programming in water resources network management. In: Zítek, P. (Ed.), Proceedings of the 16th IFAC World Congress. Vol. 16. International Federation of Automatic Control (IFAC), pp. 7-12. http://dx.doi.org/10.3182/20050703-6-CZ-1902.02172 de Rigo, D., Bosco, C., 2011. Architecture of a Pan-European Framework for Integrated Soil Water Erosion Assessment. Vol. 359 of IFIP Advances in Information and Communication Technology. Springer Boston, Berlin, Heidelberg, Ch. 34, pp. 310-318. http://dx.doi.org/10.1007/978-3-642-22285-6_34 San-Miguel-Ayanz, J., Schulte, E., Schmuck, G., Camia, A., Strobl, P., Liberta, G., Giovando, C., Boca, R., Sedano, F., Kempeneers, P., McInerney, D., Withmore, C., de Oliveira, S. S., Rodrigues, M., Durrant, T., Corti, P., Oehler, F., Vilar, L., Amatulli, G., Mar. 2012. Comprehensive monitoring of wildfires in Europe: The European Forest Fire Information System (EFFIS). In: Tiefenbacher, J. (Ed.), Approaches to Managing Disaster - Assessing Hazards, Emergencies and Disaster Impacts. InTech, Ch. 5. http://dx.doi.org/10.5772/28441 de Rigo, D., Caudullo, G., San-Miguel-Ayanz, J., Stancanelli, G., 2012. Mapping European forest tree species distribution to support pest risk assessment. In: Baker, R., Koch, F., Kriticos, D., Rafoss, T., Venette, R., van der Werf, W. (Eds.), Advancing risk assessment models for invasive alien species in the food chain: contending with climate change, economics and uncertainty. Bioforsk FOKUS 7. OECD Co-operative Research Programme on Biological Resource Management for Sustainable Agricultural Systems; Bioforsk - Norwegian Institute for Agricultural and Environmental Research. http://www.pestrisk.org/2012/BioforskFOKUS7-10_IPRMW-VI.pdf Estreguil, C., Caudullo, G., de Rigo, D., Whitmore, C., San-Miguel-Ayanz, J., 2012. Reporting on European forest fragmentation: Standardized indices and web map services. IEEE Earthzine. http://www.earthzine.org/2012/07/05/reporting-on-european-forest-fragmentation-standardized-indices-and-web-map-services/ Estreguil, C., de Rigo, D. and Caudullo, G. (exp. 2013). Towards an integrated and reproducible characterisation of habitat pattern. Submitted to Environmental Modelling & Software Amatulli, G., Camia, A., San-Miguel-Ayanz, J., 2009. Projecting future burnt area in the EU-mediterranean countries under IPCC SRES A2/B2 climate change scenarios (JRC55149), 33-38 de Rigo, D., Caudullo, G., Amatulli, G., Strobl, P., San-Miguel-Ayanz, J. (exp. 2013). Modelling tree species distribution in Europe with constrained spatial multi-frequency analysis. In prep. GRASS Development Team, 2012. Geographic Resources Analysis Support System (GRASS) Software. Open Source Geospatial Foundation. http://grass.osgeo.org http://www.spatial-ecology.net/dokuwiki/doku.php?id=wiki:firemod Neteler, M., Bowman, M. H., Landa, M., Metz, M., 2012. GRASS GIS: A multi-purpose open source GIS. Environmental Modelling & Software 31, 124-130. http://dx.doi.org/10.1016/j.envsoft.2011.11.014 Neteler, M., Mitasova, H., 2008. Open source GIS a GRASS GIS approach. ISBN: 978-0-387-35767-6 Warmerdam, F., 2008. The geospatial data abstraction library. In: Hall, G. B., Leahy, M. G. (Eds.), Open Source Approaches in Spatial Data Handling. Vol. 2 of Advances in Geographic Information Science. Springer Berlin Heidelberg, pp. 87-104. http://dx.doi.org/10.1007/978-3-540-74831-15 Open Geospatial Consortium, 2007. OpenGIS Web Processing Service version 1.0.0. No. OGC 05-007r7 in OpenGIS Standard. Open Geospatial Consortium (OGC). http://portal.opengeospatial.org/files/?artifact_id=24151 Hazzard, E., 2011. Openlayers 2.10 beginner's guide. Packt Publishing. ISBN: 1849514127 Obe, R., Hsu, L., 2011. PostGIS in Action. Manning Publications. http://dl.acm.org/citation.cfm?id=2018871 Sutton, T., 2009. Clipping data from postgis. linfiniti.com Open Source Geospatial Solutions. http://linfiniti.com/2009/09/clipping-data-from-postgis/

  19. Practices in NASA's EOSDIS to Promote Open Data and Research Integrity

    NASA Astrophysics Data System (ADS)

    Behnke, J.; Ramapriyan, H.

    2017-12-01

    The purpose of this paper is to highlight the key practices adopted by NASA in its Earth Observing System Data and Information System (EOSDIS) to promote and facilitate open data and research integrity. EOSDIS is the system that manages most of NASA's Earth science data from various sources - satellites, aircraft, field campaigns and some research projects. Since its inception in 1990 as a part of the Earth Observing System (EOS) Program, EOSDIS has been following NASA's free and open data and information policy, whereby data are shared with all users on a non-discriminatory basis and are provided at no cost. To ensure that the data are discoverable and accessible to the user community, NASA follows an evolutionary development approach, whereby the latest technologies that can be practically adopted are infused into EOSDIS. This results in continuous improvements in system capabilities such that technologies that users are accustomed to in other environments are brought to bear in their access to NASA's Earth observation data. Mechanisms have existed for ensuring that the data products offered by EOSDIS are vetted by the community before they are released. Information about data products such as Algorithm Theoretical Basis Documents and quality assessments are openly available with the products. The EOSDIS Distributed Active Archive Centers (DAACs) work with the science teams responsible for product generation to assist with proper use of metadata. The DAACs have knowledgeable staff to answer users' questions and have access to scientific experts as needed. Citation of data products in scientific papers are facilitated by assignment of Digital Object Identifiers (DOIs) - at present, over 50% of data products in EOSDIS have been assigned DOIs. NASA gathers and publishes citation metrics for the datasets offered by the DAACs. Through its Software and Services Citations Working Group, NASA is currently investigating broadening DOI assignments to promote greater provenance traceability. NASA has developed Preservation Content Specifications for Earth science data to ensure that provenance and context are captured and preserved for the future and is applying them to data and information from its missions. All these actions promote availability of information to promote integrity in scientific research.

  20. Tidal asymmetry in a funnel-shaped estuary with mixed semidiurnal tides

    NASA Astrophysics Data System (ADS)

    Gong, Wenping; Schuttelaars, Henk; Zhang, Heng

    2016-05-01

    Different types of tidal asymmetry (see review of de Swart and Zimmerman Annu Rev Fluid Mech 41: 203-229, 2009) are examined in this study. We distinguish three types of tidal asymmetry: duration and magnitude differences between flood and ebb tidal flow, duration difference between the rising and falling tides. For waterborne substance transport, the first two asymmetries are important while the last one is not. In this study, we take the Huangmaohai Estuary (HE), Pearl River Delta, China as an example to examine the spatio-temporal variations of the tidal asymmetry in a mixed semidiurnal tidal regime and to explain them by investigating the associated mechanisms. The methodology defining the tidal duration asymmetry and velocity skewness, proposed by Nidzieko (J Geophys Res 115: C08006. doi: 10.1029/2009JC005864 , 2010) and synthesized by Song et al. (J Geophys Res 116: C12007. doi: 10.1029/2011JC007270 , 2011), is utilized here and referred to as tidal duration asymmetry (TDA) and flow velocity asymmetry (FVA), respectively. The methodology is further used to quantify the flow duration asymmetry (FDA). A positive asymmetry means a shorter duration of low water slack for FDA, a shorter duration of the rising tide for TDA, and a flood dominance for FVA and vice versa. The Regional Ocean Modeling System (ROMS) model is used to provide relatively long-term water elevation and velocity data and to conduct diagnostic experiments. In the HE, the main tidal constituents are diurnal tides K 1, O 1 and semidiurnal tides M 2 and S 2. The interaction among the diurnal and semidiurnal tides generates a negative tidal asymmetry, while the interactions among semidiurnal tides and their overtides or compound tides result in a positive tidal asymmetry. The competition among the above interactions determines the FDA and TDA, whereas for the FVA, aside from the interaction among different tidal constituents, an extra component, the residual flow, plays an important role. The results show that the FDA exhibits a predominant tendency of shorter duration of low water slack, favoring the landward transport of fine sediment. The FVA demonstrates prevailing ebb dominance in the study period, favoring the seaward transport of coarse sediment. This ebb dominance is primarily induced by the interaction among the residual flow and the tidal constituents. The external TDA in the ocean experiences distinct cyclic variations with positive asymmetry when semidiurnal tides dominate and negative asymmetry during the periods when diurnal tides dominate. The funnel shape of the HE is advantageous for the development of positive tidal asymmetry as the semidiurnal tides are more amplified than the diurnal tides. The effect of river flow can enhance the ebb dominance, while the baroclinic effect is more complex. The existence of channel and shoals favors the development of residual pattern with seaward flow (ebb dominance) in the channel and landward flow (flood dominance) at the shoal when the tides are strong (semidiurnal tides dominate) and the residual pattern with landward flow (flood dominance) in the channel and seaward flow (ebb dominance) at the shoal when the baroclinic effect is dominant (diurnal tides dominate).

  1. CHERENCUBE: concept definition and implementation challenges of a Cherenkov-based detector block for PET.

    PubMed

    Somlai-Schweiger, I; Ziegler, S I

    2015-04-01

    A new concept for a depth-of-interaction (DOI) capable time-of-flight (TOF) PET detector is defined, based only on the detection of Cherenkov photons. The proposed "CHERENCUBE" consists of a cubic Cherenkov radiator with position-sensitive photodetectors covering each crystal face. By means of the spatial distribution of the detected photons and their time of arrival, the point of interaction of the gamma-ray in the crystal can be determined. This study analyzes through theoretical calculations and Monte Carlo simulations the potential advantages of the concept toward reaching a Cherenkov-only detector for TOF-PET with DOI capability. Furthermore, an algorithm for the DOI estimation is presented and the requirements for a practical implementation of the proposed concept are defined. The Monte Carlo simulations consisted of a cubic crystal with one photodetector coupled to each one of the faces of the cube. The sensitive area of the detector matched exactly the crystal size, which was varied in 1 mm steps between 1 × 1 × 1 mm(3) and 10 × 10 × 10 mm(3). For each size, five independent simulations of ten thousand 511 keV gamma-rays were triggered at a fixed distance of 10 mm. The crystal chosen was PbWO4. Its scintillation properties were simulated, but only Cherenkov photons were analyzed. Photodetectors were simulated having perfect photodetection efficiency and infinite time resolution. For every generated particle, the analysis considered its creation process, parent and daughter particles, energy, origin coordinates, trajectory, and time and position of detection. The DOI determination is based on the distribution of the emission time of all photons per event. These values are calculated as a function of the coordinates of detection and origin for every photon. The common origin is estimated by finding the distribution with the most similar emission time-points. Detection efficiency increases with crystal size from 8.2% (1 × 1 × 1 mm(3)) to 58.6% (10 × 10 × 10 mm(3)) and decreases applying a photon detection threshold of 5/10/20 photons to 6.3%/4.3%/0.7% and 49.3%/30.4%/2.8%, respectively. The detection rate in the six photodetectors is uniform due to the nearly isotropic cone emission. Most cones originated after a photoelectric effect interaction, with two dominating peaks for the kinetic energy of the electron at 422.99 and 441.47 keV. The detection distance between same-event photons defines the spatial resolution of the detector required for individual photon recognition, with 20% of the detected photons having their closest neighbor within a distance of 5% of the length of the cube. Same-event photons are detected within a time window whose width is determined by the crystal size, with values of 30 and 150 ps for a 1 × 1 × 1 mm(3) and a 10 × 10 × 10 mm(3) cube, respectively. The DOI reconstruction has an accuracy of approximately 23% of the length of the cube, with an average value of 2.2 mm for a 10 × 10 × 10 mm(3) CHERENCUBE. The proposed concept requires a detector with high photodetection efficiency. The structure of the sensitive surface of the detector should be a two dimensional array of microcells, able to provide individual detection coordinates and time stamps. The microcell size determines the ability to recognize individual photons, influencing detection efficiency. The 3D DOI recognition relies on the accuracy of the time stamps and detection coordinates, without the need for a recognition of the projected patterns of photons. The refractive index of the material defines a detector intrinsic energy-based rejection of scattered PET events at the cost of reduced sensitivity.

