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DNA barcodes of the native ray-finned fishes in Taiwan.
PubMed
Chang, Chia-Hao; Shao, Kwang-Tsao; Lin, Han-Yang; Chiu, Yung-Chieh; Lee, Mao-Ying; Liu, Shih-Hui; Lin, Pai-Lei
2017-07-01
Species identification based on the DNA sequence of a fragment of the cytochrome c oxidase subunit I gene in the mitochondrial genome, DNA barcoding, is widely applied to assist in sustainable exploitation of fish resources and the protection of fish biodiversity. The aim of this study was to establish a reliable barcoding reference database of the native ray-finned fishes in Taiwan. A total of 2993 individuals, belonging to 1245 species within 637 genera, 184 families and 29 orders of ray-finned fishes and representing approximately 40% of the recorded ray-finned fishes in Taiwan, were PCR amplified at the barcode region and bidirectionally sequenced. The mean length of the 2993 barcodes is 549 bp. Mean congeneric K2P distance (15.24%) is approximately 10-fold higher than the mean conspecific one (1.51%), but approximately 1.4-fold less than the mean genetic distance between families (20.80%). The Barcode Index Number (BIN) discordance report shows that 2993 specimens represent 1275 BINs and, among them, 86 BINs are singletons, 570 BINs are taxonomically concordant, and the other 619 BINs are taxonomically discordant. Barcode gap analysis also revealed that more than 90% of the collected fishes in this study can be discriminated by DNA barcoding. Overall, the barcoding reference database established by this study reveals the need for taxonomic revisions and voucher specimen rechecks, in addition to assisting in the management of Taiwan's fish resources and diversity. © 2016 John Wiley & Sons Ltd.
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Odor volatiles associated with microflora in damp ventilated and non-ventilated bin-stored bulk wheat.
PubMed
Tuma, D; Sinha, R N; Muir, W E; Abramson, D
1989-05-01
Western hard red spring wheat, stored at 20 and 25% moisture contents for 10 months during 1985-86, was monitored for biotic and abiotic variables in 10 unheated bins in Winnipeg, Manitoba. The major odor volatiles identified were 3-methyl-1-butanol, 3-octanone and 1-octen-3-ol. The production of these volatiles was associated and correlated with microfloral infection. Ventilation, used for cooling and drying of grain, disrupted microfloral growth patterns and production of volatiles. The highest levels of 3-methyl-1-butanol occurred in 25% moisture content wheat infected with bacteria, Penicillium spp. and Fusarium spp. In non-ventilated (control) bins with 20% moisture content wheat, 3-methyl-1-butanol was correlated with infection by members of the Aspergillus glaucus group and bacteria. In control bins, 1-octen-3-ol production was correlated with infection of wheat of both moisture contents by Penicillium spp. The fungal species, isolated from damp bin-stored wheat and tested for production of odor volatiles on wheat substrate, included Alternaria alternata (Fr.) Keissler, Aspergillus repens (Corda) Saccardo, A. flavus Link ex Fries, A. versicolor (Vuill.) Tiraboschi, Penicillium chrysogenum Thom, P. cyclopium Westling, Fusarium moniliforme Sheldon, F. semitectum (Cooke) Sacc. In the laboratory, fungus-inoculated wheat produced 3-methyl-1-butanol; 3-octanone and 1-octen-3-ol were also produced, but less frequently. Two unidentified bacterial species isolated from damp wheat and inoculated on agar produced 3-methyl-1-butanol.
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Toward zero waste: Composting and recycling for sustainable venue based events
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hottle, Troy A., E-mail: troy.hottle@asu.edu; Bilec, Melissa M., E-mail: mbilec@pitt.edu; Brown, Nicholas R., E-mail: nick.brown@asu.edu
Highlights: • Venues have billions of customers per year contributing to waste generation. • Waste audits of four university baseball games were conducted to assess venue waste. • Seven scenarios including composting were modeled using EPA’s WARM. • Findings demonstrate tradeoffs between emissions, energy, and landfill avoidance. • Sustainability of handling depends on efficacy of collection and treatment impacts. - Abstract: This study evaluated seven different waste management strategies for venue-based events and characterized the impacts of event waste management via waste audits and the Waste Reduction Model (WARM). The seven waste management scenarios included traditional waste handling methods (e.g.more » recycle and landfill) and management of the waste stream via composting, including purchasing where only compostable food service items were used during the events. Waste audits were conducted at four Arizona State University (ASU) baseball games, including a three game series. The findings demonstrate a tradeoff among CO{sub 2} equivalent emissions, energy use, and landfill diversion rates. Of