Sample records for ff coliphages structural
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2005-09-01
Escherichia coliphage virus, and ovalbumnin (OV) protein species. The work suggests certain improvements that can be made to the IMS detection System...Escherichia coliphage virus, and ovalbumin (OV) protein species. However, the origin and structural identities of the pyrolyzate peaks observed in the GC-IMS...niger), Gram-negative Pantoea agglomerans ((EH) formerly Erwinia herbicola ), ovalbumin protein (OV), and the MS-2 Escherichia coliphage virus were
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Salter, Robert S.; Durbin, Gregory W.; Conklin, Ernestine; Rosen, Jeff; Clancy, Jennifer
2010-01-01
Coliphages are microbial indicators specified in the Ground Water Rule that can be used to monitor for potential fecal contamination of drinking water. The Total Coliform Rule specifies coliform and Escherichia coli indicators for municipal water quality testing; thus, coliphage indicator use is less common and advances in detection methodology are less frequent. Coliphages are viral structures and, compared to bacterial indicators, are more resistant to disinfection and diffuse further distances from pollution sources. Therefore, coliphage presence may serve as a better predictor of groundwater quality. This study describes Fast Phage, a 16- to 24-h presence/absence modification of U.S. Environmental Protection Agency (EPA) Method 1601 for detection of coliphages in 100 ml water. The objective of the study is to demonstrate that the somatic and male-specific coliphage modifications provide results equivalent to those of Method 1601. Five laboratories compared the modifications, featuring same-day fluorescence-based prediction, to Method 1601 by using the performance-based measurement system (PBMS) criterion. This requires a minimum 50% positive response in 10 replicates of 100-ml water samples at coliphage contamination levels of 1.3 to 1.5 PFU/100 ml. The laboratories showed that Fast Phage meets PBMS criteria with 83.5 to 92.1% correlation of the same-day rapid fluorescence-based prediction with the next-day result. Somatic coliphage PBMS data are compared to manufacturer development data that followed the EPA alternative test protocol (ATP) validation approach. Statistical analysis of the data sets indicates that PBMS utilizes fewer samples than does the ATP approach but with similar conclusions. Results support testing the coliphage modifications by using an EPA-approved national PBMS approach with collaboratively shared samples. PMID:20935123
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Salter, Robert S; Durbin, Gregory W; Conklin, Ernestine; Rosen, Jeff; Clancy, Jennifer
2010-12-01
Coliphages are microbial indicators specified in the Ground Water Rule that can be used to monitor for potential fecal contamination of drinking water. The Total Coliform Rule specifies coliform and Escherichia coli indicators for municipal water quality testing; thus, coliphage indicator use is less common and advances in detection methodology are less frequent. Coliphages are viral structures and, compared to bacterial indicators, are more resistant to disinfection and diffuse further distances from pollution sources. Therefore, coliphage presence may serve as a better predictor of groundwater quality. This study describes Fast Phage, a 16- to 24-h presence/absence modification of U.S. Environmental Protection Agency (EPA) Method 1601 for detection of coliphages in 100 ml water. The objective of the study is to demonstrate that the somatic and male-specific coliphage modifications provide results equivalent to those of Method 1601. Five laboratories compared the modifications, featuring same-day fluorescence-based prediction, to Method 1601 by using the performance-based measurement system (PBMS) criterion. This requires a minimum 50% positive response in 10 replicates of 100-ml water samples at coliphage contamination levels of 1.3 to 1.5 PFU/100 ml. The laboratories showed that Fast Phage meets PBMS criteria with 83.5 to 92.1% correlation of the same-day rapid fluorescence-based prediction with the next-day result. Somatic coliphage PBMS data are compared to manufacturer development data that followed the EPA alternative test protocol (ATP) validation approach. Statistical analysis of the data sets indicates that PBMS utilizes fewer samples than does the ATP approach but with similar conclusions. Results support testing the coliphage modifications by using an EPA-approved national PBMS approach with collaboratively shared samples.
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A Structure-Function Analysis of Shiga-Like Toxin Type 2 of Enterohemorrhagic Escherichia Coli
1990-05-07
like toxins are summarized in Table 2. The genes coding for both SLT-I and SLT-II are borne on coliphage , and toxin expression by E. coli occurs as...A stock | | ’ • * suspension of toxin-converting W coliphage was prepared by inducing the phage from | "fif the E. coli C600(933W) lysogen with...mitomycin C as described previously (Marques et al., 1987). An appropriate amount of the W coliphage stock was added to an l| exponential culture of
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Inactivation Rates of Coliphages Isolated from Waste Water Treatment Plant Effluents in Georgia
Coliphages are a type of host-specific bacteriophages that infect E. coli and are found abundantly in the gut of animals, including humans. They share many structural similarities with human enteric viruses and are being evaluated as indicators for the presence of enteric viral c...
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Ecology of coliphages in southern California coastal waters.
Reyes, V C; Jiang, S C
2010-08-01
This study aims to investigate the ecology of coliphages, an important microbial pollution indicator. Specifically, our experiments address (i) the ability of environmental Escherichia coli (E. coli) to serve as hosts for coliphage replication, and (ii) the temporal and spatial distribution of coliphages in coastal waters. Water samples from three locations in California's Newport Bay watershed were tested for the presence of coliphages every 2 weeks for an entire year. A total of nine E. coli strains isolated from various sources served as hosts for coliphage detection. Coliphage occurrence was significantly different between freshwater, estuarine and coastal locations and correlated with water temperature, salinity and rainfall in the watershed. The coliphages isolated on the environmental hosts had a broad host-range relative to the coliphages isolated on an E. coli strain from sewage and a US EPA recommended strain for coliphage detection. Coliphage occurrence was related to the temperature, rainfall and salinity within the bay. The adaptation to a broad host-range may enable the proliferation of coliphages in the aquatic environment. Understanding the seasonal variation of phages is useful for establishing a background level of coliphage presence in coastal waters. The broad host-range of coliphages isolated on the environmental E. coli host calls for investigation of coliphage replication in the aquatic environment.
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Cole, Dana; Long, Sharon C; Sobsey, Mark D
2003-11-01
Male-specific (F+) coliphages have been investigated as viral indicators of fecal contamination that may provide source-specific information for impacted environmental waters. This study examined the presence and proportions of the different subgroups of F+ coliphages in a variety of fecal wastes and surface waters with well-defined potential waste impacts. Municipal wastewater samples had high proportions of F+ DNA and group II and III F+ RNA coliphages. Bovine wastewaters also contained a high proportion of F+ DNA coliphages, but group I and IV F+ RNA coliphages predominated. Swine wastewaters contained approximately equal proportions of F+ DNA and RNA coliphages, and group I and III F+ RNA coliphages were most common. Waterfowl (gull and goose) feces contained almost exclusively F+ RNA coliphages of groups I and IV. No F+ coliphages were isolated from the feces of the other species examined. F+ coliphage recovery from surface waters was influenced by precipitation events and animal or human land use. There were no significant differences in coliphage density among land use categories. Significant seasonal variation was observed in the proportions of F+ DNA and RNA coliphages. Group I F+ RNA coliphages were the vast majority (90%) of those recovered from surface waters. The percentage of group I F+ RNA coliphages detected was greatest at background sites, and the percentage of group II F+ RNA coliphages was highest at human-impacted sites. Monitoring of F+ coliphage groups can indicate the presence and major sources of microbial inputs to surface waters, but environmental effects on the relative occurrence of different groups need to be considered.
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Cole, Dana; Long, Sharon C.; Sobsey, Mark D.
2003-01-01
Male-specific (F+) coliphages have been investigated as viral indicators of fecal contamination that may provide source-specific information for impacted environmental waters. This study examined the presence and proportions of the different subgroups of F+ coliphages in a variety of fecal wastes and surface waters with well-defined potential waste impacts. Municipal wastewater samples had high proportions of F+ DNA and group II and III F+ RNA coliphages. Bovine wastewaters also contained a high proportion of F+ DNA coliphages, but group I and IV F+ RNA coliphages predominated. Swine wastewaters contained approximately equal proportions of F+ DNA and RNA coliphages, and group I and III F+ RNA coliphages were most common. Waterfowl (gull and goose) feces contained almost exclusively F+ RNA coliphages of groups I and IV. No F+ coliphages were isolated from the feces of the other species examined. F+ coliphage recovery from surface waters was influenced by precipitation events and animal or human land use. There were no significant differences in coliphage density among land use categories. Significant seasonal variation was observed in the proportions of F+ DNA and RNA coliphages. Group I F+ RNA coliphages were the vast majority (90%) of those recovered from surface waters. The percentage of group I F+ RNA coliphages detected was greatest at background sites, and the percentage of group II F+ RNA coliphages was highest at human-impacted sites. Monitoring of F+ coliphage groups can indicate the presence and major sources of microbial inputs to surface waters, but environmental effects on the relative occurrence of different groups need to be considered. PMID:14602607
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Molecular characterization of bacteriophages for microbial source tracking in Korea.
Lee, Jung Eun; Lim, Mi Young; Kim, Sei Yoon; Lee, Sunghee; Lee, Heetae; Oh, Hyun-Myung; Hur, Hor-Gil; Ko, Gwangpyo
2009-11-01
We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F+-specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F+ coliphages in all of the tested fecal samples. We further characterized 311 F+ coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F+ coliphages from various sources. F+ RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F+ RNA coliphages, most F+ coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F+ RNA coliphages isolated from various sources were divided into two main clusters. All F+ RNA coliphages isolated from human wastewater were grouped with Qbeta-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F+ RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F+ DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F+ RNA coliphages can effectively distinguish fecal sources.
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Coliphages as indicators of enteroviruses.
Stetler, R E
1984-01-01
Coliphages were monitored in conjunction with indicator bacteria and enteroviruses in a drinking-water plant modified to reduce trihalomethane production. Coliphages could be detected in the source water by direct inoculation, and sufficient coliphages were detected in enterovirus concentrates to permit following the coliphage levels through different water treatment processes. The recovery efficiency by different filter types ranged from 1 to 53%. Statistical analysis of the data indicated that enterovirus isolates were better correlated with coliphages than with total coliforms, fecal coliforms, fecal streptococci, or standard plate count organisms. Coliphages were not detected in finished water. PMID:6093694
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Concentration and recovery of coliphages from water with bituminous coal.
Dafale, Nishant; Lakhe, Shrikumar; Yadav, Krishnakant; Purohit, Hemant; Chakrabarti, Tapan
2008-03-01
Coliphages represent a process indicator for fecal pollution. The coal bed concentration method prepared for enterovirus was refined for a concentration of coliphages. A bed made from 1.5 g of 120-mesh coal powder was used for concentrating coliphage from 200 mL of a water sample with or without the addition of aluminum chloride at different pH values. The isolated E. coli strain EC-R8 was found to be more susceptible to the desired coliphage and showed significant coliphage-coliform response, with clear plaque used for further studies. The complete coliphage adsorption was achieved with the addition of 0.0005 M AlCl3 at pH 6.0. Adsorbed coliphages were eluted with 3% beef extract in Mcllvaine buffer at pH 7.1, with an average recovery of 78.74%. This concentration technique was applied for the detection of coliphages from the well water of Nagpur city (India) and found to contain coliphages in the range of 2 to 28 plaque-forming units per liter (PFU/L).
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Is the replication of somatic coliphages in water environments significant?
Jofre, J
2009-04-01
Somatic coliphages are amid several groups of bacteriophages that have been suggested as indicators in water quality assessment. One of the limitations frequently endorsed to somatic coliphages as indicators is that they can replicate in the water environment. This review intends to evaluate the significance of this potential replication. In view of: the threshold densities of somatic coliphages and host bacteria needed for productive infection to occur, the densities of both host cells supporting somatic coliphages replication and these phages in water environments, and the poor contribution of lysogenic induction to the free somatic coliphage numbers in water, it can be concluded that replication of somatic coliphages in waters is very unlikely. Consequently, the contribution of replication in the environment of somatic coliphages is expected to have a non-noticeable influence on the numbers of somatic coliphages detected in water environments. Thus, the replication in the environment should not be argued as a limitation to the use of somatic coliphages as indicators.
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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
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Coliphages and Gastrointestinal Illness in Recreational Waters
Benjamin-Chung, Jade; Arnold, Benjamin F.; Wade, Timothy J.; Schiff, Kenneth; Griffith, John F.; Dufour, Alfred P.; Weisberg, Stephen B.
2017-01-01
Background: Coliphages have been proposed as indicators of fecal contamination in recreational waters because they better mimic the persistence of pathogenic viruses in the environment and wastewater treatment than fecal indicator bacteria. We estimated the association between coliphages and gastrointestinal illness and compared it with the association with culturable enterococci. Methods: We pooled data from six prospective cohort studies that enrolled coastal beachgoers in California, Alabama, and Rhode Island. Water samples were collected and gastrointestinal illness within 10 days of the beach visit was recorded. Samples were tested for enterococci and male-specific and somatic coliphages. We estimated cumulative incidence ratios (CIR) for the association between swimming in water with detectable coliphage and gastrointestinal illness when human fecal pollution was likely present, not likely present, and under all conditions combined. The reference group was unexposed swimmers. We defined continuous and threshold-based exposures (coliphage present/absent, enterococci >35 vs. ≤35 CFU/100 ml). Results: Under all conditions combined, there was no association between gastrointestinal illness and swimming in water with detectable coliphage or enterococci. When human fecal pollution was likely present, coliphage and enterococci were associated with increased gastrointestinal illness, and there was an association between male-specific coliphage level and illness that was somewhat stronger than the association between enterococci and illness. There were no substantial differences between male-specific and somatic coliphage. Conclusions: Somatic coliphage and enterococci had similar associations with gastrointestinal illness; there was some evidence that male-specific coliphage had a stronger association with illness than enterococci in marine waters with human fecal contamination. PMID:28489717
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Benjamin-Chung, Jade; Arnold, Benjamin F; Wade, Timothy J; Schiff, Kenneth; Griffith, John F; Dufour, Alfred P; Weisberg, Stephen B; Colford, John M
2017-09-01
Coliphages have been proposed as indicators of fecal contamination in recreational waters because they better mimic the persistence of pathogenic viruses in the environment and wastewater treatment than fecal indicator bacteria. We estimated the association between coliphages and gastrointestinal illness and compared it with the association with culturable enterococci. We pooled data from six prospective cohort studies that enrolled coastal beachgoers in California, Alabama, and Rhode Island. Water samples were collected and gastrointestinal illness within 10 days of the beach visit was recorded. Samples were tested for enterococci and male-specific and somatic coliphages. We estimated cumulative incidence ratios (CIR) for the association between swimming in water with detectable coliphage and gastrointestinal illness when human fecal pollution was likely present, not likely present, and under all conditions combined. The reference group was unexposed swimmers. We defined continuous and threshold-based exposures (coliphage present/absent, enterococci >35 vs. ≤35 CFU/100 ml). Under all conditions combined, there was no association between gastrointestinal illness and swimming in water with detectable coliphage or enterococci. When human fecal pollution was likely present, coliphage and enterococci were associated with increased gastrointestinal illness, and there was an association between male-specific coliphage level and illness that was somewhat stronger than the association between enterococci and illness. There were no substantial differences between male-specific and somatic coliphage. Somatic coliphage and enterococci had similar associations with gastrointestinal illness; there was some evidence that male-specific coliphage had a stronger association with illness than enterococci in marine waters with human fecal contamination.
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Male-Specific Coliphages as Indicators of Thermal Inactivation of Pathogens in Biosolids
Nappier, Sharon P.; Aitken, Michael D.; Sobsey, Mark D.
2006-01-01
Male-specific (F+) coliphages have been proposed as a candidate indicator of fecal contamination and of virus reduction in waste treatment. However, in this and earlier work with a laboratory thermophilic anaerobic digester, a heat-resistant fraction of F+ coliphage populations indigenous to municipal wastewater and sludge was evident. We therefore isolated coliphages from municipal wastewater sludge and from biosolid samples after thermophilic anaerobic digestion to evaluate the susceptibility of specific groups to thermal inactivation. Similar numbers of F+ DNA and F+ RNA coliphages were found in untreated sludge, but the majority of isolates in digested biosolids were group I F+ RNA phages. Separate experiments on individual isolates at 53°C confirmed the apparent heat resistance of group I F+ RNA coliphages as well as the susceptibility of group III F+ RNA coliphages. Although few F+ DNA coliphages were recovered from the treated biosolid samples, thermal inactivation experiments indicated heat resistance similar to that of group I F+ RNA phages. Hence, F+ DNA coliphage reductions during thermophilic anaerobic digestion are probably related to mechanisms other than thermal inactivation. Further studies should focus on the group III F+ RNA coliphages as potential indicators of reductions of heat-resistant pathogens in thermal processes for sludge treatment. PMID:16597945
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Haramoto, E; Otagiri, M; Morita, H; Kitajima, M
2012-04-01
To determine the genogroup distribution of F-specific coliphages in aquatic environments using the plaque isolation procedure combined with genogroup-specific real-time PCR. Thirty water samples were collected from a wastewater treatment plant and a river in the Kofu basin in Japan on fine weather days. F-specific coliphages were detected in all tested samples, 187 (82%) of 227 phage plaques isolated were classified into one of the 4 F-specific RNA (F-RNA) coliphage genogroups and 24 (11%) plaques were F-specific DNA coliphages. Human genogroups II and III F-RNA coliphages were more abundant in raw sewage than animal genogroups I and IV, excluding one sample that was suspected to be heavily contaminated with sporadic heavy animal faeces. The secondary-treated sewage samples were highly contaminated with genogroup I F-RNA coliphages, probably because of different behaviours among the coliphage genogroups during wastewater treatment. The river water samples were expected to be mainly contaminated with human faeces, independent of rainfall effects. A wide range of F-specific coliphage genogroups were successfully identified in wastewater and river water samples. Our results clearly show the usefulness of the genogroup-specific real-time PCR for determining the genogroups of F-specific coliphages present in aquatic environments. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.
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Specificity of coliphages in evaluating marker efficacy: a new insight for water quality indicators.
Mookerjee, Subham; Batabyal, Prasenjit; Halder, Madhumanti; Palit, Anup
2014-11-01
Conventional procedures for qualitative assessment of coliphage are time consuming multiple step approach for achieving results. A modified and rapid technique has been introduced for determination of coliphage contamination among potable water sources during water borne outbreaks. During December 2013, 40 water samples from different potable water sources, were received for water quality analyses, from a jaundice affected Municipality of West Bengal, India. Altogether, 30% water samples were contaminated with coliform (1-20 cfu/ml) and 5% with E. coli (2-5 cfu/ml). Among post-outbreak samples, preponderance of coliform has decreased (1-4 cfu/ml) with total absence of E. coli. While standard technique has detected 55% outbreak samples with coliphage contamination, modified technique revealed that 80%, double than that of bacteriological identification rate, were contaminated with coliphages (4-20 pfu/10 ml). However, post-outbreak samples were detected with 1-5 pfu/10 ml coliphages among 20% samples. Coliphage detection rate through modified technique was nearly double (50%) than that of standard technique (27.5%). In few samples (with coliform load of 10-100 cfu/ml), while modified technique could detect coliphages among six samples (10-20 pfu/10 ml), standard protocol failed to detect coliphage in any of them. An easy, rapid and accurate modified technique has thereby been implemented for coliphage assessment from water samples. Coliform free water does not always signify pathogen free potable water and it is demonstrated that coliphage is a more reliable 'biomarker' to ascertain contamination level in potable water. Copyright © 2014 Elsevier B.V. All rights reserved.
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Agulló-Barceló, Miriam; Galofré, Belén; Sala, Lluís; García-Aljaro, Cristina; Lucena, Francisco; Jofre, Juan
2016-09-01
Bacteriophages are increasingly being used as water quality indicators. Two groups of phages infecting Escherichia coli, somatic and F-specific coliphages, are being considered as indicators of fecal and viral contamination for several types of water around the world. However, some uncertainties remain regarding which coliphages to assess. Recently, E. coli strain CB390 has been reported to be suitable for simultaneous detection of both groups, which seems to be more informative than determining only one of the groups. Here, a significant number of samples from different settings, mostly those where F-specific phages have been reported to outnumber somatic coliphages, are analyzed for somatic coliphages, F-specific RNA phages by standardized methods and coliphages detected by host strain CB390. The results presented here confirm that the numbers of phages counted using CB390 are equivalent to the sum of the somatic and F-specific coliphages counted independently in all settings. Hence the usefulness of this strain for simultaneous detection of somatic and F-specific coliphages is confirmed. Also, sets of data on the presence of coliphages in reclaimed and groundwater are reported. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Jones, Tineke H.; Brassard, Julie; Topp, Edward; Wilkes, Graham
2016-01-01
ABSTRACT From the years 2008 to 2014, a total of 1,155 water samples were collected (spring to fall) from 24 surface water sampling sites located in a mixed-used but predominantly agricultural (i.e., dairy livestock production) river basin in eastern Ontario, Canada. Water was analyzed for viable F-specific DNA (F-DNA) and F-specific RNA (F-RNA) (genogroup I [GI] to GIV) coliphage and a suite of molecularly detected viruses (norovirus [GI to GIV], torque teno virus [TTV], rotavirus, kobuvirus, adenovirus, astrovirus, hepatitis A, and hepatitis E). F-DNA and F-RNA coliphage were detected in 33 and 28% of the samples at maximum concentrations of 2,000 and 16,300 PFU · 100 ml−1, respectively. Animal TTV, human TTV, kobuvirus, astrovirus, and norovirus GIII were the most prevalent viruses, found in 23, 20, 13, 12, and 11% of samples, respectively. Viable F-DNA coliphage was found to be a modest positive indicator of molecularly detected TTV. F-RNA coliphage, unlike F-DNA coliphage, was a modest positive predictor of norovirus and rotavirus. There were, however, a number of significant negative associations among F-specific coliphage and viruses. F-DNA coliphage densities of >142 PFU · 100 ml−1 delineated conditions when ∼95% of water samples contained some type of virus. Kobuvirus was the virus most strongly related to detection of any other virus. Land use had some associations with virus/F-specific coliphage detection, but season and surface water flow were the variables that were most important for broadly delineating detection. Higher relative levels of detection of human viruses and human F-RNA coliphage were associated with higher relative degrees of upstream human land development in a catchment. IMPORTANCE This study is one of the first, to our knowledge, to evaluate relationships among F-specific coliphages and a large suite of enteric viruses in mixed-use but agriculturally dominated surface waters in Canada. This study suggested that relationships between viable F-specific coliphages and molecularly detected viruses do exist, but they are not always positive. Caution should be employed if viable F-specific coliphages are to be used as indicators of virus presence in surface waters. This study elucidates relative effects of agriculture, wildlife, and human activity on virus and F-specific coliphage detection. Seasonal and meteorological attributes play a strong role in the detection of most virus and F-specific coliphage targets. PMID:27836843
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Jones, Tineke H; Brassard, Julie; Topp, Edward; Wilkes, Graham; Lapen, David R
2017-02-01
From the years 2008 to 2014, a total of 1,155 water samples were collected (spring to fall) from 24 surface water sampling sites located in a mixed-used but predominantly agricultural (i.e., dairy livestock production) river basin in eastern Ontario, Canada. Water was analyzed for viable F-specific DNA (F-DNA) and F-specific RNA (F-RNA) (genogroup I [GI] to GIV) coliphage and a suite of molecularly detected viruses (norovirus [GI to GIV], torque teno virus [TTV], rotavirus, kobuvirus, adenovirus, astrovirus, hepatitis A, and hepatitis E). F-DNA and F-RNA coliphage were detected in 33 and 28% of the samples at maximum concentrations of 2,000 and 16,300 PFU · 100 ml -1 , respectively. Animal TTV, human TTV, kobuvirus, astrovirus, and norovirus GIII were the most prevalent viruses, found in 23, 20, 13, 12, and 11% of samples, respectively. Viable F-DNA coliphage was found to be a modest positive indicator of molecularly detected TTV. F-RNA coliphage, unlike F-DNA coliphage, was a modest positive predictor of norovirus and rotavirus. There were, however, a number of significant negative associations among F-specific coliphage and viruses. F-DNA coliphage densities of >142 PFU · 100 ml -1 delineated conditions when ∼95% of water samples contained some type of virus. Kobuvirus was the virus most strongly related to detection of any other virus. Land use had some associations with virus/F-specific coliphage detection, but season and surface water flow were the variables that were most important for broadly delineating detection. Higher relative levels of detection of human viruses and human F-RNA coliphage were associated with higher relative degrees of upstream human land development in a catchment. This study is one of the first, to our knowledge, to evaluate relationships among F-specific coliphages and a large suite of enteric viruses in mixed-use but agriculturally dominated surface waters in Canada. This study suggested that relationships between viable F-specific coliphages and molecularly detected viruses do exist, but they are not always positive. Caution should be employed if viable F-specific coliphages are to be used as indicators of virus presence in surface waters. This study elucidates relative effects of agriculture, wildlife, and human activity on virus and F-specific coliphage detection. Seasonal and meteorological attributes play a strong role in the detection of most virus and F-specific coliphage targets. © Crown copyright 2017.
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Thermal and aqueous stability improvement of graphene oxide enhanced diphenylalanine nanocomposites
NASA Astrophysics Data System (ADS)
Ryan, Kate; Neumayer, Sabine M.; Maraka, Harsha Vardhan R.; Buchete, Nicolae-Viorel; Kholkin, Andrei L.; Rice, James H.; Rodriguez, Brian J.
2017-12-01
Nanocomposites of diphenylalanine (FF) and carbon based materials provide an opportunity to overcome drawbacks associated with using FF micro- and nanostructures in nanobiotechnology applications, in particular their poor structural stability in liquid solutions. In this study, FF/graphene oxide (GO) composites were found to self-assemble into layered micro- and nanostructures, which exhibited improved thermal and aqueous stability. Dependent on the FF/GO ratio, the solubility of these structures was reduced to 35.65% after 30 min as compared to 92.4% for pure FF samples. Such functional nanocomposites may extend the use of FF structures to e.g. biosensing, electrochemical, electromechanical or electronic applications.
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Host range, immunity and antigenic properties of lambdoid coliphage HK97.
Dhillon, E K; Dhillon, T S; Lai, A N; Linn, S
1980-09-01
Temperate coliphage HK97 was isolated from pig dung. Although HK97 is antigenically unrelated to coliphage lambda, it has similar morphology, host range and immunity properties, and can recombine with it.
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Individual and Collective Protection Program
2007-11-30
98 8.2.1 PREPARATION OF STOCK SUSPENSION OF MS2 COLIPHAGE ...103 8.3.1 PROCEDURE FOR ASSAYING MS2 COLIPHAGE ...CHALLENGE NUMBER OF TEST MICROORGANISMS..................106 8.4.1 METHOD FOR DETERMINATION OF CHALLENGE NUMBER OF MS2 COLIPHAGE
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Zhao, Liling; Cao, Zanxia; Wang, Jihua
2012-01-01
To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain. PMID:22408419
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Pérez-Méndez, A; Chandler, J C; Bisha, B; Goodridge, L D
2014-08-01
Enteric viral contaminants in water represent a public health concern, thus methods for detecting these viruses or their indicator microorganisms are needed. Because enteric viruses and their viral indicators are often found at low concentrations in water, their detection requires upfront concentration methods. In this study, a strong basic anion exchange resin was evaluated as an adsorbent material for the concentration of F-RNA coliphages (MS2, Qβ, GA, and HB-P22). These coliphages are recognized as enteric virus surrogates and fecal indicator organisms. Following adsorption of the coliphages from 50ml water samples, direct RNA isolation and real time RT-PCR detection were performed. In water samples containing 10(5)pfu/ml of the F-RNA coliphages, the anion exchange resin (IRA-900) adsorbed over 96.7% of the coliphages present, improving real time RT-PCR detection by 5-7 cycles compared to direct testing. F-RNA coliphage RNA recovery using the integrated method ranged from 12.6% to 77.1%. Resin-based concentration of samples with low levels of the F-RNA coliphages allowed for 10(0)pfu/ml (MS2 and Qβ) and 10(-1)pfu/ml (GA and HB-P22) to be detected. The resin-based method offers considerable advantages in cost, speed, simplicity and field adaptability. Copyright © 2014 Elsevier B.V. All rights reserved.
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Vergara, G G R V; Goh, S G; Rezaeinejad, S; Chang, S Y; Sobsey, M D; Gin, K Y H
2015-08-01
This study aimed to evaluate the relationship between FRNA coliphages (FRNA GI to GIV) and human enteric viruses (human adenoviruses, HAdV, astroviruses, AstV, noroviruses, NoV, and rotaviruses, RoV) in a tropical urban freshwater catchment. Positive associations between human-specific coliphages and human viral pathogens substantiate their use as viral indicators and in microbial source tracking. Reverse transcription qPCR was used to measure the concentrations of viruses and FRNA coliphages in concentrated water samples. Environmental water samples were also analyzed for male-specific (F+) and somatic (Som) coliphages using plaque assay. The most abundant enteric virus was NoV (55%) followed by HAdV (33%), RoV (33%), and AstV (23%), while the most abundant FRNA genogroup was GI (85%) followed by GII (48%), GIV (8%) and GIII (7%). Concentrations of human-specific coliphages FRNA GII were positively correlated with NoV, HAdV, RoV, AstV, F+ and Som (τ = 0.5 to 0.3, P < 0.05) while concentrations of animal-specific coliphages FRNA GI were negatively correlated with HAdV and RoV (τ = -0.2, P < 0.05). This study demonstrates statistical relationships between human-specific coliphages and a suite of human enteric viruses in the environment. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Decay of Coliphages in Sewage-Contaminated Freshwater: Uncertainty and Seasonal Effects.
Wu, Jianyong; Cao, Yiping; Young, Brianna; Yuen, Yvonne; Jiang, Sharon; Melendez, Daira; Griffith, John F; Stewart, Jill R
2016-11-01
Understanding the fate of enteric viruses in water is vital for protection of water quality. However, the decay of enteric viruses is not well characterized, and its uncertainty has not been examined yet. In this study, the decay of coliphages, an indicator for enteric viruses, was investigated in situ under both sunlit and shaded conditions as well as in summer and winter. The decay rates of coliphages and their uncertainties were analyzed using a Bayesian approach. The results from the summer experiments revealed that the decay rates of somatic coliphages were significantly higher in sunlight (1.29 ± 0.06 day -1 ) than in shade (0.96 ± 0.04 day -1 ), but the decay rates of male-specific (F+) coliphages were not significantly different between sunlight (1.09 ± 0.09 day -1 ) and shaded treatments (1.11 ± 0.08 day -1 ). The decay rates of both F+ coliphages (0.25 ± 0.02 day -1 ) and somatic coliphages (0.12 ± 0.01 day -1 ) in winter were considerably lower than those in summer. Temperature and chlorophyll a (chla) concentration varied significantly (p < 0.001) between the two seasons, suggesting that these parameters might be important contributors to the seasonal variation of coliphage decay. Additionally, the Bayesian approach provided full distributions of decay rates and reduced the uncertainty, offering useful information for comparing decay rates under different conditions.
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Concentration and Quantification of Somatic and F+ Coliphage from Recreational Waters
Somatic and F+ coliphages are promising alternative fecal indicators, but current detection methods are hindered by lower levels of coliphages in surface waters compared to traditional bacterial fecal indicators. We evaluated the ability of dead-end hollow fiber ultrafiltration (...
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Surveillance of enteric viruses and coliphages in a tropical urban catchment.
Rezaeinejad, S; Vergara, G G R V; Woo, C H; Lim, T T; Sobsey, M D; Gin, K Y H
2014-07-01
An assessment of the occurrence and concentration of enteric viruses and coliphages was carried out in highly urbanized catchment waters in the tropical city-state of Singapore. Target enteric viruses in this study were noroviruses, adenoviruses, astroviruses and rotaviruses. In total, 65 water samples were collected from canals and the reservoir of the Marina catchment on a monthly basis over a period of a year. Quantitative PCR (qPCR) and single agar layer plaque assay (SAL) were used to enumerate target enteric viruses and coliphages in water samples, respectively. The most prevalent pathogen were noroviruses, detected in 37 samples (57%), particularly norovirus genogroup II (48%), with a mean concentration of 3.7 × 10(2) gene copies per liter. Rotavirus was the second most prevalent virus (40%) with a mean concentration of 2.5 × 10(2) GC/L. The mean concentrations of somatic and male-specific coliphages were 2.2 × 10(2) and 1.1 × 10(2) PFU/100 ml, respectively. The occurrence and concentration of each target virus and the ratio of somatic to male-specific coliphages varied at different sampling sites in the catchment. For sampling sites with higher frequency of occurrence and concentration of viruses, the ratio of somatic to male-specific coliphages was generally much lower than other sampling sites with lower incidences of enteric viruses. Overall, higher statistical correlation was observed between target enteric viruses than between enteric viruses and coliphages. However, male-specific coliphages were positively correlated with norovirus concentrations. A multi-level integrated surveillance system, which comprises the monitoring of bacterial indicators, coliphages and selected enteric viruses, could help to meet recreational and surface water quality criteria in a complex urbanized catchment. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Zhang, K; Farahbakhsh, K
2007-06-01
The efficacy of a conventional activated sludge wastewater treatment process and the membrane bioreactor technology in removing microbial pathogens was investigated. Total and fecal coliforms and somatic and F-specific coliphages were used as indicators of pathogenic bacteria and viruses. Up to 5.7 logs removal of coliforms and 5.5 logs of coliphages were observed in the conventional treatment process with advanced tertiary treatment. Addition of chemical coagulants seemed to improve the efficacy of primary and secondary treatment for microorganism removal. Complete removal of fecal coliforms and up to 5.8 logs removal of coliphages was observed in the MBR system. It was shown that the MBR system was capable of high removal of coliphages despite the variation in feed coliphage concentrations. The results of this study indicated that the MBR system can achieve better microbial removal in far fewer steps than the conventional activated sludge process with advanced tertiary treatment. The final effluent from either treatment processes can be potentially reused.
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Rates of inactivation of waterborne coliphages by monochloramine.
Dee, S W; Fogleman, J C
1992-01-01
A sophisticated water quality monitoring program was established to evaluate virus removal through Denver's 1-million-gal (ca. 4-million-liter)/day Direct Potable Reuse Demonstration Plant. As a comparison point for the reuse demonstration plant, Denver's main water treatment facility was also monitored for coliphage organisms. Through the routine monitoring of the main plant, it was discovered that coliphage organisms were escaping the water treatment processes. Monochloramine residuals and contact times (CT values) required to achieve 99% inactivation were determined for coliphage organisms entering and leaving this conventional water treatment plant. The coliphage tested in the effluent waters had higher CT values on the average than those of the influent waters. CT values established for some of these coliphages suggest that monochloramine alone is not capable of removing 2 orders of magnitude of these specific organisms in a typical water treatment facility. Electron micrographs revealed one distinct type of phage capable of escaping the water treatment processes and three distinct types of phages in all. Images PMID:1444427
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Background: Coliphages have been proposed as potential indicators of fecal contamination of marine recreational waters because they may better predict the presence of viruses than fecal indicator bacteria. We estimated the association between the presence of coliphages and self-r...
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Incidence of Somatic and F+ Coliphage at Three Great Lake Beaches
There is a growing interest for the potential use of coliphage as an alternative indicator to assess fecal pollution in recreational waters. Coliphage are a group of viruses that infect E. coli and are commonly used as models to infer the likely presence of human enteric viral pa...
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Incidence of somatic and F+ coliphage in Great Lake Basin recreational waters.
Wanjugi, Pauline; Sivaganesan, Mano; Korajkic, Asja; McMinn, Brian; Kelty, Catherine A; Rhodes, Eric; Cyterski, Mike; Zepp, Richard; Oshima, Kevin; Stachler, Elyse; Kinzelman, Julie; Kurdas, Stephan R; Citriglia, Mark; Hsu, Fu-Chih; Shanks, Orin C
2018-04-25
There is a growing interest for the use of coliphage as an alternative indicator to assess fecal pollution in recreational waters. Coliphage are a group of viruses that infect Escherichia coli and are considered as potential surrogates to infer the likely presence of enteric viral pathogens. We report the use of a dead-end hollow fiber ultrafiltration single agar layer method to enumerate F+ and somatic coliphage from surface waters collected from three Great Lake areas. At each location, three sites (two beaches; one river) were sampled five days a week over the 2015 beach season (n = 609 total samples). In addition, culturable E. coli and enterococci concentrations, as well as 16 water quality and recreational area parameters were assessed such as rainfall, turbidity, dissolved oxygen, pH, and ultra violet absorbance. Overall, somatic coliphage levels ranged from non-detectable to 4.39 log 10 plaque forming units per liter and were consistently higher compared to F+ (non-detectable to 3.15 log 10 PFU/L), regardless of sampling site. Coliphage concentrations weakly correlated with cultivated fecal indicator bacteria levels (E. coli and enterococci) at 75% of beach sites tested in study (r = 0.28 to 0.40). In addition, ultraviolet light absorption and water temperature were closely associated with coliphage concentrations, but not fecal indicator bacteria levels suggesting different persistence trends in Great Lake waters between indicator types (bacteria versus virus). Finally, implications for coliphage water quality management and future research directions are discussed. Copyright © 2018. Published by Elsevier Ltd.
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Somatic Coliphage Profiles of Produce and Environmental Samples from Farms in Northern México.
Bartz, Faith E; Hodge, Domonique Watson; Heredia, Norma; de Aceituno, Anna Fabiszewski; Solís, Luisa; Jaykus, Lee-Ann; Garcia, Santos; Leon, Juan S
2016-09-01
Somatic coliphages were quantified in 459 produce and environmental samples from 11 farms in Northern Mexico to compare amounts of somatic coliphages among different types of fresh produce and environmental samples across the production steps on farms. Rinsates from cantaloupe melons, jalapeño peppers, tomatoes, and the hands of workers, soil, and water were collected during 2011-2012 at four successive steps on each farm, from the field before harvest through the packing facility, and assayed by FastPhage MPN Quanti-tray method. Cantaloupe farm samples contained more coliphages than jalapeño or tomato (p range <0.01-0.03). Across production steps, jalapeños had higher coliphage percentages before harvest than during packing (p = 0.03), while tomatoes had higher coliphage concentrations at packing than all preceding production steps (p range <0.01-0.02). These findings support the use of targeted produce-specific interventions at multiple points in the process of growing and packing produce to reduce the risk of enteric virus contamination and improve food safety during fruit and vegetable production.
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Concentration and quantification of somatic and F+ coliphages from recreational waters.
McMinn, Brian R; Huff, Emma M; Rhodes, Eric R; Korajkic, Asja
2017-11-01
Somatic and F+ coliphages are promising alternative fecal indicators, but current detection methods are hindered by lower levels of coliphages in surface waters compared to traditional bacterial fecal indicators. We evaluated the ability of dead-end hollow fiber ultrafiltration (D- HFUF) and single agar layer (SAL) procedure to concentrate and enumerate coliphages from 1L and 10L volumes of ambient surface waters (lake, river, marine), river water with varying turbidities (3.74-118.7 NTU), and a simulated combined sewer overflow (CSO) event. Percentage recoveries for surface waters were 40-79% (somatic) and 35-94% (F+). The method performed equally well in all three matrices at 1L volumes, but percent recoveries were significantly higher in marine waters at 10L volumes when compared to freshwater. Percent recoveries at 1L and 10L were similar, except in river water where recoveries were significantly lower at higher volume. In highly turbid waters, D-HFUF-SAL had a recovery range of 25-77% (somatic) and 21-80% (F+). The method produced detectable levels of coliphages in diluted wastewater and in unspiked surface waters, emphasizing its applicability to CSO events and highlighting its utility in recovery of low coliphage densities from surface waters. Thus D-HFUF-SAL is a good candidate method for routine water quality monitoring of coliphages. Published by Elsevier B.V.
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Gibbons, C D; Rodríguez, R A; Tallon, L; Sobsey, M D
2010-08-01
To evaluate the electropositive, alumina nanofibre (NanoCeram) cartridge filter as a primary concentration method for recovering adenovirus, norovirus and male-specific coliphages from natural seawater. Viruses were concentrated from 40 l of natural seawater using a NanoCeram cartridge filter and eluted from the filter either by soaking the filter in eluent or by recirculating the eluent continuously through the filter using a peristaltic pump. The elution solution consisted of 3% beef extract and 0.1 mol l(-1) of glycine. The method using a peristaltic pump was more effective in removing the viruses from the filter. High recoveries of norovirus and male-specific coliphages (>96%) but not adenovirus (<3%) were observed from seawater. High adsorption to the filter was observed for adenovirus and male-specific coliphages (>98%). The adsorption and recovery of adenovirus and male-specific coliphages were also determined for fresh finished water and source water. The NanoCeram cartridge filter was an effective primary concentration method for the concentration of norovirus and male-specific coliphages from natural seawater, but not for adenovirus, in spite of the high adsorption of adenovirus to the filter. This study demonstrates that NanoCeram cartridge filter is an effective primary method for concentrating noroviruses and male-specific coliphages from seawater, thereby simplifying collection and processing of water samples for virus recovery.
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40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.
Code of Federal Regulations, 2013 CFR
2013-07-01
... for the presence of E. coli, enterococci, or coliphage: Analytical Methods for Source Water Monitoring... Microbiology, 62:3881-3884. 10 EPA Method 1601: Male-specific (F+) and Somatic Coliphage in Water by Two-step... 20460. 11 EPA Method 1602: Male-specific (F+) and Somatic Coliphage in Water by Single Agar Layer (SAL...
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40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.
Code of Federal Regulations, 2014 CFR
2014-07-01
... for the presence of E. coli, enterococci, or coliphage: Analytical Methods for Source Water Monitoring... Microbiology, 62:3881-3884. 10 EPA Method 1601: Male-specific (F+) and Somatic Coliphage in Water by Two-step... 20460. 11 EPA Method 1602: Male-specific (F+) and Somatic Coliphage in Water by Single Agar Layer (SAL...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Power, U.F.; Collins, J.K.
1989-06-01
The elimination of sewage effluent-associated poliovirus, Escherichia coli, and a 22-nm icosahedral coliphage by the common mussel, Mytilus edulis, was studied. Both laboratory-and commercial-scale recirculating, UV depuration systems were used in this study. In the laboratory system, the logarithms of the poliovirus, E. coli, and coliphage levels were reduced by 1.86, 2.9, and 2.16, respectively, within 52 h of depuration. The relative patterns and rates of elimination of the three organisms suggest that they are eliminated from mussels by different mechanisms during depuration under suitable conditions. Poliovirus was not included in experiments undertaken in the commercial-scale depuration system. The differencesmore » in the relative rates and patterns of elimination were maintained for E. coli and coliphage in this system, with the logarithm of the E. coli levels being reduced by 3.18 and the logarithm of the coliphage levels being reduced by 0.87. The results from both depuration systems suggest that E. coli is an inappropriate indicator of the efficiency of virus elimination during depuration. The coliphage used appears to be a more representative indicator. Depuration under stressful conditions appeared to have a negligible affect on poliovirus and coliphage elimination rates from mussels. However, the rate and pattern of E. coli elimination were dramatically affected by these conditions. Therefore, monitoring E. coli counts might prove useful in ensuring that mussels are functioning well during depuration.« less
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Field-based evaluation of a male-specific (F+) RNA coliphage concentration method.
Chandler, J C; Pérez-Méndez, A; Paar, J; Doolittle, M M; Bisha, B; Goodridge, L D
2017-01-01
Fecal contamination of water poses a significant risk to public health due to the potential presence of pathogens, including enteric viruses. Therefore, sensitive, reliable and easy to use methods for the concentration, detection and quantification of microorganisms associated with the safety and quality of water are needed. In this study, we performed a field evaluation of an anion exchange resin-based method to concentrate male-specific (F+) RNA coliphages (FRNA), fecal indicator organisms, from diverse environmental waters that were suspected to be contaminated with feces. In this system, FRNA coliphages are adsorbed to anion exchange resin and direct nucleic acid isolation is performed, yielding a sample amenable to real-time reverse transcriptase (RT)-PCR detection. Matrix-dependent inhibition of this method was evaluated using known quantities of spiked FRNA coliphages belonging to four genogroups (GI, GII, GII and GIV). RT-PCR-based detection was successful in 97%, 72%, 85% and 98% of the samples spiked (10 6 pfu/l) with GI, GII, GIII and GIV, respectively. Differential FRNA coliphage genogroup detection was linked to inhibitors that altered RT-PCR assay efficiency. No association between inhibition and the physicochemical properties of the water samples was apparent. Additionally, the anion exchange resin method facilitated detection of naturally present FRNA coliphages in 40 of 65 environmental water samples (61.5%), demonstrating the viability of this system to concentrate FRNA coliphages from water. Copyright © 2016 Elsevier B.V. All rights reserved.
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Hepatitis E virus and coliphages in waters proximal to swine concentrated animal feeding operations.
Gentry-Shields, Jennifer; Myers, Kevin; Pisanic, Nora; Heaney, Christopher; Stewart, Jill
2015-02-01
North Carolina is the second leading state in pork production in the United States, with over 10 million swine. Swine manure in NC is typically collected and stored in open-pit lagoons before the liquid waste is sprayed onto agricultural fields for disposal. Components of this waste may be able to impact surface water quality with the potential for human exposure. This study examined viruses of public health concern in creeks adjacent to swine concentrated animal feeding operation (CAFO) spray fields. Surface water samples (n=154) were collected from public access waters in proximity to swine CAFO spray fields for six months and were tested for hepatitis E virus (HEV) and coliphages. HEV was detected in one sample. Somatic coliphages were detected in 98% of samples (geometric mean 24 ± 4.1 PFU per 100 ml), and F+ coliphages were detected in 85% of samples (geometric mean 6.8 ± 5.0 PFU per 100 ml). Only 3% (21) of the F+ coliphage isolates were RNA phage, and all of the F+ RNA coliphages belonged to genogroup I. Although the pervasiveness of swine CAFOs in this area prevented a comparison with samples from un-impacted sites, the near ubiquity of coliphages, as well as the presence of HEV, suggests that current waste management practices may be associated with the dissemination of viruses of public health concern in waters proximal to CAFO spray fields. Copyright © 2014 Elsevier B.V. All rights reserved.
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Yazdi, Mojgan; Yavarmanesh, Masoud; Bahreini, Masumeh; Mohebbi, Mohebbat
2017-03-01
The aim of this research was to preliminary track fecal source male-specific F + RNA coliphages including human and animals in lettuce. At first, two published virus extraction procedures of ultracentrifugation and PEG precipitation were compared using DAL assay for determining the recovery efficiency in lettuce spiked artificially with three concentrations (10 2 , 10 4 , 10 6 pfu/100 ml) of MS2 coliphage. The results showed that PEG precipitation had the highest recovery in which the recovery efficiency at the spiked level of 10 6 pfu/100 ml was 16.63 %. Aqueous phase obtained from the final step of PEG method was applied for enumeration of coliphage and viral RNA extraction in naturally contaminated lettuce samples (N = 30) collected from two sources (market and farm). The samples were then analyzed based on (I, II, III, and IV primer sets) using RT-PCR method. Coliphages were detected in 9 (60 %) and 12 (80 %) out of 15 market and farm samples, respectively, using DAL assay, whereas male-specific F + RNA coliphages were detected using the RT-PCR method in 9 (60 %) and 13 (86.6 %) out of 15 samples of market and farm, respectively. Based on the results, only genotype I of male-specific F + RNA coliphages was detected in lettuce samples and no sample tested was positive for other genotypes (II, III, and IV).
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Gino, Efrat; Starosvetsky, Jeana; Armon, Robert
2007-10-01
In view of various studies looking for the merit of coliphages as indicators of water pollution with viruses originating from faecal material, a small agricultural community (population of approximately 1500 inhabitants of all ages, 2-3 km from Haifa) was selected in order to understand these bacteriophage ecology (F-RNA and somatic coliphages) in its sewer and oxidation pond system. Along the sewer lines, it was possible to isolate constantly both bacteriophage types (F-RNA and somatic coliphages) at 10(2)-10(4) plaque-forming units (pfu) ml(-1). The average numbers of somatic and F-RNA phages isolated from oxidation pond were 10(3)-10(4) pfu ml(-1); however, somatic coliphages were undetectable for several months (April-August). Significant high correlation (0.944 < R(2) < 0.99) was found between increased anionic detergent concentrations and F-RNA coliphage numbers. Infants less than 1 year old excreted both phage types and few only F-RNA coliphages (at high numbers > 10(5) pfu g(-1)) for up to 1 year. The excretion of F-RNA coliphages was highly linked to Escherichia coli F(+) harborage in the intestinal track as found in their faecal content. Finally, three bacterial hosts E. coli F(+), F(-) and CN(13) tested for survivability in sewage filtrate revealed that E. coli F(+) had the highest survivability under these conditions. Presence of somatic and F male-specific phages in sewer lines of a small community are influenced by several factors such as: anionic detergents, nutrients, temperature, source (mainly infants), shedding and survival capability of the host strain. Better understanding of coliphages ecology in sewer systems can enhance our evaluation of these proposed indicator/index microorganisms used in tracking environmental pollution of water, soil and crop contamination with faecal material containing enteric viruses.
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Antimicrobial Efficiency of Iodinated Individual Protection Filters
2004-11-01
additional 2 logs of attenuation vs. a standard COTS canister when challenged with MS2 coliphage . U U U UU 9 Joseph D. Wander 850-283-6240 NOTICES USING...versus a standard COTS canister when challenged with MS2 coliphage . INTRODUCTION Biological weapons are not new, and have been used as warfare...canisters and the iodinated clip-on prototypes were challenged with aerosolized MS2 coliphage . EXPERIMENTAL METHODS Escherichia coli (ATCC 15597) was
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Kim, Hyung-Eun; Nguyen, Thuy T M; Lee, Hongshin; Lee, Changha
2015-12-15
The inactivation of Escherichia coli and MS2 coliphage by Cu(II) is found to be significantly enhanced in the presence of hydroxylamine (HA). The addition of a small amount of HA (i.e., 5-20 μM) increased the inactivation efficacies of E. coli and MS2 coliphage by 5- to 100-fold, depending on the conditions. Dual effects were anticipated to enhance the biocidal activity of Cu(II) by the addition of HA, viz. (i) the accelerated reduction of Cu(II) into Cu(I) (a stronger biocide) and (ii) the production of reactive oxidants from the reaction of Cu(I) with dissolved oxygen (evidenced by the oxidative transformation of methanol into formaldehyde). Deaeration enhanced the inactivation of E. coli but slightly decreased the inactivation efficacy of MS2 coliphage. The addition of 10 μM hydrogen peroxide (H2O2) greatly enhanced the MS2 inactivation, whereas the same concentration of H2O2 did not significantly affect the inactivation efficacy of E. coli Observations collectively indicate that different biocidal actions lead to the inactivation of E. coli and MS2 coliphage. The toxicity of Cu(I) is dominantly responsible for the E. coli inactivation. However, for the MS2 coliphage inactivation, the oxidative damage induced by reactive oxidants is as important as the effect of Cu(I).
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Mendez, Javier; Monleon-Getino, Antonio; Jofre, Juan; Lucena, Francisco
2017-10-01
The present study aimed to establish the kinetics of the appearance of coliphage plaques using the double agar layer titration technique to evaluate the feasibility of using traditional coliphage plaque forming unit (PFU) enumeration as a rapid quantification method. Repeated measurements of the appearance of plaques of coliphages titrated according to ISO 10705-2 at different times were analysed using non-linear mixed-effects regression to determine the most suitable model of their appearance kinetics. Although this model is adequate, to simplify its applicability two linear models were developed to predict the numbers of coliphages reliably, using the PFU counts as determined by the ISO after only 3 hours of incubation. One linear model, when the number of plaques detected was between 4 and 26 PFU after 3 hours, had a linear fit of: (1.48 × Counts 3 h + 1.97); and the other, values >26 PFU, had a fit of (1.18 × Counts 3 h + 2.95). If the number of plaques detected was <4 PFU after 3 hours, we recommend incubation for (18 ± 3) hours. The study indicates that the traditional coliphage plating technique has a reasonable potential to provide results in a single working day without the need to invest in additional laboratory equipment.
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Zyara, Alyaa M; Torvinen, Eila; Veijalainen, Anna-Maria; Heinonen-Tanski, Helvi
2016-08-01
Chlorine disinfection is a globally used method to ensure the safety of drinking water. However, it has not always been successful against viruses and, therefore, it is important to find new methods to disinfect water. Seventeen different coliphages were isolated from the treated municipal wastewater. These coliphages and MS2 were treated with different dosages of chlorine in drinking water, and a combined chlorine/ultraviolet irradiation treatment for the chlorine-resistant coliphages. Chlorine disinfection with 0.3-0.5 mg/L total chlorine (free Cl-dosage 0.12-0.21 mg/L) for 10 min achieved 2.5-5.7 Log10-reductions for 11 sensitive coliphages. The six most resistant coliphages showed no reduction with these chlorine concentrations. MS2 was intermediate in chlorine resistance, and thus it is not a good indicator for viruses in chlorine disinfection. In the combined treatment total chlorine of 0.05-0.25 mg/L (free Cl-dosage 0.02-0.08 mg/L) and ultraviolet irradiation (14-22 mWs/cm(2)) were more effective than chlorine alone, and 3-5 Log10-reductions were achieved for the chlorine-resistant strains. The chlorination efficiency could be increased by higher dosages and longer contact times, but this could increase the formation of disinfection by-products. Therefore, the combination treatment is a recommended disinfection method.
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LI, PING; LUO, SHIKE; PAN, CHUNJI; CHENG, XIAOSHU
2015-01-01
Heart failure is a disease predominantly caused by an energy metabolic disorder in cardiomyocytes. The present study investigated the inhibitory effects of fenofibrate (FF) on isoproterenol (ISO)-induced hear failure in rats, and examined the underlying mechanisms. The rats were divided into CON, ISO (HF model), FF and FF+ISO (HF animals pretreated with FF) groups. The cardiac structure and function of the rats were assessed, and contents of free fatty acids and glucose metabolic products were determined. In addition, myocardial cells were isolated from neonatal rats and used in vitro to investigate the mechanisms by which FF relieves heart failure. Western blot analysis was performed to quantify the expression levels of peroxisome proliferator-activated receptor (PPAR)α and uncoupling protein 2 (UCP2). FF effectively alleviated the ISO-induced cardiac structural damage, functional decline, and fatty acid and carbohydrate metabolic abnormalities. Compared with the ISO group, the serum levels of brain natriuretic peptide (BNP), free fatty acids, lactic acid and pyruvic acid were decreased in the FF animals. In the cultured myocardial cells, lactic acid and pyruvic acid contents were lower in the supernatants obtained from the FF animals, with lower levels of mitochondrial ROS production and cell necrosis, compared with the ISO group, whereas PPARα upregulation and UCP2 downregulation occurred in the FF+ISO group. The results demonstrated that FF efficiently alleviated heart failure in the ISO-induced rat model, possibly via promoting fatty acid oxidation. PMID:26497978
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Firefly Algorithm for Structural Search.
Avendaño-Franco, Guillermo; Romero, Aldo H
2016-07-12
The problem of computational structure prediction of materials is approached using the firefly (FF) algorithm. Starting from the chemical composition and optionally using prior knowledge of similar structures, the FF method is able to predict not only known stable structures but also a variety of novel competitive metastable structures. This article focuses on the strengths and limitations of the algorithm as a multimodal global searcher. The algorithm has been implemented in software package PyChemia ( https://github.com/MaterialsDiscovery/PyChemia ), an open source python library for materials analysis. We present applications of the method to van der Waals clusters and crystal structures. The FF method is shown to be competitive when compared to other population-based global searchers.
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ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins
Song, Dong; Wang, Wei; Ye, Wei; Ji, Dingjue; Luo, Ray; Chen, Hai-Feng
2017-01-01
Intrinsically disordered proteins (IDPs) are proteins which lack of specific tertiary structure and unable to fold spontaneously without the partner binding. These IDPs are found to associate with various diseases, such as diabetes, cancer, and neurodegenerative diseases. However, current widely used force fields, such as ff99SB, ff14SB, OPLS/AA, and Charmm27 are insufficient in sampling the conformational characters of IDPs. In this study, the CMAP method was used to correct the φ/ψ distributions of disorder-promoting amino acids. The simulation results show that the force filed parameters (ff14IDPs) can improve the φ/ψ distributions of the disorder-promoting amino acids, with RMSD less than 0.10% relative to the benchmark data of IDPs. Further test suggests that the calculated secondary chemical shifts under ff14IDPs force field are in quantitative agreement with the data of NMR experiment for five tested systems. In addition, the simulation results show that ff14IDPs can still be used to model structural proteins, such as tested lysozyme and ubiquitin, with better performance in coil regions than the original general Amber force field ff14SB. These findings confirm that the newly developed Amber ff14IDPs force field is a robust model for improving the conformation sampling of IDPs. PMID:27484738
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Filamentous Phage: Structure and Biology.
Rakonjac, Jasna; Russel, Marjorie; Khanum, Sofia; Brooke, Sam J; Rajič, Marina
2017-01-01
Ff filamentous phage (fd, M13 and f1) of Escherichia coli have been the workhorse of phage display technology for the past 30 years. Dominance of Ff over other bacteriophage in display technology stems from the titres that are about 100-fold higher than any other known phage, efficacious transformation ensuring large library size and superior stability of the virion at high temperatures, detergents and pH extremes, allowing broad range of biopanning conditions in screening phage display libraries. Due to the excellent understanding of infection and assembly requirements, Ff phage have also been at the core of phage-assisted continual protein evolution strategies (PACE). This chapter will give an overview of the Ff filamentous phage structure and biology, emphasizing those properties of the Ff phage life cycle and virion that are pertinent to phage display applications.
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Surface structure and stability of partially hydroxylated silica surfaces
Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.
2017-04-04
Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less
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Microbiological, coliphages and physico-chemical assessments of the Umgeni River, South Africa.
Singh, Atheesha; Lin, Johnson
2015-01-01
The water quality of Umgeni River in KwaZulu-Natal (South Africa) was investigated from April 2011 to January 2012. Indicator bacterial populations, physico-chemical properties, heavy metal contaminants and the presence of coliphages were determined according to standard protocols. The results showed that all sampling points failed to comply with the set guidelines for turbidity, total coliform, faecal coliform and total heterotrophic counts. Salmonella spp., Shigella spp. and Vibrio cholerae were also detected in all the water samples. The somatic coliphages and F-RNA coliphages were detected more frequently in the lower reaches of the river during summer. Temperature, electrical conductivity and pH were found to have positive relationships with the microbial communities especially in the lower catchment area during spring and summer indicating the impacts of various anthropogenic activities in the surrounding areas.
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Jebri, Sihem; Jofre, Juan; Barkallah, Insaf; Saidi, Mouldi; Hmaied, Fatma
2012-07-01
The role of water in the transmission of infectious diseases is well defined; it may act as a reservoir of different types of pathogens. Enteric viruses can survive and persist for a long time in water, maintaining infectivity in many instances. This suggests the need to include virus detection in the evaluation of the microbiological quality of waters. In this study, enteric viruses (enteroviruses and hepatitis A virus (HAV)) were investigated by RT-PCR and coliphages (known as indicators of viral contamination) were enumerated with the double-layer technique agar in effluents and sewage sludge from three Tunisian wastewater treatment plants. The molecular detection of enteric viruses revealed 7.7% of positive activated sludge samples for enteroviruses. None of the samples was positive for HAV. Molecular virus detection threshold was estimated to be 10(3) PFU/100 ml. All samples contained high concentrations of coliphages except those of dry sludge. Reductions in the concentrations of bacteriophages attained by the wastewater treatment plants are of the order of magnitude as reductions described elsewhere. Peak concentrations in raw wastewater were associated with winter rains and suspended materials rate in analysed samples. Our data which is the first in North Africa showed that similar trends of coliphages distribution to other studies in other countries. No clear correlation between studied enteric viruses and coliphages concentration was proved. Coliphages abundance in collected samples should raise concerns about human enteric viruses transmission as these residues are reused in agricultural fields.
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Structure of nascent replicative form DNA of coliphage M13
DOE Office of Scientific and Technical Information (OSTI.GOV)
Dasgupta, S.; Mitra, S.
Nascent replicative form type II (RFII) DNA of coliphage M13 synthesized in an Escherichia coli mutant deficient in the 5' ..-->.. 3' exonuclease associated with DNA polymerase I contains ribonucleotides that are retained in the covalently closed RFI DNA sealed in vitro by the joint action of T5 phage DNA polymerase and T4 phage DNA ligase. These RFI molecules are labile to alkali and RNase H, unlike the RFI produced either in vivo or from RFII with E. coli DNA polymerase I and E. coli DNA ligase. The ribonucleotides are located at one site and predominantly in one strand ofmore » the nascent RF DNA. Furthermore, these molecules contain multiple small gaps, randomly located, and one large gap in the intracistronic region.« less
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Structural Shielding Design of a 6 MV Flattening Filter Free Linear Accelerator: Indian Scenario.
Mishra, Bibekananda; Selvam, T Palani; Sharma, P K Dash
2017-01-01
Detailed structural shielding of primary and secondary barriers for a 6 MV medical linear accelerator (LINAC) operated with flattening filter (FF) and flattening filter free (FFF) modes are calculated. The calculations have been carried out by two methods, one using the approach given in National Council on Radiation Protection (NCRP) Report No. 151 and the other based on the monitor units (MUs) delivered in clinical practice. Radiation survey of the installations was also carried out. NCRP approach suggests that the primary and secondary barrier thicknesses are higher by 24% and 26%. respectively, for a LINAC operated in FF mode to that of a LINAC operated in both FF and FFF modes with an assumption that only 20% of the workload is shared in FFF mode. Primary and secondary barrier thicknesses calculated from MUs delivered on clinical practice method also show the same trend and are higher by 20% and 19%, respectively, for a LINAC operated in FF mode to that of a LINAC operated in both FF and FFF modes. Overall, the barrier thickness for a LINAC operated in FF mode is higher about 20% to that of a LINAC operated in both FF and FFF modes.
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Structural Shielding Design of a 6 MV Flattening Filter Free Linear Accelerator: Indian Scenario
Mishra, Bibekananda; Selvam, T. Palani; Sharma, P. K. Dash
2017-01-01
Detailed structural shielding of primary and secondary barriers for a 6 MV medical linear accelerator (LINAC) operated with flattening filter (FF) and flattening filter free (FFF) modes are calculated. The calculations have been carried out by two methods, one using the approach given in National Council on Radiation Protection (NCRP) Report No. 151 and the other based on the monitor units (MUs) delivered in clinical practice. Radiation survey of the installations was also carried out. NCRP approach suggests that the primary and secondary barrier thicknesses are higher by 24% and 26%. respectively, for a LINAC operated in FF mode to that of a LINAC operated in both FF and FFF modes with an assumption that only 20% of the workload is shared in FFF mode. Primary and secondary barrier thicknesses calculated from MUs delivered on clinical practice method also show the same trend and are higher by 20% and 19%, respectively, for a LINAC operated in FF mode to that of a LINAC operated in both FF and FFF modes. Overall, the barrier thickness for a LINAC operated in FF mode is higher about 20% to that of a LINAC operated in both FF and FFF modes. PMID:28405104
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Espinosa, Ana C; Arias, Carlos F; Sánchez-Colón, Salvador; Mazari-Hiriart, Marisa
2009-10-27
Bacteria used as indicators for pathogenic microorganisms in water are not considered adequate as enteric virus indicators. Surface water from a tropical high-altitude system located in Mexico City that receives rainwater, treated and non-treated wastewater used for irrigation, and groundwater used for drinking, was studied. The presence of enterovirus, rotavirus, astrovirus, coliphage, coliform bacteria, and enterococci was determined during annual cycles in 2001 and 2002. Enteric viruses in concentrated water samples were detected by reverse transcriptase-polymerase chain reaction (RT-PCR). Coliphages were detected using the double agar layer method. Bacteria analyses of the water samples were carried out by membrane filtration. The presence of viruses and bacteria in the water used for irrigation showed no relationship between current bacterial indicator detection and viral presence. Coliphages showed strong association with indicator bacteria and enterovirus, but weak association with other enteric viruses. Enterovirus and rotavirus showed significant seasonal differences in water used for irrigation, although this was not clear for astrovirus. Coliphages proved to be adequate faecal pollution indicators for the irrigation water studied. Viral presence in this tropical high-altitude system showed a similar trend to data previously reported for temperate zones.
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Free Available Chlorine Disinfection Criteria for Fixed Army Installation Primary Drinking Water
1981-12-01
Buffered Water with Fuivic Acid (5 C.U.) at pH 9 and 60C ............................................ 6. FAC Disinfection of f 2 Coliphage in Buffered Water ...with and without 250 mg/L -Ca+ at pH 5, 7, and 9 and 6°C ............... 31 10. FAC Disinfection of f 2 Coliphage in Water Containing 5 NTU Bentonite2...rngi L Ca+ 2 at pH- 5, 7, and q and 60C ...... ........................ 34 13. FAC Disinfection of f 2 Coliphage in Borate-Buffered Water with 250 mg
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A facile and low-cost micro fabrication material: flash foam.
He, Yong; Xiao, Xiao; Wu, Yan; Fu, Jian-zhong
2015-08-28
Although many microfabrication methods have been reported, the preliminary replication templates used in most microfabrication still depend on the expensive and long-period photolithography. This paper explores an alternative replication templates based on a daily used material, flash foam (FF), and proposes a facile microfabrication method, flash foam stamp lithography (FFSL). When FF is exposed with a desired pattern mask, the negative of the pattern is transferred to its surface and micro structures are formed due to the shrinkage of the exposed area. As FF is commonly used in personal stamps, FFSL is very simple and cost-effective. In this paper, we demonstrated that FF is a good and low-cost template for many micro fabrication methods, such as micro casting and soft lithography. Thus, designing and fabricating micro structures at personal office immediately become possible with FFSL. Furthermore, we demonstrated that multi-scale micro structures can be easily fabricated by double exposure with FFSL. Skin textures is used as another case to demonstrate that FFSL can fabricate structures with different depth in a single exposure. As a result, FF shows a promising future in biology, and analytical chemistry, such as rapid fabrication of point of care diagnostics and microfluidic analytical devices with low cost.
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NASA Astrophysics Data System (ADS)
Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.
2018-05-01
Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.
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Self-assembly of diphenylalanine with preclick components as capping groups.
Gemma, Andrea; Mayans, Enric; Ballano, Gema; Torras, Juan; Díaz, Angélica; Jiménez, Ana I; Puiggalí, Jordi; Cativiela, Carlos; Alemán, Carlos
2017-10-11
Alkyne and azide, which are commonly used in the cycloaddition reaction recognized as "click chemistry", have been used as capping groups of two engineered diphenylalanine (FF) derivatives due to their ability to form weak intermolecular interactions (i.e. dipole-π and π-π stacking). In Poc-FF-N 3 , alkyne and azide act as N- and C-terminal capping groups, respectively, while such positions are exchanged in N 3 -FF-OPrp. The self-assembly of such two synthesized peptides has been extensively studied in their "pre-click" state, considering the influence of three different factors: the peptide concentration, the polarity of the medium, and the nature of the substrate. Poc-FF-N 3 assembles into microfibers that, depending on the medium and the substrate, can aggregate hierarchically in supramolecular structures with different morphologies. The most distinctive one corresponds to very stable birefringent dendritic-like microstructures, which are derived from the ordered agglomeration of microfibers. These branched supramolecular structures, which are observed under a variety of conditions, are relatively uncommon in short FF sequences. At the molecular level, Poc-FF-N 3 organizes in antiparallel β-sheets stabilized by N-HO intermolecular hydrogen bonds and re-enforced by weak interactions between the azide and alkyne groups of neighbouring molecules. In contrast, N 3 -FF-OPrp exhibits a very poor tendency to organize into structures with a well-defined morphology. Theoretical calculations on model complexes indicate that the tendency of the latter peptide to organize into small amorphous agglomerates is due to its poor ability to form specific intermolecular interactions in comparison with Poc-FF-N 3 . The implications of the weak interactions induced by the alkyne and azide groups, which strengthen peptidepeptide hydrogen bonds and π-ladders due to the stacked aromatic phenyl side groups, are discussed.
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Rodríguez, Roberto A; Love, David C; Stewart, Jill R; Tajuba, Julianne; Knee, Jacqueline; Dickerson, Jerold W; Webster, Laura F; Sobsey, Mark D
2012-04-01
Methods for detection of two fecal indicator viruses, F+ and somatic coliphages, were evaluated for application to recreational marine water. Marine water samples were collected during the summer of 2007 in Southern California, United States from transects along Avalon Beach (n=186 samples) and Doheny Beach (n=101 samples). Coliphage detection methods included EPA method 1601 - two-step enrichment (ENR), EPA method 1602 - single agar layer (SAL), and variations of ENR. Variations included comparison of two incubation times (overnight and 5-h incubation) and two final detection steps (lysis zone assay and a rapid latex agglutination assay). A greater number of samples were positive for somatic and F+ coliphages by ENR than by SAL (p<0.01). The standard ENR with overnight incubation and detection by lysis zone assay was the most sensitive method for the detection of F+ and somatic coliphages from marine water, although the method takes up to three days to obtain results. A rapid 5-h enrichment version of ENR also performed well, with more positive samples than SAL, and could be performed in roughly 24h. Latex agglutination-based detection methods require the least amount of time to perform, although the sensitivity was less than lysis zone-based detection methods. Rapid culture-based enrichment of coliphages in marine water may be possible by further optimizing culture-based methods for saline water conditions to generate higher viral titers than currently available, as well as increasing the sensitivity of latex agglutination detection methods. Copyright © 2012 Elsevier B.V. All rights reserved.
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Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System.
Brown, Noam; Lei, Jiangtao; Zhan, Chendi; Shimon, Linda J W; Adler-Abramovich, Lihi; Wei, Guanghong; Gazit, Ehud
2018-04-24
Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.
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Jones, T H; Muehlhauser, V; Thériault, G
2014-09-01
Increasing attention is being paid to the impact of agricultural activities on water quality to understand the impact on public health. F-RNA coliphages have been proposed as viral indicators of fecal contamination while porcine teschovirus (PTV) and porcine adenovirus (PAdV) are proposed indicators of fecal contamination of swine origin. Viruses and coliphages are present in water in very low concentrations and must be concentrated to permit their detection. There is little information comparing the effectiveness of the methods for concentrating F-RNA coliphages with concentration methods for other viruses and vice versa. The objective of this study was to compare 5 current published methods for recovering F-RNA coliphages, PTV and PAdV from river water samples concentrated by electronegative nitrocellulose membrane filters (methods A and B) or electropositive Zeta Plus 60S filters (methods C-E). Method A is used routinely for the detection of coliphages (Méndez et al., 2004) and method C (Brassard et al., 2005) is the official method in Health Canada's compendium for the detection of viruses in bottled mineral or spring water. When river water was inoculated with stocks of F-RNA MS2, PAdV, and PTV to final concentrations of 1×10(6) PFU/100 mL, 1×10(5) gc/100 mL and 3×10(5) gc/100 mL, respectively, a significantly higher recovery for each virus was consistently obtained for method A with recoveries of 52% for MS2, 95% for PAdV, and 1.5% for PTV. When method A was compared with method C for the detection of F-coliphages, PAdV and PTV in river water samples, viruses were detected with higher frequencies and at higher mean numbers with method A than with method C. With method A, F-coliphages were detected in 11/12 samples (5-154 PFU/100 mL), PTV in 12/12 samples (397-10,951 gc/100 mL), PAdV in 1/12 samples (15 gc/100 mL), and F-RNA GIII in 1/12 samples (750 gc/100 mL) while F-RNA genotypes I, II, and IV were not detected by qRT-PCR. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.
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Gerba, Charles P; Riley, Kelley R; Nwachuku, Nena; Ryu, Hodon; Abbaszadegan, Morteza
2003-07-01
The removal of the Microsporidia, Encephalitozoon intestinalis, feline calicivirus and coliphages MS-2, PRD-1, and Fr were evaluated during conventional drinking water treatment in a pilot plant. The treatment consisted of coagulation, sedimentation, and mixed media filtration. Fr coliphage was removed the most (3.21 log), followed by feline calicivirus (3.05 log), E. coli (2.67 log), E. intestinalis (2.47 log), MS-2 (2.51 log). and PRD-1 (1.85 log). With the exception of PRD-1 the greatest removal of the viruses occurred during the flocculation step of the water treatment process.
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Whitman, R.L.; Przybyla-Kelly, K.; Shively, D.A.; Nevers, M.B.; Byappanahalli, M.N.
2009-01-01
Beach sand contains fecal indicator bacteria, often in densities greatly exceeding the adjacent swimming waters. We examined the transferability of Escherichia coli and F+ coliphage (MS2) from beach sand to hands in order to estimate the potential subsequent health risk. Sand with high initial E. coli concentrations was collected from a Chicago beach. Individuals manipulated the sand for 60 seconds, and rinse water was analysed for E. coli and coliphage. E. coli densities transferred were correlated with density in sand rather than surface area of an individual's hand, and the amount of coliphage transferred from seeded sand was different among individuals. In sequential rinsing, percentage reduction was 92% for E. coli and 98% for coliphage. Using dose-response estimates developed for swimming water, it was determined that the number of individuals per thousand that would develop gastrointestinal symptoms would be 11 if all E. coli on the fingertip were ingested or 33 if all E. coli on the hand were ingested. These results suggest that beach sand may be an important medium for microbial exposure; bacteria transfer is related to initial concentration in the sand; and rinsing may be effective in limiting oral exposure to sand-borne microbes of human concern.
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Mondal, Tania; Rouch, Duncan A; Thurbon, Nerida; Smith, Stephen R; Deighton, Margaret A
2015-06-01
Factors affecting the decay of Salmonella Birkenhead and coliphage, as representatives of bacterial and viral pathogens, respectively, during mesophilic anaerobic digestion (MAD) and air drying treatment of anaerobically digested sewage sludge were investigated. Controlled concentrations of S. Birkenhead were inoculated into non-sterile, autoclaved, γ-irradiated and nutrient-supplemented sludge and cultures were incubated at 37 °C (MAD sludge treatment temperature) or 20 °C (summer air drying sludge treatment temperature). Nutrient limitation caused by microbial competition was the principal mechanism responsible for the decay of S. Birkenhead by MAD and during air drying of digested sludge. The effects of protease activity in sludge on MS2 coliphage decay in digested and air dried sludge were also investigated. MS2 coliphage showed a 3.0-3.5 log10 reduction during incubation with sludge-protease extracts at 37 °C for 25 h. Proteases produced by indigenous microbes in sludge potentially increase coliphage inactivation and may therefore have a significant role in the decay of enteric viruses in sewage sludge. The results help to explain the loss of viability of enteric bacteria and viral pathogens with treatment process time and contribute to fundamental understanding of the various biotic inactivation mechanisms operating in sludge treatment processes at mesophilic and ambient temperatures.
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2009-01-01
Background Bacteria used as indicators for pathogenic microorganisms in water are not considered adequate as enteric virus indicators. Surface water from a tropical high-altitude system located in Mexico City that receives rainwater, treated and non-treated wastewater used for irrigation, and groundwater used for drinking, was studied. Methods The presence of enterovirus, rotavirus, astrovirus, coliphage, coliform bacteria, and enterococci was determined during annual cycles in 2001 and 2002. Enteric viruses in concentrated water samples were detected by reverse transcriptase-polymerase chain reaction (RT-PCR). Coliphages were detected using the double agar layer method. Bacteria analyses of the water samples were carried out by membrane filtration. Results The presence of viruses and bacteria in the water used for irrigation showed no relationship between current bacterial indicator detection and viral presence. Coliphages showed strong association with indicator bacteria and enterovirus, but weak association with other enteric viruses. Enterovirus and rotavirus showed significant seasonal differences in water used for irrigation, although this was not clear for astrovirus. Conclusion Coliphages proved to be adequate faecal pollution indicators for the irrigation water studied. Viral presence in this tropical high-altitude system showed a similar trend to data previously reported for temperate zones. PMID:19860917
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Assessment of coliphage surrogates for testing drinking water treatment devices.
Gerba, Charles P; Abd-Elmaksoud, Sherif; Newick, Huikheng; El-Esnawy, Nagwa A; Barakat, Ahmed; Ghanem, Hossam
2015-03-01
Test protocols have been developed by the United States Environmental Protection Agency (USEPA) and the World Health Organization (WHO) to test water treatment devices/systems that are used at the individual and home levels to ensure the removal of waterborne viruses. The goal of this study was to assess if coliphage surrogates could be used in this testing in place of the currently required use of animal or human enteric viruses. Five different coliphages (MS-2, PRD1, ΦX-174, Qβ, and fr) were compared to the removal of poliovirus type 1 (LSc-2ab) by eight different water treatment devices/systems using a general case and a challenge case (high organic load, dissolved solids, and turbidity) test water as defined by the USEPA. The performance of the units was rated as a pass/fail based on a 4 log removal/inactivation of the viruses. In all cases, a failure or a pass of the units/system for poliovirus also corresponded to a pass/fail by all of the coliphages. In summary, in using pass/fail criteria as recommended under USEPA guidelines for testing water treatment device/systems, the use of coliphages should be considered as an alternative to reduce cost and time of testing such devices/systems.
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Field-based evaluation of a male-specific (F+) RNA coliphage ...