  2. CHERENCUBE: Concept definition and implementation challenges of a Cherenkov-based detector block for PET

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

    Somlai-Schweiger, I., E-mail: ian.somlai@tum.de; Ziegler, S. I.

    Purpose: A new concept for a depth-of-interaction (DOI) capable time-of-flight (TOF) PET detector is defined, based only on the detection of Cherenkov photons. The proposed “CHERENCUBE” consists of a cubic Cherenkov radiator with position-sensitive photodetectors covering each crystal face. By means of the spatial distribution of the detected photons and their time of arrival, the point of interaction of the gamma-ray in the crystal can be determined. This study analyzes through theoretical calculations and Monte Carlo simulations the potential advantages of the concept toward reaching a Cherenkov-only detector for TOF-PET with DOI capability. Furthermore, an algorithm for the DOI estimationmore » is presented and the requirements for a practical implementation of the proposed concept are defined. Methods: The Monte Carlo simulations consisted of a cubic crystal with one photodetector coupled to each one of the faces of the cube. The sensitive area of the detector matched exactly the crystal size, which was varied in 1 mm steps between 1 × 1 × 1 mm{sup 3} and 10 × 10 × 10 mm{sup 3}. For each size, five independent simulations of ten thousand 511 keV gamma-rays were triggered at a fixed distance of 10 mm. The crystal chosen was PbWO{sub 4}. Its scintillation properties were simulated, but only Cherenkov photons were analyzed. Photodetectors were simulated having perfect photodetection efficiency and infinite time resolution. For every generated particle, the analysis considered its creation process, parent and daughter particles, energy, origin coordinates, trajectory, and time and position of detection. The DOI determination is based on the distribution of the emission time of all photons per event. These values are calculated as a function of the coordinates of detection and origin for every photon. The common origin is estimated by finding the distribution with the most similar emission time-points. Results: Detection efficiency increases with crystal size from 8.2% (1 × 1 × 1 mm{sup 3}) to 58.6% (10 × 10 × 10 mm{sup 3}) and decreases applying a photon detection threshold of 5/10/20 photons to 6.3%/4.3%/0.7% and 49.3%/30.4%/2.8%, respectively. The detection rate in the six photodetectors is uniform due to the nearly isotropic cone emission. Most cones originated after a photoelectric effect interaction, with two dominating peaks for the kinetic energy of the electron at 422.99 and 441.47 keV. The detection distance between same-event photons defines the spatial resolution of the detector required for individual photon recognition, with 20% of the detected photons having their closest neighbor within a distance of 5% of the length of the cube. Same-event photons are detected within a time window whose width is determined by the crystal size, with values of 30 and 150 ps for a 1 × 1 × 1 mm{sup 3} and a 10 × 10 × 10 mm{sup 3} cube, respectively. The DOI reconstruction has an accuracy of approximately 23% of the length of the cube, with an average value of 2.2 mm for a 10 × 10 × 10 mm{sup 3} CHERENCUBE. Conclusions: The proposed concept requires a detector with high photodetection efficiency. The structure of the sensitive surface of the detector should be a two dimensional array of microcells, able to provide individual detection coordinates and time stamps. The microcell size determines the ability to recognize individual photons, influencing detection efficiency. The 3D DOI recognition relies on the accuracy of the time stamps and detection coordinates, without the need for a recognition of the projected patterns of photons. The refractive index of the material defines a detector intrinsic energy-based rejection of scattered PET events at the cost of reduced sensitivity.« less

  3. ACT-R/E: An Embodied Cognitive Architecture for Human-Robot Interaction

    DTIC Science & Technology

    2013-01-01

    Threaded Cognition: An Integrated Theory of Concurrent Multitasking . Psychological Review, 115(1), 101–130, http://dx.doi.org/10.1037/0033-295X...Trafton, Naval Research Laboratory, Washington, DC, USA Email : greg.trafton@nrl.navy.mil Laura Hiatt, Naval Research Laboratory, Washington, DC, USA Email ...laura.hiatt@nrl.navy.mil Anthony Harrison, Naval Research Laboratory, Washington, DC, USA Email : anthony.harrison@nrl.navy.mil Frank Tamborello, Naval

  4. Spin-Orbit Coupled Bose-Einstein Condensates

    DTIC Science & Technology

    2016-11-03

    generalized the new concepts to interacting spin-1/2 bosons in optical lattices and described a superfluid-to-Mott insulator transition in spin-orbit...and quantum phase transitions in topological insulators , Physical Review B, (09 2010): 0. doi: 10.1103/PhysRevB.82.115125 Christopher Varney, Kai...109.235308 J. Radi?, A. Di Ciolo, K. Sun, V. Galitski. Exotic Quantum Spin Models in Spin-Orbit-Coupled Mott Insulators , Physical Review Letters

  5. STS-87 Day 09 Highlights

    NASA Technical Reports Server (NTRS)

    1997-01-01

    On this ninth day of the STS-87 mission, the flight crew, Cmdr. Kevin R. Kregel, Pilot Steven W. Lindsey, Mission Specialists Winston E. Scott, Kalpana Chawla, and Takao Doi, and Payload Specialist Leonid K. Kadenyuk continue work with the microgravity science investigations in a special glovebox facility on the middeck. The autonomous operations with the mission's prime payload continue in the payload bay of Columbia with no interaction by the crew required.

  6. Novel Colloidal and Dynamic Interfacial Phenomena in Liquid Crystalline Systems

    DTIC Science & Technology

    2014-09-13

    Pablo. Effects of anchoring strength on the diffusivity of nanoparticles in model liquid-crystalline fluids, Soft Matter, (03 2011): 6828. doi...10.1021/la103975s Santanu Kumar Pal, Claribel Acevedo-Ve?lez, Jacob T. Hunter, Nicholas L. Abbott. Effects of Divalent Ligand Interactions on Surface...peer-reviewed journals: (c) Presentations 7 Presentation #1 (a) Electrical double layer and specific ion effects at interfaces between thermotropic

  7. Ultrafast Laser Interaction Processes for Libs and Other Sensing Technologies

    DTIC Science & Technology

    2013-04-05

    Wang. Propagation of ultrashort pulses through water, Optics Express, (02 2007): . doi: 12/02/2009 8.00 Z. Chen, S. Mao. Femtosecond laser -induced...Richardson, "Nd:YAG-CO2 double- pulse laser -induced breakdown spectroscopy for explosive residues detection" SPIE Defense, Security, Sensing; Orlando, FL... Ultrashort Pulse Laser Workshop, Directed Energy Professional Society; Newton, MA, USA; 06/29,2009. 63. Martin C. Richardson, Michael Sigman

  8. Ultrafast Laser Interaction Processes for LIBS and Other Sensing Technologies

    DTIC Science & Technology

    2013-04-05

    Propagation of ultrashort pulses through water, Optics Express, (02 2007): . doi: 12/02/2009 8.00 Z. Chen, S. Mao. Femtosecond laser -induced electronic...CO2 double- pulse laser -induced breakdown spectroscopy for explosive residues detection" SPIE Defense, Security, Sensing; Orlando, FL, USA; 04/07...Matthieu Baudelet, Michael Sigman, Paul J Dagdigian, Martin C. Richardson, "Nd:YAG-CO2 Double- Pulse Laser Induced Breakdown Spectroscopy for Explosive

  9. Eukaryotic translation initiation factor 3 plays distinct roles at the mRNA entry and exit channels of the ribosomal preinitiation complex

    PubMed Central

    Aitken, Colin Echeverría; Beznosková, Petra; Vlčkova, Vladislava; Chiu, Wen-Ling; Zhou, Fujun; Valášek, Leoš Shivaya; Hinnebusch, Alan G; Lorsch, Jon R

    2016-01-01

    Eukaryotic translation initiation factor 3 (eIF3) is a central player in recruitment of the pre-initiation complex (PIC) to mRNA. We probed the effects on mRNA recruitment of a library of S. cerevisiae eIF3 functional variants spanning its 5 essential subunits using an in vitro-reconstituted system. Mutations throughout eIF3 disrupt its interaction with the PIC and diminish its ability to accelerate recruitment to a native yeast mRNA. Alterations to the eIF3a CTD and eIF3b/i/g significantly slow mRNA recruitment, and mutations within eIF3b/i/g destabilize eIF2•GTP•Met-tRNAi binding to the PIC. Using model mRNAs lacking contacts with the 40S entry or exit channels, we uncovered a critical role for eIF3 requiring the eIF3a NTD, in stabilizing mRNA interactions at the exit channel, and an ancillary role at the entry channel requiring residues of the eIF3a CTD. These functions are redundant: defects at each channel can be rescued by filling the other channel with mRNA. DOI: http://dx.doi.org/10.7554/eLife.20934.001 PMID:27782884

  10. The nucleolar protein NIFK promotes cancer progression via CK1α/β-catenin in metastasis and Ki-67-dependent cell proliferation

    PubMed Central

    Lin, Tsung-Chieh; Su, Chia-Yi; Wu, Pei-Yu; Lai, Tsung-Ching; Pan, Wen-An; Jan, Yi-Hua; Chang, Yu-Chang; Yeh, Chi-Tai; Chen, Chi-Long; Ger, Luo-Ping; Chang, Hong-Tai; Yang, Chih-Jen; Huang, Ming-Shyan; Liu, Yu-Peng; Lin, Yuan-Feng; Shyy, John Y-J; Tsai, Ming-Daw; Hsiao, Michael

