WorldWideScience

Sample records for location analysis reveals

  1. Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.

    Science.gov (United States)

    Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A P; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N

    2016-02-01

    Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. Copyright © 2016 by the Genetics Society of America.

  2. Detailed seismotectonic analysis of Sumatra subduction zone revealed by high precision earthquake location

    Science.gov (United States)

    Sagala, Ricardo Alfencius; Harjadi, P. J. Prih; Heryandoko, Nova; Sianipar, Dimas

    2017-07-01

    Sumatra was one of the most high seismicity regions in Indonesia. The subduction of Indo-Australian plate beneath Eurasian plate in western Sumatra contributes for many significant earthquakes that occur in this area. These earthquake events can be used to analyze the seismotectonic of Sumatra subduction zone and its system. In this study we use teleseismic double-difference method to obtain more high precision earthquake distribution in Sumatra subduction zone. We use a 3D nested regional-global velocity model. We use a combination of data from both of ISC (International Seismological Center) and BMKG (Agency for Meteorology Climatology and Geophysics, Indonesia). We successfully relocate about 6886 earthquakes that occur on period of 1981-2015. We consider that this new location is more precise than the regular bulletin. The relocation results show greatly reduced of RMS residual of travel time. Using this data, we can construct a new seismotectonic map of Sumatra. A well-built geometry of subduction slab, faults and volcano arc can be obtained from the new bulletin. It is also showed that at a depth of 140-170 km, there is many events occur as moderate-to-deep earthquakes, and we consider about the relation of the slab's events with volcanic arc and inland fault system. A reliable slab model is also built from regression equation using new relocated data. We also analyze the spatial-temporal of seismotectonic using b-value mapping that inspected in detail horizontally and vertically cross-section.

  3. Location analysis for the estrogen receptor-? reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

    OpenAIRE

    Mason, Christopher E.; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M.; Kallen, Roland G.; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B.

    2010-01-01

    Location analysis for estrogen receptor-? (ER?)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ER?-bound loci and quantify the incidence of ERE sequences under two stringencies of detection:

  4. Location analysis for the estrogen receptor-α reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

    Science.gov (United States)

    Mason, Christopher E.; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M.; Kallen, Roland G.; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B.

    2010-01-01

    Location analysis for estrogen receptor-α (ERα)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERα-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: ERE sequence. We demonstrate that ∼50% of all ERα-bound loci do not have a discernable ERE and show that most ERα-bound EREs are not perfect consensus EREs. Approximately one-third of all ERα-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERα-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERα binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers. PMID:20047966

  5. Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements.

    Science.gov (United States)

    Mason, Christopher E; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M; Kallen, Roland G; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B

    2010-04-01

    Location analysis for estrogen receptor-alpha (ERalpha)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERalpha-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: ERE sequence. We demonstrate that approximately 50% of all ERalpha-bound loci do not have a discernable ERE and show that most ERalpha-bound EREs are not perfect consensus EREs. Approximately one-third of all ERalpha-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERalpha-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERalpha binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers.

  6. Recombination patterns reveal information about centromere location on linkage maps

    DEFF Research Database (Denmark)

    Limborg, Morten T.; McKinney, Garrett J.; Seeb, Lisa W.

    2016-01-01

    . mykiss) characterized by low and unevenly distributed recombination – a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations...

  7. Selective interference reveals dissociation between memory for location and colour.

    Science.gov (United States)

    Vuontela, V; Rämä, P; Raninen, A; Aronen, H J; Carlson, S

    1999-08-02

    The aim was to study whether there is indication of a dissociation in processing of visuospatial and colour information in working memory in humans. Experimental subjects performed visuospatial and colour n-back tasks with and without visuospatial and colour distractive stimuli presented in the middle of the delay period to specifically affect mnemonic processing of task-related information. In the high memory-load condition, the visuospatial, but not the colour, task was selectively disrupted by visuospatial but not colour distractors. When subvocal rehearsal of the memoranda in the colour task was prevented by articulatory suppression; colour task performance was also selectively disrupted by distractors qualitatively similar to the memoranda. The results support the suggestion that visual working memory for location is processed separate from that for colour.