Fecal contamination of water poses a significant risk to public health due to the potential presence of pathogens, including enteric viruses. Thus, sensitive, reliable and easy to use methods for the detection of microorganisms are needed to evaluate water quality. In this study, we performed a field evaluation of an anion-exchange resin based platform to concentrate F-RNA coliphages (fecal/enteric virus indicators) from diverse fecally impacted environmental waters. In this platform, F-RNA coliphages are adsorbed to anion-exchange resin and direct nucleic acid isolation is performed, yielding a sample amenable to real-time reverse transcriptase PCR detection. Matrix-dependent inhibition was evaluated using known quantities of spiked F-RNA coliphage genogroups GI, GII, GII and GIV. Detection was successful in 97%, 72%, 85% and 98% of the samples for spiked F-RNA coliphage GI, GII, GIII and GIV, respectively, and was differentially affected by inhibitory properties specific to each water sample. No association between inhibition and the water samples’ physicochemical properties was apparent. Parallel evaluations of the spiked samples with internal amplification control (IAC) reactions (a widely used control to assess inhibition) demonstrated that IAC reaction inhibition was not agreement with that observed for spiked samples, suggesting that testing of spiked samples allows for better assessments of matrix-dependent inhibition. Additionally, the anion-
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COLIPHAGES AS POTENTIAL VIRAL INDICATORS OF FECAL POLLUTION
Friedman, Stephanie D. In press. Coliphages as Potential Viral Indicators of Fecal Pollution (Abstract). To be presented at the SWS/GERS Fall Joint Society Meeting: Communication and Collaboration: Coastal Systems of the Gulf of Mexico and Southeastern United States, 6-9 October ...
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A facile and low-cost micro fabrication material: flash foam
He, Yong; Xiao, Xiao; Wu, Yan; Fu, Jian-zhong
2015-01-01
Although many microfabrication methods have been reported, the preliminary replication templates used in most microfabrication still depend on the expensive and long-period photolithography. This paper explores an alternative replication templates based on a daily used material, flash foam (FF), and proposes a facile microfabrication method, flash foam stamp lithography (FFSL). When FF is exposed with a desired pattern mask, the negative of the pattern is transferred to its surface and micro structures are formed due to the shrinkage of the exposed area. As FF is commonly used in personal stamps, FFSL is very simple and cost-effective. In this paper, we demonstrated that FF is a good and low-cost template for many micro fabrication methods, such as micro casting and soft lithography. Thus, designing and fabricating micro structures at personal office immediately become possible with FFSL. Furthermore, we demonstrated that multi-scale micro structures can be easily fabricated by double exposure with FFSL. Skin textures is used as another case to demonstrate that FFSL can fabricate structures with different depth in a single exposure. As a result, FF shows a promising future in biology, and analytical chemistry, such as rapid fabrication of point of care diagnostics and microfluidic analytical devices with low cost. PMID:26314247
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Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations
Tamamis, Phanourios; Adler-Abramovich, Lihi; Reches, Meital; Marshall, Karen; Sikorski, Pawel; Serpell, Louise; Gazit, Ehud; Archontis, Georgios
2009-01-01
Abstract Studies of peptide-based nanostructures provide general insights into biomolecular self-assembly and can lead material engineering toward technological applications. The diphenylalanine peptide (FF) self-assembles into discrete, hollow, well ordered nanotubes, and its derivatives form nanoassemblies of various morphologies. Here we demonstrate for the first time, to our knowledge, the formation of planar nanostructures with β-sheet content by the triphenylalanine peptide (FFF). We characterize these structures using various microscopy and spectroscopy techniques. We also obtain insights into the interactions and structural properties of the FF and FFF nanostructures by 0.4-μs, implicit-solvent, replica-exchange, molecular-dynamics simulations of aqueous FF and FFF solutions. In the simulations the peptides form aggregates, which often contain open or ring-like peptide networks, as well as elementary and network-containing structures with β-sheet characteristics. The networks are stabilized by polar and nonpolar interactions, and by the surrounding aggregate. In particular, the charged termini of neighbor peptides are involved in hydrogen-bonding interactions and their aromatic side chains form “T-shaped” contacts, as in three-dimensional FF crystals. These interactions may assist the FF and FFF self-assembly at the early stage, and may also stabilize the mature nanostructures. The FFF peptides have higher network propensities and increased aggregate stabilities with respect to FF, which can be interpreted energetically. PMID:19527662
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Franke, Christiane; Rechenburg, Andrea; Baumanns, Susanne; Willkomm, Marlene; Christoffels, Ekkehard; Exner, Martin; Kistemann, Thomas
2009-05-01
Different land use patterns were investigated for their potential as non-point sources of coliphage emissions into surface waters. Water samples were taken regularly at five locations in the upper reaches of the river Swist, Germany. Samples of surface and subsurface run-off were taken within the same catchment area after rainfall events using a newly developed device that made it possible to collect current concentrations of the effluent compounds. The water quality was examined for the occurrence of somatic coliphages and F(+)-specific RNA-bacteriophages as well as for various bacteria over the period of a hydrological year. The potential of various bacteria as indicators for the occurrence of phages was evaluated using statistical correlations. The load of coliphages varied depending on the land use type, but it did not differ as much as the bacterial parameters. River sections in intensively used areas turned out to be more contaminated than in less intensively used regions. The concentrations of phages from surface and subsurface run-off in most samples were quite low for all land use types and did not show conspicuous variations of surface and subsurface run-off within one land use type. Therefore, high concentrations of phages in river water cannot be explained only by non-point effluent from open ground. Following consideration of the statistical results, conventional indicator bacteria seem not to be reliable indicator organisms for coliphages and subsequently for human pathogen viruses. The detected concentrations of coliphages in several water samples of river sections surrounded by intensively used areas underpin an existing health risk in the use of river water for e.g. recreational activities or irrigation.
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BACKGROUND: Coliphages have been proposed as indicators of fecal contamination in recreational waters because they better mimic the persistence of pathogenic viruses in the environment and wastewater treatment than fecal indicator bacteria. We estimated the association between co...
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Coherent Soft X-ray Diffraction Imaging of Coliphage PR772 at the Linac Coherent Light Source
Reddy, Hemanth, K.N.
2017-01-05
A dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source.
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Interaction of human adenoviruses and coliphages with kaolinite and bentonite.
Bellou, Maria I; Syngouna, Vasiliki I; Tselepi, Maria A; Kokkinos, Petros A; Paparrodopoulos, Spyros C; Vantarakis, Apostolos; Chrysikopoulos, Constantinos V
2015-06-01
Human adenoviruses (hAdVs) are pathogenic viruses responsible for public health problems worldwide. They have also been used as viral indicators in environmental systems. Coliphages (e.g., MS2, ΦX174) have also been studied as indicators of viral pollution in fecally contaminated water. Our objective was to evaluate the distribution of three viral fecal indicators (hAdVs, MS2, and ΦΧ174), between two different phyllosilicate clays (kaolinite and bentonite) and the aqueous phase. A series of static and dynamic experiments were conducted under two different temperatures (4, 25°C) for a time period of seven days. HAdV adsorption was examined in DNase I reaction buffer (pH=7.6, and ionic strength (IS)=1.4mM), whereas coliphage adsorption in phosphate buffered saline solution (pH=7, IS=2mM). Moreover, the effect of IS on hAdV adsorption under static conditions was evaluated. The adsorption of hAdV was assessed by real-time PCR and its infectivity was tested by cultivation methods. The coliphages MS2 and ΦΧ174 were assayed by the double-layer overlay method. The experimental results have shown that coliphage adsorption onto both kaolinite and bentonite was higher for the dynamic than the static experiments; whereas hAdV adsorption was lower under dynamic conditions. The adsorption of hAdV increased with decreasing temperature, contrary to the results obtained for the coliphages. This study examines the combined effect of temperature, agitation, clay type, and IS on hAdV adsorption onto clays. The results provide useful new information on the effective removal of viral fecal indicators (MS2, ΦX174 and hAdV) from dilute aqueous solutions by adsorption onto kaolinite and bentonite. Factors enabling enteric viruses to penetrate soils, groundwater and travel long distances within aquifers are important public health issues. Because the observed adsorption behavior of surrogate coliphages MS2 and ΦΧ174 is substantially different to that of hAdV, neither MS2 nor ΦΧ174 is recommended as a suitable model for adenovirus. Copyright © 2015 Elsevier B.V. All rights reserved.
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The influence of particle size on the first flush strength of urban stormwater runoff.
Morgan, D; Johnston, P; Osei, K; Gill, L
2017-10-01
The presence of a first flush (FF) of suspended solids (SS) in stormwater runoff has important implications for the design of treatment facilities, as does the particle size of solids. Whilst numerous studies have examined the FF behaviour of SS, few have disaggregated FF trends by particle size. In this study, the FF behaviour of SS was investigated in five size ranges, sampled from an urban stormwater drainage system located in Dublin, Ireland. A weak FF was exhibited in the gross fraction of SS, with just two events from 14 transporting more than 50% of the SS mass in the first 25% of runoff, implying that treatment structures should be capable of removing SS throughout the storm event. In the majority of rain events, the FF strength increased with decreasing particle size, probably related to the lower intensities required to dislodge solids at the onset of rainfall. Although FF strength was correlated with rain event characteristics, prediction intervals were too broad to confirm FF presence based on rainfall data alone. Therefore, the design of smaller treatment volumes based on an assumption of FF must be justified by local monitoring data.
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Nkwe, Keitumetse Idah; Ateba, Collins Njie; Sithebe, Nomathamsanqa Patricia; Bezuidenhout, Cornelius Carlos
2015-07-01
Bacteriophages are regarded as enteric viral indicators in faecally contaminated water systems and may indicate the presence of human viral pollution. They are relatively resistant to inactivation by natural and treatment processes. In this study, the presence of somatic coliphages and F-RNA coliphages was investigated in potable water from rural areas in the North West province. Water samples were aseptically collected from boreholes and tap water from some rural communities in the North West Province. Physical parameters of the water, such as the temperature, pH and turbidity, were measured before sample collection. Double-agar layer assay was performed using ISO, (1995, 2000) standard methods. Bottled water was used as a negative control and the strains фX174 and MS2 as positive controls. Of the 16 water samples collected, 15 were positive for somatic bacteriophages while F-RNA coliphages were detected in only two samples. Amongst the positive samples 189 and three plaque forming units were obtained for both somatic and F-RNA coliphages, respectively. No coliphage was detected in water from Masamane tap 1. The rest of the samples obtained from various rural areas were positive and did not comply with national and international standards for potable water. This was a cause for concern and should be further investigated.
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Nkwe, Keitumetse Idah; Ateba, Collins Njie; Sithebe, Nomathamsanqa Patricia; Bezuidenhout, Cornelius Carlos
2015-01-01
Bacteriophages are regarded as enteric viral indicators in faecally contaminated water systems and may indicate the presence of human viral pollution. They are relatively resistant to inactivation by natural and treatment processes. In this study, the presence of somatic coliphages and F-RNA coliphages was investigated in potable water from rural areas in the North West province. Water samples were aseptically collected from boreholes and tap water from some rural communities in the North West Province. Physical parameters of the water, such as the temperature, pH and turbidity, were measured before sample collection. Double-agar layer assay was performed using ISO, (1995, 2000) standard methods. Bottled water was used as a negative control and the strains фX174 and MS2 as positive controls. Of the 16 water samples collected, 15 were positive for somatic bacteriophages while F-RNA coliphages were detected in only two samples. Amongst the positive samples 189 and three plaque forming units were obtained for both somatic and F-RNA coliphages, respectively. No coliphage was detected in water from Masamane tap 1. The rest of the samples obtained from various rural areas were positive and did not comply with national and international standards for potable water. This was a cause for concern and should be further investigated. PMID:26140675
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Franje, Catherine A; Chang, Shao-Kuang; Shyu, Ching-Lin; Davis, Jennifer L; Lee, Yan-Wen; Lee, Ren-Jye; Chang, Chao-Chin; Chou, Chi-Chung
2010-12-01
Heat stability of amphenicols and the relationship between structural degradation and antimicrobial activity after heating has not been well investigated. Florfenicol (FF), thiamphenicol (TAP), and chloramphenicol (CAP) were heated at 100 degrees C in water, salt water, soybean sauce and chicken meat for up to 2h. Degradation and antimicrobial activity of the compounds was evaluated using capillary electrophoresis (CE) with UV-DAD spectrometry, minimum inhibitory concentration (MIC) assay, and gas chromatography with electron impact ionization mass spectrometry (GC-EI-MS). Heat stability of amphenicols in matrices was ranked as water> or =salt water>soybean sauce>meat, suggesting that heat degradation of amphenicols was accelerated in soybean sauce and was not protected in meat. Heat stability by drug and matrices was ranked as FF>TAP=CAP in water, FF=TAP>CAP in salt water, TAP> or =FF=CAP in soybean sauce, and TAP> or =FF=CAP in meat, indicating differential heat stability of amphenicols among the 3 drugs and in different matrices. In accordance with the less than 20% degradation, the MIC against Escherichia coli and Staphylococcus aureus did not change after 2h heating in water. A 5-min heating of amphenicols in water by microwave oven generated comparable percentage degradation to boiling in water bath for 30 min to 1h. Both CE and GC-MS analysis showed that heating of FF produced TAP but not FF amine as one of its breakdown products. In conclusion, despite close similarity in structure; amphenicols exhibited differential behavior toward heating degradation in solutions and protein matrices. Although higher degradations of amphenicols were observed in soybean sauce and meat, heating treatment may generate product with antimicrobial activity (FF to TAP), therefore, heating of amphenicol residues in food cannot always be assumed safe. Copyright (c) 2010 Elsevier B.V. All rights reserved.
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Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source
Reddy, Hemanth K.N.; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A.; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G.; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A.; Kurta, Ruslan P.; Larsson, Daniel S.D.; Duane Loh, N.; Maia, Filipe R.N.C.; Mancuso, Adrian P.; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A.; Song, Changyong; Spence, John C.H.; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu
2017-01-01
Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency. PMID:28654088
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Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source
Reddy, Hemanth K. N.; Yoon, Chun Hong; Aquila, Andrew; ...
2017-06-27
Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. As a result, themore » data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.« less
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Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source.
Reddy, Hemanth K N; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A; Kurta, Ruslan P; Larsson, Daniel S D; Duane Loh, N; Maia, Filipe R N C; Mancuso, Adrian P; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A; Song, Changyong; Spence, John C H; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A; Williams, Garth J; Xavier, P Lourdu
2017-06-27
Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.
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Goals of reducing fecal contamination in recreational, drinking, shellfishing and other waters and accurately assessing risk from exposure can best be attained if tools to distinguish between sources of pollution are available. The male-specific RNA coliphage (FRNA) genogroups h...
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Past studies have indicated that sunlight plays an important role in altering densities of coliphages, other indicator microorganisms and pathogens in aquatic environments. Fate and transport modeling of bacteriophage requires mathematical relationships that describe the waveleng...
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Groundwater samples from two sites in Alabama, USA were plaque assayed for F-specific RNA (FRNA) coliphages using Salmonella typhimurium WG49 as the host bacterium. While numerous plaques were detected with WG49 (a strain possessing Escherichia coli F pili), plaques were also obs...
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Puerto Rico Strong Motion Seismic Network
NASA Astrophysics Data System (ADS)
Huerta-Lopez, C. I.; Martínez-Cruzado, J. A.; Martínez-Pagan, J.; Santana-Torres, E. X.; Torres-O, D. M.
2014-12-01
The Puerto Rico Strong Motion Seismic Network is currently in charge of the operation of: (i) free-field (ff) strong motion stations, (ii) instrumented structures (STR) (Dams, Bridges, Buildings), and (iii) the data acquisition/monitoring and analysis of earthquakes considered strong from the point of view of their intensity and magnitude. All these instruments are deployed in the Puerto Rico Island (PRI), US-, and British-Virgin Islands (BVI), and Dominican Republic (DR). The Puerto Rico Island and the Caribbean region have high potential to be affected by earthquakes that could be catastrophic for the area. The Puerto Rico Strong Motion Seismic Network (actually Puerto Rico Strong Motion Program, PRSMP) has grown since 1970's from 7 ff strong motion stations and one instrumented building with analog accelerographs to 111 ff strong motion stations and 16 instrumented buildings with digital accelerographs: PRI: 88 ff, 16 STR., DR: 13 ff, BVI: 5 ff, 2 STR collecting data via IP (internet), DU (telephone), and stand alone stations The current stage of the PRSMP seismic network, the analysis of moderate earthquakes that were recorded and/or occurred on the island, results of the intensity distribution of selected earthquakes, as well as results of dynamic parameter identification of some of the instrumented structures are here presented.
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Assignment of two new host range types to the P2 family of temperate coliphages.
Poon, A P; Dhillon, T S
1986-04-01
Six non-inducible coliphages which grow on Escherichia coli C but not on K12 (C-specific) were shown to be antigenically related to P2. All six were shown to be P4 helpers and some of them could also recombine with P2.
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Male-specific ssRNA (FRNA) coliphages belong to the family Leviviridae. Two genera subdivided into four genogroups (Levivirus, genogroups I and II and Allolevivirus, genogroups III and IV) comprise the lower taxonomic levels. Strains isolated from several continents have been p...
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Microbiological quality of Puget Sound Basin streams and identification of contaminant sources
Embrey, S.S.
2001-01-01
Fecal coliforms, Escherichia coli, enterococci, and somatic coliphages were detected in samples from 31 sites on streams draining urban and agricultural regions of the Puget Sound Basin Lowlands. Densities of bacteria in 48 and 71 percent of the samples exceeded U.S. Environmental Protection Agency's freshwater recreation criteria for Escherichia coli and enterococci, respectively, and 81 percent exceeded Washington State fecal coliform standards. Male-specific coliphages were detected in samples from 15 sites. Male-specific F+RNA coliphages isolated from samples taken at South Fork Thornton and Longfellow Creeks were serotyped as Group II, implicating humans as potential contaminant sources. These two sites are located in residential, urban areas. F+RNA coliphages in samples from 10 other sites, mostly in agricultural or rural areas, were serotyped as Group I, implicating non-human animals as likely sources. Chemicals common to wastewater, including fecal sterols, were detected in samples from several urban streams, and also implicate humans, at least in part, as possible sources of fecal bacteria and viruses to the streams.
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FF12MC: A revised AMBER forcefield and new protein simulation protocol
2016-01-01
ABSTRACT Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened C—H bonds, (ii) removal of torsions involving a nonperipheral sp3 atom, and (iii) reduced 1–4 interaction scaling factors of torsions ϕ and ψ. This article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric–isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left‐ and right‐handed configurations for C14–C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp‐cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general‐purpose AMBER forcefield FF14SB locks the C14–C38 bond to the right‐handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric–isothermal MD simulations 2–4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics. Proteins 2016; 84:1490–1516. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:27348292
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Voloshchuk, Natalya; Zhu, Anita Y; Snydacker, David; Montclare, Jin Kim
2009-09-15
To explore the impact of global incorporation of fluorinated aromatic amino acids on protein function, we investigated the effects of three monofluorinated phenylalanine analogs para-fluorophenylalanine (pFF), meta-fluorophenylalanine (mFF), and ortho-fluorophenylalanine (oFF) on the stability and enzymatic activity of the histone acetyltransferase (HAT), tGCN5. We selected this set of fluorinated amino acids because they bear the same size and overall polarity but alter in side chain shape and dipole direction. Our experiments showed that among three fluorinated amino acids, the global incorporation of pFF affords the smallest perturbation to the structure and function of tGCN5.
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Potable and monitoring wells located in close proximity to a large groundwater recharge project which utilizes a blend of surface water and reclaimed wastewater for recharge were tested for coliphage over a period of 6 months to assess the potential for virus migration. During th...
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A real-time, reverse transcription-PCR (RT-qPCR) assay was developed to differentiate the four genogroups of male-specific ssRNA coliphages (FRNA) (family Leviviridae). As FRNA display a trend of source-specificity (human sewage or animal waste) at the genogroup level, this assa...
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Inactivation of a model coliphage virus in water by iodine
NASA Technical Reports Server (NTRS)
Brion, Gail M.; Silverstein, Joann
1992-01-01
Until now, NASA's space water reuse research program has not considered the transport of water-borne infectious enteric viruses; however, viral diseases probably are a signifficant concern in long-duration space missions. To simplify monitoring and prediction of pathogen distribution, model indicator strains historically have been used. In this research, the male specific RNA coliphage MS-2 is used as a model of enteric viruses due to their similar size and biochemical composition. Inactivation of some water-borne enteric viruses by iodine has previously been characterized. In this paper, iodine inactivation of the model coliphage MS-2 in buffered water is compared with earlier bench-scale disinfection survival data and with survival in iodinated simulated shower water used in a test water recycling system.
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Shan, Tzu-Ray; van Duin, Adri C T; Thompson, Aidan P
2014-02-27
We have developed a new ReaxFF reactive force field parametrization for ammonium nitrate. Starting with an existing nitramine/TATB ReaxFF parametrization, we optimized it to reproduce electronic structure calculations for dissociation barriers, heats of formation, and crystal structure properties of ammonium nitrate phases. We have used it to predict the isothermal pressure-volume curve and the unreacted principal Hugoniot states. The predicted isothermal pressure-volume curve for phase IV solid ammonium nitrate agreed with electronic structure calculations and experimental data within 10% error for the considered range of compression. The predicted unreacted principal Hugoniot states were approximately 17% stiffer than experimental measurements. We then simulated thermal decomposition during heating to 2500 K. Thermal decomposition pathways agreed with experimental findings.
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Yong, Chin W
2016-08-22
DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.
Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less
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Baltar, Federico; Arístegui, Javier; Gasol, Josep M; Lekunberri, Itziar; Herndl, Gerhard J
2010-08-01
To investigate the effects of mesoscale eddies on prokaryotic assemblage structure and activity, we sampled two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) in the permanent eddy-field downstream the Canary Islands. The eddy stations were compared with two far-field (FF) stations located also in the Canary Current, but outside the influence of the eddy field. The distribution of prokaryotic abundance (PA), bulk prokaryotic heterotrophic activity (PHA), various indicators of single-cell activity (such as nucleic acid content, proportion of live cells, and fraction of cells actively incorporating leucine), as well as bacterial and archaeal community structure were determined from the surface to 2000 m depth. In the upper epipelagic layer (0-200 m), the effect of eddies on the prokaryotic community was more apparent, as indicated by the higher PA, PHA, fraction of living cells, and percentage of active cells incorporating leucine within eddies than at FF stations. Prokaryotic community composition differed also between eddy and FF stations in the epipelagic layer. In the mesopelagic layer (200-1000 m), there were also significant differences in PA and PHA between eddy and FF stations, although in general, there were no clear differences in community composition or single-cell activity. The effects on prokaryotic activity and community structure were stronger in AE than CE, decreasing with depth in both types of eddies. Overall, both types of eddies show distinct community compositions (as compared with FF in the epipelagic), and represent oceanic 'hotspots' of prokaryotic activity (in the epi- and mesopelagic realms).
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Reddy, Samala Murali Mohan; Shanmugam, Ganesh
2016-09-19
Although the role of intermolecular aromatic π-π interactions in the self-assembly of di-l-phenylalanine (l-Phe-l-Phe, FF), a peptide that is known for hierarchical structure, is well established, the influence of intramolecular π-π interactions on the morphology of the self-assembled structure of FF has not been studied. Herein, the role of intramolecular aromatic π-π interactions is investigated for FF and analogous alanine (Ala)-containing dipeptides, namely, l-Phe-l-Ala (FA) and l-Ala-l-Phe (AF). The results reveal that these dipeptides not only form self-assemblies, but also exhibit remarkable differences in structural morphology. The morphological differences between FF and the analogues indicate the importance of intramolecular π-π interactions, and the structural difference between FA and AF demonstrates the crucial role of the nature of intramolecular side-chain interactions (aromatic-aliphatic or aliphatic-aromatic), in addition to intermolecular interactions, in deciding the final morphology of the self-assembled structure. The current results emphasise that intramolecular aromatic π-π interaction may not be essential to induce self-assembly in smaller peptides, and π (aromatic)-alkyl or alkyl-π (aromatic) interactions may be sufficient. This work also illustrates the versatility of aromatic and a combination of aromatic and aliphatic residues in dipeptides in the formation of structurally diverse self-assembled structures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Morphology and Pattern Control of Diphenylalanine Self-Assembly via Evaporative Dewetting.
Chen, Jiarui; Qin, Shuyu; Wu, Xinglong; Chu, And Paul K
2016-01-26
Self-assembled peptide nanostructures have unique physical and biological properties and promising applications in electrical devices and functional molecular recognition. Although solution-based peptide molecules can self-assemble into different morphologies, it is challenging to control the self-assembly process. Herein, controllable self-assembly of diphenylalanine (FF) in an evaporative dewetting solution is reported. The fluid mechanical dimensionless numbers, namely Rayleigh, Marangoni, and capillary numbers, are introduced to control the interaction between the solution and FF molecules in the self-assembly process. The difference in the film thickness reflects the effects of Rayleigh and Marangoni convection, and the water vapor flow rate reveals the role of viscous fingering in the emergence of aligned FF flakes. By employing dewetting, various FF self-assembled patterns, like concentric and spokelike, and morphologies, like strips and hexagonal tubes/rods, can be produced, and there are no significant lattice structural changes in the FF nanostructures.
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Transferable Reactive Force Fields: Extensions of ReaxFF-lg to Nitromethane.
Larentzos, James P; Rice, Betsy M
2017-03-09
Transferable ReaxFF-lg models of nitromethane that predict a variety of material properties over a wide range of thermodynamic states are obtained by screening a library of ∼6600 potentials that were previously optimized through the Multiple Objective Evolutionary Strategies (MOES) approach using a training set that included information for other energetic materials composed of carbon, hydrogen, nitrogen, and oxygen. Models that best match experimental nitromethane lattice constants at 4.2 K and 1 atm are evaluated for transferability to high-pressure states at room temperature and are shown to better predict various liquid- and solid-phase structural, thermodynamic, and transport properties as compared to the existing ReaxFF and ReaxFF-lg parametrizations. Although demonstrated for an energetic material, the library of ReaxFF-lg models is supplied to the scientific community to enable new research explorations of complex reactive phenomena in a variety of materials research applications.
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NASA Astrophysics Data System (ADS)
Liu, Hao; Guo, Xiang; Han, Jingcheng; Luo, Ray; Chen, Hai-Feng
2018-06-01
Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved. In this study, molecular dynamics (MD) simulations were used to study the order-to-disorder transition kinetics of KID based on the good agreement with the experiment on its disordered-state properties. Specifically, we tested four force fields, ff99SBildn, ff99IDPs, ff14IDPSFF, and ff14IDPs in the simulations of KID and found that ff14IDPSFF can generate more diversified disordered conformers and also reproduce more accurate experimental secondary chemical shifts. Kinetics analysis of MD simulations demonstrates that the order-disorder transition of KID obeys the first-order kinetics, and the transition nucleus is I127/L128/L141. The possible transition pathways from the nucleus to the last folded residues were identified as I127-R125-L138-L141-S143-A145 and L128-R125-L138-L141-S143-A145 based on a residue-level dynamical network analysis. These computational studies not only provide testable prediction/hypothesis on the order-disorder transition of KID but also confirm that the ff14IDPSFF force field can be used to explore the correlation between the structure and function of IDPs.
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2011-01-01
We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures. Although χOL can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χOL for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χOL force field is compared with several previous glycosidic torsion parametrizations. PMID:21921995
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Lindsey, Bruce D.; Rasberry, Jennifer S.; Zimmerman, Tammy M.
2002-01-01
Samples were collected from 59 noncommunity water supplies in the Commonwealth of Pennsylvania from September 2000 to January 2001 and analyzed for pathogens and microbiological indicator organisms. The pathogens sampled were culturable viruses and Helicobacter pylori (H. pylori). The indicator organisms sampled were total coliform, Escherichia coli (E. coli), Clostridium perfringens (C. perfringens), somatic coliphage, male- specific coliphage, and enterococcus. The two primary areas sampled for the project completed by the U.S. Geological Survey, in cooperation with the Pennsylvania Department of Environmental Protection (PaDEP), were carbonate aquifers and crystalline aquifers. The results of all sampling showed culturable viruses were detected in 8 percent of the wells, H. pyloriin 7 percent of the wells, E. coli in 12 percent of the wells, total coliform in 46 percent of the wells, C. perfringens in 15 percent of the wells, somatic coliphage in 8 percent of the wells, male-specific coliphage in 5 percent of the wells, and enterococcus in 14 percent of the wells. Carbonate aquifers tended to have higher detection rates for the pathogens and indicators sampled than the crystalline aquifers. Detections of the pathogens and indicator organisms were not related statistically to the amounts of urban, agricultural, or forested area in a 1,500-foot radius around the sampled well. Somatic and male-specific coliphage showed the best relation to occurrence of culturable viruses. Culturable viruses and H. pylori were detected in wells in which no indicator organisms were present; therefore, none of the indicator organisms sampled provide complete assurance of pathogenfree water. The best predictive tool for virus screening was a combination of indicator organisms.
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Payment, P; Franco, E
1993-01-01
To find the most suitable indicator of viral and parasitic contamination of drinking water, large-volume samples were collected and analyzed for the presence of pathogens (cultivable human enteric viruses, Giardia lamblia cysts, and Cryptosporidium oocysts) and potential indicators (somatic and male-specific coliphages, Clostridium perfringens). The samples were obtained from three water treatment plants by using conventional or better treatments (ozonation, biological filtration). All samples of river water contained the microorganisms sought, and only C. perfringens counts were correlated with human enteric viruses, cysts, or oocysts. For settled and filtered water samples, all indicators were statistically correlated with human enteric viruses but not with cysts or oocysts. By using multiple regression, the somatic coliphage counts were the only explanatory variable for the human enteric virus counts in settled water, while in filtered water samples it was C. perfringens counts. Finished water samples of 1,000 liters each were free of all microorganisms, except for a single sample that contained low levels of cysts and oocysts of undetermined viability. Three of nine finished water samples of 20,000 liters each revealed residual levels of somatic coliphages at 0.03, 0.10, and 0.26 per 100 liters. Measured virus removal was more than 4 to 5 log10, and cyst removal was more than 4 log10. Coliphage and C. perfringens counts suggested that the total removal and inactivation was more than 7 log10 viable microorganisms. C. perfringens counts appear to be the most suitable indicator for the inactivation and removal of viruses in drinking water treatment.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8368831
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Nasser, Abidelfatah M; Benisti, Neta-Lee; Ofer, Naomi; Hovers, Sivan; Nitzan, Yeshayahu
2017-01-28
Advanced wastewater treatment processes are applied to prevent the environmental dissemination of pathogenic microorganisms. Giardia lamblia causes a severe disease called giardiasis, and is highly prevalent in untreated wastewater worldwide. Monitoring the microbial quality of wastewater effluents is usually based on testing for the levels of indicator microorganisms in the effluents. This study was conducted to compare the suitability of fecal coliforms, F+ coliphages and sulfide reducing clostridia (SRC) as indicators for the reduction of Giardia cysts in two full-scale wastewater treatment plants. The treatment process consists of activated sludge, coagulation, high rate filtration and either chlorine or UV disinfection. The results of the study demonstrated that Giardia cysts are highly prevalent in raw wastewater at an average concentration of 3600 cysts/L. Fecal coliforms, F+ coliphages and SRC were also detected at high concentrations in raw wastewater. Giardia cysts were efficiently removed (3.6 log 10 ) by the treatment train. The greatest reduction was observed for fecal coliforms (9.6 log 10 ) whereas the least reduction was observed for F+ coliphages (2.1 log 10 ) following chlorine disinfection. Similar reduction was observed for SRC by filtration and disinfection by either UV (3.6 log 10 ) or chlorine (3.3 log 10 ). Since F+ coliphage and SRC were found to be more resistant than fecal coliforms for the tertiary treatment processes, they may prove to be more suitable as indicators for Giardia. The results of this study demonstrated that advanced wastewater treatment may prove efficient for the removal of Giardia cysts and may prevent its transmission when treated effluents are applied for crop irrigation or streams restoration.
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Ravva, Subbarao V; Sarreal, Chester Z; Cooley, Michael B
2015-07-01
To provide data for traditional trace-back studies from fork to farm, it is necessary to determine the environmental sources for Shiga-toxigenic Escherichia coli. We developed SYBR green based reverse-transcriptase PCR methods to determine the prevalence of F+ RNA coliphages (FRNA) as indicators of fecal contamination. Male-specific coliphages, determined using a single-agar overlay method, were prevalent in all surface waters sampled for 8 months. F+ DNA coliphages (FDNA) were predominant compared to FRNA in water samples from majority of sampling locations. Most (90%) of the FRNA were sourced to humans and originated from human-impacted sites. Members of genogroup III represented 77% of FRNA originated from human sources. Furthermore, 93% of FRNA sourced to animals were also detected in water samples from human-impacted sites. Eighty percent of all FRNA were isolated during the winter months indicating seasonality in prevalence. In contrast, FDNA were more prevalent during summer months. E. coli O157:H7 and Shiga-toxigenic E. coli were detected in water samples from locations predominantly influenced by agriculture. Owing to their scarcity, their numbers could not be correlated with the prevalence of FRNA or FDNA in water samples. Both coliform bacteria and generic E. coli from agricultural or human-impacted sites were similar in numbers and thus could not be used to determine the sources of fecal contamination. Data on the prevalence of male-specific coliphages may be invaluable for predicting the sources of fecal contamination and aid in developing methods to prevent enteric pathogen contamination from likely sources during produce production.
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Application of F⁺RNA Coliphages as Source Tracking Enteric Viruses on Parsley and Leek Using RT-PCR.
Shahrampour, Dina; Yavarmanesh, Masoud; Najafi, Mohammad Bagher Habibi; Mohebbi, Mohebbat
2015-12-01
The objective of this study was to identify sources of fecal contamination in leek and parsley, by using four different F(+)RNA coliphage genogroups (IV, I indicate animal fecal contamination and II, III indicate human fecal contamination). Three different concentrations (10(2), 10(4), 10(6) pfu/ml) of MS2 coliphage were inoculated on the surface of parsley and leek samples for detection of phage recovery efficiency among two methods of elution concentration (PEG-precipitation and Ultracentrifugation) by performing double agar layer (DAL) assay in three replications. Highest recovery of MS2 was observed in PEG method and in 10(6) inoculation concentration. Accordingly, the PEG method was used for washing and isolation of potentially contaminated phages of 30 collected samples (15 samples from the market and 15 samples from the farm). The final solutions of PEG method were tested for the enumeration of plaques by DAL assay. Total RNA was then extracted from recovered phages, and RT-PCR was performed by using four primer sets I, II, III, and IV. Incidence of F(+)RNA coliphages was observed in 12/15 (80 %) and 10/15 (66/6 %) of samples were obtained from farm and market, respectively, using both DAL and RT-PCR test methods. Different genotypes (I, II, and IV) of F(+)RNA coliphages were found in farm samples, while only genotype I was detected in market samples by using the primer sets. Due to the higher frequency of genotype I and IV, the absence of genotype III, and also the low frequency of genotype II, it is concluded that the contamination of vegetable (parsley and leek) in Neyshabour, Iran is most likely originated from animal sources.
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Oishi, Wakana; Sano, Daisuke; Decrey, Loic; Kadoya, Syunsuke; Kohn, Tamar; Funamizu, Naoyuki
2017-11-15
Volume reduction (condensation) is a key for the practical usage of human urine as a fertilizer because it enables the saving of storage space and the reduction of transportation cost. However, concentrated urine may carry infectious disease risks resulting from human pathogens frequently present in excreta, though the survival of pathogens in concentrated urine is not well understood. In this study, the inactivation of MS2 coliphage, a surrogate for single-stranded RNA human enteric viruses, in concentrated synthetic urine was investigated. The infectious titer reduction of MS2 coliphage in synthetic urine samples was measured by plaque assay, and the reduction of genome copy number was monitored by reverse transcription-quantitative PCR (RTqPCR). Among chemical-physical conditions such as pH and osmotic pressure, uncharged ammonia was shown to be the predominant factor responsible for MS2 inactivation, independently of urine concentration level. The reduction rate of the viral genome number varied among genome regions, but the comprehensive reduction rate of six genome regions was well correlated with that of the infectious titer of MS2 coliphage. This indicates that genome degradation is the main mechanism driving loss of infectivity, and that RT-qPCR targeting the six genome regions can be used as a culture-independent assay for monitoring infectivity loss of the coliphage in urine. MS2 inactivation rate constants were well predicted by a model using ion composition and speciation in synthetic urine samples, which suggests that MS2 infectivity loss can be estimated solely based on the solution composition, temperature and pH, without explicitly accounting for effects of osmotic pressure. Copyright © 2017 Elsevier B.V. All rights reserved.
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Coliphage and indigenous phage in Mamala Bay, Oahu, Hawaii.
Paul, J H; Rose, J B; Jiang, S C; London, P; Xhou, X; Kellogg, C
1997-01-01
Public concern over the discharge of primarily treated sewage by two offshore outfalls in Mamala Bay, Oahu, prompted a multidisciplinary study to determine the impact of such activities on the water quality in the bay and at adjacent recreational beaches. As part of this study, we determined the abundance of coliphage as an indicator of fecal pollution along with total viral direct counts and phages infective for Vibrio parahaemoltyicus 16 at stations in Mamala Bay in four quarterly samplings over 13 months. Coliphage (< 1 to 1.2 x 10(3)/liter) were found during each quarterly sampling along an offshore transect to the Sand Island waste treatment facility outfall. The nonpoint coastal stations (Pearl Harbor, Ala Wai Canal, and Ke'ehi Lagoon) had high levels of coliphage during the storm event sampling in February 1994 but much lower levels or none when sampled during dry weather. Coliphage were absent at all samplings at Waikiki Beach and at the control station off Diamond Head. Viral direct counts in eutrophic coastal stations (Pearl Harbor, Ke'ehi Lagoon, Ala Moana Beach, and Ala Wai canal) averaged 10(9)/liter, while counts at offshore stations ranged from 9 x 10(7) to 1 x 10(9) viruses/liter, values similar to those for other marine environments. Vibriophage were found mainly in eutrophic coastal environments (Ala Wai Canal, Pearl Harbor, and Ke'ehi Lagoon) and at the Sand Island Transect stations D1 and D2. The greatest abundance was found during the storm event (February 1994) sampling. These results suggest that the Sand Island outfall influenced the water quality of the immediate surrounding waters but had little effect on the quality of the recreational beaches. Nonpoint discharge sources appeared to be more important in the distribution of fecal indicators in the coastal zone.
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Belcher, John D.; Chen, Chunsheng; Nguyen, Julia; Abdulla, Fuad; Nguyen, Phong; Nguyen, Minh; Okeley, Nicole M.; Benjamin, Dennis R.; Senter, Peter D.; Vercellotti, Gregory M.
2015-01-01
2-Fluorofucose (2FF) blocks the fucosylation and the tethering of sialyl-Lewisx tetrasaccharide and structural variants on leukocytes and red blood cells to P- and E-selectins on activated endothelial cell surfaces. Because P- and E-selectin are required for vaso-occlusion in murine sickle cell disease (SCD), we investigated whether 2FF would inhibit vaso-occlusion in SCD mice. Microvascular stasis was measured in subcutaneous venules in NY1DD and HbSS-Townes SCD mice with dorsal skin-fold chambers after infusion of hemoglobin or exposure to hypoxia/reoxygenation. 2FF in drinking water or administered by gavage inhibited stasis in sickle mice in a dose-responsive manner. Significant inhibitory effects on stasis were seen 1 day post-treatment. 2FF treatment of SCD mice also significantly reduced leukocyte rolling and adhesion along the vessel walls of SCD mice and the static adhesion of neutrophils and sickle red blood cells isolated from 2FF-treated SCD mice to resting and activated endothelial cells. Total white blood cell counts increased in response to 2FF. NF-ĸB activation and VCAM-1 and E-selectin expression were inhibited in the livers of SCD mice consistent with an overall decrease in vascular inflammation and ischemia-reperfusion physiology. Pretreatment with 2FF completely eliminated heme-induced lethality in HbSS-Townes mice, consistent with the observed anti-inflammatory and anti-adhesive properties of 2FF in SCD mice. These data suggest that 2FF may be beneficial for preventing or treating vaso-occlusive crises in SCD patients. PMID:25706118
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Atomic-scale electronic structure of the cuprate d-symmetry form factor density wave state
M. H. Hamidian; Kim, Chung Koo; Edkins, S. D.; ...
2015-10-26
Research on high-temperature superconducting cuprates is at present focused on identifying the relationship between the classic ‘pseudogap’ phenomenon 1, 2 and the more recently investigated density wave state 3–13. This state is generally characterized by a wavevector Q parallel to the planar Cu–O–Cu bonds 4–13 along with a predominantly d-symmetry form factor 14–17 (dFF-DW). To identify the microscopic mechanism giving rise to this state 18–30, one must identify the momentum-space states contributing to the dFF-DW spectral weight, determine their particle–hole phase relationship about the Fermi energy, establish whether they exhibit a characteristic energy gap, and understand the evolution of allmore » these phenomena throughout the phase diagram. Here we use energy-resolved sublattice visualization 14 of electronic structure and reveal that the characteristic energy of the dFF-DW modulations is actually the ‘pseudogap’ energy Δ 1. Moreover, we demonstrate that the dFF-DW modulations at E = –Δ 1 (filled states) occur with relative phase π compared to those at E = Δ 1 (empty states). Lastly, we show that the conventionally defined dFF-DW Q corresponds to scattering between the ‘hot frontier’ regions of momentum-space beyond which Bogoliubov quasiparticles cease to exist 30–32. These data indicate that the cuprate dFF-DW state involves particle–hole interactions focused at the pseudogap energy scale and between the four pairs of ‘hot frontier’ regions in momentum space where the pseudogap opens.« less
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NASA Astrophysics Data System (ADS)
Sengul, Mert Y.; Randall, Clive A.; van Duin, Adri C. T.
2018-04-01
The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was investigated using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ xHAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ xHAc), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental results. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations indicate that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.
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Park, Eunyoung; Lee, Cheonghoon; Bisesi, Michael; Lee, Jiyoung
2014-03-01
The disinfection efficiency of peracetic acid (PAA) was investigated on three microbial types using three different methods (filtration-based ATP (adenosine-triphosphate) bioluminescence, quantitative polymerase chain reaction (qPCR), culture-based method). Fecal indicator bacteria (Enterococcus faecium), virus indicator (male-specific (F(+)) coliphages (coliphages)), and protozoa disinfection surrogate (Bacillus subtilis spores (spores)) were tested. The mode of action for spore disinfection was visualized using scanning electron microscopy. The results indicated that PAA concentrations of 5 ppm (contact time: 5 min), 50 ppm (10 min), and 3,000 ppm (5 min) were needed to achieve 3-log reduction of E. faecium, coliphages, and spores, respectively. Scanning electron microscopy observation showed that PAA targets the external layers of spores. The lower reduction rates of tested microbes measured with qPCR suggest that qPCR may overestimate the surviving microbes. Collectively, PAA showed broad disinfection efficiency (susceptibility: E. faecium > coliphages > spores). For E. faecium and spores, ATP bioluminescence was substantially faster (∼5 min) than culture-based method (>24 h) and qPCR (2-3 h). This study suggests PAA as an effective alternative to inactivate broad types of microbial contaminants in water. Together with the use of rapid detection methods, this approach can be useful for urgent situations when timely response is needed for ensuring water quality.
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Muniesa, M; Ballesté, E; Imamovic, L; Pascual-Benito, M; Toribio-Avedillo, D; Lucena, F; Blanch, A R; Jofre, J
2018-01-01
The use of somatic coliphages as indicators of fecal and viral pollution in water and food has great potential due to the reliability, reproducibility, speed and cost effectiveness of methods for their detection. Indeed, several countries already use this approach in their water management policies. Although standardized protocols for somatic coliphage detection are available, user-friendly commercial kits would facilitate their routine implementation in laboratories. The new method presented here allows detection of up to 1 somatic coliphage in under 3.5 h, well within one working day. The method is based on a modified Escherichia coli strain with knocked-out uidB and uidC genes, which encode the transport of glucuronic acid inside cells, and overexpressing uidA, which encodes the enzyme β-glucuronidase. The enzyme accumulated in the bacterial cells only has contact with its substrate after cell lysis, such as that caused by phages, since the strain cannot internalize the substrate. When the enzyme is released into the medium, which contains a chromogen analogous to glucuronic acid, it produces a change of color from yellow to dark blue. This microbiological method for the determination of fecal pollution via the detection of culturable microorganisms can be applied to diverse sample types and volumes for qualitative (presence/absence) and quantitative analysis and is the fastest reported to date. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Lee, Hee Suk; Sobsey, Mark D
2011-06-01
The potential use of specific somatic coliphage taxonomic groups as viral indicators based on their persistence and prevalence in water was investigated. Representative type strains of the 4 major somatic coliphage taxonomic groups were seeded into reagent water and an ambient surface water source of drinking water and the survival of the added phages was measured over 90 days at temperatures of 23-25 and 4 °C. Microviridae (type strain PhiX174), Siphoviridae (type strain Lambda), and Myoviridae (type strain T4) viruses were the most persistent in water at the temperatures tested. The Microviridae (type strain PhiX174) and the Siphoviridae (type strain Lambda) were the most resistant viruses to UV radiation and the Myoviridae (type strain T4) and the Microviridae (type strain PhiX174) were the most resistant viruses to heat. Based on their greater persistence in water over time and their relative resistance to heat and/or UV radiation, the Myoviridae (type strain T4), the Microviridae (type strain PhiX174), and the Siphoviridae (type strain Lambda) were the preferred candidate somatic coliphages as fecal indicator viruses in water, with the Microviridae (type strain PhiX174) the most resistant to these conditions overall. Copyright © 2011 Elsevier Ltd. All rights reserved.
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Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor
2018-03-01
The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.
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Probing the structure of Nun transcription arrest factor bound to RNA polymerase
Mustaev, Arkady; Vitiello, Christal L.; Gottesman, Max E.
2016-01-01
The coliphage HK022 protein Nun transcription elongation arrest factor inhibits RNA polymerase translocation. In vivo, Nun acts specifically to block transcription of the coliphage λ chromosome. Using in vitro assays, we demonstrate that Nun cross-links RNA in an RNA:DNA hybrid within a ternary elongation complex (TEC). Both the 5′ and the 3′ ends of the RNA cross-link Nun, implying that Nun contacts RNA polymerase both at the upstream edge of the RNA:DNA hybrid and in the vicinity of the catalytic center. This finding suggests that Nun may inhibit translocation by more than one mechanism. Transcription elongation factor GreA efficiently blocked Nun cross-linking to the 3′ end of the transcript, whereas the highly homologous GreB factor did not. Surprisingly, both factors strongly suppressed Nun cross-linking to the 5′ end of the RNA, suggesting that GreA and GreB can enter the RNA exit channel as well as the secondary channel, where they are known to bind. These findings extend the known action mechanism for these ubiquitous cellular factors. PMID:27436904
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Griffin, Dale W.; Gibson, Charles J.; Lipp, Erin K.; Riley, Kelley; Paul, John H.; Rose, Joan B.
1999-01-01
In order to assess the microbial water quality in canal waters throughout the Florida Keys, a survey was conducted to determine the concentration of microbial fecal indicators and the presence of human pathogenic microorganisms. A total of 19 sites, including 17 canal sites and 2 nearshore water sites, were assayed for total coliforms, fecal coliforms, Escherichia coli, Clostridium perfringens, enterococci, coliphages, F-specific (F+) RNA coliphages, Giardia lamblia, Cryptosporidium parvum, and human enteric viruses (polioviruses, coxsackie A and B viruses, echoviruses, hepatitis A viruses, Norwalk viruses, and small round-structured viruses). Numbers of coliforms ranged from <1 to 1,410, E. coli organisms from <1 to 130, Clostridium spp. from <1 to 520, and enterococci from <1 to 800 CFU/100 ml of sample. Two sites were positive for coliphages, but no F+ phages were identified. The sites were ranked according to microbial water quality and compared to various water quality standards and guidelines. Seventy-nine percent of the sites were positive for the presence of enteroviruses by reverse transcriptase PCR (polioviruses, coxsackie A and B viruses, and echoviruses). Sixty-three percent of the sites were positive for the presence of hepatitis A viruses. Ten percent of the sites were positive for the presence of Norwalk viruses. Ninety-five percent of the sites were positive for at least one of the virus groups. These results indicate that the canals and nearshore waters throughout the Florida Keys are being impacted by human fecal material carrying human enteric viruses through current wastewater treatment strategies such as septic tanks. Exposure to canal waters through recreation and work may be contributing to human health risks. PMID:10473424
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Hinkle, Stephen J.; Weick, Rodney J.; Johnson, Jill M.; Cahill, Jeffery D.; Smith, Steven G.; Rich, Barbara J.
2005-01-01
The occurrence of organic wastewater compounds (components of 'personal care products' and other common household chemicals), pharmaceuticals (human prescription and nonprescription medical drugs), and coliphage (viruses that infect coliform bacteria, and found in high concentrations in municipal wastewater) in onsite wastewater (septic tank effluent) and in a shallow, unconfined, sandy aquifer that serves as the primary source of drinking water for most residents near La Pine, Oregon, was documented. Samples from two types of observation networks provided basic occurrence data for onsite wastewater and downgradient ground water. One observation network was a group of 28 traditional and innovative (advanced treatment) onsite wastewater treatment systems and associated downgradient drainfield monitoring wells, referred to as the 'innovative systems network'. The drainfield monitoring wells were located adjacent to or under onsite wastewater treatment system drainfield lines. Another observation network, termed the 'transect network', consisted of 31 wells distributed among three transects of temporary, stainless-steel-screened, direct-push monitoring wells installed along three plumes of onsite wastewater. The transect network, by virtue of its design, also provided a basis for increased understanding of the transport of analytes in natural systems. Coliphage were frequently detected in onsite wastewater. Coliphage concentrations in onsite wastewater were highly variable, ranging from less than 1 to 3,000,000 plaque forming units per 100 milliliters. Coliphage were occasionally detected (eight occurrences) at low concentrations in samples from wells located downgradient from onsite wastewater treatment system drainfield lines. However, coliphage concentrations were below method detection limits in replicate or repeat samples collected from the eight sites. The consistent absence of coliphage detections in the replicate or repeat samples is interpreted to indicate that the detections reported for ground-water samples represented low-level field or laboratory contamination, and it would appear that coliphage were effectively attenuated to less than 1 PFU/100 mL over distances of several feet of transport in the La Pine aquifer and (or) overlying unsaturated zone. Organic wastewater compounds were frequently detected in onsite wastewater. Of the 63 organic wastewater compounds in the analytical schedule, 45 were detected in the 21 samples of onsite wastewater. Concentrations of organic wastewater compounds reached a maximum of 1,300 ug/L (p-cresol). Caffeine was detected at concentrations as high as 320 ug/L. Fourteen of the 45 compounds were detected in more than 90 percent of onsite wastewater samples. Fewer (nine) organic wastewater compounds were detected in ground water, despite the presence of nitrate and chloride likely from onsite wastewater sources. The nine organic wastewater compounds that were detected in ground-water samples were acetyl-hexamethyl-tetrahydro-naphthalene (AHTN), caffeine, cholesterol, hexahydrohexamethyl-cyclopentabenzopyran, N,N-diethyl-meta-toluamide (DEET), tetrachloroethene, tris (2-chloroethyl) phosphate, tris (dichloroisopropyl) phosphate, and tributyl phosphate. Frequent detection of household-chemical type organic wastewater compounds in onsite wastewater provides evidence that some of these organic wastewater compounds may be useful indicators of human waste effluent dispersal in some hydrologic environments. The occurrence of organic wastewater compounds in ground water downgradient from onsite wastewater treatment systems demonstrates that a subgroup of organic wastewater compounds is transported in the La Pine aquifer. The consistently low concentrations (generally less than 1 ug/L) of organic wastewater compounds in water samples collected from wells located no more than 19 feet from drainfield lines indicates that the reactivity (sorption, degradation) of this suite of organic waste
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A Single Molecule Study of Two Bacteriophage Epigenetic Switches
NASA Astrophysics Data System (ADS)
Wang, Haowei
Epigenetic switches allow organisms to evolve into different states by activating/repressing different sets of genes without mutations of the underlying DNA sequence. The study of epigenetic switches is very important to understand the mechanism of human development, the origin of cancer, mental illness and fundamental processes such as gene regulation. The coliphage lambda epigenetic switch, which allows switching from lysogeny to lysis, has been studied for more than 50 years as a paradigm, and has recently received renewed attention. Atomic force microscopy (AFM) was used here to show that the lambda repressor oligomerizes on DNA, primarily as a dodecamer, to secure a DNA loop, which is the basis of the lambda switch. This study also provides support for the idea that specifically bound repressor stabilizes adjacent, non-specifically bound repressor molecules, which confers robustness to the switch. 186 is a member of a different coliphage family. One of the major differences between the two coliphage families is that lambda phages can be induced to switch from the lysogenic to the lytic state by UV radiation, but most coliphages of P2 family, to which 186 belongs, cannot. Interaction between coliphage 186 repressor and DNA is characterized by AFM and tethered particle motion (TPM). To expedite analysis of the AFM data, MatLab codes were written to automate the laborious, manual tracing procedures. The programs automatically recognize DNA segments and protein particles in an image, in order to measure the DNA length and position of bound particles as well as their height, diameter and volume. Application of these algorithms greatly improved the efficiency of AFM analysis. It was showed that 186 CI dimers form heptameric wheels, which induce DNA wrapping and different kinds of DNA looping producing various conformations of nucleoprotein complexes. Information about the dynamics of DNA wrapping and looping on 186 CI particles was also obtained by TPM.
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Mittal, Jeetain; Best, Robert B
2010-08-04
The ability to fold proteins on a computer has highlighted the fact that existing force fields tend to be biased toward a particular type of secondary structure. Consequently, force fields for folding simulations are often chosen according to the native structure, implying that they are not truly "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structures, a simple correction to the backbone potential (ff03( *)) results in an unbiased energy function. We take as examples the 35-residue alpha-helical Villin HP35 and 37 residue beta-sheet Pin WW domains, which had not previously been folded with the same force field. Starting from unfolded configurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A RMSD of the experimental structures. This demonstrates that a simple backbone correction results in a more transferable force field, an important requirement if simulations are to be used to interpret folding mechanism. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Genes and Structural Proteins of the Phage Syn5 of the Marine Cyanobacteria Synechococcus
2005-09-01
typhimurium phage P22, a podoviridae, was shown to possess extensive genomic similarity to coliphage lambda, a siphoviridae (Botstein and Herskowitz...are found among cyanobacteria in the surface waters during the winter. Temperature influences the number of infectious particles produced during lytic...grids and stained with 1% uranyl acetate for 15 minutes, washed three times in double-distilled water , stained in 1% lead citrate for 4 minutes, and
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Cohen, Dror; van Swinderen, Bruno; Tsuchiya, Naotsugu
2018-01-01
Hierarchically organized brains communicate through feedforward (FF) and feedback (FB) pathways. In mammals, FF and FB are mediated by higher and lower frequencies during wakefulness. FB is preferentially impaired by general anesthetics in multiple mammalian species. This suggests FB serves critical functions in waking brains. The brain of Drosophila melanogaster (fruit fly) is also hierarchically organized, but the presence of FB in these brains is not established. Here, we studied FB in the fly brain, by simultaneously recording local field potentials (LFPs) from low-order peripheral structures and higher-order central structures. We analyzed the data using Granger causality (GC), the first application of this analysis technique to recordings from the insect brain. Our analysis revealed that low frequencies (0.1-5 Hz) mediated FB from the center to the periphery, while higher frequencies (10-45 Hz) mediated FF in the opposite direction. Further, isoflurane anesthesia preferentially reduced FB. Our results imply that the spectral characteristics of FF and FB may be a signature of hierarchically organized brains that is conserved from insects to mammals. We speculate that general anesthetics may induce unresponsiveness across species by targeting the mechanisms that support FB.
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2018-01-01
Abstract Hierarchically organized brains communicate through feedforward (FF) and feedback (FB) pathways. In mammals, FF and FB are mediated by higher and lower frequencies during wakefulness. FB is preferentially impaired by general anesthetics in multiple mammalian species. This suggests FB serves critical functions in waking brains. The brain of Drosophila melanogaster (fruit fly) is also hierarchically organized, but the presence of FB in these brains is not established. Here, we studied FB in the fly brain, by simultaneously recording local field potentials (LFPs) from low-order peripheral structures and higher-order central structures. We analyzed the data using Granger causality (GC), the first application of this analysis technique to recordings from the insect brain. Our analysis revealed that low frequencies (0.1–5 Hz) mediated FB from the center to the periphery, while higher frequencies (10–45 Hz) mediated FF in the opposite direction. Further, isoflurane anesthesia preferentially reduced FB. Our results imply that the spectral characteristics of FF and FB may be a signature of hierarchically organized brains that is conserved from insects to mammals. We speculate that general anesthetics may induce unresponsiveness across species by targeting the mechanisms that support FB. PMID:29541686
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Haramoto, Eiji; Kitajima, Masaaki; Kishida, Naohiro; Katayama, Hiroyuki; Asami, Mari; Akiba, Michihiro
2012-09-01
A nationwide survey of viruses, protozoa, and indicator microorganisms in drinking water sources of Japan was conducted. Among 64 surface water samples collected from 16 drinking water treatment plants, 51 (80 %) samples were positive for at least one of the 11 pathogen types tested, including noroviruses of genogroups I (positive rate, 13 %) and II (2 %), human sapoviruses (5 %), human adenoviruses of serotypes 40 and 41 (39 %), Cryptosporidium oocysts (41 %), and Giardia cysts (36 %). Total coliforms, Escherichia coli, and F-specific coliphages were detected in 63 (98 %), 33 (52 %), and 17 (27 %) samples, respectively, and E. coli was judged to be the most suitable indicator of pathogen contamination of drinking water sources. Genogroup-specific real-time PCR for F-specific coliphages revealed the presence of F-specific RNA coliphages of animal genogroup I and human genogroups II and III in 13 (41 %), 12 (39 %), and 1 (3 %), respectively, of 31 plaques isolated.
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Do, Hackwon; Lee, Jun Hyuck; Lee, Sung Gu; Kim, Hak Jun
2012-07-01
Ice growth in a cold environment is fatal for polar organisms, not only because of the physical destruction of inner cell organelles but also because of the resulting chemical damage owing to processes such as osmotic shock. The properties of ice-binding proteins (IBPs), which include antifreeze proteins (AFPs), have been characterized and IBPs exhibit the ability to inhibit ice growth by binding to specific ice planes and lowering the freezing point. An ice-binding protein (FfIBP) from the Gram-negative bacterium Flavobacterium frigoris PS1, which was isolated from the Antarctic, has recently been overexpressed. Interestingly, the thermal hysteresis activity of FfIBP was approximately 2.5 K at 50 µM, which is ten times higher than that of the moderately active IBP from Arctic yeast (LeIBP). Although FfIBP closely resembles LeIBP in its amino-acid sequence, the antifreeze activity of FfIBP appears to be much greater than that of LeIBP. In an effort to understand the reason for this difference, an attempt was made to solve the crystal structure of FfIBP. Here, the crystallization and X-ray diffraction data of FfIBP are reported. FfIBP was crystallized using the hanging-drop vapour-diffusion method with 0.1 M sodium acetate pH 4.4 and 3 M sodium chloride as precipitant. A complete diffraction data set was collected to a resolution of 2.9 Å. The crystal belonged to space group P4(1)22, with unit-cell parameters a = b = 69.4, c = 178.2 Å. The asymmetric unit contained one monomer.
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Pouvreau, Maxime; Greathouse, Jeffery A.; Cygan, Randall T.; ...
2017-06-28
Molecular scale understanding of the structure and properties of aqueous interfaces with clays, metal (oxy-) hydroxides, layered double hydroxides, and other inorganic phases is strongly affected by significant degrees of structural and compositional disorder of the interfaces. ClayFF was originally developed as a robust and flexible force field for classical molecular simulations of such systems. However, despite its success, multiple limitations have also become evident with its use. One of the most important limitations is the difficulty to accurately model the edges of finite size nanoparticles or pores rather than infinitely layered periodic structures. Here we propose a systematic approachmore » to solve this problem by developing specific metal–O–H (M–O–H) bending terms for ClayFF, E bend = k (θ – θ 0) 2 to better describe the structure and dynamics of singly protonated hydroxyl groups at mineral surfaces, particularly edge surfaces. On the basis of a series of DFT calculations, the optimal values of the Al–O–H and Mg–O–H parameters for Al and Mg in octahedral coordination are determined to be θ 0,AlOH = θ 0,MgOH = 110°, k AlOH = 15 kcal mol –1 rad –2 and k MgOH = 6 kcal mol –1 rad –2. Molecular dynamics simulations were performed for fully hydrated models of the basal and edge surfaces of gibbsite, Al(OH) 3, and brucite, Mg(OH) 2, at the DFT level of theory and at the classical level, using ClayFF with and without the M–O–H term. The addition of the new bending term leads to a much more accurate representation of the orientation of O–H groups at the basal and edge surfaces. Finally, the previously observed unrealistic desorption of OH 2 groups from the particle edges within the original ClayFF model is also strongly constrained by the new modification.« less
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Evidence of neutralizing activity against T3 coliphage in oyster Crassostrea gigas hemolymph.
Bachère, E; Hervio, D; Mialhe, E; Grizel, H
1990-01-01
To investigate defense reactions of bivalve molluscs against viruses, experimental in vitro assays have been developed using T3 coliphage as a test virus. A native neutralizing factor in oyster Crassostrea gigas serum showed high individual variability and was enhanced significantly by repeated sampling of hemolymph from the same oysters. The responsible factor is apparently thermolabile and sensitive to EDTA treatment. Because of an inhibitory effect by the enzymatic inhibitor, phenylmethylsulphonyl fluoride (PMSF), the T3-neutralizing factor may be related to serine protease.
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1980-05-01
the manufacturer are to inflate the isolator to a pressure of 10 mm of water on the gauge and seal off all air lines. If the pressure drops more than 4...results of these tests, it must be borne in mind that the tests were conducted using non-pathogenic Tl coliphage virus and B. subtilis var. niger spores...order as that for Tl coliphage . Also, the procedures described in- clude a large safety factor and would be expected to be adequate to eliminate all
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Practical direct plaque assay for coliphages in 100-ml samples of drinking water.
Grabow, W O; Coubrough, P
1986-01-01
A practical single-agar-layer plaque assay for the direct detection of coliphages in 100-ml samples of water was designed and evaluated. With this assay a 100-ml sample of water, an agar medium containing divalent cations, and the host Escherichia coli C (ATCC 13706) were mixed in a single container, and the mixture was plated on 10 14-cm-diameter petri dishes. It was more sensitive, reliable, and accurate than various other methods and proved rapid, simple, and economic. PMID:3532952
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1983-11-23
during their replication in B. subtilis cells. IV. CLONING THE 0.3 GENE OF COLIPHAGE T7 IN SPP1v We are currently investigating the fidelity of synthesis...of the product of the 0.3 gene of coliphage T7 in infected cells of E.. g by determining the frequency of misincorporation of S-cysteine into this...using a sealed hydrolysis chamber. BC1 was evaporated under vacuum and the hydrolysate resuspended in water . Unlabeled cysteine (12 ug) and methionine
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Byun, Wonwoo; Lee, Jung-Min; Kim, Youngwon; Brusseau, Timothy A
2018-03-26
This study examined the accuracy of the Fitbit activity tracker (FF) for quantifying sedentary behavior (SB) and varying intensities of physical activity (PA) in 3-5-year-old children. Twenty-eight healthy preschool-aged children (Girls: 46%, Mean age: 4.8 ± 1.0 years) wore the FF and were directly observed while performing a set of various unstructured and structured free-living activities from sedentary to vigorous intensity. The classification accuracy of the FF for measuring SB, light PA (LPA), moderate-to-vigorous PA (MVPA), and total PA (TPA) was examined calculating Pearson correlation coefficients (r), mean absolute percent error (MAPE), Cohen's kappa ( k ), sensitivity (Se), specificity (Sp), and area under the receiver operating curve (ROC-AUC). The classification accuracies of the FF (ROC-AUC) were 0.92, 0.63, 0.77 and 0.92 for SB, LPA, MVPA and TPA, respectively. Similarly, values of kappa, Se, Sp and percentage of correct classification were consistently high for SB and TPA, but low for LPA and MVPA. The FF demonstrated excellent classification accuracy for assessing SB and TPA, but lower accuracy for classifying LPA and MVPA. Our findings suggest that the FF should be considered as a valid instrument for assessing time spent sedentary and overall physical activity in preschool-aged children.
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Assessment of the microbial removal capabilities of riverbank filtration
NASA Astrophysics Data System (ADS)
Partinoudi, V.; Collins, M.; Margolin, A.; Brannaka, L.
2003-04-01
Riverbank filtrate includes both groundwater and river water that has percolated through the banks or bed of a river to an extraction well. One of the primary objectives of this study was to assess the microbial removal capabilities of riverbank filtration (RBF) independent of any groundwater dilution, i.e. a worse case scenario. A total of five sites were chosen: the Pembroke Waterworks (NH), the Milford State Fish Hatchery (NH), Jackson (NH) (where an infiltration gallery exists), Louisville Water Company (KY), and Cedar Rapids (IA). This study has been monitoring total coliforms, E.coli and aerobic spore forming bacteria amongst other water quality parameters over the past twelve months. Male specific (MS2) and somatic coliphage viruses were also monitored intensively for two weeks, using a single agar overlay and a two-step enrichment method, in December 2002 in Louisville, KY and in Cedar Rapids, IA. This intensive coliphage monitoring was followed by the collection of samples for special analysis of enteric viruses (Adenovirus type 40 and 41, Astrovirus, Poliovirus, Coxsackie virus, Rotavirus and Echovirus). The virus samples were analyzed using the ICC-nPCR method, due to its high specificity and sensitivity. Typical river water total coliforms, E.coli and aerobic spore forming bacteria concentrations ranged between 43-145000 CFU/100mL, 0-24192 CFU/100mL and 83-1997 CFU/100mL, respectively. All three of these microbial concentrations were below detection limits (<1CFU/100mL) in the riverbank filtration extraction well water, even after eliminating the “dilution” effects with groundwater. The male specific and the somatic coliphages ranged between 328-491 PFU/25mL and 3-21 PFU/25mL, respectively, in the river water. The concentration of the male specific coliphages was reduced by as much as 77% by the riverbank passage whereas the concentrations of the somatic coliphages were reduced by 100%. In summary the sites evaluated in this study indicated the conservative effectiveness of RBF in removing bacteria and virus indicators. Any groundwater dilution with the RBF extract should contribute to even lower microbial concentrations.
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Mackowiak, Martin; Leifels, Mats; Hamza, Ibrahim Ahmed; Jurzik, Lars; Wingender, Jost
2018-06-01
Fecal contamination of surface water is commonly evaluated by quantification of bacterial or viral indicators such as Escherichia coli and coliphages, or by direct testing for pathogens such as enteric viruses. Retention of fecally derived organisms in biofilms and sediments is less frequently considered. In this study, we assessed the distribution of E. coli, somatic coliphages, and enteric viruses including human adenovirus (HAdV), enterovirus (EV), norovirus genogroup GII (NoV GII) and group A rotavirus (RoV) in an urban river environment in Germany. 24 samples each of water, epilithic biofilms and sediments were examined. E. coli and somatic coliphages were prevalent not only in the flowing water, but also in epilithic biofilms and sediments, where they were accumulated compared to the overlying water. During enhanced rainfall, E. coli and coliphage concentrations increased by approximately 2.5 and 1 log unit, respectively, in the flowing water, whereas concentrations did not change significantly in epilithic biofilms and sediments. The occurrence of human enteric viruses detected by qPCR was higher in water than in biofilms and sediments. 87.5% of all water samples were positive for HAdV. Enteric viruses found less frequently were EV, RoV and NoV GII in 20.8%, 16.7% and 8.3% of the water samples, respectively. In epilithic biofilms and sediments, HAdV was found in 54.2% and 50.0% of the samples, respectively, and EV was found in 4.2% of both biofilm and sediment samples. RoV and NoV GII were not detected in any of the biofilms and sediments. Overall, the prevalence of enteric viruses was in the order of HAdV > EV > RoV ≥ NoV GII. In conclusion, epilithic biofilms and sediments can be reservoirs for fecal indicators and enteric viruses and thus should be taken into consideration when assessing microbial pollution of surface water environments. Copyright © 2018 Elsevier B.V. All rights reserved.
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Chloroform-Treated Filamentous Phage as a Bioreceptor for Piezoelectric Sensors
2005-01-01
Gels were rinsed in double-deionized water (DDH2O) then treated by immersion in 0.2 N NaOH for 1 h, 1 M Tris-HCl (pH 7.5) for 15 min, and 0.05 M...Filamentous bacteriophage contract into hollow spherical particles upon exposure to a chloroform- water interface. Cell 23, 747- 753. Manning, M...Chrysogelos, S., Griffith, J., 1981. Mechanism of coliphage M13 contraction: intermediate structures trapped at low temperatures. J. Virol. 40, 912-919. Naylor
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Novel approach for modifying microporous filters for virus concentration from water.
Preston, D R; Vasudevan, T V; Bitton, G; Farrah, S R; Morel, J L
1988-01-01
Electronegative microporous filters composed of epoxyfiberglass (Filterite) were treated with cationic polymers to enhance their virus-adsorbing properties. This novel and inexpensive approach to microporous filter modification entails soaking filters in an aqueous solution of a cationic polymer such as polyethyleneimine (PEI) for 2 h at room temperature and then allowing the filters to air dry overnight on absorbent paper towels. PEI-treated filters were evaluated for coliphage (MS2, T2, and phi X174) and enterovirus (poliovirus type 1 and coxsackievirus type B5) adsorption from buffer at pH 3.5 to 9.0 and for indigenous coliphages from unchlorinated secondary effluent at ambient pH. Adsorbed viruses were recovered with 3% beef extract (pH 9). Several other cationic polymers were used to modify epoxyfiberglass filters and were evaluated for their ability to concentrate viruses from water. Zeta potentials of disrupted filter material indicated that electronegative epoxyfiberglass filters were made more electropositive when treated with cationic polymers. In general, epoxyfiberglass filters treated with cationic polymers were found to adsorb a greater percentage of coliphages and enteroviruses than were untreated filters. PMID:2843091
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Sprenger, C; Lorenzen, G; Grunert, A; Ronghang, M; Dizer, H; Selinka, H-C; Girones, R; Lopez-Pila, J M; Mittal, A K; Szewzyk, R
2014-06-01
Emerging countries frequently afflicted by waterborne diseases require safe and cost-efficient production of drinking water, a task that is becoming more challenging as many rivers carry a high degree of pollution. A study was conducted on the banks of the Yamuna River, Delhi, India, to ascertain if riverbank filtration (RBF) can significantly improve the quality of the highly polluted surface water in terms of virus removal (coliphages, enteric viruses). Human adenoviruses and noroviruses, both present in the Yamuna River in the range of 10(5) genomes/100 mL, were undetectable after 50 m infiltration and approximately 119 days of underground passage. Indigenous somatic coliphages, used as surrogates of human pathogenic viruses, underwent approximately 5 log10 removal after only 3.8 m of RBF. The initial removal after 1 m was 3.3 log10, and the removal between 1 and 2.4 m and between 2.4 and 3.8 m was 0.7 log10 each. RBF is therefore an excellent candidate to improve the water situation in emerging countries with respect to virus removal.
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Meher, Biswa Ranjan; Kumar, Mattaparthi Venkata Satish; Bandyopadhyay, Pradipta
2014-01-01
The dynamics of HIV-1 protease (HIV-pr), a drug target for HIV infection, has been studied extensively by both computational and experimental methods. The flap dynamics of HIV-pr is considered to be more important for better ligand binding and enzymatic actions. Moreover, it has been demonstrated that the drug-induced mutations can change the flap dynamics of HIV-pr affecting the binding affinity of the ligands. Therefore, detailed understanding of flap dynamics is essential for designing better inhibitors. Previous computational investigations observed significant variation in the flap opening in nanosecond time scale indicating that the dynamics is highly sensitive to the simulation protocols. To understand the sensitivity of the flap dynamics on the force field and simulation protocol, molecular dynamics simulations of HIV-pr have been performed with two different AMBER force fields, ff99 and ff02. Two different trajectories (20 ns each) were obtained using the ff99 and ff02 force field. The results showed polarizable force field (ff02) make the flap tighter than the nonpolarizable force field (ff99). Some polar interactions and hydrogen bonds involving flap residues were found to be stronger with ff02 force field. The formation of interchain hydrophobic cluster (between flap tip of one chain and active site wall of another chain) was found to be dominant in the semi-open structures obtained from the simulations irrespective of the force field. It is proposed that an inhibitor, which will promote this interchain hydrophobic clustering, may make the flaps more rigid, and presumably the effect of mutation would be small on ligand binding.
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Nomura, Ken-Ichi; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya; van Duin, Adri C T; Goddard, William A
2007-10-05
Mechanical stimuli in energetic materials initiate chemical reactions at shock fronts prior to detonation. Shock sensitivity measurements provide widely varying results, and quantum-mechanical calculations are unable to handle systems large enough to describe shock structure. Recent developments in reactive force-field molecular dynamics (ReaxFF-MD) combined with advances in parallel computing have paved the way to accurately simulate reaction pathways along with the structure of shock fronts. Our multimillion-atom ReaxFF-MD simulations of l,3,5-trinitro-l,3,5-triazine (RDX) reveal that detonation is preceded by a transition from a diffuse shock front with well-ordered molecular dipoles behind it to a disordered dipole distribution behind a sharp front.
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Skraber, S; Gassilloud, B; Schwartzbrod, L; Gantzer, C
2004-07-01
The microbiological quality of water is currently assessed by search for fecal bacteria indicators. There is, however, a body of knowledge demonstrating that bacterial indicators are less resistant to environmental factors than human pathogenic viruses and therefore underestimate the viral risk. As river water is often used as a resource for drinking water production, it is particularly important to obtain a valid estimation of the health hazard, including specific viral risk. This work was conducted to compare the survival of infectious Poliovirus-1 used as a pathogenic virus model to the persistence of, on the one hand, thermotolerant coliforms commonly used as indicators and on the other hand, to somatic coliphages and Poliovirus-1 genome considered as potential indicators. We studied the behavior of infectious Poliovirus-1 and the three (potential) indicators of viral contamination in river water at three different temperatures (4 degrees C,18 degrees C and 25 degrees C). This experiment was performed twice with river water sampled at two different periods, once in winter and once in summer. Our results showed that the survival of thermotolerant coliforms can be 1.5-fold lower than infectious Poliovirus-1. In contrast, under all our experimental conditions, somatic coliphages and Poliovirus-1 genome persisted longer than infectious Poliovirus-1, surviving, respectively, 2-6-fold and about 2-fold longer than infectious Poliovirus-1. According to our results exclusively based on survival capacity, somatic coliphages and viral genome, unlike thermotolerant coliforms appear to be better indicators of viral contamination in river water. Moreover, the disappearance of viral genome is well-correlated to that one of infectious virus irrespective of the conditions tested.
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Yoshimura, Masato; Chen, Nai Chi; Guan, Hong Hsiang; Chuankhayan, Phimonphan; Lin, Chien Chih; Nakagawa, Atsushi; Chen, Chun Jung
2016-07-01
Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures.
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Park, Jun-Sang; Zhang, Xuan; Kenesei, Peter; ...
2017-08-31
A suite of non-destructive, three-dimensional X-ray microscopy techniques have recently been developed and used to characterize the microstructures of polycrystalline materials. These techniques utilize high-energy synchrotron radiation and include near-field and far-field diffraction microscopy (NF- and FF-HEDM, respectively) and absorption tomography. Several compatible sample environments have also been developed, enabling a wide range of 3D studies of material evolution. In this article, the FF-HEDM technique is described in detail, including its implementation at the 1-ID beamline of the Advanced Photon Source. Examples of how the information obtained from FF-HEDM can be used to deepen our understanding of structure-property-processing relationships inmore » selected materials are presented.« less
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Jofre, J; Ollé, E; Ribas, F; Vidal, A; Lucena, F
1995-01-01
The presence of bacteriophages at different stages in three drinking water treatment plants was evaluated to study the usefulness of phages as model organisms for assessing the efficiency of the processes. The bacteriophages tested were somatic coliphages, F-specific coliphages, and phages infecting Bacteroides fragilis. The presence of enteroviruses and currently used bacterial indicators was also determined. Most bacteriophages were removed during the prechlorination-flocculation-sedimentation step. In these particular treatment plants, which include prechlorination, phages were, in general, more resistant to the treatment processes than present bacterial indicators, with the exception, in some cases, of clostridia. Bacteriophages infecting B. fragilis were found to be more resistant to water treatment than either somatic or F-specific coliphages or even clostridia. Enteric viruses were found only in untreated water in low numbers, and consequently, the efficiency of the plants in the removal of viruses could not be evaluated with precision. The numbers and frequencies of detection of the various microorganisms in water samples taken in the distribution network served by the three plants confirm the results found in the finished water at the plants. PMID:7574632
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Rijal, G K; Fujioka, R S
2003-01-01
Aluminum reflectors were added to solar units designed to inactivate faecal microorganisms (faecal coliform, E. coli, enterococci, FRNA coliphage, C. perfringens) in stream water and diluted sewage by the two mechanisms (solar heat, solar UV) known to inactivate microorganisms. During sunny conditions, solar units with and without reflectors inactivated E. coli to <1 CFU/100 ml to meet drinking water standards. Solar units with reflectors disinfected the water sooner by increasing the water temperature by 8-10 degrees C to 64-75 degrees C. However, FRNA coliphages were still detected in these samples, indicating that this treatment may not inactivate pathogenic human enteric viruses. During cloudy conditions, reflectors only increased the water temperature by 3-4 degrees C to a maximum of 43-49 degrees C and E. coli was not completely inactivated. Under sunny and cloudy conditions, the UV wavelengths of sunlight worked synergistically with increasing water temperatures and were able to disinfect microorganisms at temperatures (45-56 degrees C), which were not effective in inactivating microorganisms. Relative resistance to the solar disinfecting effects were C. perfringens > FRNA coliphages > enterococci > E. coli > faecal coliform.