the seven waste management scenarios assessed, the recycling scenarios provide the greatest reductions in CO{sub 2} eq. emissions and energy use because of the retention of high value materials but are compounded by the difficulty in managing a two or three bin collection system. The compost only scenario achieves complete landfill diversion but does not perform as well with respect to CO{sub 2} eq. emissions or energy. The three game series was used to test the impact of staffed bins on contamination rates; the first game served as a baseline, the second game employed staffed bins, and the third game had non staffed bins to determine the effect of staffing on contamination rates. Contamination rates in both the recycling and compost bins were tracked throughout the series. Contamination rates were reduced from 34% in the first game to 11% on the second night (with the staffed bins) and 23% contamination rates at the third game.« less
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Dark Energy Survey Year 1 Results: redshift distributions of the weak-lensing source galaxies
NASA Astrophysics Data System (ADS)
Hoyle, B.; Gruen, D.; Bernstein, G. M.; Rau, M. M.; De Vicente, J.; Hartley, W. G.; Gaztanaga, E.; DeRose, J.; Troxel, M. A.; Davis, C.; Alarcon, A.; MacCrann, N.; Prat, J.; Sánchez, C.; Sheldon, E.; Wechsler, R. H.; Asorey, J.; Becker, M. R.; Bonnett, C.; Carnero Rosell, A.; Carollo, D.; Carrasco Kind, M.; Castander, F. J.; Cawthon, R.; Chang, C.; Childress, M.; Davis, T. M.; Drlica-Wagner, A.; Gatti, M.; Glazebrook, K.; Gschwend, J.; Hinton, S. R.; Hoormann, J. K.; Kim, A. G.; King, A.; Kuehn, K.; Lewis, G.; Lidman, C.; Lin, H.; Macaulay, E.; Maia, M. A. G.; Martini, P.; Mudd, D.; Möller, A.; Nichol, R. C.; Ogando, R. L. C.; Rollins, R. P.; Roodman, A.; Ross, A. J.; Rozo, E.; Rykoff, E. S.; Samuroff, S.; Sevilla-Noarbe, I.; Sharp, R.; Sommer, N. E.; Tucker, B. E.; Uddin, S. A.; Varga, T. N.; Vielzeuf, P.; Yuan, F.; Zhang, B.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Bechtol, K.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Busha, M. T.; Capozzi, D.; Carretero, J.; Crocce, M.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Eifler, T. F.; Estrada, J.; Evrard, A. E.; Fernandez, E.; Flaugher, B.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gerdes, D. W.; Giannantonio, T.; Goldstein, D. A.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Jarvis, M.; Jeltema, T.; Johnson, M. W. G.; Johnson, M. D.; Kirk, D.; Krause, E.; Kuhlmann, S.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; March, M.; Marshall, J. L.; Melchior, P.; Menanteau, F.; Miquel, R.; Nord, B.; O'Neill, C. R.; Plazas, A. A.; Romer, A. K.; Sako, M.; Sanchez, E.; Santiago, B.; Scarpine, V.; Schindler, R.; Schubnell, M.; Smith, M.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Tucker, D. L.; Vikram, V.; Walker, A. R.; Weller, J.; Wester, W.; Wolf, R. C.; Yanny, B.; Zuntz, J.
2018-07-01
We describe the derivation and validation of redshift distribution estimates and their uncertainties for the populations of galaxies used as weak-lensing sources in the Dark Energy Survey (DES) Year 1 cosmological analyses. The Bayesian Photometric Redshift (BPZ) code is used to assign galaxies to four redshift bins between z ≈ 0.2 and ≈1.3, and to produce initial estimates of the lensing-weighted redshift distributions n^i_PZ(z)∝ dn^i/dz for members of bin i. Accurate determination of cosmological parameters depends critically on knowledge of ni, but is insensitive to bin assignments or redshift errors for individual galaxies. The cosmological analyses allow for shifts n^i(z)=n^i_PZ(z-Δ z^i) to correct the mean redshift of ni(z) for biases in n^i_PZ. The Δzi are constrained by comparison of independently estimated 30-band photometric redshifts of galaxies in the Cosmic Evolution Survey (COSMOS) field to BPZ estimates made from the DES griz fluxes, for a sample matched in fluxes, pre-seeing size, and lensing weight to the DES weak-lensing sources. In companion papers, the Δzi of the three lowest redshift bins are further constrained by the angular clustering of the source galaxies around red galaxies with secure photometric redshifts at 0.15 < z < 0.9. This paper details the BPZ and COSMOS procedures, and demonstrates that the cosmological inference is insensitive to details of the ni(z) beyond the choice of Δzi. The clustering and COSMOS validation methods produce consistent estimates of Δzi in the bins where both can be applied, with combined uncertainties of σ_{Δ z^i}=0.015, 0.013, 0.011, and 0.022 in the four bins. Repeating the photo-z procedure instead using the Directional Neighbourhood Fitting algorithm, or using the ni(z) estimated from the matched sample in COSMOS, yields no discernible difference in cosmological inferences.
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Receptor protein of Lysinibacillus sphaericus mosquito-larvicidal toxin displays amylomaltase activity.