    2016-01-01

    Nucleolar protein interacting with the FHA domain of pKi-67 (NIFK) is a Ki-67-interacting protein. However, its precise function in cancer remains largely uninvestigated. Here we show the clinical significance and metastatic mechanism of NIFK in lung cancer. NIFK expression is clinically associated with poor prognosis and metastasis. Furthermore, NIFK enhances Ki-67-dependent proliferation, and promotes migration, invasion in vitro and metastasis in vivo via downregulation of casein kinase 1α (CK1α), a suppressor of pro-metastatic TCF4/β-catenin signaling. Inversely, CK1α is upregulated upon NIFK knockdown. The silencing of CK1α expression in NIFK-silenced cells restores TCF4/β-catenin transcriptional activity, cell migration, and metastasis. Furthermore, RUNX1 is identified as a transcription factor of CSNK1A1 (CK1α) that is negatively regulated by NIFK. Our results demonstrate the prognostic value of NIFK, and suggest that NIFK is required for lung cancer progression via the RUNX1-dependent CK1α repression, which activates TCF4/β-catenin signaling in metastasis and the Ki-67-dependent regulation in cell proliferation. DOI: http://dx.doi.org/10.7554/eLife.11288.001 PMID:26984280

  11. Aerosol patterns and aerosol-cloud-interactions off the West African Coast based on the A-train formation

    NASA Astrophysics Data System (ADS)

    Fuchs, Julia; Bendix, Jörg; Cermak, Jan

    2013-04-01

    In this study, spatial and temporal aerosol patterns off the Western African coast are characterized and related to cloud properties, based on satellite data Atmospheric aerosols play a key role in atmospheric processes and influence our environmental system in a complex way. Their identification, characterization, transport patterns as well as their interactions with clouds pose major challenges. Especially the last aspect reveals major uncertainties in terms of the Earth's radiation budget as reported in the IPCC's Fourth Assessment Report (IPCC, 2007). Western and Southern Africa are dominated by two well-known source types of atmospheric aerosols. First, the Saharan Desert is the world's largest aeolian dust emitting source region. Second, biomass burning aerosol is commonly transported off-shore further south (Kaufman et al., 2005). Both aerosol types influence Earth's climate in different manners and can be detected by the MODIS (MODerate resolution Imaging Spectrometer) sensor onboard the EOS platforms as they propagate to the Central and Southern Atlantic. The motivation of this study was to reveal the seasonal pattern of the Saharan dust transport based on an observation period of 11 years and trying to explain the meteorological mechanisms. North African dust plumes are transported along a latitude of 19°N in July and 6°N in January. The seasonally fluctuating intensities adapt to the annual cycle of wind and precipitation regimes. A strong relationship is found between the spatial shift of the Azores High and the Saharan dust load over the middle Atlantic Ocean. Monthly Aerosol Optical Thickness products of Terra MODIS and NCEP-DOE (National Centers for Environmental Predictions) Reanalysis II data are used for this purpose. The relationship between aerosol and cloud droplet parameters is blurred by high sensitivities to aerosol size and composition (Feingold, 2003; McFiggans et al., 2006) as well as meteorological context (Ackerman et al., 2004). Satellite data from the A-train formation, including the Aqua, CloudSat and CALIPSO (Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation) are used to analyze aerosol-cloud-interactions in detail, along with re-analysis data to constrain by meteorological conditions. Information about the vertical and geographical distribution of different aerosol types and cloud parameters will lead to a process-oriented understanding of these issues on a regional scale. Ackerman, A., Kirkpatrick, M., Stevens, D., & Toon, O. (2004). The impact of humidity above stratiform clouds on indirect aerosol climate forcing. Nature, 432(December), 1014-1017. doi:10.1038/nature03137.1. Feingold, G. (2003). First measurements of the Twomey indirect effect using ground-based remote sensors. Geophysical Research Letters, 30(6), 1287. doi:10.1029/2002GL016633 IPCC. (2007). Climate Change 2007: The Physical Science Basis. Contribution of Working group I to the Fourth Assessment Report of the Interfovernmental Panel on climate Change. Change [Solomon, S., D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt, M.Tignor and H.L. Miller (eds.)]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA. Kaufman, Y. J., Koren, I., Remer, L. A., Tanré, D., Ginoux, P., & Fan, S. (2005). Dust transport and deposition observed from the Terra-Moderate Resolution Imaging Spectroradiometer (MODIS) spacecraft over the Atlantic Ocean. Journal of Geophysical Research, 110(D10), 1-16. doi:10.1029/2003JD004436 McFiggans, G., Artaxo, P., Baltensperger, U., Coe, H., Facchini, M. C., Feingold, G., Fuzzi, S., et al. (2006). The effect of physical and chemical aerosol properties on warm cloud droplet activation. Atmospheric Chemistry and Physics, 6(9), 2593-2649. doi:10.5194/acp-6-2593-2006

  12. An edge-readout, multilayer detector for positron emission tomography.

    PubMed

    Li, Xin; Ruiz-Gonzalez, Maria; Furenlid, Lars R

    2018-06-01

    We present a novel gamma-ray-detector design based on total internal reflection (TIR) of scintillation photons within a crystal that addresses many limitations of traditional PET detectors. Our approach has appealing features, including submillimeter lateral resolution, DOI positioning from layer thickness, and excellent energy resolution. The design places light sensors on the edges of a stack of scintillator slabs separated by small air gaps and exploits the phenomenon that more than 80% of scintillation light emitted during a gamma-ray event reaches the edges of a thin crystal with polished faces due to TIR. Gamma-ray stopping power is achieved by stacking multiple layers, and DOI is determined by which layer the gamma ray interacts in. The concept of edge readouts of a thin slab was verified by Monte Carlo simulation of scintillation light transport. An LYSO crystal of dimensions 50.8 mm × 50.8 mm × 3.0 mm was modeled with five rectangular SiPMs placed along each edge face. The mean-detector-response functions (MDRFs) were calculated by simulating signals from 511 keV gamma-ray interactions in a grid of locations. Simulations were carried out to study the influence of choice of scintillator material and dimensions, gamma-ray photon energies, introduction of laser or mechanically induced optical barriers (LIOBs, MIOBs), and refractive indices of optical-coupling media and SiPM windows. We also analyzed timing performance including influence of gamma-ray interaction position and presence of optical barriers. We also modeled and built a prototype detector, a 27.4 mm × 27.4 mm × 3.0 mm CsI(Tl) crystal with 4 SiPMs per edge to experimentally validate the results predicted by the simulations. The prototype detector used CsI(Tl) crystals from Proteus outfitted with 16 Hamamatsu model S13360-6050PE MPPCs read out by an AiT-16-channel readout. The MDRFs were measured by scanning the detector with a collimated beam of 662-keV photons from a 137 Cs source. The spatial resolution was experimentally determined by imaging a tungsten slit that created a beam of 0.44 mm (FWHM) width normal to the detector surface. The energy resolution was evaluated by analyzing list-mode data from flood illumination by the 137 Cs source. We find that in a block-detector-sized LYSO layer read out by five SiPMs per edge, illuminated by 511-keV photons, the average resolution is 1.49 mm (FWHM). With the introduction of optical barriers, average spatial resolution improves to 0.56 mm (FWHM). The DOI resolution is the layer thickness of 3.0 mm. We also find that optical-coupling media and SiPM-window materials have an impact on spatial resolution. The timing simulation with LYSO crystal yields a coincidence resolving time (CRT) of 200-400 ps, which is slightly position dependent. And the introduction of optical barriers has minimum influence. The prototype CsI(Tl) detector, with a smaller area and fewer SiPMs, was measured to have central-area spatial resolutions of 0.70 and 0.39 mm without and with optical barriers, respectively. These results match well with our simulations. An energy resolution of 6.4% was achieved at 662 keV. A detector design based on a stack of monolithic scintillator layers that uses edge readouts offers several advantages over current block detectors for PET. For example, there is no tradeoff between spatial resolution and detection sensitivity since no reflector material displaces scintillator crystal, and submillimeter resolution can be achieved. DOI information is readily available, and excellent timing and energy resolutions are possible. © 2018 The Authors. Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

  13. DOIDB: Reusing DataCite's search software as metadata portal for GFZ Data Services

    NASA Astrophysics Data System (ADS)

    Elger, K.; Ulbricht, D.; Bertelmann, R.

    2016-12-01

    GFZ Data Services is the central service point for the publication of research data at the Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences (GFZ). It provides data publishing services to scientists of GFZ, associated projects, and associated institutions. The publishing services aim to make research data and physical samples visible and citable, by assigning persistent identifiers (DOI, IGSN) and by complementing existing IT infrastructure. To integrate several research domains a modular software stack that is made of free software components has been created to manage data and metadata as well as register persistent identifiers [1]. Pivotal component for the registration of DOIs is the DOIDB. It has been derived from three software components provided by DataCite [2] that moderate the registration of DOIs and the deposition of metadata, allow the dissemination of metadata, and provide a user interface to navigate and discover datasets. The DOIDB acts as a proxy to the DataCite infrastructure and in addition to the DataCite metadata schema, it allows to deposit and disseminate metadata following the schemas ISO19139 and NASA GCMD DIF. The search component has been modified to meet the requirements of a geosciences metadata portal. In particular, the search component has been altered to make use of Apache SOLRs capability to index and query spatial coordinates. Furthermore, the user interface has been adjusted to provide a first impression of the data by showing a map, summary information and subjects. DOIDB and its components are available on GitHub [3].We present a software solution for registration of DOIs that allows to integrate existing data systems, keeps track of registered DOIs, and provides a metadata portal to discover datasets [4]. [1] Ulbricht, D.; Elger, K.; Bertelmann, R.; Klump, J. panMetaDocs, eSciDoc, and DOIDB—An Infrastructure for the Curation and Publication of File-Based Datasets for GFZ Data Services. ISPRS Int. J. Geo-Inf. 2016, 5, 25. http://doi.org/10.3390/ijgi5030025[2] https://github.com/datacite[3] https://github.com/ulbricht/search/tree/doidb , https://github.com/ulbricht/mds/tree/doidb , https://github.com/ulbricht/oaip/tree/doidb[4] http://doidb.wdc-terra.org

  14. Metal alkyls programmed to generate metal alkylidenes by α-H abstraction: prognosis from NMR chemical shift† †Electronic supplementary information (ESI) available: Experimental and computational details, NMR spectra, results of NMR calculations and NCS analysis, graphical representation of shielding tensors, molecular orbital diagrams of selected compounds, optimized structures for all calculated species. See DOI: 10.1039/c7sc05039a

    PubMed Central

    Gordon, Christopher P.; Yamamoto, Keishi; Searles, Keith; Shirase, Satoru

    2018-01-01

    Metal alkylidenes, which are key organometallic intermediates in reactions such as olefination or alkene and alkane metathesis, are typically generated from metal dialkyl compounds [M](CH2R)2 that show distinctively deshielded chemical shifts for their α-carbons. Experimental solid-state NMR measurements combined with DFT/ZORA calculations and a chemical shift tensor analysis reveal that this remarkable deshielding originates from an empty metal d-orbital oriented in the M–Cα–Cα′ plane, interacting with the Cα p-orbital lying in the same plane. This π-type interaction inscribes some alkylidene character into Cα that favors alkylidene generation via α-H abstraction. The extent of the deshielding and the anisotropy of the alkyl chemical shift tensors distinguishes [M](CH2R)2 compounds that form alkylidenes from those that do not, relating the reactivity to molecular orbitals of the respective molecules. The α-carbon chemical shifts and tensor orientations thus predict the reactivity of metal alkyl compounds towards alkylidene generation. PMID:29675237

  15. New coordination features; a bridging pyridine and the forced shortest non-covalent distance between two CO3 2– species† †Electronic supplementary information (ESI) available: Mass Spectrometry and BVS analysis CCDC 996546–996548. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc02491e Click here for additional data file. Click here for additional data file.