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Francy, Donna S; Stelzer, Erin A; Bushon, Rebecca N; Brady, Amie M G; Williston, Ashley G; Riddell, Kimberly R; Borchardt, Mark A; Spencer, Susan K; Gellner, Terry M
2012-09-01
Log removals of bacterial indicators, coliphage, and enteric viruses were studied in three membrane bioreactor (MBR) activated-sludge and two conventional secondary activated-sludge municipal wastewater treatment plants during three recreational seasons (May-Oct.) when disinfection of effluents is required. In total, 73 regular samples were collected from key locations throughout treatment processes: post-preliminary, post-MBR, post-secondary, post-tertiary, and post-disinfection (UV or chlorine). Out of 19 post-preliminary samples, adenovirus by quantitative polymerase chain reaction (qPCR) was detected in all 19, enterovirus by quantitative reverse transcription polymerase chain reaction (qRT-PCR) was detected in 15, and norovirus GI by qRT-PCR was detected in 11. Norovirus GII and Hepatitis A virus were not detected in any samples, and rotavirus was detected in one sample but could not be quantified. Although culturable viruses were found in 12 out of 19 post-preliminary samples, they were not detected in any post-secondary, post-MBR, post-ultraviolet, or post-chlorine samples. Median log removals for all organisms were higher for MBR secondary treatment (3.02 to >6.73) than for conventional secondary (1.53-4.19) treatment. Ultraviolet disinfection after MBR treatment provided little additional log removal of any organism except for somatic coliphage (>2.18), whereas ultraviolet or chlorine disinfection after conventional secondary treatment provided significant log removals (above the analytical variability) of all bacterial indicators (1.18-3.89) and somatic and F-specific coliphage (0.71 and >2.98). Median log removals of adenovirus across disinfection were low in both MBR and conventional secondary plants (no removal detected and 0.24), and few removals of individual samples were near or above the analytical variability of 1.2 log genomic copies per liter. Based on qualitative examinations of plots showing reductions of organisms throughout treatment processes, somatic coliphage may best represent the removal of viruses across secondary treatment in both MBR and conventional secondary plants. F-specific coliphage and Escherichia coli may best represent the removal of viruses across the disinfection process in MBR facilities, but none of the indicators represented the removal of viruses across disinfection in conventional secondary plants. Published by Elsevier Ltd.
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Francy, Donna S.; Erin, A. Stelzer; Bushon, Rebecca N.; Brady, Amie M.G.; Williston, Ashley G.; Riddell, Kimberly R.; Borchardt, Mark A.; Spencer, Susan K.; Gellner, Terry M.
2012-01-01
Log removals of bacterial indicators, coliphage, and enteric viruses were studied in three membrane bioreactor (MBR) activated-sludge and two conventional secondary activated-sludge municipal wastewater treatment plants during three recreational seasons (May-Oct.) when disinfection of effluents is required. In total, 73 regular samples were collected from key locations throughout treatment processes: post-preliminary, post-MBR, post-secondary, post-tertiary, and post-disinfection (UV or chlorine). Out of 19 post-preliminary samples, adenovirus by quantitative polymerase chain reaction (qPCR) was detected in all 19, enterovirus by quantitative reverse transcription polymerase chain reaction (qRT-PCR) was detected in 15, and norovirus GI by qRT-PCR was detected in 11. Norovirus GII and Hepatitis A virus were not detected in any samples, and rotavirus was detected in one sample but could not be quantified. Although culturable viruses were found in 12 out of 19 post-preliminary samples, they were not detected in any post-secondary, post-MBR, post-ultraviolet, or post-chlorine samples. Median log removals for all organisms were higher for MBR secondary treatment (3.02 to >6.73) than for conventional secondary (1.53-4.19) treatment. Ultraviolet disinfection after MBR treatment provided little additional log removal of any organism except for somatic coliphage (>2.18), whereas ultraviolet or chlorine disinfection after conventional secondary treatment provided significant log removals (above the analytical variability) of all bacterial indicators (1.18-3.89) and somatic and F-specific coliphage (0.71 and >2.98). Median log removals of adenovirus across disinfection were low in both MBR and conventional secondary plants (no removal detected and 0.24), and few removals of individual samples were near or above the analytical variability of 1.2 log genomic copies per liter. Based on qualitative examinations of plots showing reductions of organisms throughout treatment processes, somatic coliphage may best represent the removal of viruses across secondary treatment in both MBR and conventional secondary plants. F-specific coliphage and Escherichia coli may best represent the removal of viruses across the disinfection process in MBR facilities, but none of the indicators represented the removal of viruses across disinfection in conventional secondary plants.
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Characterization and mechanical properties investigation of TiN-Ag films onto Ti-6Al-4V
NASA Astrophysics Data System (ADS)
Du, Dongxing; Liu, Daoxin; Zhang, Xiaohua; Tang, Jingang; Xiang, Dinggen
2016-03-01
To investigate their effect on fretting fatigue (FF) resistance of a Ti-6Al-4V alloy, hard solid lubricating composite films of TiN with varying silver contents (TiN-Ag) were deposited on a Ti-6Al-4V alloy using ion-assisted magnetron sputtering. The surface morphology and structure were analyzed by atomic force microscopy, X-ray diffractometry, X-ray photoelectron spectroscopy, and transmission electron microscopy. The hardness, bonding strength, and toughness of films were tested using a micro-hardness tester, scratch tester, and a repeated press-press test system that was manufactured in-house, respectively. The FF resistance of TiN-Ag composite films was studied using self-developed devices. The results show that the FF resistance of a titanium alloy can be improved by TiN-Ag composite films, which were fabricated using hard TiN coating doped with soft Ag. The FF life of Ag0.5, Ag2, Ag5, Ag10 and Ag20 composite films is 2.41, 3.18, 3.20, 2.94 and 2.87 times as great as that of the titanium alloy, respectively. This is because the composite films have the better toughness, friction lubrication, and high bonding strength. When the atomic fraction of Ag changes from 2% to 5%, the FF resistance of the composite films shows the best performance. This is attributed to the surface integrity of the composite film is sufficiently fine to prevent the initiation and early propagation of FF cracks.
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Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel
2018-04-05
Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.
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NASA Technical Reports Server (NTRS)
Borner, A.; Swaminathan-Gopalan, K.; Stephani, Kelly; Poovathingal, S.; Murray, V. J.; Minton, T. K.; Panerai, F.; Mansour, N. N.
2017-01-01
A collaborative effort between the University of Illinois at Urbana-Champaign (UIUC), NASA Ames Research Center (ARC) and Montana State University (MSU) succeeded at developing a new finite-rate carbon oxidation model from molecular beam scattering experiments on vitreous carbon (VC). We now aim to use the direct simulation Monte Carlo (DSMC) code SPARTA to apply the model to each fiber of the porous fibrous Thermal Protection Systems (TPS) material FiberForm (FF). The detailed micro-structure of FF was obtained from X-ray micro-tomography and then used in DSMC. Both experiments and simulations show that the CO/O products ratio increased at all temperatures from VC to FF. We postulate this is due to the larger number of collisions an O atom encounters inside the porous FF material compared to the flat surface of VC. For the simulations, we particularly focused on the lowest and highest temperatures studied experimentally, 1023 K and 1823 K, and found good agreement between the finite-rate DSMC simulations and experiments.
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The social cost of alcohol, tobacco and illicit drugs in France, 1997.
Fenoglio, Philippe; Parel, Véronique; Kopp, Pierre
2003-01-01
AIM, DESIGN AND SETTING: The economic costs of alcohol, tobacco and illicit drugs to French society are estimated using a cost of illness framework. For the cause of disease or death (using ICD-9 categories), pooled relative risk estimates from meta-analyses were combined with prevalence data by age and gender to derive the proportion attributable to alcohol, tobacco and/or illicit drugs. The resulting estimates of attributable deaths and hospitalizations were used to calculate the associated health care, law enforcement, productivity and other costs. The results were compared with those of other studies, and sensitivity analyses were conducted by alternative ways of measuring risk attribution and costs. The use of alcohol, tobacco and illicit drugs cost more than 200 billion francs (FF) in France in 1997, representing 3714 FF per capita or 2.7% of the gross domestic product (GDP). Alcohol is the drug that gives rise to the greatest cost in France, i.e. 115420.91 million FF (1.42% of GDP) or an expenditure per capita of 1966 FF in 1997. Alcohol takes more than half of the social cost of drugs to society. The greatest share of the social cost of alcohol comes from the loss of productivity (57555.66 million FF), due to premature death (53168.60 million FF), morbidity (3884.0 million FF) and imprisonment (503.06 million FF). Tobacco leads to a social cost of 89256.90 million FF, that is an expenditure per capita of 1520.56 FF or 1.1% of GDP. Productivity losses amount to 50446.70 million FF, with losses of 42765.80 million FF as a result of premature death and 7680.90 million FF linked to morbidity. Health care costs for tobacco occupy second place at 26973.70 million FF. Illicit drugs generate a social cost of 13350.28 million FF, that is an expenditure per capita of 227.43 FF or 0.16% of GDP. Productivity losses reach 6099.19 million FF, with 5246.92 million FF linked to imprisonment and 852.27 million FF to premature death. The cost of enforcing the law for illicit drugs occupies second place at 3911.46 million FF, followed by health care costs of 1524.51 million FF. Substance abuse exact a considerable toll from French society in terms of illness, injury, death and economic costs. Copyright 2003 S. Karger AG, Basel
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Correlative super-resolution fluorescence microscopy combined with optical coherence microscopy
NASA Astrophysics Data System (ADS)
Kim, Sungho; Kim, Gyeong Tae; Jang, Soohyun; Shim, Sang-Hee; Bae, Sung Chul
2015-03-01
Recent development of super-resolution fluorescence imaging technique such as stochastic optical reconstruction microscopy (STORM) and photoactived localization microscope (PALM) has brought us beyond the diffraction limits. It allows numerous opportunities in biology because vast amount of formerly obscured molecular structures, due to lack of spatial resolution, now can be directly observed. A drawback of fluorescence imaging, however, is that it lacks complete structural information. For this reason, we have developed a super-resolution multimodal imaging system based on STORM and full-field optical coherence microscopy (FF-OCM). FF-OCM is a type of interferometry systems based on a broadband light source and a bulk Michelson interferometer, which provides label-free and non-invasive visualization of biological samples. The integration between the two systems is simple because both systems use a wide-field illumination scheme and a conventional microscope. This combined imaging system gives us both functional information at a molecular level (~20nm) and structural information at the sub-cellular level (~1μm). For thick samples such as tissue slices, while FF-OCM is readily capable of imaging the 3D architecture, STORM suffer from aberrations and high background fluorescence that substantially degrade the resolution. In order to correct the aberrations in thick tissues, we employed an adaptive optics system in the detection path of the STORM microscope. We used our multimodal system to obtain images on brain tissue samples with structural and functional information.
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Ahalawat, Navjeet; Arora, Simran; Murarka, Rajesh K
2015-08-27
The human cluster determinant 4 (CD4), expressed primarily on the surface of T helper cells, serves as a coreceptor in T-cell receptor recognition of MHC II antigen complexes. Besides its cellular functions, CD4 serves as a primary receptor of human immunodeficiency virus (HIV) type 1. The cytoplasmic tail of CD4 (residues 402-419) is known to be involved in direct interaction with the HIV-1 proteins Vpu and Nef. These two viral accessory proteins (Vpu and Nef) downregulate CD4 in HIV-1 infected cells by multiple strategies and make the body susceptible to all forms of infections. In this work, we carried out extensive replica exchange molecular dynamics simulations in explicit water with three popular protein force fields Amber ff99SB, Amber ff99SB*-ILDN, and CHARMM36 to characterize the equilibrium conformational ensemble of CD4-tail (402-419) and further validated the simulated ensembles with known NMR data. We found that ff99SB*-ILDN gives a better description of the structural ensemble of this peptide compared with ff99SB and CHARMM36. The peptide adopts multiple distinct conformations with varying degree of residual secondary structures. In particular, we observed 28, 7, and 5% average α-helical, β-strand, and 3(10)-helix content, respectively, for ff99SB*-ILDN. The peptide chain shows the tendency of helix formation in a cooperative manner, seeding at residues 407-410, and subsequently extending toward both ends of the chain. Furthermore, we constructed Markov state model (MSM) from large-scale molecular dynamics simulations to study the dynamics of transitions between different metastable states explored by this peptide. The mean first passage times computed from MSM indicate rapid interconversion of these states, and the time scales of transitions range from several nanoseconds to hundreds of microseconds. Our results show good agreement with experimental data and could help to understand the key molecular mechanisms of T-cell activation and HIV-mediated receptor interference.
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Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung
2016-01-01
Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Pouvreau, Maxime; Greathouse, Jeffery A.; Cygan, Randall T.
Molecular scale understanding of the structure and properties of aqueous interfaces with clays, metal (oxy-) hydroxides, layered double hydroxides, and other inorganic phases is strongly affected by significant degrees of structural and compositional disorder of the interfaces. ClayFF was originally developed as a robust and flexible force field for classical molecular simulations of such systems. However, despite its success, multiple limitations have also become evident with its use. One of the most important limitations is the difficulty to accurately model the edges of finite size nanoparticles or pores rather than infinitely layered periodic structures. Here we propose a systematic approachmore » to solve this problem by developing specific metal–O–H (M–O–H) bending terms for ClayFF, E bend = k (θ – θ 0) 2 to better describe the structure and dynamics of singly protonated hydroxyl groups at mineral surfaces, particularly edge surfaces. On the basis of a series of DFT calculations, the optimal values of the Al–O–H and Mg–O–H parameters for Al and Mg in octahedral coordination are determined to be θ 0,AlOH = θ 0,MgOH = 110°, k AlOH = 15 kcal mol –1 rad –2 and k MgOH = 6 kcal mol –1 rad –2. Molecular dynamics simulations were performed for fully hydrated models of the basal and edge surfaces of gibbsite, Al(OH) 3, and brucite, Mg(OH) 2, at the DFT level of theory and at the classical level, using ClayFF with and without the M–O–H term. The addition of the new bending term leads to a much more accurate representation of the orientation of O–H groups at the basal and edge surfaces. Finally, the previously observed unrealistic desorption of OH 2 groups from the particle edges within the original ClayFF model is also strongly constrained by the new modification.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Niyogi, S.K.; Mitra, S.
Escherichia coli RNA polymerase binds specifically to the single-stranded circular DNA of coliphage M13 in the presence of a saturating concentration of the bacterial DNA binding protein presumably as an essential step in the synthesis of the RNA primer required for synthesizing the complementary DNA strand in parental replicative-form DNA. The RNA polymerase-protected DNA regions were isolated after extensive digestion with pancreatic DNase, S1 endonuclease of Aspergillus oryzae, and exonuclease I of E. coli. The physicochemical properties of the RNA polymerase-protected segments (called PI and PII) were compared with those of the naturally occurring hairpin regions.
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NASA Astrophysics Data System (ADS)
Zarnescu, Livia; Leung, Michael C.; Abeyta, Michael; Sudkamp, Helge; Baer, Thomas; Behr, Barry; Ellerbee, Audrey K.
2015-09-01
Vitrification is an increasingly popular method of embryo cryopreservation that is used in assisted reproductive technology. Although vitrification has high post-thaw survival rates compared to other freezing techniques, its long-term effects on embryo development are still poorly understood. We demonstrate an application of full-field optical coherence tomography (FF-OCT) to visualize the effects of vitrification on live single-cell (2 pronuclear) mouse embryos without harmful labels. Using FF-OCT, we observed that vitrification causes a significant increase in the aggregation of structures within the embryo cytoplasm, consistent with reports in literature based on fluorescence techniques. We quantify the degree of aggregation with an objective metric, the cytoplasmic aggregation (CA) score, and observe a high degree of correlation between the CA scores of FF-OCT images of embryos and of fluorescence images of their mitochondria. Our results indicate that FF-OCT shows promise as a label-free assessment of the effects of vitrification on embryo mitochondria distribution. The CA score provides a quantitative metric to describe the degree to which embryos have been affected by vitrification and could aid clinicians in selecting embryos for transfer.
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1984-10-01
is ready for engagement. The SCAS pitch, roll, and yaw engage switches energize the appropriate channels of the SCAS and the electrical solenoid valves ...I 4i TFF FF iff iT1Ii F1T ’I" 114~~~~7. FF+4441UF - - 4-� 1;4 444 1~ FF1 111410 4 IB1: TIF FF 1F V4j UVFFtli T FF’HI F F FF F F tF1 F ’’ ’-FF11 1
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Ff-nano, short functionalized nanorods derived from Ff (f1, fd, or M13) filamentous bacteriophage
Sattar, Sadia; Bennett, Nicholas J.; Wen, Wesley X.; Guthrie, Jenness M.; Blackwell, Len F.; Conway, James F.; Rakonjac, Jasna
2015-01-01
F-specific filamentous phage of Escherichia coli (Ff: f1, M13, or fd) are long thin filaments (860 nm × 6 nm). They have been a major workhorse in display technologies and bionanotechnology; however, some applications are limited by the high length-to-diameter ratio of Ff. Furthermore, use of functionalized Ff outside of laboratory containment is in part hampered by the fact that they are genetically modified viruses. We have now developed a system for production and purification of very short functionalized Ff-phage-derived nanorods, named Ff-nano, that are only 50 nm in length. In contrast to standard Ff-derived vectors that replicate in E. coli and contain antibiotic-resistance genes, Ff-nano are protein-DNA complexes that cannot replicate on their own and do not contain any coding sequences. These nanorods show an increased resistance to heating at 70∘C in 1% SDS in comparison to the full-length Ff phage of the same coat composition. We demonstrate that functionalized Ff-nano particles are suitable for application as detection particles in sensitive and quantitative “dipstick” lateral flow diagnostic assay for human plasma fibronectin. PMID:25941520
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Ff-nano, short functionalized nanorods derived from Ff (f1, fd, or M13) filamentous bacteriophage.
Sattar, Sadia; Bennett, Nicholas J; Wen, Wesley X; Guthrie, Jenness M; Blackwell, Len F; Conway, James F; Rakonjac, Jasna
2015-01-01
F-specific filamentous phage of Escherichia coli (Ff: f1, M13, or fd) are long thin filaments (860 nm × 6 nm). They have been a major workhorse in display technologies and bionanotechnology; however, some applications are limited by the high length-to-diameter ratio of Ff. Furthermore, use of functionalized Ff outside of laboratory containment is in part hampered by the fact that they are genetically modified viruses. We have now developed a system for production and purification of very short functionalized Ff-phage-derived nanorods, named Ff-nano, that are only 50 nm in length. In contrast to standard Ff-derived vectors that replicate in E. coli and contain antibiotic-resistance genes, Ff-nano are protein-DNA complexes that cannot replicate on their own and do not contain any coding sequences. These nanorods show an increased resistance to heating at 70(∘)C in 1% SDS in comparison to the full-length Ff phage of the same coat composition. We demonstrate that functionalized Ff-nano particles are suitable for application as detection particles in sensitive and quantitative "dipstick" lateral flow diagnostic assay for human plasma fibronectin.
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Qualitative investigation of fresh human scalp hair with full-field optical coherence tomography
NASA Astrophysics Data System (ADS)
Choi, Woo June; Pi, Long-Quan; Min, Gihyeon; Lee, Won-Soo; Lee, Byeong Ha
2012-03-01
We have investigated depth-resolved cellular structures of unmodified fresh human scalp hairs with ultrahigh-resolution full-field optical coherence tomography (FF-OCT). The Linnik-type white light interference microscope has been home-implemented to observe the micro-internal layers of human hairs in their natural environment. In hair shafts, FF-OCT has qualitatively revealed the cellular hair compartments of cuticle and cortex layers involved in keratin filaments and melanin granules. No significant difference between black and white hair shafts was observed except for absence of only the melanin granules in the white hair, reflecting that the density of the melanin granules directly affects the hair color. Anatomical description of plucked hair bulbs was also obtained with the FF-OCT in three-dimensions. We expect this approach will be useful for evaluating cellular alteration of natural hairs on cosmetic assessment or diagnosis of hair diseases.
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Enterococcus phages as potential tool for identifying sewage inputs in the Great Lakes region
Vijayavel, K.; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Ebdon, J.; Taylor, H.; Kashian, D.R.
2014-01-01
Bacteriophages are viruses living in bacteria that can be used as a tool to detect fecal contamination in surface waters around the world. However, the lack of a universal host strain makes them unsuitable for tracking fecal sources. We evaluated the suitability of two newly isolated Enterococcus host strains (ENT-49 and ENT-55) capable for identifying sewage contamination in impacted waters by targeting phages specific to these hosts. Both host strains were isolated from wastewater samples and identified as E. faecium by 16S rRNA gene sequencing. Occurrence of Enterococcus phages was evaluated in sewage samples (n = 15) from five wastewater treatment plants and in fecal samples from twenty-two species of wild and domesticated animals (individual samples; n = 22). Levels of Enterococcus phages, F + coliphages, Escherichia coli and enterococci were examined from four rivers, four beaches, and three harbors. Enterococcus phages enumeration was at similar levels (Mean = 6.72 Log PFU/100 mL) to F + coliphages in all wastewater samples, but were absent from all non-human fecal sources tested. The phages infecting Enterococcus spp. and F + coliphages were not detected in the river samples (detection threshold < 10 PFU/100 mL), but were present in the beach and harbor samples (range = 1.83 to 2.86 Log PFU/100 mL). Slightly higher concentrations (range = 3.22 to 3.69 Log MPN/100 mL) of E. coli and enterococci when compared to F + coliphages and Enterococcus phages, were observed in the river, beach and harbor samples. Our findings suggest that the bacteriophages associated with these particular Enterococcus host strains offer potentially sensitive and human-source specific indicators of enteric pathogen risk.
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2016-01-01
We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642
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Comparison of CIGS solar cells made with different structures and fabrication techniques
Mansfield, Lorelle M.; Garris, Rebekah L.; Counts, Kahl D.; ...
2016-11-03
Cu(In, Ga)Se2 (CIGS)-based solar cells from six fabricators were characterized and compared. The devices had differing substrates, absorber deposition processes, buffer materials, and contact materials. The effective bandgaps of devices varied from 1.05 to 1.22 eV, with the lowest optical bandgaps occurring in those with metal-precursor absorber processes. Devices with Zn(O, S) or thin CdS buffers had quantum efficiencies above 90% down to 400 nm. Most voltages were 250-300 mV below the Shockley-Queisser limit for their bandgap. Electroluminescence intensity tracked well with the respective voltage deficits. Fill factor (FF) was as high as 95% of the maximum for each device'smore » respective current and voltage, with higher FF corresponding to lower diode quality factors (~1.3). An in-depth analysis of FF losses determined that diode quality reflected in the quality factor, voltage-dependent photocurrent, and, to a lesser extent, the parasitic resistances are the limiting factors. As a result, different absorber processes and device structures led to a range of electrical and physical characteristics, yet this investigation showed that multiple fabrication pathways could lead to high-quality and high-efficiency solar cells.« less
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Comparison of CIGS solar cells made with different structures and fabrication techniques
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mansfield, Lorelle M.; Garris, Rebekah L.; Counts, Kahl D.
Cu(In, Ga)Se2 (CIGS)-based solar cells from six fabricators were characterized and compared. The devices had differing substrates, absorber deposition processes, buffer materials, and contact materials. The effective bandgaps of devices varied from 1.05 to 1.22 eV, with the lowest optical bandgaps occurring in those with metal-precursor absorber processes. Devices with Zn(O, S) or thin CdS buffers had quantum efficiencies above 90% down to 400 nm. Most voltages were 250-300 mV below the Shockley-Queisser limit for their bandgap. Electroluminescence intensity tracked well with the respective voltage deficits. Fill factor (FF) was as high as 95% of the maximum for each device'smore » respective current and voltage, with higher FF corresponding to lower diode quality factors (~1.3). An in-depth analysis of FF losses determined that diode quality reflected in the quality factor, voltage-dependent photocurrent, and, to a lesser extent, the parasitic resistances are the limiting factors. As a result, different absorber processes and device structures led to a range of electrical and physical characteristics, yet this investigation showed that multiple fabrication pathways could lead to high-quality and high-efficiency solar cells.« less
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A Review of the Growth of the Fast Food Industry in China and Its Potential Impact on Obesity.
Wang, Youfa; Wang, Liang; Xue, Hong; Qu, Weidong
2016-11-09
The fast-food (FF) industry and obesity rates have rapidly increased in China. This study examined the FF industry growth in China, key factors contributing to the growth, and the association between FF consumption (FFC) and obesity. We collected related data from multiple sources and conducted analysis including linear regression analysis on the increase in FF revenue. It was found that FF industry in China is large, with over two million FF facilities. Its total revenue (in million US$) increased from 10,464 in 1999 to 94,218 in 2013, and by 13% annually since 2008. Increased income, urbanization, busier lifestyle, speedy FF service, assurance of food safety, new brands and foods have stimulated demand for FF. Studies have linked FFC with obesity risk, including a few reporting a positive association between FFC and obesity in China. Rapid expansion of Western-style FF restaurants has also stimulated local FF industry growth. Government regulation and public health education need to address the health consequences of rapidly increasing FFC. Lessons learned in China will help other countries.
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A Review of the Growth of the Fast Food Industry in China and Its Potential Impact on Obesity
Wang, Youfa; Wang, Liang; Xue, Hong; Qu, Weidong
2016-01-01
The fast-food (FF) industry and obesity rates have rapidly increased in China. This study examined the FF industry growth in China, key factors contributing to the growth, and the association between FF consumption (FFC) and obesity. We collected related data from multiple sources and conducted analysis including linear regression analysis on the increase in FF revenue. It was found that FF industry in China is large, with over two million FF facilities. Its total revenue (in million US$) increased from 10,464 in 1999 to 94,218 in 2013, and by 13% annually since 2008. Increased income, urbanization, busier lifestyle, speedy FF service, assurance of food safety, new brands and foods have stimulated demand for FF. Studies have linked FFC with obesity risk, including a few reporting a positive association between FFC and obesity in China. Rapid expansion of Western-style FF restaurants has also stimulated local FF industry growth. Government regulation and public health education need to address the health consequences of rapidly increasing FFC. Lessons learned in China will help other countries. PMID:27834887
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A NASTRAN Vibration Model of the AH-1G Helicopter Airframe. Volume 2
1974-06-01
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NASA Astrophysics Data System (ADS)
Harms, F.; Dalimier, E.; Vermeulen, P.; Fragola, A.; Boccara, A. C.
2012-03-01
Optical Coherence Tomography (OCT) is an efficient technique for in-depth optical biopsy of biological tissues, relying on interferometric selection of ballistic photons. Full-Field Optical Coherence Tomography (FF-OCT) is an alternative approach to Fourier-domain OCT (spectral or swept-source), allowing parallel acquisition of en-face optical sections. Using medium numerical aperture objective, it is possible to reach an isotropic resolution of about 1x1x1 ìm. After stitching a grid of acquired images, FF-OCT gives access to the architecture of the tissue, for both macroscopic and microscopic structures, in a non-invasive process, which makes the technique particularly suitable for applications in pathology. Here we report a multimodal approach to FF-OCT, combining two Full-Field techniques for collecting a backscattered endogeneous OCT image and a fluorescence exogeneous image in parallel. Considering pathological diagnosis of cancer, visualization of cell nuclei is of paramount importance. OCT images, even for the highest resolution, usually fail to identify individual nuclei due to the nature of the optical contrast used. We have built a multimodal optical microscope based on the combination of FF-OCT and Structured Illumination Microscopy (SIM). We used x30 immersion objectives, with a numerical aperture of 1.05, allowing for sub-micron transverse resolution. Fluorescent staining of nuclei was obtained using specific fluorescent dyes such as acridine orange. We present multimodal images of healthy and pathological skin tissue at various scales. This instrumental development paves the way for improvements of standard pathology procedures, as a faster, non sacrificial, operator independent digital optical method compared to frozen sections.
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Kolodinsky, Jane; Labrecque, JoAnne; Doyon, Maurice; Reynolds, Travis; Oble, Frédéric; Bellavance, François; Marquis, Marie
2008-01-01
Functional foods (FF)--foods containing nutritional supplements in addition to natural nutrients--have an increasing presence in the marketplace. Expanding on previous research, the authors investigated college students' acceptance of FF. In September--March 2004, 811 undergraduates in Canada, the United States, and France participated in the study. A self-administered questionnaire measured students' general food attitudes and beliefs as well as FF-related knowledge, attitudes, beliefs, and purchase intention. Overall, participants slightly favored FF over traditional foods. However, although most respondents associated FF with positive health benefits, many remained dubious of currently available FF information. In terms of culture and sex, the authors found small but significant divergences in FF knowledge, attitudes, and behaviors. Stronger labeling and education efforts may increase cross-cultural acceptance of FF by college students.
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Chung, Pak-Kwong; Zhao, Yanan; Liu, Jing-Dong; Quach, Binh
This study aimed to explore the relationship between the functional fitness (FF) and health-related quality of life (HRQoL) in older adults, and to identify the key subdimensions of FF and HRQoL influencing their overall relationship. This cross-sectional study was performed among 851 independent community members (65-84 years; men=402). The Senior Fitness Test and the Short Form 36 Health Survey were used to measure FF and HRQoL, respectively. A canonical correlation analysis was conducted using seven fitness variables as predictors of eight HRQoL variables to examine the relationship between FF and HRQoL. The overall FF was positively correlated with the overall HRQoL in both men (canonical correlation=0.350) and women (canonical correlation=0.456). The up-and-go and 2-min step contributed the most to FF, and physical functioning contributed the most to HRQOL among men. Conversely, the up-and-go and 30-s chair stand contributed the most to FF, and physical functioning contributed the most to HRQoL in women. There were positive and moderate relationships between overall FF and overall HRQOL in older adults. The FF has a significant influence on HRQoL, particularly physical functioning. The main FF components influencing the relationship between FF and HRQoL in men are balance and agility and aerobic endurance, whereas in women they are balance and agility and lower extremity muscle strength. Results from this study facilitate comprehensively understanding the relationship between FF and HRQoL, and generating critical insight into HRQoL improvement from the perspective of FF enhancement. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
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Hayes, Jacqueline F; Altman, Myra; Kolko, Rachel P; Balantekin, Katherine N; Holland, Jodi Cahill; Stein, Richard I; Saelens, Brian E; Welch, R Robinson; Perri, Michael G; Schechtman, Kenneth B; Epstein, Leonard H; Wilfley, Denise E
2016-10-01
Food fussiness (FF), or the frequent rejection of both familiar and unfamiliar foods, is common among children and, given its link to poor diet quality, may contribute to the onset and/or maintenance of childhood obesity. This study examined child FF in association with anthropometric variables and diet in children with overweight/obesity participating in family-based behavioral weight loss treatment (FBT). Change in FF was assessed in relation to FBT outcome, including whether change in diet quality mediated the relation between change in FF and change in child weight. Child (N = 170; age = 9.41 ± 1.23) height and weight were measured, and parents completed FF questionnaires and three 24-h recalls of child diet at baseline and post-treatment. Healthy Eating Index-2005 scores were calculated. At baseline, child FF was related to lower vegetable intake. Average child FF decreased from start to end of FBT. Greater decreases in FF were associated with greater reductions in child body mass index and improved overall diet quality. Overall, diet quality change through FBT mediated the relation between child FF change and child body mass index change. Children with high FF can benefit from FBT, and addressing FF may be important in childhood obesity treatment to maximize weight outcomes. © 2016 The Obesity Society.
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Chemical shift-based MRI to measure fat fractions in dystrophic skeletal muscle
Triplett, William T.; Baligand, Celine; Forbes, Sean C.; Willcocks, Rebecca J.; Lott, Donovan J.; DeVos, Soren; Pollaro, Jim; Rooney, William D.; Sweeney, H. Lee; Bönnemann, Carsten; Wang, Dah-Jyuu; Vandenborne, Krista; Walter, Glenn A.
2014-01-01
Purpose The relationship between FF determined based on multiple TE, unipolar GE images and 1H-MRS was evaluated using different models for fat-water decomposition, signal-to-noise ratios (SNR), and excitation flip angles. Methods A combination of single voxel proton spectroscopy (1H-MRS) and gradient echo (GE) imaging was used to determine muscle fat fractions (FF) in both normal and dystrophic muscles. In order to cover a large range of FF, the soleus and vastus lateralis muscles of 22 unaffected control (CON), 16 subjects with Collagen VI (COL6), and 71 subjects with Duchenne muscular dystrophy (DMD) were studied. 1H-MRS based FF were corrected for the increased muscle 1H2O T1 and T2 values observed in dystrophic muscles. Results Excellent agreement was found between co-registered FF derived from GE images fit to a multipeak model with noise bias correction and the relaxation corrected 1H-MRS FF (y= 0.93×+0.003; R2=0.96) across the full range of FF. Relaxation corrected 1H-MRS FF and imaging based FF were significantly elevated (p<0.01) in both COL6 and DMD muscles. Conclusion FF, T2, and T1 were all sensitive to muscle involvement in dystrophic muscle. MRI offered an additional advantage over single voxel spectroscopy in that the tissue heterogeneity in FF could be readily determined. PMID:24006208
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Paar, Jack; Doolittle, Mark M; Varma, Manju; Siefring, Shawn; Oshima, Kevin; Haugland, Richard A
2015-05-01
A method, incorporating recently improved reverse transcriptase-PCR primer/probe assays and including controls for detecting interferences in RNA recovery and analysis, was developed for the direct, culture-independent detection of genetic markers from FRNA coliphage genogroups I, II & IV in water samples. Results were obtained from an initial evaluation of the performance of this method in analyses of waste water, ambient surface water and stormwater drain and outfall samples from predominantly urban locations. The evaluation also included a comparison of the occurrence of the FRNA genetic markers with genetic markers from general and human-related bacterial fecal indicators determined by current or pending EPA-validated qPCR methods. Strong associations were observed between the occurrence of the putatively human related FRNA genogroup II marker and the densities of the bacterial markers in the stormwater drain and outfall samples. However fewer samples were positive for FRNA coliphage compared to either the general bacterial fecal indicator or the human-related bacterial fecal indicator markers particularly for ambient water samples. Together, these methods show promise as complementary tools for the identification of contaminated storm water drainage systems as well as the determination of human and non-human sources of contamination. Published by Elsevier B.V.
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González-Zamora, Arturo; Arroyo-Rodríguez, Víctor; Escobar, Federico; Rös, Matthias; Oyama, Ken; Ibarra-Manríquez, Guillermo; Stoner, Kathryn E.; Chapman, Colin A.
2014-01-01
The repeated use of sleeping sites by frugivorous vertebrates promotes the deposition and aggregation of copious amounts of seeds in these sites. This spatially contagious pattern of seed deposition has key implications for seed dispersal, particularly because such patterns can persist through recruitment. Assessing the seed rain patterns in sleeping sites thus represents a fundamental step in understanding the spatial structure and regeneration of plant assemblages. We evaluated the seed rain produced by spider monkeys (Ateles geoffroyi) in latrines located beneath 60 sleeping trees in two continuous forest sites (CFS) and three forest fragments (FF) in the Lacandona rainforest, Mexico. We tested for differences among latrines, among sites, and between forest conditions in the abundance, diversity (α-, β- and, γ-components) and evenness of seed assemblages. We recorded 45,919 seeds ≥5 mm (in length) from 68 species. The abundance of seeds was 1.7 times higher in FF than in CFS, particularly because of the dominance of a few plant species. As a consequence, community evenness tended to be lower within FF. β-diversity of common and dominant species was two times greater among FF than between CFS. Although mean α-diversity per latrine did not differ among sites, the greater β-diversity among latrines in CFS increased γ-diversity in these sites, particularly when considering common and dominant species. Our results support the hypothesis that fruit scarcity in FF can ‘force’ spider monkeys to deplete the available fruit patches more intensively than in CFS. This feeding strategy can limit the effectiveness of spider monkeys as seed dispersers in FF, because (i) it can limit the number of seed dispersers visiting such fruit patches; (ii) it increases seed dispersal limitation; and (iii) it can contribute to the floristic homogenization (i.e., reduced β-diversity among latrines) in fragmented landscapes. PMID:24586705
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Microbial (Pathogen)/Recreational Water Quality Criteria
Documents pertaining to Recreational Human Health Ambient Water Quality Criteria for Microbial Organisms (Pathogens). These documents include safe levels for cyanotoxins microcystin and cylindrospermopsin, and Coliphage to protect human health.
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Abdelrahman, Mostafa; El-Sayed, Magdi; Sato, Shusei; Hirakawa, Hideki; Ito, Shin-ichi; Tanaka, Keisuke; Mine, Yoko; Sugiyama, Nobuo; Suzuki, Minoru; Yamauchi, Naoki
2017-01-01
The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium’s defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway in Allium species is poorly understood. The monosomic addition lines (MALs) of the Japanese bunching onion (A. fistulosum, FF) with an extra chromosome from the shallot (A. cepa Aggregatum group, AA) are powerful genetic resources that enable us to understand many physiological traits of Allium. In the present study, we were able to isolate and identify Alliospiroside A saponin compound in A. fistulosum with extra chromosome 2A from shallot (FF2A) and its role in the defense mechanism against Fusarium pathogens. Furthermore, to gain molecular insight into the Allium saponin biosynthesis pathway, high-throughput RNA-Seq of the root, bulb, and leaf of AA, MALs, and FF was carried out using Illumina's HiSeq 2500 platform. An open access Allium Transcript Database (Allium TDB, http://alliumtdb.kazusa.or.jp) was generated based on RNA-Seq data. The resulting assembled transcripts were functionally annotated, revealing 50 unigenes involved in saponin biosynthesis. Differential gene expression (DGE) analyses of AA and MALs as compared with FF (as a control) revealed a strong up-regulation of the saponin downstream pathway, including cytochrome P450, glycosyltransferase, and beta-glucosidase in chromosome 2A. An understanding of the saponin compounds and biosynthesis-related genes would facilitate the development of plants with unique saponin content and, subsequently, improved disease resistance. PMID:28800607
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Abdelrahman, Mostafa; El-Sayed, Magdi; Sato, Shusei; Hirakawa, Hideki; Ito, Shin-Ichi; Tanaka, Keisuke; Mine, Yoko; Sugiyama, Nobuo; Suzuki, Yutaka; Yamauchi, Naoki; Shigyo, Masayoshi
2017-01-01
The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium's defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway in Allium species is poorly understood. The monosomic addition lines (MALs) of the Japanese bunching onion (A. fistulosum, FF) with an extra chromosome from the shallot (A. cepa Aggregatum group, AA) are powerful genetic resources that enable us to understand many physiological traits of Allium. In the present study, we were able to isolate and identify Alliospiroside A saponin compound in A. fistulosum with extra chromosome 2A from shallot (FF2A) and its role in the defense mechanism against Fusarium pathogens. Furthermore, to gain molecular insight into the Allium saponin biosynthesis pathway, high-throughput RNA-Seq of the root, bulb, and leaf of AA, MALs, and FF was carried out using Illumina's HiSeq 2500 platform. An open access Allium Transcript Database (Allium TDB, http://alliumtdb.kazusa.or.jp) was generated based on RNA-Seq data. The resulting assembled transcripts were functionally annotated, revealing 50 unigenes involved in saponin biosynthesis. Differential gene expression (DGE) analyses of AA and MALs as compared with FF (as a control) revealed a strong up-regulation of the saponin downstream pathway, including cytochrome P450, glycosyltransferase, and beta-glucosidase in chromosome 2A. An understanding of the saponin compounds and biosynthesis-related genes would facilitate the development of plants with unique saponin content and, subsequently, improved disease resistance.
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Hayashi, Tatsuya; Saitoh, Satoshi; Takahashi, Junji; Tsuji, Yoshinori; Ikeda, Kenji; Kobayashi, Masahiro; Kawamura, Yusuke; Fujii, Takeshi; Inoue, Masafumi; Miyati, Tosiaki; Kumada, Hiromitsu
2017-04-01
The two-point Dixon method for magnetic resonance imaging (MRI) is commonly used to non-invasively measure fat deposition in the liver. The aim of the present study was to assess the usefulness of MRI-fat fraction (MRI-FF) using the two-point Dixon method based on the non-alcoholic fatty liver disease activity score. This retrospective study included 106 patients who underwent liver MRI and MR spectroscopy, and 201 patients who underwent liver MRI and histological assessment. The relationship between MRI-FF and MR spectroscopy-fat fraction was used to estimate the corrected MRI-FF for hepatic multi-peaks of fat. Then, a color FF map was generated with the corrected MRI-FF based on the non-alcoholic fatty liver disease activity score. We defined FF variability as the standard deviation of FF in regions of interest. Uniformity of hepatic fat was visually graded on a three-point scale using both gray-scale and color FF maps. Confounding effects of histology (iron, inflammation and fibrosis) on corrected MRI-FF were assessed by multiple linear regression. The linear correlations between MRI-FF and MR spectroscopy-fat fraction, and between corrected MRI-FF and histological steatosis were strong (R 2 = 0.90 and R 2 = 0.88, respectively). Liver fat variability significantly increased with visual fat uniformity grade using both of the maps (ρ = 0.67-0.69, both P < 0.001). Hepatic iron, inflammation and fibrosis had no significant confounding effects on the corrected MRI-FF (all P > 0.05). The two-point Dixon method and the gray-scale or color FF maps based on the non-alcoholic fatty liver disease activity score were useful for fat quantification in the liver of patients without severe iron deposition. © 2016 The Japan Society of Hepatology.
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Failure kinetics in borosilicate glass during rod impact
DOE Office of Scientific and Technical Information (OSTI.GOV)
Orphal, Dennis L.; Anderson, Charles E. Jr.; Behner, Thilo
2007-12-12
Failure front (FF) and penetration velocity have been measured for long gold rods impacting and penetrating borosilicate (BS) glass. Data are obtained by visualizing simultaneously FF propagation with a high speed camera and rod penetration with flash X-rays. Results for BS glass are qualitatively similar to those of DEDF (PbO) glass. FF velocity rapidly decreases from an initial value to a lower, approximately constant value. FF velocity increases with impact velocity, v{sub p}. The FF velocity remains significantly lower than the shear velocity, even at the highest impact velocity tested, about 2.5 km/s. The ratio of the FF velocity tomore » the rod penetration velocity, v{sub F}/u, decreases with increasing v{sub p} and appears to be approaching v{sub F}/u = 1 asymptotically, as observed previously for DEDF glass. The separation of the FF and the tip of the rod decreases with increasing impact velocity. Importantly, since v{sub F}/u{>=}1, the gold rod is always penetrating glass behind the FF.« less
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ReaxFF Reactive Force-Field Study of Molybdenum Disulfide (MoS2).
Ostadhossein, Alireza; Rahnamoun, Ali; Wang, Yuanxi; Zhao, Peng; Zhang, Sulin; Crespi, Vincent H; van Duin, Adri C T
2017-02-02
Two-dimensional layers of molybdenum disulfide, MoS 2 , have been recognized as promising materials for nanoelectronics due to their exceptional electronic and optical properties. Here we develop a new ReaxFF reactive potential that can accurately describe the thermodynamic and structural properties of MoS 2 sheets, guided by extensive density functional theory simulations. This potential is then applied to the formation energies of five different types of vacancies, various vacancy migration barriers, and the transition barrier between the semiconducting 2H and metallic 1T phases. The energetics of ripplocations, a recently observed defect in van der Waals layers, is examined, and the interplay between these defects and sulfur vacancies is studied. As strain engineering of MoS 2 sheets is an effective way to manipulate the sheets' electronic and optical properties, the new ReaxFF description can provide valuable insights into morphological changes that occur under various loading conditions and defect distributions, thus allowing one to tailor the electronic properties of these 2D crystals.
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Giddings, Elise M.; Oblinger, Carolyn J.
2004-01-01
Water quality in the Newfound Creek watershed has been shown to be affected by bacteria, sediment, and nutrients. In this study, Escherichia coli (E. coli) bacteria were sampled at five sites in Newfound Creek and five tributary sites during low flow on May 28, 2003, and high flow on November 19, 2003. In addition, a subset of five sites was sampled for fecal coliform bacteria, E. coli bacteria in streambed sediments (low flow only), and coliphage virus for serotyping. Coliphage virus serotyping has been used to identify human and animal sources of bacterial contamination. A streamflow gage was installed and operated to support ongoing water-quality studies in the watershed. Fecal coliform densities ranged from 92 to 27,000 colony-forming units per 100 milliliters of water for E. coli and 140 to an estimated 29,000 colony-forming units per 100 milliliters of water for fecal coliform during the two sampling visits. Ninety percent of the E. coli and fecal coliform samples exceeded corresponding U.S. Environmental Protection Agency or North Carolina water-quality criteria for recreational and ambient waters. During low flow, the middle part of the Newfound Creek watershed and the Dix Creek tributary had the highest densities of E. coli bacteria. During the high-flow sampling, all tributaries contained high densities of E. coli bacteria, although Dix Creek and Round Hill Branch were the largest contributors of these bacteria to Newfound Creek. Coliphage virus serotyping results were inconclusive because most samples did not contain the male-specific RNA coliphage needed for serotyping. Positive results indicated, however, that during low flow, non-human sources of bacteria were present in Sluder Branch, and during high flow, human sources of bacteria were present in Round Hill Branch. Sampling of bacteria in streambed sediments during low flow indicated that sediments do not appear to be a substantial source of bacteria relative to the water column, with the exception of an area near the confluence of Sluder Branch and Newfound Creek.
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Burbano-Rosero, E. M.; Ueda-Ito, M.; Kisielius, J. J.; Nagasse-Sugahara, T. K.; Almeida, B. C.; Souza, C. P.; Markman, C.; Martins, G. G.; Albertini, L.; Rivera, I. N. G.
2011-01-01
Bacteriophages are the most abundant and genetically diverse viruses on Earth, with complex ecology in both quantitative and qualitative terms. Somatic coliphages (SC) have been reported to be good indicators of fecal pollution in seawater. This study focused on determining the concentration of SC and their diversity by electron microscopy of seawater, plankton, and bivalve samples collected at three coastal regions in São Paulo, Brazil. The SC counts varied from <1 to 3.4 × 103 PFU/100 ml in seawater (73 samples tested), from <1 to 4.7 × 102 PFU/g in plankton (46 samples tested), and from <1 to 2.2 × 101 PFU/g in bivalves (11 samples tested). In seawater samples, a relationship between the thermotolerant coliforms and Escherichia coli and SC was observed at the three regions (P = 0.0001) according to the anthropogenic activities present at each region. However, SC were found in plankton samples from three regions: Baixada Santista (17/20), Canal de São Sebastião (6/14), and Ubatuba (3/12). In seawater samples collected from Baixada Santista, four morphotypes were observed: A1 (4.5%), B1 (50%), C1 (36.4%), and D1 (9.1%). One coliphage, Siphoviridae type T1, had the longest tail: between 939 and 995 nm. In plankton samples, Siphoviridae (65.8%), Podoviridae (15.8%), Microviridae (15.8%), and Myoviridae (2.6%) were found. In bivalves, only the morphotype B1 was observed. These SC were associated with enteric hosts: enterobacteria, E. coli, Proteus, Salmonella, and Yersinia. Baixada Santista is an area containing a high level of fecal pollution compared to those in the Canal de São Sebastião and Ubatuba. This is the first report of coliphage diversity in seawater, plankton, and bivalve samples collected from São Paulo coastal regions. A better characterization of SC diversity in coastal environments will help with the management and evaluation of the microbiological risks for recreation, seafood cultivation, and consumption. PMID:21531842
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Secure TRNG with random phase stimulation
NASA Astrophysics Data System (ADS)
Wieczorek, Piotr Z.
2017-08-01
In this paper a novel TRNG concept is proposed which is a vital part of cryptographic systems. The proposed TRNG involves phase variability of a pair of ring oscillators (ROs) to force the multiple metastable events in a flip-flop (FF). In the solution, the ROs are periodically activated to ensure the violation of the FF timing and resultant state randomness, while the TRNG circuit adapts the structure of ROs to obtain the maximum entropy and circuit security. The TRNG can be implemented in inexpensive re-programmable devices (CPLDs or FPGAs) without the use of Digital Clock Managers (DCMs). Preliminary test results proved the circuit's immunity to the intentional frequency injection attacks.
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Gao, Feng; Li, Zhiwei; Chang, Qingbo; Gao, Mengchun; She, Zonglian; Wu, Juan; Jin, Chunji; Zheng, Dong; Guo, Liang; Zhao, Yangguo; Wang, Sen
2018-02-01
The effects of florfenicol (FF) on the performance, microbial activity and microbial community of a sequencing batch biofilm reactor (SBBR) were evaluated in treating mariculture wastewater. The chemical oxygen demand (COD) and nitrogen removal were inhibited at high FF concentrations. The specific oxygen utilization rate (SOUR), specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR) and specific nitrate reduction rate (SNRR) were decreased with an increase in the FF concentration from 0 to 35 mg/L. The chemical compositions of loosely bound extracellular polymeric substances (LB-EPS) and tightly bound EPS (TB-EPS) could be affected with an increase in the FF concentration. The high-throughput sequencing indicated some obvious variations in the microbial community at different FF concentrations. The relative abundance of Nitrosomonas and Nitrospira showed a decreasing tendency with an increase in the FF concentration, suggesting that FF could affect the nitrification process of SBBR. Some genera capable of reducing nitrate to nitrogen gas could be inhibited by the addition of FF in the influent, such as Azospirillum and Hyphomicrobium.
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Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique
2015-05-15
QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Ray, Jaideep; Lee, Jina; Lefantzi, Sophia
2013-09-01
The estimation of fossil-fuel CO2 emissions (ffCO2) from limited ground-based and satellite measurements of CO2 concentrations will form a key component of the monitoring of treaties aimed at the abatement of greenhouse gas emissions. The limited nature of the measured data leads to a severely-underdetermined estimation problem. If the estimation is performed at fine spatial resolutions, it can also be computationally expensive. In order to enable such estimations, advances are needed in the spatial representation of ffCO2 emissions, scalable inversion algorithms and the identification of observables to measure. To that end, we investigate parsimonious spatial parameterizations of ffCO2 emissions whichmore » can be used in atmospheric inversions. We devise and test three random field models, based on wavelets, Gaussian kernels and covariance structures derived from easily-observed proxies of human activity. In doing so, we constructed a novel inversion algorithm, based on compressive sensing and sparse reconstruction, to perform the estimation. We also address scalable ensemble Kalman filters as an inversion mechanism and quantify the impact of Gaussian assumptions inherent in them. We find that the assumption does not impact the estimates of mean ffCO2 source strengths appreciably, but a comparison with Markov chain Monte Carlo estimates show significant differences in the variance of the source strengths. Finally, we study if the very different spatial natures of biogenic and ffCO2 emissions can be used to estimate them, in a disaggregated fashion, solely from CO2 concentration measurements, without extra information from products of incomplete combustion e.g., CO. We find that this is possible during the winter months, though the errors can be as large as 50%.« less
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Skaat, Hadas; Chen, Ravit; Grinberg, Igor; Margel, Shlomo
2012-09-10
Protein aggregation into amyloid fibrils is implicated in the pathogenesis of many neurodegenerative diseases. Engineered nanoparticles have emerged as a potential approach to alter the kinetics of protein fibrillation process. Yet, there are only a few reports describing the use of nanoparticles for inhibition of amyloid-β 40 (Aβ(40)) peptide aggregation, involved in Alzheimer's disease (AD). In the present study, we designed new uniform biocompatible amino-acid-based polymer nanoparticles containing hydrophobic dipeptides in the polymer side chains. The dipeptide residues were designed similarly to the hydrophobic core sequence of Aβ. Poly(N-acryloyl-L-phenylalanyl-L-phenylalanine methyl ester) (polyA-FF-ME) nanoparticles of 57 ± 6 nm were synthesized by dispersion polymerization of the monomer A-FF-ME in 2-methoxy ethanol, followed by precipitation of the obtained polymer in aqueous solution. Cell viability assay confirmed that no significant cytotoxic effect of the polyA-FF-ME nanoparticles on different human cell lines, e.g., PC-12 and SH-SY5Y, was observed. A significantly slow secondary structure transition from random coil to β-sheets during Aβ(40) fibril formation was observed in the presence of these nanoparticles, resulting in significant inhibition of Aβ(40) fibrillation kinetics. However, the polyA-FF-ME analogous nanoparticles containing the L-alanyl-L-alanine (AA) dipeptide in the polymer side groups, polyA-AA-ME nanoparticles, accelerate the Aβ(40) fibrillation kinetics. The polyA-FF-ME nanoparticles and the polyA-AA-ME nanoparticles may therefore contribute to a mechanistic understanding of the fibrillation process, leading to the development of therapeutic strategies against amyloid-related diseases.
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Song, Yijun; Zhou, Xiya; Huang, Saiqiong; Li, Xiaohong; Qi, Qingwei; Jiang, Yulin; Liu, Yiqian; Ma, Chengcheng; Li, Zhifeng; Xu, Mengnan; Cram, David S; Liu, Juntao
2016-05-01
Calculation of the fetal DNA fraction (FF) is important for reliable and accurate noninvasive prenatal testing (NIPT) for fetal genetic abnormalities. The aim of the study was to develop and validate a novel method for FF determination. FF was calculated using the chromosome Y (ChrY) sequence read assay and by circulating single molecule amplification and re-sequencing technology of 76 autosomal SNPs. By Pearson correlation for FF (4.73-22.11%) in 33 male pregnancy samples, the R(2) co-efficient for the 76-SNP versus the ChrY assay was 0.9572 (p<0.001). In addition, the co-efficient of variation (CV) of FF measurement by the 76-SNP assay was low (0.15-0.35). As a control, the FF measurement for four non-pregnant plasma samples was virtually zero. In prospective longitudinal studies of 14 women with normal pregnancies, FF generally increased with gestational age. However, in eight women (71%) there was a significant decrease in FF between the first trimester (11-13 weeks) and the second trimester (15-19 weeks), and this was attributable to significant maternal weight gain. The novel 76-SNP cSMART assay has the precision to accurately measure FF in all pregnancies at a detection threshold of 5%. Based on FF trends in individual pregnancies, our results suggest that the end of the first trimester may be a more optimal window for performing NIPT. Copyright © 2016 Elsevier B.V. All rights reserved.
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Polsky, Sarit; Beck, Jimikaye; Stark, Rebecca A.; Pan, Zhaoxing; Hill, James O.; Peters, John C.
2014-01-01
Adults often consume more fat than is recommended. We examined factors that may improve liking of reduced fat and reduced saturated fat foods, including the addition of herbs and spices and habitual consumption of different high-fat and low-fat food items. We randomized adults to taste three different conditions: full fat (FF), reduced fat with no added spice (RF), and reduced fat plus spice (RFS). Subjects rated their liking of French toast, sausage and the overall meal, or chicken, vegetables, pasta and the overall meal on a nine-point hedonic Likert scale. Overall liking of the RF breakfast and lunch meals were lower than the FF and RFS versions (Breakfast: 6.50 RF vs. 6.84 FF, p=0.0061; 6.50 RF vs. 6.82 RFS, p=0.0030; Lunch: 6.35 RF vs. 6.94 FF, p<0.0001; 6.35 RF vs. 6.71 RFS, p=0.0061). RFS and FF breakfast and lunch meals, French toast, chicken and vegetable likings were similar. FF and RFS conditions were liked more than RF for the breakfast and lunch meals, French toast, chicken entrée and vegetables. Liking of all three sausage conditions were similar. FF Pasta was liked more than RFS and RF (7.47 FF vs. 6.42 RFS, p<0.0001; 7.47 FF vs. 6.47 RF, p<0.0001). Habitual consumption of roasted chicken was associated with reduced liking of FF chicken (r = −0.23, p=0.004) and FF pasta (r = −0.23, p=0.005). Herbs and spices may be useful for improving the liking of lower-fat foods and helping Americans maintain a diet consistent with the US Dietary Guidelines. PMID:25219391
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Fildes, Alison; van Jaarsveld, Cornelia H M; Cooke, Lucy; Wardle, Jane; Llewellyn, Clare H
2016-04-01
Food fussiness (FF) is common in early childhood and is often associated with the rejection of nutrient-dense foods such as vegetables and fruit. FF and liking for vegetables and fruit are likely all heritable phenotypes; the genetic influence underlying FF may explain the observed genetic influence on liking for vegetables and fruit. Twin analyses make it possible to get a broad-based estimate of the extent of the shared genetic influence that underlies these traits. We quantified the extent of the shared genetic influence that underlies FF and liking for vegetables and fruit in early childhood with the use of a twin design. Data were from the Gemini cohort, which is a population-based sample of twins born in England and Wales in 2007. Parents of 3-y-old twins (n= 1330 pairs) completed questionnaire measures of their children's food preferences (liking for vegetables and fruit) and the FF scale from the Children's Eating Behavior Questionnaire. Multivariate quantitative genetic modeling was used to estimate common genetic influences that underlie FF and liking for vegetables and fruit. Genetic correlations were significant and moderate to large in size between FF and liking for both vegetables (-0.65) and fruit (-0.43), which indicated that a substantial proportion of the genes that influence FF also influence liking. Common genes that underlie FF and liking for vegetables and fruit largely explained the observed phenotypic correlations between them (68-70%). FF and liking for fruit and vegetables in young children share a large proportion of common genetic factors. The genetic influence on FF may determine why fussy children typically reject fruit and vegetables.
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Characterizing Uncertainties in Atmospheric Inversions of Fossil Fuel CO2 Emissions in California
NASA Astrophysics Data System (ADS)
Brophy, K. J.; Graven, H. D.; Manning, A.; Arnold, T.; Fischer, M. L.; Jeong, S.; Cui, X.; Parazoo, N.
2016-12-01
In 2006 California passed a law requiring greenhouse gas emissions be reduced to 1990 levels by 2020, equivalent to a 20% reduction over 2006-2020. Assessing compliance with greenhouse gas mitigation policies requires accurate determination of emissions, particularly for CO2 emitted by fossil fuel combustion (ffCO2). We found differences in inventory-based ffCO2 flux estimates for California total emissions of 11% (standard deviation relative to the mean), and even larger differences on some smaller sub-state levels. Top-down studies may be useful for validating ffCO2 flux estimates, but top-down studies of CO2 typically focus on biospheric CO2 fluxes and they are not yet well-developed for ffCO2. Implementing top-down studies of ffCO2 requires observations of a fossil fuel combustion tracer such as 14C to distinguish ffCO2 from biospheric CO2. However, even if a large number of 14C observations are available, multiple other sources of uncertainty will contribute to the uncertainty in posterior ffCO2 flux estimates. With a Bayesian inverse modelling approach, we use simulated atmospheric observations of ffCO2 at a network of 11 tower sites across California in an observing system simulation experiment to investigate uncertainties. We use four different prior ffCO2 flux estimates, two different atmospheric transport models, different types of spatial aggregation, and different assumptions for observational and model transport uncertainties to investigate contributions to posterior ffCO2 emission uncertainties. We show how various sources of uncertainty compare and which uncertainties are likely to limit top-down estimation of ffCO2 fluxes in California.
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Association between lysyl oxidase and fibrotic focus in relation with inflammation in breast cancer
Jeong, Young Ju; Park, Sung Hwan; Mun, Sung Hee; Kwak, Sang Gyu; Lee, Sun-Jae; Oh, Hoon Kyu
2018-01-01
We hypothesized that lysyl oxidase (LOX) contributes to the formation of fibrotic focus (FF) in association with inflammation and serves a significant role in breast carcinogenesis. In the present study, the association between the expression of LOX family members and FF with regards to with inflammation was analyzed, and the prognostic significance of LOX and FF in breast cancer was investigated. Immunohistochemical staining for LOX, LOX-like protein (LOXL) 1, LOXL2 and LOXL3 was performed in primary breast cancer tissues. The status of FF within the tumor was assessed, including size and grade. Levels of inflammatory markers, intratumoral and peritumoral lymphocyte infiltration were also evaluated. The clinicopathological characteristics were evaluated from the medical records of patients. In the present study, the expression of LOX family members was not associated with the presence of FF. FF was identified to be associated with intratumoral and peritumoral inflammation, tumor stage, larger tumor size, lymph node metastasis, high histologic grade, and p53 expression. LOX and LOXL3 were associated with intratumoral, and peritumoral inflammation. Furthermore, LOXL1 was associated with intratumoral inflammation and interleukin-4. In addition, LOX was associated with cluster of differentiation 8+ T cells. LOXL3 was associated with expression of ER and PR, and molecular subtype. In the survival analysis, overall survival time was statistically significantly longer in the FF-negative compared with that in the FF-positive group. In conclusion, it was demonstrated that FF and the expression of LOX family members were associated with inflammation in breast cancer. FF was associated with poor prognostic markers of breast cancer. Further studies are required to clarify the mechanisms underlying the association between the LOX family, FF and inflammation in breast cancer. PMID:29434955
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Li, Liyun; Ferin, Michel; Sauer, Mark V; Lobo, Roger A
2012-12-01
We aimed to characterize the association between levels of serum and follicular fluid (FF) adipocytokines, reflected by the leptin to adiponectin ratio (L:A ratio), and oocyte quality and in vitro embryo development in women undergoing assisted reproduction. We also aimed to assess whether follicular hormonal pathways mediate this interaction. We prospectively collected FF from up to four individual preovulatory follicles (n = 76) and fasting sera from women (n = 31) without endocrinopathies undergoing in vitro fertilization (IVF) at a university-based center for assisted reproduction. Leptin, total adiponectin, insulin, insulin-like growth factor 1 (IGF-1), and ovarian steriods were measured using enzyme immunoassay. Oocyte maturity, fertilization, and embryo development were assessed. FF leptin was similar to serum levels while FF adiponectin was lower. FF leptin (27.10 ± 4.05 ng/mL) and the L:A ratio (11.48E-3 ± 2.57E-3) were related to FF insulin (R (2) = 0.370 and 0.419, p < 0.001) but not to ovarian steroids or IGF-1, whereas FF adiponectin ( 4.22 ± 0.52 ug/mL) correlated only with leptin (R (2) = -0.138, p = 0.001). Oocytes from a high FF L:A ratio environment were 81 % (RR 1.81 [95%CI 0.97-3.37]) more likely to undergo successful cleavage and 117 % (RR 2.17 [95 % CI 1.06-4.44]) more likely to obtain viable cleavage morphology compared to a low FF L:A ratio environment, even when adjusted for FF insulin, an independent predictor of cleavage. Certain adipocytokines, particularly the L:A ratio in the FF of the preovulatory follicle, are related to successful in vitro embryo development. This action may be independent of FF insulin.
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Kise, Yoshitaka; Chikui, Toru; Yamashita, Yasuo; Kobayashi, Koji; Yoshiura, Kazunori
2017-08-01
To estimate the fat fraction (FF) in the salivary glands (SGs) by the mDIXON method and the 1 H-MR spectroscopy (MRS) method, and to compare the results. 16 healthy volunteers were enrolled. mDIXON Quant and MRS (point-resolved spectroscopy: PRESS) with a single TE were employed to measure the FF in the parotid gland (PG) and submandibular gland (SMG). Multiple TEs were applied in 10 volunteers to correct for T 2 decay. In addition, we assumed that the 1.3 ppm peak accounted for 60% of the total fat peak and estimated the FF (MRS all) as a gold standard. On mDIXON Quant images, volumes of interest were set on the bilateral SGs and we obtained the FF (mDIXON) of each volume of interest. There was a strong correlation between the results of the mDIXON Quant method and the MRS (single TE) method (R 2 = 0.960, slope = 0.900). Using PRESS with multiple TEs, there was also a strong correlation between FF (mDIXON) and FF (MRS all) (R 2 = 0.963, slope = 1.18). FF (MRS all) was 24.9±12.7% in the PG and 4.5±3.0% in the SMG, while FF (mDIXON) was 29.4±16.2% in the PG and 6.4±4.7% in the SMG. There were no significant differences between the two methods, but the Bland-Altman plot showed that FF (mDIXON) was slightly larger than FF (MRS all) for small FF areas. The mDIXON Quant method could be clinically useful for evaluating the FF of SGs, but the absolute values need careful interpretation. Advance in knowledge: This study suggested the potential clinical usefulness of the mDIXON Quant method for the SGs.
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Atmospheric Fossil Fuel CO2 Tracing By 14C In Some Chinese Cities
NASA Astrophysics Data System (ADS)
Zhou, W.; Niu, Z.; Zhu, Y., Sr.
2016-12-01
CO2 plays an important role in global climate as a primary greenhouse gas in the atmosphere. Moreover, it has been shown that more than 70% of global fossil fuel CO2 (CO2ff) emissions are concentrated in urban areas (Duren and Miller, 2012). Our study focuses on atmospheric CO2ff concentrations in 15 Chinese cities using accelerator mass spectrometer (AMS) to measure 14C. Our objectives are: (1) to document atmospheric CO2ff concentrations in a variety of urban environments, (2) to differentiate the spatial-temporal variations in CO2ff among these cities, and (3) to ascertain the factors that control the observed variations. For about two years (winter 2014 to winter 2016), the CO2ff concentrations we observed from all sites varied from 5.1±4.5 ppm to 65.8±39.0 ppm. We observed that inland cities display much higher CO2ff concentrations and overall temporal variations than coastal cities in winter, and that northern cities have higher CO2ff concentrations than those of southern cities in winter. For inland cities relatively high CO2ff values are observed in winter and low values in summer; while seasonal variations are not distinct in the coastal cities. No significant (p > 0.05) differences in CO2ff values are found between weekdays and weekends as was shown previously in Xi'an (Zhou et al., 2014). Diurnal CO2ff variations are plainly evident, with high values between midnight and 4:00 am, and during morning and afternoon rush hours (Niu et al., 2016). The high CO2ff concentrations in northern inland cities in winter results mainly from the substantial consumption of fossil fuels for heating. The high CO2ff concentrations seen in diurnal measurements result mainly from variations in atmospheric dispersion, and from vehicle emissions related to traffic flows. The inter-annual variations in CO2ff in cities could provide a useful reference for local governments to develop policy around the effect of energy conservation and emission reduction strategies.
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Interactions of pharmacokinetic profile of different parts from Ginkgo biloba extract in rats.
Guan, HanLiang; Qian, Dawei; Ren, Hao; Zhang, Wei; Nie, Hui; Shang, Erxing; Duan, Jinao
2014-08-08
Extracts from Ginkgo biloba L. leaves confer their therapeutic effects through the synergistic actions of flavonoid and terpenoid components, but some non-flavonoid and non-terpenoid components also exist in this extract. In the study of this paper, an investigation was carried out to compare the pharmacokinetic parameters of fourteen compounds to clarify the influences of non-flavonoid and non-terpenoid fraction (WEF) on the pharmacokinetics profile of the flavonoid fraction (FF) and the terpene lactone fraction (TLF) from Ginkgo biloba extracts. A selective and sensitive UPLC-MS/MS method was established to determine the plasma concentrations of the fourteen compounds to compare the pharmacokinetic parameters after orally administration of FF, TLF, FF-WEF, FF-TLF, TLF-WEF and FF-TLF-WEF with approximately the same dose. At different time points, the concentration of rutin (1), isoquercitrin (2), quercetin 3-O-[4-O-(-β-D-glucosyl)-α-L-rhamnoside] (3), ginkgolide C (4), bilobalide (5), quercitrin (6), ginkgolide B (7), ginkgolide A (8), luteolin (9), quercetin (10), apigenin (11), kaempferol (12), isorhamnetin (13), genkwanin (14) in rat plasma were determined and main pharmacokinetic parameters including T1/2, Tmax, Cmax and AUC were calculated using the DAS 3.2 software package. The statistical analysis was performed using the Student׳s t-test with P<0.05 as the level of significance. FF and WEF had no effect on the pharmacokinetic behaviors and parameters of the four terpene lactones, but the pharmacokinetic profiles and parameters of flavonoids changed while co-administered with non-flavonoid components. It was found that Cmax and AUC of six flavonoid aglycones in group FF-WEF, FF-TLF and FF-TLF-WEF had varying degrees of reduction in comparison with group FF, especially in group FF-TLF-WEF. On the contrary, the values of Cmax, Tmax and AUC of four flavonoid glycosides in group FF-TLF-WEF were significantly increased compared with those in group FF. These results indicate that non-flavonoid components in Ginkgo biloba extracts could increase the absorption and improve the bioavailability of flavonoid glycosides but decrease the absorption and reduce the bioavailability of flavonoid aglycones. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
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Zhang, Luzheng; Zybin, Sergey V; van Duin, Adri C T; Dasgupta, Siddharth; Goddard, William A; Kober, Edward M
2009-10-08
We report molecular dynamics (MD) simulations using the first-principles-based ReaxFF reactive force field to study the thermal decomposition of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at various densities and temperatures. TATB is known to produce a large amount (15-30%) of high-molecular-weight carbon clusters, whereas detonation of nitramines such as HMX and RDX (1,3,5-trinitroperhydro-1,3,5-triazine) generate predominantly low-molecular-weight products. In agreement with experimental observation, these simulations predict that TATB decomposition quickly (by 30 ps) initiates the formation of large carbonaceous clusters (more than 4000 amu, or approximately 15-30% of the total system mass), and HMX decomposition leads almost exclusively to small-molecule products. We find that HMX decomposes readily on this time scale at lower temperatures, for which the decomposition rate of TATB is about an order of magnitude slower. Analyzing the ReaxFF MD results leads to the detailed atomistic structure of this carbon-rich phase of TATB and allows characterization of the kinetics and chemistry related to this phase and their dependence on system density and temperature. The carbon-rich phase formed from TATB contains mainly polyaromatic rings with large oxygen content, leading to graphitic regions. We use these results to describe the initial reaction steps of thermal decomposition of HMX and TATB in terms of the rates for forming primary and secondary products, allowing comparison to experimentally derived models. These studies show that MD using the ReaxFF reactive force field provides detailed atomistic information that explains such macroscopic observations as the dramatic difference in carbon cluster formation between TATB and HMX. This shows that ReaxFF MD captures the fundamental differences in the mechanisms of such systems and illustrates how the ReaxFF may be applied to model complex chemical phenomena in energetic materials. The studies here illustrate this for modestly sized systems and modest periods; however, ReaxFF calculations of reactive processes have already been reported on systems with approximately 10(6) atoms. Thus, with suitable computational facilities, one can study the atomistic level chemical processes in complex systems under extreme conditions.
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Effects of rare earth oxide additive on surface and tribological properties of polyimide composites
NASA Astrophysics Data System (ADS)
Pan, Zihe; Wang, Tianchang; Chen, Li; Idziak, Stefan; Huang, Zhaohui; Zhao, Boxin
2017-09-01
Rare earth oxide La2O3 microparticles-reinforced polyimide (PI) composites (La-PI-Cs) were fabricated, aiming to improve the tribological property of PI. Surface roughness, surface composition, bulk structure, friction force (Ff) and coefficient of friction (COF) at macro/micro preload, and anti-wear performances of La-PI-Cs were studied and compared with neat PI. With La2O3 microparticles, La-PI-Cs showed larger surface roughness, lower surface energy, and higher hydrophobicity than neat PI, and displayed beneficial layered structure different from the compact structure of PI. Owing to these advantages, La-PI-Cs were found to show a 70% reduction in Ff and COF, and a 30% reduction in wear rate, indicating significantly lowered friction and enhanced anti-wear properties after adding La2O3 microparticles. Our research findings demonstrated an easy and low cost method to fabricate polymer composites with low friction and high wear resistance, and help meet the demanding of polymer composites with high tribological performances in broaden applications.
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Brown, Sean G.; Costello, Sarah; Kelly, Mark C.; Ramalingam, Mythili; Drew, Ellen; Publicover, Stephen J.; Barratt, Christopher L.R.; Da Silva, Sarah Martins
2017-01-01
Abstract STUDY QUESTION Does progesterone in human follicular fluid (hFF) activate CatSper and do other components of hFF modulate this effect and/or contribute separately to hFF-induced Ca2+ signaling? SUMMARY ANSWER hFF potently stimulates CatSper and increases [Ca2+]i, primarily due to high concentrations of progesterone, however, other components of hFF also contribute to [Ca2+]i signaling, including modulation of CatSper channel activity and inhibition of [Ca2+]i oscillations. WHAT IS KNOWN ALREADY CatSper, the principal Ca2+ channel in spermatozoa, is progesterone-sensitive and essential for fertility. Both hFF and progesterone, which is present in hFF, influence sperm function and increase their [Ca2+]i. STUDY DESIGN, SIZE, DURATION This basic medical research study used semen samples from >40 donors and hFF from >50 patients who were undergoing surgical oocyte retrieval for IVF/ICSI. PARTICIPANTS/MATERIALS, SETTING, METHODS Semen donors and patients were recruited in accordance with local ethics approval (13/ES/0091) from the East of Scotland Research Ethics Service REC1. Activities of CatSper and KSper were assessed by patch clamp electrophysiology. Sperm [Ca2+]i responses were examined in sperm populations and single cells. Computer-assisted sperm analysis (CASA) parameters and penetration into viscous media were used to assess functional effects. MAIN RESULTS AND THE ROLE OF CHANCE hFF and progesterone significantly potentiated CatSper currents. Under quasi-physiological conditions, hFF (up to 50%) failed to alter membrane K+ conductance or current reversal potential. hFF and progesterone (at an equivalent concentration) stimulated similar biphasic [Ca2+]i signals both in sperm populations and single cells. At a high hFF concentration (10%), the sustained (plateau) component of the [Ca2+]i signal was consistently greater than that induced by progesterone alone. In single cell recordings, 1% hFF-induced [Ca2+]i oscillations similarly to progesterone but with 10% hFF generation of [Ca2+]i oscillations was suppressed. After treatment to ‘strip’ lipid-derived mediators, hFF failed to significantly stimulate CatSper currents but induced small [Ca2+]i responses that were greater than those induced by the equivalent concentration of progesterone after stripping. Similar [Ca2+]i responses were observed when sperm pretreated with 3 μM progesterone (to desensitize progesterone responses) were stimulated with hFF or stripped hFF. hFF stimulated viscous media penetration and was more effective than the equivalent does of progesterone. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION This was an in vitro study. Caution must be taken when extrapolating these results in vivo. WIDER IMPLICATIONS OF THE FINDINGS This study directly demonstrates that hFF activates CatSper and establishes that the biologically important effects of hFF reflect, at least in part, action on this channel, primarily via progesterone. However, these experiments also demonstrate that other components of hFF both contribute to the [Ca2+]i signal and modulate the activation of CatSper. Simple in vitro experiments performed out of the context of the complex in vivo environment need to be interpreted with caution. STUDY FUNDING/COMPETING INTEREST(S) Funding was provided by MRC (MR/K013343/1, MR/012492/1) (S.G.B., S.J.P., C.L.R.B.) and University of Abertay (sabbatical for S.G.B.). Additional funding was provided by TENOVUS SCOTLAND (S.M.D.S.), Chief Scientist Office/NHS Research Scotland (S.M.D.S). C.L.R.B. is EIC of MHR and Chair of the WHO ESG on Diagnosis of Male infertility. The remaining authors have no conlicts of interest. PMID:28938737
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Hambly, Emma; Tétart, Francoise; Desplats, Carine; Wilson, William H.; Krisch, Henry M.; Mann, Nicholas H.
2001-01-01
Sequence analysis of a 10-kb region of the genome of the marine cyanomyovirus S-PM2 reveals a homology to coliphage T4 that extends as a contiguous block from gene (g)18 to g23. The order of the S-PM2 genes in this region is similar to that of T4, but there are insertions and deletions of small ORFs of unknown function. In T4, g18 codes for the tail sheath, g19, the tail tube, g20, the head portal protein, g21, the prohead core protein, g22, a scaffolding protein, and g23, the major capsid protein. Thus, the entire module that determines the structural components of the phage head and contractile tail is conserved between T4 and this cyanophage. The significant differences in the morphology of these phages must reflect the considerable divergence of the amino acid sequence of their homologous virion proteins, which uniformly exceeds 50%. We suggest that their enormous diversity in the sea could be a result of genetic shuffling between disparate phages mediated by such commonly shared modules. These conserved sequences could facilitate genetic exchange by providing partially homologous substrates for recombination between otherwise divergent phage genomes. Such a mechanism would thus expand the pool of phage genes accessible by recombination to all those phages that share common modules. PMID:11553768
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Force field dependent solution properties of glycine oligomers
Drake, Justin A.
2015-01-01
Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623
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Somatic coliphages as surrogates for enteroviruses in sludge hygienization treatments.
Martín-Díaz, Julia; Casas-Mangas, Raquel; García-Aljaro, Cristina; Blanch, Anicet R; Lucena, Francisco
2016-01-01
Conventional bacterial indicators present serious drawbacks giving information about viral pathogens persistence during sludge hygienization treatments. This calls for the search of alternative viral indicators. Somatic coliphages' (SOMCPH) ability for acting as surrogates for enteroviruses was assessed in 47 sludge samples subjected to novel treatment processes. SOMCPH, infectious enteroviruses and genome copies of enteroviruses were monitored. Only one of these groups, the bacteriophages, was present in the sludge at concentrations that allowed the evaluation of treatment's performance. An indicator/pathogen relationship of 4 log10 (PFU/g dw) was found between SOMCPH and infective enteroviruses and their detection accuracy was assessed. The obtained results and the existence of rapid and standardized methods encourage the inclusion of SOMCPH quantification in future sludge directives. In addition, an existing real-time quantitative polymerase chain reaction (RT-qPCR) for enteroviruses was adapted and applied.