PubMed
Sharma, Mahima; Gupta, Gagan D; Kumar, Vinay
2018-02-01
The activated binary toxin (BinAB) from Lysinibacillus sphaericus binds to surface receptor protein (Cqm1) on the midgut cell membrane and kills Culex quinquefasciatus larvae on internalization. Cqm1 is attached to cells via a glycosyl-phosphatidylinositol (GPI) anchor. It has been classified as a member of glycoside hydrolase family 13 of the CAZy database. Here, we report characterization of the ordered domain (residues 23-560) of Cqm1. Gene expressing Cqm1 of BinAB susceptible mosquito was chemically synthesized and the protein was purified using E. coli expression system. Values for the Michaelis-Menten kinetics parameters towards 4-nitrophenyl α-D-glucopyranoside (α-pNPG) substrate were estimated to be 0.44 mM (Km) and 1.9 s -1 (kcat). Thin layer chromatography experiments established Cqm1 as α-glucosidase competent to cleave α-1,4-glycosidic bonds of maltose and maltotriose with high glycosyltransferase activity to form glucose-oligomers. The observed hydrolysis and synthesis of glucose-oligomers is consistent with open and accessible active-site in the structural model. The protein also hydrolyses glycogen and sucrose. These activities suggest that Cqm1 may be involved in carbohydrate metabolism in mosquitoes. Further, toxic BinA component does not inhibit α-glucosidase activity of Cqm1, while BinB reduced the activity by nearly 50%. The surface plasmon resonance study reveals strong binding of BinB with Cqm1 (Kd, 9.8 nM). BinA interaction with Cqm1 however, is 1000-fold weaker. Notably the estimated Kd values match well with dissociation constants reported earlier with larvae brush border membrane fractions. The Cqm1 protein forms a stable dimer that is consistent with its apical localization in lipid rafts. Its melting temperature (T m ) as observed by thermofluor-shift assay is 51.5 °C and Ca 2+ provides structural stability to the protein. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Dark Energy Survey Year 1 Results: Redshift distributions of the weak lensing source galaxies
NASA Astrophysics Data System (ADS)
Hoyle, B.; Gruen, D.; Bernstein, G. M.; Rau, M. M.; De Vicente, J.; Hartley, W. G.; Gaztanaga, E.; DeRose, J.; Troxel, M. A.; Davis, C.; Alarcon, A.; MacCrann, N.; Prat, J.; Sánchez, C.; Sheldon, E.; Wechsler, R. H.; Asorey, J.; Becker, M. R.; Bonnett, C.; Carnero Rosell, A.; Carollo, D.; Carrasco Kind, M.; Castander, F. J.; Cawthon, R.; Chang, C.; Childress, M.; Davis, T. M.; Drlica-Wagner, A.; Gatti, M.; Glazebrook, K.; Gschwend, J.; Hinton, S. R.; Hoormann, J. K.; Kim, A. G.; King, A.; Kuehn, K.; Lewis, G.; Lidman, C.; Lin, H.; Macaulay, E.; Maia, M. A. G.; Martini, P.; Mudd, D.; Möller, A.; Nichol, R. C.; Ogando, R. L. C.; Rollins, R. P.; Roodman, A.; Ross, A. J.; Rozo, E.; Rykoff, E. S.; Samuroff, S.; Sevilla-Noarbe, I.; Sharp, R.; Sommer, N. E.; Tucker, B. E.; Uddin, S. A.; Varga, T. N.; Vielzeuf, P.; Yuan, F.; Zhang, B.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Bechtol, K.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Busha, M. T.; Capozzi, D.; Carretero, J.; Crocce, M.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Eifler, T. F.; Estrada, J.; Evrard, A. E.; Fernandez, E.; Flaugher, B.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gerdes, D. W.; Giannantonio, T.; Goldstein, D. A.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Jarvis, M.; Jeltema, T.; Johnson, M. W. G.; Johnson, M. D.; Kirk, D.; Krause, E.; Kuhlmann, S.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; March, M.; Marshall, J. L.; Melchior, P.; Menanteau, F.; Miquel, R.; Nord, B.; O'Neill, C. R.; Plazas, A. A.; Romer, A. K.; Sako, M.; Sanchez, E.; Santiago, B.; Scarpine, V.; Schindler, R.; Schubnell, M.; Smith, M.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Tucker, D. L.; Vikram, V.; Walker, A. R.; Weller, J.; Wester, W.; Wolf, R. C.; Yanny, B.; Zuntz, J.; DES Collaboration
2018-04-01
We describe the derivation and validation of redshift distribution estimates and their uncertainties for the populations of galaxies used as weak lensing sources in the Dark Energy Survey (DES) Year 1 cosmological analyses. The Bayesian Photometric Redshift (BPZ) code is used to assign galaxies to four redshift bins between z ≈ 0.2 and ≈1.3, and to produce initial estimates of the lensing-weighted redshift distributions n^i_PZ(z)∝ dn^i/dz for members of bin i. Accurate determination of cosmological parameters depends critically on knowledge of ni but is insensitive to bin assignments or redshift errors for individual galaxies. The cosmological analyses allow for shifts n^i(z)=n^i_PZ(z-Δ z^i) to correct the mean redshift of ni(z) for biases in n^i_PZ. The Δzi are constrained by comparison of independently estimated 30-band photometric redshifts of galaxies in the COSMOS field to BPZ estimates made from the DES griz fluxes, for a sample matched in fluxes, pre-seeing size, and lensing weight to the DES weak-lensing sources. In companion papers, the Δzi of the three lowest redshift bins are further constrained by the angular clustering of the source galaxies around red galaxies with secure photometric redshifts at 0.15 < z < 0.9. This paper details the BPZ and COSMOS procedures, and demonstrates that the cosmological inference is insensitive to details of the ni(z) beyond the choice of Δzi. The clustering and COSMOS validation methods produce consistent estimates of Δzi in the bins where both can be applied, with combined uncertainties of σ _{Δ z^i}=0.015, 0.013, 0.011, and 0.022 in the four bins. Repeating the photo-z proceedure instead using the Directional Neighborhood Fitting (DNF) algorithm, or using the ni(z) estimated from the matched sample in COSMOS, yields no discernible difference in cosmological inferences.
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Fully integrated sub 100ps photon counting platform
NASA Astrophysics Data System (ADS)
Buckley, S. J.; Bellis, S. J.; Rosinger, P.; Jackson, J. C.