  8. Cluster analysis for determining distribution center location

    Science.gov (United States)

    Lestari Widaningrum, Dyah; Andika, Aditya; Murphiyanto, Richard Dimas Julian

    2017-12-01

    Determination of distribution facilities is highly important to survive in the high level of competition in today’s business world. Companies can operate multiple distribution centers to mitigate supply chain risk. Thus, new problems arise, namely how many and where the facilities should be provided. This study examines a fast-food restaurant brand, which located in the Greater Jakarta. This brand is included in the category of top 5 fast food restaurant chain based on retail sales. There were three stages in this study, compiling spatial data, cluster analysis, and network analysis. Cluster analysis results are used to consider the location of the additional distribution center. Network analysis results show a more efficient process referring to a shorter distance to the distribution process.

  9. Simulation analysis for hyperbola locating accuracy

    International Nuclear Information System (INIS)

    Wang Changli; Liu Daizhi

    2004-01-01

    In the system of the hyperbola location, the geometric shape of the detecting stations has an important influence on the locating accuracy. At first, this paper simulates the process of the hyperbola location by the computer, and then analyzes the influence of the geometric shape on the locating errors and gives the computer simulation results, finally, discusses the problems that require attention in course of selecting the detecting station. The conclusion has practicality. (authors)

  10. Heat Retreat Locations in Cities - The Survey-Based Location Analysis of Heat Relief

    Science.gov (United States)

    Neht, Alice; Maximini, Claudia; Prenger-Berninghoff, Kathrin

    2017-12-01

    The adaptation of cities to climate change effects is one of the major strategies in urban planning to encounter the challenges of climate change (IPCC 2014). One of the fields of climate change adaption is dealing with heat events that occur more frequently and with greater intensity. Cities in particular are vulnerable to these events due to high population and infrastructure density. Proceeding urbanization calls for the existence of sufficient heat retreat locations (HRL) to enable relief for the population from heat in summer. This is why an extensive analysis of HRL is needed. This paper aims at the development of a survey-based location analysis of heat relief by identifying user groups, locations and characteristics of HRL based on a home survey that was conducted in three German cities. Key results of the study show that the majority of the participants of the survey are users of existing HRL, are affected by heat, and perceive heat as a burden in summer. Moreover, HRL that are located in close proximity are preferred by most users while their effect depends on the regional context that has to be considered in the analysis. Hence, this research presents an approach to heat relief that underlines the importance of HRL in cities by referring to selected examples of HRL types in densely populated areas of cities. HRL should especially be established and secured in densely built-up areas of cities. According to results of the survey, most HRL are located in public spaces, and the overall accessibility of HRL turned out to be an issue.

  11. Continuous wavelet transform analysis and modal location analysis acoustic emission source location for nuclear piping crack growth monitoring

    International Nuclear Information System (INIS)

    Shukri Mohd

    2013-01-01

    Full-text: Source location is an important feature of acoustic emission (AE) damage monitoring in nuclear piping. The ability to accurately locate sources can assist in source characterisation and early warning of failure. This paper describe the development of a novelAE source location technique termed Wavelet Transform analysis and Modal Location (WTML) based on Lamb wave theory and time-frequency analysis that can be used for global monitoring of plate like steel structures. Source location was performed on a steel pipe of 1500 mm long and 220 mm outer diameter with nominal thickness of 5 mm under a planar location test setup using H-N sources. The accuracy of the new technique was compared with other AE source location methods such as the time of arrival (TOA) technique and DeltaTlocation. The results of the study show that the WTML method produces more accurate location results compared with TOA and triple point filtering location methods. The accuracy of the WTML approach is comparable with the deltaT location method but requires no initial acoustic calibration of the structure. (author)

  12. Continuous wavelet transform analysis and modal location analysis acoustic emission source location for nuclear piping crack growth monitoring

    International Nuclear Information System (INIS)