    PubMed Central

    Velasco, V.; Aguilà, D.; Barrios, L. A.; Borilovic, I.; Roubeau, O.; Ribas-Ariño, J.; Fumanal, M.; Teat, S. J.

    2015-01-01

    The aerobic reaction of the multidentate ligand 2,6-bis-(3-oxo-3-(2-hydroxyphenyl)-propionyl)-pyridine, H4L, with Co(ii) salts in strong basic conditions produces the clusters [Co4(L)2(OH)(py)7]NO3 (1) and [Co8Na4(L)4(OH)2(CO3)2(py)10](BF4)2 (2). Analysis of their structure unveils unusual coordination features including a very rare bridging pyridine ligand or two trapped carbonate anions within one coordination cage, forced to stay at an extremely close distance (d O···O = 1.946 Å). This unprecedented non-bonding proximity represents a meeting point between long covalent interactions and “intermolecular” contacts. These original motifs have been analysed here through DFT calculations, which have yielded interaction energies and the reduced repulsion energy experimented by both CO3 2– anions when located in close proximity inside the coordination cage. PMID:28616127

  16. Anion dependent self-assembly of 56-metal Cd-Ln nanoclusters with enhanced near-infrared luminescence properties

    NASA Astrophysics Data System (ADS)

    Yang, Xiaoping; Schipper, Desmond; Zhang, Lijie; Yang, Keqin; Huang, Shaoming; Jiang, Jijun; Su, Chengyong; Jones, Richard A.

    2014-08-01

    Two series of Cd-Ln clusters: nano-drum [Ln8Cd24L12(OAc)48] and nano-double-drum [Ln12Cd44L20Cl30(OAc)54] (Ln = Nd and Yb) were prepared using a flexible Schiff base ligand bearing two aryl-Br groups. Chloride (Cl-) ions, together with the interactions of Br with other electronegative atoms, play a key role in the formation of the nano-double-drums. The structures were studied by TEM and photophysical properties were determined.Two series of Cd-Ln clusters: nano-drum [Ln8Cd24L12(OAc)48] and nano-double-drum [Ln12Cd44L20Cl30(OAc)54] (Ln = Nd and Yb) were prepared using a flexible Schiff base ligand bearing two aryl-Br groups. Chloride (Cl-) ions, together with the interactions of Br with other electronegative atoms, play a key role in the formation of the nano-double-drums. The structures were studied by TEM and photophysical properties were determined. Electronic supplementary information (ESI) available: Full experimental and characterization details for 1-4. CCDC 972369-972372. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4nr03075c

  17. 77 FR 21992 - Proposed Renewal of Information Collection: Applicant Background Survey

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-12

    ... Force representation for many mission critical occupations. The DOI Strategic Plan identifies the job.... Frequency of Response: One per job application. (2) Annual reporting and record keeping burden: Average reporting burden per application: 5 minutes. Total annual reporting: 1,119 hours. (3) Description of the...

  18. 75 FR 68814 - BOEMRE Information Collection Activity: 1010-0149, Platforms and Structures, Extension of a...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-09

    ... Interior; Bureau of Ocean Energy Management, Regulation and Enforcement; Attention: Cheryl Blundon; 381... special benefits. Under the Department of the Interior's (DOI) implementing policy, BOEMRE is required to charge fees for services that provide special benefits or privileges to an identifiable non-Federal...

  19. 43 CFR 17.332 - Mediation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Mediation. 17.332 Section 17.332 Public..., and Enforcement Procedures § 17.332 Mediation. (a) Referral of complaints for mediation. DOI will... participate in the mediation process to the extent necessary to reach an agreement or make an informed...

  20. Web Sites for Every Department Course

    ERIC Educational Resources Information Center

    Naveh, Gali; Tubin, Dorit; Pliskin, Nava

    2006-01-01

    Purpose: To study the implementation of a learning content management system (LCMS) at one department of a university in light of Rogers' diffusion of innovation (DOI) theory and in comparison to known critical success factors (CSFs) in implementation of information systems. Design/methodology/approach: A case study approach was used to examine…

  1. 25 CFR 900.2 - Purpose and scope.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Privacy Act. (f) Information collection. The Office of Management and Budget has approved, under 44 U.S.C... INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR, AND INDIAN HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN... contracts by the Department of Health and Human Services (DHHS) and the Department of the Interior (DOI) in...

  2. Unravelling the mechanisms of vibrational relaxation in solution† †All experimental data are archived in the University of Bristol's Research Data Storage Facility (DOI: 10.5523/bris.2vk036f35m5aq2dnlb79c0wcsh). ‡ ‡Electronic supplementary information (ESI) available: Further discussion of spectral lineshapes, concentration dependence of transient absorption data, theoretical calculations, IR-pump IR-probe spectra, transient absorption spectra including animation of spectra. See DOI: 10.1039/c6sc05234g Click here for additional data file. Click here for additional data file.

    PubMed Central

    Grubb, Michael P.; Coulter, Philip M.; Marroux, Hugo J. B.

    2017-01-01

    We present a systematic study of the mode-specific vibrational relaxation of NO2 in six weakly-interacting solvents (perfluorohexane, perfluoromethylcyclohexane, perfluorodecalin, carbon tetrachloride, chloroform, and d-chloroform), chosen to elucidate the dominant energy transfer mechanisms in the solution phase. Broadband transient vibrational absorption spectroscopy has allowed us to extract quantum state-resolved relaxation dynamics of the two distinct NO2 fragments produced from the 340 nm photolysis of N2O4 → NO2(X) + NO2(A) and their separate paths to thermal equilibrium. Distinct relaxation pathways are observed for the NO2 bending and stretching modes, even at energies as high as 7000 cm–1 above the potential minimum. Vibrational energy transfer is governed by different interaction mechanisms in the various solvent environments, and proceeds with timescales ranging from 20–1100 ps. NO2 relaxation rates in the perfluorocarbon solvents are identical despite differences in acceptor mode state densities, infrared absorption cross sections, and local solvent structure. Vibrational energy is shown to be transferred to non-vibrational solvent degrees of freedom (V-T) through impulsive collisions with the perfluorocarbon molecules. Conversely, NO2 relaxation in chlorinated solvents is reliant on vibrational resonances (V-V) while V-T energy transfer is inefficient and thermal excitation of the surrounding solvent molecules inhibits faster vibrational relaxation through direct complexation. Intramolecular vibrational redistribution allows the symmetric stretch of NO2 to act as a gateway for antisymmetric stretch energy to exit the molecule. This study establishes an unprecedented level of detail for the cooling dynamics of a solvated small molecule, and provides a benchmark system for future theoretical studies of vibrational relaxation processes in solution. PMID:28451375

  3. Isolation of 2-deoxy-scyllo-inosose (DOI)-assimilating yeasts and cloning and characterization of the DOI reductase gene of Cryptococcus podzolicus ND1.

    PubMed

    Ara, Satoshi; Yamazaki, Harutake; Takaku, Hiroaki

    2018-04-01

    2-Deoxy-scyllo-inosose (DOI) is the first intermediate in the 2-deoxystreptamine-containing aminoglycoside antibiotic biosynthesis pathway and has a six-membered carbocycle structure. DOI is a valuable material because it is easily converted to aromatic compounds and carbasugar derivatives. In this study, we isolated yeast strains capable of assimilating DOI as a carbon source. One of the strains, Cryptococcus podzolicus ND1, mainly converted DOI to scyllo-quercitol and (-)-vibo-quercitol, which is a valuable compound used as an antihypoglycemia agent and as a heat storage material. An NADH-dependent DOI reductase coding gene, DOIR, from C. podzolicus ND1 was cloned and successfully overexpressed in Escherichia coli. The purified protein catalyzed the irreversible reduction of DOI with NADH and converted DOI into (-)-vibo-quercitol. The enzyme had an optimal pH of 8.5 and optimal temperature of 35°C, respectively. The k cat of this enzyme was 9.98 s -1 , and the K m values for DOI and NADH were 4.38 and 0.24 mM, respectively. The enzyme showed a strong preference for NADH and showed no activity with NADPH. Multiple-alignment analysis of DOI reductase revealed that it belongs to the GFO_IDH_MocA protein family and is an inositol dehydrogenase homolog in other fungi, such as Cryptococcus gattii, and bacteria, such as Bacillus subtilis. This is the first identification of a DOI-assimilating yeast and a gene involved in DOI metabolism in fungi. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  4. Ground-Atmosphere Interactions at Gale: Determination of the Surface Energy Budget, Thermal Inertia and Water Sorption on the Regolith

    NASA Astrophysics Data System (ADS)

    Martinez, German; Renno, Nilton; Fischer, Erik; Borlina, Caue; Hallet, Bernard; De la Torre Juarez, Manuel; Vasavada, Aswhin; Gomez-Elvira, Javier

    2014-05-01

    The analysis of the Surface Energy Budget (SEB) yields insights into the local climate and the soil-atmosphere interactions, while the analysis of the thermal inertia of the shallow subsurface augments surface observations, providing information about the local geology. The Mars Global Surveyor Thermal Emission Spectrometer and the Mars Odyssey Thermal Emission Imaging System have measured near subsurface thermal inertia from orbit at scales of ~104 m2 to ~10 km2. Here we report analysis of the thermal inertia at a few locations at Gale Crater at scales of 100 m2. The thermal inertia is calculated by solving the heat conduction equation in the soil using hourly measurements by the Rover Environmental Station (REMS) ground temperature sensor as an upper boundary condition. Three Sols representative of different environmental conditions and soil properties, namely, Sol 82 at Rocknest (RCK), Sol 112 at Point Lake (PL) and Sol 139 at Yellowknife Bay (YKB) are analyzed in detail. The largest thermal inertia (I) value is found at YKB, I = 445 J m-2 K-1 s-1/2 or 445 tiu (thermal inertia unit), followed by PL with I= 300 tiu and RCK withI = 280 tiu [1]. These values are consistent with the type of terrain imaged by MastCam and with previous satellite estimates at Gale Crater [2,3]. The SEB is calculated by using all REMS data products as well as dust opacity values derived from MastCam measurements, whereas previously, the SEB has been calculated using numerical models only [4]. At each location and during the daytime, the SEB is dominated by the downwelling shortwave (SW) solar radiation (~450-500 W/m2) and the upwelling longwave (LW) radiation emitted by the surface (~300-400 W/m2). The sum of these two terms accounts for at least 70% of the net surface heating rate between 0900 and 1400 local solar time. At nighttime, the SEB is dominated by the upwelling LW radiation emitted by the surface (~50-100 W/m2) and the downwelling LW radiation from the atmosphere (~50 W/m2). When the wind speeds exceed 10 m/s at night, the turbulent heat flux can be as large as 25 W/m2, thus playing a secondary but significant role in the SEB. Finally, we estimate the amount of adsorbed water exchanged between the shallow subsurface and the atmosphere at diurnal time scales. We use subsurface temperature profiles, obtained by solving the heat conduction equation in the soil using the calculated value of I, and adsorption and desorption isotherms [5] to analyze critically the correlation between the soil wetness measured by the Dynamic Albedo of Neutrons instrument and the relative humidity measured by REMS. Acknowledgement: This research is supported by a grant from the Mars Science Laboratory and NASA Astrobiology Program Award #09-EXOB09-0050. References: [1] Martinez, G.M. et al. (2014), JGR (submitted). [2] Pelkey, S. M., and B. M. Jakosky (2002), doi:10.1006/icar.2002.6978. [3] Fergason, R., P. et al. (2012), doi:10.1007/s11214-012-9891-3. [4] Savijärvi, H., and A. Määttänen (2010), doi:10.1002/qj.650. [5] Pommerol, A. et al. (2009), doi:10.1016/j.icarus.2009.06.013.