2007-02-01
Current state of the art high resolution counting modules, specifically designed for high timing resolution applications, are largely based on a computer card format. This has tended to result in a costly solution that is restricted to the computer it resides in. We describe a four channel timing module that interfaces to a computer via a USB port and operates with a resolution of less than 100 picoseconds. The core design of the system is an advanced field programmable gate array (FPGA) interfacing to a precision time interval measurement module, mass memory block and a high speed USB 2.0 serial data port. The FPGA design allows the module to operate in a number of modes allowing both continuous recording of photon events (time-tagging) and repetitive time binning. In time-tag mode the system reports, for each photon event, the high resolution time along with the chronological time (macro time) and the channel ID. The time-tags are uploaded in real time to a host computer via a high speed USB port allowing continuous storage to computer memory of up to 4 millions photons per second. In time-bin mode, binning is carried out with count rates up to 10 million photons per second. Each curve resides in a block of 128,000 time-bins each with a resolution programmable down to less than 100 picoseconds. Each bin has a limit of 65535 hits allowing autonomous curve recording until a bin reaches the maximum count or the system is commanded to halt. Due to the large memory storage, several curves/experiments can be stored in the system prior to uploading to the host computer for analysis. This makes this module ideal for integration into high timing resolution specific applications such as laser ranging and fluorescence lifetime imaging using techniques such as time correlated single photon counting (TCSPC).
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The Impact of Aerosols on Cloud and Precipitation Processes: Cloud-Resolving Model Simulations
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo; Khain, A.; Simpson, S.; Johnson, D.; Li, X.; Remer, L.
2003-01-01
Cloud microphysics are inevitably affected by the smoke particle (CCN, cloud condensation nuclei) size distributions below the clouds. Therefore, size distributions parameterized as spectral bin microphysics are needed to explicitly study the effects of atmospheric aerosol concentration on cloud development, rainfall production, and rainfall rates for convective clouds. Recently, two detailed spectral-bin microphysical schemes were implemented into the Goddard Cumulus Ensemble (GCE) model. The formulation for the explicit spectral-bin microphysical processes is based on solving stochastic kinetic equations for the size distribution functions of water droplets (i.e., cloud droplets and raindrops), and several types of ice particles [i.e.,pristine ice crystals (columnar and plate-like), snow (dendrites and aggregates), graupel and frozen drops/hail]. Each type is described by a special size distribution function containing many categories (i.e. 33 bins). Atmospheric aerosols are also described using number density size-distribution functions.A spectral-bin microphysical model is very expensive from a from a computational point of view and has only been implemented into the 2D version of the GCE at the present time. The model is tested by studying the evolution of deep tropical clouds in the west Pacific warm pool region using identical thermodynamic conditions but with different concentrations of CCN: a low "clean" concentration and a high "dirty" concentration. Besides the initial differences in aerosol concentration, preliminary results indicate that the low CCN concentration case produces rainfall at the surface sooner than the high CCN case but has less cloud water mass aloft. Because the spectral-bin model explicitly calculates and allows for the examination of both the mass and number concentration of species in each size categor, a detailed analysis of the instantaneous size spectrum can be obtained for the two cases. It is shown that since the low CCN case produces fewer droplets, larger sized develop due to the greater condensational and collectional growth, leading to a broader size spectrum in comparison to the high CCN case.
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The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments
PubMed Central
2009-01-01
Background The characterisation, or binning, of metagenome fragments is an important first step to further downstream analysis of microbial consortia. Here, we propose a one-dimensional signature, OFDEG, derived from the oligonucleotide frequency profile of a DNA sequence, and show that it is possible to obtain a meaningful phylogenetic signal for relatively short DNA sequences. The one-dimensional signal is essentially a compact representation of higher dimensional feature spaces of greater complexity and is intended to improve on the tetranucleotide frequency feature space preferred by current compositional binning methods. Results We compare the fidelity of OFDEG against tetranucleotide frequency in both an unsupervised and semi-supervised setting on simulated metagenome benchmark data. Four tests were conducted using assembler output of Arachne and phrap, and for each, performance was evaluated on contigs which are greater than or equal to 8 kbp in length and contigs which are composed of at least 10 reads. Using both G-C content in conjunction with OFDEG gave an average accuracy of 96.75% (semi-supervised) and 95.19% (unsupervised), versus 94.25% (semi-supervised) and 82.35% (unsupervised) for tetranucleotide frequency. Conclusion We have presented an observation of an alternative characteristic of DNA sequences. The proposed feature representation has proven to be more beneficial than the existing tetranucleotide frequency space to the metagenome binning problem. We do note, however, that our observation of OFDEG deserves further anlaysis and investigation. Unsupervised clustering revealed OFDEG related features performed better than standard tetranucleotide frequency in representing a relevant organism specific signal. Further improvement in binning accuracy is given by semi-supervised classification using OFDEG. The emphasis on a feature-driven, bottom-up approach to the problem of binning reveals promising avenues for future development of techniques to characterise short environmental sequences without bias toward cultivable organisms. PMID:19958473
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Bright high z SnIa: A challenge for ΛCDM
NASA Astrophysics Data System (ADS)
Perivolaropoulos, L.; Shafieloo, A.