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Water quality indicators: bacteria, coliphages, enteric viruses.
Lin, Johnson; Ganesh, Atheesha
2013-12-01
Water quality through the presence of pathogenic enteric microorganisms may affect human health. Coliform bacteria, Escherichia coli and coliphages are normally used as indicators of water quality. However, the presence of above-mentioned indicators do not always suggest the presence of human enteric viruses. It is important to study human enteric viruses in water. Human enteric viruses can tolerate fluctuating environmental conditions and survive in the environment for long periods of time becoming causal agents of diarrhoeal diseases. Therefore, the potential of human pathogenic viruses as significant indicators of water quality is emerging. Human Adenoviruses and other viruses have been proposed as suitable indices for the effective identification of such organisms of human origin contaminating water systems. This article reports on the recent developments in the management of water quality specifically focusing on human enteric viruses as indicators.
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Pulsed high voltage electric discharge disinfection of microbially contaminated liquids.
Anpilov, A M; Barkhudarov, E M; Christofi, N; Kop'ev, V A; Kossyi, I A; Taktakishvili, M I; Zadiraka, Y
2002-01-01
To examine the use of a novel multielectrode slipping surface discharge (SSD) treatment system, capable of pulsed plasma discharge directly in water, in killing micro-organisms. Potable water containing Escherichia coli and somatic coliphages was treated with pulsed electric discharges generated by the SSD. The SSD system was highly efficient in the microbial disinfection of water with a low energy utilization (eta approximately 10-4 kW h l-1). The SSD treatment was effective in the destruction of E. coli and its coliphages through the generation of u.v. radiation, ozone and free radicals. The non-thermal treatment method can be used for the eradication of micro-organisms in a range of contaminated liquids, including milk, negating the use of pasteurization. The method utilizes multipoint electric discharges capable of treating large volumes of liquid under static and flowing regimes.
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Inactivation of coliphage Q beta by potassium ferrate.
Kazama, F
1994-05-15
The kinetics of inactivation of a bacteriophage by potassium ferrate were studied with the F-specific RNA-coliphage Q beta. Inactivation in phosphate buffer (pH 6, 7 and 8) containing ferrate could be described by Hom's model. The inactivation rate depended on the pH. However, the relative effects of ferrate concentration and exposure time on inactivation were not affected by a change in pH from 6 to 8. In a study of the mechanism by which ferrate inactivated the virus, the efficiency of viral inactivation after ferrate decomposed in buffer was assayed. Inactivation was still effective and still followed Hom's equation after the complete decomposition of ferrate ion; however, the efficiency of that inactivation disappeared when sodium thiosulfate was added, suggesting that long-lived oxidative intermediates capable of viral inactivation were generated during the decomposition of ferrate ions.
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Searching for sterile neutrinos in dynamical dark energy cosmologies
NASA Astrophysics Data System (ADS)
Feng, Lu; Zhang, Jing-Fei; Zhang, Xin
2018-05-01
We investigate how the dark energy properties change the cosmological limits on sterile neutrino parameters by using recent cosmological observations. We consider the simplest dynamical dark energy models, the wCDM model and the holographic dark energy (HDE) model, to make an analysis. The cosmological observations used in this work include the Planck 2015 CMB temperature and polarization data, the baryon acoustic oscillation data, the type Ia supernova data, the Hubble constant direct measurement data, and the Planck CMB lensing data. We find that, m v,terile ff < 0.2675 eV and Ne f f < 3.5718 for ACDM cosmology, m v,terile ff < 0.5313 eV and Ne f f < 3.5008 for wCDM cosmology, and raffterile < 0.1989 eV and Ne f f < 3.6701 for HDE cosmology, from the constraints of the combination of these data. Thus, without the addition of measurements of growth of structure, only upper limits on both m v,terile ff and Ne f f can be derived, indicating that no evidence of the existence of a sterile neutrino species with eV-scale mass is found in this analysis. Moreover, compared to the ACDM model, in the wCDM model the limit on m v,terile ff becomes much looser, but in the HDE model the limit becomes much tighter. Therefore, the dark energy properties could significantly influence the constraint limits of sterile neutrino parameters.
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Dysfunctional role of parietal lobe during self-face recognition in schizophrenia.
Yun, Je-Yeon; Hur, Ji-Won; Jung, Wi Hoon; Jang, Joon Hwan; Youn, Tak; Kang, Do-Hyung; Park, Sohee; Kwon, Jun Soo
2014-01-01
Anomalous sense of self is central to schizophrenia yet difficult to demonstrate empirically. The present study examined the effective neural network connectivity underlying self-face recognition in patients with schizophrenia (SZ) using [15O]H2O Positron Emission Tomography (PET) and Structural Equation Modeling. Eight SZ and eight age-matched healthy controls (CO) underwent six consecutive [15O]H2O PET scans during self-face (SF) and famous face (FF) recognition blocks, each of which was repeated three times. There were no behavioral performance differences between the SF and FF blocks in SZ. Moreover, voxel-based analyses of data from SZ revealed no significant differences in the regional cerebral blood flow (rCBF) levels between the SF and FF recognition conditions. Further effective connectivity analyses for SZ also showed a similar pattern of effective connectivity network across the SF and FF recognition. On the other hand, comparison of SF recognition effective connectivity network between SZ and CO demonstrated significantly attenuated effective connectivity strength not only between the right supramarginal gyrus and left inferior temporal gyrus, but also between the cuneus and right medial prefrontal cortex in SZ. These findings support a conceptual model that posits a causal relationship between disrupted self-other discrimination and attenuated effective connectivity among the right supramarginal gyrus, cuneus, and prefronto-temporal brain areas involved in the SF recognition network of SZ. © 2013.
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Amarasiri, Mohan; Kitajima, Masaaki; Nguyen, Thanh H; Okabe, Satoshi; Sano, Daisuke
2017-09-15
The multiple-barrier concept is widely employed in international and domestic guidelines for wastewater reclamation and reuse for microbiological risk management, in which a wastewater reclamation system is designed to achieve guideline values of the performance target of microbe reduction. Enteric viruses are one of the pathogens for which the target reduction values are stipulated in guidelines, but frequent monitoring to validate human virus removal efficacy is challenging in a daily operation due to the cumbersome procedures for virus quantification in wastewater. Bacteriophages have been the first choice surrogate for this task, because of the well-characterized nature of strains and the presence of established protocols for quantification. Here, we performed a meta-analysis to calculate the average log 10 reduction values (LRVs) of somatic coliphages, F-specific phages, MS2 coliphage and T4 phage by membrane bioreactor, activated sludge, constructed wetlands, pond systems, microfiltration and ultrafiltration. The calculated LRVs of bacteriophages were then compared with reported human enteric virus LRVs. MS2 coliphage LRVs in MBR processes were shown to be lower than those of norovirus GII and enterovirus, suggesting it as a possible validation and operational monitoring tool. The other bacteriophages provided higher LRVs compared to human viruses. The data sets on LRVs of human viruses and bacteriophages are scarce except for MBR and conventional activated sludge processes, which highlights the necessity of investigating LRVs of human viruses and bacteriophages in multiple treatment unit processes. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Zanetti, F; De Luca, G; Sacchetti, R; Stampi, S
2007-11-01
The aim of the study was to assess the efficiency of low doses of peracetic acid against viral and bacterial indicators in wastewater and to evaluate if the treatment allows regulatory requirements to be satisfied. A total of 31 samplings were carried out, each involving the collection of secondary effluent and of effluent disinfected with 1.2 or 1.5 mg l(-1) of peracetic acid (contact time 20 minutes). In each sample were measured: somatic coliphages, F-specific RNA bacteriophages, Escherichia coli, total and faecal coliforms, enterococci. Peracetic acid disinfection showed significant differences between the reductions of the microorganisms tested: E. coli showed the highest reduction (1.78 and 2.43 Log respectively with 1.2 and 1.5 mg l(-1) of peracetic acid) and phages the lowest (ranging between 0.52 and 0.60 Log). Only a concentration of 1.5 mg l(-1) of peracetic acid would enable the effluent to be discharged into surface waters in compliance with Italian regulations. The variability of microbial resistance against the peracetic acid disinfection treatment, underlines the importance of assessing disinfection efficiency by using more than one indicator microorganism. The detection of E. coli could be usefully accompanied by tests for more resistant microorganisms such as enterococci or coliphages. In conclusion, peracetic acid can be used for the disinfection of effluents even at low doses, with the advantage of reducing costs and preventing the formation of significant amounts of genotoxic by-products.
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Haramoto, Eiji; Yamada, Kaoru; Nishida, Kei
2011-12-01
Limited information is available on the prevalence of waterborne pathogens in aquatic environments in developing countries. In this study, water samples were collected from nine shallow wells and a river in the Kathmandu Valley, Nepal, during the rainy season in 2009 and were subjected to detection of waterborne protozoa, viruses and coliphages using a recently developed method for simultaneous concentration of protozoa and viruses in water. Escherichia coli and total coliforms were also tested as indicator bacteria. At least one type of the five pathogens tested (Cryptosporidium, Giardia, human adenoviruses, and noroviruses of genogroups I and II) was detected in five groundwater samples (56%) (1000 ml each) from shallow wells. Compared with groundwater samples, the pathogens were more abundant in the river water sample (100ml); the concentrations of Cryptosporidium and Giardia were 140 oocysts/l and 8500 cysts/l, respectively, and the mean threshold cycle (Ct) values in real-time RT-PCR were 34.3, 36.8 and 34.0 for human adenoviruses and noroviruses of genogroups I and II, respectively. Genotyping of F-RNA coliphages by real-time RT-PCR was successfully used to differentiate human and animal faecal contamination in the samples. Moreover, for the groundwater samples, protozoa and viruses were detected only in E. coli-positive samples, suggesting that E. coli may be an appropriate indicator of pathogen contamination of valley groundwater. Copyright © 2011 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.
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Muniesa, Maite; Lucena, Francisco; Blanch, Anicet R; Payán, Andrey; Jofre, Juan
2012-12-01
Water contaminated with human faeces is a risk to human health and management of water bodies can be improved by determining the sources of faecal pollution. Field studies show that existing methods are insufficient and that different markers are required. This study proposes the combined use of two microbial indicators, the concentrations of which are presented as ratios. This provides a more reliable approach to identifying faecal sources as it avoids variation due to treatment or ageing of the contamination. Among other indicators, bacteriophages have been proposed as rapid and cheap indicators of faecal pollution. Samples analysed in this study were derived from wastewater treatment plants (raw sewage, secondary and tertiary effluents and raw sewage sludge) river water, seawater and animal related wastewater. The abundance ratios of faecal coliforms and Bacteroides phages, either strain RYC2056 (non-specific for faecal origin) or strain GA17 (specific for human pollution), and among somatic coliphages and phages infecting both Bacteroides strains, were evaluated. The results indicate that the ratio of somatic coliphages and phages infecting Bacteroides strain GA17, which is specific to human faecal sources, provides a robust method for discriminating samples, even those presenting different levels and ages of pollution, and allows samples polluted with human faeces to be distinguished from those containing animal faecal pollution. This method allows the generation of numerical data that can be further applied to numerical methods for faecal pollution discrimination. Copyright © 2012 Elsevier Ltd. All rights reserved.
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Kennedy, Lisa M; Watson-Leung, Trudy L; Poirier, David G
2016-10-01
Three Hyalella azteca cultures were reared on different diets since birth, reflecting the recommended diets of various investigators. The 3 diets consisted of fish flakes (FF), a mixture of fish flakes supplemented with the diatom Thalassiosira weissflogii (FF-D), and a mixture of fish flakes supplemented with yeast, cereal grass media, and trout chow (FF-YCT). The 3 diets were evaluated by comparing 20 wk of culturing data, along with the organism's response to standard 96-h toxicity testing with ammonium chloride over a range of pH and temperature. Hyalella azteca fed the FF-D diet had the highest overall survival rate (96.6%, standard deviation [SD] 4.3%) compared to those fed the FF diet (92.0%, SD 12.7%), or the FF-YCT diet (91.1%, SD 14.8%), although difference in survival was not statistically significant. Organisms fed the FF-D diet produced a higher number of young per week per adult (6.1, SD 2.8) than the FF diet (5.1, SD 2.2), or the FF-YCT diet (4.0, SD 1.2), although differences were not statistically significant. Of the diets evaluated, H. azteca reared on the FF-D diet were often significantly more resistant to total and un-ionized ammonia toxicity in acute 96-h testing than those reared on the other 2 diets across the 2 temperatures and 5 pHs tested, suggesting this may be the most optimal diet for this species. Environ Toxicol Chem 2016;35:2416-2424. © 2016 SETAC. © 2016 SETAC.
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Espinal, Allyson C; Wang, Dan; Yan, Li; Liu, Song; Tang, Li; Hu, Qiang; Morrison, Carl D; Ambrosone, Christine B; Higgins, Michael J; Sucheston-Campbell, Lara E
2017-02-28
DNA from archival formalin-fixed and paraffin embedded (FFPE) tissue is an invaluable resource for genome-wide methylation studies although concerns about poor quality may limit its use. In this study, we compared DNA methylation profiles of breast tumors using DNA from fresh-frozen (FF) tissues and three types of matched FFPE samples. For 9/10 patients, correlation and unsupervised clustering analysis revealed that the FF and FFPE samples were consistently correlated with each other and clustered into distinct subgroups. Greater than 84% of the top 100 loci previously shown to differentiate ER+ and ER- tumors in FF tissues were also FFPE DML. Weighted Correlation Gene Network Analyses (WCGNA) grouped the DML loci into 16 modules in FF tissue, with ~85% of the module membership preserved across tissue types. Restored FFPE and matched FF samples were profiled using the Illumina Infinium HumanMethylation450K platform. Methylation levels (β-values) across all loci and the top 100 loci previously shown to differentiate tumors by estrogen receptor status (ER+ or ER-) in a larger FF study, were compared between matched FF and FFPE samples using Pearson's correlation, hierarchical clustering and WCGNA. Positive predictive values and sensitivity levels for detecting differentially methylated loci (DML) in FF samples were calculated in an independent FFPE cohort. FFPE breast tumors samples show lower overall detection of DMLs versus FF, however FFPE and FF DMLs compare favorably. These results support the emerging consensus that the 450K platform can be employed to investigate epigenetics in large sets of archival FFPE tissues.
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Matera, Maria Gabriella; Capuano, Annalisa; Cazzola, Mario
2015-02-01
Fluticasone furoate/vilanterol (FF/VI) is a novel inhaled corticosteroid/long-acting β₂-agonist (ICS/LABA) fixed dose combination that, by simplifying the dosing schedule, allows, for the first time in a member of the ICS/LABA class, a shift from twice-daily to once-daily treatment. FF/VI is delivered via a novel, single-step activation, multi-dose dry powder inhaler for oral inhalation, Ellipta. Regrettably, there are no head-to-head trials that have shown superiority in the safety or efficacy of FF versus other ICSs, but evidence shows that VI has a quicker onset of effect versus salmeterol. However, the clinical utility of this effect in a maintenance medication is still questionable. Furthermore, benefits of FF/VI over twice-daily ICS/LABA comparator have not been shown yet and, in addition, its adverse event profile is generally consistent with the known class effects of an ICS/LABA fixed dose combination. In particular, there is an increase in the risk of pneumonia among patients treated with FF/VI relative to VI, mainly among those who benefit most from FF/VI. Nevertheless, the interesting pharmacological profiles of both FF and VI, the possibility that FF/VI can be administered once-daily, and the attractive characteristics of Ellipta are important features that could help FF/VI to be a successful combination in the treatment of chronic obstructive pulmonary disease.
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Hao, Jiuxiao; Wang, Hui; Wang, Xiujin
2018-04-01
The feast-to-famine ratio (F/F) represents the extent of selective pressure during polyhydroxyalkanoate (PHA) culture selection. This study evaluated the effects of F/F on a new PHA production system by an enriched culture with valerate-dominant sludge hydrolysate and selected the optimal F/F. After the original F/F 1/3 was modified to 1/1, 1/2, 1/4, and 1/5, F/F did not affect their lengths of feast phase, but affected their biomass growth behaviors during the famine phase and PHA-producing abilities. The optimal F/F was 1/2, and compared with 1/3, it increased the maximal PHA content and the fraction of 3-hydroxyvalerate (3HV) and 3-hydroxy-2-methylvalerate (3H2MV) monomers, with higher productivity and better polymer properties. Although F/F 1/2 impaired the advantage of the dominant genus Delftia, it improved the PHA production rate while decreased biomass growth rate, meanwhile enhancing the utilization and conversion of valerate. These findings indicate that in contrast to previous studies using acetate-dominant substrate for PHA production, the new system fed by valerate-dominant substrate can adopt a higher F/F.
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Liu, Jin; Ke, Bowen; Wang, Xiaojia; Li, Fengshan; Li, Tao; Bayliss, Douglas A.; Chen, Xiangdong
2015-01-01
Background HCN1 channels have been identified as targets of ketamine to produce hypnosis. Volatile anesthetics also inhibit HCN1 channels. However, the effects of HCN1 channels on volatile anesthetics in vivo is still elusive. This study uses global and conditional HCN1 knockout mice to evaluate how HCN1 channels affect the actions of volatile anesthetics. Methods Minimum alveolar concentrations (MAC) of isoflurane and sevoflurane that induced immobility (MAC of immobility) and/or hypnosis (MAC of hypnosis) were determined in wild-type (WT) mice, global HCN1 channel knockout mice (HCN1−/−), floxed HCN1 channel gene (HCN1f/f) mice and forebrain-selective HCN1 channel knockout (HCN1f/f: cre) mice. Immobility of mice was defined as no purposeful reactions to tail-clamping stimulus and hypnosis was defined as loss of righting reflex (LORR). The amnestic effects of isoflurane and sevoflurane were evaluated by fear-potentiated startle in these four strains of mice. Results All MAC values were expressed as mean ± SEM. For MAC of immobility of isoflurane, no significant difference was found among wild-type, HCN1−/−, HCN1f/f and HCN1f/f: cre mice (all ~1.24-1.29% isoflurane). For both HCN1−/− and HCN1f/f: cre mice, the MAC of hypnosis for isoflurane (each ~1.05% isoflurane) were significantly increased over their nonknockout controls: HCN1−/− vs. wild-type (0.86±0.03%, P<0.001) and HCN1f/f: cre vs. HCN1f/f mice (0.84±0.03%, P<0.001); no significant difference was found between HCN1−/− and HCN1f/f: cre mice. For MAC of immobility of sevoflurane, no significant difference was found among wild-type, HCN1−/−, HCN1f/f and HCN1f/f: cre mice (all ~2.6-2.7% sevoflurane). For both HCN1−/− and HCN1f/f: cre mice, the MAC of hypnosis for sevoflurane (each ~1.90% sevoflurane) was significantly increased over their nonknockout controls: HCN1−/− vs. wild-type (1.58±0.05%, P<0.001) and HCN1f/f: cre vs. HCN1f/f mice (1.56±0.05%, P<0.001). No significant difference was found between HCN1−/− and HCN1f/f: cre mice. By fear-potentiated startle experiments, amnestic effects of isoflurane and sevoflurane were significantly attenuated in HCN1−/− and HCN1f/f: cre mice (both P<0.002 vs. wild-type or HCN1f/f mice). No significant difference was found between HCN1−/− and HCN1f/f: cre mice. Conclusions Forebrain HCN1 channels contribute to hypnotic and amnestic effects of volatile anesthetics, but HCN1 channels are not involved in the immobilizing actions of volatile anesthetics. PMID:26287296
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Roche, S M; Jones-Bitton, A; Meehan, M; Von Massow, M; Kelton, D F
2015-08-01
This study evaluated a participatory-based, experiential learning program, Ontario Focus Farms (FF), which aimed to change dairy producer behavior to control Johne's disease (JD) in Ontario, Canada. The goals were to (1) assess the effect of FF on participating dairy producers' knowledge, attitudes, and behavior with regard to JD control; (2) compare changes in these factors among FF participants to changes among a group of nonparticipating dairy producers; and (3) describe the characteristics of producers who made at least one on-farm management change. Pre- and post-FF intervention questionnaires collected data on respondents' knowledge, attitudes, behavior, herd production, and demographic information; before and after JD-risk assessments were used to assess respondents' on-farm risk of JD transmission. Overall, 176 dairy producers participated in the FF process; 39.8% (70/176) of FF and 14.6% (52/357) of control participants responded to both the pre- and postintervention questionnaires. Upon comparison, FF respondents were more likely to be younger, have larger herds, and have higher management scores. The proportion of FF participants who reported making at least one on-farm change (81%) was significantly higher than that of control respondents (38%). Overall, FF respondents significantly changed their risk score in 4 out of 5 risk areas and had an average reduction of 13 points in their overall risk score between before and after risk assessments. Control respondents' risk assessment scores did not significantly change during the study period. In a JD knowledge assessment, FF and control respondents exhibited a moderate knowledge score before the intervention period, with median scores of 75.9% (22/29) in each group. The FF respondents significantly increased their score at the postintervention assessment, with a median of 82.8% (24/29); control-respondent scores did not significantly change. Both FF and control respondents held strong positive attitudes toward JD control and felt a moderate amount of social pressure from veterinarians and industry organizations to make on-farm changes. However, they questioned their ability to effectively control JD on the farm. Last, participating in FF, having a moderate herd management score, having a positive perception about the practicality of on-farm recommendations, and having a singular learning preference were associated with increased odds of making an on-farm change. Overall, the FF process appears to be effective at influencing producer behavior toward implementing on-farm management practices for JD control. Future JD control programs should consider implementing peer-learning extension processes, such as FF, in combination with other extension approaches, to influence producer behavior. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
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Zhao, Yangyang; Dong, Xiaoyan; Yu, Linling; Liu, Yang; Sun, Yan
2018-05-18
Previously, we have studied protein adsorption and chromatographic behaviors on poly(ethylenimine) (PEI)-grafted Sepharose FF anion-exchange resins, and found that protein uptake rates increased greatly when PEI grafting density reached over a critical ionic capacity (cIC) due to the occurrence of the "chain delivery" effect. Moreover, by partial charge neutralization of starting resin FF-PEI-L740 (IC = 740 mmol/L, larger than the cIC) with sodium acetate to FF-PEI-R440, it exhibited a three-fold increase in uptake rate over FF-PEI-L740. In this work, to take the advantages of PEI and extend the applications of the PEI-grafted resins in cation-exchange chromatography, a series of cation exchangers of five different ICs were developed. First, the charged of FF-PEI-L740 was reversed from positive to negative by reaction with excess succinic anhydride, which created a cation-exchanger with an IC of 970 mmol/L (FF-FEI-C970). FF-PEI-C970 was further modified with ethanolamine for partial charge neutralizations, leading to the preparation of four charge-reduced cation exchangers with IC values (in mmol/L) of 780, 630, 560 and 430, which were denoted as FF-PEI-CR780, -CR630 -CR560 and -CR430, respectively. Protein adsorption and chromatographic behaviors were investigated using lysozyme (Lys) as the model protein. It was found that, the resins of high and moderate IC values (IC ≥ 560 mmol/L) afforded adsorption capacities up to over 230 mg/mL. Besides, the uptake rate, represented by the effective pore diffusivity (D e/ D 0 ), exhibited significant increase from 0.067 (FF-PEI-C970 and FF-PEI-CR780) to 0.343 (FF-PEI-CR630 and FF-PEI-CR560) and then to 1.035 (FF-PEI-CR430) with decreasing IC. It was considered that decreasing IC led to the decreased protein binding sites (binding strength), which encouraged the occurrence of the "chain delivery" effect. Moreover, the resins of high and moderate IC values, particularly, the resins of moderate IC values (FF-PEI-CR630 and FF-PEI-CR560), presented both high adsorption capacities and uptake kinetics at 0-100 mmol/L NaCl. Besides, dynamic binding capacity achieved 150 mg/mL for the resins of moderate IC values at 0 mmol/L NaCl concentration, and afforded >110 mg/mL for the resin of high IC values at 0-100 mmol/L NaCl concentration. The results proved the excellent IEC performance of the PEI-derived cation exchangers. Copyright © 2018 Elsevier B.V. All rights reserved.
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The burden and undertreatment of fragility fractures among senior women.
Rodrigues, Ana M; Eusébio, Mónica; Santos, Maria José; Gouveia, Nélia; Tavares, Viviana; Coelho, Pedro S; Mendes, Jorge M; Branco, Jaime C; Canhão, Helena
2018-03-07
Using a large population database, we showed that fragility fractures were highly prevalent in senior women and were associated with significant physical disability. However, treatment rates were low because osteoporosis treatment was not prescribed or not agreed to by the majority of women with prevalent fragility fractures. The purpose of the study is to estimate prevalence of fragility fractures (FF), risk factors, and treatment rates in senior women and to assess impact of FF on physical function and quality of life. Women aged 65 years and older from the EpiReumaPt study (2011-2013) were evaluated. Rheumatologists collected data regarding FF, clinical risk factors for fractures, and osteoporosis (OP) treatment. Health-related quality of life (EQ5D) and physical function (HAQ) were analyzed. Peripheral dual-energy X-ray absorptiometry was performed. FF was defined as any self-reported low-impact fracture that occurred after 40 years of age. Prevalence estimates of FF were calculated. Among 3877 subjects evaluated in EpiReumaPt, 884 were senior women. The estimated prevalence of FF was 20.7%. Lower leg was the most frequent fracture site reported (37.8%) followed by wrist (18.6%). Only 7.1% of the senior women reporting a prevalent FF were under treatment for OP, and 13.9% never had treatment. OP treatment was not prescribed in 47.7% of FF women, and 23.4% refused treatment. Age (OR = 2.46, 95% CI 1.11-5.47), obesity (OR = 2.05, 95% CI 1.14-3.70), and low wrist BMD (OR = 2.29; 95% CI 1.20, 4.35; p = 0.012) were positively associated with prevalent FF. A significantly higher proportion of women in the lowest quintile of wrist bone mineral density reported FF (OR = 2.29, 95% CI 1.20-4.35). FF were associated with greater physical disability (β = 0.33, 95% CI 0.13-0.51) independent of other comorbidities. FF was frequently reported among senior women as an important cause of physical disability. However, the prevalence of OP treatment was low, which constitutes a public health problem in this vulnerable group.
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Yan, Li; Liu, Song; Tang, Li; Hu, Qiang; Morrison, Carl D.; Ambrosone, Christine B.; Higgins, Michael J.; Sucheston-Campbell, Lara E.
2017-01-01
Background DNA from archival formalin-fixed and paraffin embedded (FFPE) tissue is an invaluable resource for genome-wide methylation studies although concerns about poor quality may limit its use. In this study, we compared DNA methylation profiles of breast tumors using DNA from fresh-frozen (FF) tissues and three types of matched FFPE samples. Results For 9/10 patients, correlation and unsupervised clustering analysis revealed that the FF and FFPE samples were consistently correlated with each other and clustered into distinct subgroups. Greater than 84% of the top 100 loci previously shown to differentiate ER+ and ER– tumors in FF tissues were also FFPE DML. Weighted Correlation Gene Network Analyses (WCGNA) grouped the DML loci into 16 modules in FF tissue, with ~85% of the module membership preserved across tissue types. Materials and Methods Restored FFPE and matched FF samples were profiled using the Illumina Infinium HumanMethylation450K platform. Methylation levels (β-values) across all loci and the top 100 loci previously shown to differentiate tumors by estrogen receptor status (ER+ or ER−) in a larger FF study, were compared between matched FF and FFPE samples using Pearson's correlation, hierarchical clustering and WCGNA. Positive predictive values and sensitivity levels for detecting differentially methylated loci (DML) in FF samples were calculated in an independent FFPE cohort. Conclusions FFPE breast tumors samples show lower overall detection of DMLs versus FF, however FFPE and FF DMLs compare favorably. These results support the emerging consensus that the 450K platform can be employed to investigate epigenetics in large sets of archival FFPE tissues. PMID:28118602
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Castro, Angela M.; Lupu, Traian S.; Weinheimer, Carla; Smith, Craig; Kovacs, Attila
2016-01-01
Fibroblast growth factor (FGF) signaling is cardioprotective in various models of myocardial infarction. FGF receptors (FGFRs) are expressed in multiple cell types in the adult heart, but the cell type-specific FGFR signaling that mediates different cardioprotective endpoints is not known. To determine the requirement for FGFR signaling in endothelium in cardiac ischemia-reperfusion injury, we conditionally inactivated the Fgfr1 and Fgfr2 genes in endothelial cells with Tie2-Cre (Tie2-Cre, Fgfr1f/f, Fgfr2f/f DCKO mice). Tie2-Cre, Fgfr1f/f, Fgfr2f/f DCKO mice had normal baseline cardiac morphometry, function, and vessel density. When subjected to closed-chest, regional cardiac ischemia-reperfusion injury, Tie2-Cre, Fgfr1f/f, Fgfr2f/f DCKO mice showed a significantly increased hypokinetic area at 7 days, but not 1 day, after reperfusion. Tie2-Cre, Fgfr1f/f, Fgfr2f/f DCKO mice also showed significantly worsened cardiac function compared with controls at 7 days but not 1 day after reperfusion. Pathophysiological analysis showed significantly decreased vessel density, increased endothelial cell apoptosis, and worsened tissue hypoxia in the peri-infarct area at 7 days following reperfusion. Notably, Tie2-Cre, Fgfr1f/f, Fgfr2f/f DCKO mice showed no impairment in the cardiac hypertrophic response. These data demonstrate an essential role for FGFR1 and FGFR2 in endothelial cells for cardiac functional recovery and vascular remodeling following in vivo cardiac ischemia-reperfusion injury, without affecting the cardiac hypertrophic response. This study suggests the potential for therapeutic benefit from activation of endothelial FGFR pathways following ischemic injury to the heart. PMID:26747503
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Circulating fetal cell-free DNA fractions differ in autosomal aneuploidies and monosomy X.
Rava, Richard P; Srinivasan, Anupama; Sehnert, Amy J; Bianchi, Diana W
2014-01-01
Noninvasive prenatal testing based on massively parallel sequencing (MPS) of cell-free DNA in maternal plasma has become rapidly integrated into clinical practice for detecting fetal chromosomal aneuploidy. We directly determined the fetal fraction (FF) from results obtained with MPS tag counting and examined the relationships of FF to such biological parameters as fetal karyotype and maternal demographics. FF was determined from samples previously collected for the MELISSA (Maternal Blood Is Source to Accurately Diagnose Fetal Aneuploidy) study. Samples were resequenced, analyzed blindly, and aligned to the human genome (assembly hg19). FF was calculated in pregnancies with male or aneuploid fetuses by means of an equation that incorporated the ratio of the tags in these samples to those of a euploid training set. The mean (SD) FF from euploid male pregnancies was 0.126 (0.052) (n = 160). Weak but statistically significant correlations were found between FF and the maternal body mass index (r(2) = 0.18; P = 2.3 × 10(-8)) and between FF and gestational age (r(2) = 0.02; P = 0.047). No relationship with maternal ethnicity or age was observed. Mean FF values for trisomies 21 (n = 90), 18 (n = 38), and 13 (n = 16) and for monosomy X (n = 20) were 0.135 (0.051), 0.089 (0.039), 0.090 (0.062), and 0.106 (0.045), respectively. MPS tag-count data can be used to determine FF directly and accurately. Compared with male euploid fetuses, the FF is higher in maternal plasma when the fetus has trisomy 21 and is lower when the fetus has trisomy 18, 13, or monosomy X. The different biologies of these aneuploidies have practical implications for the determination of cutoff values, which in turn will affect the diagnostic sensitivity and specificity of the test.
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House, Stacey L; Castro, Angela M; Lupu, Traian S; Weinheimer, Carla; Smith, Craig; Kovacs, Attila; Ornitz, David M
2016-03-01
Fibroblast growth factor (FGF) signaling is cardioprotective in various models of myocardial infarction. FGF receptors (FGFRs) are expressed in multiple cell types in the adult heart, but the cell type-specific FGFR signaling that mediates different cardioprotective endpoints is not known. To determine the requirement for FGFR signaling in endothelium in cardiac ischemia-reperfusion injury, we conditionally inactivated the Fgfr1 and Fgfr2 genes in endothelial cells with Tie2-Cre (Tie2-Cre, Fgfr1(f/f), Fgfr2(f/f) DCKO mice). Tie2-Cre, Fgfr1(f/f), Fgfr2(f/f) DCKO mice had normal baseline cardiac morphometry, function, and vessel density. When subjected to closed-chest, regional cardiac ischemia-reperfusion injury, Tie2-Cre, Fgfr1(f/f), Fgfr2(f/f) DCKO mice showed a significantly increased hypokinetic area at 7 days, but not 1 day, after reperfusion. Tie2-Cre, Fgfr1(f/f), Fgfr2(f/f) DCKO mice also showed significantly worsened cardiac function compared with controls at 7 days but not 1 day after reperfusion. Pathophysiological analysis showed significantly decreased vessel density, increased endothelial cell apoptosis, and worsened tissue hypoxia in the peri-infarct area at 7 days following reperfusion. Notably, Tie2-Cre, Fgfr1(f/f), Fgfr2(f/f) DCKO mice showed no impairment in the cardiac hypertrophic response. These data demonstrate an essential role for FGFR1 and FGFR2 in endothelial cells for cardiac functional recovery and vascular remodeling following in vivo cardiac ischemia-reperfusion injury, without affecting the cardiac hypertrophic response. This study suggests the potential for therapeutic benefit from activation of endothelial FGFR pathways following ischemic injury to the heart. Copyright © 2016 the American Physiological Society.
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The Geography of Fast Food Outlets: A Review
Fraser, Lorna K.; Edwards, Kimberly L.; Cade, Janet; Clarke, Graham P.
2010-01-01
The availability of food high in fat, salt and sugar through Fast Food (FF) or takeaway outlets, is implicated in the causal pathway for the obesity epidemic. This review aims to summarise this body of research and highlight areas for future work. Thirty three studies were found that had assessed the geography of these outlets. Fourteen studies showed a positive association between availability of FF outlets and increasing deprivation. Another 13 studies also included overweight or obesity data and showed conflicting results between obesity/overweight and FF outlet availability. There is some evidence that FF availability is associated with lower fruit and vegetable intake. There is potential for land use policies to have an influence on the location of new FF outlets. Further research should incorporate good quality data on FF consumption, weight and physical activity. PMID:20623025
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The geography of Fast Food outlets: a review.
Fraser, Lorna K; Edwards, Kimberly L; Cade, Janet; Clarke, Graham P
2010-05-01
The availability of food high in fat, salt and sugar through Fast Food (FF) or takeaway outlets, is implicated in the causal pathway for the obesity epidemic. This review aims to summarise this body of research and highlight areas for future work. Thirty three studies were found that had assessed the geography of these outlets. Fourteen studies showed a positive association between availability of FF outlets and increasing deprivation. Another 13 studies also included overweight or obesity data and showed conflicting results between obesity/overweight and FF outlet availability. There is some evidence that FF availability is associated with lower fruit and vegetable intake. There is potential for land use policies to have an influence on the location of new FF outlets. Further research should incorporate good quality data on FF consumption, weight and physical activity.
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Cao, Ye; Liu, Xia -Ji; He, Lianyi; ...
2015-02-09
We theoretically investigate the superfluid density and Berezinskii-Kosterlitz-Thouless (BKT) transition of a two-dimensional Rashba spin-orbit-coupled atomic Fermi gas with both in-plane and out-of-plane Zeeman fields. It was recently predicted that, by tuning the two Zeeman fields, the system may exhibit different exotic Fulde-Ferrell (FF) superfluid phases, including the gapped FF, gapless FF, gapless topological FF, and gapped topological FF states. Due to the FF paring, we show that the superfluid density (tensor) of the system becomes anisotropic. When an in-plane Zeeman field is applied along the x direction, the tensor component along the y direction n s,yy is generally largermore » than n s,xx in most parameter space. At zero temperature, there is always a discontinuity jump in n s,xx as the system evolves from a gapped FF into a gapless FF state. With increasing temperature, such a jump is gradually washed out. The critical BKT temperature has been calculated as functions of the spin-orbit-coupling strength, interatomic interaction strength, and in-plane and out-of-plane Zeeman fields. We predict that the novel FF superfluid phases have a significant critical BKT temperature, typically at the order of 0.1T F, where T F is the Fermi degenerate temperature. Furthermore, their observation is within the reach of current experimental techniques in cold-atom laboratories.« less
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Bruening, Meg; MacLehose, Richard; Eisenberg, Marla E; Nanney, Marilyn S; Story, Mary; Neumark-Sztainer, Dianne
2014-01-01
To assess associations between adolescents and their friends with regard to sugar-sweetened beverage (SSB)/diet soda intake and fast-food (FF) restaurant visits. Population-based, cross-sectional survey study with direct measures from friends. Twenty Minneapolis/St Paul schools during 2009-2010. Adolescents (n = 2,043; mean age, 14.2 ± 1.9 years; 46.2% female; 80% non-white). Adolescent SSB/diet soda intake and FF visits. Generalized estimating equation logistic models were used to examine associations between adolescents' SSB/diet soda intake and FF visits and similar behaviors in nominated friends (friend groups and best friends). School-level (middle vs high school) interactions were assessed. Significant associations were found between adolescents and friends behaviors for each of the beverages assessed (P < .05), but they varied by friendship type and school level. Five of 6 models of FF visits (including all FF visits) were significantly associated (P < .05) among adolescents and their friends. Significant interactions by school level were present among adolescents' and friends' FF visits, with associations generally for high school participants compared with middle school participants (P < .05). Findings suggest that for many beverages and FF restaurant types, friends' behaviors are associated, especially FF visits for older adolescents. Nutrition education efforts may benefit by integrating knowledge of the impact of adolescents' friends on FF visits. Copyright © 2014 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.
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Bruening, Meg; MacLehose, Richard; Eisenberg, Marla E; Nanney, Marilyn S.; Story, Mary; Neumark-Sztainer, Dianne
2016-01-01
Objective To assess associations between adolescents and their friends with regard to sugar-sweetened beverage (SSB)/diet soda intake, and fast food (FF) restaurant visits. Design Population-based, cross-sectional survey study with direct measures from friends. Setting Twenty Minneapolis/St. Paul schools during 2009–2010. Participants Adolescents (n=2,043; mean age=14.2±1.9; 46.2% female; 80% non-white). Main outcome measures Adolescent SSB/diet soda intake and FF visits. Analysis Generalized estimating equation logistic models were used to examine associations between adolescents’ SSB/diet soda intake and FF visits and similar behaviors in nominated friends (friend groups, best friends). School-level (middle vs. high school) interactions were assessed. Results Significant associations were found between adolescents and friends behaviors for each of the beverages assessed (P<0.05), but varied by friendship type and school level. Five of six models of FF visits (including all FF visits) were significantly associated (P <0.05) among adolescents and their friends. Significant interactions by school level were present among adolescents’ and friends’ FF visits, with associations generally for high school participants compared to middle school participants (P <0.05). Conclusions and implications Findings suggest for many beverages and FF restaurant types, friends’ behaviors are associated, especially FF visits for older adolescents. Nutrition education efforts may benefit by integrating the knowledge of the impact of adolescents’ friends on FF visits. PMID:24735768
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Lewandowska, Aleksandra E; Macur, Katarzyna; Czaplewska, Paulina; Liss, Joanna; Łukaszuk, Krzysztof; Ołdziej, Stanisław
2017-08-04
Human follicular fluid (hFF) is a natural environment of oocyte maturation, and some components of hFF could be used to judge oocyte capability for fertilization and further development. In our pilot small-scale study three samples from four donors (12 samples in total) were analyzed to determine which hFF proteins/peptides could be used to differentiate individual oocytes and which are patient-specific. Ultrafiltration was used to fractionate hFF to high-molecular-weight (HMW) proteome (>10 kDa) and low-molecular-weight (LMW) peptidome (<10 kDa) fractions. HMW and LMW compositions were analyzed using LC-MS in SWATH data acquisition and processing methodology. In total we were able to identify 158 proteins, from which 59 were never reported before as hFF components. 55 (45 not reported before) proteins were found by analyzing LMW fraction, 67 (14 not reported before) were found by analyzing HMW fraction, and 36 were identified in both fractions of hFF. We were able to perform quantitative analysis for 72 proteins from HMW fraction of hFF. We found that concentrations of 11 proteins varied substantially among hFF samples from single donors, and those proteins are promising targets to identify biomarkers useful in oocyte quality assessment.
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Base-unpaired regions in supercoiled replicative form DNA of coliphage M13
DOE Office of Scientific and Technical Information (OSTI.GOV)
Dasgupta, S.; Allison, D.P.; Snyder, C.E.
Superhelical covalently closed circular replicative form DNA (RF I) of coliphage M13 appears as a relaxed molecule that has a base-unpaired region in the form of a bubble (100 to 200 base pairs long) seen in electron micrographs when spread in the presence of formaldehyde and formamide or after pretreatment with glyoxal. S1 endonuclease, specific for single-stranded DNA, converts superhelical M13 RF I DNA, but not nonsuperhelical M13 RF I to a significant extent, into unit-length linear molecules by sequential nicking of two strands. The locations of S1 nuclease-susceptible sites and glyoxal-fixed base-unpaired regions were both related to the fivemore » A-T-rich regions in M13 RF DNA. While S1 nuclease does not show preference for any of these sites, glyoxal-fixed bubbles occur predominantly at the major A-T-rich region in M13 RF DNA.« less
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Praveen, Chandni; Jesudhasan, Palmy R; Reimers, Robert S; Pillai, Suresh D
2013-09-01
Microbial pathogens in municipal sewage sludges need to be inactivated prior to environmental disposal. The efficacy of high energy (10 MeV) e-beam irradiation to inactivate a variety of selected microbial pathogens and indicator organisms in aerobically and anaerobically digested sewage sludge was evaluated. Both bacterial and viral pathogens and indicator organisms are susceptible to e-beam irradiation. However, as expected there was a significant difference in their respective e-beam irradiation sensitivity. Somatic coliphages, bacterial endospores and enteric viruses were more resistant compared to bacterial pathogens. The current US EPA mandated 10 kGy minimum dose was capable of achieving significant reduction of both bacterial and viral pathogens. Somatic coliphages can be used as a microbial indicator for monitoring e-beam processes in terms of pathogen inactivation in sewage sludges. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Assessing fossil fuel CO2 emissions in California using atmospheric observations and models
NASA Astrophysics Data System (ADS)
Graven, H.; Fischer, M. L.; Lueker, T.; Jeong, S.; Guilderson, T. P.; Keeling, R. F.; Bambha, R.; Brophy, K.; Callahan, W.; Cui, X.; Frankenberg, C.; Gurney, K. R.; LaFranchi, B. W.; Lehman, S. J.; Michelsen, H.; Miller, J. B.; Newman, S.; Paplawsky, W.; Parazoo, N. C.; Sloop, C.; Walker, S. J.
2018-06-01
Analysis systems incorporating atmospheric observations could provide a powerful tool for validating fossil fuel CO2 (ffCO2) emissions reported for individual regions, provided that fossil fuel sources can be separated from other CO2 sources or sinks and atmospheric transport can be accurately accounted for. We quantified ffCO2 by measuring radiocarbon (14C) in CO2, an accurate fossil-carbon tracer, at nine observation sites in California for three months in 2014–15. There is strong agreement between the measurements and ffCO2 simulated using a high-resolution atmospheric model and a spatiotemporally-resolved fossil fuel flux estimate. Inverse estimates of total in-state ffCO2 emissions are consistent with the California Air Resources Board’s reported ffCO2 emissions, providing tentative validation of California’s reported ffCO2 emissions in 2014–15. Continuing this prototype analysis system could provide critical independent evaluation of reported ffCO2 emissions and emissions reductions in California, and the system could be expanded to other, more data-poor regions.
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High-resolution handheld rigid endomicroscope based on full-field optical coherence tomography
NASA Astrophysics Data System (ADS)
Benoit a la Guillaume, Emilie; Martins, Franck; Boccara, Claude; Harms, Fabrice
2016-02-01
Full-field optical coherence tomography (FF-OCT) is a powerful tool for nondestructive assessment of biological tissue, i.e., for the structural examination of tissue in depth at a cellular resolution. Mostly known as a microscopy device for ex vivo analysis, FF-OCT has also been adapted to endoscopy setups since it shows good potential for in situ cancer diagnosis and biopsy guidance. Nevertheless, all the attempts to perform endoscopic FF-OCT imaging did not go beyond lab setups. We describe here, to the best of our knowledge, the first handheld FF-OCT endoscope based on a tandem interferometry assembly using incoherent illumination. A common-path passive imaging interferometer at the tip of an optical probe makes it robust and insensitive to environmental perturbations, and a low finesse Fabry-Perot processing interferometer guarantees a compact system. A good resolution (2.7 μm transverse and 6 μm axial) is maintained through the long distance, small diameter relay optics of the probe, and a good signal-to-noise ratio is achieved in a limited 100 ms acquisition time. High-resolution images and a movie of a rat brain slice have been recorded by moving the contact endoscope over the surface of the sample, allowing for tissue microscopic exploration at 20 μm under the surface. These promising ex vivo results open new perspectives for in vivo imaging of biological tissue, in particular, in the field of cancer and surgical margin assessment.
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A comparison of 2 evaporative cooling systems on a commercial dairy farm in Saudi Arabia.
Ortiz, X A; Smith, J F; Villar, F; Hall, L; Allen, J; Oddy, A; Al-Haddad, A; Lyle, P; Collier, R J
2015-12-01
Efficacy of 2 cooling systems (Korral Kool, KK, Korral Kool Inc., Mesa, AZ; FlipFan dairy system, FF, Schaefer Ventilation Equipment LLC, Sauk Rapids, MN) was estimated utilizing 400 multiparous Holstein dairy cows randomly assigned to 1 of 4 cooled California-style shade pens (2 shade pens per cooling system). Each shaded pen contained 100 cows (days in milk=58±39, milk production=56±18 kg/d, and lactation=3±1). Production data (milk yield and reproductive performance) were collected during 3mo (June-August, 2013) and physiological responses (core body temperature, respiration rates, surface temperatures, and resting time) were measured in June and July to estimate responses of cows to the 2 different cooling systems. Water and electricity consumption were recorded for each system. Cows in the KK system displayed slightly lower respiration rates in the month of June and lower surface temperatures in June and July. However, no differences were observed in the core body temperature of cows, resting time, feed intake, milk yield, services/cow, and conception rate between systems. The FF system used less water and electricity during this study. In conclusion, both cooling systems (KK and FF) were effective in mitigating the negative effects of heat stress on cows housed in arid environments, whereas the FF system consumed less water and electricity and did not require use of curtains on the shade structure. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
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Commercial off-the-Shelf (COTS) Refractory Material Evaluation
NASA Technical Reports Server (NTRS)
Calle, Luz Marina; Kolody, Mark R.; Curran, Jerome P.; Back, Teddy; Hintze, Paul E.; Parlier, Christopher R.; Sampson, Jeffrey W.; Perusich, Stephen; Bucherl, Cori
2009-01-01
Fondu Fyre (FF) is currently the only refractory material qualified for use in the flame trench at KSC's Shuttle Launch Pads 39A and 39B. However, the material is not used as it was qualified and has undergone increasingly frequent and severe degradation due to the launch blasts. This degradation is costly as well as dangerous for launch infrastructure, crew and vehicle. FF is applied at the pad via the gunnite process, where wetted refractory material is sprayed onto a steel grid mounted on a support structure. The water content in this process can be manually adjusted by operators, causing distinct visual and physical discrepancies among repair areas. Since the application process is unlikely to change for new refractory materials, it is important to understand the effects of water content on commercial off-the-shelf (COTS) refractory materials. The purpose of this study was to evaluate the performance of the FF with respect to various water contents as well as heat treatments, to simulate aging and exposure to the blast. Initial results indicated that different water contents and heat treatments result in distinct differences in crushing strength, apparent porosity and bulk density. However, water content became an insignificant factor in both crush strength and porosity when FF was cured to at least 1500 deg. Additionally, inspection of the material's surface microstructure by scanning electron microscopy indicated distinguishable characteristics for different heat treatment levels. Results from this study will help guide future studies on the development and identification of new refractory materials.
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ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
2015-01-01
We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard–Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields. PMID:25328495
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Trade-offs of the opto-electrical properties of a-Si:H solar cells based on MOCVD BZO films.
Chen, Ze; Zhang, Xiao-dan; Liang, Jun-hui; Fang, Jia; Liang, Xue-jiao; Sun, Jian; Zhang, De-kun; Chen, Xin-liang; Huang, Qian; Zhao, Ying
2015-01-07
Boron-doped zinc oxide (BZO) films, deposited by metal-organic chemical vapor deposition (MOCVD), have been widely used as front electrodes in thin-film solar cells due to their native pyramidal surface structure, which results in efficient light trapping. This light trapping effect can enhance the short-circuit current density (Jsc) of solar cells. However, nanocracks or voids in the silicon active layer may form when the surface morphology of the BZO is too sharp; this usually leads to degraded electrical properties of the cells, such as open-circuit voltage (Voc) and the fill factor (FF), which in turn decreases efficiency (Eff) [Bailat et al., Photovoltaic Energy Conversion, Conference Record of the 2006 IEEE 4th World Conference on. IEEE, 2006, vol. 2, pp. 1533-1536]. In this paper, an etching and coating method was proposed to modify the sharp "pyramids" on the surface of the BZO films. As a result, an evident enhancement was achieved for these modified, BZO-based cells' Voc, FF, and Eff, although the Jsc exhibited a small decrease. In order to increase the Jsc and maintain the improved electrical properties (Voc, FF) of the cell, a thin BZO coating, deposited by MOCVD, was introduced to coat the sputtering-treated BZO film. Finally, we optimized the trade-off among the Voc, FF, and Jsc, that is, we identified a regime with an increase of the Jsc as well as a further improvement of the other electrical properties.
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Fulde–Ferrell superfluids in spinless ultracold Fermi gases
NASA Astrophysics Data System (ADS)
Zheng, Zhen-Fei; Guo, Guang-Can; Zheng, Zhen; Zou, Xu-Bo
2018-06-01
The Fulde–Ferrell (FF) superfluid phase, in which fermions form finite momentum Cooper pairings, is well studied in spin-singlet superfluids in past decades. Different from previous works that engineer the FF state in spinful cold atoms, we show that the FF state can emerge in spinless Fermi gases confined in optical lattice associated with nearest-neighbor interactions. The mechanism of the spinless FF state relies on the split Fermi surfaces by tuning the chemistry potential, which naturally gives rise to finite momentum Cooper pairings. The phase transition is accompanied by changed Chern numbers, in which, different from the conventional picture, the band gap does not close. By beyond-mean-field calculations, we find the finite momentum pairing is more robust, yielding the system promising for maintaining the FF state at finite temperature. Finally we present the possible realization and detection scheme of the spinless FF state.
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Topological superfluids with finite-momentum pairing and Majorana fermions.
Qu, Chunlei; Zheng, Zhen; Gong, Ming; Xu, Yong; Mao, Li; Zou, Xubo; Guo, Guangcan; Zhang, Chuanwei
2013-01-01
Majorana fermions (MFs), quantum particles that are their own antiparticles, are not only of fundamental importance in elementary particle physics and dark matter, but also building blocks for fault-tolerant quantum computation. Recently MFs have been intensively studied in solid state and cold atomic systems. These studies are generally based on superconducting pairing with zero total momentum. On the other hand, finite total momentum Cooper pairings, known as Fulde-Ferrell (FF) Larkin-Ovchinnikov (LO) states, were widely studied in many branches of physics. However, whether FF and LO superconductors can support MFs has not been explored. Here we show that MFs can exist in certain types of gapped FF states, yielding a new quantum matter: topological FF superfluids/superconductors. We demonstrate the existence of such topological FF superfluids and the associated MFs using spin-orbit-coupled degenerate Fermi gases and derive their parameter regions. The implementation of topological FF superconductors in semiconductor/superconductor heterostructures is also discussed.
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Jolly-Breithaupt, M L; Nuttelman, B L; Schneider, C J; Burken, D B; Gramkow, J L; Shreck, A L; MacDonald, J C; Klopfenstein, T J; Erickson, G E
2018-05-04
Three experiments evaluated the effects of corn oil removal using centrifugation in ethanol plants, on animal performance and digestion characteristics by finishing cattle fed by-products. In Exp. 1, 225 crossbred steers (300 ± 9.1 kg) were utilized in a randomized block design with a 2 × 2 + 1 factorial arrangement of treatments. Factors consisted of oil concentration [de-oiled (DO) or full fat (FF)] and by-product type [condensed distillers solubles (CDS) or modified distillers grains plus solubles (MDGS)] compared to a corn-based control. Fat concentration was 6.0% for DO CDS, 21.1% for FF CDS, 9.2% for DO MDGS, and 11.8% for FF MDGS. No oil concentration by by-product type interactions (P ≥ 0.17) were observed. There were no differences in DMI, ADG, or G:F between DO and FF CDS (P ≥ 0.29) or DO and FF MDGS (P ≥ 0.58). No differences (P ≥ 0.25) due to oil concentration were observed for carcass characteristics. Experiment 2 was a 5 × 5 Latin Square digestion trial with treatments similar to Exp. 1. Fat concentration was 8.7% or 15.4% for DO or FF CDS and 9.2% or 12.3% for DO or FF MDGS. Intake and total tract digestibility of fat were greater (P ≤ 0.02) for FF CDS compared with DO CDS. Digestible energy (megacalorie per kilogram), adjusted for intake, was greater (P = 0.02) for steers fed FF CDS compared to DO CDS. Average ruminal pH for cattle fed FF MDGS was greater than DO MDGS (P = 0.06). In Exp. 3, 336 yearling, crossbred steers (352 ± 19 kg) were utilized in a randomized block design with a 2 × 3 + 1 factorial arrangement of treatments. Factors included oil concentration (DO or FF) and inclusion [35%, 50%, and 65% wet distillers grains plus solubles (WDGS)] along with a corn-based control. The fat concentrations of DO and FF WDGS were 7.9% and 12.4%, respectively. A linear interaction (P < 0.01) was observed for DMI, which produced different slopes for DO and FF WDGS. No linear or quadratic interactions were observed for BW, ADG, or G:F (P ≥ 0.31). For the main effect of oil concentration, there were no statistical differences (P > 0.19) for final BW, ADG, or G:F. No statistical differences were observed for all carcass traits (P ≥ 0.34). Corn oil removal via centrifugation had minimal impact on finishing performance suggesting that cattle fed DO by-products will have similar performance to cattle fed FF by-products in dry-rolled and high-moisture corn diets.
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Evaluating UV-C LED disinfection performance and ...
This study evaluated ultraviolet (UV) light emitting diodes (LEDs) emitting at 260 nm, 280 nm, and the combination of 260|280 nm together for their efficacy at inactivating Escherichia. coli, MS2 coliphage, human adenovirus type 2 (HAdV2), and Bacillus pumilus spores; research included an evaluation of genomic damage. Inactivation by the LEDs was compared with the efficacy of conventional UV sources, the low-pressure (LP) and medium-pressure (MP) mercury vapor lamps. The work also calculated the electrical energy per order of reduction of the microorganisms by the five UV sources.For E. coli, all five UV sources yielded similar inactivation rates. For MS2 coliphage, the 260 nm LED was most effective. For HAdV2 and B. pumilus, the MP UV lamp was significantly more effective than the LP UV and UVC LED sources. When considering electrical energy per order of reduction, the LP UV lamp was the most efficient for E. coli and MS2, and the MPUV and LPUV were equally efficient for HAdV2 and B. pumilus spores. Among the UVC LEDs, the 280 nm LED unit required the least energy per log reduction of E. coli and HAdV2. The 280 nm and 260|280 nm LED units were equally efficient per log reduction of B. pumilus spores, and the 260 nm LED unit required the lowest energy per order of reduction of MS2 coliphage. The combination of the 260 nm and 280 nm UV LED wavelengths was also evaluated for potential synergistic effects. No dual-wavelength synergy was detected for inactivation of
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NASA Astrophysics Data System (ADS)
Fout, G. Shay; Borchardt, Mark A.; Kieke, Burney A.; Karim, Mohammad R.
2017-06-01
Groundwater quality is often evaluated using microbial indicators. This study examines data from 12 international groundwater studies (conducted 1992-2013) of 718 public drinking-water systems located in a range of hydrogeological settings. Focus was on testing the value of indicator organisms for identifying virus-contaminated wells. One or more indicators and viruses were present in 37 and 15% of 2,273 samples and 44 and 27% of 746 wells, respectively. Escherichia coli ( E. coli) and somatic coliphage are 7-9 times more likely to be associated with culturable virus-positive samples when the indicator is present versus when it is absent, while F-specific and somatic coliphages are 8-9 times more likely to be associated with culturable virus-positive wells. However, single indicators are only marginally associated with viruses detected by molecular methods, and all microbial indicators have low sensitivity and positive predictive values for virus occurrence, whether by culturable or molecular assays, i.e., indicators are often absent when viruses are present and the indicators have a high false-positive rate. Wells were divided into three susceptibility subsets based on presence of (1) total coliform bacteria or (2) multiple indicators, or (3) location of wells in karst, fractured bedrock, or gravel/cobble settings. Better associations of some indicators with viruses were observed for (1) and (3). Findings indicate the best indicators are E. coli or somatic coliphage, although both indicators may underestimate virus occurrence. Repeat sampling for indicators improves evaluation of the potential for viral contamination in a well.
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Hygienization performances of innovative sludge treatment solutions to assure safe land spreading.
Levantesi, C; Beimfohr, C; Blanch, A R; Carducci, A; Gianico, A; Lucena, F; Tomei, M C; Mininni, G
2015-05-01
The present research aims at the evaluation of the hygienization performances of innovative sludge treatment processes applied for the separated treatment of secondary sludge. Namely, two digestion pretreatments (sonication and thermal hydrolysis) and two sequential biological processes (mesophilic/thermophilic and anaerobic/aerobic digestion) were compared to the mesophilic (MAD) and thermophilic anaerobic digestion (TAD). Microbial indicators (Escherichia coli, somatic coliphages and Clostridium perfringens spores) and pathogens (Salmonella and enteroviruses), which show different resistances to treatment processes, were monitored in untreated and treated sludge. Overall, microbial load in secondary sludge was shown to be similar or lower than previously reported in literature for mixed sludge. Notably, the anaerobic/aerobic digestion process increased the removal of E. coli and somatic coliphages compared to the simple MAD and always achieved the hygienization requirement (2-log-unit removal of E. coli) proposed by EU Commission in the 3rd Working Document on sludge (April 2000) for the use of treated sludges in agriculture with restriction on their application. The microbial quality limits for the unrestricted use of sludge in agriculture (no Salmonella in 50 g wet weight (WW) and E. coli <500 CFU/g) were always met when thermal digestion or pretreatment was applied; however, the required removal level (6-log-unit removal of E. coli) could not be assessed due to the low level of this microorganism in raw sludge. Observed levels of indicator removal showed a higher resistance of viral particles to thermal treatment compared with bacterial cells and confirmed the suitability of somatic coliphages as indicators in thermal treatment processes.
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Griffin, Dale W.; Stokes, Rodger; Rose, J.B.; Paul, J.H.
2000-01-01
A microbiological water quality study of Homosassa Springs State Wildlife Park (HSSWP) and surrounding areas was undertaken. Samples were collected in November of 1997 (seven sites) and again in November of 1998 (nine sites). Fecal bacterial concentrations (total and fecal coliforms, Clostridium perfringens, and enterococci) were measured as relative indicators of fecal contamination. F+-specific coliphage genotyping was performed to determine the source of fecal contamination at the study sites. Bacterial levels were considerably higher at most sites in the 1997 sampling compared to the 1998 sampling, probably because of the greater rainfall that year. In November of 1997, 2 of the 7 sites were in violation of all indicator standards and guidance levels. In November of 1998, 1 of 9 sites was in violation of all indicator standard and guidance levels. The highest concentrations of all fecal indicators were found at a station downstream of the animal holding pens in HSSWP. The lowest levels of indicators were found at the Homosassa Main Spring vent. Levels of fecal indicators downstream of HSSWP (near the point of confluence with the river) were equivalent to those found in the Southeastern Fork and areas upstream of the park influences. F+ specific RNA coliphage analysis indicated that fecal contamination at all sites that tested positive was from animal sources (mammals and birds). These results suggest that animal (indigenous and those in HSSWP) and not human sources influenced microbial water quality in the area of Homosassa River covered by this study.
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Hesse, Bernhard; Salome, Murielle; Castillo-Michel, Hiram; Cotte, Marine; Fayard, Barbara; Sahle, Christoph J; De Nolf, Wout; Hradilova, Jana; Masic, Admir; Kanngießer, Birgit; Bohner, Marc; Varga, Peter; Raum, Kay; Schrof, Susanne
2016-04-05
Here, we show results on X-ray absorption near edge structure spectroscopy in both transmission and X-ray fluorescence full-field mode (FF-XANES) at the calcium K-edge on human bone tissue in healthy and diseased conditions and for different tissue maturation stages. We observe that the dominating spectral differences originating from different tissue regions, which are well pronounced in the white line and postedge structures are associated with polarization effects. These polarization effects dominate the spectral variance and must be well understood and modeled before analyzing the very subtle spectral variations related to the bone tissue variations itself. However, these modulations in the fine structure of the spectra can potentially be of high interest to quantify orientations of the apatite crystals in highly structured tissue matrices such as bone. Due to the extremely short wavelengths of X-rays, FF-XANES overcomes the limited spatial resolution of other optical and spectroscopic techniques exploiting visible light. Since the field of view in FF-XANES is rather large the acquisition times for analyzing the same region are short compared to, for example, X-ray diffraction techniques. Our results on the angular absorption dependence were verified by both site-matched polarized Raman spectroscopy, which has been shown to be sensitive to the orientation of bone building blocks and by mathematical simulations of the angular absorbance dependence. As an outlook we further demonstrate the polarization based assessment of calcium-containing crystal orientation and specification of calcium in a beta-tricalcium phosphate (β-Ca3(PO4)2 scaffold implanted into ovine bone. Regarding the use of XANES to assess chemical properties of Ca in human bone tissue our data suggest that neither the anatomical site (tibia vs jaw) nor pathology (healthy vs necrotic jaw bone tissue) affected the averaged spectral shape of the XANES spectra.
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Quantifying fossil fuel CO2 from continuous measurements of APO: a novel approach
NASA Astrophysics Data System (ADS)
Pickers, Penelope; Manning, Andrew C.; Forster, Grant L.; van der Laan, Sander; Wilson, Phil A.; Wenger, Angelina; Meijer, Harro A. J.; Oram, David E.; Sturges, William T.
2016-04-01
Using atmospheric measurements to accurately quantify CO2 emissions from fossil fuel sources requires the separation of biospheric and anthropogenic CO2 fluxes. The ability to quantify the fossil fuel component of CO2 (ffCO2) from atmospheric measurements enables more accurate 'top-down' verification of CO2 emissions inventories, which frequently have large uncertainty. Typically, ffCO2 is quantified (in ppm units) from discrete atmospheric measurements of Δ14CO2, combined with higher resolution atmospheric CO measurements, and with knowledge of CO:ffCO2 ratios. In the United Kingdom (UK), however, measurements of Δ14CO2 are often significantly biased by nuclear power plant influences, which limit the use of this approach. We present a novel approach for quantifying ffCO2 using measurements of APO (Atmospheric Potential Oxygen; a tracer derived from concurrent measurements of CO2 and O2) from two measurement sites in Norfolk, UK. Our approach is similar to that used for quantifying ffCO2 from CO measurements (ffCO2(CO)), whereby ffCO2(APO) = (APOmeas - APObg)/RAPO, where (APOmeas - APObg) is the APO deviation from the background, and RAPO is the APO:CO2 combustion ratio for fossil fuel. Time varying values of RAPO are calculated from the global gridded COFFEE (CO2 release and Oxygen uptake from Fossil Fuel Emission Estimate) dataset, combined with NAME (Numerical Atmospheric-dispersion Modelling Environment) transport model footprints. We compare our ffCO2(APO) results to results obtained using the ffCO2(CO) method, using CO:CO2 fossil fuel emission ratios (RCO) from the EDGAR (Emission Database for Global Atmospheric Research) database. We find that the APO ffCO2 quantification method is more precise than the CO method, owing primarily to a smaller range of possible APO:CO2 fossil fuel emission ratios, compared to the CO:CO2 emission ratio range. Using a long-term dataset of atmospheric O2, CO2, CO and Δ14CO2 from Lutjewad, The Netherlands, we examine the accuracy of our ffCO2(APO) method, and assess the potential of using APO to quantify ffCO2 independently from Δ14CO2 measurements, which, as well as being unreliable in many UK regions, are very costly. Using APO to quantify ffCO2 has significant policy relevance, with the potential to provide more accurate and more precise top-down verification of fossil fuel emissions.
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Ingle, Mary E; Bloom, Michael S; Parsons, Patrick J; Steuerwald, Amy J; Kruger, Pamela; Fujimoto, Victor Y
2017-02-01
A hypothesis-generating pilot study exploring associations between essential trace elements measured in follicular fluid (FF) and urine and in vitro fertilization (IVF) endpoints. We recruited 58 women undergoing IVF between 2007 and 2008, and measured cobalt, chromium, copper, manganese, molybdenum, and zinc in FF (n = 46) and urine (n = 45) by inductively coupled plasma mass spectrometry (ICP-MS). We used multivariable regression models to assess the impact of FF and urine trace elements on IVF outcomes, adjusted for age, body mass index, race, and cigarette smoking. Trace elements were mostly present at lower concentrations in FF than in urine. The average number of oocytes retrieved was positively associated with higher urine cobalt, chromium, copper, and molybdenum concentrations. FF chromium and manganese were negatively associated with the proportion of mature oocytes, yet urine manganese had a positive association. FF zinc was inversely associated with average oocyte fertilization. Urine trace elements were significant positive predictors for the total number of embryos generated. FF copper predicted lower embryo fragmentation while urine copper was associated with higher embryo cell number and urine manganese with higher embryo fragmentation. No associations were detected for implantation, pregnancy, or live birth. Our results suggest the importance of trace elements in both FF and urine for intermediate, although not necessarily clinical, IVF endpoints. The results differed using FF or urine biomarkers of exposure, which may have implications for the design of clinical and epidemiologic investigations. These initial findings will form the basis of a more definitive future study.
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Gonchar, Yuri; Burkhalter, Andreas
2003-11-26
Processing of visual information is performed in different cortical areas that are interconnected by feedforward (FF) and feedback (FB) pathways. Although FF and FB inputs are excitatory, their influences on pyramidal neurons also depend on the outputs of GABAergic neurons, which receive FF and FB inputs. Rat visual cortex contains at least three different families of GABAergic neurons that express parvalbumin (PV), calretinin (CR), and somatostatin (SOM) (Gonchar and Burkhalter, 1997). To examine whether pathway-specific inhibition (Shao and Burkhalter, 1996) is attributable to distinct connections with GABAergic neurons, we traced FF and FB inputs to PV, CR, and SOM neurons in layers 1-2/3 of area 17 and the secondary lateromedial area in rat visual cortex. We found that in layer 2/3 maximally 2% of FF and FB inputs go to CR and SOM neurons. This contrasts with 12-13% of FF and FB inputs onto layer 2/3 PV neurons. Unlike inputs to layer 2/3, connections to layer 1, which contains CR but lacks SOM and PV somata, are pathway-specific: 21% of FB inputs go to CR neurons, whereas FF inputs to layer 1 and its CR neurons are absent. These findings suggest that FF and FB influences on layer 2/3 pyramidal neurons mainly involve disynaptic connections via PV neurons that control the spike outputs to axons and proximal dendrites. Unlike FF input, FB input in addition makes a disynaptic link via CR neurons, which may influence the excitability of distal pyramidal cell dendrites in layer 1.
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Using Theoretical Descriptions in Structure Activity Relations. 3. Electronic Descriptors
1988-08-01
Activity Relationships (QSAR) have been used successfully in the past to develop predictive equations for several biological and physical properties...Linear Free Energy Relationships (,FF.3) and is based on work by Hammet in which he derived electronic descriptors for the dissociation of substituted...structure of a compound and its activity in a system. Several different structural descriptors have been used in QSAR equations . These range from
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Alsulays, Bader B; Park, Jun-Bom; Alshehri, Sultan M; Morott, Joseph T; Alshahrani, Saad M; Tiwari, Roshan V; Alshetaili, Abdullah S; Majumdar, Soumyajit; Langley, Nigel; Kolter, Karl; Gryczke, Andreas; Repka, Michael A
2015-10-01
The objective of this study was to investigate the extrudability, drug release, and stability of fenofibrate (FF) formulations utilizing various hot-melt extrusion processing parameters and polyvinylpyrrolidone (PVP) polymers of various molecular weights. The different PVP grades selected for this study were Kollidon ® 12 PF (K12), Kollidon ® 30 (K30), and Kollidon ® 90 F (K90). FF was extruded with these polymers at three drug loadings (15%, 25%, and 35% w/w). Additionally, for FF combined with each of the successfully extruded PVP grades (K12 and K30), the effects of two levels of processing parameters for screw design, screw speed, and barrel temperature were assessed. It was found that the FF with (K90) was not extrudable up to 35% drug loading. With low drug loading, the polymer viscosity significantly influenced the release of FF. The crystallinity remaining was vital in the highest drug-loaded formulation dissolution profile, and the glass transition temperature of the polymer significantly affected its stability. Modifying the screw configuration resulted in more than 95% post-extrusion drug content of the FF-K30 formulations. In contrast to FF-K30 formulations, FF release and stability with K12 were significantly influenced by the extrusion temperature and screw speed.
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Niu, Zhenchuan; Zhou, Weijian; Wu, Shugang; Cheng, Peng; Lu, Xuefeng; Xiong, Xiaohu; Du, Hua; Fu, Yunchong; Wang, Gehui
2016-06-07
One year of atmospheric Δ(14)CO2 were observed in 2014 in the inland city of Beijing and coastal city of Xiamen, China, to trace temporal CO2ff variations and to determine the factors influencing them. The average CO2ff concentrations at the sampling sites in Beijing and Xiamen were 39.7 ± 36.1 ppm and 13.6 ± 12.3 ppm, respectively. These contributed 75.2 ± 14.6% and 59.1 ± 26.8% to their respective annual ΔCO2 offsets over background CO2 concentrations. Significantly (p < 0.05) high CO2ff values were observed in winter in Beijing. We did not find any significant differences in CO2ff values between weekdays and weekends. Diurnal CO2ff variations were plainly evident, with high values between midnight and 4:00, and during morning and afternoon rush hours. The sampling site in the inland city of Beijing displayed much higher CO2ff inputs and overall temporal variations than the site in the coastal city of Xiamen. The variations of CO2ff at both sites were controlled by a combination of emission sources, topography, and atmospheric dispersion. In particular, diurnal observations at the urban site in Beijing showed that CO2ff was easily accumulated under the southeast wind conditions.
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Tang, Honghong; Mai, Xiaoqin; Wang, Shun; Zhu, Chaozhe; Krueger, Frank; Liu, Chao
2016-01-01
In daily life, interpersonal interactions are influenced by uncertainty about other people's intentions. Face-to-face (FF) interaction reduces such uncertainty by providing external visible cues such as facial expression or body gestures and facilitates shared intentionality to promote belief of cooperative decisions and actual cooperative behaviors in interaction. However, so far little is known about interpersonal brain synchronization between two people engaged in naturally occurring FF interactions. In this study, we combined an adapted ultimatum game with functional near-infrared spectroscopy (fNIRS) hyperscanning to investigate how FF interaction impacts interpersonal brain synchronization during economic exchange. Pairs of strangers interacted repeatedly either FF or face-blocked (FB), while their activation was simultaneously measured in the right temporo-parietal junction (rTPJ) and the control region, right dorsolateral prefrontal cortex (rDLPFC). Behaviorally, FF interactions increased shared intentionality between strangers, leading more positive belief of cooperative decisions and more actual gains in the game. FNIRS results indicated increased interpersonal brain synchronizations during FF interactions in rTPJ (but not in rDLPFC) with greater shared intentionality between partners. These results highlighted the importance of rTPJ in collaborative social interactions during FF economic exchange and warrant future research that combines FF interactions with fNIRS hyperscanning to study social brain disorders such as autism. © The Author (2015). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.
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Pfannmüller, Andreas; Wagner, Dominik; Sieber, Christian; Schönig, Birgit; Boeckstaens, Mélanie; Marini, Anna Maria; Tudzynski, Bettina
2015-01-01
The rice pathogenic fungus Fusarium fujikuroi is well known for the production of a broad spectrum of secondary metabolites (SMs) such as gibberellic acids (GAs), mycotoxins and pigments. The biosynthesis of most of these SMs strictly depends on nitrogen availability and of the activity of permeases of nitrogen sources, e.g. the ammonium and amino acid permeases. One of the three ammonium permeases, MepB, was recently shown to act not only as a transporter but also as a nitrogen sensor affecting the production of nitrogen-repressed SMs. Here we describe the identification of a general amino acid permease, FfGap1, among the 99 putative amino acid permeases (AAPs) in the genome of F. fujikuroi. FfGap1 is able to fully restore growth of the yeast gap1∆ mutant on several amino acids including citrulline and tryptophane. In S. cerevisiae, Gap1 activity is regulated by shuttling between the plasma membrane (nitrogen limiting conditions) and the vacuole (nitrogen sufficiency), which we also show for FfGap1. In yeast, the Npr1 serine/threonine kinase stabilizes the Gap1 position at the plasma membrane. Here, we identified and characterized three NPR1-homologous genes, encoding the putative protein kinases FfNpr1-1, FfNpr1-2 and FfNpr1-3 with significant similarity to yeast Npr1. Complementation of the yeast npr1Δ mutant with each of the three F. fujikuroi NPR1 homologues, resulted in partial restoration of ammonium, arginine and proline uptake by FfNPR1-1 while none of the three kinases affect growth on different nitrogen sources and nitrogen-dependent sorting of FfGap1 in F. fujikuroi. However, exchange of the putative ubiquitin-target lysine 9 (K9A) and 15 (K15A) residues of FfGap1 resulted in extended localization to the plasma membrane and increased protein stability independently of nitrogen availability. These data suggest a similar regulation of FfGap1 by nitrogen-dependent ubiquitination, but differences regarding the role of Fusarium Npr1 homologues compared to yeast. PMID:25909858
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Mönkäre, Tiina J; Palmroth, Marja R T; Rintala, Jukka A
2017-02-01
Increasing interest for the landfill mining and the amount of fine fraction (FF) in landfills (40-70% (w/w) of landfill content) mean that sustainable treatment and utilization methods for FF are needed. For this study FF (<20mm) was mined from a municipal solid waste (MSW) landfill operated from 1967 to 1989. FF, which resembles soil, was stabilized in laboratory scale reactors in two phases: first, anaerobically for 101days and second, for 72days using four different methods: anaerobic with the addition of moisture (water) or inoculum (sewage sludge) and aerobic with continuous water washing, with, or without, bulking material. The aim was to evaluate the effect on the stability of mined FF, which has been rarely reported, and to study the quality and quantity of gas and leachate produced during the stabilization experiment. The study showed that aerobic treatment reduced respiration activity (final values 0.9-1.1mgO 2 /gTS) and residual methane potential (1.1LCH 4 /kgTS) better than anaerobic methods (1.8-2.3mg O 2 /g TS and 1.3-2.4L CH 4 /kg TS, respectively). Bulking material mixed in FF in one aerobic reactor had no effect on the stability of FF. The benefit of anaerobic treatment was the production of methane, which could be utilized as energy. Even though the inoculum addition increased methane production from FF about 30%, but the methane production was still relatively low (in total 1.5-1.7L CH 4 /kg TS). Continuous water washing was essential to remove leachable organic matter and soluble nutrients from FF, while increasing the volume of leachate collected. In the aerobic treatment, nitrogen was oxidized into nitrite and nitrate and then washed out in the leachate. Both anaerobic and aerobic methods could be used for FF stabilization. The use of FF, in landscaping for example, is possible because its nutrient content (4gN/kg TS and 1g P/kg TS) can increase the nutrient content of soil, but this may have limitations due to the possible presence of heavy metal and other contaminants. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Matsumura, Keisuke; Yoshizaki, Soichi; Maitani, Masato M; Wada, Yuji; Ogomi, Yuhei; Hayase, Shuzi; Kaiho, Tatsuo; Fuse, Shinichiro; Tanaka, Hiroshi; Takahashi, Takashi
2015-06-26
This one-pot, four-component coupling approach (Suzuki-Miyaura coupling/C-H direct arylation/Knoevenagel condensation) was developed for the rapid synthesis of thiophene-based organic dyes for dye-sensitized solar cells (DSSCs). Seven thiophene-based, organic dyes of various donor structures with/without the use of a 3,4-ethylenedioxythiophene (EDOT) moiety were successfully synthesized in good yields based on a readily available thiophene boronic acid pinacol ester scaffold (one-pot, 3-step, 35-61%). Evaluation of the photovoltaic properties of the solar cells that were prepared using the synthesized dyes revealed that the introduction of an EDOT structure beside a cyanoacrylic acid moiety improved the short-circuit current (Jsc) while decreasing the fill factor (FF). The donor structure significantly influenced the open-circuit voltage (Voc), the FF, and the power conversion efficiency (PCE). The use of a n-hexyloxyphenyl amine donor, and our originally developed, rigid, and nonplanar donor, both promoted good cell performance (η=5.2-5.6%). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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NASA Astrophysics Data System (ADS)
Krog, Jesper S.; Forslund, Anita; Larsen, Lars E.; Dalsgaard, Anders; Kjaer, Jeanne; Olsen, Preben; Schultz, Anna Charlotte
2017-06-01
The amount of animal manure used in modern agriculture is increasing due to the increase in global animal production. Pig slurry is known to contain zoonotic bacteria such as E. coli, Salmonella spp. and Campylobacter spp., and viruses such as hepatitis E virus and group A rotavirus. Coliform bacteria, present in manure, have previously been shown to leach into tile drains. This poses a potential threat to aquatic environments and may also influence the quality of drinking water. As knowledge is especially scarce about the fate of viruses when applied to fields in natural settings, this project sets out to investigate the leaching potential of six different microorganisms: E. coli and Enterococcus spp. (detected by colony assay), somatic coliphages (using plaque assays), and hepatitis E virus, porcine circovirus type 2, and group A rotavirus (by real-time polymerase chain reaction). All six microorganisms leached through the soil entering the tile drains situated at 1-m depth the first day following pig slurry application. The leaching pattern of group A rotavirus differed substantially from the pattern for somatic coliphages, which are otherwise used as indicators for virus contamination. Furthermore, group A rotavirus was detected in monitoring wells at 3.5-m depth up to 2 months after pig slurry application. The detection of viral genomic material in drainage water and shallow groundwater signifies a potential hazard to human health that needs to be investigated further, as water reservoirs used for recreational use and drinking water are potentially contaminated with zoonotic pathogens.