  5. New Rodent Population Models May Inform Human Health Risk Assessment and Identification of Genetic Susceptibility to Environmental Exposures.

    PubMed

    Harrill, Alison H; McAllister, Kimberly A

    2017-08-15

    This paper provides an introduction for environmental health scientists to emerging population-based rodent resources. Mouse reference populations provide an opportunity to model environmental exposures and gene-environment interactions in human disease and to inform human health risk assessment. This review will describe several mouse populations for toxicity assessment, including older models such as the Mouse Diversity Panel (MDP), and newer models that include the Collaborative Cross (CC) and Diversity Outbred (DO) models. This review will outline the features of the MDP, CC, and DO mouse models and will discuss published case studies investigating the use of these mouse population resources in each step of the risk assessment paradigm. These unique resources have the potential to be powerful tools for generating hypotheses related to gene-environment interplay in human disease, performing controlled exposure studies to understand the differential responses in humans for susceptibility or resistance to environmental exposures, and identifying gene variants that influence sensitivity to toxicity and disease states. These new resources offer substantial advances to classical toxicity testing paradigms by including genetically sensitive individuals that may inform toxicity risks for sensitive subpopulations. Both in vivo and complementary in vitro resources provide platforms with which to reduce uncertainty by providing population-level data around biological variability. https://doi.org/10.1289/EHP1274.

  6. New Rodent Population Models May Inform Human Health Risk Assessment and Identification of Genetic Susceptibility to Environmental Exposures

    PubMed Central

    Harrill, Alison H.

    2017-01-01

    Background: This paper provides an introduction for environmental health scientists to emerging population-based rodent resources. Mouse reference populations provide an opportunity to model environmental exposures and gene–environment interactions in human disease and to inform human health risk assessment. Objectives: This review will describe several mouse populations for toxicity assessment, including older models such as the Mouse Diversity Panel (MDP), and newer models that include the Collaborative Cross (CC) and Diversity Outbred (DO) models. Methods: This review will outline the features of the MDP, CC, and DO mouse models and will discuss published case studies investigating the use of these mouse population resources in each step of the risk assessment paradigm. Discussion: These unique resources have the potential to be powerful tools for generating hypotheses related to gene–environment interplay in human disease, performing controlled exposure studies to understand the differential responses in humans for susceptibility or resistance to environmental exposures, and identifying gene variants that influence sensitivity to toxicity and disease states. Conclusions: These new resources offer substantial advances to classical toxicity testing paradigms by including genetically sensitive individuals that may inform toxicity risks for sensitive subpopulations. Both in vivo and complementary in vitro resources provide platforms with which to reduce uncertainty by providing population-level data around biological variability. https://doi.org/10.1289/EHP1274 PMID:28886592

  7. Finding the target sites of RNA-binding proteins

    PubMed Central

    Li, Xiao; Kazan, Hilal; Lipshitz, Howard D; Morris, Quaid D

    2014-01-01

    RNA–protein interactions differ from DNA–protein interactions because of the central role of RNA secondary structure. Some RNA-binding domains (RBDs) recognize their target sites mainly by their shape and geometry and others are sequence-specific but are sensitive to secondary structure context. A number of small- and large-scale experimental approaches have been developed to measure RNAs associated in vitro and in vivo with RNA-binding proteins (RBPs). Generalizing outside of the experimental conditions tested by these assays requires computational motif finding. Often RBP motif finding is done by adapting DNA motif finding methods; but modeling secondary structure context leads to better recovery of RBP-binding preferences. Genome-wide assessment of mRNA secondary structure has recently become possible, but these data must be combined with computational predictions of secondary structure before they add value in predicting in vivo binding. There are two main approaches to incorporating structural information into motif models: supplementing primary sequence motif models with preferred secondary structure contexts (e.g., MEMERIS and RNAcontext) and directly modeling secondary structure recognized by the RBP using stochastic context-free grammars (e.g., CMfinder and RNApromo). The former better reconstruct known binding preferences for sequence-specific RBPs but are not suitable for modeling RBPs that recognize shape and geometry of RNAs. Future work in RBP motif finding should incorporate interactions between multiple RBDs and multiple RBPs in binding to RNA. WIREs RNA 2014, 5:111–130. doi: 10.1002/wrna.1201 PMID:24217996

  8. Interaction between single gold atom and the graphene edge: A study via aberration-corrected transmission electron microscopy

    NASA Astrophysics Data System (ADS)

    Wang, Hongtao; Li, Kun; Cheng, Yingchun; Wang, Qingxiao; Yao, Yingbang; Schwingenschlögl, Udo; Zhang, Xixiang; Yang, Wei

    2012-04-01

    Interaction between single noble metal atoms and graphene edges has been investigated via aberration-corrected and monochromated transmission electron microscopy. A collective motion of the Au atom and the nearby carbon atoms is observed in transition between energy-favorable configurations. Most trapping and detrapping processes are assisted by the dangling carbon atoms, which are more susceptible to knock-on displacements by electron irradiation. Thermal energy is lower than the activation barriers in transition among different energy-favorable configurations, which suggests electron-beam irradiation can be an efficient way of engineering the graphene edge with metal atoms.Interaction between single noble metal atoms and graphene edges has been investigated via aberration-corrected and monochromated transmission electron microscopy. A collective motion of the Au atom and the nearby carbon atoms is observed in transition between energy-favorable configurations. Most trapping and detrapping processes are assisted by the dangling carbon atoms, which are more susceptible to knock-on displacements by electron irradiation. Thermal energy is lower than the activation barriers in transition among different energy-favorable configurations, which suggests electron-beam irradiation can be an efficient way of engineering the graphene edge with metal atoms. Electronic supplementary information (ESI) available: Additional Figures for characterization of mono-layer CVD graphene samples with free edges and Pt atoms decorations and analysis of the effect of electron irradiation; supporting movie on edge evolution. See DOI: 10.1039/c2nr00059h

  9. Regulation of Serotonin-Induced Trafficking and Migration of Eosinophils

    PubMed Central

    Kang, Bit Na; Ha, Sung Gil; Bahaie, Nooshin S.; Hosseinkhani, M. Reza; Ge, Xiao Na; Blumenthal, Malcolm N.; Rao, Savita P.; Sriramarao, P.

    2013-01-01

    Association of the neurotransmitter serotonin (5-HT) with the pathogenesis of allergic asthma is well recognized and its role as a chemoattractant for eosinophils (Eos) in vitro and in vivo has been previously demonstrated. Here we have examined the regulation of 5-HT-induced human and murine Eos trafficking and migration at a cellular and molecular level. Eos from allergic donors and bone marrow-derived murine Eos (BM-Eos) were found to predominantly express the 5-HT2A receptor. Exposure to 5-HT or 2,5-dimethoxy-4-iodoamphetamine (DOI), a 5-HT2A/C selective agonist, induced rolling of human Eos and AML14.3D10 human Eos-like cells on vascular cell adhesion molecule (VCAM)-1 under conditions of flow in vitro coupled with distinct cytoskeletal and cell shape changes as well as phosphorylation of MAPK. Blockade of 5-HT2A or of ROCK MAPK, PI3K, PKC and calmodulin, but not Gαi-proteins, with specific inhibitors inhibited DOI-induced rolling, actin polymerization and changes in morphology of VCAM-1-adherent AML14.3D10 cells. More extensive studies with murine BM-Eos demonstrated the role of 5-HT in promoting rolling in vivo within inflamed post-capillary venules of the mouse cremaster microcirculation and confirmed that down-stream signaling of 5-HT2A activation involves ROCK, MAPK, PI3K, PKC and calmodulin similar to AML14.3D10 cells. DOI-induced migration of BM-Eos is also dependent on these signaling molecules and requires Ca2+. Further, activation of 5-HT2A with DOI led to an increase in intracellular Ca2+ levels in murine BM-Eos. Overall, these data demonstrate that 5-HT (or DOI)/5-HT2A interaction regulates Eos trafficking and migration by promoting actin polymerization associated with changes in cell shape/morphology that favor cellular trafficking and recruitment via activation of specific intracellular signaling molecules (ROCK, MAPK, PI3K and the PKC-calmodulin pathway). PMID:23372779

  10. The effect of plasma inhomogeneities on (i) radio emission generation by non-gyrotropic electron beams and (ii) particle acceleration by Langmuir waves

    NASA Astrophysics Data System (ADS)

    Tsiklauri, David

    2015-04-01

    Extensive particle-in-cell simulations of fast electron beams injected in a background magnetised plasma with a decreasing density profile were carried out. These simulations were intended to further shed light on a newly proposed mechanism for the generation of electromagnetic waves in type III solar radio bursts [1]. Here recent progress in an alternative to the plasma emission model using Particle-In-Cell, self-consistent electromagnetic wave emission simulations of solar type III radio bursts will be presented. In particular, (i) Fourier space drift (refraction) of non-gyrotropic electron beam-generated wave packets, caused by the density gradient [1,2], (ii) parameter space investigation of numerical runs [3], (iii) concurrent generation of whistler waves [4] and a separate problem of (iv) electron acceleration by Langmuir waves in a background magnetised plasma with an increasing density profile [5] will be discussed. In all considered cases the density inhomogeneity-induced wave refraction plays a crucial role. In the case of non-gyrotropic electron beam, the wave refraction transforms the generated wave packets from standing into freely escaping EM radiation. In the case of electron acceleration by Langmuir waves, a positive density gradient in the direction of wave propagation causes a decrease in the wavenumber, and hence a higher phase velocity vph = ω/k. The k-shifted wave is then subject to absorption by a faster electron by wave-particle interaction. The overall effect is an increased number of high energy electrons in the energy spectrum. [1] D. Tsiklauri, Phys. Plasmas 18, 052903 (2011); http://dx.doi.org/10.1063/1.3590928 [2] H. Schmitz, D. Tsiklauri, Phys. Plasmas 20, 062903 (2013); http://dx.doi.org/10.1063/1.4812453 [3] R. Pechhacker, D. Tsiklauri, Phys. Plasmas 19, 112903 (2012); http://dx.doi.org/10.1063/1.4768429 [4] M. Skender, D. Tsiklauri, Phys. Plasmas 21, 042904 (2014); http://dx.doi.org/10.1063/1.4871723 [5] R. Pechhacker, D. Tsiklauri, Phys. Plasmas 21, 012903 (2014); http://dx.doi.org/10.1063/1.4863494 This research is funded by the Leverhulme Trust Research Project Grant RPG-311