2009-06-01
It has recently been pointed out by Kowalski et. al. [Astrophys. J. 686, 749 (2008).ASJOAB0004-637X10.1086/589937] that there is “an unexpected brightness of the SnIa data at z>1.” We quantify this statement by constructing a new statistic which is applicable directly on the type Ia supernova (SnIa) distance moduli. This statistic is designed to pick up systematic brightness trends of SnIa data points with respect to a best fit cosmological model at high redshifts. It is based on binning the normalized differences between the SnIa distance moduli and the corresponding best fit values in the context of a specific cosmological model (e.g. ΛCDM). These differences are normalized by the standard errors of the observed distance moduli. We then focus on the highest redshift bin and extend its size toward lower redshifts until the binned normalized difference (BND) changes sign (crosses 0) at a redshift zc (bin size Nc). The bin size Nc of this crossing (the statistical variable) is then compared with the corresponding crossing bin size Nmc for Monte Carlo data realizations based on the best fit model. We find that the crossing bin size Nc obtained from the Union08 and Gold06 data with respect to the best fit ΛCDM model is anomalously large compared to Nmc of the corresponding Monte Carlo data sets obtained from the best fit ΛCDM in each case. In particular, only 2.2% of the Monte Carlo ΛCDM data sets are consistent with the Gold06 value of Nc while the corresponding probability for the Union08 value of Nc is 5.3%. Thus, according to this statistic, the probability that the high redshift brightness bias of the Union08 and Gold06 data sets is realized in the context of a (w0,w1)=(-1,0) model (ΛCDM cosmology) is less than 6%. The corresponding realization probability in the context of a (w0,w1)=(-1.4,2) model is more than 30% for both the Union08 and the Gold06 data sets indicating a much better consistency for this model with respect to the BND statistic.
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SU-F-J-136: Impact of Audiovisual Biofeedback On Interfraction Motion Over a Course of Liver Cancer Stereotactic Body Radiotherapy
DOE Office of Scientific and Technical Information (OSTI.GOV)
Pollock, S; Tse, R; Martin, D
Purpose: In abdominal radiotherapy inconsistent interfraction respiratory motion can result in deviations during treatment from what was planned in terms of target position and motion. Audiovisual biofeedback (AVB) is an interactive respiratory guide that produces a guiding interface that the patient follows over a course of radiotherapy to facilitate regular respiratory motion. This study assessed the impact of AVB on interfraction motion consistency over a course of liver cancer SBRT. Methods: Five liver cancer patients have been recruited into this study, 3 followed AVB over their course of SBRT and 2 were free breathing (FB). Respiratory signals from the Varianmore » RPM were obtained during 4DCT and each treatment fraction. Respiratory signals were organized into 10 respiratory bins, and interfraction consistency was quantified by the difference between each treatment fraction respiratory bin and each respiratory bin from 4DCT. Interfraction consistency was considered as both the relative difference (as a percentage) and absolute difference (in centimeters) between treatment respiratory bins and 4DCT respiratory bins. Results: The relative difference between 4DCT and treatment respiratory bins was 22 ± 16% for FB, and 15 ± 10% for AVB, an improvement of 32% (p < 0.001) with AVB. The absolute difference between 4DCT and treatment respiratory bins was 0.15 ± 0.10 cm for FB, and 0.14 ± 0.13 cm for AVB, an improvement of 4% (p = 0.6) with AVB. Conclusion: This was the first study to compare the impact of AVB breathing guidance on interfraction motion consistency over a course of radiotherapy. AVB demonstrated to significantly reduce the relative difference between 4DCT and treatment respiratory motion, but the absolute differences were comparable, largely due to one AVB patient exhibiting a larger amplitude than the other patients. This study demonstrates the potential benefit of AVB in reducing motion variations during treatment from what was planned. Paul Keall, Sean Pollock, Ricky OBrien and Kuldeep Makhija are shareholders of Respiratory Innovations, an Australian company that is developing a device to improve breathing stability. No funding or support was provided by Respiratory Innovations. Paul Keall is one of the inventors of US patent # 7955270.« less
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Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes
DOE Office of Scientific and Technical Information (OSTI.GOV)
White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya
ABSTRACT Soil metagenomics has been touted as the “grand challenge” for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87.7 Gbp of rapid-mode read data (~250 bp), plus 69.6 Gbp (>1.5 kbp) from Moleculo sequencing. The Moleculo data alone yielded over 5,600more » reads of >10 kbp in length, and over 95% of the unassembled reads mapped to contigs of >1.5 kbp. Hybrid assembly of all data resulted in more than 10,000 contigs over 10 kbp in length. We mapped three replicate metatranscriptomes derived from the same parent soil to the Moleculo subassembly and found that 95% of the predicted genes, based on their assignments to Enzyme Commission (EC) numbers, were expressed. The Moleculo subassembly also enabled binning of >100 microbial genome bins. We obtained via direct binning the first complete genome, that of “CandidatusPseudomonas sp. strain JKJ-1” from a native soil metagenome. By mapping metatranscriptome sequence reads back to the bins, we found that several bins corresponding to low-relative-abundanceAcidobacteriawere highly transcriptionally active, whereas bins corresponding to high-relative-abundanceVerrucomicrobiawere not. These results demonstrate that Moleculo sequencing provides a significant advance for resolving complex soil microbial communities. IMPORTANCESoil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their functional roles in ecosystem stability and responses to environmental perturbations. This knowledge gap is largely due to the difficulty in culturing the majority of soil microbes. Thus, use of culture-independent approaches, such as metagenomics, promises the direct assessment of the functional potential of soil microbiomes. Soil is, however, a challenge for metagenomic assembly due to its high microbial diversity and variable evenness, resulting in low coverage and uneven sampling of microbial genomes. Despite increasingly large soil metagenome data volumes (>200 Gbp), the majority of the data do not assemble. Here, we used the cutting-edge approach of synthetic long-read sequencing technology (Moleculo) to assemble soil metagenome sequence data into long contigs and used the assemblies for binning of genomes. Author Video: Anauthor video summaryof this article is available.« less
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Detecting the contagion effect in mass killings; a constructive example of the statistical advantages of unbinned likelihood methods.