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Risley, Casey A.L.; Zydlewski, Joseph D.
2011-01-01
Assessing the Effects of Catch-and-Release Regulations on a Brook Trout Population Using an Age-Structured Model: North American Journal of Fisheries Management: Vol 30, No 6 var _prum=[['id','54ff88bcabe53dc41d1004a5'],['mark','firstbyte',(new Date()).getTime()
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Niu, Zhenchuan; Zhou, Weijian; Feng, Xue; Feng, Tian; Wu, Shugang; Cheng, Peng; Lu, Xuefeng; Du, Hua; Xiong, Xiaohu; Fu, Yunchong
2018-06-01
Radiocarbon ( 14 C) is the most accurate tracer available for quantifying atmospheric CO 2 derived from fossil fuel (CO 2ff ), but it is expensive and time-consuming to measure. Here, we used common hourly Air Quality Index (AQI) pollutants (AQI, PM 2.5 , PM 10 , and CO) to indirectly trace diurnal CO 2ff variations during certain days at the urban sites in Beijing and Xiamen, China, based on linear relationships between AQI pollutants and CO 2ff traced by 14 C ([Formula: see text]) for semimonthly samples obtained in 2014. We validated these indirectly traced CO 2ff (CO 2ff-in ) concentrations against [Formula: see text] concentrations traced by simultaneous diurnal 14 CO 2 observations. Significant (p < 0.05) strong correlations were observed between each of the separate AQI pollutants and [Formula: see text] for the semimonthly samples. Diurnal variations in CO 2ff traced by each of the AQI pollutants generally showed similar trends to those of [Formula: see text], with high agreement at the sampling site in Beijing and relatively poor agreement at the sampling site in Xiamen. AQI pollutant tracers showed high normalized root-mean-square (NRMS) errors for the summer diurnal samples due to low [Formula: see text] concentrations. After the removal of these summer samples, the NRMS errors for AQI pollutant tracers were in the range of 31.6-64.2%. CO generally showed a high agreement and low NRMS errors among these indirect tracers. Based on these linear relationships, monthly CO 2ff averages at the sampling sites in Beijing and Xiamen were traced using CO concentration as a tracer. The monthly CO 2ff averages at the Beijing site showed a shallow U-type variation. These results indicate that CO can be used to trace CO 2ff variations in Chinese cities with CO 2ff concentrations above 5 ppm.
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Kerwin, Edward; Barnes, Neil; Gibbs, Michael; Leather, David; Forth, Richard; Jacques, Loretta; Yates, Louisa J
2017-08-07
Symptoms, including night-time awakenings, affect the quality of life of people with asthma. Fluticasone furoate/vilanterol (FF/VI) reduces exacerbations, improves lung function, and rescue-free and symptom-free 24-hour periods in patients with asthma. These post-hoc analyses compared daytime and night-time symptoms in patients with asthma who received FF/VI, versus FF, fluticasone propionate (FP) or placebo. Daytime and night-time symptoms were collected via electronic daily diary cards in three Phase III randomized studies of once-daily FF/VI in patients with uncontrolled asthma on inhaled corticosteroids (ICS) ±long-acting beta 2 -agonists (LABA) (n = 609/1039/586). Endpoints included: change from baseline in symptom-free days and nights (analyzed by Analysis of Covariance, covariates: baseline, region, sex, age, treatment), time for patients to achieve 7 consecutive symptom-free nights (analyzed by Cox proportional hazards model, covariates as above), and proportion of patients experiencing 100% symptom-free nights per week (analyzed by logistic regression, covariates: percentage of symptom-free nights, sex, age, treatment). Improvements in symptom-free days and nights were generally observed for all treatments. More patients who received FF/VI experienced 100% symptom-free nights in the last week of the treatment period than patients who received ICS alone or placebo. FF/VI also reduced time to 7 consecutive symptom-free nights. Patients with at least one night of symptoms at baseline experienced an additional 2.7 and 2.0 symptom-free nights per week with FF/VI 100/25 µg, versus 1.9 and 1.7 with FF alone; similar findings were seen with FF/VI 200/25 µg. Benefits in terms of symptom-free days and nights were observed for patients receiving FF/VI versus comparators in these post-hoc analyses.
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Chen, Yingming; Wang, Bing-Zhong
2014-07-14
Time-reversal (TR) phase prints are first used in far-field (FF) detection of sub-wavelength (SW) deformable scatterers without any extra metal structure positioned in the vicinity of the target. The 2D prints derive from discrete short-time Fourier transform of 1D TR electromagnetic (EM) signals. Because the time-invariant intensive background interference is effectively centralized by TR technique, the time-variant weak indication from FF SW scatterers can be highlighted. This method shows a different use of TR technique in which the focus peak of TR EM waves is unusually removed and the most useful information is conveyed by the other part.
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Zuckerwar, Allan J; Herring, G C; Elbing, Brian R
2006-01-01
A free-field (FF) substitution method for calibrating the pressure sensitivity of microphones at frequencies up to 80 kHz is demonstrated with both grazing and normal-incidence geometries. The substitution-based method, as opposed to a simultaneous method, avoids problems associated with the nonuniformity of the sound field and, as applied here, uses a 1/4-in. air-condenser pressure microphone as a known reference. Best results were obtained with a centrifugal fan, which is used as a random, broadband sound source. A broadband source minimizes reflection-related interferences that can plague FF measurements. Calibrations were performed on 1/4-in. FF air-condenser, electret, and microelectromechanical systems (MEMS) microphones in an anechoic chamber. The uncertainty of this FF method is estimated by comparing the pressure sensitivity of an air-condenser FF microphone, as derived from the FF measurement, with that of an electrostatic actuator calibration. The root-mean-square difference is found to be +/- 0.3 dB over the range 1-80 kHz, and the combined standard uncertainty of the FF method, including other significant contributions, is +/- 0.41 dB.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Orimoto, Yuuichi, E-mail: orimoto.yuuichi.888@m.kyushu-u.ac.jp; Aoki, Yuriko; Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012
An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method,more » and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.« less
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Orimoto, Yuuichi; Aoki, Yuriko
2016-07-14
An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between "choose-maximum" (choose a base pair giving the maximum β for each step) and "choose-minimum" (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.
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Information Hiding based Trusted Computing System Design
2014-07-18
ABSTRACT 15. SUBJECT TERMS 18. NUMBER OF PAGES 19a. NAME OF RESPONSIBLE PERSON a. REPORT b . ABSTRACT c. THIS PAGE 17. LIMITATION OF...system with two flip flops (FF) and some logic gates (Figure 1 ( b )). First, from Figure 1(a), we see that when the system is at state B and input is 0...FF2 is 1, which reflects the current state B , if input = 0, we can easily verify that FF1 remains unchanged, but FF2 changes to 0. This means that
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Validation and Application of the ReaxFF Reactive Force Field to Hydrocarbon Oxidation Kinetics
2016-06-23
AFRL-AFOSR-VA-TR-2016-0278 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics Adrianus Van Duin...application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-14-1-0355 5c. PROGRAM...Chenoweth Dec14 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics DISTRIBUTION A: Distribution approved for
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Laser Cooling and Slowing of a Diatomic Molecule
2013-12-01
mirror ( Semrock , FF669-Di01) before passing through the interaction region along the 3 mm axis of the slit. Windows are home-made Brewster windows (See... Semrock FF669-Di01 and Semrock FF741-Di01) and a polarizing beam splitter (PBS) to produce a single beam with 1e2 full width intensity waist d = 3.4 mm...pixels as possible, thereby reducing read noise and dark current noise. Behind the camera lens is a single interference filter ( Semrock , FF01-650/60, 24
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The interaction of metergoline, a 5-HT receptor blocker, and dexfenfluramine in human feeding.
Goodall, E; Silverstone, T
1988-01-01
Use of the 5-HT antagonist metergoline (MTG) has shown that dexfenfluramine (d-FF) influences food intake in animals via serotoninergic neurones. This study examined the interaction between d-FF and MTG in humans. Healthy male volunteers reported singly at 8:45 A.M. on four weekly occasions following an overnight fast. At 9:00 A.M. they received 30 mg d-FF or matching placebo and at 11:00 A.M. 4 mg MTG or placebo. Hunger and satiety were assessed hourly using visual analog scales (VAS). Subjects had access to a 4-channel automated food dispenser (AFD) from 1:15 to 3:15 P.M. Delivery and recording of each portion of known energy value was contingent on an appropriate button push. Subjects were offered two nonsweet snacks, plus fruit and a chocolate biscuit chosen to each subject's preference. Results for 13 subjects are reported. d-FF reduced hunger VAS, MTG had no effect on hunger and did not attenuate the effect of d-FF. d-FF reduced total food intake by 1306 kJ (312 kcal p less than 0.01) at 120 min. MTG increased food intake and attenuated the effect of d-FF on food intake but not significantly. d-FF markedly reduced the intake of nonsweet food; this was attenuated by MTG which alone had no effect on nonsweet food. d-FF had no effect on the intake of sweet tasting food during the first hour; by 120 min it had reduced energy intake by 342 kJ (82 kcal, t = 1.34, n.s.).(ABSTRACT TRUNCATED AT 250 WORDS)
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Ling, Z; Yonghong, L; Changqing, S; Junfeng, L; Li, Z; Chunyu, J; Xianqiang, L
2017-06-01
To effectively control bovine mastitis, tilmicosin (TIL)- and florfenicol (FF)-loaded solid lipid nanoparticles (SLN) with hydrogenated castor oil (HCO) were prepared by a hot homogenization and ultrasonication method. In vitro antibacterial activity, properties, and pharmacokinetics of the TIL-FF-SLN were studied. The results demonstrated that TIL and FF had a synergistic or additive antibacterial activity against Streptococcus dysgalactiae, Streptococcus uberis, and Streptococcus agalactiae. The size, polydispersity index, and zeta potential of nanoparticles were 289.1 ± 13.7 nm, 0.31 ± 0.05, and -26.7 ± 1.3 mV, respectively. The encapsulation efficiencies for TIL and FF were 62.3 ± 5.9% and 85.1 ± 5.2%, and the loading capacities for TIL and FF were 8.2 ± 0.6% and 3.3 ± 0.2%, respectively. The TIL-FF-SLN showed no irritation in the injection site and sustained release in vitro. After medication, TIL and FF could maintain about 0.1 μg/mL for 122 and 6 h. Compared to the control solution, the SLN increased the area under the concentration-time curve (AUC 0-t ), elimination half-life (T ½ke ), and mean residence time (MRT) of TIL by 33.09-, 23.29-, and 37.53-fold, and 1.69-, 5.00-, and 3.83-fold for FF, respectively. These results of this exploratory study suggest that the HCO-SLN could be a useful system for the delivery of TIL and FF for bovine mastitis therapy. © 2016 John Wiley & Sons Ltd.
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Dalton, Madeline A; Longacre, Meghan R; Drake, Keith M; Cleveland, Lauren P; Harris, Jennifer L; Hendricks, Kristy; Titus, Linda J
2017-06-01
To determine whether exposure to child-targeted fast-food (FF) television (TV) advertising is associated with children's FF intake in a non-experimental setting. Cross-sectional survey conducted April-December 2013. Parents reported their pre-school child's TV viewing time, channels watched and past-week FF consumption. Responses were combined with a list of FF commercials (ads) aired on children's TV channels during the same period to calculate children's exposure to child-targeted TV ads for the following chain FF restaurants: McDonald's, Subway and Wendy's (MSW). Paediatric and Women, Infants, and Children (WIC) clinics in New Hampshire, USA. Parents (n 548) with a child of pre-school age. Children's mean age was 4·4 years; 43·2 % ate MSW in the past week. Among the 40·8 % exposed to MSW ads, 23·3 % had low, 34·2 % moderate and 42·5 % high exposure. McDonald's accounted for over 70 % of children's MSW ad exposure and consumption. Children's MSW consumption was significantly associated with their ad exposure, but not overall TV viewing time. After adjusting for demographics, socio-economic status and other screen time, moderate MSW ad exposure was associated with a 31 % (95 % CI 1·12, 1·53) increase and high MSW ad exposure with a 26 % (95 % CI 1·13, 1·41) increase in the likelihood of consuming MSW in the past week. Further adjustment for parent FF consumption did not change the findings substantially. Exposure to child-targeted FF TV advertising is positively associated with FF consumption among children of pre-school age, highlighting the vulnerability of young children to persuasive advertising and supporting recommendations to limit child-directed FF marketing.
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Molecular dynamical simulations of melting Al nanoparticles using a reaxff reactive force field
NASA Astrophysics Data System (ADS)
Liu, Junpeng; Wang, Mengjun; Liu, Pingan
2018-06-01
Molecular dynamics simulations were performed to study thermal properties and melting points of Al nanoparticles by using a reactive force field under canonical (NVT) ensembles. Al nanoparticles (particle size 2–4 nm) were considered in simulations. A combination of structural and thermodynamic parameters such as the Lindemann index, heat capacities, potential energy and radial-distribution functions was employed to decide melting points. We used annealing technique to obtain the initial Al nanoparticle model. Comparison was made between ReaxFF results and other simulation results. We found that ReaxFF force field is reasonable to describe Al cluster melting behavior. The linear relationship between particle size and melting points was found. After validating the ReaxFF force field, more attention was paid on thermal properties of Al nanoparticles with different defect concentrations. 4 nm Al nanoparticles with different defect concentrations (5%–20%) were considered in this paper. Our results revealed that: the melting points are irrelevant with defect concentration at a certain particle size. The extra storage energy of Al nanoparticles is proportional to nanoparticles’ defect concentration, when defect concentration is 5%–15%. While the particle with 20% defect concentration is similar to the cluster with 10% defect concentration. After melting, the extra energy of all nanoparticles decreases sharply, and the extra storage energy is nearly zero at 600 K. The centro-symmetry parameter analysis shows structure evolution of different models during melting processes.
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Follicular fluid total antioxidant capacity levels in PCOS.
Yilmaz, Nafiye; Inal, Hasan Ali; Gorkem, Umit; Sargin Oruc, Ayla; Yilmaz, Saynur; Turkkani, Ayten
2016-07-01
In this study, our aim was to assess total antioxidant capacity (TAC) levels in follicular fluid (FF) and their relationship to clinical pregnancy rates in PCOS patients undergoing assisted reproduction (ART). Twenty-two women with polycystic ovary syndrome (PCOS) (Group 1) and 41 women without PCOS (Group 2) were included in this study. Clinical and laboratory parameters and FF TAC levels were investigated. No statistically significant differences were found between the groups with regard to age and baseline parameters. Although we could not demonstrate a significant difference in FF TAC levels between the two groups (p=0.469), there was a significant positive correlation between FF TAC and clinical pregnancy rates, BMI, and the duration of infertility for the entire group (r=0.254, p=0.048; r=0.312, p=0.013; r=0.259, p=0.040; respectively). Owing to the correlation between FF TAC and the clinical pregnancy rates, further studies evaluating the impact of FF TAC levels on ART outcomes in patients with PCOS and other etiologies of infertility are needed.
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PCOS women show significantly higher homocysteine level, independent to glucose and E2 level
Eskandari, Zahra; Sadrkhanlou, Rajab-Ali; Nejati, Vahid; Tizro, Gholamreza
2016-01-01
Background: It is reasonable to think that some biochemical characteristics of follicular fluid (FF) surrounding the oocyte may play a critical role in determining the quality of oocyte and the subsequent potential needed to achieve fertilization and embryo development. Objective: This study was carried out to evaluate the levels of FF homocysteine (Hcy) in IVF candidate polycystic ovary syndrome (PCOS) women and any relationships with FF glucose and estradiol (E2) levels. Materials and Methods: In this case control study which was performed in Dr. Tizro Day Care and IVF Center 70 infertile patients were enrolled in two groups: comprising 35 PCOS and 35 non PCOS women. Long protocol was performed for all patients. FF Hcy, glucose and E2 levels were analyzed at the time of oocyte retrieval. Results: It was observed that FF Hcy level was significantly higher in PCOS patients compared with non PCOSs (p<0.01). Observations demonstrated that in PCOS group, the Hcy level increased independent to E2, glucose levels, BMI and age, while the PCOS group showed significantly higher BMI compared with non-PCOS group (p=0.03). However, no significant differences were revealed between groups for FF glucose and E2 levels. Conclusion: Present data showed that although FF glucose and E2 levels were constant in PCOS and non PCOS patients, but the FF Hcy levels in PCOS were significantly increased (p=0.01). PMID:27679823
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Nian, Li; Gao, Ke; Jiang, Yufeng; Rong, Qikun; Hu, Xiaowen; Yuan, Dong; Liu, Feng; Peng, Xiaobin; Russell, Thomas P; Zhou, Guofu
2017-08-01
High-efficiency small-molecule-based organic photovoltaics (SM-OPVs) using two electron donors (p-DTS(FBTTh 2 ) 2 and ZnP) with distinctively different absorption and structural features are reported. Such a combination works well and synergically improves device short-circuit current density (J sc ) to 17.99 mA cm -2 and fill factor (FF) to 77.19%, yielding a milestone efficiency of 11%. To the best of our knowledge, this is the highest power conversion efficiency reported for SM-OPVs to date and the first time to combine high J sc over 17 mA cm -2 and high FF over 77% into one SM-OPV. The strategy of using multicomponent materials, with a selecting role of balancing varied electronic and structural necessities can be an important route to further developing higher performance devices. This development is important, which broadens the dimension and versatility of existing materials without much chemistry input. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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6. FF coal pulverizer (ball mill inside). GG building in ...
6. FF coal pulverizer (ball mill inside). GG building in background did preliminary crushing; pulverizer to left, coal conveyor and air cleaning towers to right; conveyor on left brought crushed coal to FF. Looking north/northeast - Rouge Steel Company, 3001 Miller Road, Dearborn, MI
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kuess, Peter, E-mail: Peter.kuess@meduniwien.ac.at
Purpose: For commercially available linear accelerators (Linacs), the electron energies of flattening filter free (FFF) and flattened (FF) beams are either identical or the electron energy of the FFF beam is increased to match the percentage depth dose curve (PDD) of the FF beam (in reference geometry). This study focuses on the primary dose components of FFF beams for both kinds of settings, studied on the same Linac. Methods: The measurements were conducted on a VersaHD Linac (Elekta, Crawley, UK) for both FF and FFF beams with nominal energies of 6 and 10 MV. In the clinical setting of themore » VersaHD, the energy of FFF{sub M} (Matched) beams is set to match the PDDs of the FF beams. In contrast the incident electron beam of the FFF{sub U} beam was set to the same energy as for the FF beam. Half value layers (HVLs) and a dual parameter beam quality specifier (DPBQS) were determined. Results: For the 6 MV FFF{sub M} beam, HVL and DPBQS values were very similar compared to those of the 6 MV FF beam, while for the 10 MV FFF{sub M} and FF beams, only %dd(10){sub x} and HVL values were comparable (differences below 1.5%). This shows that matching the PDD at one depth does not guarantee other beam quality dependent parameters to be matched. For FFF{sub U} beams, all investigated beam quality specifiers were significantly different compared to those for FF beams of the same nominal accelerator potential. The DPBQS of the 6 MV FF and FFF{sub M} beams was equal within the measurement uncertainty and was comparable to published data of a machine with similar TPR{sub 20,10} and %dd(10){sub x}. In contrast to that, the DPBQS’s two parameters of the 10 MV FFF{sub M} beam were substantially higher compared to those for the 10 MV FF beam. Conclusions: PDD-matched FF and FFF beams of both nominal accelerator potentials were observed to have similar HVL values, indicating similarity of their primary dose components. Using the DPBQS revealed that the mean attenuation coefficient was found to be the same within the uncertainty of 0.8% for 6 MV FF and 6 MV FFF{sub M} beams, while for 10 MV beams, they differed by 6.4%. This shows that the DPBQS can provide a differentiation of photon beam characteristics that would remain hidden by the use of a single beam quality specifier, such as %dd(10){sub x} or HVL.« less
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Bayesian energy landscape tilting: towards concordant models of molecular ensembles.
Beauchamp, Kyle A; Pande, Vijay S; Das, Rhiju
2014-03-18
Predicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computational model inaccuracies and data uncertainties. Building on recent proposals from maximum entropy theory and nonequilibrium thermodynamics, we address these issues through a Bayesian energy landscape tilting (BELT) scheme for computing Bayesian hyperensembles over conformational ensembles. BELT uses Markov chain Monte Carlo to directly sample maximum-entropy conformational ensembles consistent with a set of input experimental observables. To test this framework, we apply BELT to model trialanine, starting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and OPLS-AA. BELT incorporation of limited chemical shift and (3)J measurements gives convergent values of the peptide's α, β, and PPII conformational populations in all cases. As a test of predictive power, all five BELT hyperensembles recover set-aside measurements not used in the fitting and report accurate errors, even when starting from highly inaccurate simulations. BELT's principled framework thus enables practical predictions for complex biomolecular systems from discordant simulations and sparse data. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Intergenerational redistribution in a small open economy with endogenous fertility.
Kolmar, M
1997-08-01
The literature comparing fully funded (FF) and pay-as-you-go (PAYG) financed public pension systems in small, open economies stresses the importance of the Aaron condition as an empirical measure to decide which system can be expected to lead to a higher long-run welfare. A country with a PAYG system has a higher level of utility than a country with a FF system if the growth rate of total wage income exceeds the interest rate. Endogenizing population growth makes one determinant of the growth rate of wage incomes endogenous. The author demonstrates why the Aaron condition ceases to be a good indicator in this case. For PAYG-financed pension systems, claims can be calculated according to individual contributions or the number of children in a family. Analysis determined that for both structural determinants there is no interior solution of the problem of intergenerational utility maximization. Pure systems are therefore always welfare maximizing. Moreover, children-related pension claims induce a fiscal externality which tends to be positive. The determination of the optimal contribution rate shows that the Aaron condition is generally a misleading indicator for the comparison of FF and PAYG-financed pension systems.
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Monitoring programs for recreational waters utilize indicator bacteria concentrations as predictors of sewage-exposure related illness risks. However, most illnesses contracted through exposure to recreational waters may be of viral etiology. Identifying the fecal sources (non-...
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Nespoli performs periodic maintenance on the PuFF Experiment
2011-02-14
ISS026-E-027009 (14 Feb. 2011) --- European Space Agency (ESA) astronaut Paolo Nespoli, Expedition 26 flight engineer, performs periodic maintenance on the Pulmonary Function in Flight (PuFF) experiment by re-greasing the PuFF calibration syringe in the Columbus laboratory of the International Space Station.
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Atmospheric pressure ionization-tandem mass spectrometry of the phenicol drug family.
Alechaga, Élida; Moyano, Encarnación; Galceran, M Teresa
2013-11-01
In this work, the mass spectrometry behaviour of the veterinary drug family of phenicols, including chloramphenicol (CAP) and its related compounds thiamphenicol (TAP), florfenicol (FF) and FF amine (FFA), was studied. Several atmospheric pressure ionization sources, electrospray (ESI), atmospheric pressure chemical ionization and atmospheric pressure photoionization were compared. In all atmospheric pressure ionization sources, CAP, TAP and FF were ionized in both positive and negative modes; while for the metabolite FFA, only positive ionization was possible. In general, in positive mode, [M + H](+) dominated the mass spectrum for FFA, while the other compounds, CAP, TAP and FF, with lower proton affinity showed intense adducts with species present in the mobile phase. In negative mode, ESI and atmospheric pressure photoionization showed the deprotonated molecule [M-H](-), while atmospheric pressure chemical ionization provided the radical molecular ion by electron capture. All these ions were characterized by tandem mass spectrometry using the combined information obtained by multistage mass spectrometry and high-resolution mass spectrometry in a quadrupole-Orbitrap instrument. In general, the fragmentation occurred via cyclization and losses or fragmentation of the N-(alkyl)acetamide group, and common fragmentation pathways were established for this family of compounds. A new chemical structure for the product ion at m/z 257 for CAP, on the basis of the MS(3) and MS(4) spectra is proposed. Thermally assisted ESI and selected reaction monitoring are proposed for the determination of these compounds by ultra high-performance liquid chromatography coupled to tandem mass spectrometry, achieving instrumental detection limits down to 0.1 pg. Copyright © 2013 John Wiley & Sons, Ltd.
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Time Correlations of Lightning Flash Sequences in Thunderstorms Revealed by Fractal Analysis
NASA Astrophysics Data System (ADS)
Gou, Xueqiang; Chen, Mingli; Zhang, Guangshu
2018-01-01
By using the data of lightning detection and ranging system at the Kennedy Space Center, the temporal fractal and correlation of interevent time series of lightning flash sequences in thunderstorms have been investigated with Allan factor (AF), Fano factor (FF), and detrended fluctuation analysis (DFA) methods. AF, FF, and DFA methods are powerful tools to detect the time-scaling structures and correlations in point processes. Totally 40 thunderstorms with distinguishing features of a single-cell storm and apparent increase and decrease in the total flash rate were selected for the analysis. It is found that the time-scaling exponents for AF (
α AF) and FF (α FF) analyses are 1.62 and 0.95 in average, respectively, indicating a strong time correlation of the lightning flash sequences. DFA analysis shows that there is a crossover phenomenon—a crossover timescale (τ c ) ranging from 54 to 195 s with an average of 114 s. The occurrence of a lightning flash in a thunderstorm behaves randomly at timescales <τ c but shows strong time correlation at scales >τ c . Physically, these may imply that the establishment of an extensive strong electric field necessary for the occurrence of a lightning flash needs a timescale >τ c , which behaves strongly time correlated. But the initiation of a lightning flash within a well-established extensive strong electric field may involve the heterogeneities of the electric field at a timescale <τ c , which behave randomly. -
Multiscale Architectures and Parallel Algorithms for Video Object Tracking
2011-10-01
0 4 : if FIFO1 contains nDt frames then 5: Partition data into blocks. 6: Put SPE control block information...char buf 4 = FF; vec to r unsigned char buf 5 = FF; vec to r unsigned char buf 6 = FF; vec to r unsigned char buf 7 = FF; for ( j = 0 ; j < s i z e ; j...Public Release; Distribution Unlimited 8 7 u 6 ill :J (;) 5 E -;::; c 0 4 ~ u Q) X 3 Q) 8 7 6 u Q) Ul 5 :J (;) E :;::; 4 c 0
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"Atypical" chronic wasting disease in PRNP genotype 225FF mule deer.
Wolfe, Lisa L; Fox, Karen A; Miller, Michael W
2014-07-01
We compared mule deer (Odocoileus hemionus) of two different PRNP genotypes (225SS, 225FF) for susceptibility to chronic wasting disease (CWD) in the face of environmental exposure to infectivity. All three 225SS deer had immunohistochemistry (IHC)-positive tonsil biopsies by 710 days postexposure (dpe), developed classic clinical signs by 723-1,200 dpe, and showed gross and microscopic pathology, enzyme-linked immunosorbent assay (ELISA) results, and IHC staining typical of prion disease in mule deer. In contrast, although all three 225FF deer also became infected, the two individuals surviving >720 dpe had consistently negative biopsies, developed more-subtle clinical signs of CWD, and died 924 or 1,783 dpe. The 225FF deer were "suspect" by ELISA postmortem but showed negative or equivocal IHC staining of lymphoid tissues; both clinically affected 225FF deer had spongiform encephalopathy in the absence of IHC staining in the brain tissue. The experimental cases resembled three cases encountered among five additional captive 225FF deer that were not part of our experiment but also died from CWD. Aside from differences in clinical disease presentation and detection, 225FF mule deer also showed other, more-subtle, atypical traits that may help to explain the rarity of this genotype in natural populations, even in the presence of enzootic CWD.
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NASA Astrophysics Data System (ADS)
Koller, Thomas; Ramos, Javier; Garrido, Nuno M.; Fröba, Andreas P.; Economou, Ioannis G.
2012-06-01
Three united-atom (UA) force fields are presented for the ionic liquid 1-ethyl-3-methylimidazolium tetracyanoborate, abbreviated as [EMIM]+[B(CN)4]-. The atomistic charges were calculated based on the restrained electrostatic potential (RESP) of the isolated ions (abbreviated as force field 1, FF-1) and the ensemble averaged RESP (EA-RESP) method from the most stable ion pair configurations obtained by MP2/6-31G*+ calculations (abbreviated as FF-2 and FF-3). Non-electrostatic parameters for both ions were taken from the literature and Lennard-Jones parameters for the [B(CN)4]- anion were fitted in two different ways to reproduce the experimental liquid density. Molecular dynamics (MD) simulations were performed over a wide temperature range to identify the effect of the electrostatic and non-electrostatic potential on the liquid density and on transport properties such as self-diffusion coefficient and viscosity. Predicted liquid densities for the three parameter sets deviate less than 0.5% from experimental data. The molecular mobility with FF-2 and FF-3 using reduced charge sets is appreciably faster than that obtained with FF-1. FF-3 presents a refined non-electrostatic potential that leads to a notable improvement in both transport properties when compared to experimental data.
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Evaluation of bakanae disease progression caused by Fusarium fujikuroi in Oryza sativa L.
Hwang, In Sun; Kang, Woo-Ri; Hwang, Duk-Ju; Bae, Shin-Chul; Yun, Sung-Hwan; Ahn, Il-Pyung
2013-12-01
Bakanae disease caused by Fusarium fujikuroi is an important fungal disease in rice. Among the seven strains isolated from symptomatic rice grains in this study, one strain, FfB14, triggered severe root growth inhibition and decay in the crown and root of rice seedlings. The remaining six strains caused typical Bakanae symptoms such as etiolation and abnormal succulent rice growth. To reveal the relationship between mycelial growth in the infected tissues and Bakanae disease progression, we have established a reliable quantification method using real time PCR that employs a primer pair and dual-labeled probe specific to a unigene encoding F. fujikuroi PNG1 (FfPNG1), which is located upstream of the fumonisin biosynthesis gene cluster. Plotting the crossing point (CP) values from the infected tissue DNAs on a standard curve revealed the active fungal growth of FfB14 in the root and crown of rice seedlings, while the growth rate of FfB20 in rice was more than 4 times lower than FfB14. Massive infective mycelial growth of FfB14 was evident in rice stems and crown; however, FfB20 did not exhibit vigorous growth. Our quantitative evaluation system is applicable for the identification of fungal virulence factors other than gibberellin.
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High pressure-induced inactivation of Qbeta coliphage and c2 phage in oysters and in culture media.
Smiddy, Mary; Kelly, Alan L; Patterson, Margaret F; Hill, Colin
2006-02-01
High pressure (HP) treatment inactivates bacteria in shellfish, but its effects on viruses in shellfish have not yet been determined, although viral illness is frequently associated with shellfish consumption. The aim of this study was to investigate the baroresistance of two bacteriophage viruses, Qbeta coliphage and c2 phage, in oysters and in culture media. High numbers (>or=10(7) ml(-1) or g(-1)) of both phages were obtained in culture media and in oysters. Samples were HP treated at 200-800 MPa at 20 degrees C for up to 30 min. Little or no inactivation of either phage was observed in oysters or in culture media after treatment at
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Ryu, Hodon; Alum, Absar; Alvarez, Maria; Mendoza, Jose; Abbaszadegan, Morteza
2005-06-01
Increased reliance of urban populations on Rio Grande water has necessitated an expanded microbial surveillance of the river to help identify and evaluate sources of human pathogens, which could pose a public health risk. The objectives of this study were to investigate microbial and chemical water quality in Rio Grande water and to perform risk assessment analyses for Cryptosporidium. No oocysts in any of the ten-litre samples were detected. However, the limit of detection in the water samples ranged between 20 and 200 oocysts/100 L. The limits of detection obtained in this study would result in one to two orders of magnitude higher risk of infection for Cryptosporidium than the U.S.EPA annual acceptable risk level of 10(-4). The bacterial data showed the significance of animal farming and raw sewage as sources of fecal pollution. Male specific and somatic coliphages were detected in 52% (11/21) and 62% (24/39) of the samples, respectively. Somatic coliphages were greater by one order of magnitude, and were better correlated with total (r2 = 0.6801; p < or = 0.05) and fecal coliform bacteria (r2 = 0.7366; p < or = 0.05) than male specific coliphages. The dissolved organic carbon (DOC) and specific ultraviolet absorbance (SUVA) values ranged 2.58-5.59mg/L and 1.23-2.29 m(-1) (mg/I)(-1), respectively. Low SUVA values of raw water condition make it difficult to remove DOC during physical and chemical treatment processes. The microbial and chemical data provided from this study can help drinking water utilities to maintain balance between greater microbial inactivation and reduced disinfection by-products (DBPs) formation.
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Kator, H; Rhodes, M
2001-06-01
Declining oyster (Crassostrea virginica) production in the Chesapeake Bay has stimulated aquaculture based on floats for off-bottom culture. While advantages of off-bottom culture are significant, the increased use of floating containers raises public health and microbiological concerns, because oysters in floats may be more susceptible to fecal contamination from storm runoff compared to those cultured on-bottom. We conducted four commercial-scale studies with market-size oysters naturally contaminated with fecal coliforms (FC) and a candidate viral indicator, F-specific RNA (FRNA) coliphage. To facilitate sampling and to test for location effects, 12 replicate subsamples, each consisting of 15 to 20 randomly selected oysters in plastic mesh bags, were placed at four characteristic locations within a 0.6- by 3.0-m "Taylor" float, and the remaining oysters were added to a depth not exceeding 15.2 cm. The float containing approximately 3,000 oysters was relaid in the York River, Virginia, for 14 days. During relay, increases in shellfish FC densities followed rain events such that final mean levels exceeded initial levels or did not meet an arbitrary product end point of 50 FC/100 ml. FRNA coliphage densities decreased to undetectable levels within 14 days (16 to 28 degrees C) in all but the last experiment, when temperatures fell between 12 and 16 degrees C. Friedman (nonparametric analysis of variance) tests performed on FC/Escherichia coli and FRNA densities indicated no differences in counts as a function of location within the float. The public health consequences of these observations are discussed, and future research and educational needs are identified.
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Volkova, Victoriya V; Lu, Zhao; Besser, Thomas; Gröhn, Yrjö T
2014-07-01
Animal-associated bacterial communities are infected by bacteriophages, although the dynamics of these infections are poorly understood. Transduction by bacteriophages may contribute to transfer of antimicrobial resistance genes, but the relative importance of transduction among other gene transfer mechanisms is unknown. We therefore developed a candidate deterministic mathematical model of the infection dynamics of enteric coliphages in commensal Escherichia coli in the large intestine of cattle. We assumed the phages were associated with the intestine and were predominantly temperate. Model simulations demonstrated how, given the bacterial ecology and infection dynamics, most (>90%) commensal enteric E. coli bacteria may become lysogens of enteric coliphages during intestinal transit. Using the model and the most liberal assumptions about transduction efficiency and resistance gene frequency, we approximated the upper numerical limits ("worst-case scenario") of gene transfer through specialized and generalized transduction in E. coli by enteric coliphages when the transduced genetic segment is picked at random. The estimates were consistent with a relatively small contribution of transduction to lateral gene spread; for example, generalized transduction delivered the chromosomal resistance gene to up to 8 E. coli bacteria/hour within the population of 1.47 × 10(8) E. coli bacteria/liter luminal contents. In comparison, the plasmidic blaCMY-2 gene carried by ~2% of enteric E. coli was transferred by conjugation at a rate at least 1.4 × 10(3) times greater than our generalized transduction estimate. The estimated numbers of transductants varied nonlinearly depending on the ecology of bacteria available for phages to infect, that is, on the assumed rates of turnover and replication of enteric E. coli. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
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Lu, Zhao; Besser, Thomas; Gröhn, Yrjö T.
2014-01-01
Animal-associated bacterial communities are infected by bacteriophages, although the dynamics of these infections are poorly understood. Transduction by bacteriophages may contribute to transfer of antimicrobial resistance genes, but the relative importance of transduction among other gene transfer mechanisms is unknown. We therefore developed a candidate deterministic mathematical model of the infection dynamics of enteric coliphages in commensal Escherichia coli in the large intestine of cattle. We assumed the phages were associated with the intestine and were predominantly temperate. Model simulations demonstrated how, given the bacterial ecology and infection dynamics, most (>90%) commensal enteric E. coli bacteria may become lysogens of enteric coliphages during intestinal transit. Using the model and the most liberal assumptions about transduction efficiency and resistance gene frequency, we approximated the upper numerical limits (“worst-case scenario”) of gene transfer through specialized and generalized transduction in E. coli by enteric coliphages when the transduced genetic segment is picked at random. The estimates were consistent with a relatively small contribution of transduction to lateral gene spread; for example, generalized transduction delivered the chromosomal resistance gene to up to 8 E. coli bacteria/hour within the population of 1.47 × 108 E. coli bacteria/liter luminal contents. In comparison, the plasmidic blaCMY-2 gene carried by ∼2% of enteric E. coli was transferred by conjugation at a rate at least 1.4 × 103 times greater than our generalized transduction estimate. The estimated numbers of transductants varied nonlinearly depending on the ecology of bacteria available for phages to infect, that is, on the assumed rates of turnover and replication of enteric E. coli. PMID:24814786
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Quantifying viruses and bacteria in wastewater—Results, interpretation methods, and quality control
Francy, Donna S.; Stelzer, Erin A.; Bushon, Rebecca N.; Brady, Amie M.G.; Mailot, Brian E.; Spencer, Susan K.; Borchardt, Mark A.; Elber, Ashley G.; Riddell, Kimberly R.; Gellner, Terry M.
2011-01-01
Membrane bioreactors (MBR), used for wastewater treatment in Ohio and elsewhere in the United States, have pore sizes small enough to theoretically reduce concentrations of protozoa and bacteria, but not viruses. Sampling for viruses in wastewater is seldom done and not required. Instead, the bacterial indicators Escherichia coli (E. coli) and fecal coliforms are the required microbial measures of effluents for wastewater-discharge permits. Information is needed on the effectiveness of MBRs in removing human enteric viruses from wastewaters, particularly as compared to conventional wastewater treatment before and after disinfection. A total of 73 regular and 28 quality-control (QC) samples were collected at three MBR and two conventional wastewater plants in Ohio during 23 regular and 3 QC sampling trips in 2008-10. Samples were collected at various stages in the treatment processes and analyzed for bacterial indicators E. coli, fecal coliforms, and enterococci by membrane filtration; somatic and F-specific coliphage by the single agar layer (SAL) method; adenovirus, enterovirus, norovirus GI and GII, rotavirus, and hepatitis A virus by molecular methods; and viruses by cell culture. While addressing the main objective of the study-comparing removal of viruses and bacterial indicators in MBR and conventional plants-it was realized that work was needed to identify data analysis and quantification methods for interpreting enteric virus and QC data. Therefore, methods for quantifying viruses, qualifying results, and applying QC data to interpretations are described in this report. During each regular sampling trip, samples were collected (1) before conventional or MBR treatment (post-preliminary), (2) after secondary or MBR treatment (post-secondary or post-MBR), (3) after tertiary treatment (one conventional plant only), and (4) after disinfection (post-disinfection). Glass-wool fiber filtration was used to concentrate enteric viruses from large volumes, and small volume grab samples were collected for direct-plating analyses for bacterial indicators and coliphage. After filtration, the viruses were eluted from the filter and further concentrated. The final concentrated sample volume (FCSV) was used for enteric virus analysis by use of two methods-cell culture and a molecular method, polymerase chain reaction (PCR). Quantitative PCR (qPCR) for DNA viruses and quantitative reverse-transcriptase PCR (qRT-PCR) for RNA viruses were used in this study. To support data interpretations, the assay limit of detection (ALOD) was set for each virus assay and used to determine sample reporting limits (SRLs). For qPCR and qRT-PCR the ALOD was an estimated value because it was not established according to established method detection limit procedures. The SRLs were different for each sample because effective sample volumes (the volume of the original sample that was actually used in each analysis) were different for each sample. Effective sample volumes were much less than the original sample volumes because of reductions from processing steps and (or) from when dilutions were made to minimize the effects from PCR-inhibiting substances. Codes were used to further qualify the virus data and indicate the level of uncertainty associated with each measurement. Quality-control samples were used to support data interpretations. Field and laboratory blanks for bacteria, coliphage, and enteric viruses were all below detection, indicating that it was unlikely that samples were contaminated from equipment or processing procedures. The absolute value log differences (AVLDs) between concurrent replicate pairs were calculated to identify the variability associated with each measurement. For bacterial indicators and coliphage, the AVLD results indicated that concentrations <10 colony-forming units or plaque-forming units per 100 mL can differ between replicates by as much as 1 log, whereas higher concentrations can differ by as much as 0.3 log. The AVLD results for viruses indicated that differences between replicates can be as great as 1.2 log genomic copies per liter, regardless of the concentration of virus. Relatively large differences in molecular results for viruses between replicate pairs were likely due to lack of precision for samples with small effective volumes. Concentrations of E. coli, fecal coliforms, enterococci, and somatic and F-specific coliphage in post-secondary and post-tertiary samples in conventional plants were higher than those in post-MBR samples. In post-MBR and post-secondary samples, concentrations of somatic coliphage were higher than F-specific coliphage. In post-disinfection samples from two MBR plants (the third MBR plant had operational issues) and the ultraviolet conventional plant, concentrations for all bacterial indicators and coliphage were near or below detection; from the chlorine conventional plant, concentrations in post-disinfection samples were in the single or double digits. All of the plants met the National Pollutant Discharge Elimination System required effluent limits established for fecal coliforms. Norovirus GII and hepatitis A virus were not detected in any samples, and rotavirus was detected in one sample but could not be quantified. Adenovirus was found in 100 percent, enterovirus in over one-half, and norovirus GI in about one-half of post-preliminary wastewater samples. Adenovirus and enterovirus were detected throughout the treatment processes, and norovirus GI was detected less often than the other two enteric viruses. Culturable viruses were detected in post-preliminary samples and in only two post-treatment samples from the plant with operational issues.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Chung, J; Kim, J; Kang, S
2015-06-15
Purpose: The purpose of this study is to access VMAT-SABR plan using flattening filter (FF) and flattening filter-free (FFF) beam, and compare the verification results for all pretreatment plans. Methods: SABR plans for 20 prostate patients were optimized in the Eclipse treatment planning system. A prescription dose was 42.7 Gy/7 fractions. Four SABR plans for each patient were calculated using Acuros XB algorithm with both FF and FFF beams of 6- and 10-MV. The dose-volume histograms (DVH) and technical parameters were recorded and compared. A pretreatment verification was performed and the gamma analysis was used to quantify the agreement betweenmore » calculations and measurements. Results: For each patient, the DVHs are closely similar for plans of four different beams. There are small differences showed in dose distributions and corresponding DVHs when comparing the each plan related to the same patient. Sparing on bladder and rectum was slightly better on plans with 10-MV FF and FFF than with 6-MV FF and FFF, but this difference was negligible. However, there was no significance in the other OARs. The mean agreement of 3%/3mm criteria was higher than 97% in all plans. The mean MUs and deliver time employed was 1701±101 and 3.02±0.17 min for 6-MV FF, 1870±116 and 1.69±0.08 min for 6-MV FFF, 1471±86 and 2.68±0.14 min for 10-MV FF, and 1619±101 and 0.98±0.04 min for 10-MV FFF, respectively. Conclusion: Dose distributions on prostate SABR plans using FFF beams were similar to those generated by FF beams. However, the use of FFF beam offers a clear benefit in delivery time when compared to FF beam. Verification of pretreatment also represented the acceptable and comparable results in all plans using FF beam as well as FFF beam. Therefore, this study suggests that the use of FFF beam is feasible and efficient technique for prostate SABR.« less
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Vulnerability Situations associated with Flash Flood Casualties in the United States
NASA Astrophysics Data System (ADS)
Terti, G.; Ruin, I.; Anquetin, S.; Gourley, J. J.
2015-12-01
In the United States (U.S.) flash flooding (FF hereafter) is one of the leading cause of weather-related deaths. Because FF events can be distinguished from riverine floods by their fast response to rainfall and resulting impacts signature, analyzing FF-specific impact datasets seems a good way to identify the juxtaposition of social and physical circumstances leading to those impacts. This communication focuses on conceptual and methodological developments allowing testing hypotheses on FF-specific vulnerability factors through the analysis of human impact datasets. We hypothesize that the intersection of the spatio-temporal context of the FF phenomena with the distribution of people and their characteristics across space and time reveals various paths of vulnerability through the expression of different accidents' circumstances (i.e., vehicle-related, inside buildings, open-air, campsites). We argue that vulnerability and the resulting impacts vary dynamically throughout the day according to the location/situation under concern. In order to test FF-specific contextual vulnerability factors at the scale of the continental US, 1075 fatalities reported between 1996 and 2014 in the Storm Data publication of the U.S. National Climatic Data Center (NCDC) are analyzed to statistically explore the timing, the duration and the location of the FF event, and the age and gender of the victims and the circumstance (i.e. location/activity) of their death. In this objective, a re-classification of the individual fatality circumstances and a discretization of the time in qualitative time-steps are performed to obtain possible trends and patterns in the occurrence of fatalities in certain circumstances and time (e.g., day vs night). The findings highlight the importance of situation-specific assessment of FF fatalities to guide the development of FF-specific vulnerability and impacts prediction modeling. Such analysis can provide valuable knowledge when the National Weather Service issues FF warning and emergencies. This is because targeted warnings can be communicated when we can relate the location of risky incidents in space (e.g., roads, campsites, mobile homes) with specific vulnerable groups (e.g., certain age groups, gender).
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Tang, Jie; Suga, Nobuo
2009-01-01
In auditory cortex of the mustached bat, the FF (F means frequency modulation), dorsal fringe (DF) and ventral fringe (VF) areas consist of “combination-sensitive” neurons tuned to the pair of an emitted biosonar pulse and its echo with a specific delay (best delay: BD). The DF and VF areas are hierarchically at a higher level than the FF area. Focal electric stimulation of the FF area evokes “centrifugal” BD shifts of DF neurons, i.e., shifts away from the BD of the stimulated FF neurons, whereas stimulation of the DF neurons evokes “centripetal” BD shifts of FF neurons, i.e., shifts toward the BD of the stimulated DF neurons. In our current studies, we found that the feed forward projection from FF neurons evokes centrifugal BD shifts of VF neurons, that the feedback projection from VF neurons evokes centripetal BD shifts of FF neurons, that the contralateral projection from DF neurons evokes centripetal BD shifts of DF neurons, and that the centripetal BD shifts evoked by the DF and VF neurons are 2.5 times larger than the centrifugal BD shifts evoked by the FF neurons. The centrifugal BD shifts shape the selective neural representation of a specific target-distance, whereas the centripetal BD shifts expand the representation of the selected specific target-distance to focus on the processing of the target information at a specific distance. The centrifugal and centripetal BD shifts evoked by the feed forward and feedback projections promote finer analysis of a target at shorter distances. PMID:19494145
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Bioluminescent system for dynamic imaging of cell and animal behavior
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hara-Miyauchi, Chikako; Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Saitama 351-0198; Department of Biophysics and Biochemistry, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo 113-8510
2012-03-09
Highlights: Black-Right-Pointing-Pointer We combined a yellow variant of GFP and firefly luciferase to make ffLuc-cp156. Black-Right-Pointing-Pointer ffLuc-cp156 showed improved photon yield in cultured cells and transgenic mice. Black-Right-Pointing-Pointer ffLuc-cp156 enabled video-rate bioluminescence imaging of freely-moving animals. Black-Right-Pointing-Pointer ffLuc-cp156 mice enabled tracking real-time drug delivery in conscious animals. -- Abstract: The current utility of bioluminescence imaging is constrained by a low photon yield that limits temporal sensitivity. Here, we describe an imaging method that uses a chemiluminescent/fluorescent protein, ffLuc-cp156, which consists of a yellow variant of Aequorea GFP and firefly luciferase. We report an improvement in photon yield by over threemore » orders of magnitude over current bioluminescent systems. We imaged cellular movement at high resolution including neuronal growth cones and microglial cell protrusions. Transgenic ffLuc-cp156 mice enabled video-rate bioluminescence imaging of freely moving animals, which may provide a reliable assay for drug distribution in behaving animals for pre-clinical studies.« less
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The influence of herbs and spices on overall liking of reduced fat food.
Peters, John C; Polsky, Sarit; Stark, Rebecca; Zhaoxing, Pan; Hill, James O
2014-08-01
Most adults consume more fat than is recommended in the Dietary Guidelines for Americans. We examined whether adding herbs and spices to reduced-fat foods would improve their consumer liking. We recruited adults 18-65 years old to taste three lunch conditions: full fat (FF), reduced fat with no added spice (RF), and reduced fat plus spice (RFS). Subjects rated their liking of a meatloaf entrée, vegetable side dish, pasta side dish, and overall meal on a 9-point hedonic Likert scale. Subjects came weekly for 3 weeks to consume meals and were randomized to the condition order. We enrolled 148 subjects who were predominantly female (n = 101, 68%), had a mean age of 35.9 years, and body mass index of 24.4 kg/m2. Subjects reported habitual diets as 36% of total calories from fat (2005 Block Food Frequency Questionnaire). Reducing fat content alone significantly dropped overall liking of the meal compared with FF and RFS conditions (6.29 RF vs. 7.05 FF, P < 0.0001; 6.29 RF vs. 6.98 RFS, P ≤ 0.0001). The RFS overall meal was liked as well as the FF condition. FF and RFS conditions were liked significantly more than RF conditions for each meal item. Liking of FF and RFS meatloaf and vegetables were not significantly different from one another. Pasta FF and RFS conditions were rated significantly differently from each other (7.33 FF vs. 6.61 RFS, P < 0.0001). Adding herbs and spices to reduced fat foods restored liking of the overall meal, meatloaf, and vegetables to that of FF conditions, and significantly improved the liking of RF pasta. Herbs and spices can be a useful tool to improve liking of foods consistent with national guidelines. Copyright © 2014 The Author. Published by Elsevier Ltd.. All rights reserved.
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Merhi, Zaher; Irani, Mohamad; Doswell, Angela D; Ambroggio, Jennifer
2014-02-01
The interaction of advanced glycation end-products (AGEs) with their cellular receptor (RAGE) is implicated in the pathogenesis of abnormal ovarian follicular growth. RAGE has a circulating secretory receptor form, soluble RAGE (sRAGE), which neutralizes the action of AGEs and might exert a protective role on the follicular environment. The objective of the study was to investigate whether serum or follicular fluid (FF) sRAGE levels are associated with markers of ovarian reserve. Serum anti-Mullerian hormone (AMH) and sRAGE protein levels were correlated in 31 reproductive-aged women. An additional 33 women who underwent oocyte retrieval for in vitro fertilization were enrolled. AMH and its receptor (AMHR-II) mRNA levels were quantified in cumulus granulosa cells and FF sRAGE and AMH protein levels were measured. Granulosa cell AMH and AMHR-II gene expression, serum and FF AMH and sRAGE protein concentration, and number of oocytes retrieved were measured. In the serum, sRAGE levels were negatively correlated with body mass index (BMI) (r = -0.5, P < .001) but not with age or serum AMH. The higher the FF sRAGE, the lower the number of international units of gonadotropin needed per cycle independent of age, BMI, or day 3 FSH level (r = -0.4, P = .04). After adjusting for age, BMI, day 3 FSH, and the total dose of gonadotropins, FF sRAGE predicted the number of oocytes retrieved (R(2) = 0.27, P = .045). FF sRAGE positively correlated with FF AMH levels (r = 0.5, P = .0085). RT-PCR results showed no correlation between the FF sRAGE and AMH or AMHR-II mRNA levels. These data support a relationship between FF sRAGE and measures of ovarian reserve. The pathological significance of the harmful inflammatory AGEs in follicular health clearly requires further investigation. Targeting AGEs might offer potential therapeutic options for the treatment of diminished ovarian response.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, W; Zhang, J; Lu, J
Purpose: To compare the dosimetric difference of volumetric modulated arc therapy(VMAT) for preoperative radiotherapy rectal cancer using 6MV X-ray flattening filter free(FFF) and flattening filter(FF) modes. Methods: FF-VMAT and FFF-VMAT plans were designed to 15 rectal cancer patients with preoperative radiotherapy by planning treatment system(Eclipse 10.0),respectively. Dose prescription was 50 Gy in 25 fractions. All plans were normalized to 50 Gy to 95% of PTV. The Dose Volume Histogram (DVH), target and risk organ doses, conformity indexes (CI), homogeneity indexes (HI), low dose volume of normal tissue(BP), monitor units(MU) and treatment time (TT) were compared between the two kinds ofmore » plans. Results: FF-VMAT provided the lower Dmean, V105, HI, and higher CI as compared with FFF-VMAT. The small intestine of D5, Bladder of D5, Dmean, V40, V50, L-femoral head of V40, R-femoral head of Dmean were lower in FF-VMAT than in FFF-VMAT. FF-VMAT had higher BP of V5, but no significantly different of V10, V15, V20, V30 as compared with FFF-VMAT. FF-VMAT reduceed the monitor units(MU) by 21%(P<0.05), as well as the treatment time(TT) was no significantly different(P>0.05), as compared with FFF-VMAT. Conclusion: The plan qualities of FF and FFF VMAT plans were comparable and both clinically acceptable. FF-VMAT as compared with FFF-VMAT, showing better target coverage, some of OARs sparing, the MUs of FFF-VMAT were higher than FF-VMAT, yet were delivered within the same time. This work was supported by the Medical Scientific Research Foundation of Guangdong Procvince (A2014455 to Changchun Ma)« less
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Dalton, Madeline A; Longacre, Meghan R; Drake, Keith M; Cleveland, Lauren P; Harris, Jennifer L; Hendricks, Kristy; Titus, Linda J
2017-01-01
Objective To determine whether exposure to child-targeted fast-food (FF) television (TV) advertising is associated with children’s FF intake in a non-experimental setting. Design Cross-sectional survey conducted April–December 2013. Parents reported their pre-school child’s TV viewing time, channels watched and past-week FF consumption. Responses were combined with a list of FF commercials (ads) aired on children’s TV channels during the same period to calculate children’s exposure to child-targeted TV ads for the following chain FF restaurants: McDonald’s, Subway and Wendy’s (MSW). Setting Paediatric and Women, Infants, and Children (WIC) clinics in New Hampshire, USA. Subjects Parents (n 548) with a child of pre-school age. Results Children’s mean age was 4·4 years; 43·2 % ate MSW in the past week. Among the 40·8 % exposed to MSW ads, 23·3 % had low, 34·2 % moderate and 42·5 % high exposure. McDonald’s accounted for over 70 % of children’s MSW ad exposure and consumption. Children’s MSW consumption was significantly associated with their ad exposure, but not overall TV viewing time. After adjusting for demographics, socio-economic status and other screen time, moderate MSW ad exposure was associated with a 31 % (95 % CI 1·12, 1·53) increase and high MSW ad exposure with a 26 % (95 % CI 1·13, 1·41) increase in the likelihood of consuming MSW in the past week. Further adjustment for parent FF consumption did not change the findings substantially. Conclusions Exposure to child-targeted FF TV advertising is positively associated with FF consumption among children of pre-school age, highlighting the vulnerability of young children to persuasive advertising and supporting recommendations to limit child-directed FF marketing. PMID:28416041
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Wilsey, Laura; Gowrisankaran, Sowjanya; Cull, Grant; Hardin, Christy; Burgoyne, Claude F; Fortune, Brad
2017-04-01
To compare diagnostic performance and structure-function correlations of multifocal electroretinogram (mfERG), full-field flash ERG (ff-ERG) photopic negative response (PhNR) and transient pattern-reversal ERG (PERG) in a non-human primate (NHP) model of experimental glaucoma (EG). At baseline and after induction of chronic unilateral IOP elevation, 43 NHP had alternating weekly recordings of retinal nerve fiber layer thickness (RNFLT) by spectral domain OCT (Spectralis) and retinal function by mfERG (7F slow-sequence stimulus, VERIS), ff-ERG (red 0.42 log cd-s/m 2 flashes on blue 30 scotopic cd/m 2 background, LKC UTAS-E3000), and PERG (0.8° checks, 99% contrast, 100 cd/m 2 mean, 5 reversals/s, VERIS). All NHP were followed at least until HRT-confirmed optic nerve head posterior deformation, most to later stages. mfERG responses were filtered into low- and high-frequency components (LFC, HFC, >75 Hz). Peak-to-trough amplitudes of LFC features (N1, P1, N2) and HFC RMS amplitudes were measured and ratios calculated for HFC:P1 and N2:P1. ff-ERG parameters included A-wave (at 10 ms), B-wave (trough-to-peak) and PhNR (baseline-to-trough) amplitudes as well as PhNR:B-wave ratio. PERG parameters included P50 and N95 amplitudes as well as N95:P50 ratio and N95 slope. Diagnostic performance of retinal function parameters was compared using the area under the receiver operating characteristic curve (A-ROC) to discriminate between EG and control eyes. Correlations to RNFLT were compared using Steiger's test. Study duration was 15 ± 8 months. At final follow-up, structural damage in EG eyes measured by RNFLT ranged from 9% above baseline (BL) to 58% below BL; 29/43 EG eyes (67%) and 0/43 of the fellow control eyes exhibited significant (>7%) loss of RNFLT from BL. Using raw parameter values, the largest A-ROC findings for mfERG were: HFC (0.82) and HFC:P1 (0.90); for ff-ERG: PhNR (0.90) and PhNR:B-wave (0.88) and for PERG: P50 (0.64) and N95 (0.61). A-ROC increased when data were expressed as % change from BL, but the pattern of results persisted. At 95% specificity, the diagnostic sensitivity of mfERG HFC:P1 ratio was best, followed by PhNR and PERG. The correlation to RNFLT was stronger for mfERG HFC (R = 0.65) than for PhNR (R = 0.59) or PERG N95 (R = 0.36), (p = 0.20, p = 0.0006, respectively). The PhNR flagged a few EG eyes at the final time point that had not been flagged by mfERG HFC or PERG. Diagnostic performance and structure-function correlation were strongest for mfERG HFC as compared with ff-ERG PhNR or PERG in NHP EG.
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Kopf, Thomas; Schaefer, Hans-Ludwig; Troetzmueller, Martin; Koefeler, Harald; Broenstrup, Mark; Konovalova, Tatiana; Schmitz, Gerd
2014-01-01
Fenofibrate (FF) lowers plasma triglycerides via PPARα activation. Here, we analyzed lipidomic changes upon FF treatment of fructose fed rats. Three groups with 6 animals each were defined as control, fructose-fed and fructose-fed/FF treated. Male Wistar Unilever Rats were subjected to 10% fructose-feeding for 20 days. On day 14, fenofibrate treatment (100 mg/kg p.o.) was initiated and maintained for 7 days. Lipid species in serum were analyzed using mass spectrometry (ESI-MS/MS; LC-FT-MS, GC-MS) on days 0, 14 and 20 in all three groups. In addition, lipid levels in liver and intestine were determined. Short-chain TAGs increased in serum and liver upon fructose-feeding, while almost all TAG-species decreased under FF treatment. Long-chain unsaturated DAG-levels (36:1, 36:2, 36:4, 38:3, 38:4, 38:5) increased upon FF treatment in rat liver and decreased in rat serum. FAs, especially short-chain FAs (12:0, 14:0, 16:0) increased during fructose-challenge. VLDL secretion increased upon fructose-feeding and together with FA-levels decreased to control levels during FF treatment. Fructose challenge of de novo fatty acid synthesis through fatty acid synthase (FAS) may enhance the release of FAs ≤ 16:0 chain length, a process reversed by FF-mediated PPARα-activation.
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Security Informatics Research Challenges for Mitigating Cyber Friendly Fire
DOE Office of Scientific and Technical Information (OSTI.GOV)
Carroll, Thomas E.; Greitzer, Frank L.; Roberts, Adam D.
This paper addresses cognitive implications and research needs surrounding the problem of cyber friendly re (FF). We dene cyber FF as intentional o*ensive or defensive cyber/electronic actions intended to protect cyber systems against enemy forces or to attack enemy cyber systems, which unintentionally harms the mission e*ectiveness of friendly or neutral forces. We describe examples of cyber FF and discuss how it ts within a general conceptual framework for cyber security failures. Because it involves human failure, cyber FF may be considered to belong to a sub-class of cyber security failures characterized as unintentional insider threats. Cyber FF is closelymore » related to combat friendly re in that maintaining situation awareness (SA) is paramount to avoiding unintended consequences. Cyber SA concerns knowledge of a system's topology (connectedness and relationships of the nodes in a system), and critical knowledge elements such as the characteristics and vulnerabilities of the components that comprise the system and its nodes, the nature of the activities or work performed, and the available defensive and o*ensive countermeasures that may be applied to thwart network attacks. We describe a test bed designed to support empirical research on factors a*ecting cyber FF. Finally, we discuss mitigation strategies to combat cyber FF, including both training concepts and suggestions for decision aids and visualization approaches.« less
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Code of Federal Regulations, 2010 CFR
2010-07-01
... the requirements of 40 CFR part 61, subpart FF, and the waste requirements for ethylene production... (CONTINUED) National Emission Standards for Ethylene Manufacturing Process Units: Heat Exchange Systems and... requirements of 40 CFR part 61, subpart FF, and the waste requirements for ethylene production sources? The...
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Effects of milk replacer program fed 2 or 4 times daily on nutrient intake and calf growth.
Kmicikewycz, A D; da Silva, D N L; Linn, J G; Litherland, N B
2013-02-01
The aims of this study were to determine if feeding frequency (FF) of milk replacer (MR; meals/d) alters starter intake, growth, and efficiency of growth in nursery calves fed a conventional or accelerated MR. We hypothesized that smaller and more frequent MR meals would increase starter intake and growth when greater amounts of MR nutrients are fed to nursery calves. Forty-eight Holstein and Holstein-cross heifer and bull calves were assigned to treatments in a 2 × 2 factorial arrangement of MR and FF. Treatments included (1) standard 20% CP and 20% fat MR fed at 1.5% of body weight (BW; 2 meals/d; STD2), (2) standard 20% CP and 20% fat MR fed at 1.5% of BW (4 meals/d; STD4), (3) modified 26% CP and 18% fat MR fed at 2.0% of BW (2 meals/d; MOD2), and (4) modified 26% CP and 18% fat MR fed at 2.0% of BW (4 meals/d; MOD4; n=12). All calves were fed at 0600 and 1700 h and STD4 and MOD4 calves were fed 2 additional meals at 1100 and 1400 h, resulting in the same amount of MR offered for the 2 × and 4 × treatments. Treatments were fed from d 2 to 42 of age and all MR feeding rates were adjusted weekly to maintain MR solids intakes at 1.5 or 2.0% of BW for STD and MOD diets, respectively, and were reconstituted to 15% total solids. Milk replacer FF was reduced by 50% on d 36 and calves were weaned on d 42. Calves were housed in hutches bedded with straw and offered water and a texturized 18% CP starter ad libitum. Calf body weight and body structure were measured weekly and starter intake and fecal scores were measured daily. Through both 42 and 56 d, calves fed MOD had greater CP and fat intake, resulting in increased average daily gain, heart girth, circulating nonesterified fatty acids (NEFA), and muscle total lipid compared with calves fed STD diets. Calves fed MOD diets consumed less starter grain than STD calves but total dry matter intake was similar among treatments. Increased FF for STD calves resulted in greater starter intake at weaning but increasing FF of MOD calves did not have this effect. Due to differences in starter intake, total dry matter by calves through d 56 was similar across treatments. Additionally, increased FF tended to increase serum NEFA concentrations. Serum NEFA concentration was negatively correlated with starter intake. The BW of calves fed STD2 and STD4 treatments almost doubled and the BW of calves on the MOD2 and MOD4 treatments doubled by d 56. Increased FF of the conventional MR program but not accelerated MR program increased starter intake. Increased FF did not affect growth, starter intake, or gain:feed ratio. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
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Field-based evaluation of a male-specific (F+) RNA coliphage concentration method
Fecal contamination of water poses a significant risk to public health due to the potential presence of pathogens, including enteric viruses. Thus, sensitive, reliable and easy to use methods for the detection of microorganisms are needed to evaluate water quality. In this stud...
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Dillow, Jonathan J.A.; Banks, William S.L.; Smigaj, Michael J.
2002-01-01
The U.S. Geological Survey, in cooperation with the Maryland Department of the Environment and the Wisconsin State Laboratory of Hygiene, conducted a study to characterize the occurrence and distribution of viral contamination in small (withdrawing less than 10,000 gallons per day) public water-supply wells screened in the shallow aquifer in the Piedmont Physiographic Province in Baltimore and Harford Counties, Maryland. Two hundred sixty-three small public water-supply wells were in operation in these counties during the spring of 2000. Ninety-one of these sites were selected for sampling using a methodology that distributed the samples evenly over the population and the spatial extent of the study area. Each site, and its potential susceptibility to microbiological contamination, was evaluated with regard to hole depth, casing interval, and open interval. Each site was evaluated using characteristics such as on-site geology and on-site land use.Samples were collected by pumping between 200 and 400 gallons of untreated well water through an electropositive cartridge filter. Water concentrates were subjected to cell-culture assay for the detection of culturable viruses and reverse-transcription polymerase chain reaction/gene probe assays to detect viral ribonucleic acid; grab samples were analyzed for somatic and male-specific coliphages, Bacteroides fragilis, Clostridium perfringens, enterococci, Escherichia coli, total coliforms, total oxidized nitrogen, nitrite, organic nitrogen, total phosphate, ortho-phosphate, calcium, magnesium, sodium, potas-sium, chloride, sulfate, iron, acid-neutralizing capacity, pH, specific conductance, temperature, and dissolved oxygen.One sample tested positive for the presence of the ribonucleic acid of rotavirus through poly-merase chain-reaction analysis. Twenty-nine per-cent of the samples (26 of 90) had bacterial con-tamination. About 7 percent of the samples (6 of 90) were contaminated with either male-specific coliphage, somatic coliphage, or bacteriophages of Bacteroides fragilis. About 3 percent of the sam-ples (3 of 87) had oxidized nitrogen concentra-tions that exceeded the U.S. Environmental Protection Agency?s Maximum Contaminant Level of 10.0 milligrams per liter. A statistical analysis showed that no significant relation exists between the presence of bacteria or coliphage and all variables, except the mean temperature of the water sample as measured in the field. Additionally, the concentration of total coliform bacteria had a statistically significant, moderately strong cor-relation with the concentration of sulfate and sample pH as measured at the U.S. Geological Survey National Water-Quality Laboratory in Denver, Colorado.
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Banks, William S.L.; Battigelli, David A.
2002-01-01
The U.S. Geological Survey, in cooperation with the Maryland Department of the Environment and the Wisconsin State Laboratory of Hygiene, conducted a study to characterize the occurrence and distribution of viral contamination in small (withdrawing less than 10,000 gallons per day) public water-supply wells screened in the shallow aquifer in the Piedmont Physiographic Province in Baltimore and Harford Counties, Maryland. Two hundred sixty-three small public water-supply wells were in operation in these counties during the spring of 2000. Ninety-one of these sites were selected for sampling using a methodology that distributed the samples evenly over the population and the spatial extent of the study area. Each site, and its potential susceptibility to microbiological contamination, was evaluated with regard to hole depth, casing interval, and open interval. Each site was evaluated using characteristics such as on-site geology and on-site land use.Samples were collected by pumping between 200 and 400 gallons of untreated well water through an electropositive cartridge filter. Water concentrates were subjected to cell-culture assay for the detection of culturable viruses and reverse-transcription polymerase chain reaction/gene probe assays to detect viral ribonucleic acid; grab samples were analyzed for somatic and male-specific coliphages, Bacteroides fragilis, Clostridium perfringens, enterococci, Escherichia coli, total coliforms, total oxidized nitrogen, nitrite, organic nitrogen, total phosphate, ortho-phosphate, calcium, magnesium, sodium, potas-sium, chloride, sulfate, iron, acid-neutralizing capacity, pH, specific conductance, temperature, and dissolved oxygen.One sample tested positive for the presence of the ribonucleic acid of rotavirus through poly-merase chain-reaction analysis. Twenty-nine per-cent of the samples (26 of 90) had bacterial con-tamination. About 7 percent of the samples (6 of 90) were contaminated with either male-specific coliphage, somatic coliphage, or bacteriophages of Bacteroides fragilis. About 3 percent of the sam-ples (3 of 87) had oxidized nitrogen concentra-tions that exceeded the U.S. Environmental Protection Agency?s Maximum Contaminant Level of 10.0 milligrams per liter. A statistical analysis showed that no significant relation exists between the presence of bacteria or coliphage and all variables, except the mean temperature of the water sample as measured in the field. Additionally, the concentration of total coliform bacteria had a statistically significant, moderately strong cor-relation with the concentration of sulfate and sample pH as measured at the U.S. Geological Survey National Water-Quality Laboratory in Denver, Colorado.
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Characterization of a ViI-like Phage Specific to Escherichia coli O157:H7
2011-01-01
Phage vB_EcoM_CBA120 (CBA120), isolated against Escherichia coli O157:H7 from a cattle feedlot, is morphologically very similar to the classic phage ViI of Salmonella enterica serovar Typhi. Until recently, little was known genetically or physiologically about the ViI-like phages, and none targeting E. coli have been described in the literature. The genome of CBA120 has been fully sequenced and is highly similar to those of both ViI and the Shigella phage AG3. The core set of structural and replication-related proteins of CBA120 are homologous to those from T-even phages, but generally are more closely related to those from T4-like phages of Vibrio, Aeromonas and cyanobacteria than those of the Enterobacteriaceae. The baseplate and method of adhesion to the host are, however, very different from those of either T4 or the cyanophages. None of the outer baseplate proteins are conserved. Instead of T4's long and short tail fibers, CBA120, like ViI, encodes tail spikes related to those normally seen on podoviruses. The 158 kb genome, like that of T4, is circularly permuted and terminally redundant, but unlike T4 CBA120 does not substitute hmdCyt for cytosine in its DNA. However, in contrast to other coliphages, CBA120 and related coliphages we have isolated cannot incorporate 3H-thymidine (3H-dThd) into their DNA. Protein sequence comparisons cluster the putative "thymidylate synthase" of CBA120, ViI and AG3 much more closely with those of Delftia phage φW-14, Bacillus subtilis phage SPO1, and Pseudomonas phage YuA, all known to produce and incorporate hydroxymethyluracil (hmdUra). PMID:21899740
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Chen, Mianmian; Xu, Juntian; Yao, Huochun; Lu, Chengping; Zhang, Wei
2016-05-10
Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. Due to the drug residues and increased antibiotic resistance caused by antibiotic use, bacteriophages and other alternative therapeutic agents are expected to control APEC infection in poultry. Two APEC phages, named P483 and P694, were isolated from the feces from the farmers market in China. We then studied their biological properties, and carried out high-throughput genome sequencing and homology analyses of these phages. Assembly results of high-throughput sequencing showed that the structures of both P483 and P694 genomes consist of linear and double-stranded DNA. Results of the electron microscopy and homology analysis revealed that both P483 and P694 belong to T7-like virus which is a member of the Podoviridae family of the Caudovirales order. Comparative genomic analysis showed that most of the predicted proteins of these two phages showed strongest sequence similarity to the Enterobacteria phages BA14 and 285P, Erwinia phage FE44, and Kluyvera phage Kvp1; however, some proteins such as gp0.6a, gp1.7 and gp17 showed lower similarity (<85%) with the homologs of other phages in the T7 subgroup. We also found some unique characteristics of P483 and P694, such as the two types of the genes of P694 and no lytic activity of P694 against its host bacteria in liquid medium. Our results serve to further our understanding of phage evolution of T7-like coliphages and provide the potential application of the phages as therapeutic agents for the treatment of diseases. Copyright © 2016 Elsevier B.V. All rights reserved.
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Characterization of Five Podoviridae Phages Infecting Citrobacter freundii
Hamdi, Sana; Rousseau, Geneviève M.; Labrie, Simon J.; Kourda, Rim S.; Tremblay, Denise M.; Moineau, Sylvain; Slama, Karim B.
2016-01-01
Citrobacter freundii causes opportunistic infections in humans and animals, which are becoming difficult to treat due to increased antibiotic resistance. The aim of this study was to explore phages as potential antimicrobial agents against this opportunistic pathogen. We isolated and characterized five new virulent phages, SH1, SH2, SH3, SH4, and SH5 from sewage samples in Tunisia. Morphological and genomic analyses revealed that the five C. freundii phages belong to the Caudovirales order, Podoviridae family, and Autographivirinae subfamily. Their linear double-stranded DNA genomes range from 39,158 to 39,832 bp and are terminally redundant with direct repeats between 183 and 242 bp. The five genomes share the same organization as coliphage T7. Based on genomic comparisons and on the phylogeny of the DNA polymerases, we assigned the five phages to the T7virus genus but separated them into two different groups. Phages SH1 and SH2 are very similar to previously characterized phages phiYeO3-12 and phiSG-JL2, infecting, respectively, Yersinia enterocolitica and Salmonella enterica, as well as sharing more than 80% identity with most genes of coliphage T7. Phages SH3, SH4, and SH5 are very similar to phages K1F and Dev2, infecting, respectively, Escherichia coli and Cronobacter turicensis. Several structural proteins of phages SH1, SH3, and SH4 were detected by mass spectrometry. The five phages were also stable from pH 5 to 10. No genes coding for known virulence factors or integrases were found, suggesting that the five isolated phages could be good candidates for therapeutic applications to prevent or treat C. freundii infections. In addition, this study increases our knowledge about the evolutionary relationships within the T7virus genus. PMID:27446058
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Polsky, Sarit; Beck, Jimikaye; Stark, Rebecca A; Pan, Zhaoxing; Hill, James O; Peters, John C
2014-10-01
Adults often consume more fat than is recommended. We examined factors that may improve liking of reduced fat and reduced saturated fat foods, including the addition of herbs and spices and habitual consumption of different high-fat and low-fat food items. We randomized adults to taste 3 different conditions: full fat (FF), reduced fat with no added spice (RF), and reduced fat plus spice (RFS). Subjects rated their liking of French toast, sausage and the overall meal, or chicken, vegetables, pasta, and the overall meal on a 9-point hedonic Likert scale. Overall liking of the RF breakfast and lunch meals were lower than the FF and RFS versions (breakfast: 6.50 RF compared with 6.84 FF, P = 0.0061; 6.50 RF compared with 6.82 RFS, P = 0.0030; lunch: 6.35 RF compared with 6.94 FF, P < 0.0001; 6.35 RF compared with 6.71 RFS, P = 0.0061). RFS and FF breakfast and lunch meals, French toast, chicken, and vegetable likings were similar. FF and RFS conditions were liked more than RF for the breakfast and lunch meals, French toast, chicken entrée, and vegetables. Liking of all 3 sausage conditions was similar. FF pasta was liked more than RFS and RF (7.47 FF compared with 6.42 RFS, P < 0.0001; 7.47 FF compared with 6.47 RF, P < 0.0001). Habitual consumption of roasted chicken was associated with reduced liking of FF chicken (r = -0.23, P = 0.004) and FF pasta (r = -0.23, P = 0.005). Herbs and spices may be useful for improving the liking of lower fat foods and helping Americans maintain a diet consistent with the U.S. Dietary Guidelines. Americans consume more fat than is recommended in the Dietary Guidelines for Americans. This study shows that you can take foods like French toast, chicken, or a vegetable side and cut the fat and calories by up to 50% while restoring flavor with herbs and spices. People typically use butter, cheese, or fatty meat to enhance the flavor of their food. We found that even when we reduced the fat in our meals by using lower fat dairy and meat products but then added herbs and spices, we were able to deliver the flavor people desire for a fraction of the calories. © 2014 Institute of Food Technologists®
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Links between the charge model and bonded parameter force constants in biomolecular force fields
NASA Astrophysics Data System (ADS)
Cerutti, David S.; Debiec, Karl T.; Case, David A.; Chong, Lillian T.