  11. Improvement of crystal identification performance for a four-layer DOI detector composed of crystals segmented by laser processing

    NASA Astrophysics Data System (ADS)

    Mohammadi, Akram; Inadama, Naoko; Yoshida, Eiji; Nishikido, Fumihiko; Shimizu, Keiji; Yamaya, Taiga

    2017-09-01

    We have developed a four-layer depth of interaction (DOI) detector with single-side photon readout, in which segmented crystals with the patterned reflector insertion are separately identified by the Anger-type calculation. Optical conditions between segmented crystals, where there is no reflector, affect crystal identification ability. Our objective of this work was to improve crystal identification performance of the four-layer DOI detector that uses crystals segmented with a recently developed laser processing technique to include laser processed boundaries (LPBs). The detector consisted of 2 × 2 × 4mm3 LYSO crystals and a 4 × 4 array multianode photomultiplier tube (PMT) with 4.5 mm anode pitch. The 2D position map of the detector was calculated by the Anger calculation method. At first, influence of optical condition on crystal identification was evaluated for a one-layer detector consisting of a 2 × 2 crystal array with three different optical conditions between the crystals: crystals stuck together using room temperature vulcanized (RTV) rubber, crystals with air coupling and segmented crystals with LPBs. The crystal array with LPBs gave the shortest distance between crystal responses in the 2D position map compared with the crystal array coupled with RTV rubber or air due to the great amount of cross-talk between segmented crystals with LPBs. These results were used to find optical conditions offering the optimum distance between crystal responses in the 2D position map for the four-layer DOI detector. Crystal identification performance for the four-layer DOI detector consisting of an 8 × 8 array of crystals segmented with LPBs was examined and it was not acceptable for the crystals in the first layer. The crystal identification was improved for the first layer by changing the optical conditions between all 2 × 2 crystal arrays of the first layer to RTV coupling. More improvement was observed by combining different optical conditions between all crystals of the first layer and some crystals of the second and the third layers of the segmented array.

  12. A hybrid parallel architecture for electrostatic interactions in the simulation of dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Yang, Sheng-Chun; Lu, Zhong-Yuan; Qian, Hu-Jun; Wang, Yong-Lei; Han, Jie-Ping

    2017-11-01

    In this work, we upgraded the electrostatic interaction method of CU-ENUF (Yang, et al., 2016) which first applied CUNFFT (nonequispaced Fourier transforms based on CUDA) to the reciprocal-space electrostatic computation and made the computation of electrostatic interaction done thoroughly in GPU. The upgraded edition of CU-ENUF runs concurrently in a hybrid parallel way that enables the computation parallelizing on multiple computer nodes firstly, then further on the installed GPU in each computer. By this parallel strategy, the size of simulation system will be never restricted to the throughput of a single CPU or GPU. The most critical technical problem is how to parallelize a CUNFFT in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Furthermore, the upgraded method is capable of computing electrostatic interactions for both the atomistic molecular dynamics (MD) and the dissipative particle dynamics (DPD). Finally, the benchmarks conducted for validation and performance indicate that the upgraded method is able to not only present a good precision when setting suitable parameters, but also give an efficient way to compute electrostatic interactions for huge simulation systems. Program Files doi:http://dx.doi.org/10.17632/zncf24fhpv.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: C, C++, and CUDA C Supplementary material: The program is designed for effective electrostatic interactions of large-scale simulation systems, which runs on particular computers equipped with NVIDIA GPUs. It has been tested on (a) single computer node with Intel(R) Core(TM) i7-3770@ 3.40 GHz (CPU) and GTX 980 Ti (GPU), and (b) MPI parallel computer nodes with the same configurations. Nature of problem: For molecular dynamics simulation, the electrostatic interaction is the most time-consuming computation because of its long-range feature and slow convergence in simulation space, which approximately take up most of the total simulation time. Although the parallel method CU-ENUF (Yang et al., 2016) based on GPU has achieved a qualitative leap compared with previous methods in electrostatic interactions computation, the computation capability is limited to the throughput capacity of a single GPU for super-scale simulation system. Therefore, we should look for an effective method to handle the calculation of electrostatic interactions efficiently for a simulation system with super-scale size. Solution method: We constructed a hybrid parallel architecture, in which CPU and GPU are combined to accelerate the electrostatic computation effectively. Firstly, the simulation system is divided into many subtasks via domain-decomposition method. Then MPI (Message Passing Interface) is used to implement the CPU-parallel computation with each computer node corresponding to a particular subtask, and furthermore each subtask in one computer node will be executed in GPU in parallel efficiently. In this hybrid parallel method, the most critical technical problem is how to parallelize a CUNFFT (nonequispaced fast Fourier transform based on CUDA) in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Restrictions: The HP-ENUF is mainly oriented to super-scale system simulations, in which the performance superiority is shown adequately. However, for a small simulation system containing less than 106 particles, the mode of multiple computer nodes has no apparent efficiency advantage or even lower efficiency due to the serious network delay among computer nodes, than the mode of single computer node. References: (1) S.-C. Yang, H.-J. Qian, Z.-Y. Lu, Appl. Comput. Harmon. Anal. 2016, http://dx.doi.org/10.1016/j.acha.2016.04.009. (2) S.-C. Yang, Y.-L. Wang, G.-S. Jiao, H.-J. Qian, Z.-Y. Lu, J. Comput. Chem. 37 (2016) 378. (3) S.-C. Yang, Y.-L. Zhu, H.-J. Qian, Z.-Y. Lu, Appl. Chem. Res. Chin. Univ., 2017, http://dx.doi.org/10.1007/s40242-016-6354-5. (4) Y.-L. Zhu, H. Liu, Z.-W. Li, H.-J. Qian, G. Milano, Z.-Y. Lu, J. Comput. Chem. 34 (2013) 2197.

  13. First Human Brain Imaging by the jPET-D4 Prototype With a Pre-Computed System Matrix

    NASA Astrophysics Data System (ADS)

    Yamaya, Taiga; Yoshida, Eiji; Obi, Takashi; Ito, Hiroshi; Yoshikawa, Kyosan; Murayama, Hideo

    2008-10-01

    The jPET-D4 is a novel brain PET scanner which aims to achieve not only high spatial resolution but also high scanner sensitivity by using 4-layer depth-of-interaction (DOI) information. The dimensions of a system matrix for the jPET-D4 are 3.3 billion (lines-of-response) times 5 million (image elements) when a standard field-of-view (FOV) of 25 cm diameter is sampled with a (1.5 mm)3 voxel . The size of the system matrix is estimated as 117 petabytes (PB) with the accuracy of 8 bytes per element. An on-the-fly calculation is usually used to deal with such a huge system matrix. However we cannot avoid extension of the calculation time when we improve the accuracy of system modeling. In this work, we implemented an alternative approach based on pre-calculation of the system matrix. A histogram-based 3D OS-EM algorithm was implemented on a desktop workstation with 32 GB memory installed. The 117 PB system matrix was compressed under the limited amount of computer memory by (1) eliminating zero elements, (2) applying the DOI compression (DOIC) method and (3) applying rotational symmetry and an axial shift property of the crystal arrangement. Spanning, which degrades axial resolution, was not applied. The system modeling and the DOIC method, which had been validated in 2D image reconstruction, were expanded into 3D implementation. In particular, a new system model including the DOIC transformation was introduced to suppress resolution loss caused by the DOIC method. Experimental results showed that the jPET-D4 has almost uniform spatial resolution of better than 3 mm over the FOV. Finally the first human brain images were obtained with the jPET-D4.

  14. New scaling relation for information transfer in biological networks

    PubMed Central

    Kim, Hyunju; Davies, Paul; Walker, Sara Imari

    2015-01-01

    We quantify characteristics of the informational architecture of two representative biological networks: the Boolean network model for the cell-cycle regulatory network of the fission yeast Schizosaccharomyces pombe (Davidich et al. 2008 PLoS ONE 3, e1672 (doi:10.1371/journal.pone.0001672)) and that of the budding yeast Saccharomyces cerevisiae (Li et al. 2004 Proc. Natl Acad. Sci. USA 101, 4781–4786 (doi:10.1073/pnas.0305937101)). We compare our results for these biological networks with the same analysis performed on ensembles of two different types of random networks: Erdös–Rényi and scale-free. We show that both biological networks share features in common that are not shared by either random network ensemble. In particular, the biological networks in our study process more information than the random networks on average. Both biological networks also exhibit a scaling relation in information transferred between nodes that distinguishes them from random, where the biological networks stand out as distinct even when compared with random networks that share important topological properties, such as degree distribution, with the biological network. We show that the most biologically distinct regime of this scaling relation is associated with a subset of control nodes that regulate the dynamics and function of each respective biological network. Information processing in biological networks is therefore interpreted as an emergent property of topology (causal structure) and dynamics (function). Our results demonstrate quantitatively how the informational architecture of biologically evolved networks can distinguish them from other classes of network architecture that do not share the same informational properties. PMID:26701883

  15. Lorentz microscopy sheds light on the role of dipolar interactions in magnetic hyperthermia

    NASA Astrophysics Data System (ADS)

    Campanini, M.; Ciprian, R.; Bedogni, E.; Mega, A.; Chiesi, V.; Casoli, F.; de Julián Fernández, C.; Rotunno, E.; Rossi, F.; Secchi, A.; Bigi, F.; Salviati, G.; Magén, C.; Grillo, V.; Albertini, F.

    2015-04-01

    Monodispersed Fe3O4 nanoparticles with comparable size distributions have been synthesized by two different synthesis routes, co-precipitation and thermal decomposition. Thanks to the different steric stabilizations, the described samples can be considered as a model system to investigate the effects of magnetic dipolar interactions on the aggregation states of the nanoparticles. Moreover, the presence of magnetic dipolar interactions can strongly affect the nanoparticle efficiency as a hyperthermic mediator. In this paper, we present a novel way to visualize and map the magnetic dipolar interactions in different kinds of nanoparticle aggregates by the use of Lorentz microscopy, an easy and reliable in-line electron holographic technique. By exploiting Lorentz microscopy, which is complementary to the magnetic measurements, it is possible to correlate the interaction degrees of magnetic nanoparticles with their magnetic behaviors. In particular, we demonstrate that Lorentz microscopy is successful in visualizing the magnetic configurations stabilized by dipolar interactions, thus paving the way to the comprehension of the power loss mechanisms for different nanoparticle aggregates.Monodispersed Fe3O4 nanoparticles with comparable size distributions have been synthesized by two different synthesis routes, co-precipitation and thermal decomposition. Thanks to the different steric stabilizations, the described samples can be considered as a model system to investigate the effects of magnetic dipolar interactions on the aggregation states of the nanoparticles. Moreover, the presence of magnetic dipolar interactions can strongly affect the nanoparticle efficiency as a hyperthermic mediator. In this paper, we present a novel way to visualize and map the magnetic dipolar interactions in different kinds of nanoparticle aggregates by the use of Lorentz microscopy, an easy and reliable in-line electron holographic technique. By exploiting Lorentz microscopy, which is complementary to the magnetic measurements, it is possible to correlate the interaction degrees of magnetic nanoparticles with their magnetic behaviors. In particular, we demonstrate that Lorentz microscopy is successful in visualizing the magnetic configurations stabilized by dipolar interactions, thus paving the way to the comprehension of the power loss mechanisms for different nanoparticle aggregates. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00273g

  16. Magic informationally complete POVMs with permutations

    NASA Astrophysics Data System (ADS)

    Planat, Michel; Gedik, Zafer

    2017-09-01

    Eigenstates of permutation gates are either stabilizer states (for gates in the Pauli group) or magic states, thus allowing universal quantum computation (Planat, Rukhsan-Ul-Haq 2017 Adv. Math. Phys. 2017, 5287862 (doi:10.1155/2017/5287862)). We show in this paper that a subset of such magic states, when acting on the generalized Pauli group, define (asymmetric) informationally complete POVMs. Such informationally complete POVMs, investigated in dimensions 2-12, exhibit simple finite geometries in their projector products and, for dimensions 4 and 8 and 9, relate to two-qubit, three-qubit and two-qutrit contextuality.