PubMed
Towers, Sherry; Mubayi, Anuj; Castillo-Chavez, Carlos
2018-01-01
When attempting to statistically distinguish between a null and an alternative hypothesis, many researchers in the life and social sciences turn to binned statistical analysis methods, or methods that are simply based on the moments of a distribution (such as the mean, and variance). These methods have the advantage of simplicity of implementation, and simplicity of explanation. However, when null and alternative hypotheses manifest themselves in subtle differences in patterns in the data, binned analysis methods may be insensitive to these differences, and researchers may erroneously fail to reject the null hypothesis when in fact more sensitive statistical analysis methods might produce a different result when the null hypothesis is actually false. Here, with a focus on two recent conflicting studies of contagion in mass killings as instructive examples, we discuss how the use of unbinned likelihood methods makes optimal use of the information in the data; a fact that has been long known in statistical theory, but perhaps is not as widely appreciated amongst general researchers in the life and social sciences. In 2015, Towers et al published a paper that quantified the long-suspected contagion effect in mass killings. However, in 2017, Lankford & Tomek subsequently published a paper, based upon the same data, that claimed to contradict the results of the earlier study. The former used unbinned likelihood methods, and the latter used binned methods, and comparison of distribution moments. Using these analyses, we also discuss how visualization of the data can aid in determination of the most appropriate statistical analysis methods to distinguish between a null and alternate hypothesis. We also discuss the importance of assessment of the robustness of analysis results to methodological assumptions made (for example, arbitrary choices of number of bins and bin widths when using binned methods); an issue that is widely overlooked in the literature, but is critical to analysis reproducibility and robustness. When an analysis cannot distinguish between a null and alternate hypothesis, care must be taken to ensure that the analysis methodology itself maximizes the use of information in the data that can distinguish between the two hypotheses. The use of binned methods by Lankford & Tomek (2017), that examined how many mass killings fell within a 14 day window from a previous mass killing, substantially reduced the sensitivity of their analysis to contagion effects. The unbinned likelihood methods used by Towers et al (2015) did not suffer from this problem. While a binned analysis might be favorable for simplicity and clarity of presentation, unbinned likelihood methods are preferable when effects might be somewhat subtle.
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Detecting the contagion effect in mass killings; a constructive example of the statistical advantages of unbinned likelihood methods
PubMed Central
Mubayi, Anuj; Castillo-Chavez, Carlos
2018-01-01
Background When attempting to statistically distinguish between a null and an alternative hypothesis, many researchers in the life and social sciences turn to binned statistical analysis methods, or methods that are simply based on the moments of a distribution (such as the mean, and variance). These methods have the advantage of simplicity of implementation, and simplicity of explanation. However, when null and alternative hypotheses manifest themselves in subtle differences in patterns in the data, binned analysis methods may be insensitive to these differences, and researchers may erroneously fail to reject the null hypothesis when in fact more sensitive statistical analysis methods might produce a different result when the null hypothesis is actually false. Here, with a focus on two recent conflicting studies of contagion in mass killings as instructive examples, we discuss how the use of unbinned likelihood methods makes optimal use of the information in the data; a fact that has been long known in statistical theory, but perhaps is not as widely appreciated amongst general researchers in the life and social sciences. Methods In 2015, Towers et al published a paper that quantified the long-suspected contagion effect in mass killings. However, in 2017, Lankford & Tomek subsequently published a paper, based upon the same data, that claimed to contradict the results of the earlier study. The former used unbinned likelihood methods, and the latter used binned methods, and comparison of distribution moments. Using these analyses, we also discuss how visualization of the data can aid in determination of the most appropriate statistical analysis methods to distinguish between a null and alternate hypothesis. We also discuss the importance of assessment of the robustness of analysis results to methodological assumptions made (for example, arbitrary choices of number of bins and bin widths when using binned methods); an issue that is widely overlooked in the literature, but is critical to analysis reproducibility and robustness. Conclusions When an analysis cannot distinguish between a null and alternate hypothesis, care must be taken to ensure that the analysis methodology itself maximizes the use of information in the data that can distinguish between the two hypotheses. The use of binned methods by Lankford & Tomek (2017), that examined how many mass killings fell within a 14 day window from a previous mass killing, substantially reduced the sensitivity of their analysis to contagion effects. The unbinned likelihood methods used by Towers et al (2015) did not suffer from this problem. While a binned analysis might be favorable for simplicity and clarity of presentation, unbinned likelihood methods are preferable when effects might be somewhat subtle. PMID:29742115
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Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes
PubMed Central