2017-10-01
The ff15ipq protein force field is a fixed charge model built by automated tools based on the two charge sets of the implicitly polarized charge method: one set (appropriate for vacuum) for deriving bonded parameters and the other (appropriate for aqueous solution) for running simulations. The duality is intended to treat water-induced electronic polarization with an understanding that fitting data for bonded parameters will come from quantum mechanical calculations in the gas phase. In this study, we compare ff15ipq to two alternatives produced with the same fitting software and a further expanded data set but following more conventional methods for tailoring bonded parameters (harmonic angle terms and torsion potentials) to the charge model. First, ff15ipq-Qsolv derives bonded parameters in the context of the ff15ipq solution phase charge set. Second, ff15ipq-Vac takes ff15ipq's bonded parameters and runs simulations with the vacuum phase charge set used to derive those parameters. The IPolQ charge model and associated protocol for deriving bonded parameters are shown to be an incremental improvement over protocols that do not account for the material phases of each source of their fitting data. Both force fields incorporating the polarized charge set depict stable globular proteins and have varying degrees of success modeling the metastability of short (5-19 residues) peptides. In this particular case, ff15ipq-Qsolv increases stability in a number of α -helices, correctly obtaining 70% helical character in the K19 system at 275 K and showing appropriately diminishing content up to 325 K, but overestimating the helical fraction of AAQAA3 by 50% or more, forming long-lived α -helices in simulations of a β -hairpin, and increasing the likelihood that the disordered p53 N-terminal peptide will also form a helix. This may indicate a systematic bias imparted by the ff15ipq-Qsolv parameter development strategy, which has the hallmarks of strategies used to develop other popular force fields, and may explain some of the need for manual corrections in this force fields' evolution. In contrast, ff15ipq-Vac incorrectly depicts globular protein unfolding in numerous systems tested, including Trp cage, villin, lysozyme, and GB3, and does not perform any better than ff15ipq or ff15ipq-Qsolv in tests on short peptides. We analyze the free energy surfaces of individual amino acid dipeptides and the electrostatic potential energy surfaces of each charge model to explain the differences.
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Vural, Fisun; Vural, Birol; Doğer, Emek; Çakıroğlu, Yiğit; Çekmen, Mustafa
2016-10-01
The aim of this study is to investigate the association of perifollicular blood flow (PFBF) with follicular fluid EG-VEGF, inhibin-a, and insulin-like growth factor-1 (IGF-1) concentrations, endometrial vascularity, and IVF outcomes. Forty women with tubal factor infertility were included in a prospective cohort study. Each woman underwent IVF/ICSI procedure. Individual follicles of ≥16 mm (n = 156) were evaluated by power Doppler analysis and categorized as well-vascularized follicles (WVFs) or poorly vascularized follicles (PVFs). WVFs referred to those with perifollicular vascularity of 51-100 %. Each follicular fluid (FF) was individually aspirated and FF/serum EG-VEGF, inhibin-a, and FF IGF-1 levels were evaluated. Zones III-IV endometrial vascularity was classified as a well-vascularized endometrium (WVE). The presence of a WVE and mature oocytes, in addition to the embryo quality and clinical pregnancy rate (CPR), were recorded for each follicle. The main outcome measures were FF serum EG-VEGF, inhibin-a, IGF-1 levels, and WVE and IVF outcome per PFBF. For WVFs, the level of FF EG-VEGF (p = 0.008), oocyte quality (p = 0.001), embryo quality (p = 0.002), a WVE (p = 0.001), and CPR (p = 0.04) increased significantly. The pregnant group was characterized by increased numbers of WVFs (p = 0.044), a WVE (p = 0.022), and increased levels of FF IGF-1 (p = 0.001) and serum EG-VEGF (p = 0.03). FF IGF-1 >50 ng/mL (AUC 0.72) had 75 % sensitivity and 64 % specificity for predicting CPR. WVFs yield high-quality oocytes and embryos, a WVE, increased FF EG-VEGF levels, and increased CPRs.
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Wang, Hanyu; Ouyang, Yidan; Zhou, Chang; Xiao, Difan; Guo, Yaping; Wu, Lan; Li, Xi; Gu, Yunfu; Xiang, Quanju; Zhao, Ke; Yu, Xiumei; Zou, Likou; Ma, Menggen
2017-12-01
Aldehydes generated as by-products during the pretreatment of lignocellulose are the key inhibitors to Saccharomyces cerevisiae, which is considered as the most promising microorganism for industrial production of biofuel, xylitol as well as other special chemicals from lignocellulose. S. cerevisiae has the inherent ability to in situ detoxify aldehydes to corresponding alcohols by multiple aldehyde reductases. Herein, we report that an uncharacterized open reading frame YKL071W from S. cerevisiae encodes a novel "classical" short-chain dehydrogenase/reductase (SDR) protein with NADH-dependent enzymatic activities for reduction of furfural (FF), glycolaldehyde (GA), formaldehyde (FA), and benzaldehyde (BZA). This enzyme showed much better specific activities for reduction of GA and FF than FA and BZA, and displayed much higher Km and Kcat/Km but lower Vmax and Kcat for reduction of GA than FF. For this enzyme, the optimum pH was 5.5 and 6.0 for reduction of GA and FF, and the optimum temperature was 30 °C for reduction of GA and FF. Both pH and temperature affected stability of this enzyme in a similar trend for reduction of GA and FF. Cu 2+ , Zn 2+ , Ni 2+ , and Fe 3+ had severe inhibition effects on enzyme activities of Ykl071wp for reduction of GA and FF. Transcription of YKL071W in S. cerevisiae was significantly upregulated under GA and FF stress conditions, and its transcription is most probably regulated by transcription factor genes of YAP1, CAD1, PDR3, and STB5. This research provides guidelines to identify more uncharacterized genes with reductase activities for detoxification of aldehydes derived from lignocellulose in S. cerevisiae.
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Gruber, Allison H; Umberger, Brian R; Braun, Barry; Hamill, Joseph
2013-07-15
It continues to be argued that a forefoot (FF) strike pattern during running is more economical than a rearfoot (RF) pattern; however, previous studies using one habitual footstrike group have found no difference in running economy between footstrike patterns. We aimed to conduct a more extensive study by including both habitual RF and FF runners. The purposes of this study were to determine whether there were differences in running economy between these groups and whether running economy would change when they ran with the alternative footstrike pattern. Nineteen habitual RF and 18 habitual FF runners performed the RF and FF patterns on a treadmill at 3.0, 3.5, and 4.0 m/s. Steady-state rates of oxygen consumption (Vo2, ml·kg(-1)·min(-1)) and carbohydrate contribution to total energy expenditure (%CHO) were determined by indirect calorimetry for each footstrike pattern and speed condition. A mixed-model ANOVA was used to assess the differences in each variable between groups and footstrike patterns (α = 0.05). No differences in Vo2 or %CHO were detected between groups when running with their habitual footstrike pattern. The RF pattern resulted in lower Vo2 and %CHO compared with the FF pattern at the slow and medium speeds in the RF group (P < 0.05) but not in the FF group (P > 0.05). At the fast speed, a significant footstrike pattern main effect indicated that Vo2 was greater with the FF pattern than with the RF pattern (P < 0.05), but %CHO was not different (P > 0.05). The results suggest that the FF pattern is not more economical than the RF pattern.
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van Ditzhuijzen, Nienke S.; Kurata, Mie; van den Heuvel, Mieke; Sorop, Oana; van Duin, Richard W. B.; Krabbendam-Peters, Ilona; Ligthart, Jurgen; Witberg, Karen; Murawska, Magdalena; Bouma, Brett; Villiger, Martin; Garcia-Garcia, Hector M.; Serruys, Patrick W.; Zijlstra, Felix; van Soest, Gijs; Duncker, Dirk-Jan; Regar, Evelyn; van Beusekom, Heleen M. M.
2017-01-01
Background DM remains a risk factor for poor outcome after stent-implantation, but little is known if and how DM affects the vascular response to BVS. Aim The aim of our study was to examine coronary responses to bioresorbable vascular scaffolds (BVS) in swine with and without diabetes mellitus fed a ‘fast-food’ diet (FF-DM and FF-NDM, respectively) by sequential optical coherence tomography (OCT)-imaging and histology. Methods Fifteen male swine were evaluated. Eight received streptozotocin-injection to induce DM. After 9 months (M), 32 single BVS were implanted in epicardial arteries with a stent to artery (S/A)-ratio of 1.1:1 under quantitative coronary angiography (QCA) and OCT guidance. Lumen, scaffold, neointimal coverage and composition were assessed by QCA, OCT and near-infrared spectroscopy (NIRS) pre- and/or post-procedure, at 3M and 6M. Additionally, polarization-sensitive (PS)-OCT was performed in 7 swine at 6M. After sacrifice at 3M and 6M, histology and polymer degradation analysis were performed. Results Late lumen loss was high (~60%) within the first 3M after BVS-implantation (P<0.01 FF-DM vs. FF-NDM) and stabilized between 3M and 6M (<5% change in FF-DM, ~10% in FF-NDM; P>0.20). Neointimal coverage was highly heterogeneous in all swine (DM vs. NDM P>0.05), with focal lipid accumulation, irregular collagen distribution and neointimal calcification. Likewise, polymer mass loss was low (~2% at 3M, ~5% at 6M;P>0.20) and not associated with DM or inflammation. Conclusion Scaffold coverage showed signs of neo-atherosclerosis in all FF-DM and FF-NDM swine, scaffold polymer was preserved and the vascular response to BVS was not influenced by diabetes. PMID:28898243
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van Ditzhuijzen, Nienke S; Kurata, Mie; van den Heuvel, Mieke; Sorop, Oana; van Duin, Richard W B; Krabbendam-Peters, Ilona; Ligthart, Jurgen; Witberg, Karen; Murawska, Magdalena; Bouma, Brett; Villiger, Martin; Garcia-Garcia, Hector M; Serruys, Patrick W; Zijlstra, Felix; van Soest, Gijs; Duncker, Dirk-Jan; Regar, Evelyn; van Beusekom, Heleen M M
2017-01-01
DM remains a risk factor for poor outcome after stent-implantation, but little is known if and how DM affects the vascular response to BVS. The aim of our study was to examine coronary responses to bioresorbable vascular scaffolds (BVS) in swine with and without diabetes mellitus fed a 'fast-food' diet (FF-DM and FF-NDM, respectively) by sequential optical coherence tomography (OCT)-imaging and histology. Fifteen male swine were evaluated. Eight received streptozotocin-injection to induce DM. After 9 months (M), 32 single BVS were implanted in epicardial arteries with a stent to artery (S/A)-ratio of 1.1:1 under quantitative coronary angiography (QCA) and OCT guidance. Lumen, scaffold, neointimal coverage and composition were assessed by QCA, OCT and near-infrared spectroscopy (NIRS) pre- and/or post-procedure, at 3M and 6M. Additionally, polarization-sensitive (PS)-OCT was performed in 7 swine at 6M. After sacrifice at 3M and 6M, histology and polymer degradation analysis were performed. Late lumen loss was high (~60%) within the first 3M after BVS-implantation (P<0.01 FF-DM vs. FF-NDM) and stabilized between 3M and 6M (<5% change in FF-DM, ~10% in FF-NDM; P>0.20). Neointimal coverage was highly heterogeneous in all swine (DM vs. NDM P>0.05), with focal lipid accumulation, irregular collagen distribution and neointimal calcification. Likewise, polymer mass loss was low (~2% at 3M, ~5% at 6M;P>0.20) and not associated with DM or inflammation. Scaffold coverage showed signs of neo-atherosclerosis in all FF-DM and FF-NDM swine, scaffold polymer was preserved and the vascular response to BVS was not influenced by diabetes.
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Ling, Z; Yonghong, L; Junfeng, L; Li, Z; Xianqiang, L
2018-04-01
The combined antibacterial effects of tilmicosin (TIL) and florfenicol (FF) against Actinobacillus pleuropneumoniae (APP) (n = 2), Streptococcus suis (S. suis) (n = 2), and Haemophilus parasuis (HPS) (n = 2) were evaluated by chekerboard test and time-kill assays. The pharmacokinetics (PKs) of TIL- and FF-loaded hydrogenated castor oil (HCO)-solid lipid nanoparticles (SLN) were performed in healthy pigs. The results indicated that TIL and FF showed synergistic or additive antibacterial activities against APP, S. suis and HPS with the fractional inhibitory concentration (FIC) ranging from 0.375 to 0.75. The time-kill assays showed that 1/2 minimum inhibitory concentration (MIC) TIL combined with 1/2 MIC FF had a stronger ability to inhibit the growth of APP, S. suis, and HPS than 1 MIC TIL or 1 MIC FF, respectively. After oral administration, plasma TIL and FF concentrations could maintain about 0.1 μg/ml for 192 and 176 hr. The SLN prolonged the last time point with detectable concentrations (T last ), area under the concentration-time curve (AUC 0-t ), elimination half-life (T ½ke ), and mean residence time (MRT) by 3.1, 5.6, 12.7, 3.4-fold of the active pharmaceutical ingredient (API) of TIL and 11.8, 16.5, 18.1, 12.1-fold of the API of FF, respectively. This study suggests that the TIL-FF-SLN could be a useful oral formulation for the treatment of APP, S. suis, and HPS infection in pigs. © 2017 John Wiley & Sons Ltd.
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A statistical approach for isolating fossil fuel emissions in atmospheric inverse problems
Yadav, Vineet; Michalak, Anna M.; Ray, Jaideep; ...
2016-10-27
We study independent verification and quantification of fossil fuel (FF) emissions that constitutes a considerable scientific challenge. By coupling atmospheric observations of CO 2 with models of atmospheric transport, inverse models offer the possibility of overcoming this challenge. However, disaggregating the biospheric and FF flux components of terrestrial fluxes from CO 2 concentration measurements has proven to be difficult, due to observational and modeling limitations. In this study, we propose a statistical inverse modeling scheme for disaggregating winter time fluxes on the basis of their unique error covariances and covariates, where these covariances and covariates are representative of the underlyingmore » processes affecting FF and biospheric fluxes. The application of the method is demonstrated with one synthetic and two real data prototypical inversions by using in situ CO 2 measurements over North America. Also, inversions are performed only for the month of January, as predominance of biospheric CO 2 signal relative to FF CO 2 signal and observational limitations preclude disaggregation of the fluxes in other months. The quality of disaggregation is assessed primarily through examination of a posteriori covariance between disaggregated FF and biospheric fluxes at regional scales. Findings indicate that the proposed method is able to robustly disaggregate fluxes regionally at monthly temporal resolution with a posteriori cross covariance lower than 0.15 µmol m -2 s -1 between FF and biospheric fluxes. Error covariance models and covariates based on temporally varying FF inventory data provide a more robust disaggregation over static proxies (e.g., nightlight intensity and population density). However, the synthetic data case study shows that disaggregation is possible even in absence of detailed temporally varying FF inventory data.« less
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Aoki, Takatoshi; Yamaguchi, Shinpei; Kinoshita, Shunsuke; Hayashida, Yoshiko; Korogi, Yukunori
2016-09-01
To determine the reproducibility of the quantitative chemical shift-based water-fat separation method with a multiecho gradient echo sequence [iteraterative decomposition of water and fat with echo asymmetry and least-squares estimation quantitation sequence (IDEAL-IQ)] for assessing bone marrow fat fraction (FF); to evaluate variation of FF at different bone sites; and to investigate its association with age and menopause. 31 consecutive females who underwent pelvic iterative decomposition of water and fat with echo asymmetry and least-squares estimation at 3-T MRI were included in this study. Quantitative FF using IDEAL-IQ of four bone sites were analyzed. The coefficients of variance (CV) on each site were evaluated repeatedly 10 times to assess the reproducibility. Correlations between FF and age were evaluated on each site, and the FFs between pre- and post-menopausal groups were compared. The CV in the quantification of marrow FF ranged from 0.69% to 1.70%. A statistically significant correlation was established between the FF and the age in lumbar vertebral body, ilium and intertrochanteric region of the femur (p < 0.001). The average FF of post-menopausal females was significantly higher than that of pre-menopausal females in these sites (p < 0.05). In the greater trochanter of the femur, there was no significant correlation between FF and age. In vivo IDEAL-IQ would provide reliable quantification of bone marrow fat. IDEAL-IQ is simple to perform in a short time and may be practical for providing information on bone quality in clinical settings.
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Lin, C-Y; Huang, W-Y; Jen, Y-M; Chen, C-M; Su, Y-F; Chao, H-L; Lin, C-S
2014-08-01
The aim of this study was to compare high-dose volumetric modulated arc therapy (VMAT) and fixed-field intensity-modulated radiotherapy (ff-IMRT) plans for the treatment of patients with middle-thoracic esophageal cancer. Eight patients with cT2-3N0M0 middle-thoracic esophageal cancer were enrolled. The treatment planning system was the version 9 of the Pinnacle(3) with SmartArc (Philips Healthcare, Fitchburg, WI, USA). VMAT and ff-IMRT treatment plans were generated for each case, and both techniques were used to deliver 50 Gy to the planning target volume (PTV(50)) and then provided a 16-Gy boost (PTV(66)). The VMAT plans provided superior PTV(66) coverage compared with the ff-IMRT plans (P = 0.034), whereas the ff-IMRT plans provided more appropriate dose homogeneity to the PTV(50) (P = 0.017). In the lung, the V(5) and V(10) were lower for the ff-IMRT plans than for the VMAT plans, whereas the V(20) was lower for the VMAT plans. The delivery time was significantly shorter for the VMAT plans than for the ff-IMRT plans (P = 0.012). In addition, the VMAT plans delivered fewer monitor units. The VMAT technique required a shorter planning time than the ff-IMRT technique (3.8 ± 0.8 hours vs. 5.4 ± 0.6 hours, P = 0.011). The major advantages of VMAT plans are higher efficiency and an approximately 50% reduction in delivery time compared with the ff-IMRT plans, with comparable plan quality. Further clinical investigations to evaluate the use of high-dose VMAT for the treatment of esophageal cancer are warranted. © 2013 Wiley Periodicals, Inc. and the International Society for Diseases of the Esophagus.
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Srinivasan, Sriram Goverapet; Adri C. T. van Duin; Ganesh, Panchapakesan
2015-01-06
In this paper, we report the development of a ReaxFF reactive potential that can accurately describe the chemistry and dynamics of carbon condensed phases. Density functional theory (DFT)-based calculations were performed to obtain the equation of state for graphite and diamond and the formation energies of defects in graphene and amorphous phases from fullerenes. The DFT data were used to reparametrize ReaxFF CHO, resulting in a new potential called ReaxFF C-2013. ReaxFF C-2013 accurately predicts the atomization energy of graphite and closely reproduces the DFT-based energy difference between graphite and diamond, and the barrier for transition from graphite to diamond.more » ReaxFF C-2013 also accurately predicts the DFT-based energy barrier for Stone–Wales transformation in a C 60(I h) fullerene through the concerted rotation of a C 2 unit. Later, MD simulations of a C 180 fullerene using ReaxFF C-2013 suggested that the thermal fragmentation of these giant fullerenes is an exponential function of time. An Arrhenius-type equation was fit to the decay rate, giving an activation energy of 7.66 eV for the loss of carbon atoms from the fullerene. Although the decay of the molecule occurs primarily via the loss of C 2 units, we observed that, with an increase in temperature, the probability of loss of larger fragments increases. Finally, the ReaxFF C-2013 potential developed in this work, and the results obtained on fullerene fragmentation, provide an important step toward the full computational chemical modeling of coal pyrolysis, soot incandescence, high temperature erosion of graphitic rocket nozzles, and ablation of carbon-based spacecraft materials during atmospheric reentry.« less
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Zhang, Xiudong; Bai, Yuanyuan; Cao, Xuefei; Sun, Runcang
2017-08-01
Herein, an efficient biphasic pretreatment process was developed to improve the production of furfural (FF) and glucose from Eucalyptus. The influence of formic acid and NaCl on FF production from xylose in water and various biphasic systems was investigated. Results showed that the addition of formic acid and NaCl significantly promoted the FF yield, and the biphasic system of MIBK (methyl isobutyl ketone)/water exhibited the best performance for FF production. Then the Eucalyptus was pretreated in the MIBK/water system, and a maximum FF yield of 82.0% was achieved at 180°C for 60min. Surface of the pretreated Eucalyptus became relatively rough and loose, and its crystallinity index increased obviously due to the removal of hemicelluloses and lignin. The pretreated Eucalyptus samples showed much higher enzymatic hydrolysis rates (26.2-70.7%) than the raw Eucalyptus (14.5%). Copyright © 2017 Elsevier Ltd. All rights reserved.
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Thermoluminescence response of flat optical fiber subjected to 9 MeV electron irradiations
NASA Astrophysics Data System (ADS)
Hashim, S.; Omar, S. S. Che; Ibrahim, S. A.; Hassan, W. M. S. Wan; Ung, N. M.; Mahdiraji, G. A.; Bradley, D. A.; Alzimami, K.
2015-01-01
We describe the efforts of finding a new thermoluminescent (TL) media using pure silica flat optical fiber (FF). The present study investigates the dose response, sensitivity, minimum detectable dose and glow curve of FF subjected to 9 MeV electron irradiations with various dose ranges from 0 Gy to 2.5 Gy. The above-mentioned TL properties of the FF are compared with commercially available TLD-100 rods. The TL measurements of the TL media exhibit a linear dose response over the delivered dose using a linear accelerator. We found that the sensitivity of TLD-100 is markedly 6 times greater than that of FF optical fiber. The minimum detectable dose was found to be 0.09 mGy for TLD-100 and 8.22 mGy for FF. Our work may contribute towards the development of a new dosimeter for personal monitoring purposes.
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Consistency of Fear of Failure Score Meanings among 8- to 18-Year-Old Female Athletes
ERIC Educational Resources Information Center
Conroy, David E.; Coatsworth, J. Douglas; Kaye, Miranda P.
2007-01-01
Fear of failure (FF) energizes individuals to avoid failure because of the learned aversive consequences of failing (e.g., shame). Although FF is socialized in childhood, little is known about the meaning of scores from FF measures used with children and adolescents. This study addresses that void by establishing a preliminary nomological network…
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Code of Federal Regulations, 2014 CFR
2014-07-01
... the requirements of 40 CFR part 61, subpart FF, and the waste requirements for ethylene production... Waste Operations Background for Waste Requirements § 63.1092 What are the major differences between the requirements of 40 CFR part 61, subpart FF, and the waste requirements for ethylene production sources? The...
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Huang, Yongdong; Bi, Jingxiu; Zhao, Lan; Ma, Guanghui; Su, Zhiguo
2010-12-01
Ion-exchange chromatography (IEC) using commercial ionic absorbents is a widely used technique for protein purification. Protein adsorption onto ion-exchange adsorbents often involves a multipoint adsorption. In IEC of multimeric proteins or "soft" proteins, the intense multipoint binding would make the further desorption difficult, even lead to the destruction of protein structure and the loss of its biological activity. In this paper, DEAE Sepharose FF adsorbents with controllable ligand densities from 0.020 to 0.183 mmol/ml were synthesized, and then the effect of ligand density on the static ion-exchange adsorption of bovine serum albumin (BSA) onto DEAE Sepharose FF was studied by batch adsorption technique. Steric mass-action (SMA) model was employed to analyze the static adsorption behavior. The results showed that the SMA model parameters, equilibrium constant (K(a)), characteristic number of binding sites (υ) and steric factor (σ), increased gradually with ligand density. Thus, it was feasible to regulate BSA multipoint adsorption by modulating the ligand density of ion-exchange adsorbent. Furthermore, IEC of hepatitis B surface antigen (HBsAg) using DEAE Sepharose FF adsorbents with different ligand densities was carried out, and the activity recovery of HBsAg was improved from 42% to 67% when the ligand density was decreased from 0.183 to 0.020 mmol/ml. Taking the activity recovery of HBsAg, the purification factor and the binding capacity into account, DEAE Sepharose FF with a ligand density of 0.041 mmol/ml was most effective for the purification of HBsAg. Such a strategy may also be beneficial for the purification of macromolecules and multimeric proteins. Copyright © 2010 Elsevier Inc. All rights reserved.
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Fuster, Melissa
2017-01-01
The study was conducted to understand fried-food (FF) consumption among Hispanic Caribbean (HC) communities in New York City. Data were collected through qualitative interviews with 23 adults self-identified as Cuban, Dominican, or Puerto Rican. Most informants considered FFs an important part of their traditional diet. Potential explanations included taste, cost, convenience, and the emotive values attached to FF. FF consumption was contextualized in local foodscapes. Results include strategies to diminish FF consumption and differences across HC groups and migratory generations. The relevance for future nutrition interventions addressing health disparities in this community is discussed.
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Bacteriophages are likely the most abundant entities in the aquatic environment, yet knowledge of their ecology is limited. During a fecal source-tracking study, two genetically novel Leviviridae strains were discovered. Although the novel strains were isolated from coastal wat...
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Evaluating UV-C LED disinfection performance and investigating potential dual-wavelength synergy
This study evaluated ultraviolet (UV) light emitting diodes (LEDs) emitting at 260 nm, 280 nm, and the combination of 260|280 nm together for their efficacy at inactivating Escherichia. coli, MS2 coliphage, human adenovirus type 2 (HAdV2), and Bacillus pumilus spores; research in...
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Studies have demonstrated that fecal indicator bacteria (FIB) and pathogens may be present in beach sand and suggest an increased risk of enteric illness among beachgoers contacting sand. During the 2007 National Epidemiological and Environmental Assessment of Recreational (NEEAR...
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INACTIVATION KINETICS OF MONOCHLORAMINE ON MONODISPERSED HEPATITIS A VIRUS AND MS2
The purpose of this study was to further characterize the disinfecting capabilities of preformed monochloramine using hepatitis A virus and the model coliphage MS2. he EPA has identified the latter virus as a model organism in developing CT values and conducting pilot plant studi...
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NASA Astrophysics Data System (ADS)
Cailleaud, Emilie; Guérin, Frédéric; Bouillon, Steven; Sarrazin, Max; Serça, Dominique
2014-05-01
At the Petit Saut Reservoir (PSR, French Guiana, South America), vertical profiles were performed at 5 stations in the open waters (OW) and 6 stations in two shallow flooded forest (FF) areas between April 2012 and September 2013. Measurements included physico-chemical parameters, ammonium, nitrate and dissolved greenhouse gas (CO2, CH4, N2O) concentrations, dissolved and particulate organic carbon (DOC, POC) and nitrogen (PN), δ13C-POC and δ15N-PN . The diffusive fluxes were calculated from surface concentrations. The aim of this study was to estimate the spatial variations of greenhouse gas emissions at a dentrical hydroelectric reservoir located in the tropics and flooding primary forest. Twenty years after impoundment, the water column of the PSR is permanently and tightly stratified thermally in the FF whereas in the OW, the thermal gradients are not as stable. The different hydrodynamical behaviours between the two different zones have significant consequences on the biogeochemistry: oxygen barely diffuses down to the hypolimnion in the FF whereas destratification occurs sporadically during the rainy season in the OW. Although we found the same range of POC in the FF and the OW (2.5-29 μmol L-1) and 20% more DOC at the bottom of OW than in the FF (229-878 μmol L-1), CO2 and CH4 concentrations were always significantly higher in the FF (CO2: 11-1412 μmol L-1, CH4: 0.001-1015 μmol L-1) than in the OW. On average, the CO2 concentrations were 30-40% higher in the FF than in the OW and the CH4 concentrations were three times higher in the FF than in the OW. The δ13C-POC and C:N values did not suggest substantial differences in the sources of OM between the FF and OW. At all stations, POC at the bottom has an isotopic signature slightly lighter than the terrestrial OM in the surrounding forest whereas the isotopic signature of surface POM would result from phytoplankton and methanotrophs. The vertical profiles of nitrogen compounds reveal that the main source of nitrogen in the water column of the PSR is the NH4+ produced during the mineralisation of the OM at the bottom of the reservoir. In OW, the production of NO3- and N2O is enhanced compared to the FF. As a result, N2O concentrations are three times higher at the bottom of OW but surface concentrations are similar in the FF and OW. CO2 diffusive fluxes are 40% higher and CH4 diffusive fluxes are three times higher in FF (CO2: 42±20 mmol m-2 d-1 ; CH4: 0.7±1.4 mmol m-2 d-1) than in OW (CO2: 27±17 mmol m-2 d-1 ; CH4: 0.2±0.3 mmol m-2 d-1). In shallow FF, average CH4 ebullition is 3±10 mmol m-2 d-1 whereas ebullition was never observed in OW. N2O emissions did not exhibit any spatial variability (9±4 μmol m-2 d-1). At the PSR, FF which represents one third of the surface area, is responsible of half of the GHG emissions from the reservoir. This implies that the emissions from most of the tropical reservoirs flooding primary forest need to be reassessed since FF environments are usually overlooked.
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NASA Astrophysics Data System (ADS)
Valentini, Paolo; Schwartzentruber, Thomas E.; Cozmuta, Ioana
2011-12-01
Atomic-level Grand Canonical Monte Carlo (GCMC) simulations equipped with a reactive force field (ReaxFF) are used to study atomic oxygen adsorption on a Pt(111) surface. The off-lattice GCMC calculations presented here rely solely on the interatomic potential and do not necessitate the pre-computation of surface adlayer structures and their interpolation. As such, they provide a predictive description of adsorbate phases. In this study, validation is obtained with experimental evidence (steric heats of adsorption and isotherms) as well as DFT-based state diagrams available in the literature. The ReaxFF computed steric heats of adsorption agree well with experimental data, and this study clearly shows that indirect dissociative adsorption of O2 on Pt(111) is an activated process at non-zero coverages, with an activation energy that monotonically increases with coverage. At a coverage of 0.25 ML, a highly ordered p(2 × 2) adlayer is found, in agreement with several low-energy electron diffraction observations. Isotherms obtained from the GCMC simulations compare qualitatively and quantitatively well with previous DFT-based state diagrams, but are in disagreement with the experimental data sets available. ReaxFF GCMC simulations at very high coverages show that O atoms prefer to bind in fcc hollow sites, at least up to 0.8 ML considered in the present work. At moderate coverages, little to no disorder appears in the Pt lattice. At high coverages, some Pt atoms markedly protrude out of the surface plane. This observation is in qualitative agreement with recent STM images of an oxygen covered Pt surface. The use of the GCMC technique based on a transferable potential is particularly valuable to produce more realistic systems (adsorbent and adsorbate) to be used in subsequent dynamical simulations (Molecular Dynamics) to address recombination reactions (via either Eley-Rideal or Langmuir-Hinshelwood mechanisms) on variously covered surfaces. By using GCMC and Molecular Dynamics simulations, the ReaxFF force field can be a valuable tool for understanding heterogeneous catalysis on a solid surface. Finally, the use of a reactive potential is a necessary requirement to investigate problems where dissociative adsorption occurs, as typical of many important catalytic processes.
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Niu, Zhenchuan; Zhou, Weijian; Zhang, Xiaoshan; Wang, Sen; Zhang, Dongxia; Lu, Xuefeng; Cheng, Peng; Wu, Shugang; Xiong, Xiaohu; Du, Hua; Fu, Yunchong
2016-01-01
Atmospheric fossil fuel CO2 (CO2ff ) information is an important reference for local government to formulate energy-saving and emission reduction in China. The CO2ff spatial distribution in Beijing City was traced by Δ(14)C in the leaves of gingko (Ginkgo biloba L.) from late March to September in 2009. The Δ(14)C values were in the range of -35.2 ± 2.8∼15.5 ± 3.2 ‰ (average 3.4 ± 11.8 ‰), with high values found at suburban sites (average 12.8 ± 3.1 ‰) and low values at road sites (average -8.4 ± 18.1 ‰). The CO2ff concentrations varied from 11.6 ± 3.7 to 32.5 ± 9.0 ppm, with an average of 16.4 ± 4.9 ppm. The CO2ff distribution in Beijing City showed spatial heterogeneity. CO2ff hotspots were found at road sites resulted from the emission from vehicles, while low CO2ff concentrations were found at suburban sites because of the less usage of fossil fuels. Additionally, CO2ff concentrations in the northwest area were generally higher than those in the southeast area due to the disadvantageous topography.
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[Correlation between vertebral bone marrow fat and abdomen fat: a prospective study].
Zhang, Xiao-Dong; Zhao, Yin-Xia; Zhao, Wen-Ji; Zhang, Ling-Yan; Yan, Jie-Wen; Hao, Shuai; Lu, Xiong-Guang; Zhao, Jing; Li, Shao-Lin
2016-02-01
To investigate the correlation between the lumbar bone marrow fat and abdominal fat. A total of 68 individuals (32 men and 36 women, aged 21-74 years with a median of 49.5 years) were included in this study. All the subjects underwent spectroscopic examination of the third lumber vertebra with the single voxel method on a 1.5T MR scanner to measure the fat fraction (FF%). Quantitative CT was also performed for measurement of the abdomen subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT). The measurements were compared between subjects aged ≥50 years and those below 50 years, respectively,in male or female subjects. In male subjects, BMI, FF%, VAT or SAT showed no significant differences between the two age groups (P>0.05), and FF% was not correlated with BMI, VAT or SAT (r=0.109, 0.034, 0.066, respectively; P>0.05). In the female subjects, BMI, FF%, VAT and SAT differed significantly between the two age groups (P<0.05), and in ≥50 years group, FF% showed a positive correlation with VAT (r=0.499, P<0.05) but was not correlated with SAT (r=0.221, P>0.05); in<50 years group, FF% was not correlated with VAT or SAT (r=0.076, -0.067, respectively; P>0.05). FF% is positively correlated with VAT in female subjects aged beyond 50 years, but is not correlated with VAT or SAT in male subjects or in younger female subjects.
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Cheng, Jun; He, Jun; Liu, Huaping; Cai, Hao; Hong, Guini; Zhang, Jiahui; Li, Na; Ao, Lu; Guo, Zheng
2017-01-01
Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that expression measurements of thousands of genes had at least two-fold change in FFPE samples compared with paired FF samples. Therefore, for a transcriptional signature based on risk scores summarized from the expression levels of the signature genes, the risk score thresholds trained from FFPE (or FF) samples could not be applied to FF (or FFPE) samples. On the other hand, we found that more than 90% of the relative expression orderings (REOs) of gene pairs in the FF samples were maintained in their paired FFPE samples and largely unaffected by the storage time. The result suggested that the REOs of gene pairs were highly robust against partial RNA degradation in FFPE samples. Finally, as a case study, we developed a REOs-based signature to distinguish liver cirrhosis from hepatocellular carcinoma (HCC) using FFPE samples. The signature was validated in four datasets of FFPE samples and eight datasets of FF samples. In conclusion, the valuable FFPE samples can be fully exploited to identify REOs-based diagnostic and prognostic signatures which could be robustly applicable to both FF samples and FFPE samples with degraded RNA. PMID:28036264
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Anatomy of hierarchy: Feedforward and feedback pathways in macaque visual cortex
Markov, Nikola T; Vezoli, Julien; Chameau, Pascal; Falchier, Arnaud; Quilodran, René; Huissoud, Cyril; Lamy, Camille; Misery, Pierre; Giroud, Pascale; Ullman, Shimon; Barone, Pascal; Dehay, Colette; Knoblauch, Kenneth; Kennedy, Henry
2013-01-01
The laminar location of the cell bodies and terminals of interareal connections determines the hierarchical structural organization of the cortex and has been intensively studied. However, we still have only a rudimentary understanding of the connectional principles of feedforward (FF) and feedback (FB) pathways. Quantitative analysis of retrograde tracers was used to extend the notion that the laminar distribution of neurons interconnecting visual areas provides an index of hierarchical distance (percentage of supragranular labeled neurons [SLN]). We show that: 1) SLN values constrain models of cortical hierarchy, revealing previously unsuspected areal relations; 2) SLN reflects the operation of a combinatorial distance rule acting differentially on sets of connections between areas; 3) Supragranular layers contain highly segregated bottom-up and top-down streams, both of which exhibit point-to-point connectivity. This contrasts with the infragranular layers, which contain diffuse bottom-up and top-down streams; 4) Cell filling of the parent neurons of FF and FB pathways provides further evidence of compartmentalization; 5) FF pathways have higher weights, cross fewer hierarchical levels, and are less numerous than FB pathways. Taken together, the present results suggest that cortical hierarchies are built from supra- and infragranular counterstreams. This compartmentalized dual counterstream organization allows point-to-point connectivity in both bottom-up and top-down directions. PMID:23983048
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Zang, Hongjun; Chen, Eugene Y X
2015-03-30
There is increasing interest in the upgrading of C5 furfural (FF) and C6 5-hydroxymethyl furfural (HMF) into C10 and C12 furoins as higher energy-density intermediates for renewable chemicals, materials, and biofuels. This work utilizes the organocatalytic approach, using the in situ generated N,S-heterocyclic carbene catalyst derived from thiazolium ionic liquids (ILs), to achieve highly efficient self-coupling reactions of FF and HMF. Specifically, variations of the thiazolium IL structure have led to the most active and efficient catalyst system of the current series, which is derived from a new thiazolium IL carrying the electron-donating acetate group at the 5-ring position. For FF coupling by this IL (0.1 mol %, 60 °C, 1 h), when combined with Et3N, furoin was obtained in >99% yield. A 97% yield of the C12 furoin was also achieved from the HMF coupling by this catalyst system (10 mol % loading, 120 °C, 3 h). On the other hand, the thiazolium IL bearing the electron-withdrawing group at the 5-ring position is the least active and efficient catalyst. The mechanistic aspects of the coupling reaction by the thiazolium catalyst system have also been examined and a mechanism has been proposed.
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Force Field Model of Periodic Trends in Biomolecular Halogen Bonds
Scholfield, Matthew R.; Ford, Melissa Coates; Vander Zanden, Crystal M.; Billman, M. Marie; Ho, P. Shing; Rappé, Anthony K.
2016-01-01
The study of the noncovalent interaction now defined as a halogen bond (X-bond) has become one of the fastest growing areas in experimental and theoretical chemistry—its applications as a design tool are highly extensive. The significance of the interaction in biology has only recently been recognized, but has now become important in medicinal chemistry. We had previously derived a set of empirical potential energy functions to model the structure-energy relationships for bromines in biomolecular X-bonds (BXBs). Here, we have extended this force field for BXBs (ffBXB) to the halogens (Cl, Br, and I) that are commonly seen to form stable X-bonds. The ffBXB calculated energies show a remarkable one-to-one linear relationship to explicit BXB energies determined from an experimental DNA junction system, thereby validating the approach and the model. The resulting parameters allow us to interpret the stabilizing effects of BXBs in terms of well-defined physical properties of the halogen atoms, including their size, shape, and charge, showing periodic trends that are predictable along the Group VII column of elements. Consequently, we have established the ffBXB as accurate computational tool that can be applied to, for example, for the design of new therapeutic compounds against clinically important targets and new biomolecular based materials. PMID:25338128
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... difficile - fecal transplant; Pseudomembranous colitis - fecal transplant References Ferri FF. Clostridium difficile infection. In: Ferri FF, ed. Ferri's Clinical Advisor 2017. Philadelphia, PA: ...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Liu, Hao; Li, Yufeng; Wang, Shuai
Air-void structure was introduced in GaN-based blue light-emitting diodes (LED) with one-step growth on periodic laser drilling patterned sapphire substrate, which free of any photolithography or wet/dry etching process. The influence of filling factors (FF) of air-void on crystal quality and optical performance were investigate. Transmission electron microscopy images and micro-Raman spectroscopy indicated that the dislocation was bended and the partially compressed strain was released. When FF was 55.43%, compared with the LED structure grown on flat sapphire substrate, the incorporation of air-void was observed to reduce the compressed stress of ∼20% and the luminance intensity has improved by 128%.more » Together with the simulated reflection intensity enhancement by finite difference time-domain (FDTD) method, we attribute the enhanced optical performance to the combined contribution of strong back-side light reflection of air-void and better GaN epitaxial quality. This approach provides a simple replacement to the conventional air-void embedded LED process.« less
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Composite Structural Analysis of Flat-Back Shaped Blade for Multi-MW Class Wind Turbine
NASA Astrophysics Data System (ADS)
Kim, Soo-Hyun; Bang, Hyung-Joon; Shin, Hyung-Ki; Jang, Moon-Seok
2014-06-01
This paper provides an overview of failure mode estimation based on 3D structural finite element (FE) analysis of the flat-back shaped wind turbine blade. Buckling stability, fiber failure (FF), and inter-fiber failure (IFF) analyses were performed to account for delamination or matrix failure of composite materials and to predict the realistic behavior of the entire blade region. Puck's fracture criteria were used for IFF evaluation. Blade design loads applicable to multi-megawatt (MW) wind turbine systems were calculated according to the Germanischer Lloyd (GL) guideline and the International Electrotechnical Commission (IEC) 61400-1 standard, under Class IIA wind conditions. After the post-processing of final load results, a number of principal load cases were selected and converted into applied forces at the each section along the blade's radius of the FE model. Nonlinear static analyses were performed for laminate failure, FF, and IFF check. For buckling stability, linear eigenvalue analysis was performed. As a result, we were able to estimate the failure mode and locate the major weak point.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kawahara, D; Medical and Dental Sciences Course, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima; Ozawa, S
Purpose: SBRT combining transarterial chemoembolization with Lipiodol is expected to improve local control. Our showed that the dose enhancement effect in the Lipiodol with 10X flattening filter free (FFF) was inserted. This study was to investigate the energy fluence variations of electron in the Lipiodol using flattened (FF) and FFF beams. Methods: FF and FFF for 6X and 10X beams by TrueBeam were used in this study. The Lipiodol (3 X 3 X 3 cm{sup 3}) was located at the depth of 5 cm in water, the dose enhancement factor (DEF) and energy fluence were calculated by Monte Carlo (MC)more » calculations (PHITS). Results: DEFs with FF and FFF of 6X were 17.1% and 24.3% at rebuild-up region in the Lipiodol (5.3cm depth), 7.0% and 17.0% at the center of Lipiodol (6.5cm depth), and −13.2% and −8.2% at behind Lipiodol (8.3cm depth). DEFs with FF and FFF of 10X were 21.7% and 15.3% at rebuild-up region, 8.2% and 10.5% at the center of Lipiodol, and −14.0% and −8.6% at behind Lipiodol. Spectral results showed that the FFF beam contained more low-energy (0–0.3MeV) component of electrons than FF beam, and FF beam contained more high-energy (over 0.3MeV) electrons than FFF beam in Lipiodol. Behind the Lipiodol, build-down effect with FF beam was larger than FFF beam because FF beam contained more high energy electrons. The difference of DEFs between FFF and FF beams for 6X were larger than for 10X. This is because 10X beam contained more high-energy electrons. Conclusion: It was found that the 6XFFF beam gives the largest change of energy fluence and the largest DEF in this study. These phenomena are mainly caused by component of low-energy electrons, and this energy is almost correspond to the boundary of photo electronic dominant and Compton scattering dominant region for photon beams.« less
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Mercier, Manuel R; Schwartz, Sophie; Spinelli, Laurent; Michel, Christoph M; Blanke, Olaf
2017-03-01
The main model of visual processing in primates proposes an anatomo-functional distinction between the dorsal stream, specialized in spatio-temporal information, and the ventral stream, processing essentially form information. However, these two pathways also communicate to share much visual information. These dorso-ventral interactions have been studied using form-from-motion (FfM) stimuli, revealing that FfM perception first activates dorsal regions (e.g., MT+/V5), followed by successive activations of ventral regions (e.g., LOC). However, relatively little is known about the implications of focal brain damage of visual areas on these dorso-ventral interactions. In the present case report, we investigated the dynamics of dorsal and ventral activations related to FfM perception (using topographical ERP analysis and electrical source imaging) in a patient suffering from a deficit in FfM perception due to right extrastriate brain damage in the ventral stream. Despite the patient's FfM impairment, both successful (observed for the highest level of FfM signal) and absent/failed FfM perception evoked the same temporal sequence of three processing states observed previously in healthy subjects. During the first period, brain source localization revealed cortical activations along the dorsal stream, currently associated with preserved elementary motion processing. During the latter two periods, the patterns of activity differed from normal subjects: activations were observed in the ventral stream (as reported for normal subjects), but also in the dorsal pathway, with the strongest and most sustained activity localized in the parieto-occipital regions. On the other hand, absent/failed FfM perception was characterized by weaker brain activity, restricted to the more lateral regions. This study shows that in the present case report, successful FfM perception, while following the same temporal sequence of processing steps as in normal subjects, evoked different patterns of brain activity. By revealing a brain circuit involving the most rostral part of the dorsal pathway, this study provides further support for neuro-imaging studies and brain lesion investigations that have suggested the existence of different brain circuits associated with different profiles of interaction between the dorsal and the ventral streams.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Yu, S; Roa, D; Hanna, N
2015-06-15
Purpose: Flattening Filter Free (FFF) beams offer the potential for higher dose rates, short treatment time, and lower out of field dose. Therefore, the aim of this study was to investigate the dosimetric effects and out of field dose of Volumetric Modulated Arc Therapy (VMAT) plans using FFF vs Flattening Filtering (FF) beams for partial brain irradiation. Methods: Ten brain patients treated with a 6FF beam from a Truebeam STX were analyzed retrospectively for this study. These plans (46Gy at 2 Gy per fraction) were re-optimized for 6FFF beams using the same dose constraints as the original plans. PTV coverage,more » PTV Dmax, total MUs, and mean dose to organs-at-risk (OAR) were evaluated. In addition, the out-of-field dose for 6FF and 6FFF plans for one patient was measured on an anthropomorphic phantom. TLDs were placed inside (central axis) and outside (surface) the phantom at distances ranging from 0.5 cm to 17 cm from the field edge. Paired T-test was used for statistical analysis. Results: PTV coverage and PTV Dmax were comparable for the FF and FFF plans with 95.9% versus 95.6% and 111.2% versus 111.9%, respectively. Mean dose to the OARs were 3.7% less for FFF than FF plans (p<0.0001). Total MUs were, on average, 12.5% greater for FFF than FF plans with 481±55 MU (FFF) versus 429±50 MU (FF), p=0.0003. On average, the measured out of field dose was 24% less for FFF compared to FF, p<0.0001. A similar beam-on time was observed for the FFF and FF treatment. Conclusion: It is beneficial to use 6FFF beams for regular fractionated brain VMAT treatments. VMAT treatment plans using FFF beams can achieve comparable PTV coverage but with more OAR sparing. The out of field dose is significant less with mean reduction of 24%.« less
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Francy, Donna S.; Bushon, Rebecca N.; Stopar, Julie; Luzano, Emma J.; Fout, G. Shay
2004-01-01
A study of small public ground-water-supply wells that produce water from discontinuous sand and gravel aquifers was done from July 1999 through July 2001 in southeastern Michigan. Samples were collected to determine the occurrence of viral pathogens and microbiological indicators of fecal contamination (indicators), determine whether indicators are adequate predictors of the presence of enteric viruses, and determine the factors that affect the presence of enteric viruses. Small systems are those that serve less than 3,300 people. Samples were analyzed for specific enteric viruses by reverse transcriptase-polymerase chain reaction (RT-PCR), for culturable viruses by cell culture, and for the indicators total coliforms, Escherichia coli (E. coli), enterococci, and F-specific and somatic coliphage. Ancillary environmental and water-quality data were collected or compiled. A total of 169 regular samples and 32 replicate pairs were collected from 38 wells. Replicate pairs were samples collected at the same well on the same date. One well was sampled 6 times, 30 wells were sampled five times, 6 wells were sampled twice, and 1 well was sampled once. By use of RT-PCR, enterovirus was found in four wells (10.5 percent) and hepatitis A virus (HAV) in five wells (13.2 percent). In two of these wells, investigators found both enterovirus and HAV, but on different sampling dates. Culturable viruses were found one time in two wells (5.9 percent), and neither of these wells was positive for viruses by use of RT-PCR on any sampling date. If results for all viruses are combined, 9 of the 38 small public-supply wells were positive for enteric viruses (23.7 percent) by either cell culture or RT-PCR. One or more indicators were found in 18 of 38 wells. Total coliforms, E. coli, enterococci, and F-specific and somatic coliphage were found in 34.2, 10.5, 15.8, 5.9, and 5.9 percent, respectively, of the wells tested. In only 3 out of 18 wells were samples positive for an indicator on more than one date at the same well. The co-occurrence of enteric viruses and any indicator was 55.6 percent; five out of the nine virus-positive wells were also found to be positive for an indicator. Two wells with detections of viruses had a detection of total coliforms, one well had a detection of E. coli, one of enterococci, and one of F-specific coliphage. On a per sample basis, of 11 samples that were positive for enteric viruses, indicator bacteria co-occurred in only 2 samples, and coliphage were not present in any. More virus-positive samples were found at sites served by septic systems than those served by sewerlines. Sampling condition (ground water or a mixture of tank and ground water), distance to septic system, type of and distance to nearest surface-water body, well characteristics, or land use were not related to the presence of viruses or indicators. Among continuous water-quality variables, statistically significant relations were found between total coliforms and dissolved organic carbon and between total coliforms and iron. There was a statistically significant relation between chloride concentrations >20 mg/L and detections of total coliforms. Presence of nitrate and nitrite was related to the presence of other indicators (E. coli, enterococci, and F-specific and somatic coliphage) or enteric viruses, but not to total coliforms. The data indicated that chloride-to-bromide (C1:Br) ratios may be useful as a screening tool for total coliforms and enteric viruses but not for E. coli, enterococci, and F-specific and somatic coliphage. This study provides evidence for fecal contamination of ground water from small public-supply wells, at least on an intermittent basis. Collecting data on multiple lines of evidence would be needed to reliably predict the presence of enteric viruses and protect public health. Future data collection toward this end could include repeat sampling several times a year for different indicators, measuring dissolv
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Bělohlávek, Jan; Mlček, Mikuláš; Huptych, Michal; Svoboda, Tomáš; Havránek, Stěpán; Ošt'ádal, Petr; Bouček, Tomáš; Kovárník, Tomáš; Mlejnský, František; Mrázek, Vratislav; Bělohlávek, Marek; Aschermann, Michael; Linhart, Aleš; Kittnar, Otomar
2012-12-12
Extracorporeal membrane oxygenation (ECMO) is increasingly used in cardiac arrest (CA). Adequacy of carotid and coronary blood flows (CaBF, CoBF) and coronary perfusion pressure (CoPP) in ECMO treated CA is not well established. This study compares femoro-femoral (FF) to femoro-subclavian (FS) ECMO and intraaortic balloon counterpulsation (IABP) contribution based on CaBF, CoBF, CoPP, myocardial and brain oxygenation in experimental CA managed by ECMO. In 11 female pigs (50.3 ± 3.4 kg), CA was randomly treated by FF versus FS ECMO ± IABP. Animals under general anesthesia had undergone 15 minutes of ventricular fibrillation (VF) with ECMO flow of 5 to 10 mL/kg/min simulating low-flow CA followed by continued VF with ECMO flow of 100 mL/kg/min. CaBF and CoBF were measured by a Doppler flow wire, cerebral and peripheral oxygenation by near infrared spectroscopy. CoPP, myocardial oxygen metabolism and resuscitability were determined. CaBF reached values > 80% of baseline in all regimens. CoBF > 80% was reached only by the FF ECMO, 90.0% (66.1, 98.6). Addition of IABP to FF ECMO decreased CoBF to 60.7% (55.1, 86.2) of baseline, P = 0.004. FS ECMO produced 70.0% (49.1, 113.2) of baseline CoBF, significantly lower than FF, P = 0.039. Addition of IABP to FS did not change the CoBF; however, it provided significantly higher flow, 76.7% (71.9, 111.2) of baseline, compared to FF + IABP, P = 0.026. Both brain and peripheral regional oxygen saturations decreased after induction of CA to 23% (15.0, 32.3) and 34% (23.5, 34.0), respectively, and normalized after ECMO institution. For brain saturations, all regimens reached values exceeding 80% of baseline, none of the comparisons between respective treatment approaches differed significantly. After a decline to 15 mmHg (9.5, 20.8) during CA, CoPP gradually rose with time to 68 mmHg (43.3, 84.0), P = 0 .003, with best recovery on FF ECMO. Resuscitability of the animals was high, both 5 and 60 minutes return of spontaneous circulation occured in eight animals (73%). In a pig model of CA, both FF and FS ECMO assure adequate brain perfusion and oxygenation. FF ECMO offers better CoBF than FS ECMO. Addition of IABP to FF ECMO worsens CoBF. FF ECMO, more than FS ECMO, increases CoPP over time.
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2012-01-01
Introduction Extracorporeal membrane oxygenation (ECMO) is increasingly used in cardiac arrest (CA). Adequacy of carotid and coronary blood flows (CaBF, CoBF) and coronary perfusion pressure (CoPP) in ECMO treated CA is not well established. This study compares femoro-femoral (FF) to femoro-subclavian (FS) ECMO and intraaortic balloon counterpulsation (IABP) contribution based on CaBF, CoBF, CoPP, myocardial and brain oxygenation in experimental CA managed by ECMO. Methods In 11 female pigs (50.3 ± 3.4 kg), CA was randomly treated by FF versus FS ECMO ± IABP. Animals under general anesthesia had undergone 15 minutes of ventricular fibrillation (VF) with ECMO flow of 5 to 10 mL/kg/min simulating low-flow CA followed by continued VF with ECMO flow of 100 mL/kg/min. CaBF and CoBF were measured by a Doppler flow wire, cerebral and peripheral oxygenation by near infrared spectroscopy. CoPP, myocardial oxygen metabolism and resuscitability were determined. Results CaBF reached values > 80% of baseline in all regimens. CoBF > 80% was reached only by the FF ECMO, 90.0% (66.1, 98.6). Addition of IABP to FF ECMO decreased CoBF to 60.7% (55.1, 86.2) of baseline, P = 0.004. FS ECMO produced 70.0% (49.1, 113.2) of baseline CoBF, significantly lower than FF, P = 0.039. Addition of IABP to FS did not change the CoBF; however, it provided significantly higher flow, 76.7% (71.9, 111.2) of baseline, compared to FF + IABP, P = 0.026. Both brain and peripheral regional oxygen saturations decreased after induction of CA to 23% (15.0, 32.3) and 34% (23.5, 34.0), respectively, and normalized after ECMO institution. For brain saturations, all regimens reached values exceeding 80% of baseline, none of the comparisons between respective treatment approaches differed significantly. After a decline to 15 mmHg (9.5, 20.8) during CA, CoPP gradually rose with time to 68 mmHg (43.3, 84.0), P = 0 .003, with best recovery on FF ECMO. Resuscitability of the animals was high, both 5 and 60 minutes return of spontaneous circulation occured in eight animals (73%). Conclusions In a pig model of CA, both FF and FS ECMO assure adequate brain perfusion and oxygenation. FF ECMO offers better CoBF than FS ECMO. Addition of IABP to FF ECMO worsens CoBF. FF ECMO, more than FS ECMO, increases CoPP over time. PMID:22424292
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Membrane triangles with corner drilling freedoms. III - Implementation and performance evaluation
NASA Technical Reports Server (NTRS)
Felippa, Carlos A.; Alexander, Scott
1992-01-01
This paper completes a three-part series on the formulation of 3-node, 9-dof membrane triangles with corner drilling freedoms based on parametrized variational principles. The first four sections cover element implementation details including determination of optimal parameters and treatment of distributed loads. Then three elements of this type, labeled ALL, FF and EFF-ANDES, are tested on standard plane stress problems. ALL represents numerically integrated versions of Allman's 1988 triangle; FF is based on the free formulation triangle presented by Bergan and Felippa in 1985; and EFF-ANDES represent two different formulations of the optimal triangle derived in Parts I and II. The numerical studies indicate that the ALL, FF and EFF-ANDES elements are comparable in accuracy for elements of unitary aspect ratios. The ALL elements are found to stiffen rapidly in inplane bending for high aspect ratios, whereas the FF and EFF elements maintain accuracy. The EFF and ANDES implementations have a moderate edge in formation speed over the FF.
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Free-field Calibration of the Pressure Sensitivity of Microphones at Frequencies up to 80 kHz
NASA Technical Reports Server (NTRS)
Herring, G. C.; Zuckerwar, Allan J.; Elbing, Brian R.
2006-01-01
A free-field (FF) substitution method for calibrating the pressure sensitivity of microphones at frequencies up to 80 kHz is demonstrated with both grazing and normal incidence geometries. The substitution-based method, as opposed to a simultaneous method, avoids problems associated with the non-uniformity of the sound field and, as applied here, uses a 1/2 -inch air-condenser pressure microphone as a known reference. Best results were obtained with a centrifugal fan, which is used as a random, broadband sound source. A broadband source minimizes reflection-related interferences that often plague FF measurements. Calibrations were performed on 1/4-inch FF air-condenser, electret, and micro-electromechanical systems (MEMS) microphones in an anechoic chamber. The accuracy of this FF method is estimated by comparing the pressure sensitivity of an air-condenser microphone, as derived from the FF measurement, with that of an electrostatic actuator calibration and is typically 0.3 dB (95% confidence), over the range 2-80 kHz.
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Fill factor in organic solar cells can exceed the Shockley-Queisser limit
NASA Astrophysics Data System (ADS)
Trukhanov, Vasily A.; Bruevich, Vladimir V.; Paraschuk, Dmitry Yu.
2015-06-01
The ultimate efficiency of organic solar cells (OSC) is under active debate. The solar cell efficiency is calculated from the current-voltage characteristic as a product of the open-circuit voltage (VOC), short-circuit current (JSC), and the fill factor (FF). While the factors limiting VOC and JSC for OSC were extensively studied, the ultimate FF for OSC is scarcely explored. Using numerical drift-diffusion modeling, we have found that the FF in OSC can exceed the Shockley-Queisser limit (SQL) established for inorganic p-n junction solar cells. Comparing charge generation and recombination in organic donor-acceptor bilayer heterojunction and inorganic p-n junction, we show that such distinctive properties of OSC as interface charge generation and heterojunction facilitate high FF, but the necessary condition for FF exceeding the SQL in OSC is field-dependence of charge recombination at the donor-acceptor interface. These findings can serve as a guideline for further improvement of OSC.
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Xia, Lan; Zhao, Xiaoming; Sun, Yun; Hong, Yan; Gao, Yuping; Hu, Shuanggang
2014-01-01
Objective: To establish a gas chromatography/mass spectrometry (GC/MS)-based metabolomics method to compare the metabolites in the follicular fluid (FF) from patients with in vitro fertilization (IVF) and repeated IVF failure (RIF). Methods: A prospective study was employed in Center for Reprodutive Medcine, Renji Hospital, Shanghai, China, between January and October 2010. FF samples were collected from 13 patients with RIF and 15 patients who achieved pregnancy after the first IVF cycle. Results: Partial least squares (PLS) discriminant analysis of the PCA data revealed that the samples were scattered into two different regions. FF from the two groups differed with respect to 20 metabolites. FF from RIF group showed elevated levels of several amino acids (valine, threonine, isoleucine, cysteine, serine, proline, alanine, phenylalanine, lysine, methionine and ornithine), and reduced levels of dicarboxylic acids, cholesterol and some organic acids. Conclusions: The studies corroborated successful determination of the levels of metabolite in the FF. PMID:25400819
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Beta endorphin in serum and follicular fluid of PCOS- and non-PCOS women.
Jaschke, Nikolai; Lunger, Fabian; Wildt, Ludwig; Seeber, Beata
2018-07-01
To compare the concentrations of beta endorphin in serum and follicular fluid (FF) of PCOS- and non-PCOS women. Secondarily, to investigate associations between beta endorphin and other parameters. Fifty-nine women undergoing in vitro fertilization (IVF) were included in the study. Sixteen were stratified to the PCOS group using the Rotterdam criteria. The remaining 43 women served as controls. Follicular fluid was collected during oocyte retrieval and peripheral blood sampling was performed on the same day. Beta endorphin concentrations in serum and follicular fluid, serum levels of insulin, glucose, LH, estradiol and progesterone were measured. Additionally, testosterone was measured before starting the stimulation protocol. There was no difference in beta endorphin levels between PCOS- and non-PCOS women. The concentration of the peptide was higher in serum than in FF, likely due to collection of FF after ovulation induction and corresponding to the early luteal phase. We found a significant correlation between the number of mature Metaphase II (MII) oocytes retrieved and beta endorphin concentration in FF. In women with biochemical hyperandrogenemia, beta endorphin levels in FF correlated with testosterone levels. Beta Endorphin concentrations in serum and FF do not differ between PCOS- and non PCOS-women undergoing IVF. However, together with sex hormones, beta endorphin might play a key role in oocyte maturation.
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Sex differences in the fetal heart rate variability indices of twins.
Tendais, Iva; Figueiredo, Bárbara; Gonçalves, Hernâni; Bernardes, João; Ayres-de-Campos, Diogo; Montenegro, Nuno
2015-03-01
To evaluate the differences in linear and complex heart rate dynamics in twin pairs according to fetal sex combination [male-female (MF), male-male (MM), and female-female (FF)]. Fourteen twin pairs (6 MF, 3 MM, and 5 FF) were monitored between 31 and 36.4 weeks of gestation. Twenty-six fetal heart rate (FHR) recordings of both twins were simultaneously acquired and analyzed with a system for computerized analysis of cardiotocograms. Linear and nonlinear FHR indices were calculated. Overall, MM twins presented higher intrapair average in linear indices than the other pairs, whereas FF twins showed higher sympathetic-vagal balance. MF twins exhibited higher intrapair average in entropy indices and MM twins presented lower entropy values than FF twins considering the (automatically selected) threshold rLu. MM twin pairs showed higher intrapair differences in linear heart rate indices than MF and FF twins, whereas FF twins exhibited lower intrapair differences in entropy indices. The results of this exploratory study suggest that twins have sex-specific differences in linear and nonlinear indices of FHR. MM twins expressed signs of a more active autonomic nervous system and MF twins showed the most active complexity control system. These results suggest that fetal sex combination should be taken into consideration when performing detailed evaluation of the FHR in twins.
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Pulmonary Function in Flight (PuFF) Experiment
NASA Technical Reports Server (NTRS)
2003-01-01
In this International Space Station (ISS) onboard photo, Expedition Six Science Officer Donald R. Pettit works to set up the Pulmonary Function in Flight (PuFF) experiment hardware in the Destiny Laboratory. Expedition Six is the fourth and final crew to perform the PuFF experiment. The PuFF experiment was developed to better understand what effects long term exposure to microgravity may have on the lungs. The focus is on measuring changes in the everness of gas exchange in the lungs, and on detecting changes in respiratory muscle strength. It allows astronauts to measure blood flow through the lungs, the ability of the lung to take up oxygen, and lung volumes. Each PuFF session includes five lung function tests, which involve breathing only cabin air. For each planned extravehicular (EVA) activity, a crew member performs a PuFF test within one week prior to the EVA. Following the EVA, those crew members perform another test to document the effect of exposure of the lungs to the low-pressure environment of the space suits. This experiment utilizes the Gas Analyzer System for Metabolic Analysis Physiology, or GASMAP, located in the Human Research Facility (HRF), along with a variety of other Puff equipment including a manual breathing valve, flow meter, pressure-flow module, pressure and volume calibration syringes, and disposable mouth pieces.
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Analysis of the FF Aqr spectra
NASA Astrophysics Data System (ADS)
Shimanskaya, N. N.; Bikmaev, I. F.; Shimansky, V. V.
2011-07-01
We determine the atmospheric parameters of the secondary in the close binary system FF Aqr and analyze its chemical composition. A series of high-resolution spectra are taken at different orbital phases using the coude echelle spectrometer of the 1.5-m Russian-Turkish Telescope (RTT150). We show that the absorption line intensity of heavy elements varies with phase due to the spotty nature of the cool component. We determine the abundances of heavy elements in the star's atmosphere by modelling the synthetic spectra and performing a differential analysis of the chemical composition of FF Aqr relative to the solar composition. Our analysis of the averaged spectrum of FF Aqr yielded 539 abundance estimates for 21 chemical elements. We found the metallicity of the star ([ Fe/H] = -0.11 ± 0.08) to be close solar, in agreement with the hypothesis that FF Aqr should belong to the Galactic disk. The inferred chemical composition of the objects exhibits no anomalous abundances of the α-, r-, and s-process elements like those earlier found in other systems (IN Com, LW Hya, V471 Tau). The lack of such anomalies in FF Aqr must be due to the fact that the elements heavier than 16 O cannot be synthesized in the core of the primary during the last stages of its evolution.
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NASA Astrophysics Data System (ADS)
Li, Huiyan; Wan, Huiying; Xia, Tian; Chen, Maohua; Zhang, Yun; Luo, Xiaoming; Li, Xiaohong
2015-07-01
Therapeutic angiogenesis remains the most effective method to re-establish a proper blood flow in ischemic tissues. There is a great clinical need to identify an injectable format to achieve a well accumulation following local administration and a sustained delivery of biological factors at the ischemic sites. In the current study, fragmented nanofibers with loaded traditional Chinese medicines, astragaloside IV (AT), the main active ingredient of astragalus, and ferulic acid (FA), the main ingredient of angelica, were proposed to promote the microvessel formation after intramuscular injection into ischemic hindlimbs. Fragmented fibers with average lengths of 5 (FF-5), 20 (FF-20) and 80 μm (FF-80) were constructed by the cryocutting of aligned electrospun fibers. Their dispersion in sodium alginate solution (0.2%) indicated good injectability. After injection into the quadriceps muscles of the hindlimbs, FF-20 and FF-80 fiber fragments showed higher tissue retentions than FF-5, and around 90% of the injected doses were determined after 7 days. On a hindlimb ischemia model established by ligating the femoral arteries, intramuscular injection of the mixtures of FA-loaded and AT-loaded FF-20 fiber fragments substantially reduced the muscle degeneration with minimal fibrosis formation, significantly enhanced the neovessel formation and hindlimb perfusion in the ischemic tissues, and efficiently promoted the limb salvage with few limb losses. Along with the easy manipulation and lower invasiveness for in vivo administration, fragmented fibers should become potential drug carriers for disease treatment, wound recovery and tissue repair after local injection.
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Naji, Mohammad; Nekoonam, Saeid; Aleyasin, Ashraf; Arefian, Ehsan; Mahdian, Reza; Azizi, Elham; Shabani Nashtaei, Maryam; Amidi, Fardin
2018-01-01
Polycystic ovary syndrome (PCOS) is one of the most common endocrinopathies that affects women in reproductive age. MicroRNAs (miRNAs) play crucial roles in normal function of female reproductive system and folliculogenesis. Deregulated expression of miRNAs in PCOS condition may be significantly implicated in the pathogenesis of PCOS. We determined relative expression of miR-15a, miR-145, and miR-182 in granulosa-lutein cells (GLCs), follicular fluid (FF), and serum of PCOS patients. Human subjects were divided into PCOS (n = 20) and control (n = 21) groups. GLCs, FF, and serum were isolated and stored. RNA isolation was performed and cDNA was reversely transcribed using specific stem-loop RT primers. Relative expression of miRNAs was calculated after normalization against U6 expression. Correlation of miRNAs' expression level with basic clinical features and predictive value of miRNAs in FF and serum were appraised. Relative expression of miR-145 and miR-182 in GLCs was significantly decreased in PCOS, but miR-182 in FF of PCOS patients revealed up-regulated levels. Significant correlations between level of miRNAs in FF and serum and hormonal profile of subjects were observed. MiR-182 in FF showed a significant predictive value with AUC of 0.73, 76.4% sensitivity, and 70.5% specificity which was improved after combination of miR-182 and miR-145. A significant dysregulation of miR-145 and miR-182 in GLCs of PCOS may indicate their involvement in pathogenesis of PCOS. Differential up-regulation of miR-182 in FF of PCOS patients with its promising predictive values for discrimination of PCOS reinforced the importance of studying miRNAs' profile in FF.
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Kawahara, Daisuke; Ozawa, Shuichi; Saito, Akito; Kimura, Tomoki; Suzuki, Tatsuhiko; Tsuneda, Masato; Tanaka, Sodai; Nakashima, Takeo; Ohno, Yoshimi; Murakami, Yuji; Nagata, Yasushi
2018-03-01
Lipiodol, which was used in transcatheter arterial chemoembolization before liver stereotactic body radiation therapy (SBRT), remains in SBRT. Previous we reported the dose enhancement in Lipiodol using 10 MV (10×) FFF beam. In this study, we compared the dose enhancement in Lipiodol and evaluated the probability of electron generation (PEG) for the dose enhancement using flattening filter (FF) and flattening filter free (FFF) beams. FF and FFF for 6 MV (6×) and 10× beams were delivered by TrueBeam. The dose enhancement factor (DEF), energy spectrum, and PEG was calculated using Monte Carlo (MC) code BEAMnrc and heavy ion transport code system (PHITS). DEFs for FF and FFF 6× beams were 7.0% and 17.0% at the center of Lipiodol (depth, 6.5 cm). DEFs for FF and FFF 10× beams were 8.2% and 10.5% at the center of Lipiodol. Spectral analysis revealed that the FFF beams contained more low-energy (0-0.3 MeV) electrons than the FF beams, and the FF beams contained more high-energy (>0.3 MeV) electrons than the FFF beams in Lipiodol. The difference between FFF and FF beam DEFs was larger for 6× than for 10×. This occurred because the 10× beams contained more high-energy electrons. The PEGs for photoelectric absorption and Compton scattering for the FFF beams were higher than those for the FF beams. The PEG for the photoelectric absorption was higher than that for Compton scattering. FFF beam contained more low-energy photons and it contributed to the dose enhancement. Energy spectra and PEGs are useful for analyzing the mechanisms of dose enhancement. © 2018 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.
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Clark, Katy M.; Li, Ming; Zhu, Bingquan; Liang, Furong; Shao, Jie; Zhang, Yueyang; Ji, Chai; Zhao, Zhengyan; Kaciroti, Niko; Lozoff, Betsy
2016-01-01
Objective To assess associations between breastfeeding and iron status at 9 months in two samples of Chinese infants. Study design Associations between feeding at 9 months (breastfed [BF] as sole milk source, mixed-fed [MF], or formula-fed [FF]) and iron deficiency anemia (IDA), iron deficiency (ID), and iron sufficiency were determined in infants from Zhejiang and Hebei provinces (ns = 142 and 813). ID was defined as body iron < 0 mg/kg, IDA as ID + hemoglobin < 110 g/L. Multiple logistic regression assessed associations between feeding pattern and iron status. Results Breastfeeding was associated with iron status (P-values < .001). In Zhejiang, 27.5% of BF infants had IDA compared with 0% of FF infants. The odds of ID/IDA were increased in BF and MF infants compared with FF: BF vs. FF odds ratio (OR): 28.8, 95% CI: 3.7–226.4; MF vs. FF OR: 11.0, 95% CI: 1.2–103.2. In Hebei, 44.0% of BF infants had IDA compared with 2.8% of FF infants. With covariable adjustment, odds of IDA were increased in BF and MF groups: BF vs. FF OR: 78.8, 95% CI: 27.2–228.1; MF vs. FF OR: 21.0, 95% CI: 7.3–60.9. Conclusions In both cohorts, the odds of ID/IDA at 9 months were increased in BF and MF infants, and ID/IDA was common. Although the benefits of breastfeeding are indisputable, these findings add to the evidence that breastfeeding in later infancy identifies infants at risk for ID/IDA in many settings. Protocols for detecting and preventing ID/IDA in BF infants are needed. Trial registration ClinicalTrials.gov: NCT00642863 and NCT00613717 PMID:27836288
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Chimote, Natachandra M; Nath, Nirmalendu M; Chimote, Nishad N; Chimote, Bindu N
2015-01-01
To investigate if the level of dehydroepiandrosterone sulfate (DHEA-s) in follicular fluid (FF) influences the competence of oocytes to fertilize, develop to the blastocyst stage, and produce a viable pregnancy in conventional in vitro fertilization (IVF) cycles. Prospective study of age-matched, nonpolycystic ovary syndrome (PCOS) women undergoing antagonist stimulation protocol involving conventional insemination and day 5 blastocyst transfer. FF levels of DHEA-s and E2 were measured by a radio-immuno-assay method using diagnostic kits. Fertilization rate, embryo development to the blastocyst stage and live birth rate were main outcome measures. Cycles were divided into pregnant/nonpregnant groups and also into low/medium/high FF DHEA-s groups. Statistical analysis was done by GraphPad Prism V software. FF DHEA-s levels were significantly higher in pregnant (n = 111) compared to nonpregnant (n = 381) group (1599 ± 77.45 vs. 1372 ± 40.47 ng/ml; P = 0.01). High (n = 134) FF DHEA-s group had significantly higher percentage of metaphase II (MII) oocytes (91.5 vs. 85.54 vs. 79.44%, P < 0.0001), fertilization rate (78.86 vs. 74.16 vs. 71.26%, P < 0.0001), cleavage rate (83.67 vs. 69.1 vs. 66.17%, P = 0.0002), blastocyst formation rate (37.15 vs. 33.01 vs. 26.95%, P < 0.0001), and live birth rate (29.85 vs. 22.22 vs. 14.78%, P = 0.017) compared to medium (n = 243) and low (n = 115) FF DHEA-s groups, respectively despite comparable number of oocytes retrieved and number of blastocysts transferred. FF DHEA-s levels correlated significantly with the attainment of MII oocytes (Pearson r = 0.41) and fertilization rates (Pearson r = 0.35). FF DHEA-s level influences the oocyte maturation process and is predictive of fertilization, embryo development to the blastocyst stage and live birth rates in non-PCOS women undergoing conventional IVF cycles.
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Lundström, Elin; Strand, Robin; Johansson, Lars; Bergsten, Peter; Ahlström, Håkan; Kullberg, Joel
2015-01-01
Objectives To evaluate whether a water-fat magnetic resonance imaging (MRI) cooling-reheating protocol could be used to detect changes in lipid content and perfusion in the main human brown adipose tissue (BAT) depot after a three-hour long mild cold exposure. Materials and Methods Nine volunteers were investigated with chemical-shift-encoded water-fat MRI at baseline, after a three-hour long cold exposure and after subsequent short reheating. Changes in fat fraction (FF) and R2*, related to ambient temperature, were quantified within cervical-supraclavicular adipose tissue (considered as suspected BAT, denoted sBAT) after semi-automatic segmentation. In addition, FF and R2* were quantified fully automatically in subcutaneous adipose tissue (not considered as suspected BAT, denoted SAT) for comparison. By assuming different time scales for the regulation of lipid turnover and perfusion in BAT, the changes were determined as resulting from either altered absolute fat content (lipid-related) or altered absolute water content (perfusion-related). Results sBAT-FF decreased after cold exposure (mean change in percentage points = -1.94 pp, P = 0.021) whereas no change was observed in SAT-FF (mean = 0.23 pp, P = 0.314). sBAT-R2* tended to increase (mean = 0.65 s-1, P = 0.051) and SAT-R2* increased (mean = 0.40 s-1, P = 0.038) after cold exposure. sBAT-FF remained decreased after reheating (mean = -1.92 pp, P = 0.008, compared to baseline) whereas SAT-FF decreased (mean = -0.79 pp, P = 0.008, compared to after cold exposure). Conclusions The sustained low sBAT-FF after reheating suggests lipid consumption, rather than altered perfusion, as the main cause to the decreased sBAT-FF. The results obtained demonstrate the use of the cooling-reheating protocol for detecting changes in the cervical-supraclavicular fat depot, being the main human brown adipose tissue depot, in terms of lipid content and perfusion. PMID:25928226
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Carve, Megan; Coggan, Timothy L; Myers, Jackie H; Clarke, Bradley; Nugegoda, Dayanthi; Shimeta, Jeff
2018-02-01
The herbicide Fusilade Forte ® (FF) is widely applied in agricultural weed management and in the management of the invasive saltmarsh grass, Spartina anglica (ricegrass or cordgrass). FF (active ingredient fluazifop-P acid, FPA) is selective for poaceous grasses. Its primary mode of action is inhibition of the acetyl coenzyme-A carboxylase (ACCase) specific to this taxonomic group, and its secondary mode is by promotion of oxidative stress. FF is applied to S. anglica infestations in the intertidal zone, in proximity to seagrass meadows. Despite the potential for vital seagrass ecosystems to be exposed to FF, there is limited knowledge of any potential impacts. We investigated impacts of FPA on the endemic Australian seagrass, Zostera nigricaulis, measuring ACCase activity and parameters that reflect oxidative stress: photosynthetic performance, lipid peroxidation and photosynthetic pigment content. Seagrass was exposed to FF (0.01-10mgL -1 FPA and a control) for 7d, followed by a 7-d recovery in uncontaminated seawater. An enzyme assay demonstrated that FPA ≤10mgL -1 did not inhibit the activity of ACCase isolated from Z. nigricaulis, demonstrating that this seagrass is resistant to FF's primary mode of action. However, physiological impacts occurred following 7 days exposure to ≥0.1mgL -1 FPA, including up to a 72% reduction in photosynthetic pigment concentration. After 7-d recovery, photosynthetic pigment content improved in treatment plants; however, treated plants exhibited higher levels of lipid peroxidation. This study demonstrates that while Z. nigricaulis is resistant to FF's primary mode of action, significant physiological impacts occur following 7 days exposure to ≥0.1mgL -1 FPA. This study provides valuable information on the effects of FF on a non-target species that can better inform approaches to Spartina management in coastal seagrass ecosystems. Copyright © 2017 Elsevier B.V. All rights reserved.