  17. Water resources of Calcasieu Parish, Louisiana

    USGS Publications Warehouse

    White, Vincent E.; Prakken, Lawrence B.

    2017-01-12

    Information concerning the availability, use, and quality of water in Calcasieu Parish, Louisiana, is critical for proper water-resource management. The purpose of this fact sheet is to present information that can be used by water managers, parish residents, and others for stewardship of this vital resource. Information on the availability, past and current use, use trends, and water quality from groundwater and surface-water sources in the parish is presented. Previously published reports and data stored in the U.S. Geological Survey’s National Water Information System (http://dx.doi.org/10.5066/F7P55KJN) are the primary sources of the information presented here.

  18. Reliability beyond Theory and into Practice

    ERIC Educational Resources Information Center

    Sijtsma, Klaas

    2009-01-01

    The critical reactions of Bentler (2009, doi: 10.1007/s11336-008-9100-1), Green and Yang (2009a, doi: 10.1007/s11336-008-9098-4 ; 2009b, doi: 10.1007/s11336-008-9099-3), and Revelle and Zinbarg (2009, doi: 10.1007/s11336-008-9102-z) to Sijtsma's (2009, doi: 10.1007/s11336-008-9101-0) paper on Cronbach's alpha are addressed. The dissemination of…

  19. Link-Prediction Enhanced Consensus Clustering for Complex Networks (Open Access)

    DTIC Science & Technology

    2016-05-20

    92:022816. Available from: http://link.aps.org/doi/10.1103/PhysRevE.92.022816. doi: 10. 1103 /PhysRevE.92.022816 16. Aldecoa R, Marín I. Exploring the...from: http://link.aps.org/doi/10.1103/PhysRevE.80.056117. doi: 10. 1103 /PhysRevE.80.056117 18. Dahlin J, Svenson P. Ensemble approaches for improving...046110. Available from: http://link.aps.org/doi/10.1103/PhysRevE.81.046110. doi: 10. 1103 /PhysRevE.81.046110 28. Gfeller D, Chappelier JC, De Los Rios P

  20. It takes two to tango to the melanosome

    PubMed Central

    Lakkaraju, Aparna; Carvajal-Gonzalez, Jose Maria

    2009-01-01

    The role of clathrin adaptor proteins in sorting cargo in the biosynthetic and recycling routes is an area of intense research. In this issue, Delevoye et al. (2009. J. Cell Biol. doi:10.1083/jcb.200907122) show that a close interaction between the clathrin adaptor AP-1 and a kinesin motor KIF13A is essential for delivering melanogenic enzymes from recycling endosomes to nascent melanosomes and for organelle biogenesis. PMID:19841135

  1. A hierarchical, retinotopic proto-organization of the primate visual system at birth

    PubMed Central

    Arcaro, Michael J; Livingstone, Margaret S

    2017-01-01

    The adult primate visual system comprises a series of hierarchically organized areas. Each cortical area contains a topographic map of visual space, with different areas extracting different kinds of information from the retinal input. Here we asked to what extent the newborn visual system resembles the adult organization. We find that hierarchical, topographic organization is present at birth and therefore constitutes a proto-organization for the entire primate visual system. Even within inferior temporal cortex, this proto-organization was already present, prior to the emergence of category selectivity (e.g., faces or scenes). We propose that this topographic organization provides the scaffolding for the subsequent development of visual cortex that commences at the onset of visual experience DOI: http://dx.doi.org/10.7554/eLife.26196.001 PMID:28671063

  2. CORRIGENDUM to The impact of prehabilitation on post-surgical complications in patients undergoing non-urgent cardiovascular surgical intervention: Systematic review and meta-analysis.

    PubMed

    2018-06-01

    The impact of prehabilitation on post-surgical complications in patients undergoing non-urgent cardiovascular surgical intervention: Systematic review and meta-analysis by F Marmelo et al. European Journal of Preventive Cardiology January 2018 25: 404-417, DOI: 2016 doi: 10.1177/2047487317752373 The third author's name, affiliation and Funding information were incorrect, the correct details are below: Daniel Moreira-Gonçalves Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Portugal CIAFEL, Faculdade de Desporto, Universidade do Porto, Portugal Funding D.M.G is supported by an individual fellowship grant from Fundação para a Ciência e Tecnologia (SFRH/BPD/90010/ 2012) This has been corrected in the online article.

  3. Identifying resource manager information needs for the North Pacific Landscape Conservation Cooperative

    USGS Publications Warehouse

    Woodward, Andrea; Liedtke, Theresa; Jenni, Karen

    2014-01-01

    Landscape Conservation Cooperatives (LCCs) are a network of 22 public-private partnerships, defined by ecoregion, that share and provide science to ensure the sustainability of land, water, wildlife and cultural resources in North America. LLCs were established by the U.S. Department of Interior (DOI) in recognition that response to climate change must be coordinated on a landscape-level basis because important resources, ecosystem processes and resource management challenges extend beyond national wildlife refuges, Bureau of Land Management lands, national parks, and even international boundaries. Therefore, DOI agencies must work with other Federal, State, Tribal (U.S. indigenous peoples), First Nation (Canadian indigenous peoples), and local governments, as well as private landowners, to develop landscape-level strategies for understanding and responding to climate change.

  4. Interneuronal mechanisms of hippocampal theta oscillations in a full-scale model of the rodent CA1 circuit

    PubMed Central

    Bezaire, Marianne J; Raikov, Ivan; Burk, Kelly; Vyas, Dhrumil; Soltesz, Ivan

    2016-01-01

    The hippocampal theta rhythm plays important roles in information processing; however, the mechanisms of its generation are not well understood. We developed a data-driven, supercomputer-based, full-scale (1:1) model of the rodent CA1 area and studied its interneurons during theta oscillations. Theta rhythm with phase-locked gamma oscillations and phase-preferential discharges of distinct interneuronal types spontaneously emerged from the isolated CA1 circuit without rhythmic inputs. Perturbation experiments identified parvalbumin-expressing interneurons and neurogliaform cells, as well as interneuronal diversity itself, as important factors in theta generation. These simulations reveal new insights into the spatiotemporal organization of the CA1 circuit during theta oscillations. DOI: http://dx.doi.org/10.7554/eLife.18566.001 PMID:28009257

  5. National Satellite Land Remote Sensing Data Archive

    USGS Publications Warehouse

    Faundeen, John L.; Kelly, Francis P.; Holm, Thomas M.; Nolt, Jenna E.

    2013-01-01

    The National Satellite Land Remote Sensing Data Archive (NSLRSDA) resides at the U.S. Geological Survey's (USGS) Earth Resources Observation and Science (EROS) Center. Through the Land Remote Sensing Policy Act of 1992, the U.S. Congress directed the Department of the Interior (DOI) to establish a permanent Government archive containing satellite remote sensing data of the Earth's land surface and to make this data easily accessible and readily available. This unique DOI/USGS archive provides a comprehensive, permanent, and impartial observational record of the planet's land surface obtained throughout more than five decades of satellite remote sensing. Satellite-derived data and information products are primary sources used to detect and understand changes such as deforestation, desertification, agricultural crop vigor, water quality, invasive plant species, and certain natural hazards such as flood extent and wildfire scars.

  6. Two months of disdrometer data in the Paris area

    NASA Astrophysics Data System (ADS)

    Gires, Auguste; Tchiguirinskaia, Ioulia; Schertzer, Daniel

    2018-05-01

    The Hydrology, Meteorology, and Complexity laboratory of École des Ponts ParisTech (hmco.enpc.fr) has made a data set of optical disdrometer measurements available that come from a campaign involving three collocated devices from two different manufacturers, relying on different underlying technologies (one Campbell Scientific PWS100 and two OTT Parsivel2 instruments). The campaign took place in January-February 2016 in the Paris area (France). Disdrometers provide access to information on the size and velocity of drops falling through the sampling area of the devices of roughly a few tens of cm2. It enables the drop size distribution to be estimated and rainfall microphysics, kinetic energy, or radar quantities, for example, to be studied further. Raw data, i.e. basically a matrix containing a number of drops according to classes of size and velocity, along with more aggregated ones, such as the rain rate or drop size distribution with filtering, are available. Link to the data set: https://zenodo.org/record/1240168 (DOI: https://doi.org/10.5281/zenodo.1240168).

  7. USGS Information Technology Strategic Plan: Fiscal Years 2007-2011

    USGS Publications Warehouse

    ,

    2006-01-01

    Introduction: The acquisition, management, communication, and long-term stewardship of natural science data, information, and knowledge are fundamental mission responsibilities of the U.S. Geological Survey (USGS). USGS scientists collect, maintain, and exchange raw scientific data and interpret and analyze it to produce a wide variety of science-based products. Managers throughout the Bureau access, summarize, and analyze administrative or business-related information to budget, plan, evaluate, and report on programs and projects. Information professionals manage the extensive and growing stores of irreplaceable scientific information and knowledge in numerous databases, archives, libraries, and other digital and nondigital holdings. Information is the primary currency of the USGS, and it flows to scientists, managers, partners, and a wide base of customers, including local, State, and Federal agencies, private sector organizations, and individual citizens. Supporting these information flows is an infrastructure of computer systems, telecommunications equipment, software applications, digital and nondigital data stores and archives, technical expertise, and information policies and procedures. This infrastructure has evolved over many years and consists of tools and technologies acquired or built to address the specific requirements of particular projects or programs. Developed independently, the elements of this infrastructure were typically not designed to facilitate the exchange of data and information across programs or disciplines, to allow for sharing of information resources or expertise, or to be combined into a Bureauwide and broader information infrastructure. The challenge to the Bureau is to wisely and effectively use its information resources to create a more Integrated Information Environment that can reduce costs, enhance the discovery and delivery of scientific products, and improve support for science. This Information Technology Strategic Plan for the USGS outlines key information technology (IT) strategic goals and objectives that will support the Bureau's science mission, while also aligning with the Department of the Interior (DOI) IT Strategic Plan and the DOI Government Performance and Results Act (GPRA) Strategic Plan.

  8. Response of radiation belt simulations to different radial diffusion coefficients

    NASA Astrophysics Data System (ADS)

    Drozdov, A.; Shprits, Y.; Subbotin, D.; Kellerman, A. C.