White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya; Zucker, Jeremy D.; Brislawn, Colin J.; Nicora, Carrie D.; Fansler, Sarah J.; Glaesemann, Kurt R.; Glass, Kevin
2016-01-01
ABSTRACT Soil metagenomics has been touted as the “grand challenge” for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87.7 Gbp of rapid-mode read data (~250 bp), plus 69.6 Gbp (>1.5 kbp) from Moleculo sequencing. The Moleculo data alone yielded over 5,600 reads of >10 kbp in length, and over 95% of the unassembled reads mapped to contigs of >1.5 kbp. Hybrid assembly of all data resulted in more than 10,000 contigs over 10 kbp in length. We mapped three replicate metatranscriptomes derived from the same parent soil to the Moleculo subassembly and found that 95% of the predicted genes, based on their assignments to Enzyme Commission (EC) numbers, were expressed. The Moleculo subassembly also enabled binning of >100 microbial genome bins. We obtained via direct binning the first complete genome, that of “Candidatus Pseudomonas sp. strain JKJ-1” from a native soil metagenome. By mapping metatranscriptome sequence reads back to the bins, we found that several bins corresponding to low-relative-abundance Acidobacteria were highly transcriptionally active, whereas bins corresponding to high-relative-abundance Verrucomicrobia were not. These results demonstrate that Moleculo sequencing provides a significant advance for resolving complex soil microbial communities. IMPORTANCE Soil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their functional roles in ecosystem stability and responses to environmental perturbations. This knowledge gap is largely due to the difficulty in culturing the majority of soil microbes. Thus, use of culture-independent approaches, such as metagenomics, promises the direct assessment of the functional potential of soil microbiomes. Soil is, however, a challenge for metagenomic assembly due to its high microbial diversity and variable evenness, resulting in low coverage and uneven sampling of microbial genomes. Despite increasingly large soil metagenome data volumes (>200 Gbp), the majority of the data do not assemble. Here, we used the cutting-edge approach of synthetic long-read sequencing technology (Moleculo) to assemble soil metagenome sequence data into long contigs and used the assemblies for binning of genomes. Author Video: An author video summary of this article is available. PMID:27822530
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Evaluation of respiratory and cardiac motion correction schemes in dual gated PET/CT cardiac imaging.
PubMed
Lamare, F; Le Maitre, A; Dawood, M; Schäfers, K P; Fernandez, P; Rimoldi, O E; Visvikis, D
2014-07-01
Cardiac imaging suffers from both respiratory and cardiac motion. One of the proposed solutions involves double gated acquisitions. Although such an approach may lead to both respiratory and cardiac motion compensation there are issues associated with (a) the combination of data from cardiac and respiratory motion bins, and (b) poor statistical quality images as a result of using only part of the acquired data. The main objective of this work was to evaluate different schemes of combining binned data in order to identify the best strategy to reconstruct motion free cardiac images from dual gated positron emission tomography (PET) acquisitions. A digital phantom study as well as seven human studies were used in this evaluation. PET data were acquired in list mode (LM). A real-time position management system and an electrocardiogram device were used to provide the respiratory and cardiac motion triggers registered within the LM file. Acquired data were subsequently binned considering four and six cardiac gates, or the diastole only in combination with eight respiratory amplitude gates. PET images were corrected for attenuation, but no randoms nor scatter corrections were included. Reconstructed images from each of the bins considered above were subsequently used in combination with an affine or an elastic registration algorithm to derive transformation parameters allowing the combination of all acquired data in a particular position in the cardiac and respiratory cycles. Images were assessed in terms of signal-to-noise ratio (SNR), contrast, image profile, coefficient-of-variation (COV), and relative difference of the recovered activity concentration. Regardless of the considered motion compensation strategy, the nonrigid motion model performed better than the affine model, leading to higher SNR and contrast combined with a lower COV. Nevertheless, when compensating for respiration only, no statistically significant differences were observed in the performance of the two motion models considered. Superior image SNR and contrast were seen using the affine respiratory motion model in combination with the diastole cardiac bin in comparison to the use of the whole cardiac cycle. In contrast, when simultaneously correcting for cardiac beating and respiration, the elastic respiratory motion model outperformed the affine model. In this context, four cardiac bins associated with eight respiratory amplitude bins seemed to be adequate. Considering the compensation of respiratory motion effects only, both affine and elastic based approaches led to an accurate resizing and positioning of the myocardium. The use of the diastolic phase combined with an affine model based respiratory motion correction may therefore be a simple approach leading to significant quality improvements in cardiac PET imaging. However, the best performance was obtained with the combined correction for both cardiac and respiratory movements considering all the dual-gated bins independently through the use of an elastic model based motion compensation.
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Image quality in thoracic 4D cone-beam CT: A sensitivity analysis of respiratory signal, binning method, reconstruction algorithm, and projection angular spacing
DOE Office of Scientific and Technical Information (OSTI.GOV)
Shieh, Chun-Chien; Kipritidis, John; O’Brien, Ricky T.