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Lundström, Elin; Strand, Robin; Johansson, Lars; Bergsten, Peter; Ahlström, Håkan; Kullberg, Joel
2015-01-01
To evaluate whether a water-fat magnetic resonance imaging (MRI) cooling-reheating protocol could be used to detect changes in lipid content and perfusion in the main human brown adipose tissue (BAT) depot after a three-hour long mild cold exposure. Nine volunteers were investigated with chemical-shift-encoded water-fat MRI at baseline, after a three-hour long cold exposure and after subsequent short reheating. Changes in fat fraction (FF) and R2*, related to ambient temperature, were quantified within cervical-supraclavicular adipose tissue (considered as suspected BAT, denoted sBAT) after semi-automatic segmentation. In addition, FF and R2* were quantified fully automatically in subcutaneous adipose tissue (not considered as suspected BAT, denoted SAT) for comparison. By assuming different time scales for the regulation of lipid turnover and perfusion in BAT, the changes were determined as resulting from either altered absolute fat content (lipid-related) or altered absolute water content (perfusion-related). sBAT-FF decreased after cold exposure (mean change in percentage points = -1.94 pp, P = 0.021) whereas no change was observed in SAT-FF (mean = 0.23 pp, P = 0.314). sBAT-R2* tended to increase (mean = 0.65 s-1, P = 0.051) and SAT-R2* increased (mean = 0.40 s-1, P = 0.038) after cold exposure. sBAT-FF remained decreased after reheating (mean = -1.92 pp, P = 0.008, compared to baseline) whereas SAT-FF decreased (mean = -0.79 pp, P = 0.008, compared to after cold exposure). The sustained low sBAT-FF after reheating suggests lipid consumption, rather than altered perfusion, as the main cause to the decreased sBAT-FF. The results obtained demonstrate the use of the cooling-reheating protocol for detecting changes in the cervical-supraclavicular fat depot, being the main human brown adipose tissue depot, in terms of lipid content and perfusion.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Barbiero, Sara; Specialty School in Medical Physics, University of Pisa, Pisa; Rink, Alexandra
2016-01-01
Purpose: To report on single-fraction stereotactic body radiotherapy (RT) (SBRT) with flattening filter (FF)–free (FFF) volumetric modulated arc therapy (VMAT) for lung cancer and to compare dosimetric results with VMAT with FF. Methods and materials: Overall, 25 patients were treated with 6-MV FFF VMAT (Varian TrueBeam STx LINAC) to a prescribed dose of 24 Gy in a single fraction. Treatment plans were recreated using FF VMAT. Dose-volume indices, monitor units (MU), and treatment times were compared between FFF and FF VMAT techniques. Results: Dose constraints to PTV, spinal cord, and lungs were reached in FFF and FF plans. In FFFmore » plans, average conformity index was 1.13 (95% CI: 1.07 to1.38). Maximum doses to spinal cord, heart, esophagus, and trachea were 2.9 Gy (95% CI: 0.4 to 6.7 Gy), 0.8 Gy (95% CI: 0 to 3.6 Gy), 3.3 Gy (95% CI: 0.02 to 13.9 Gy), and 1.5 Gy (95% CI: 0 to 4.9 Gy), respectively. Average V7 Gy, V7.4 Gy, and mean dose to the healthy lung were 126.5 cc (95% CI: 41.3 to 248.9 cc), 107.3 cc (95% CI: 18.7 to 232.8 cc), and 1.1 Gy (95% CI: 0.3 to 2.2 Gy), respectively. No statistically significant differences were found in dosimetric results and MU between FF and FFF treatments. Treatment time was reduced by an average factor of 2.31 (95% CI: 2.15 to 2.43) from FF treatments to FFF, and the difference was statistically significant. Conclusions: FFF VMAT for lung SBRT provides equivalent dosimetric results to the target and organs at risk as FF VMAT while significantly reducing treatment time.« less
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Cohen, Itay; Kayode, Olumide; Hockla, Alexandra; Sankaran, Banumathi; Radisky, Derek C; Radisky, Evette S; Papo, Niv
2016-05-15
Engineered protein therapeutics offer advantages, including strong target affinity, selectivity and low toxicity, but like natural proteins can be susceptible to proteolytic degradation, thereby limiting their effectiveness. A compelling therapeutic target is mesotrypsin, a protease up-regulated with tumour progression, associated with poor prognosis, and implicated in tumour growth and progression of many cancers. However, with its unique capability for cleavage and inactivation of proteinaceous inhibitors, mesotrypsin presents a formidable challenge to the development of biological inhibitors. We used a powerful yeast display platform for directed evolution, employing a novel multi-modal library screening strategy, to engineer the human amyloid precursor protein Kunitz protease inhibitor domain (APPI) simultaneously for increased proteolytic stability, stronger binding affinity and improved selectivity for mesotrypsin inhibition. We identified a triple mutant APPIM17G/I18F/F34V, with a mesotrypsin inhibition constant (Ki) of 89 pM, as the strongest mesotrypsin inhibitor yet reported; this variant displays 1459-fold improved affinity, up to 350 000-fold greater specificity and 83-fold improved proteolytic stability compared with wild-type APPI. We demonstrated that APPIM17G/I18F/F34V acts as a functional inhibitor in cell-based models of mesotrypsin-dependent prostate cancer cellular invasiveness. Additionally, by solving the crystal structure of the APPIM17G/I18F/F34V-mesotrypsin complex, we obtained new insights into the structural and mechanistic basis for improved binding and proteolytic resistance. Our study identifies a promising mesotrypsin inhibitor as a starting point for development of anticancer protein therapeutics and establishes proof-of-principle for a novel library screening approach that will be widely applicable for simultaneously evolving proteolytic stability in tandem with desired functionality for diverse protein scaffolds. © 2016 Authors; published by Portland Press Limited.
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Cu(In,Ga)Se2 Solar Cells with Amorphous In2O3-Based Front Contact Layers.
Koida, Takashi; Ueno, Yuko; Nishinaga, Jiro; Higuchi, Hirohumi; Takahashi, Hideki; Iioka, Masayuki; Shibata, Hajime; Niki, Shigeru
2017-09-06
Amorphous (a-) In 2 O 3 -based front contact layers composed of transparent conducting oxide (TCO) and transparent oxide semiconductor (TOS) layers were proved to be effective in enhancing the short-circuit current density (J sc ) of Cu(In,Ga)Se 2 (CIGS) solar cells with a glass/Mo/CIGS/CdS/TOS/TCO structure, while maintaining high fill factor (FF) and open-circuit voltage (V oc ). An n-type a-In-Ga-Zn-O layer was introduced between the CdS and TCO layers. Unlike unintentionally doped ZnO broadly used as TOS layers in CIGS solar cells, the grain-boundary(GB)-free amorphous structure of the a-In-Ga-Zn-O layers allowed high electron mobility with superior control over the carrier density (N). High FF and V oc values were achieved in solar cells containing a-In-Ga-Zn-O layers with N values broadly ranging from 2 × 10 15 to 3 × 10 18 cm -3 . The decrease in FF and V oc produced by the electronic inhomogeneity of solar cells was mitigated by controlling the series resistance within the TOS layer of CIGS solar cells. In addition, a-In 2 O 3 :H and a-In-Zn-O layers exhibited higher electron mobilities than the ZnO:Al layers conventionally used as TCO layers in CIGS solar cells. The In 2 O 3 -based layers exhibited lower free carrier absorption while maintaining similar sheet resistance than ZnO:Al. The TCO and TOS materials and their combinations did not significantly change the V oc of the CIGS solar cells and the mini-modules.
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Petit, Valérie; Sandoz, Laurence; Garcia-Rodenas, Clara L
2017-06-01
Gastrointestinal tolerance and fat and calcium (Ca) absorption are different between breast-fed (BF) and formula-fed (FF) infants. Certain components and/or structural particularities in human milk (HM), can contribute to favorable outcomes in BF infants. In HM, the long-chain saturated fatty acid (LCSFA) palmitic acid has a different stereospecific distribution (sn-2 position) compared to most infant formula (IF) (primarily sn-1, 3 positions), which may contribute to unfavorable outcomes. Evidence suggests palmitic acid is important in the formation of stool FA-mineral (or FA-Ca) soaps, associated with harder stools in FF infants. Partial replacement by structured palmitic acid-rich triacylglycerols (TAGs) promotes palmitic acid absorption. However, evidence for stool softening, improved fat absorption and reduced Ca excretion in stools is inconsistent. IFs with less palmitic acid can improve fat and Ca absorption, and stool consistency. The presence of other LCSFAs (myristic and stearic acids) in sn-1, 3 positions may also contribute to reduced absorption of fat and Ca, and stool hardness, in FF infants. Nevertheless, little attention has been given to modifying these other LCSFAs in IF. We review literature comparing the effect of HM and IF with different lipid compositions on stool patterns and/or fat and Ca absorption in healthy, term infants. Based on available data, we estimate a maximum level for sn-1, 3 LCSFAs of 13% of TAGs, under which fat and Ca absorption and stool consistency are improved. IF designed according to this threshold could efficiently improve nutrient absorption and stool patterns in healthy infants who cannot be breast-fed. Copyright © 2017 Elsevier Ltd. All rights reserved.
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40 CFR 141.202 - Tier 1 Public Notice-Form, manner, and frequency of notice.
Code of Federal Regulations, 2012 CFR
2012-07-01
...) Detection of E. coli, enterococci, or coliphage in source water samples as specified in § 141.402(a) and... (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Public Notification of Drinking Water Violations § 141.202 Tier 1 Public Notice—Form, manner, and frequency of notice. (a) Which...
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Removal of micro-organisms in a small-scale hydroponics wastewater treatment system.
Ottoson, J; Norström, A; Dalhammar, G
2005-01-01
To measure the microbial removal capacity of a small-scale hydroponics wastewater treatment plant. Paired samples were taken from untreated, partly-treated and treated wastewater and analysed for faecal microbial indicators, i.e. coliforms, Escherichia coli, enterococci, Clostridium perfringens spores and somatic coliphages, by culture based methods. Escherichia coli was never detected in effluent water after >5.8-log removal. Enterococci, coliforms, spores and coliphages were removed by 4.5, 4.1, 2.3 and 2.5 log respectively. Most of the removal (60-87%) took place in the latter part of the system because of settling, normal inactivation (retention time 12.7 d) and sand filtration. Time-dependent log-linear removal was shown for spores (k = -0.17 log d(-1), r(2) = 0.99). Hydroponics wastewater treatment removed micro-organisms satisfactorily. Investigations on the microbial removal capacity of hydroponics have only been performed for bacterial indicators. In this study it has been shown that virus and (oo)cyst process indicators were removed and that hydroponics can be an alternative to conventional wastewater treatment.
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Gaudin, O G; Meley, B; Chomel, J J; Viac, J
1976-01-01
A survey was carried out from March 1972 to February 1973 to identify viral flora found in the river Furan ater St. Etienne. The 54 samples examined revealed the following data: 1) more accurate results are obtained when viral concentration values are expressed in terms of m3/sec., taking into account the flow of the river and eliminating the seasonal dilution factor; 2) rates of enteroviruses remain constant throughout the year, in spite of a relatively rapid spontaneous inactivation of the viruses; 3) rates of coliphages vary considerably according to seasons, with a notable increase in summer; 4) the two previous data are unrelated; 5) 147 enterovirus strains were isolated, of which 44% were polioviruses; 6) virulent and attenuated types 2 and 3 polioviruses were found simultaneously at certain periods; 7) only virulent strains of type 1 poliovirus were isolated; 8) this type of survey may be useful in controlling the endemic residual poliomyelitis in the region of St. Etienne.
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Base Structure Annex to Manpower Requirements Report for FY 1985.
1984-01-01
A 04 .I S DEPARTMENT OF DEFENSE BASE STRUCTURE ANNEX Toct 00 Manpower Requirements Report for FY 1985 JANUARY 1984 DTIC ELECTE FEB 2 7 4 >~fB OFFICE...JANUARY 1984 DTIC S ELECTE FEB27 1984 Prepared by Office of the Assistant Secretary of Defense (Manpower, Installations and Logistics) D&MM_ ffA-1ENo...individuals - Intelligence and Camunications 604 Individuals - Airlift/Sealift Forces 605 tndividua~ s - Guard and Reserves 609 Individ&ls - Training
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Ferri FF. Normal pressure hydrocephalus. In: Ferri FF, ed. Ferri's Clinical Advisor 2016 . Philadelphia, PA: Elsevier; 2016:chap 648. Rosenberg GA. Brain edema and disorders of cerebrospinal fluid circulation. ...
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Guilt by Association-Based Discovery of Botnet Footprints
2010-11-01
our fast flux database using our Fast Flux Monitor ( FFM ); a Web service application designed to detect whether a domain exhibits fast flux (FF) or...double flux (DF) behaviour. The primary technical components of FFM include: (1) sensors which perform real-time detection of FF service networks...sensors for our FFM active sensors: (1) FF Activity Index, (2) Footprint Index, and (3) Time To Live (TTL), and (4) Guilt by Association Score. In
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Characterization of pixel sensor designed in 180 nm SOI CMOS technology
NASA Astrophysics Data System (ADS)
Benka, T.; Havranek, M.; Hejtmanek, M.; Jakovenko, J.; Janoska, Z.; Marcisovska, M.; Marcisovsky, M.; Neue, G.; Tomasek, L.; Vrba, V.
2018-01-01
A new type of X-ray imaging Monolithic Active Pixel Sensor (MAPS), X-CHIP-02, was developed using a 180 nm deep submicron Silicon On Insulator (SOI) CMOS commercial technology. Two pixel matrices were integrated into the prototype chip, which differ by the pixel pitch of 50 μm and 100 μm. The X-CHIP-02 contains several test structures, which are useful for characterization of individual blocks. The sensitive part of the pixel integrated in the handle wafer is one of the key structures designed for testing. The purpose of this structure is to determine the capacitance of the sensitive part (diode in the MAPS pixel). The measured capacitance is 2.9 fF for 50 μm pixel pitch and 4.8 fF for 100 μm pixel pitch at -100 V (default operational voltage). This structure was used to measure the IV characteristics of the sensitive diode. In this work, we report on a circuit designed for precise determination of sensor capacitance and IV characteristics of both pixel types with respect to X-ray irradiation. The motivation for measurement of the sensor capacitance was its importance for the design of front-end amplifier circuits. The design of pixel elements, as well as circuit simulation and laboratory measurement techniques are described. The experimental results are of great importance for further development of MAPS sensors in this technology.
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16 CFR 1630.61 - Hide carpets and rugs-alternative washing procedure.
Code of Federal Regulations, 2011 CFR
2011-01-01
... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 1-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...
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16 CFR 1630.61 - Hide carpets and rugs-alternative washing procedure.
Code of Federal Regulations, 2014 CFR
2014-01-01
... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 1-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...
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16 CFR 1630.61 - Hide carpets and rugs-alternative washing procedure.
Code of Federal Regulations, 2012 CFR
2012-01-01
... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 1-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...
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16 CFR 1631.61 - Hide carpets and rugs-alternative washing procedure.
Code of Federal Regulations, 2011 CFR
2011-01-01
... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 2-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...
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16 CFR 1631.61 - Hide carpets and rugs-alternative washing procedure.
Code of Federal Regulations, 2014 CFR
2014-01-01
... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 2-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...
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16 CFR 1631.61 - Hide carpets and rugs-alternative washing procedure.
Code of Federal Regulations, 2012 CFR
2012-01-01
... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 2-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...
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1987-07-01
frozen rockfill dams on permafrost. In Proceedings of Conference on Buildings and Structures on Perma- frost, Noril’sk, Vol. III, p. 137-144. Sukhanov ...Razzorenov, F.F. (1968) Reed, R.E. (1966) Sleptsov, D.N. (1972) Stankevich, lu.N. (1964) Stavrovskll, A.P. (1977) Sukhanov , G.K. et al. (1978) *Thornton
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Bartz, Faith E.; Lickness, Jacquelyn Sunshine; Heredia, Norma; Fabiszewski de Aceituno, Anna; Newman, Kira L.; Hodge, Domonique Watson; Jaykus, Lee-Ann; García, Santos
2017-01-01
ABSTRACT To improve food safety on farms, it is critical to quantify the impact of environmental microbial contamination sources on fresh produce. However, studies are hampered by difficulties achieving study designs with powered sample sizes to elucidate relationships between environmental and produce contamination. Our goal was to quantify, in the agricultural production environment, the relationship between microbial contamination on hands, soil, and water and contamination on fresh produce. In 11 farms and packing facilities in northern Mexico, we applied a matched study design: composite samples (n = 636, equivalent to 11,046 units) of produce rinses were matched to water, soil, and worker hand rinses during two growing seasons. Microbial indicators (coliforms, Escherichia coli, Enterococcus spp., and somatic coliphage) were quantified from composite samples. Statistical measures of association and correlations were calculated through Spearman's correlation, linear regression, and logistic regression models. The concentrations of all microbial indicators were positively correlated between produce and hands (ρ range, 0.41 to 0.75; P < 0.01). When E. coli was present on hands, the handled produce was nine times more likely to contain E. coli (P < 0.05). Similarly, when coliphage was present on hands, the handled produce was eight times more likely to contain coliphage (P < 0.05). There were relatively low concentrations of indicators in soil and water samples, and a few sporadic significant associations were observed between contamination of soil and water and contamination of produce. This methodology provides a foundation for future field studies, and results highlight the need for interventions surrounding farmworker hygiene and sanitation to reduce microbial contamination of farmworkers' hands. IMPORTANCE This study of the relationships between microbes on produce and in the farm environment can be used to support the design of targeted interventions to prevent or reduce microbial contamination of fresh produce with associated reductions in foodborne illness. PMID:28363965
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Bartz, Faith E; Lickness, Jacquelyn Sunshine; Heredia, Norma; Fabiszewski de Aceituno, Anna; Newman, Kira L; Hodge, Domonique Watson; Jaykus, Lee-Ann; García, Santos; Leon, Juan S
2017-06-01
To improve food safety on farms, it is critical to quantify the impact of environmental microbial contamination sources on fresh produce. However, studies are hampered by difficulties achieving study designs with powered sample sizes to elucidate relationships between environmental and produce contamination. Our goal was to quantify, in the agricultural production environment, the relationship between microbial contamination on hands, soil, and water and contamination on fresh produce. In 11 farms and packing facilities in northern Mexico, we applied a matched study design: composite samples ( n = 636, equivalent to 11,046 units) of produce rinses were matched to water, soil, and worker hand rinses during two growing seasons. Microbial indicators (coliforms, Escherichia coli , Enterococcus spp., and somatic coliphage) were quantified from composite samples. Statistical measures of association and correlations were calculated through Spearman's correlation, linear regression, and logistic regression models. The concentrations of all microbial indicators were positively correlated between produce and hands (ρ range, 0.41 to 0.75; P < 0.01). When E. coli was present on hands, the handled produce was nine times more likely to contain E. coli ( P < 0.05). Similarly, when coliphage was present on hands, the handled produce was eight times more likely to contain coliphage ( P < 0.05). There were relatively low concentrations of indicators in soil and water samples, and a few sporadic significant associations were observed between contamination of soil and water and contamination of produce. This methodology provides a foundation for future field studies, and results highlight the need for interventions surrounding farmworker hygiene and sanitation to reduce microbial contamination of farmworkers' hands. IMPORTANCE This study of the relationships between microbes on produce and in the farm environment can be used to support the design of targeted interventions to prevent or reduce microbial contamination of fresh produce with associated reductions in foodborne illness. Copyright © 2017 American Society for Microbiology.
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Meschke, J S; Sobsey, M D
2003-01-01
Norwalk-like viruses (NLVs) are important agents of waterborne illness and have been linked to several groundwater-related outbreaks. The presence of human enteric viruses, in particular the presence of NLVs, is difficult to detect in the environment. Consequently, surrogate organisms are typically used as indicators of viruses from faecal contamination. Whether traditional bacterial indicators are reliable indicators for viral pathogens remains uncertain. Few studies have directly compared mobility and reduction of bacterial indicators (e.g. coliforms, Escherichia coli) and other surrogate indicators (coliphages) with pathogenic human viruses in soil systems. In this study the mobility and comparative reduction of the prototype NLV, Norwalk Virus (NV), was compared to poliovirus 1 (PV1), a bacterial indicator (E coli, EC) and a viral indicator (coliphage MS2) through miniature soil columns. Replicate, 10 cm deep, miniature columns were prepared using three soils representing a range of soil textures (sand, organic muck, and clay). Columns were initially conditioned, then incubated at 10-14 degrees C, dosed twice weekly for 8 weeks with one column pore volume of virus-seeded groundwater per dose, followed by 8 weeks of dosing with one column pore volume per dose of unseeded, simulated rainwater. Columns were allowed to drain after each dosing until an effluent volume equivalent to an applied dose was collected. Column effluents and doses were assayed for all viruses and EC. Rapid mobility with minimal reduction was observed for all organisms in the sand. Similar reductions were observed in organic muck for most organisms but NV showed a greater reduction. No organisms were shown to pass through the clay columns. Elution of viruses, in particular PV1, from the columns was gradual. After cessation of microbe dosing, E. coli was less detectable than viruses in column effluents and, therefore, unreliable as a virus indicator.
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McLaughlin, M.R.; Rose, J.B.
2006-01-01
Traditional fecal coliform bacterial indicators have been found to be severely limited in determining the significance and sources of fecal contamination in ambient waters of tropical and subtropical regions. The bacteriophages that infect Bacteroides fragilis have been suggested as better fecal indicators and at least one type may be human specific. In this study, the phages that infect B. fragilis host RYC2056 (RYC), including phage B56-3, and host ATCC 51477-HSP40 (HSP), including the human specific phage B40-8, were evaluated in the drainage basins of Tampa Bay, 7 samples (n = 62), or 11%, tested positive for the presence of phages infecting the host HSP, whereas 28 samples, or 45%, tested positive using the host RYC. A survival study was also done to compare the persistence of phages B56-3 and B40-8 to MS2 coliphage in seawater at various temperatures. The decay rates for MS2 were 0.239 log 10 d-1 at 10??C, but increased to 0.896 at 20??C and 2.62 log10 d-1 at 30??C. The two B. fragilis phages persisted much longer in the seawater compared to the coliphage and showed little variation between the temperatures. All sewage influents sampled from area wastewater treatment plants contained phages that infected the two B. fragilis hosts at levels from 1.2 ?? 104 to 1.11 ?? 10 5 pfu 100 ml-1 for host RYC and 67 to 350 pfu 100 ml -1 for host HSP. Of the 7 chlorinated effluent samples tested, 3 were positive for the presence of the phage using the host RYC and the phage enrichment method, with levels estimated to be <10 pfu 100 ml-1. No phages were detected using the host HSP in the treated sewage effluent. Coliphages were found in 3 of the 7 effluent samples at a range of 30 to 1.2 ?? 103 pfu 100 ml-1. ?? 2006 Estuarine Research Federation.
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Liu, Na; Yu, Linling; Sun, Yan
2015-07-24
In the previous studies on protein adsorption to poly(ethylenimine) (PEI)-grafted Sepharose FF resins, a critical ionic capacity (600mmol/L) of PEI-Sepharose resins was found for the adsorption of bovine serum albumin (BSA), above which both protein capacity and uptake rate increased drastically. In this work, the influence of counterions on the PEI-Sepharose resin with an ionic capacity of 683mmol/L (FF-PEI-L680) was investigated with sodium salts of SCN(-), Cl(-), HPO4(2-) and SO4(2-). Linear gradient elution, batch adsorption and breakthrough experiments showed that counterion preference, effective pore diffusion coefficient (De) and dynamic binding capacity (DBC) values increased in the order of SCN(-), Cl(-), HPO4(2-) and SO4(2-), while static adsorption capacity decreased in this order. It is considered that higher counterion preference of the ion exchange groups resulted in lower protein binding strength and adsorption capacity, while the De value increased due to the enhanced "chain delivery" effect (a kind of surface diffusion). Besides, the DBC value was mainly dependent on De value. In particular, SO4(2-) was the most favorable counterion for the PEI-Sepharose resin, which gave rise to the highest De value (De/D0=1.17, D0 is protein diffusivity in free solution) and DBC value (118mg/mL at a residence time of 2min). Moreover, the effects of counterions on BSA adsorption to DEAE Sepharose FF and Q Sepharose FF, which were non-grafted resins, were also studied for comparisons. It was found that the counterion preferences of the two non-grafted resins were different from each other and also different from that of FF-PEI-L680. The different counterion preferences were attributed to the differences in the ion-exchange ligand chemistries. In addition, the De values for DEAE Sepharose FF and Q Sepharose FF kept unchanged. The low counterion sensitivity of De values could be interpreted as the lack of "chain delivery" effect for the non-grafted resins. The results indicate that protein adsorption and chromatographic performance with PEI-Sepharose can be improved by proper counterions. For the four counterions tested, SO4(2-) was the most favorable for providing the best adsorption and elution outcomes with FF-PEI-L680. Copyright © 2015 Elsevier B.V. All rights reserved.
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Indrova, E; Dolezel, R; Novakova-Mala, J; Pechova, A; Zavadilova, M; Cech, S
2017-02-01
Acid-base balance is one of the most vigorously regulated variables of the body, including genital organs. Subacute ruminal acidosis is a common disturbance in dairy cows that disturbs several biochemical indices in the blood, cerebrospinal fluid, and urine. The possible negative effects of metabolic acidosis on the follicular fluid (FF) composition and, subsequently, on oocyte quality, are not fully elucidated. This study aimed to evaluate the changes in acid-base balance (ABB) in FF and blood during acute metabolic acidosis in dairy heifers. Ten Holstein heifers were stimulated with FSH in eight decreasing doses at 12-hour intervals (D0-D3). Acidosis was induced by oral administration of sucrose at 9 g/kg of body weight, dissolved in 10 L of warm tap water, at D3. Samples were collected from each cow at 0, 8, 12, 16, 24, 32, 40, and 48 hours after treatment. Samples of FF, obtained by transvaginal follicular aspiration, and peripheral blood were examined for ABB parameters: pH, pCO 2 , pO 2 , HCO 3 - , and base excess (BE). A significant decrease in pH, HCO 3 - , and BE values in the blood, as well as FF, occurred after sucrose treatment. The lowest pH values occurred in blood at 16 hours, and in FF at 24 hours, after treatment (7.30 ± 0.05 and 7.33 ± 0.05, respectively). The lowest HCO 3 - values in blood (18.75 ± 3.2 mmol/L) and FF (18.07 ± 2.84 mmol/L) occurred 24 hours after treatment, as did the lowest BE values (-6.61 ± 3.7 mmol/L and -7.53 ± 3.89 mmol/L, in blood and FF, respectively). Significant correlations for HCO 3 - (r = 0.928), BE (r = 0.946), pH (r = 0.889), and pCO 2 (r = 0.522) existed between blood and FF samples. The results demonstrated that metabolic acute acidosis substantially influences the characteristics of both serum and FF. Copyright © 2016 Elsevier Inc. All rights reserved.
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Scoglio, M E; Grillo, O C; Munaò, F; Di Pietro, A; Squeri, L
1989-01-01
Most pollution of drinking water is caused by inadequacy of the uptake and distribution systems, by insufficient upkeep of the sewage system and by defects or breaks in the disinfection processes. This may be the cause of waterborne epidemic outbreaks and therefore it is necessary carry out routine controls by simple and rapid tests for the detection of intestinal organisms. In the light of minor hepatitis A epidemics occurred in the town of Messina, we have carried out a study to determine the drinking water quality. To this end, in addition to the traditional tests recommended by CEE and required by the 8/2/1985 DPCM (37 degrees C and 20 degrees C viable count, total and faecal coliforms and faecal streptococci), we have carried out P. aeruginosa, coliphages and gram-negative endotoxins tests, in 74 water samples drawn on way in and way out of the tanks and along the piping system. Only 12.5% of the sixteen water samples drawn on way in (before disinfection system) was in compliance with the law. 75% of these samples showed positivity for faecal streptococci. The water quality was lower in the fourteen water samples drawn on way out of the tanks (7.1% was in compliance with the law). The percent of positivity along the piping system for total and faecal coliforms and for faecal streptococci was 34.1, 15.9 and 59.1 respectively. Coliphages were always absent. P. aeruginosa was almost always present in way in water (93.7%). Moreover this microorganism was recovered in 85.7% of the samples drawn on the way out and in 77.3% along the piping system. In the same drawing places endotoxins were present at high percentage (100%, 85.7% and 90.9%). These values come from high test sensitivity and poor water quality. Finally we have pointed out the importance of all the parameters examined. The significance of coliform bacteria is known, but we consider very important, as organisms indicative of pollution, the enterococci, since they P. aeruginosa may survive long time in fresh water though it is not autoctone, but, in general, of faecal origin. Several soluble antigens of this microorganism as well as enterococci show positive LAL tests (1-5-6). The endotoxin content in fresh water reflects the degree of bacterial contamination. We believe, therefore, it is needed to fix an upper limit to endotoxins in drinking water. Coliphages concentrations could be correlated with enteric virus concentrations but the ratio of coliforms to coliphages is about 100:1. Therefore this indicator of viral pollution is helpful only for highly polluted surface waters.
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Atmospheric measurement of point source fossil fuel CO2 emissions
NASA Astrophysics Data System (ADS)
Turnbull, J. C.; Keller, E. D.; Baisden, W. T.; Brailsford, G.; Bromley, T.; Norris, M.; Zondervan, A.
2013-11-01
We use the Kapuni Gas Treatment Plant to examine methodologies for atmospheric monitoring of point source fossil fuel CO2 (CO2ff) emissions. The Kapuni plant, located in rural New Zealand, removes CO2 from locally extracted natural gas and vents that CO2 to the atmosphere, at a rate of ~0.1 Tg carbon per year. The plant is located in a rural dairy farming area, with no other significant CO2ff sources nearby, but large, diurnally varying, biospheric CO2 fluxes from the surrounding highly productive agricultural grassland. We made flask measurements of CO2 and 14CO2 (from which we derive the CO2ff component) and in situ measurements of CO2 downwind of the Kapuni plant, using a Helikite to sample transects across the emission plume from the surface up to 100 m a.g.l. We also determined the surface CO2ff content averaged over several weeks from the 14CO2 content of grass samples collected from the surrounding area. We use the WindTrax plume dispersion model to compare the atmospheric observations with the emissions reported by the Kapuni plant, and to determine how well atmospheric measurements can constrain the emissions. The model has difficulty accurately capturing the fluctuations and short-term variability in the Helikite samples, but does quite well in representing the observed CO2ff in 15 min averaged surface flask samples and in ~1 week integrated CO2ff averages from grass samples. In this pilot study, we found that using grass samples, the modeled and observed CO2ff emissions averaged over one week agreed to within 30%. The results imply that greater verification accuracy may be achieved by including more detailed meteorological observations and refining 14CO2 sampling strategies.
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Atmospheric measurement of point source fossil CO2 emissions
NASA Astrophysics Data System (ADS)
Turnbull, J. C.; Keller, E. D.; Baisden, T.; Brailsford, G.; Bromley, T.; Norris, M.; Zondervan, A.
2014-05-01
We use the Kapuni Gas Treatment Plant to examine methodologies for atmospheric monitoring of point source fossil fuel CO2 (CO2ff) emissions. The Kapuni plant, located in rural New Zealand, removes CO2 from locally extracted natural gas and vents that CO2 to the atmosphere, at a rate of ~0.1 Tg carbon per year. The plant is located in a rural dairy farming area, with no other significant CO2ff sources nearby, but large, diurnally varying, biospheric CO2 fluxes from the surrounding highly productive agricultural grassland. We made flask measurements of CO2 and 14CO2 (from which we derive the CO2ff component) and in situ measurements of CO2 downwind of the Kapuni plant, using a Helikite to sample transects across the emission plume from the surface up to 100 m above ground level. We also determined the surface CO2ff content averaged over several weeks from the 14C content of grass samples collected from the surrounding area. We use the WindTrax plume dispersion model to compare the atmospheric observations with the emissions reported by the Kapuni plant, and to determine how well atmospheric measurements can constrain the emissions. The model has difficulty accurately capturing the fluctuations and short-term variability in the Helikite samples, but does quite well in representing the observed CO2ff in 15 min averaged surface flask samples and in ~ one week integrated CO2ff averages from grass samples. In this pilot study, we found that using grass samples, the modeled and observed CO2ff emissions averaged over one week agreed to within 30%. The results imply that greater verification accuracy may be achieved by including more detailed meteorological observations and refining 14C sampling strategies.
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Human Brown Adipose Tissue Temperature and Fat Fraction Are Related to Its Metabolic Activity.
Koskensalo, Kalle; Raiko, Juho; Saari, Teemu; Saunavaara, Virva; Eskola, Olli; Nuutila, Pirjo; Saunavaara, Jani; Parkkola, Riitta; Virtanen, Kirsi A
2017-04-01
The metabolic activity of human brown adipose tissue (BAT) has been previously examined using positron emission tomography (PET). The aim of this study was to use proton magnetic resonance spectroscopy (1H MRS) to investigate whether the temperature and the fat fraction (FF) of BAT and white adipose tissue (WAT) are associated with BAT metabolic activity determined by deoxy-2-18F-fluoro-d-glucose (18F-FDG)-PET. Ten healthy subjects (four women, six men; 25 to 45 years of age) were studied using PET-magnetic resonance imaging during acute cold exposure and at ambient room temperature. BAT and subcutaneous WAT 1H MRS were measured. The tissue temperature and the FF were derived from the spectra. Tissue metabolic activity was studied through glucose uptake using dynamic FDG PET scanning during cold exposure. A 2-hour hyperinsulinemic euglycemic clamp was performed on eight subjects. The metabolic activity of BAT associated directly with the heat production capacity and inversely with the FF of the tissue. In addition, the lipid-burning capacity of BAT associated with whole-body insulin sensitivity. During cold exposure, the FF of BAT was lower than at room temperature, and cold-induced FF of BAT associated inversely with high-density lipoprotein and directly with low-density lipoprotein cholesterol. Both 1H MRS-derived temperature and FF are promising methods to study BAT activity noninvasively. The association between the lipid-burning capacity of BAT and whole-body insulin sensitivity emphasizes the role of BAT in glucose handling. Furthermore, the relation of FF to high-density lipoprotein and low-density lipoprotein cholesterol suggests that BAT has a role in lipid clearance, thus protecting tissues from excess lipid load. Copyright © 2017 Endocrine Society
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NASA Astrophysics Data System (ADS)
Sahu, L. K.; Kondo, Y.; Moteki, N.; Takegawa, N.; Zhao, Y.; Vay, S. A.; Diskin, G. S.; Wisthaler, A.; Huey, L. G.
2009-12-01
Measurements of black carbon (BC) and other chemical species were made from the NASA DC-8 aircraft during the CARB campaign conducted over California in June 2008. We operated an SP2 system that measured BC and scattering particles. The vertical profiles of BC and scattering particles show enhancements in the lower troposphere. We have used relations of CO-CH3CN-SO2 to identify the sources of major plumes. The plumes originating from anthropogenic activities, mainly due to the use of fossil fuels (FF), were observed near the surface. However, the influence of smoke plumes from wild fire or biomass-burning (BB) sources was observed up to 3 km. Overall, the 1-minute average BC mass concentrations were in the ranges of about 90-500 ng/m3 and 300-700 ng/m3 in FF and BB plumes, respectively. The shell/core diameter ratios were much lagerer in BB plumes than those in FF plumes. Namely, the median shell/core ratios were 1.2-1.4 for FF plumes, while they were 1.4-1.7 for BB plumes. In both FF and BB plumes, the mass-size distributions of BC were single mode lognormal. However, the mass median diameters FF plumes were considerably smaller. The BC-CO2 regression slopes were 19±9 ng m-3/ppmv and 270±90 ng m-3/ppmv for FF and BB plumes, respectively. On the other hand the regression slopes of BC-CO were about 3.3 ng m-3/ppbv in both the plumes. Conversely, the regression slopes of BC with other co-emitted combustions products can be used to estimate the contributions of emissions from different sources.
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Agarwal, Khushbu; Sharma, Uma; Mathur, Sandeep; Seenu, Vurthaluru; Parshad, Rajinder; Jagannathan, Naranamangalam R
2018-06-01
To evaluate the utility of fat fraction (FF) for the differentiation of different breast tissues and in various breast tumor subtypes using in vivo proton ( 1 H) magnetic resonance spectroscopy (MRS). 1 H MRS was performed on 68 malignant, 35 benign, and 30 healthy volunteers at 1.5 T. Malignant breast tissues of patients were characterized into different subtypes based on the differences in the expression of hormone receptors and the FF was calculated. Further, the sensitivity and specificity of FF to differentiate malignant from benign and from normal breast tissues of healthy volunteers was determined using receiver operator curve (ROC) analysis. A significantly lower FF of malignant (median 0.12; range 0.01-0.70) compared to benign lesions (median 0.28; range 0.02-0.71) and normal breast tissue of healthy volunteers (median 0.39; range 0.06-0.76) was observed. No significant difference in FF was seen between benign lesions and normal breast tissues of healthy volunteers. Sensitivity and specificity of 75% and 68.6%, respectively was obtained to differentiate malignant from benign lesions. For the differentiation of malignant from healthy breast tissues, 76% sensitivity and 74.5% specificity was achieved. Higher FF was seen in patients with ER-/PR- status as compared to ER+/PR+ patients. Similarly, FF of HER2neu+ tumors were significantly higher than in HER2neu- breast tumors. The results showed the potential of in vivo 1 H MRS in providing insight into the changes in the fat content of different types of breast tissues and in various breast tumor subtypes. Copyright © 2018 Elsevier Inc. All rights reserved.
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Leemans, Bart; Gadella, Bart M; Stout, Tom A E; Nelis, Hilde; Hoogewijs, Maarten; Van Soom, Ann
2015-09-01
Induction of hyperactivated motility is considered essential for triggering the release of oviduct-bound mammalian spermatozoa in preparation for fertilization. In this study, oviduct-bound stallion spermatozoa were exposed for 2 h to: i) pre-ovulatory and ii) post-ovulatory oviductal fluid; iii) 100% and iv) 10% follicular fluid (FF); v) cumulus cells, vi) mature equine oocytes, vii) capacitating and viii) non-capacitating medium. None of these triggered sperm release or hyperactivated motility. Interestingly, native FF was detrimental to sperm viability, an effect that was negated by heat inactivation, charcoal treatment and 30 kDa filtration alone or in combination. Moreover, sperm suspensions exposed to treated FF at pH 7.9 but not pH 7.4 showed Ca(2+)-dependent hypermotility. Fluo-4 AM staining of sperm showed elevated cytoplasmic Ca(2+) in hyperactivated stallion spermatozoa exposed to treated FF at pH 7.9 compared to a modest response in defined capacitating conditions at pH 7.9 and no response in treated FF at pH 7.4. Moreover, 1 h incubation in alkaline, treated FF induced protein tyrosine phosphorylation in 20% of spermatozoa. None of the conditions tested induced widespread release of sperm pre-bound to oviduct epithelium. However, the hyperactivating conditions did induce release of 70-120 spermatozoa per oviduct explant, of which 48% showed protein tyrosine phosphorylation and all were acrosome-intact, but capable of acrosomal exocytosis in response to calcium ionophore. We conclude that, in the presence of elevated pH and extracellular Ca(2+), a heat-resistant, hydrophilic, <30 kDa component of FF can trigger protein tyrosine phosphorylation, elevated cytoplasmic Ca(2+) and hyperactivated motility in stallion sperm, but infrequent release of sperm pre-bound to oviduct epithelium. © 2015 Society for Reproduction and Fertility.
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Li, Fang; Li, Feng; Zhao, Ting; Mao, Guanghua; Zou, Ye; Zheng, Daheng; Takase, Mohammed; Feng, Weiwei; Wu, Xiangyang; Yang, Liuqing
2013-08-01
The industrial solid wastes generated during the production of silymarin from the fruits of milk thistle Silybum marianum was used as the substrate. Preparation and evaluation of the feeds produced by solid-state fermentation (SSF) of the industrial solid wastes was carried out. The protein content of the fermented feed (FF) from a combination of Aspergillus niger and Candida tropicalis was the highest among the examined strains. The optimal process parameters for protein enrichment with SSF using A. niger and C. tropicalis included incubation temperature of 30.8 °C, fermentation time of 87.0 h, and initial moisture content of 59.7 %. Under these conditions, the value additions of FF occurred. The fiber of FF was decreased by 25.07 %, while the digestibility of protein, protein content, and the ratio of total essential amino acids to total amino acids were increased by 79.85, 16.22, and 8.21 %, respectively. The analysis indicated that FF contained 1.44 mg/kg flavonoids and 0.5 mg/kg silybin, which significantly increased by 2.42 and 1.63 times, respectively than those in unfermented substrates. FF recorded reduced molecular weight of proteins from 20.1 to 44.3 kDa to below 14.3 kDa. The results of feeding trial of FF replacement with soybean meal in broilers diets for 8 weeks showed that FF significantly improved carcass characteristics including abdominal fat rate, serum biochemical parameters including aspartate transaminase, blood urea nitrogen and high density lipoprotein cholesterol, and immune responses of broilers. A potential feed quality improvement was achieved through mixed strains SSF of industrial solid wastes of S. marianum fruits.
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Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.
Zheng, Mo; Li, Xiaoxia; Guo, Li
2013-04-01
Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. Copyright © 2013 Elsevier Inc. All rights reserved.
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Differences in Postprandial Lipid Response to Breast- or Formula-feeding in 8-Week-Old Infants.
Teller, Inga C; Schoen, Stefanie; van de Heijning, Bert; van der Beek, Eline M; Sauer, Pieter J J
2017-04-01
Lipids play important roles in infant growth and development. In this exploratory observational single-center study, we investigated postmeal responses of infants to dietary lipids and differences between breast-feeding (BF) and formula-feeding (FF). Two capillary blood samples were collected from each subject, before and randomly assigned at either 30, 60, 90, 120, 180, or 240 minutes after their respective feeding, followed by measurement of lipid-related plasma parameter concentrations using enzyme-linked immunosorbent assay-based or combined enzymatic and colorimetric methods. The intermeal interval before testing was shorter in the BF (182.91 ± 22.85 minutes, n = 33) versus FF group (214.1 ± 30.76 minutes, n = 34); BF subjects fed 5 minutes longer (BF 20.27 ± 7.7 minutes; FF 14.82 ± 3.57 minutes). Composite postmeal concentration profiles were generated from 59 plasma sample pairs with sufficient volume (BF = 30): triglyceride (TG) baselines were not different. A TG difference was indicated for BF over FF subjects at 30 minutes, for FF over BF subjects at 60 minutes when corrected for baseline. TG responses in both groups appeared and seemed to clear much faster than those reported for adults. The TG:apolipoprotein B48 (ApoB48) ratio suggests that chylomicrons in BF subjects may carry a higher fat load (P < 0.05), compensated by a higher chylomicron number in FF subjects (P < 0.05). Cholesterol in BF subjects was higher and showed an increase after feeding when corrected for baseline. Our results indicate that lipids from either BF or FF may be handled differently in young healthy infants.
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Isolated free intra-abdominal fluid on CT in blunt trauma: The continued diagnostic dilemma.
Kong, Victor Y; Jeetoo, Damon; Naidoo, Leah C; Oosthuizen, George V; Clarke, Damian L
2015-01-01
The clinical significance of isolated free fluid (FF) without solid organ injury on computed to- mography (CT) continues to pose significant dilemma in the management of patients with blunt abdominal trauma (BAT). We reviewed the incidence of FF and the clinical outcome amongst patients with blunt abdominal trauma in a metropolitan trauma service in South Africa. We performed a retrospective study of 121 consecutive CT scans over a period of 12 months to determine the incidence of isolated FF and the clinical outcome of patients managed in a large metropolitan trauma service. Of the 121 CTs, FF was identified in 36 patients (30%). Seven patients (6%) had isolated FF. Of the 29 patients who had free fluid and associated organ injuries, 33 organ injuries were identified. 86% (25/ 29) of all 29 patients had a single organ injury and 14% had multiple organ injuries. There were 26 solid organ injuries and 7 hollow organ injuries. The 33 organs injured were: spleen, 12; liver, 8; kidney, 5; pancreas, 2; small bowel, 4; duodenum, 1. Six (21%) patients required operative management for small bowel perforations in 4 cases and pancreatic tail injury in 2 cases. All 7 patients with isolated FF were initially observed, and 3 (43%) were eventually subjected to operative intervention. They were found to have an intra-peritoneal bladder rupture in 1 case, a non-expanding zone 3 haematoma in 1 case, and a negative laparotomy in 1 case. Four (57%) patients were successfully managed without surgical interventions. Isolated FF is uncommon and the clinical significance remains unclear. Provided that reli- able serial physical examination can be performed by experienced surgeons, an initial non-operative approach should be considered.
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2011-05-04
pubs.acs.org/JPCB Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics Si-ping Han,†,‡ Adri C. T. van...ABSTRACT: We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH3NO2) using molec- ular dynamics...with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000
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Chattopadhyay, Tanay
2010-10-01
A flip-flop (FF) is a kind of latch and the simplest form of memory device, which stores various values either temporarily or permanently. Optical FF memories form a fundamental building block for all-optical packet switches in next-generation communication networks. An all-optical clocked delay FF using a single terahertz optical asymmetric demultiplexer-based interferometric switch is proposed and described. Numerical simulation results are also reported.
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Vegetation limits the impact of a warm climate on boreal wildfires.
Girardin, Martin P; Ali, Adam A; Carcaillet, Christopher; Blarquez, Olivier; Hély, Christelle; Terrier, Aurélie; Genries, Aurélie; Bergeron, Yves
2013-09-01
Strategic introduction of less flammable broadleaf vegetation into landscapes was suggested as a management strategy for decreasing the risk of boreal wildfires projected under climatic change. However, the realization and strength of this offsetting effect in an actual environment remain to be demonstrated. Here we combined paleoecological data, global climate models and wildfire modelling to assess regional fire frequency (RegFF, i.e. the number of fires through time) in boreal forests as it relates to tree species composition and climate over millennial time-scales. Lacustrine charcoals from northern landscapes of eastern boreal Canada indicate that RegFF during the mid-Holocene (6000-3000 yr ago) was significantly higher than pre-industrial RegFF (AD c. 1750). In southern landscapes, RegFF was not significantly higher than the pre-industrial RegFF in spite of the declining drought severity. The modelling experiment indicates that the high fire risk brought about by a warmer and drier climate in the south during the mid-Holocene was offset by a higher broadleaf component. Our data highlight an important function for broadleaf vegetation in determining boreal RegFF in a warmer climate. We estimate that its feedback may be large enough to offset the projected climate change impacts on drought conditions. © 2013 Her Majesty the Queen in Right of Canada New Phytologist © 2013 New Phytologist Trust.
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Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts.
Kim, Sung K; Hannum, Gregory; Geis, Jennifer; Tynan, John; Hogg, Grant; Zhao, Chen; Jensen, Taylor J; Mazloom, Amin R; Oeth, Paul; Ehrich, Mathias; van den Boom, Dirk; Deciu, Cosmin
2015-08-01
This study introduces a novel method, referred to as SeqFF, for estimating the fetal DNA fraction in the plasma of pregnant women and to infer the underlying mechanism that allows for such statistical modeling. Autosomal regional read counts from whole-genome massively parallel single-end sequencing of circulating cell-free DNA (ccfDNA) from the plasma of 25 312 pregnant women were used to train a multivariate model. The pretrained model was then applied to 505 pregnant samples to assess the performance of SeqFF against known methodologies for fetal DNA fraction calculations. Pearson's correlation between chromosome Y and SeqFF for pregnancies with male fetuses from two independent cohorts ranged from 0.932 to 0.938. Comparison between a single-nucleotide polymorphism-based approach and SeqFF yielded a Pearson's correlation of 0.921. Paired-end sequencing suggests that shorter ccfDNA, that is, less than 150 bp in length, is nonuniformly distributed across the genome. Regions exhibiting an increased proportion of short ccfDNA, which are more likely of fetal origin, tend to provide more information in the SeqFF calculations. SeqFF is a robust and direct method to determine fetal DNA fraction. Furthermore, the method is applicable to both male and female pregnancies and can greatly improve the accuracy of noninvasive prenatal testing for fetal copy number variation. © 2015 John Wiley & Sons, Ltd.
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Cox, D N; Koster, A; Russell, C G
2004-08-01
The widespread use of dietary supplements and so-called 'functional foods' is thought to be partially motivated by self-control of health. However, whilst consumers want foods associated with well-being or disease prevention, they are unlikely to be willing to compromise on taste or technology. This presents a dilemma for promoters of functional foods. Middle-aged consumers' intentions to consume functional foods or supplements that may improve memory were tested within an adaptation of Protection Motivation theory (PMT). Participants evaluated text descriptions of four products described as: having an unpleasant bitter taste (Natural-FF); having 'additives' to reduce bitterness (Sweetened-FF); being genetically modified to enhance function (GM-FF) and Supplements. Participants were recruited as being of high and low perceived vulnerability to memory failure. In total, 290 middle-aged consumers (aged 40-60 years) participated in the study. Motivations to consume the GM-FF were the lowest. There were gender differences between intention to consume the supplements, Natural-FF and Sweetened-FF and product differences within genders. Women were less favourable than men in their attitudes towards genetic modification in general. Regression analyses indicated that PM predictors of intention to consume functional foods or supplements explained 59-63% of the variance (R2). Overall, perceived 'efficacy' (of the behaviour) and self-efficacy were the most important predictors of intentions to consume.
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Role of vascular endothelial cell growth factor in Ovarian Hyperstimulation Syndrome.
Levin, E R; Rosen, G F; Cassidenti, D L; Yee, B; Meldrum, D; Wisot, A; Pedram, A
1998-01-01
Controlled ovarian hyperstimulation with gonadotropins is followed by Ovarian Hyperstimulation Syndrome (OHSS) in some women. An unidentified capillary permeability factor from the ovary has been implicated, and vascular endothelial cell growth/permeability factor (VEGF) is a candidate protein. Follicular fluids (FF) from 80 women who received hormonal induction for infertility were studied. FFs were grouped according to oocyte production, from group I (0-7 oocytes) through group IV (23-31 oocytes). Group IV was comprised of four women with the most severe symptoms of OHSS. Endothelial cell (EC) permeability induced by the individual FF was highly correlated to oocytes produced (r2 = 0.73, P < 0.001). Group IV FF stimulated a 63+/-4% greater permeability than FF from group I patients (P < 0. 01), reversed 98% by anti-VEGF antibody. Group IV fluids contained the VEGF165 isoform and significantly greater concentrations of VEGF as compared with group I (1,105+/-87 pg/ml vs. 353+/-28 pg/ml, P < 0. 05). Significant cytoskeletal rearrangement of F-actin into stress fibers and a destruction of ZO-1 tight junction protein alignment was caused by group IV FF, mediated in part by nitric oxide. These mechanisms, which lead to increased EC permeability, were reversed by the VEGF antibody. Our results indicate that VEGF is the FF factor responsible for increased vascular permeability, thereby contributing to the pathogenesis of OHSS. PMID:9835623
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Dietz, Carin H J T; Kroon, Maaike C; Di Stefano, Michela; van Sint Annaland, Martin; Gallucci, Fausto
2017-12-14
For the first time, 12 different supported deep eutectic solvent (DES) liquid membranes were prepared and characterized. These membranes consist of a polymeric support impregnated with a hydrophobic DES. First, the different membranes were characterized and their stability in water and air was determined. Subsequently, the supported DES liquid membranes were applied for the recovery of furfural (FF) and hydroxymethylfurfural (HMF) from aqueous solutions. The effects of substrate properties (e.g. pore size), DES properties (e.g. viscosity) and concentrations of FF and HMF in the feed phase on the observed diffusivities and permeabilities were assessed. It was found that the addition of DES enhances the transport of FF and HMF through the polymeric membrane support. In particular, the use of the DES consisting of thymol + lidocaine (in the molar ratio 2 : 1) impregnated in a polyethylene support resulted in enhanced transport for both FF and HMF, and is most interesting for (in situ) isolation of FF and HMF from aqueous solutions, e.g. in biorefinery processes.
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Yun, Kang-Seop; Pai, Sung Jin; Yeo, Byung Chul; Lee, Kwang-Ryeol; Kim, Sun-Jae; Han, Sang Soo
2017-07-06
We propose the ReaxFF reactive force field as a simulation protocol for predicting the evolution of solid-electrolyte interphase (SEI) components such as gases (C 2 H 4 , CO, CO 2 , CH 4 , and C 2 H 6 ), and inorganic (Li 2 CO 3 , Li 2 O, and LiF) and organic (ROLi and ROCO 2 Li: R = -CH 3 or -C 2 H 5 ) products that are generated by the chemical reactions between the anodes and liquid electrolytes. ReaxFF was developed from ab initio results, and a molecular dynamics simulation with ReaxFF realized the prediction of SEI formation under real experimental conditions and with a reasonable computational cost. We report the effects on SEI formation of different kinds of Si anodes (pristine Si and SiO x ), of the different types and compositions of various carbonate electrolytes, and of the additives. From the results, we expect that ReaxFF will be very useful for the development of novel electrolytes or additives and for further advances in Li-ion battery technology.
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The impact of follicular fluid adiponectin and ghrelin levels based on BMI on IVF outcomes in PCOS.
Inal, H A; Yilmaz, N; Gorkem, U; Oruc, A S; Timur, H
2016-04-01
This study aimed at evaluating the effects of polycystic ovary syndrome (PCOS) and body mass index (BMI) on follicular fluid (FF) adiponectin and ghrelin levels, and on in vitro fertilization outcomes in patients who underwent controlled ovarian hyperstimulation. This prospective cross-sectional study was performed with a total of 120 primary infertile women [group 1; non-PCOS = 60 (BMI <25 = 30, BMI ≥25 = 30) and group 2; PCOS = 60 (BMI <25 = 30, BMI ≥25 = 30)]. On the day of oocyte pickup, FF samples were collected. The FF adiponectin levels were lower in the lean PCOS group than the lean non-PCOS group (p = 0.001), and these levels were lower in the overweight non-PCOS group compared to lean non-PCOS group (0.001). However, there was no difference in the FF ghrelin levels between the groups. Additionally, we could not find a relationship between clinical pregnancy and adiponectin and ghrelin levels. The FF adiponectin and ghrelin levels have no effects on clinical pregnancy in PCOS. Therefore, further studies are needed to elucidate this issue.
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First High Resolution IR Study of the νb{14} (a') A-Type Band Near 421.847 \\wn of 2-^{13}C-PROPENE
NASA Astrophysics Data System (ADS)
Daunt, S. J.; Grzywacz, Robert; Billinghurst, Brant E.
2017-06-01
This is is the first high resolution IR study of any band of the 2-^{13}C-propene species. There have been only two previous high resolution studies of vibration-rotation bands of the normal species. The band examined here is the νb{14} (A') CCC skeletal bending near 421.847 \\wn which has an A-Type asymmetric rotor structure. The spectra were recorded on the FTS at the Far-IR beamline of the Canadian Light Source with a resolution of Δν = 0.0009 \\wn. We have assigned and fitted around 2200 transitions and determined ground and upper state rotational constants. Lines with J up to 49 and K up to 12 were included. The subbands with K greater than 12 were perturbed and show torsional splittings that vary from small to extremely large. The fitting was done with the PGOPHER program of Colin Western. The GS constants are in good agreement with the MW constants reported recently by Craig, Groner and co-workers. Ainetschian, Fraser, Ortigoso & Pate, J. Chem. Phys. 100, 729 ff. (1994); Lafferty, Flaud & Herman, J. Mol. Struct. 780-781, 65 ff. (2006). Western, J. Quant. Spectrosc. Rad. Transf. 186, 221 ff. (2017). Paper M109, 71st ISMS Symposium (2016); J. Mol. Spectrosc. 328, 1-6 (2016).
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Zhang, Tao; Han, Han; Zou, Yunlong; Lee, Ying-Chi; Oshima, Hiroya; Wong, Ken-Tsung; Holmes, Russell J
2017-08-02
We report a promising set of donor-acceptor-acceptor (D-A-A) electron-donor materials based on coplanar thieno[3,2-b]/[2,3-b]indole, benzo[c][1,2,5]thiadiazole, and dicyanovinylene, which are found to show broadband absorption with high extinction coefficients. The role of the regioisomeric electron-donating thienoindole moiety on the physical and structural properties is examined. Bulk heterojunction (BHJ) organic photovoltaic cells (OPVs) based on the thieno[2,3-b]indole-based electron donor NTU-2, using C 70 as an electron acceptor, show a champion power conversion efficiency of 5.2% under AM 1.5G solar simulated illumination. This efficiency is limited by a low fill factor (FF), as has previously been the case in D-A-A systems. In order to identify the origin of the limited FF, further insight into donor layer charge-transport behavior is realized by examining planar heterojunction OPVs, with emphasis on the evolution of film morphology with thermal annealing. Compared to as-deposited OPVs that exhibit insufficient donor crystallinity, crystalline OPVs based on annealed thin films show an increase in the short-circuit current density, FF, and power conversion efficiency. These results suggest that that the crystallization of D-A-A molecules might not be realized spontaneously at room temperature and that further processing is needed to realize efficient charge transport in these materials.
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Follicular Fluid redox involvement for ovarian follicle growth.
Freitas, Cláudia; Neto, Ana Catarina; Matos, Liliana; Silva, Elisabete; Ribeiro, Ângela; Silva-Carvalho, João Luís; Almeida, Henrique
2017-07-12
As the human ovarian follicle enlarges in the course of a regular cycle or following controlled ovarian stimulation, the changes in its structure reveal the oocyte environment composed of cumulus oophorus cells and the follicular fluid (FF).In contrast to the dynamic nature of cells, the fluid compartment appears as a reservoir rich in biomolecules. In some aspects, it is similar to the plasma, but it also exhibits differences that likely relate to its specific localization around the oocyte. The chemical composition indicates that the follicular fluid is able to detect and buffer excessive amounts of reactive oxygen species, employing a variety of antioxidants, some of them components of the intracellular milieu.An important part is played by albumin through specific cysteine residues. But the fluid contains other molecules whose cysteine residues may be involved in sensing and buffering the local oxidative conditions. How these molecules are recruited and regulated to intervene such process is unknown but it is a critical issue in reproduction.In fact, important proteins in the FF, that regulate follicle growth and oocyte quality, exhibit cysteine residues at specific points, whose untoward oxidation would result in functional loss. Therefore, preservation of controlled oxidative conditions in the FF is a requirement for the fine-tuned oocyte maturation process. In contrast, its disturbance enhances the susceptibility to the establishment of reproductive disorders that would require the intervention of reproductive medicine technology.
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Zang, Hongjun; Chen, Eugene Y. X.
2015-01-01
There is increasing interest in the upgrading of C5 furfural (FF) and C6 5-hydroxymethyl furfural (HMF) into C10 and C12 furoins as higher energy-density intermediates for renewable chemicals, materials, and biofuels. This work utilizes the organocatalytic approach, using the in situ generated N,S-heterocyclic carbene catalyst derived from thiazolium ionic liquids (ILs), to achieve highly efficient self-coupling reactions of FF and HMF. Specifically, variations of the thiazolium IL structure have led to the most active and efficient catalyst system of the current series, which is derived from a new thiazolium IL carrying the electron-donating acetate group at the 5-ring position. For FF coupling by this IL (0.1 mol %, 60 °C, 1 h), when combined with Et3N, furoin was obtained in >99% yield. A 97% yield of the C12 furoin was also achieved from the HMF coupling by this catalyst system (10 mol % loading, 120 °C, 3 h). On the other hand, the thiazolium IL bearing the electron-withdrawing group at the 5-ring position is the least active and efficient catalyst. The mechanistic aspects of the coupling reaction by the thiazolium catalyst system have also been examined and a mechanism has been proposed. PMID:25830482
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Variability of visual responses of superior colliculus neurons depends on stimulus velocity.
Mochol, Gabriela; Wójcik, Daniel K; Wypych, Marek; Wróbel, Andrzej; Waleszczyk, Wioletta J
2010-03-03
Visually responding neurons in the superficial, retinorecipient layers of the cat superior colliculus receive input from two primarily parallel information processing channels, Y and W, which is reflected in their velocity response profiles. We quantified the time-dependent variability of responses of these neurons to stimuli moving with different velocities by Fano factor (FF) calculated in discrete time windows. The FF for cells responding to low-velocity stimuli, thus receiving W inputs, increased with the increase in the firing rate. In contrast, the dynamics of activity of the cells responding to fast moving stimuli, processed by Y pathway, correlated negatively with FF whether the response was excitatory or suppressive. These observations were tested against several types of surrogate data. Whereas Poisson description failed to reproduce the variability of all collicular responses, the inclusion of secondary structure to the generating point process recovered most of the observed features of responses to fast moving stimuli. Neither model could reproduce the variability of low-velocity responses, which suggests that, in this case, more complex time dependencies need to be taken into account. Our results indicate that Y and W channels may differ in reliability of responses to visual stimulation. Apart from previously reported morphological and physiological differences of the cells belonging to Y and W channels, this is a new feature distinguishing these two pathways.
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Karadağ, Bergüzar; Yücel, Nilgün Candan
2017-12-01
To elucidate the physiological mechanism of salt stress mitigated by cinnamic acid (CA) and fish flour (FF) pretreatment, wheat was pretreated with 20, 50 and 100 ppm CA and 1 g/10 mL FF for 2 d and was then cultivated. We investigated whether exogenous CA + FF could protect wheat from salt stress and examined whether the protective effect was associated with the regulation of seed vigor, antioxidant defense systems, phenolic biosynthesis and lipid peroxidation. At 2 days exogenous CA did not influence seed vigor. Salt stress increased the phenolic biosynthesis, but the CA + FF-combined pretreatment enhanced the phenolic biosynthesis even more under salt stress and decreased lipid peroxidation to some extent, enhancing the tolerance of wheat to salt stress.
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Development of a Charge-Implicit ReaxFF Potential for Hydrocarbon Systems.
Kański, Michał; Maciążek, Dawid; Postawa, Zbigniew; Ashraf, Chowdhury M; van Duin, Adri C T; Garrison, Barbara J
2018-01-18
Molecular dynamics (MD) simulations continue to make important contributions to understanding chemical and physical processes. Concomitant with the growth of MD simulations is the need to have interaction potentials that both represent the chemistry of the system and are computationally efficient. We propose a modification to the ReaxFF potential for carbon and hydrogen that eliminates the time-consuming charge equilibration, eliminates the acknowledged flaws of the electronegativity equalization method, includes an expanded training set for condensed phases, has a repulsive wall for simulations of energetic particle bombardment, and is compatible with the LAMMPS code. This charge-implicit ReaxFF potential is five times faster than the conventional ReaxFF potential for a simulation of keV particle bombardment with a sample size of over 800 000 atoms.
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Eva, Kevin W; Macala, Catherine
2014-06-01
The multiple mini-interview (MMI), used to facilitate the selection of applicants in health professional programmes, has been shown to be capable of generating reliable data predictive of success. It is a process rather than a single instrument and therefore its psychometric properties can be expected to vary according to the stations generated, the alignment between the stations and the qualities an institution prioritises, and the outcomes used. The purpose of this study was to explore the MMI's test characteristics when station type is manipulated. A 12-station MMI was established in which four stations were presented in three different ways. These included: situational judgement (SJ) stations, in which applicants were asked to imagine what they would do in specific situations; behavioural interview (BI) stations, in which applicants were asked to recall what they did in experienced situations, and free form (FF) stations, which were unstructured in that the examiner was simply given a brief explanation of the intent of the station without further guidance on how to conduct the discussion. Four circuits of the 12 stations were run with one examiner within each station. Candidates and examiners were surveyed regarding their experience. The reliability of the scores derived from the assessment was analysed separately for each station type. A total of 41 medical school candidates participated after completing the regular admission process. Although the score assigned did not differ across station type, BI stations more reliably differentiated between candidates (g = 0.77) than did the other station types (SJ, g = 0.69; FF, g = 0.66). The correlation between actual MMI scores and BI stations was also greatest (BI, r = 0.57; SJ, r = 0.45; FF, r = 0.42). Candidates' opinions indicated that FF stations were more anxiety-provoking, less clear, and more difficult than structured stations (SJ and BI stations). Examiner opinions indicated equivalence on these measures. The results suggest that structuring stations has value, although that value was gained only through the use of BI stations, in which candidates were asked to recall and discuss a specific experience of relevance to the purpose of the interview station. © 2014 John Wiley & Sons Ltd.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Niyogi, S.K.; Mitra, S.
With precise conditions of digestion with single-strand-specific nucleases, namely, endonuclease S1 of Aspergillus oryzae and exonuclease I of Escherichia coli, nuclease-resistant DNA cores can be obtained reproducibly from single-stranded M13 DNA. The DNA cores are composed almost exclusively of two sizes (60 and 44 nucleotides long). These have high (G + C)-contents relative to that of intact M13 DNA, and arise from restricted regions of the M13 genome. The resistance of these fragments to single-strand-specific nucleases and their nondenaturability strongly suggest the presence of double-stranded segments in these core pieces. That the core pieces are only partially double-stranded is shownmore » by their lack of complete base complementarity and their pattern of elution from hydroxyapatite.« less
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A complete method, incorporating recently improved reverse transcriptase-PCR primer/probe assays and including controls for determining interferences to phage recoveries from water sample concentrates and for detecting interferences to their analysis, was developed for the direct...
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40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.
Code of Federal Regulations, 2011 CFR
2011-07-01
... approves the use of E. coli as a fecal indicator for source water monitoring under this paragraph (a). If the repeat sample collected from the ground water source is E.coli positive, the system must comply... listed in the in paragraph (c)(2) of this section for the presence of E. coli, enterococci, or coliphage...
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40 CFR 141.202 - Tier 1 Public Notice-Form, manner, and frequency of notice.
Code of Federal Regulations, 2013 CFR
2013-07-01
..., or coliphage in source water samples as specified in § 141.402(a) and § 141.402(b); (9) Other... (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Public Notification of Drinking Water Violations § 141.202 Tier 1 Public Notice—Form, manner, and frequency of notice. (a) Which...
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A complete method, incorporating recently improved reverse transcriptase-PCR primer/probe assays and including controls for determining interferences to phage recoveries from water sample concentrates and for detecting interferences to their analysis, was developed for the direct...
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40 CFR 141.202 - Tier 1 Public Notice-Form, manner, and frequency of notice.
Code of Federal Regulations, 2014 CFR
2014-07-01
..., or coliphage in source water samples as specified in § 141.402(a) and § 141.402(b); (9) Other... (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Public Notification of Drinking Water Violations § 141.202 Tier 1 Public Notice—Form, manner, and frequency of notice. (a) Which...
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The purpose of this verification was a cut fiber challenge study for the Dow Chemical Company SFD-2880 UF membrane module. MS2 coliphage virus was the surrogate challenge organism. The challenge tests followed the requirements of the Department of Health Victoria (Australia) Dr...
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The Dow SFD-2880 UF module was tested for removal of microorganisms using live Cryptosporidium parvum oocysts, endospores of the bacteria Bacillus alrophaeus, and the MS2 coliphage virus according to the product-specific challenge testing requirements of the EPA Long-Term 2 Enhan...
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USDA-ARS?s Scientific Manuscript database
F+ RNA coliphages (FRNA) are used to source-track fecal contamination and as surrogates for enteric pathogen persistence in the environment. However, the environmental persistence of FRNA is not clearly understood and thus we evaluated the survival of prototype and environmental isolates of FRNA rep...
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... Concepts and Clinical Practice . 8th ed. Philadelphia, PA: Elsevier Saunders; 2014:chap 58. Ferri FF. Plantar fasciitis. ... FF ed. Ferri's Clinical Advisor 2016 . Philadelphia, PA: Elsevier; 2016:970. Kadakia AR. Heel pain and plantar ...
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... Nelson Textbook of Pediatrics . 20th ed. Philadelphia, PA: Elsevier; 2016:chap 545. Ferri FF. Testicular torsion. In: ... FF, ed. Ferri's Clinical Advisor 2018 . Philadelphia, PA: Elsevier; 2017:1255-1255. Kryger JV. Acute and chronic ...
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NASA Astrophysics Data System (ADS)
Michalzik, Beate; Bischoff, Sebastian; Schwarz, Martin; Siemens, Jan; Thieme, Lisa; Wilcke, Wolfgang
2016-04-01
The amount and chemical nature of water-bound organic matter is a prerequisite for advancing our understanding of the C and nutrient cycling and associated ecosystem processes. While many investigations have addressed the nature and dynamics of DOM in terrestrial ecosystems, only a few have investigated the dynamics and composition of water-bound total OM (TOM) including the particulate organic matter fraction (POM; 0.45 μm < POM < 500 μm). Since water-bound element and nutrient concentrations are conventionally measured after 0.45 μm-filtration, the exclusion of the POM fraction results in misleading inferences and budgeting gaps of nutrient and energy fluxes in terrestrial ecosystems. Furthermore, tree species differ in leaf composition (e.g. nutrient, polyphenols content) and leaf litter quality, which in turn affect a variety of ecosystem processes. Nevertheless, the composition and amount of DOM and TOM derived from living plant material via throughfall (TF), stemflow (SF) and its compositional fate traversing the forest floor (FF) are insufficiently understood. In particular we asked: How do tree species and forest types affect the amount of dissolved and particulate C and N in TF and FF solutions and thus the input into the mineral soil? Do functional properties (e.g. aromaticity) of DOM and TOM differ in TF, SF and FF solutions collected in beech and spruce stands and among different beech stands across Germany? To monitor (mineral) soil input fluxes of DOM and POM in different spruce and beech forests, we fortnightly sampled TF and FF solution over three years (2010-2012) in the "Hainich-Dün-Exploratory", Thuringia, Central Germany, which forms part of the DFG SPP 1374 "Exploratories for Large-scale and Long-term Functional Biodiversity Research". To characterize chemical properties of DOM and TOM, we applied solid-state 13C NMR spectroscopy to TF, SF and FF solutions from three European beech regions across Germany and from Norway spruce sites of the Hainich-Dün-Exploratory. Fluxes of POC and PN were highly variable between years and added significantly to the annual budgets of DOC and DN in TF and FF solutions especially in beech forests. The non-consideration of these particle-bound element fluxes remarkable underestimates the TOC input to the soil by 30 to 40% and those of TN by 10 to 20%. We therefore emphasize the imperative to include POC and PN fluxes into C and N budgeting of forest ecosystems. 13C NMR spectroscopy revealed remarkable tree-species related differences in the composition of DOM and TOM. Compared to DOM, TOM generally showed higher intensities for the alkyl C region and lower ones for lignin-derived and aromatic C of the aryl C region resulting in lower aromaticity indices and a diminished degree of humification. Differences in the structural composition of DOM and TOM under beech lessened in the order: throughfall > stemflow > forest floor leachate. Compared to spruce, TF DOM under beech concordantly showed the highest intensities of aromatic and phenolic C and lowest ones of alkyl-C. Phenolic compounds are known for their allelopathic potential successfully impairing competing plants and hence altering ecosystem structure and functions - mechanisms being still imperfectly understood.
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... eds. Seidel's Guide to Physical Examination . 8th ed. Elsevier Mosby; 2015:chap 8. Ferri FF. Ehlers-Danlos ... FF, ed. Ferri's Clinical Advisor 2016 . Philadelphia, PA: Elsevier; 2016:451-451. Gorgas DL, McGrath JL. Vital ...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Lu, Yunxia, E-mail: wwwdluyx@sina.com; The Comprehensive Laboratory, Anhui Medical University, Hefei, Anhui 230032; Cheng, Jingjing
Fenofibrate (FF) is widely used to lower blood lipids in clinical practice, but whether its protective effect on endothelium-dependent vasodilatation (EDV) in thoracic aorta is related with endoplasmic reticulum (ER) stress remains unknown. In this study, female Sprauge Dawley rats were divided into standard chow diets (SCD), high-fat diets (HFD) and HFD plus FF treatment group (HFD + FF) randomly. The rats of latter two groups were given HFD feeding for 5 months, then HFD + FF rats were treated with FF (30 mg/kg, once daily) via gavage for another 2 months. The pathological and tensional changes, protein expression of eNOS, and ER stress relatedmore » genes in thoracic aorta were measured. Then impacts of palmitic acid (PA) and FF on EDV of thoracic aorta from normal female SD rats were observed. Ultimately the expression of ER stress related genes were assessed in primary mouse aortic endothelial cells (MAEC) treated by fenofibric acid (FA) and PA. We found that FF treatment improved serum lipid levels and pathological changes in thoracic aorta, accompanied with decreased ER stress and increased phosphorylation of eNOS. FF pretreatment also improved EDV impaired by different concentrations of PA treatment. The dose- and time-dependent inhibition of cell proliferation by PA were inverted by FA pretreatment. Phosphorylation of eNOS and expression of ER stress related genes were all inverted by FA pretreatment in PA-treated MAEC. Our findings show that fenofibrate recovers damaged EDV by chronic HFD feeding and acute stimulation of PA, this effect is related with decreased ER stress and increased phosphorylation of eNOS. - Highlights: • Fenofibrate treatment improved pathological changes in thoracic aorta by chronic high-fat-diet feeding. • Fenofibrate pretreatment improved endothelium-dependent vasodilation impaired by different concentrations of palmitic acid. • The inhibition of proliferation in endothelial cells by palmitic acid were inverted by fenofibric acid. • Phosphorylation of eNOS and expression of ER stress related genes were inverted by fenofibrate or fenofibric acid.« less
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Miller, A; McLeod, L; Alhayyani, S; Szczepny, A; Watkins, D N; Chen, W; Enriori, P; Ferlin, W; Ruwanpura, S; Jenkins, B J
2017-05-25
Lung cancer is the leading cause of cancer death worldwide, and is frequently associated with the devastating paraneoplastic syndrome of cachexia. The potent immunomodulatory cytokine interleukin (IL)-6 has been linked with the development of lung cancer as well as cachexia; however, the mechanisms by which IL-6 promotes muscle wasting in lung cancer cachexia are ill-defined. In this study, we report that the gp130 F/F knock-in mouse model displaying hyperactivation of the latent transcription factor STAT3 via the common IL-6 cytokine family signalling receptor, gp130, develops cachexia during Kras-driven lung carcinogenesis. Specifically, exacerbated weight loss, early mortality and reduced muscle and adipose tissue mass were features of the gp130 F/F :Kras G12D model, but not parental Kras G12D mice in which STAT3 was not hyperactivated. Gene expression profiling of muscle tissue in cachectic gp130 F/F :Kras G12D mice revealed the upregulation of IL-6 and STAT3-target genes compared with Kras G12D muscle tissue. These cachectic features of gp130 F/F :Kras G12D mice were abrogated upon the genetic normalization of STAT3 activation or ablation of IL-6 in gp130 F/F :Kras G12D :Stat3 -/+ or gp130 F/F :Kras G12D :Il6 -/- mice, respectively. Furthermore, protein levels of the soluble IL-6 receptor (sIL-6R), which is the central facilitator of IL-6 trans-signalling, were elevated in cachectic muscle from gp130 F/F :Kras G12D mice, and the specific blockade of IL-6 trans-signalling, but not classical signalling, with an anti-IL-6R antibody ameliorated cachexia-related characteristics in gp130 F/F :Kras G12D mice. Collectively, these preclinical findings identify trans-signalling via STAT3 as the signalling modality by which IL-6 promotes muscle wasting in lung cancer cachexia, and therefore support the clinical evaluation of the IL-6 trans-signalling/STAT3 axis as a therapeutic target in advanced lung cancer patients presenting with cachexia.
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Factors that contribute to the botulinal safety of reduced-fat and fat-free process chesse products.
Glass, Kathleen A; Johnson, Eric A
2004-08-01
The effects of fat, type of natural cheese, and adjunct process cheese ingredients were evaluated to determine factors that contribute to the botulinal safety of reduced-fat (RF) process cheese products stored at 30 degrees C. In the first set of experiments, pasteurized process cheese products (PPCPs) were formulated using full-fat (FF) Cheddar, 30% RF Cheddar, or skim milk (SM) cheese as cheese-base types and were standardized to 59% moisture, pH 5.75, 2.8 or 3.2% total salts, and 15 to 19% fat. Subsequent trials evaluated the effect of fat levels and adjunct ingredients in PPCPs made with SM, RF, and FF cheese (final fat levels, less than 1, 13, and 24%, respectively). When fat levels of PPCPs were comparable (15.1, 19.1, and 16.2 for product manufactured with SC, RE and FF cheese, respectively), botulinal toxin production was delayed for up to 2 days in PPCPs formulated with SM compared with RF or FF cheese; however, the effect was not statistically significant. When fat levels were reduced to less than 1% in SM PPCPs, toxin production was delayed 2 weeks in products made with SM compared with RF or FF cheese manufactured with 13 or 24% fat, respectively. The antibotulinal effect of adjunct ingredients varied among the products manufactured with different fat levels. Sodium lactate significantly delayed toxin production (P < 0.05) for all fat levels tested, whereas beta-glucan fat replacer did not delay toxin production. An enzyme-modified cheese used as a flavor enhancer significantly delayed toxin production (P < 0.05) in SM (less than 1% fat) products but had little to no inhibitory effect in RF (13% fat) and FF (24% fat) cheese products. Similarly, monolaurin increased the time to detectable toxin in SM products but was ineffective in RF or FF cheese products. These results verify that RF PPCPs exhibit greater safety than FF products and that safety may be enhanced by using certain adjunct ingredients as antimicrobials.