    2013-12-01

    Resonant interactions between Ultra Low Frequency (ULF) waves and relativistic electrons may violate the third adiabatic invariant of motion, which produces radial diffusion in the electron radiation belts. This process plays an important role in the formation and structure of the outer electron radiation belt and is important for electron acceleration and losses in that region. Two parameterizations of the resonant wave-particle interaction of electrons with ULF waves in the magnetosphere by Brautigam and Albert [2000] and Ozeke et al. [2012] are evaluated using the Versatile Electron Radiation Belt (VERB) diffusion code to estimate their relative effect on the radiation belt simulation. The period of investigation includes quiet time and storm time geomagnetic activity and is compared to data based on satellite observations. Our calculations take into account wave-particle interactions represented by radial diffusion transport, local acceleration, losses due to pitch-angle diffusion, and mixed diffusion. We show that the results of the 3D diffusion simulations depend on the assumed parametrization of waves. The differences between the simulations and potential missing physical mechanisms are discussed. References Brautigam, D. H., and J. M. Albert (2000), Radial diffusion analysis of outer radiation belt electrons during the October 9, 1990, magnetic storm, J. Geophys. Res., 105(A1), 291-309, doi:10.1029/1999JA900344 Ozeke, L. G., I. R. Mann, K. R. Murphy, I. J. Rae, D. K. Milling, S. R. Elkington, A. A. Chan, and H. J. Singer (2012), ULF wave derived radiation belt radial diffusion coefficients, J. Geophys. Res., 117, A04222, doi:10.1029/2011JA017463.

  9. 78 FR 52431 - Amendments to ONRR's Service of Official Correspondence

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-23

    ... shelf, Electronic funds transfers, Geothermal energy, Indians--lands, Mineral royalties, Oil and gas... site at http://www.doi.gov/ocio/information_management/iq.cfm . Effects on the Energy Supply (E.O. 13211) This direct final rule is not a significant energy action under the definition in E.O. 13211, and...

  10. ACHP | The Protection of Indian Sacred Sites

    Science.gov Websites

    signatories issued an action plan for implementation of the MOU and in March 2014, issued a progress report , Action Plan, Progress Report, and other information may be accessed by clicking the links below: 2016 Action Plan ACHP News Announcement Department of the Interior Press Release DOI/Forest Service Updates

  11. Use of Informal Networks to Resolve Logistics-related Issues in Humanitarian Assistance Disaster Response

    DTIC Science & Technology

    2011-06-01

    efforts and the situation objectively and were not tempted to cast themselves in a favorable light ( Podsakoff & Organ, 1986). The AARs and CDRs were...Management.13(3), 146-156. doi: 10.1108/ 13673270910962932. Podsakoff , P.M., & Organ, D.W. (1986). Self-Reports in Organizational Research: Problems

  12. 76 FR 23816 - Agency Information Collection Request; 60-Day Public Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-28

    ...,292 1 60 437,520 DOI Grant Applicant 41 1 60 2,460 DOT Grant Applicant 370 1 60 22,200 ED Grant Applicant 2,000 1 60 120,000 HHS Grant Applicant 62,133 1 60 3,727,980 NARA Grant Applicant 1 1 60 60 NASA...

  13. 76 FR 60004 - Proposed Information Collection; Comment Request; Data Collection and Verification for the Marine...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-28

    ... Collection; Comment Request; Data Collection and Verification for the Marine Protected Areas Inventory AGENCY... developing a national system of marine protected areas (MPAs). These departments are working closely with... Administration (NOAA) and DOI have created the Marine Protected Areas Inventory, an online spatial database that...

  14. 77 FR 52340 - Meeting of the Secretarial Commission on Indian Trust Administration and Reform

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-29

    ... session the evening of September 13, 2012, at the United Tribes Technical College. DATES: The Commission's... held in the afternoon (time to be determined) on September 12, 2012, and the youth outreach session... Tribes Technical College; further information on these locations will be available at http://www.doi.gov...

  15. Working Memory Encoding Delays Top-Down Attention to Visual Cortex

    ERIC Educational Resources Information Center

    Scalf, Paige E.; Dux, Paul E.; Marois, Rene

    2011-01-01

    The encoding of information from one event into working memory can delay high-level, central decision-making processes for subsequent events [e.g., Jolicoeur, P., & Dell'Acqua, R. The demonstration of short-term consolidation. "Cognitive Psychology, 36", 138-202, 1998, doi:10.1006/cogp.1998.0684]. Working memory, however, is also believed to…

  16. Northern Prairie Wildlife Research Center

    USGS Publications Warehouse

    ,

    2009-01-01

    The Northern Prairie Wildlife Research Center (NPWRC) conducts integrated research to fulfill the Department of the Interior's responsibilities to the Nation's natural resources. Located on 600 acres along the James River Valley near Jamestown, North Dakota, the NPWRC develops and disseminates scientific information needed to understand, conserve, and wisely manage the Nation's biological resources. Research emphasis is primarily on midcontinental plant and animal species and ecosystems of the United States. During the center's 40-year history, its scientists have earned an international reputation for leadership and expertise on the biology of waterfowl and grassland birds, wetland ecology and classification, mammalian behavior and ecology, grassland ecosystems, and application of statistics and geographic information systems. To address current science challenges, NPWRC scientists collaborate with researchers from other U.S. Geological Survey centers and disciplines (Biology, Geography, Geology, and Water) and with biologists and managers in the Department of the Interior (DOI), other Federal agencies, State agencies, universities, and nongovernmental organizations. Expanding upon its scientific expertise and leadership, the NPWRC is moving in new directions, including invasive plant species, restoration of native habitats, carbon sequestration and marketing, and ungulate management on DOI lands.

  17. Microtubules provide directional information for core PCP function

    PubMed Central

    Matis, Maja; Russler-Germain, David A; Hu, Qie; Tomlin, Claire J; Axelrod, Jeffrey D

    2014-01-01

    Planar cell polarity (PCP) signaling controls the polarization of cells within the plane of an epithelium. Two molecular modules composed of Fat(Ft)/Dachsous(Ds)/Four-jointed(Fj) and a ‘PCP-core’ including Frizzled(Fz) and Dishevelled(Dsh) contribute to polarization of individual cells. How polarity is globally coordinated with tissue axes is unresolved. Consistent with previous results, we find that the Ft/Ds/Fj-module has an effect on a MT-cytoskeleton. Here, we provide evidence for the model that the Ft/Ds/Fj-module provides directional information to the core-module through this MT organizing function. We show Ft/Ds/Fj-dependent initial polarization of the apical MT-cytoskeleton prior to global alignment of the core-module, reveal that the anchoring of apical non-centrosomal MTs at apical junctions is polarized, observe that directional trafficking of vesicles containing Dsh depends on Ft, and demonstrate the feasibility of this model by mathematical simulation. Together, these results support the hypothesis that Ft/Ds/Fj provides a signal to orient core PCP function via MT polarization. DOI: http://dx.doi.org/10.7554/eLife.02893.001 PMID:25124458

  18. Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus

    PubMed Central

    Wheeler, Diek W; White, Charise M; Rees, Christopher L; Komendantov, Alexander O; Hamilton, David J; Ascoli, Giorgio A

    2015-01-01

    Hippocampome.org is a comprehensive knowledge base of neuron types in the rodent hippocampal formation (dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex). Although the hippocampal literature is remarkably information-rich, neuron properties are often reported with incompletely defined and notoriously inconsistent terminology, creating a formidable challenge for data integration. Our extensive literature mining and data reconciliation identified 122 neuron types based on neurotransmitter, axonal and dendritic patterns, synaptic specificity, electrophysiology, and molecular biomarkers. All ∼3700 annotated properties are individually supported by specific evidence (∼14,000 pieces) in peer-reviewed publications. Systematic analysis of this unprecedented amount of machine-readable information reveals novel correlations among neuron types and properties, the potential connectivity of the full hippocampal circuitry, and outstanding knowledge gaps. User-friendly browsing and online querying of Hippocampome.org may aid design and interpretation of both experiments and simulations. This powerful, simple, and extensible neuron classification endeavor is unique in its detail, utility, and completeness. DOI: http://dx.doi.org/10.7554/eLife.09960.001 PMID:26402459

  19. The right hippocampus leads the bilateral integration of gamma-parsed lateralized information

    PubMed Central

    Benito, Nuria; Martín-Vázquez, Gonzalo; Makarova, Julia; Makarov, Valeri A; Herreras, Oscar

    2016-01-01

    It is unclear whether the two hippocampal lobes convey similar or different activities and how they cooperate. Spatial discrimination of electric fields in anesthetized rats allowed us to compare the pathway-specific field potentials corresponding to the gamma-paced CA3 output (CA1 Schaffer potentials) and CA3 somatic inhibition within and between sides. Bilateral excitatory Schaffer gamma waves are generally larger and lead from the right hemisphere with only moderate covariation of amplitude, and drive CA1 pyramidal units more strongly than unilateral waves. CA3 waves lock to the ipsilateral Schaffer potentials, although bilateral coherence was weak. Notably, Schaffer activity may run laterally, as seen after the disruption of the connecting pathways. Thus, asymmetric operations promote the entrainment of CA3-autonomous gamma oscillators bilaterally, synchronizing lateralized gamma strings to converge optimally on CA1 targets. The findings support the view that interhippocampal connections integrate different aspects of information that flow through the left and right lobes. DOI: http://dx.doi.org/10.7554/eLife.16658.001 PMID:27599221

  20. Implementing DOIs for Oceanographic Satellite Data at PO.DAAC

    NASA Astrophysics Data System (ADS)

    Hausman, J.; Tauer, E.; Chung, N.; Chen, C.; Moroni, D. F.

    2013-12-01

    The Physical Oceanographic Distributed Active Archive Center (PO.DAAC) is NASA's archive for physical oceanographic satellite data. It distributes over 500 datasets from gravity, ocean wind, sea surface topography, sea ice, ocean currents, salinity, and sea surface temperature satellite missions. A dataset is a collection of granules/files that share the same mission/project, versioning, processing level, spatial, and temporal characteristics. The large number of datasets is partially due to the number of satellite missions, but mostly because a single satellite mission typically has multiple versions or even temporal and spatial resolutions of data. As a result, a user might mistake one dataset for a different dataset from the same satellite mission. Due to the PO.DAAC'S vast variety and volume of data and growing requirements to report dataset usage, it has begun implementing DOIs for the datasets it archives and distributes. However, this was not as simple as registering a name for a DOI and providing a URL. Before implementing DOIs multiple questions needed to be answered. What are the sponsor and end-user expectations regarding DOIs? At what level does a DOI get assigned (dataset, file/granule)? Do all data get a DOI, or only selected data? How do we create a DOI? How do we create landing pages and manage them? What changes need to be made to the data archive, life cycle policy and web portal to accommodate DOIs? What if the data also exists at another archive and a DOI already exists? How is a DOI included if the data were obtained via a subsetting tool? How does a researcher or author provide a unique, definitive reference (standard citation) for a given dataset? This presentation will discuss how these questions were answered through changes in policy, process, and system design. Implementing DOIs is not a trivial undertaking, but as DOIs are rapidly becoming the de facto approach, it is worth the effort. Researchers have historically referenced the source satellite and data center (or archive), but scientific writings do not typically provide enough detail to point to a singular, uniquely identifiable dataset. DOIs provide the means to help researchers be precise in their data citations and provide needed clarity, standardization and permanence.

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