Purpose: Respiratory signal, binning method, and reconstruction algorithm are three major controllable factors affecting image quality in thoracic 4D cone-beam CT (4D-CBCT), which is widely used in image guided radiotherapy (IGRT). Previous studies have investigated each of these factors individually, but no integrated sensitivity analysis has been performed. In addition, projection angular spacing is also a key factor in reconstruction, but how it affects image quality is not obvious. An investigation of the impacts of these four factors on image quality can help determine the most effective strategy in improving 4D-CBCT for IGRT. Methods: Fourteen 4D-CBCT patient projection datasets withmore » various respiratory motion features were reconstructed with the following controllable factors: (i) respiratory signal (real-time position management, projection image intensity analysis, or fiducial marker tracking), (ii) binning method (phase, displacement, or equal-projection-density displacement binning), and (iii) reconstruction algorithm [Feldkamp–Davis–Kress (FDK), McKinnon–Bates (MKB), or adaptive-steepest-descent projection-onto-convex-sets (ASD-POCS)]. The image quality was quantified using signal-to-noise ratio (SNR), contrast-to-noise ratio, and edge-response width in order to assess noise/streaking and blur. The SNR values were also analyzed with respect to the maximum, mean, and root-mean-squared-error (RMSE) projection angular spacing to investigate how projection angular spacing affects image quality. Results: The choice of respiratory signals was found to have no significant impact on image quality. Displacement-based binning was found to be less prone to motion artifacts compared to phase binning in more than half of the cases, but was shown to suffer from large interbin image quality variation and large projection angular gaps. Both MKB and ASD-POCS resulted in noticeably improved image quality almost 100% of the time relative to FDK. In addition, SNR values were found to increase with decreasing RMSE values of projection angular gaps with strong correlations (r ≈ −0.7) regardless of the reconstruction algorithm used. Conclusions: Based on the authors’ results, displacement-based binning methods, better reconstruction algorithms, and the acquisition of even projection angular views are the most important factors to consider for improving thoracic 4D-CBCT image quality. In view of the practical issues with displacement-based binning and the fact that projection angular spacing is not currently directly controllable, development of better reconstruction algorithms represents the most effective strategy for improving image quality in thoracic 4D-CBCT for IGRT applications at the current stage.« less
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3013/9975 Surveillance Program Interim Summary Report
DOE Office of Scientific and Technical Information (OSTI.GOV)
Dunn, K.; Hackney, B.; McClard, J.
2011-06-22
The K-Area Materials Storage (KAMS) Documented Safety Analysis (DSA) requires a surveillance program to monitor the safety performance of 3013 containers and 9975 shipping packages stored in KAMS. The SRS surveillance program [Reference 1] outlines activities for field surveillance and laboratory tests that demonstrate the packages meet the functional performance requirements described in the DSA. The SRS program also supports the complexwide Integrated Surveillance Program (ISP) [Reference 2] for 3013 containers. The purpose of this report is to provide a summary of the SRS portion of the surveillance program activities through fiscal year 2010 (FY10) and formally communicate the interpretationmore » of these results by the Surveillance Program Authority (SPA). Surveillance for the initial 3013 container random sampling of the Innocuous bin and the Pressure bin has been completed and there has been no indication of corrosion or significant pressurization. The maximum pressure observed was less than 50 psig, which is well below the design pressure of 699 psig for the 3013 container [Reference 3]. The data collected during surveillance of these bins has been evaluated by the Materials Identification and Surveillance (MIS) Working Group and no additional surveillance is necessary for these bins at least through FY13. A decision will be made whether additional surveillance of these bins is needed during future years of storage and as additional containers are generated. Based on the data collected to date, the SPA concludes that 3013 containers in these bins can continue to be safely stored in KAMS. This year, 13 destructive examinations (DE) were performed on random samples from the Pressure & Corrosion bin. To date, DE has been completed for approximately 30% of the random samples from the Pressure & Corrosion bin. In addition, DE has been performed on 6 engineering judgment (EJ) containers, for a total of 17 to date. This includes one container that exceeded the 3013 Standard moisture limit which was opened at LANL. The container pieces and an oxide sample were sent to SRNL for examination in FY11. No significant pressurization has been observed for the Pressure & Corrosion bin containers. Relatively minor corrosion has been observed on some convenience containers and the inside of two inner containers. While the limited extent of corrosion does not jeopardize the integrity of the outer 3013 containers, it does highlight the importance of continuing to perform DE and the Shelf Life program to assure that the corrosion rate is not accelerating or changing to a different corrosion mechanism (e.g., stress corrosion cracking). Statistical sampling is currently scheduled to be completed in FY17, but there is a proposed reduction of the number of DE's per year for FY11 and beyond which may delay the completion date. Since 3013 containers are stored inside 9975 containers, surveillances of 9975 containers are performed in conjunction with 3013 container surveillances. Results of 9975 container nondestructive examinations (NDEs) and DEs indicate that the containers will provide adequate protection of the 3013 containers in K-Area storage for at least 15 years [Reference 4].« less
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Research and Development of a New Waste Collection Bin to Facilitate Education in Plastic Recycling
ERIC Educational Resources Information Center
Chow, Cheuk-fai; So, Wing-Mui Winnie; Cheung, Tsz-Yan
2016-01-01
Plastic recycling has been an alternative method for solid waste management apart from landfill and incineration. However, recycling quality is affected when all plastics are discarded into a single recycling bin that increases cross contaminations and operation cost to the recycling industry. Following the engineering design process, a new…
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Test Anxiety & Its Relation to Perceived Academic Self-Efficacy among Al Hussein Bin Talal University Students
ERIC Educational Resources Information Center
sa'ad alzboon, Habis
2016-01-01
This study aimed to identify the degree of perceived academic self-efficacy and the relationship nature between test anxiety and perceived academic self-efficacy among students of Al Hussein Bin Talal University (AHU). Moreover, to identify the degree of available statistical significance differences that are attributed to gender, college and…