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Wolthers, Ole D; Stone, Sally; Bareille, Philippe; Tomkins, Susan; Khindri, Sanjeev
2017-06-01
A dry powder inhaler formulation of the inhaled corticosteroid fluticasone furoate (FF) is being evaluated for use in children. An important potential risk associated with the use of inhaled corticosteroids in children is growth suppression. Therefore, the aim of this study was to assess the short-term lower leg growth in children with asthma treated for 2 weeks with inhaled FF versus placebo from the ELLIPTA inhaler. Prepubertal children with persistent asthma (n = 60; aged 5 to <12 years) were recruited into a randomized, double-blind, placebo-controlled, 2-way crossover, noninferiority study. The study consisted of four 2-week periods: run-in, 2 treatment periods, 1 washout period, and a 1-week follow-up period. Interventions were FF 50 µg and placebo once daily in the evening. Lower leg length was measured by using knemometry. The randomized ITT population comprised 36 boys and 24 girls with a mean age of 8.7 (standard deviation, 1.5; range, 5-11) years; 58% had a duration of asthma ≥5 years. Fifty-eight subjects completed both treatment periods. The least squares mean growth rate was 0.31 mm/week during treatment with FF and 0.36 mm/week during the placebo period. The difference in adjusted least squares mean growth rates between FF and placebo was -0.052 mm/week with a 95% CI of -0.122 to 0.018. This finding was greater than the prespecified noninferiority margin of -0.20 mm/week. The overall incidence of adverse events was 35% with placebo and 22% with FF. Inhaled FF 50 µg provided once daily for 2 weeks was noninferior to placebo in terms of effects on short-term lower leg growth in children with asthma. To further quantify the risk of growth suppression in children, intermediate-term growth studies should be conducted. Inhaled FF 50 µg was well tolerated in this study population. ClinicalTrials.gov identifier: NCT02502734. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
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Jaramillo, Diego; Bedoya, Maria A; Wang, Dah-Jyuu; Pena, Andres H; Delgado, Jorge; Jaimes, Camilo; Ho-Fung, Victor; Kaplan, Paige
2015-06-01
The objective of our study was to use proton MR spectroscopy (MRS) to quantitatively evaluate bone marrow infiltration by measuring the fat fraction (FF) and to compare the FF with semiquantitative bone marrow MRI scores and clinical status in children treated for type 1 Gaucher disease (GD). Over a 2-year period, we prospectively evaluated 10 treated GD patients (six males, four females; median age, 15.1 years) and 10 healthy age-matched control subjects (five males, five females; median age, 15.3 years) using 3-T proton MRS of L5 and the femoral neck. Water and lipid AUCs were measured to calculate the FF. Two blinded pediatric musculoskeletal radiologists performed a semiquantitative analysis of the conventional MR images using the bone marrow burden score and modified Spanish MRI score. We evaluated symptoms, spleen and liver volumes, platelet levels, hemoglobin levels, and bone complications. In the femur, the FF was higher in the control subjects (median, 0.71) than the GD patients (0.54) (p = 0.02). In L5, the difference in FF--higher FF in control subjects (0.37) than in GD patients (0.26)--was not significant (p = 0.16). In both groups and both regions, the FF increased with patient age (p < 0.02). Semiquantitative scores showed no differences between control subjects and treated GD patients (p > 0.11). Eight of 10 GD patients were asymptomatic and two had chronic bone pain. The median age of patients at symptom onset was 4.0 years, the median age of patients at the initiation of enzyme replacement therapy was 4.3 years, and the median treatment duration was 10.2 years. Hemoglobin level, platelet count, and liver volume at MRI were normal. Mean pretreatment spleen volume (15.4-fold above normal) decreased to 2.8-fold above normal at the time of MRI (p = 0.01). Proton MRS detected FF differences that were undetectable using conventional MRI; for that reason, proton MRS can be used to optimize treatment of GD patients.
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16 CFR § 1630.61 - Hide carpets and rugs-alternative washing procedure.
Code of Federal Regulations, 2013 CFR
2013-01-01
... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 1-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...
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16 CFR § 1631.61 - Hide carpets and rugs-alternative washing procedure.
Code of Federal Regulations, 2013 CFR
2013-01-01
... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 2-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...
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NASA Astrophysics Data System (ADS)
Turnbull, J. C.; Cambaliza, M. L.; Sweeney, C.; Karion, A.; Newberger, T.; Tans, P. P.; Lehman, S.; Davis, K. J.; Miles, N. L.; Richardson, S.; Lauvaux, T.; Shepson, P.; Gurney, K. R.; Song, Y.; Razlivanov, I. N.
2012-12-01
Emissions of fossil fuel CO2 (CO2ff) from anthropogenic sources are the primary driver of observed increases in the atmospheric CO2 burden, and hence global warming. Quantification of the magnitude of fossil fuel CO2 emissions is vital to improving our understanding of the global and regional carbon cycle, and independent evaluation of reported emissions is essential to the success of any emission reduction efforts. The urban scale is of particular interest, because ~75% CO2ff is emitted from urban regions, and cities are leading the way in attempts to reduce emissions. Measurements of 14CO2 can be used to determine CO2ff, yet existing 14C measurement techniques require laborious laboratory analysis and measurements are often insufficient for inferring an urban emission flux. This presentation will focus on how 14CO2 measurements can be combined with those of more easily measured ancillary tracers to obtain high resolution CO2ff mixing ratio estimates and then infer the emission flux. A pilot study over Sacramento, California showed strong correlations between CO2ff and carbon monoxide (CO) and demonstrated an ability to quantify the urban flux, albeit with large uncertainties. The Indianapolis Flux Project (INFLUX) aims to develop and assess methods to quantify urban greenhouse gas emissions. Indianapolis was chosen as an ideal test case because it has relatively straightforward meteorology; a contained, isolated, urban region; and substantial and well-known fossil fuel CO2 emissions. INFLUX incorporates atmospheric measurements of a suite of gases and isotopes including 14C from light aircraft and from a network of existing tall towers surrounding the Indianapolis urban area. The recently added CO2ff content is calculated from measurements of 14C in CO2, and then convolved with atmospheric transport models and ancillary data to estimate the urban CO2ff emission flux. Significant innovations in sample collection include: collection of hourly averaged samples to remove short term atmospheric variability; and direct measurement of the background signal from towers immediately upwind of the urban area and from the boundary layer. We find that CO2ff and other anthropogenic trace gases are consistently enhanced at a tower site downwind of the city. Measurements made directly over or very close to the urban area show only weak correlations between CO2ff and trace gases associated with combustion, likely because the urban plume is not yet well mixed. Total CO2 is also consistently enhanced in the downwind samples, even in summer. In winter, total CO2 enhancement is slightly higher than the fossil fuel CO2 enhancement, in agreement with Indiana's requirement for 10% bioethanol use in gasoline. This result implies that the enhancement in total CO2 can be used to infer CO2ff emissions for Indianapolis during winter. We therefore use the high resolution in situ total CO2 measurements in a simple mass balance model to estimate the urban CO2ff emissions. An initial comparison shows a ~20% difference between the top-down and bottom-up methods.
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Vashishta, Priya; Kalia, Rajiv K; Nakano, Aiichiro
2006-03-02
We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to coexistence of brittle grains and soft amorphous-like grain boundary phases. Simulations predict a crossover from intergranular continuous deformation to intragrain discrete deformation at a critical indentation depth.
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Microbiota in fermented feed and swine gut.
Wang, Cheng; Shi, Changyou; Zhang, Yu; Song, Deguang; Lu, Zeqing; Wang, Yizhen
2018-04-01
Development of alternatives to antibiotic growth promoters (AGP) used in swine production requires a better understanding of their impacts on the gut microbiota. Supplementing fermented feed (FF) in swine diets as a novel nutritional strategy to reduce the use of AGP and feed price, can positively affect the porcine gut microbiota, thereby improving pig productivities. Previous studies have noted the potential effects of FF on the shift in benefit of the swine microbiota in different regions of the gastrointestinal tract (GIT). The positive influences of FF on swine gut microbiota may be due to the beneficial effects of both pre- and probiotics. Necessarily, some methods should be adopted to properly ferment and evaluate the feed and avoid undesired problems. In this mini-review, we mainly discuss the microbiota in both fermented feed and swine gut and how FF influences swine gut microbiota.
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Influence of follicular fluid and cumulus cells on oocyte quality: clinical implications.
Da Broi, M G; Giorgi, V S I; Wang, F; Keefe, D L; Albertini, D; Navarro, P A
2018-03-02
An equilibrium needs to be established by the cellular and acellular components of the ovarian follicle if developmental competence is to be acquired by the oocyte. Both cumulus cells (CCs) and follicular fluid (FF) are critical determinants for oocyte quality. Understanding how CCs and FF influence oocyte quality in the presence of deleterious systemic or pelvic conditions may impact clinical decisions in the course of managing infertility. Given that the functional integrities of FF and CCs are susceptible to concurrent pathological conditions, it is important to understand how pathophysiological factors influence natural fertility and the outcomes of pregnancy arising from the use of assisted reproduction technologies (ARTs). Accordingly, this review discusses the roles of CCs and FF in ensuring oocyte competence and present new insights on pathological conditions that may interfere with oocyte quality by altering the intrafollicular environment.
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NASA Astrophysics Data System (ADS)
Yoshihara, K.; van Mierlo, M.; Ng, A.; Shankar Kumar, B.; De Ruiter, A.; Komatsu, Y.; Horiguchi, H.; Hashimoto, H.
2008-08-01
This paper introduces the Japan Canada Joint Collaboration Satellites - Formation Flying (JC2Sat-FF) project. JC2Sat-FF is a joint project between the Canadian Space Agency (CSA) and the Japan Aerospace Exploration Agency (JAXA) with the end goal of building, launching and operating two 20kg- class nanosatellites for technical demonstration of formation flight (FF) using differential drag technique, relative navigation using commercial off-the-shelf (COTS) dual band GPS receivers and far infra-red radiance measurement. A unique aspect of this project is that the two JC2Sats are developed by a united small team consisting of engineers and researchers from both agencies. Technical exchange in this international team gives stimulation to the members and generates a synergistic effect for the project.
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NASA Astrophysics Data System (ADS)
Gjuraj, Daniel; Daunt, S. J.; Grzywacz, Robert; Lafferty, Walter; Flaud, Jean-Marie; Billinghurst, Brant E.
2017-06-01
As part of our project on the study of isotopologues of propane we have taken the spectra of the 2-D and 2,2-D_2 substituted species. There have been no studies of these species since the early IR studies. We recorded high resolution (Δν = 0.0009 \\wn) FTS data on the Canadian Light Source Far-IR beamline. The spectra of all bands of both species in the region examined (500 - 1250 \\wn) show torsionally perturbed lines, all but one band appearing globally perturbed. Virtually all bands were not amenable to analysis at present except for the νb{15} (B_{1}) A-type band centered at 954.709 \\wn. One can still see a few perturbed lines with torsional components but overall most lines were single and could be readily assigned using traditional methods. The spectrum is modelled well using PGOPHER. No MW determined GS constants were available so we have analyzed about 3500 levels to determine both ground state and upper state rotational constants. Friedman & Turkevich, J. Chem. Phys. 17, 1012 ff. (1949) McMurry, Thornton & Condon, J. Chem. Phys. 17, 918 ff. (1949) McMurry & Thornton, J. Chem. Phys. 19, 1014 ff.(1951) Gayles & King, Spectrochim. Acta 21, 543 ff.(1965) Kondo & Saeki, Spectrochim. Acta 29A, 735 ff. (1973) Western, J. Quant. Spectrosc. Rad. Transf. 186, 221 ff. (2017).
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Ruiz Hidalgo, Irene; Rodriguez, Pablo; Rozema, Jos J; Ní Dhubhghaill, Sorcha; Zakaria, Nadia; Tassignon, Marie-José; Koppen, Carina
2016-06-01
To evaluate the performance of a support vector machine algorithm that automatically and objectively identifies corneal patterns based on a combination of 22 parameters obtained from Pentacam measurements and to compare this method with other known keratoconus (KC) classification methods. Pentacam data from 860 eyes were included in the study and divided into 5 groups: 454 KC, 67 forme fruste (FF), 28 astigmatic, 117 after refractive surgery (PR), and 194 normal eyes (N). Twenty-two parameters were used for classification using a support vector machine algorithm developed in Weka, a machine-learning computer software. The cross-validation accuracy for 3 different classification tasks (KC vs. N, FF vs. N and all 5 groups) was calculated and compared with other known classification methods. The accuracy achieved in the KC versus N discrimination task was 98.9%, with 99.1% sensitivity and 98.5% specificity for KC detection. The accuracy in the FF versus N task was 93.1%, with 79.1% sensitivity and 97.9% specificity for the FF discrimination. Finally, for the 5-groups classification, the accuracy was 88.8%, with a weighted average sensitivity of 89.0% and specificity of 95.2%. Despite using the strictest definition for FF KC, the present study obtained comparable or better results than the single-parameter methods and indices reported in the literature. In some cases, direct comparisons with the literature were not possible because of differences in the compositions and definitions of the study groups, especially the FF KC.
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Segregation of feedforward and feedback projections in mouse visual cortex
Berezovskii, Vladimir K.; Nassi, Jonathan J.; Born, Richard T.
2011-01-01
Hierarchical organization is a common feature of mammalian neocortex. Neurons that send their axons from lower to higher areas of the hierarchy are referred to as “feedforward” (FF) neurons, whereas those projecting in the opposite direction are called “feedback” (FB) neurons. Anatomical, functional and theoretical studies suggest that these different classes of projections play fundamentally different roles in perception. In primates, laminar differences in projection patterns often distinguish the two projection streams. In rodents, however, these differences are less clear, despite an established hierarchy of visual areas. Thus the rodent provides a strong test of the hypothesis that FF and FB neurons form distinct populations. We tested this hypothesis by injecting retrograde tracers into two different hierarchical levels of mouse visual cortex (areas 17 and AL) and then determining the relative proportions of double-labeled FB and FF neurons in an area intermediate to them (LM). Despite finding singly labeled neurons densely intermingled with no laminar segregation, we found few double-labeled neurons (~5% of each singly labeled population). We also examined the development of FF and FB connections. FF connections were present at the earliest time-point we examined (postnatal day two, P2), while FB connections were not detectable until P11. Our findings indicate that, even in cortices without laminar segregation of FF and FB neurons, the two projection systems are largely distinct at the neuronal level and also differ with respect to the timing of their outgrowth. PMID:21618232
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Guo, Lingling; Song, Shanshan; Liu, Liqiang; Peng, Juan; Kuang, Hua; Xu, Chuanlai
2015-09-01
Rapid and sensitive indirect competitive enzyme-linked immunosorbent assays (ic-ELISA) and gold nanoparticle immunochromatographic strip tests were developed to detect thiamphenicol (TAP), florfenicol (FF) and chloramphenicol (CAP) in milk and honey samples. The generic monoclonal antibody for TAP, FF and CAP was prepared based on a hapten [D-threo-1-(4-aminophenyl)-2- dichloroacetylamino-1,3-propanediol], and the haptenwas linked to a carrier protein using the diazotization method. After the optimization of several parameters (coating, pH, sodium chloride content and methanol content), the ic-ELISA was established. The quantitative working range for TAP was 0.11-1.36 ng/mL, with an IC50 of 0.39 ng/mL. The optimized ELISA showed cross-reactivity to CAP (300%) and FF (15.6%), with IC50 values of 0.13 and 2.5 ng/mL, respectively. The analytical recovery of TAP, FF and CAP in milk and honey samples in the ic-ELISA ranged from 81.2 to 112.9%. Based on this monoclonal antibody, a rapid and sensitive immunochromatographic test strip was also developed. This strip had a detection limit of 1 ng/mL for TAP, FF and CAP in milk and honey samples. Moreover, the test was completed within 10 min. Our results showed that the proposed ic-ELISA and immunochromatographic test strip method are highly useful screening tools for TAP, FF and CAP detection in milk and honey samples. Copyright © 2015 John Wiley & Sons, Ltd.
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Dobson, Melissa E.; Diallo-Krou, Ericka; Grachtchouk, Vladimir; Yu, Jingcheng; Colby, Lesley A.; Wilkinson, John E.; Giordano, Thomas J.
2011-01-01
Approximately 35% of follicular thyroid carcinomas harbor a chromosomal translocation that results in expression of a paired box gene 8-peroxisome proliferator-activated receptor γ gene (PPARγ) fusion protein (PPFP). To better understand the oncogenic role of PPFP and its relationship to endogenous PPARγ, we generated a transgenic mouse model that combines Cre-dependent PPFP expression (PPFP;Cre) with homozygous deletion of floxed Pten (PtenFF;Cre), both thyroid specific. Although neither PPFP;Cre nor PtenFF;Cre mice develop thyroid tumors, the combined PPFP;PtenFF;Cre mice develop metastatic thyroid cancer, consistent with patient data that PPFP is occasionally found in benign thyroid adenomas and that PPFP carcinomas have increased phosphorylated AKT/protein kinase B. We then tested the effects of the PPARγ agonist pioglitazone in our mouse model. Pioglitazone had no effect on PtenFF;Cre mouse thyroids. However, the thyroids in pioglitazone-fed PPFP;PtenFF;Cre mice decreased 7-fold in size, and metastatic disease was prevented. Remarkably, pioglitazone caused an adipogenic response in the PPFP;PtenFF;Cre thyroids characterized by lipid accumulation and the induction of a broad array of adipocyte PPARγ target genes. These data indicate that, in the presence of pioglitazone, PPFP has PPARγ-like activity that results in trans-differentiation of thyroid carcinoma cells into adipocyte-like cells. Furthermore, the data predict that pioglitazone will be therapeutic in patients with PPFP-positive carcinomas. PMID:21952241
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Rowe, Fiona J.; Noonan, Carmel; Manuel, Melanie
2013-01-01
Aim. To compare semikinetic perimetry (SKP) on Octopus 900 perimetry to a peripheral static programme with Humphrey automated perimetry. Methods. Prospective cross-section study comparing Humphrey full field (FF) 120 two zone programme to a screening protocol for SKP on Octopus perimetry. Results were independently graded for presence/absence of field defect plus type and location of defect. Results. 64 patients (113 eyes) underwent dual perimetry assessment. Mean duration of assessment for SKP was 4.54 minutes ±0.18 and 6.17 ± 0.12 for FF120 (P = 0.0001). 80% of results were correctly matched for normal or abnormal visual fields using the I4e target versus FF120, and 73.5% were correctly matched using the I2e target versus FF120. When comparing Octopus results with combined I4e and I2e isopters to the FF120 result, a match for normal or abnormal fields was recorded in 87%. Conclusions. Humphrey perimetry test duration was generally longer than Octopus SKP. In the absence of kinetic perimetry, peripheral static suprathreshold programme options such as FF120 may be useful for detection of visual field defects. However, statokinetic dissociation may occur. Octopus SKP utilising both I4e and I2e targets provides detailed information of both the defect depth and size and may provide a more representative view of the actual visual field defect. PMID:24558605
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Final report of the APMP water flow key comparison: APMP.M.FF-K1
NASA Astrophysics Data System (ADS)
Lee, Kwang-Bock; Chun, Sejong; Terao, Yoshiya; Thai, Nguyen Hong; Tsair Yang, Cheng; Tao, Meng; Gutkin, Mikhail B.
2011-01-01
The key comparison, APMP.M.FF-K1, was undertaken by APMP/TCFF, the Technical Committee for Fluid Flow (TCFF) under the Asia Pacific Metrology Program (APMP). One objective of the key comparison was to demonstrate the degree of equivalence among six participating laboratories (KRISS, NMIJ, VMI, CMS, NIM and VNIIM) in water flow rate metrology by comparing the results with the key comparison reference value (KCRV) determined from the CCM.FF-K1 key comparison. The other objective of this key comparison was to provide supporting evidence for the calibration and measurement capabilities (CMCs), which had been declared by the participating laboratories during this key comparison. The Transfer Standard Package (TSP) was a Coriolis mass flowmeter, which had been used in the CCM.FF-K1 key comparison. Because the K-factors in the APMP.M.FF-K1 key comparison were slightly lower than the K-factors of the CCM.FF-K1 key comparison due to long-term drifts of the TSP, a correction value D was introduced. The value of D was given by a weighted sum between two link laboratories (NMIJ and KRISS), which participated in both the CCM.FF-K1 and the APMP.M.FF-K1 key comparisons. By this correction, the K-factors were laid between 12.004 and 12.017 at either low (Re = 254 000) or high (Re = 561 000) flow rates. Most of the calibration data were within expected uncertainty bounds. However, some data showed undulations, which gave large fluctuations of the metering factor at Re = 561 000. Calculation of degrees of equivalence showed that all the participating laboratories had deviations between -0.009 and 0.007 pulses/kg from the CCM.FF-K1 KCRV at either the low or the high flow rates. In case of En calculation, all the participating laboratories showed values less than 1, indicating that the corrected K-factors of all the laboratories were equivalent with the KCRV at both Re = 254 000 and 561 000. When the corrected K-factors from two participating laboratories were compared, all the numbers of equivalence showed values less than 1, indicating equivalence. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).
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Grzywacz, Joseph G; Lipscomb, Hester J; Casanova, Vanessa; Neis, Barbara; Fraser, Clermont; Monaghan, Paul; Vallejos, Quirina M
2013-08-01
There is widespread agreement that work organization is an important element of occupational safety and health, but the health effects of many aspects of work organization are likely to vary considerably across different sectors of work and geographies. We examined existing employment policies and work organization-related research relevant specifically to immigrant workers in the Agriculture, Forestry, and Fishing (AgFF) Sector of the US workforce focusing, when possible, on the southeastern US. A number of specific aspects of work organization within AgFF subsectors have been described, but most of this literature exists outside the purview of occupational health. There are few studies that directly examine how attributes of work organization relevant to the AgFF Sector affect workers', much less immigrant workers', occupational health exposures and outcomes. In contrast to the broader literature, research linking occupational health outcomes to work organization in the AgFF Sector is limited and weak. A systematic program of research and intervention is needed to develop strategies that eliminate or substantially mitigate the deleterious health effects of occupational exposures whose origins likely lie in the organization of AgFF work. Copyright © 2013 Wiley Periodicals, Inc.
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Albertson, Timothy E.; Richards, John R.; Zeki, Amir A.
2015-01-01
The treatment of persistent asthma has been aided by the recent approval of new medications. The combined inhaled corticosteroid (ICS)/long-acting β2 agonist (LABA) powder inhaler fluticasone furoate (FF)/vilanterol trifenatate (VI) is one of these new agents, which was recently approved as a maintenance therapy for persistent asthma. This once-daily ICS/LABA inhaler has previously been approved and used in chronic obstructive pulmonary disease as a maintenance therapy. Both FF and VI individually have been shown to have efficacy in the treatment of persistent asthma; the combination of FF/VI at the dose of 100/25 μg daily improves trough peak expiratory flows and forced expiratory volume in 1 s. It also reduces the frequency of asthma exacerbations in patients with persistent asthma. The once-daily dosing is well tolerated, with limited clinically significant adverse events; the once-daily inhaled dosing regimen should also improve medication adherence. The data supporting the use of the FF/VI inhaler in persistent asthma are reviewed. The dry powder inhaler of FF/VI (100/25 μg) is an effective and well tolerated once-daily maintenance treatment for patients with persistent asthma. PMID:26668137
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Daily, Michael D; Baer, Marcel D; Mundy, Christopher J
2016-03-10
The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described.
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40 CFR 141.202 - Tier 1 Public Notice-Form, manner, and frequency of notice.
Code of Federal Regulations, 2010 CFR
2010-07-01
... fecal coliform or E. coli are present in the water distribution system (as specified in § 141.63(b)), or when the water system fails to test for fecal coliforms or E. coli when any repeat sample tests...) Detection of E. coli, enterococci, or coliphage in source water samples as specified in § 141.402(a) and...
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40 CFR 141.202 - Tier 1 Public Notice-Form, manner, and frequency of notice.
Code of Federal Regulations, 2011 CFR
2011-07-01
... fecal coliform or E. coli are present in the water distribution system (as specified in § 141.63(b)), or when the water system fails to test for fecal coliforms or E. coli when any repeat sample tests...) Detection of E. coli, enterococci, or coliphage in source water samples as specified in § 141.402(a) and...
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1979-09-01
was funded under Civil Works Project CWIS 31280, Evaluation of Existing Facilities for Waste- water Land Treatment. Robert Emerson of the Atmospheric...20 Estimation of Coliphage .................................. 23 Fluorescein Dye Runs ..................................... 23 Chemicai and...California Water Pollletion Control Board 1957) in which data were obtained on the travel of coliform bacteria from spray operations using
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Use of tracers and isotopes to evaluate vulnerability of water in domestic wells to septic waste
Verstraeten, Ingrid M.; Fetterman, G.S.; Meyer, M.J.; Bullen, T.; Sebree, S.K.
2005-01-01
In Nebraska, a large number (>200) of shallow sand-point and cased wells completed in coarse alluvial sediments along rivers and lakes still are used to obtain drinking water for human consumption, even though construction of sand-point wells for consumptive uses has been banned since 1987. The quality of water from shallow domestic wells potentially vulnerable to seepage from septic systems was evaluated by analyzing for the presence of tracers and multiple isotopes. Samples were collected from 26 sand-point and perforated, cased domestic wells and were analyzed for bacteria, coliphages, nitrogen species, nitrogen and boron isotopes, dissolved organic carbon (DOC), prescription and nonprescription drugs, or organic waste water contaminants. At least 13 of the 26 domestic well samples showed some evidence of septic system effects based on the results of several tracers including DOC, coliphages, NH4+, NO3-, N2, ?? 15N[NO3-] and boron isotopes, and antibiotics and other drugs. Sand-point wells within 30 m of a septic system and <14 m deep in a shallow, thin aquifer had the most tracers detected and the highest values, indicating the greatest vulnerability to contamination from septic waste. Copyright ?? 2005 National Ground Water Association.
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[Spring water quality assessment regarding the problem of endemic fluorosis].
Leshchenko, D V; Mialo, O A; Beliakova, M B; Beliaeva, E A; Samoukina, A M; Chervinets, Iu V; Ivanova, O V
2013-01-01
A possible variant for reducing the consumption of fluoride by population of Tver region is the use of water with low fluoride content, such as spring water. Assessment of drinking suitability of spring water (the content of physiologically important mineral elements and microbial purity) is relevant to our region. Water samples from 6 spring-water source of Tver region were studied during the year. The content of fluoride and calcium were measured by using an ion-selective electrodes. Microbiological purity tested by the presence of total coliform bacteria, thermotolerant coliform bacteria, coliphages and total microbial numbers. The analysis of some mineral components in spring water of Tver region showed that calcium content was in range 33-88 mg/l, that satisfied the recommended value; fluoride concentration is less then 0.5 mg/l. In all spring water samples total coliforms, thermotolerant coliforms and coliphages were absent. The total microbial number was in standard range, except of two spring-water source in the autumn and summer. The data suppose that spring water of Tver region can be used as a component of diet normalizing the fluoride consumption at risk of dental fluorosis in children.
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Global occurrence of Torque teno virus in water systems.
Charest, A J; Plummer, J D; Long, S C; Carducci, A; Verani, M; Sidhu, J P S
2015-09-01
Bacterial indicator organisms are used globally to assess the microbiological safety of waters. However, waterborne viral outbreaks have occurred in drinking water systems despite negative bacterial results. Using viral markers may therefore provide more accurate health risk assessment data. In this study, fecal, wastewater, stormwater, surface water (fresh and salt), groundwater, and drinking water samples were analyzed for the presence or concentration of traditional indicators, innovative indicators and viral markers. Samples were obtained in the United States, Italy, and Australia and results compared to those reported for studies conducted in Asia and South America as well. Indicators included total coliforms, Escherichia coli, enterococci, male-specific coliphages, somatic coliphages and microviradae. Viral markers included adenovirus, polyomavirus, and a potential new surrogate, Torque teno virus (TTV). TTV was more frequently found in wastewaters (38-100%) and waters influenced by waste discharges (25%) than in surface waters used as drinking water sources (5%). TTV was also specific to human rather than animal feces. While TTV numbers were strongly correlated to other viral markers in wastewaters, suggesting its utility as a fecal contamination marker, data limitations and TTV presence in treated drinking waters demonstrates that additional research is needed on this potential viral indicator.
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Santiago-Rodriguez, Tasha M; Toranzos, Gary A; Arce-Nazario, Javier A
2016-10-01
Urbanization affects the microbial loading into tropical streams, but its impact on water quality varies across watersheds. Rainfall in tropical environments also complicates microbial dynamics due to high seasonal and annual variations. Understanding the dynamics of fecal contamination in tropical surface waters may be further hindered by limitations from the utilization of traditional microbial indicators. We measured traditional (Enterococcus spp. and Escherichia coli), as well as alternate (enterophages and coliphages) indicators of fecal contamination in a tropical watershed in Puerto Rico during a 1-year period, and examined their relationship with rainfall events across an urbanization gradient. Enterococcus spp. and E. coli concentrations were 4 to 5 logs higher in non-urbanized or pristine sites when compared to enterophages and coliphages, suggesting that traditional fecal indicator bacteria may be natural inhabitants of pristine tropical waters. All of the tested indicators were positively correlated with rainfall and urbanization, except in the most urbanized sites, where rainfall may have had a dilution effect. The present study indicates that utilizing novel indicators of microbial water quality may improve the assessment of fecal contamination and pathogen risk for tropical watersheds.
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Wu, Jinling; Li, Haitao; Huang, Xia
2010-03-01
The membrane bioreactor (MBR) features many advantages, such as its excellent effluent quality and compactness. Moreover, the MBR is well known for its disinfectant capacity. This paper investigates virus removal performance for municipal wastewater using a submerged MBR and the operational conditions affecting the virus removal using indigenous somatic coliphages (SC) as an indicator for viruses. The results revealed that the municipal wastewater acquired by the Qinghe Municipal Wastewater Treatment Plant, Beijing, contained an SC concentration of (2.81+/-1.51)x10(4)PFU ml(-1), which varies seasonally due to spontaneous decay. In the MBR system, the biomass process dominates SC removal. Membrane rejection is an essential supplement of biomass process for SC removal. In this paper, the relative contributions of biomass process and membrane rejection during the start-up and steady operational periods are discussed in detail. The major factors affecting SC removal are biodegradation, membrane pore size, and gel layer formation on the membrane. During long-term experiments, it was demonstrated that high inoculated sludge concentration, long hydraulic retention time, moderate fouling layer, and non-frequent chemical cleaning are favorable for high SC removal in MBR systems. Copyright 2009 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Skuce, A. G.
2014-12-01
The direct, non-climate, contribution of carbon dioxide and water emissions from fossil-fuel (FF) combustion to the volume and mass of the oceans has been omitted from estimates of sea-level rise (SLR) in IPCC reports. Following the method of Gornitz et al. (1997), H2O emissions are estimated using carbon emissions from the Carbon Dioxide Information Analysis Center, along with typical carbon and hydrogen contents of FF. Historic H2O emissions from 1750 to 2010 amount to 430 ±50 PgH2O, equivalent to 1.2 ±0.2 mmSLR. Sometime in this decade the volume of H2O from historic FF combustion will exceed the volume of Lake Erie (480 km3). CO2 dissolved in the ocean increases the seawater volume by 31-33 mL mol-1 CO2. From 1750 to 2010, 370 ±70 PgCO2 from FF combustion has dissolved in the oceans, causing 0.7 ±0.2 mmSLR. Combined H2O+CO2emissions from FF have therefore added 1.9 ±0.4 mm to sea levels in the Industrial Era. Combustion of FF in 2010 resulted in emissions of 32 PgCO2 and 12 ±1 PgH2O. SLR contributions for that year from FF emissions were 0.033 ±0.005 mm from H2O and 0.011±0.003 mm from dissolved CO2, a total rate of 0.044 ±0.008 mm yr-1. Emissions incorporated in socio-economic models underlying the RCP 8.5 and 2.6 scenarios are used along with concentration-driven CMIP5 Earth System Models results to estimate future sea-level rise from FF combustion. From 2010 to 2100, RCP8.5 and 2.6 models respectively produce 9 ±2 mmSLR and 5 ±1 mmSLR from FF H2O+CO2. For perspective, these amounts are larger than the modelled contributions from loss of glaciers in the Andes. The direct contribution of FF emissions to SLR is small (1-2%) relative to current rates and projected estimates under RCP scenarios up to 2100. The magnitude is similar to SLR estimates from other minor sources such as the melting of floating ice, land-use emissions and produced water from oil operations, none of which are currently included in SLR assessments. As uncertainties in observations and contributions are reduced, small contribution factors, hitherto neglected, will become relatively more important in balancing the books. ReferenceGornitz, V., C. Rosenzweig, and D. Hillel, 1997: Effects of anthropogenic intervention in the land hydrological cycle on global sea level rise. Global and Planetary Change, 14, 147-161. DOI: 10.1016/S0921-8181(96)00008-2
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Adaptive accelerated ReaxFF reactive dynamics with validation from simulating hydrogen combustion.
Cheng, Tao; Jaramillo-Botero, Andrés; Goddard, William A; Sun, Huai
2014-07-02
We develop here the methodology for dramatically accelerating the ReaxFF reactive force field based reactive molecular dynamics (RMD) simulations through use of the bond boost concept (BB), which we validate here for describing hydrogen combustion. The bond order, undercoordination, and overcoordination concepts of ReaxFF ensure that the BB correctly adapts to the instantaneous configurations in the reactive system to automatically identify the reactions appropriate to receive the bond boost. We refer to this as adaptive Accelerated ReaxFF Reactive Dynamics or aARRDyn. To validate the aARRDyn methodology, we determined the detailed sequence of reactions for hydrogen combustion with and without the BB. We validate that the kinetics and reaction mechanisms (that is the detailed sequences of reactive intermediates and their subsequent transformation to others) for H2 oxidation obtained from aARRDyn agrees well with the brute force reactive molecular dynamics (BF-RMD) at 2498 K. Using aARRDyn, we then extend our simulations to the whole range of combustion temperatures from ignition (798 K) to flame temperature (2998K), and demonstrate that, over this full temperature range, the reaction rates predicted by aARRDyn agree well with the BF-RMD values, extrapolated to lower temperatures. For the aARRDyn simulation at 798 K we find that the time period for half the H2 to form H2O product is ∼538 s, whereas the computational cost was just 1289 ps, a speed increase of ∼0.42 trillion (10(12)) over BF-RMD. In carrying out these RMD simulations we found that the ReaxFF-COH2008 version of the ReaxFF force field was not accurate for such intermediates as H3O. Consequently we reoptimized the fit to a quantum mechanics (QM) level, leading to the ReaxFF-OH2014 force field that was used in the simulations.
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Total renin after gonadotropin stimulation in polycystic ovarian disease.
Matinlauri, I; Anttila, L; Jaatinen, T A; Koskinen, P; Aalto, M; Irjala, K; Nikkanen, V
1995-02-01
To examine the influence of polycystic ovarian disease (PCOD) on the levels of total renin in plasma and follicular fluid (FF) after stimulation with hMG. Comparative study of the plasma and FF concentrations of total renin in women with and without PCOD after stimulation with hMG. In vitro fertilization-embryo transfer program at the Department of Obstetrics and Gynecology, the University Central Hospital of Turku, Finland. Thirty-six women undergoing IVF-ET for infertility with (n = 10) or without (n = 26) ultrasonographically diagnosed PCOD. Of the latter group, 15 women had tubal infertility, and the rest suffered from an anovulatory infertility and reacted with PCO-like ovarian response to stimulation. The concentrations of total renin in plasma and FF, serum E2, and protein in FF. The concentrations of plasma total renin after the gonadotropin stimulation were significantly higher in the PCOD and PCO-like groups when compared with the tubal group. The concentration of total renin in FF and the ratio of total renin per protein in FF were higher in the PCOD and PCO-like groups than in the tubal group, but the differences did not reach statistical significance. Positive correlations were found between the plasma total renin and serum E2 concentrations in the PCO-like and in the tubal group and between plasma total renin concentrations and the number of mature follicles in all groups. Follicular fluid total renin did not correlate with FF protein in any group. All findings were independent of the total hMG dosage used and the body mass index of the patients. In the present study the concentrations of total renin in plasma were enhanced markedly after gonadotropin stimulation in women with PCOD compared with women having tubal infertility. The pattern of the hormonal secretions revealed a group of infertile patients reacting biochemically like women with PCOD.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kainz, K; Lawton, C; Li, X
2015-06-15
Purpose: To compare the dosimetry and delivery of burst-mode modulated arc radiotherapy using flattening-filter-free (FFF) and flattening-filtered (FF) beams. Methods: Burst-mode modulated arc therapy (mARC, Siemens) plans were generated for six prostate cases with FFF and FF beam models, using the Elekta Monaco v. 5.00 planning system. One 360-degree arc was used for five cases, and for one case two 360-degree coplanar arcs were used. The maximum number of optimization points (OPs) per arc was set to 91, and OPs with less than 4 MU were disregarded. All plans were delivered on the Siemens Artiste linear accelerator with 6MV FFmore » (300 MU/min) and comparable-energy FFF (2000 MU/min, labeled as 7UF) beams. Results: For all cases studied, the plans with FFF beams exhibited DVHs for the PTV, rectum, and bladder that were nearly identical to those for the plans with FF beams. The FFF plan yielded reduced dose to the right femoral head for 5 cases, and lower mean dose to the left femoral head for 4 cases. For all but the two-arc case, the FFF and FF plans resulted in an identical number of segments. The total number of MUs was slightly lower for the FF plans for five cases. The total delivery time per fraction was substantially lower for the FFF plans, ranging from 25 to 50 percent among all cases, as compared to the FF plans. Conclusion: For mARC plans, FFF and FF beams provided comparable PTV coverage and rectum and bladder sparing. For the femoral heads, the mean dose was slightly lower in most cases when using the FFF beam. Although the flat beam plans typically required slightly fewer MUs, FFF beams required substantially less time to deliver a plan of similar quality. This work was supported by Siemens Medical Solutions and the MCW Cancer Center Fotsch Foundation.« less
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Nishimura, Jihei; Dewa, Yasuaki; Muguruma, Masako; Kuroiwa, Yuichi; Yasuno, Hiroaki; Shima, Tomomi; Jin, Mailan; Takahashi, Miwa; Umemura, Takashi; Mitsumori, Kunitoshi
2007-05-01
To investigate the relationship between fenofibrate (FF) and oxidative stress, enzymatic, histopathological, and molecular biological analyses were performed in the liver of male F344 rats fed 2 doses of FF (Experiment 1; 0 and 6000 ppm) for 3 weeks and 3 doses (Experiment 2; 0, 3000, and 6000 ppm) for 9 weeks. FF treatment increased the activity of enzymes such as carnitine acetyltransferase, carnitine palmitoyltransferase, fatty acyl-CoA oxidizing system, and catalase in the liver. However, it decreased those of superoxide dismutase in the liver in both experiments. Increased 8-hydroxy-2'-deoxyguanosine levels in liver DNA and lipofuscin accumulation were observed in the treated rats of Experiment 2. In vitro measurement of reactive oxygen species (ROS) in rat liver microsomes revealed a dose-dependent increase due to FF treatment. Microarray (only Experiment 1) or real-time reverse transcription-polymerase chain reaction analyses revealed that the expression levels of metabolism and DNA repair-related genes such as Aco, Cyp4a1, Cat, Yc2, Gpx2, Apex1, Xrcc5, Mgmt, Mlh1, Gadd45a, and Nbn were increased in FF-treated rats. These results provide evidence of a direct or indirect relationship between oxidative stress and FF treatment. In addition, increases in the expression levels of cell cycle-related genes such as Chek1, Cdc25a, and Ccdn1; increases in the expression levels of cell proliferation-related genes such as Hdgfrp3 and Vegfb; and fluctuations in the expression levels of apoptosis-related genes such as Casp11 and Trp53inp1 were observed in these rats. This suggests that cell proliferation induction, apoptosis suppression, and DNA damage due to oxidative stresses are probably involved in the mechanism of hepatocarcinogenesis due to FF in rats.
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Diané, Abdoulaye; Pierce, W David; Russell, James C; Heth, C Donald; Vine, Donna F; Richard, Denis; Proctor, Spencer D
2014-03-14
We hypothesised that hypothalamic feeding-related neuropeptides are differentially expressed in obese-prone and lean-prone rats and trigger overeating-induced obesity. To test this hypothesis, in the present study, we measured energy balance and hypothalamic neuropeptide Y (NPY) and pro-opiomelanocortin (POMC) mRNA expressions in male JCR:LA-cp rats. We compared, in independent cohorts, free-feeding obese-prone (Obese-FF) and lean-prone (Lean-FF) rats at pre-weaning (10 d old), weaning (21-25 d old) and early adulthood (8-12 weeks). A group of Obese-pair-feeding (PF) rats pair-fed to the Lean-FF rats was included in the adult cohort. The body weights of 10-d-old Obese-FF and Lean-FF pups were not significantly different. However, when the pups were shifted from dams' milk to solid food (weaning), the obese-prone rats exhibited more energy intake over the days than the lean-prone rats and higher body and fat pad weights and fasting plasma glucose, leptin, insulin and lipid levels. These differences were consistent with higher energy consumption and lower energy expenditure. In the young adult cohort, the differences between the Obese-FF and Lean-FF rats became more pronounced, yielding significant age effects on most of the parameters of the metabolic syndrome, which were reduced in the Obese-PF rats. The obese-prone rats displayed higher NPY expression than the lean-prone rats at pre-weaning and weaning, and the expression levels did not differ by age. In contrast, POMC expression exhibited significant age-by-genotype differences. At pre-weaning, there was no genotype difference in POMC expression, but in the weanling cohort, obese-prone pups exhibited lower POMC expression than the lean-prone rats. This genotype difference became more pronounced at adulthood. Overall, the development of hyperphagia-induced obesity in obese-prone JCR rats is related to POMC expression down-regulation in the presence of established NPY overexpression.
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Hollingsworth, Julia; Lau, Angela; Tone, Alicia; Kollara, Alexandra; Allen, Lisa; Colgan, Terence J; Dube, Valerie; Rosen, Barry; Murphy, K Joan; Greenblatt, Ellen M; Feigenberg, Tomer; Virtanen, Carl; Brown, Theodore J
2018-05-28
Germline BRCA1 or BRCA2 mutations (mtBRCA1 and mtBRCA2) increase risk for high-grade serous ovarian cancer (HGSOC), the most commonly diagnosed epithelial ovarian cancer histotype. Other identified risk factors for this cancer, which originates primarily in the distal fallopian tube epithelium (FTE), implicate ovulation, during which the FTE cells become transiently exposed to follicular fluid (FF). To test whether mtBRCA1 or mtBRCA2 nonmalignant FTE cells respond differently to periovulatory FF exposure than control patient FTE cells, gene expression profiles from primary FTE cultures derived from BRCA1 or BRCA2 mutation carriers or control patients were compared at baseline, 24 hours after FF exposure, and 24 hours after FF replacement with culture medium. Hierarchical clustering revealed both FF exposure and BRCA mutation status affect gene expression, with BRCA1 mutation having the greatest impact. Gene set enrichment analysis revealed increased NFκB and EGFR signaling at baseline in mtBRCA1 samples, with increased interferon target gene expression, including members of the ISGylation pathway, observed after recovery from FF exposure. Gene set enrichment analysis did not identify altered pathway signaling in mtBRCA2 samples. An inverse relationship between EGFR signaling and ISGylation with BRCA1 protein levels was verified in an immortalized FTE cell line, OE-E6/E7, stably transfected with BRCA1 cDNA. Suppression of ISG15 and ISGylated protein levels by increased BRCA1 expression was found to be mediated by decreased NFκB signaling. These studies indicate that increased NFκB signaling associated with decreased BRCA1 expression results in increased ISG15 and protein ISGylation following FF exposure, which may be involved in predisposition to HGSOC. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.
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Hsieh, Chih-Chen; Jain, Semant; Larson, Ronald G
2006-01-28
A very stiff finitely extensible nonlinear elastic (FENE)-Fraenkel spring is proposed to replace the rigid rod in the bead-rod model. This allows the adoption of a fast predictor-corrector method so that large time steps can be taken in Brownian dynamics (BD) simulations without over- or understretching the stiff springs. In contrast to the simple bead-rod model, BD simulations with beads and FENE-Fraenkel (FF) springs yield a random-walk configuration at equilibrium. We compare the simulation results of the free-draining bead-FF-spring model with those for the bead-rod model in relaxation, start-up of uniaxial extensional, and simple shear flows, and find that both methods generate nearly identical results. The computational cost per time step for a free-draining BD simulation with the proposed bead-FF-spring model is about twice as high as the traditional bead-rod model with the midpoint algorithm of Liu [J. Chem. Phys. 90, 5826 (1989)]. Nevertheless, computations with the bead-FF-spring model are as efficient as those with the bead-rod model in extensional flow because the former allows larger time steps. Moreover, the Brownian contribution to the stress for the bead-FF-spring model is isotropic and therefore simplifies the calculation of the polymer stresses. In addition, hydrodynamic interaction can more easily be incorporated into the bead-FF-spring model than into the bead-rod model since the metric force arising from the non-Cartesian coordinates used in bead-rod simulations is absent from bead-spring simulations. Finally, with our newly developed bead-FF-spring model, existing computer codes for the bead-spring models can trivially be converted to ones for effective bead-rod simulations merely by replacing the usual FENE or Cohen spring law with a FENE-Fraenkel law, and this convertibility provides a very convenient way to perform multiscale BD simulations.
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Respiratory protection from isocyanate exposure in the autobody repair and refinishing industry.
Liu, Youcheng; Stowe, Meredith H; Bello, Dhimiter; Woskie, Susan R; Sparer, Judy; Gore, Rebecca; Youngs, Fred; Cullen, Mark R; Redlich, Carrie A
2006-05-01
This study, part of the Survey of Painters and Repairers of Auto bodies by Yale (SPRAY), evaluated the effectiveness of respiratory protection against exposure to aliphatic polyisocyanates. A total of 36 shops were assessed for respiratory protection program completeness; 142 workers were measured for respirator fit factor (FF) using PortaCount Plus respirator fit tester. Twenty-two painters from 21 shops were sampled using NIOSH method 5525 to determine the workplace protection factor (WPF) of negative pressure, air-purifying half-facepiece respirators equipped with organic vapor cartridges and paint prefilters during spray-painting and priming activities. Only 11 shops (30%) had written respiratory protection programs. Eighty percent of all fit tested workers passed the test on the first try with FF >or= 100, and 92% passed the second test after respirator use training. Overall geometric mean (GM) FF was 1012 for all fit tested workers. Significant differences on pass rate (92% vs. 72%) and on FF (1990 vs. 736) were found between previously fit tested workers vs. nontested workers. Twenty-nine WPF samples were collected. The outside facepiece GM concentration of total isocyanate group (NCO) was 378.4 micro g NCO/m(3) with 96% concentrations exceeding the U.K. short-term exposure limit, 70 micro g NCO/m(3), but no in-facepiece concentrations exceeded the limit. The GM WPF of total NCO was 319 (GSD 4) and the 5th percentile was 54. WPF of total NCO was positively correlated with the duration of painting task. FF positively correlated with WPF when FF was
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NASA Astrophysics Data System (ADS)
Hsieh, Chih-Chen; Jain, Semant; Larson, Ronald G.
2006-01-01
A very stiff finitely extensible nonlinear elastic (FENE)-Fraenkel spring is proposed to replace the rigid rod in the bead-rod model. This allows the adoption of a fast predictor-corrector method so that large time steps can be taken in Brownian dynamics (BD) simulations without over- or understretching the stiff springs. In contrast to the simple bead-rod model, BD simulations with beads and FENE-Fraenkel (FF) springs yield a random-walk configuration at equilibrium. We compare the simulation results of the free-draining bead-FF-spring model with those for the bead-rod model in relaxation, start-up of uniaxial extensional, and simple shear flows, and find that both methods generate nearly identical results. The computational cost per time step for a free-draining BD simulation with the proposed bead-FF-spring model is about twice as high as the traditional bead-rod model with the midpoint algorithm of Liu [J. Chem. Phys. 90, 5826 (1989)]. Nevertheless, computations with the bead-FF-spring model are as efficient as those with the bead-rod model in extensional flow because the former allows larger time steps. Moreover, the Brownian contribution to the stress for the bead-FF-spring model is isotropic and therefore simplifies the calculation of the polymer stresses. In addition, hydrodynamic interaction can more easily be incorporated into the bead-FF-spring model than into the bead-rod model since the metric force arising from the non-Cartesian coordinates used in bead-rod simulations is absent from bead-spring simulations. Finally, with our newly developed bead-FF-spring model, existing computer codes for the bead-spring models can trivially be converted to ones for effective bead-rod simulations merely by replacing the usual FENE or Cohen spring law with a FENE-Fraenkel law, and this convertibility provides a very convenient way to perform multiscale BD simulations.
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Balakrishnan, Swati; Sarma, Siddhartha P
2017-08-22
Aromatic interactions are an important force in protein folding as they combine the stability of a hydrophobic interaction with the selectivity of a hydrogen bond. Much of our understanding of aromatic interactions comes from "bioinformatics" based analyses of protein structures and from the contribution of these interactions to stabilizing secondary structure motifs in model peptides. In this study, the structural consequences of aromatic interactions on protein folding have been explored in engineered mutants of the molten globule protein apo-cytochrome b 5 . Structural changes from disorder to order due to aromatic interactions in two variants of the protein, viz., WF-cytb5 and FF-cytb5, result in significant long-range secondary and tertiary structure. The results show that 54 and 52% of the residues in WF-cytb5 and FF-cytb5, respectively, occupy ordered regions versus 26% in apo-cytochrome b 5 . The interactions between the aromatic groups are offset-stacked and edge-to-face for the Trp-Phe and Phe-Phe mutants, respectively. Urea denaturation studies indicate that both mutants have a C m higher than that of apo-cytochrome b 5 and are more stable to chaotropic agents than apo-cytochrome b 5 . The introduction of these aromatic residues also results in "trimer" interactions with existing aromatic groups, reaffirming the selectivity of the aromatic interactions. These studies provide insights into the aromatic interactions that drive disorder-to-order transitions in intrinsically disordered regions of proteins and will aid in de novo protein design beyond small peptide scaffolds.
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NASA Astrophysics Data System (ADS)
Heredia, A.; Bdikin, I.; Kopyl, S.; Mishina, E.; Semin, S.; Sigov, A.; German, K.; Bystrov, V.; Gracio, J.; Kholkin, A. L.
2010-11-01
Diphenylalanine (FF) peptide nanotubes (PNTs) represent a unique class of self-assembled functional biomaterials owing to a wide range of useful properties including nanostructural variability, mechanical rigidity and chemical stability. In addition, strong piezoelectric activity has recently been observed paving the way to their use as nanoscale sensors and actuators. In this work, we fabricated both horizontal and vertical FF PNTs and examined their optical second harmonic generation and local piezoresponse as a function of temperature. The measurements show a gradual decrease in polarization with increasing temperature accompanied by an irreversible phase transition into another crystalline phase at about 140-150 °C. The results are corroborated by the molecular dynamic simulations predicting an order-disorder phase transition into a centrosymmetric (possibly, orthorhombic) phase with antiparallel polarization orientation in neighbouring FF rings. Partial piezoresponse hysteresis indicates incomplete polarization switching due to the high coercive field in FF PNTs.
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Lee, James T; Liau, Joy; Murphy, Paul; Schroeder, Michael E; Sirlin, Claude B; Bydder, Mark
2012-05-01
The purpose of this study was to investigate the relationship between liver fat fraction (FF) and diffusion parameters derived from the intravoxel incoherent motion (IVIM) model. Thirty-six subjects with suspected nonalcoholic fatty liver disease underwent diffusion-weighted magnetic resonance imaging with 10 b-values and spoiled gradient recalled echo imaging with six echoes for fat quantification. Correlations were measured between FF, transverse relaxivity (R2), diffusivity (D) and perfusion fraction (f). The primary finding was that no significant correlation was obtained for D vs. FF or f vs. FF. Significant correlations were obtained for D vs. R2 (r=-0.490, P=.002) and f vs. D (r=-0.458, P=.005). The conclusion is that hepatic steatosis does not affect measurement of perfusion or diffusion and therefore is unlikely to confound the use of apparent diffusivity to evaluate hepatic fibrosis. Copyright © 2012 Elsevier Inc. All rights reserved.
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Universal dimer–dimer scattering in lattice effective field theory
DOE Office of Scientific and Technical Information (OSTI.GOV)
Elhatisari, Serdar; Katterjohn, Kris; Lee, Dean
We consider two-component fermions with short-range interactions and large scattering length. This system has universal properties that are realized in several different fields of physics. In the limit of large fermion–fermion scattering length a ff and zero-range interaction, all properties of the system scale proportionally with a ff. For the case with shallow bound dimers, we calculate the dimer–dimer scattering phase shifts using lattice effective field theory. We extract the universal dimer–dimer scattering length a dd/a ff=0.618(30) and effective range r dd/a ff=-0.431(48). This result for the effective range is the first calculation with quantified and controlled systematic errors. Wemore » also benchmark our methods by computing the fermion–dimer scattering parameters and testing some predictions of conformal scaling of irrelevant operators near the unitarity limit.« less
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NASA Astrophysics Data System (ADS)
Gan, Zhixing; Zhou, Weiping; Chen, Zhihui; Wang, Huan; Di, Yunsong; Huang, Shisong
2016-11-01
A diphenylalanine (L-Phe-L-Phe, FF)-carbon nitride composite film is designed and fabricated to visualize the deep ultraviolet (DUV, 245-290 nm) photons. The FF film, composed of diphenylalanine molecules, doped with carbon nitrides shows blue emission under excitation of DUV light, which makes the DUV beam observable. Both Förster resonance energy transfer and cascade photon reabsorption contribute to the conversion of photon energy. First, the FF is excited by the DUV photons. On one hand, the energy transfers to the embedded carbon nitrides through nonradiative dipole-dipole couplings. On the other hand, the 284 nm photons emitted from the FF would further excite the carbon nitrides, which will finally convert to blue fluorescence. Herein, the experimental demonstration of a simple device for the visualization of high DUV fluxes is reported.
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Wettability and friction coefficient of micro-magnet arrayed surface
NASA Astrophysics Data System (ADS)
Huang, Wei; Liao, Sijie; Wang, Xiaolei
2012-01-01
Surface coating is an important part of surface engineering and it has been successfully used in many applications to improve the performance of surfaces. In this paper, magnetic arrayed films with different thicknesses were fabricated on the surface of 316 stainless steel disks. Controllable colloid - ferrofluids (FF) was chosen as lubricant, which can be adsorbed on the magnetic surface. The wettability of the micro-magnet arrayed surface was evaluated by measuring the contract angle of FF drops on surface. Tribological experiments were carried out to investigate the effects of magnetic film thickness on frictional properties when lubricated by FF under plane contact condition. It was found that the magnetic arrayed surface with thicker magnetic films presented larger contract angle. The frictional test results showed that samples with thicker magnetic films could reduce friction and wear more efficiently at higher sliding velocity under the lubrication of FF.
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Universal dimer–dimer scattering in lattice effective field theory
Elhatisari, Serdar; Katterjohn, Kris; Lee, Dean; ...
2017-03-14
We consider two-component fermions with short-range interactions and large scattering length. This system has universal properties that are realized in several different fields of physics. In the limit of large fermion–fermion scattering length a ff and zero-range interaction, all properties of the system scale proportionally with a ff. For the case with shallow bound dimers, we calculate the dimer–dimer scattering phase shifts using lattice effective field theory. We extract the universal dimer–dimer scattering length a dd/a ff=0.618(30) and effective range r dd/a ff=-0.431(48). This result for the effective range is the first calculation with quantified and controlled systematic errors. Wemore » also benchmark our methods by computing the fermion–dimer scattering parameters and testing some predictions of conformal scaling of irrelevant operators near the unitarity limit.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Lynch, Vickie E.; Borreguero, Jose M.; Bhowmik, Debsindhu
Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parametersmore » which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.« less
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Pauli, Samuel A; Session, Donna R; Shang, Weirong; Easley, Kirk; Wieser, Friedrich; Taylor, Robert N; Pierzchalski, Keely; Napoli, Joseph L; Kane, Maureen A; Sidell, Neil
2013-09-01
Retinol (ROL) and its biologically active metabolite, all-trans retinoic acid (ATRA), are essential for a number of reproductive processes. However, there is a paucity of information regarding their roles in ovarian folliculogenesis, oocyte maturation, and early embryogenesis. The objectives of this study were to quantify and compare peripheral plasma (PP) and follicular fluid (FF) retinoid levels, including ATRA in women undergoing in vitro fertilization (IVF) and to investigate the relationship between retinoid levels and embryo quality. Retinoid levels were evaluated in PP and FF from 79 women undergoing IVF at the time of oocyte retrieval and corresponding embryo quality assessed on a daily basis after retrieval for 3 days until uterine transfer. Analysis compared the retinoid levels with day 3 embryo grades and between endometriosis versus control patients. Results demonstrated distinctive levels of retinoid metabolites and isomers in FF versus PP. There was a significantly larger percentage of high-quality grade I embryos derived from the largest versus smallest follicles. An increase in follicle size also correlated with a >50% increase in FF ROL and ATRA concentrations. Independent of follicle size, FF yielding grade I versus nongrade I embryos showed higher mean levels of ATRA but not ROL. In a nested case-control analysis, control participants had 50% higher mean levels of ATRA in their FF and PP than women with endometriosis. These findings strongly support the proposition that ATRA plays a fundamental role in oocyte development and quality, and that reduced ATRA synthesis may contribute to decreased fecundity of participants with endometriosis.
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Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.
Vanommeslaeghe, K; MacKerell, A D
2012-12-21
Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF's complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/ .
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Neutron production from flattening filter free high energy medical linac: A Monte Carlo study
NASA Astrophysics Data System (ADS)
Najem, M. A.; Abolaban, F. A.; Podolyák, Z.; Spyrou, N. M.
2015-11-01
One of the problems arising from using a conventional linac at high energy (>8 MV) is the production of neutrons. One way to reduce neutron production is to remove the flattening filter (FF). The main purpose of this work was to study the effect of FF removal on neutron fluence and neutron dose equivalent inside the treatment room at different photon beam energies. Several simulations based on Monte Carlo techniques were carried out in order to calculate the neutron fluence at different locations in the treatment room from different linac energies with and without a FF. In addition, a step-and-shoot intensity modulated radiotherapy (SnS IMRT) for prostate cancer was modelled using the 15 MV photon beam with and without a FF on a water phantom to calculate the neutron dose received in a full treatment. The results obtained show a significant drop-off in neutrons fluence and dose equivalent when the FF was removed. For example, the neutron fluence was decreased by 54%, 76% and 75% for 10, 15 and 18 MV, respectively. This can decrease the neutron dose to the patient as well as reduce the shielding cost of the treatment room. The neutron dose equivalent of the SnS IMRT for prostate cancer was reduced significantly by 71.3% when the FF was removed. It can be concluded that the flattening filter removal from the head of the linac could reduce the risk of causing secondary cancers and the shielding cost of radiotherapy treatment rooms.
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Analysis of Follicular Fluid Retinoids in Women Undergoing In Vitro Fertilization
Pauli, Samuel A.; Session, Donna R.; Shang, Weirong; Easley, Kirk; Wieser, Friedrich; Taylor, Robert N.; Pierzchalski, Keely; Napoli, Joseph L.; Kane, Maureen A.
2013-01-01
Retinol (ROL) and its biologically active metabolite, all-trans retinoic acid (ATRA), are essential for a number of reproductive processes. However, there is a paucity of information regarding their roles in ovarian folliculogenesis, oocyte maturation, and early embryogenesis. The objectives of this study were to quantify and compare peripheral plasma (PP) and follicular fluid (FF) retinoid levels, including ATRA in women undergoing in vitro fertilization (IVF) and to investigate the relationship between retinoid levels and embryo quality. Retinoid levels were evaluated in PP and FF from 79 women undergoing IVF at the time of oocyte retrieval and corresponding embryo quality assessed on a daily basis after retrieval for 3 days until uterine transfer. Analysis compared the retinoid levels with day 3 embryo grades and between endometriosis versus control patients. Results demonstrated distinctive levels of retinoid metabolites and isomers in FF versus PP. There was a significantly larger percentage of high-quality grade I embryos derived from the largest versus smallest follicles. An increase in follicle size also correlated with a >50% increase in FF ROL and ATRA concentrations. Independent of follicle size, FF yielding grade I versus nongrade I embryos showed higher mean levels of ATRA but not ROL. In a nested case–control analysis, control participants had 50% higher mean levels of ATRA in their FF and PP than women with endometriosis. These findings strongly support the proposition that ATRA plays a fundamental role in oocyte development and quality, and that reduced ATRA synthesis may contribute to decreased fecundity of participants with endometriosis. PMID:23427183
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McCallister, Andrew; Zhang, Le; Burant, Alex; Katz, Laurence; Branca, Rosa Tamara
2017-11-01
To assess the spatial correlation between MRI and 18F-fludeoxyglucose positron emission tomography (FDG-PET) maps of human brown adipose tissue (BAT) and to measure differences in fat fraction (FF) between glucose avid and non-avid regions of the supraclavicular fat depot using a hybrid FDG-PET/MR scanner. In 16 healthy volunteers, mean age of 30 and body mass index of 26, FF, R2*, and FDG uptake maps were acquired simultaneously using a hybrid PET/MR system while employing an individualized cooling protocol to maximally stimulate BAT. Fourteen of the 16 volunteers reported BAT-positive FDG-PET scans. MR FF maps of BAT correlate well with combined FDG-PET/MR maps of BAT only in subjects with intense glucose uptake. The results indicate that the extent of the spatial correlation positively correlates with maximum FDG uptake in the supraclavicular fat depot. No consistent, significant differences were found in FF or R2* between FDG avid and non-avid supraclavicular fat regions. In a few FDG-positive subjects, a small but significant linear decrease in BAT FF was observed during BAT stimulation. MR FF, when used in conjunction with FDG uptake maps, can be seen as a valuable, radiation-free alternative to CT and can be used to measure tissue hydration and lipid consumption in some subjects. Magn Reson Med 78:1922-1932, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.
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303-K Storage Facility closure plan. Revision 2
DOE Office of Scientific and Technical Information (OSTI.GOV)
Not Available
1993-12-15
Recyclable scrap uranium with zircaloy-2 and copper silicon alloy, uranium-titanium alloy, beryllium/zircaloy-2 alloy, and zircaloy-2 chips and fines were secured in concrete billets (7.5-gallon containers) in the 303-K Storage Facility, located in the 300 Area. The beryllium/zircaloy-2 alloy and zircaloy-2 chips and fines are designated as mixed waste with the characteristic of ignitability. The concretion process reduced the ignitability of the fines and chips for safe storage and shipment. This process has been discontinued and the 303-K Storage Facility is now undergoing closure as defined in the Resource Conservation and Recovery Act (RCRA) of 1976 and the Washington Administrative Codemore » (WAC) Dangerous Waste Regulations, WAC 173-303-040. This closure plan presents a description of the 303-K Storage Facility, the history of materials and waste managed, and the procedures that will be followed to close the 303-K Storage Facility. The 303-K Storage Facility is located within the 300-FF-3 (source) and 300-FF-5 (groundwater) operable units, as designated in the Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) (Ecology et al. 1992). Contamination in the operable units 300-FF-3 and 300-FF-5 is scheduled to be addressed through the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) of 1980 remedial action process. Therefore, all soil remedial action at the 304 Facility will be conducted as part of the CERCLA remedial action of operable units 300-FF-3 and 300-FF-5.« less
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Cheng, Baochang; Yan, Yufei; Qi, Jingjing; Deng, Lianfu; Shao, Zeng-Wu; Zhang, Ke-Qin; Li, Bin; Sun, Ziling; Li, Xinming
2018-04-18
Silk fibroin (SF) from Bombyx mori has received increasing interest in biomedical fields, because of its slow biodegradability, good biocompatibility, and low immunogenicity. Although SF-based hydrogels have been studied intensively as a potential matrix for tissue engineering, weak gelation performance and low mechanical strength are major limitations that hamper their widespread applicability. Therefore, searching for new strategies to improve the SF gelation property is highly desirable in tissue engineering research. Herein, we report a facile approach to induce rapid gelation of SF by a small peptide gelator (e.g., NapFF). Following the simple mixing of SF and NapFF in water, a stable hydrogel of SF was obtained in a short time period at physiological pH, and the minimum gelation concentration of SF can reach as low as 0.1%. In this process of gelation, NapFF not only can behave itself as a gelator for supramolecular self-assembly, but also can trigger the conformational transition of the SF molecule from random coil to β-sheet structure via hydrophobic and hydrogen-bonding interactions. More importantly, for the generation of a scaffold with favorable cell-surface interactions, a new peptide gelator (NapFFRGD) with Arg-Gly-Asp (RGD) domain was applied to functionalize SF hydrogel with improved bioactivity for cell adhesion and growth. Following encapsulating the vascular endothelial growth factor (VEGF), the SF gel was subcutaneously injected in mice, and served as an effective matrix to trigger the generation of new blood capillaries in vivo.
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5. Historic American Buildings Survey Frank O. Branzetti, Photographer July ...
5. Historic American Buildings Survey Frank O. Branzetti, Photographer July 8, 1940 (ff) 4- MILE STONE, opp. 862 HUNTINGTON AVE., ROXBURY - Milestones D, Y, Z, AA, BB, FF & NN, Various Roxbury locations, Roxbury, Suffolk County, MA
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CO2 Emissions from the Los Angeles Basin During Spring of 2010 - Measurements vs. Model
NASA Astrophysics Data System (ADS)
Newman, S.; Jeong, S.; Fischer, M. L.; Xu, X.; Gurney, K. R.; Alvarez, S. L.; Rappenglueck, B.; Haman, C. L.; Lefer, B. L.; Miller, C. E.; Yung, Y. L.
2011-12-01
More than half of the world's population now lives in urban areas, contributing large fluxes of greenhouse gas to the atmosphere. Quantifying the spatiotemporal distribution of these emissions is critical for providing independent verification of future mitigation activities. We have used high precision measurements of CO2 and CO to determine the contribution of fossil fuel combustion (ffCO2 mixing ratio) to the total CO2 emissions in the Los Angeles basin during the CalNex-LA ground campaign of May-June 2010 in Pasadena. The ratio of COxs/CO2xs (the excess of each species above free tropospheric levels) varies significantly by time of day, giving a proxy for the fraction of ffCO2/CO2xs. Using an emission ratio for CO/CO2 for fossil fuel combustion of 0.011±0.002 (Wunch et al., 2009, Geophys Res Lett 36, L15810), we determined that burning of fossil fuels contributed ~50% overnight - 100% during midday of the total local contribution, resulting in ffCO2 of 13 - 23 ppm, respectively. These values compare very well with those calculated from Δ14C for measurements of two samples aggregated from 7-8 flask samples collected at 14:00 PST on alternate days during the first and second half of the CalNex-LA campaign: 17 and 24 ppm ffCO2, respectively. We then compared the measured values of ffCO2 with predictions combining a diurnally averaged version of the Vulcan 2.0 ffCO2 emission inventory (http://www.purdue.edu/eas/carbon/vulcan/index.php) and mesoscale transport computed with the Weather Research and Forecast (WRF) and Stochastic Time-Inverted Lagrangian Transport (STILT) models. To evaluate transport model uncertainty, we compared predicted and measured planetary boundary layer height (PBLH) and found WRF predictions compared favorably with ceilometer measurements made during the day at the Pasadena site. Initial comparison of the diurnal cycle of ffCO2 determined by the CO/CO2 ratios to that predicted with a temporally constant map of diurnal mean emissions shows the prediction to have a larger diurnal amplitude than the measurements, suggesting that the diurnal cycle of emitted ffCO2 compensates for daytime dilution in the PBL.
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Lötvall, Jan; Bleecker, Eugene R; Busse, William W; O'Byrne, Paul M; Woodcock, Ashley; Kerwin, Edward M; Stone, Sally; Forth, Richard; Jacques, Loretta; Bateman, Eric D
2014-01-01
Inhaled corticosteroids (ICSs) improve asthma disease control; once-daily ICS administration may have advantages for patients. Our objective was to assess the efficacy and safety of the novel ICS fluticasone furoate (FF) over 24 weeks versus placebo. This was a 24-week double-blind, double-dummy, placebo- and active-controlled study (NCT01159912) of 343 asthma patients (≥12 years) not controlled by their current ICS. Patients were randomised (1:1:1) to FF100 μg, placebo (both administered once-daily [OD] via ELLIPTA™ dry powder inhaler in the evening) or fluticasone propionate (FP) 250 μg (administered twice-daily (BD) via DISKUS™/ACCUHALER™). Primary endpoint was change from baseline in pre-dose evening forced expiratory volume in 1s (FEV1) at Week 24; change from baseline in % rescue-free 24-h periods was a powered secondary endpoint. Adverse events (AEs) were assessed. FF100 μg OD and FP250 μg BD significantly improved pre-dose evening FEV1 compared with placebo at Week 24 (+146 ml [p = 0.009] and +145 ml [p = 0.011], respectively). Percentage of rescue-free 24-h periods was increased with FF100 μg OD (+14.8%) and FP250 μg BD (+17.9%) compared to placebo (both p < 0.001). On-treatment AEs were reported by 53% (FF100 μg OD), 42% (FP250 μg BD) and 40% (placebo) of patients. On-treatment severe asthma exacerbations were lower with FF100 μg OD (3%) and FP250 μg BD (2%) than placebo (7%). There was significant suppression of urinary cortisol at week 24 with FF100 μg OD (p = 0.030) and FP250 μg BD (p = 0.036) relative to placebo. FF100 μg OD, administered in the evening, achieves significant improvements in lung function and rescue inhaler use over 24 weeks, comparable to FP250 μg BD with similar safety profile. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.
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Manenti, Guglielmo; Capuani, Silvia; Fanucci, Ezio; Assako, Elie Parfait; Masala, Salvatore; Sorge, Roberto; Iundusi, Riccardo; Tarantino, Umberto; Simonetti, Giovanni
2013-07-01
We assessed the potential of diffusion tensor imaging (DTI) in combination with proton magnetic resonance spectroscopy (1H-MRS), in cancellous bone quality evaluation of the femoral neck in postmenopausal women. DTI allows for non-invasive microarchitectural characterization of heterogeneous tissue. In this work we hypothesized that DTI parameters mean diffusivity (MD) and fractional anisotropy (FA) of bone marrow water, can provide information about microstructural changes that occur with the development of osteoporosis disease. Because osteoporosis is associated with increased bone marrow fat content, which in principal can alter DTI parameters, the goal of this study was to examine the potential of MD and FA, in combination with bone marrow fat fraction (FF), to discriminate between healthy, osteopenic and osteoporotic subjects, classified according to DXA criteria. Forty postmenopausal women (mean age, 68.7 years; range 52-81 years), underwent a Dual-energy X-ray absorptiometry (DXA) examination in femoral neck, to be classified as healthy (n=12), osteopenic (n=14) and osteoporotic (n=14) subjects. 1H-MRS and DTI (with b value=2500 s/mm2) of femoral neck were obtained in each subject at 3T. The study protocol was approved by local Ethics Committee. MD, FA, FF and MD/FF, FA/FF were obtained and compared among the three bone-density groups. One-way ANOVA with multiple comparisons Bonferroni test and Pearson correlation analysis were applied. Receiver operating characteristic (ROC) curve analysis was also performed. Reproducibility of DTI measures was satisfactory. CV was approximately 2%-3% for MD and 4%-5% for FA measurements. Moreover, no significant difference was found in both MD and FA measurements between two separate sessions (median 34 days apart) comprised of six healthy volunteers. FF was able to discriminate between healthy and osteoporotic subjects only. Conversely MD and FA were able to discriminate healthy from osteopenic and healthy from osteoporotic subjects, but they were not able to discriminate between osteopenic and osteoporotic patients. A significant correlation between MD and FF was observed in healthy group only. A moderate correlation was found between MD and T-score when all groups together are considered. No significant correlation was found between MD and T-score within groups. A significant positive correlation between FA and FF was found in both osteopenic and osteoporotic groups. Vice-versa no correlation between FA and FF was observed in healthy group. A high significant positive correlation was found between FA and T-score in all groups together, in healthy and in osteoporotic groups. MD/FF and FA/FF are characterized by a higher sensitivity and specificity compared to MD and FA in the discrimination between healthy, and osteoporotic subjects. MD/FF vs. FA/FF graph extracted from femoral neck, identify all healthy individuals according to DXA results. DTI-(1)H-MRS protocol performed in femoral neck seems to be highly sensitive and specific in identifying healthy subjects. A MR exam is more expensive when compared to a DXA investigation. However, even though DXA BMD evaluation has been the accepted standard for osteoporosis diagnosis, DXA result has a low predictive value on patients' risk for future fractures. Thus, new approaches for examining patients at risk for developing osteoporosis would be desirable. Preliminary results showed here suggest that future studies on a larger population based on DTI assessment in the femoral neck, in combination with 1H-MRS investigations, might allow screening of high-risk populations and the establishment of cut-off values of normality, with potential application of the method to single subjects. Copyright © 2013 Elsevier Inc. All rights reserved.
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Li, Jiang; Liu, Jun-Ling; Zhou, Hong-Jun; Fu, Yao
2016-06-08
Iron-based heterogeneous catalysts, which were generally prepared by pyrolysis of iron complexes on supports at elevated temperature, were found to be capable of catalyzing the transfer hydrogenation of furfural (FF) to furfuryl alcohol (FFA). The effects of metal precursor, nitrogen precursor, pyrolysis temperature, and support on catalytic performance were examined thoroughly, and a comprehensive study of the reaction parameters was also performed. The highest selectivity of FFA reached 83.0 % with a FF conversion of 91.6 % under the optimal reaction condition. Catalyst characterization suggested that iron cations coordinated by pyridinic nitrogen functionalities were responsible for the enhanced catalytic activity. The iron catalyst could be recycled without significant loss of catalytic activity for five runs, and the destruction of the nitrogen-iron species, the presence of crystallized Fe2 O3 phase, and the pore structure change were the main reasons for catalyst deactivation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Liquid Adsorption of Organic Compounds on Hematite α-Fe2O3 Using ReaxFF.
Chia, Chung-Lim; Avendaño, Carlos; Siperstein, Flor R; Filip, Sorin
2017-10-24
ReaxFF-based molecular dynamics simulations are used in this work to study the effect of the polarity of adsorbed molecules in the liquid phase on the structure and polarization of hematite (α-Fe 2 O 3 ). We compared the adsorption of organic molecules with different polarities on a rigid hematite surface and on a flexible and polarizable surface. We show that the displacements of surface atoms and surface polarization in a flexible hematite model are proportional to the adsorbed molecule's polarity. The increase in electrostatic interactions resulting from charge transfer in the outermost solid atoms in a flexible hematite model results in better-defined adsorbed layers that are less ordered than those obtained assuming a rigid solid. These results suggest that care must be taken when parametrizing empirical transferable force fields because the calculated charges on a solid slab in vacuum may not be representative of a real system, especially when the solid is in contact with a polar liquid.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Speelman, Amy L.; Zhang, Bo; Silakov, Alexey
2016-06-06
Dinitrosyl iron complexes (DNICs) are among the most abundant NO-derived cellular species. Monomeric DNICs can exist in the {Fe(NO) 2} 9 or {Fe(NO) 2} 10 oxidation state (in the Enemark -Feltham notation). However, experimental studies of analogous DNICs in both oxidation states are rare, which prevents a thorough understanding of the di ff erences in the electronic structures of these species. Here, the {Fe(NO) 2} 9 DNIC [Fe(dmp)(NO) 2](OTf) ( 1 ; dmp = 2,9-dimethyl-1,10- phenanthroline) is synthesized from a ferrous precursor via an unusual pathway, involving disproportionation of an {FeNO} 7 complex to yield the {Fe(NO) 2} 9 DNICmore » and a ferric species, which is subsequently reduced by NO gas to generate a ferrous complex that re-enters the reaction cycle. In contrast to most {Fe(NO) 2} 9 DNICs with neutral N-donor ligands, 1 exhibits high solution stability and can be characterized structurally and spectroscopically. Reduction of 1 yields the corresponding {Fe(NO) 2} 10 DNIC [Fe(dmp)(NO) 2](2). The Mo ssbauer isomer shift of 2 is 0.08 mm/s smaller than that of 1 , which indicates that the iron center is slightly more oxidized in the reduced complex. The nuclear resonance vibrational spectra (NRVS) of 1 and 2 are distinct and provide direct experimental insight into di ff erences in bonding in these complexes. In particular, the symmetric out-of-plane Fe -N - O bending mode is shifted to higher energy by 188 cm -1 in 2 in comparison to 1 . Using quantum chemistry centered normal coordinate analysis (QCC-NCA), this is shown to arise from an increase in Fe - NO bond order and a sti ff ening of the Fe(NO) 2 unit upon reduction of 1 to 2 . DFT calculations demonstrate that the changes in bonding arise from an iron- centered reduction which leads to a distinct increase in Fe - NO π -back-bonding in {Fe(NO) 2} 10 DNICs in comparison to the corresponding {Fe(NO) 2} 9 complexes, in agreement with all experimental findings. Finally, the implications of the electronic structure of DNICs for their reactivity are discussed, especially with respect to N-N bond formation in NO reductases.« less
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Nanostructures nucleation in carbon-metal gaseous phase: A molecular dynamics study
NASA Astrophysics Data System (ADS)
Galiullina, G. M.; Orekhov, N. D.; Stegailov, V. V.
2018-01-01
We perform nonequilibrium molecular dynamics simulation of carbon nanoclusters nucleation and early stages of growth from the gaseous phase. We analyze the catalytic effect of iron atoms on the nucleation kinetics and structure of the resultant nanoparticles. Reactive Force Field (ReaxFF) is used in the simulations for the description of bond formation and dissociation during the nucleation process at the nanoscale. The catalytic effect of iron reveals itself even on nanosecond simulation times: iron atoms accelerate the process of clustering but result in less graphitized carbon structures.
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Unorthodox theoretical methods
DOE Office of Scientific and Technical Information (OSTI.GOV)
Nedd, Sean
2012-01-01
The use of the ReaxFF force field to correlate with NMR mobilities of amine catalytic substituents on a mesoporous silica nanosphere surface is considered. The interfacing of the ReaxFF force field within the Surface Integrated Molecular Orbital/Molecular Mechanics (SIMOMM) method, in order to replicate earlier SIMOMM published data and to compare with the ReaxFF data, is discussed. The development of a new correlation consistent Composite Approach (ccCA) is presented, which incorporates the completely renormalized coupled cluster method with singles, doubles and non-iterative triples corrections towards the determination of heats of formations and reaction pathways which contain biradical species.