    Mohd, Shukri; Holford, Karen M.; Pullin, Rhys

    2014-01-01

    Source location is an important feature of acoustic emission (AE) damage monitoring in nuclear piping. The ability to accurately locate sources can assist in source characterisation and early warning of failure. This paper describe the development of a novelAE source location technique termed 'Wavelet Transform analysis and Modal Location (WTML)' based on Lamb wave theory and time-frequency analysis that can be used for global monitoring of plate like steel structures. Source location was performed on a steel pipe of 1500 mm long and 220 mm outer diameter with nominal thickness of 5 mm under a planar location test setup using H-N sources. The accuracy of the new technique was compared with other AE source location methods such as the time of arrival (TOA) techniqueand DeltaTlocation. Theresults of the study show that the WTML method produces more accurate location resultscompared with TOA and triple point filtering location methods. The accuracy of the WTML approach is comparable with the deltaT location method but requires no initial acoustic calibration of the structure

  13. Continuous wavelet transform analysis and modal location analysis acoustic emission source location for nuclear piping crack growth monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Mohd, Shukri [Nondestructive Testing Group, Industrial Technology Division, Malaysian Nuclear Agency, 43000, Bangi, Selangor (Malaysia); Holford, Karen M.; Pullin, Rhys [Cardiff School of Engineering, Cardiff University, Queen' s Buildings, The Parade, CARDIFF CF24 3AA (United Kingdom)

    2014-02-12

    Source location is an important feature of acoustic emission (AE) damage monitoring in nuclear piping. The ability to accurately locate sources can assist in source characterisation and early warning of failure. This paper describe the development of a novelAE source location technique termed 'Wavelet Transform analysis and Modal Location (WTML)' based on Lamb wave theory and time-frequency analysis that can be used for global monitoring of plate like steel structures. Source location was performed on a steel pipe of 1500 mm long and 220 mm outer diameter with nominal thickness of 5 mm under a planar location test setup using H-N sources. The accuracy of the new technique was compared with other AE source location methods such as the time of arrival (TOA) techniqueand DeltaTlocation. Theresults of the study show that the WTML method produces more accurate location resultscompared with TOA and triple point filtering location methods. The accuracy of the WTML approach is comparable with the deltaT location method but requires no initial acoustic calibration of the structure.

  14. Location Analysis of Freight Distribution Terminal of Jakarta City, Indonesia

    Directory of Open Access Journals (Sweden)

    Nahry Nahry

    2016-03-01

    Full Text Available Currently Jakarta has two freight terminals, namely Pulo Gebang and Tanah Merdeka. But, both terminals are just functioned for parking and have not been utilized properly yet, e.g. for consolidation. Goods consolidation, which is usually performed in distribution terminal, may reduce number of freight flow within the city. This paper is aimed to determine the best location of distribution terminal in Jakarta among those two terminals and two additional alternative sites, namely Lodan and Rawa Buaya. It is initialized by the identification of important factors that affect the location selection. It is carried out by Likert analysis through the questionnaires distributed to logistics firms. The best location is determined by applying Overlay Analysis using ArcGIS 9.2. Four grid maps are produced to represent the accessibility, cost, time, and environment factors as the important factors of location. The result shows that the ranking from the best is; Lodan, Tanah Merdeka, Pulo Gebang, and Rawa Buaya.

  15. Quantitative imaging analysis of posterior fossa ependymoma location in children.

    Science.gov (United States)

    Sabin, Noah D; Merchant, Thomas E; Li, Xingyu; Li, Yimei; Klimo, Paul; Boop, Frederick A; Ellison, David W; Ogg, Robert J

    2016-08-01

    Imaging descriptions of posterior fossa ependymoma in children have focused on magnetic resonance imaging (MRI) signal and local anatomic relationships with imaging location only recently used to classify these neoplasms. We developed a quantitative method for analyzing the location of ependymoma in the posterior fossa, tested its effectiveness in distinguishing groups of tumors, and examined potential associations of distinct tumor groups with treatment and prognostic factors. Pre-operative MRI examinations of the brain for 38 children with histopathologically proven posterior fossa ependymoma were analyzed. Tumor margin contours and anatomic landmarks were manually marked and used to calculate the centroid of each tumor. Landmarks were used to calculate a transformation to align, scale, and rotate each patient's image coordinates to a common coordinate space. Hierarchical cluster analysis of the location and morphological variables was performed to detect multivariate patterns in tumor characteristics. The ependymomas were also characterized as "central" or "lateral" based on published radiological criteria. Therapeutic details and demographic, recurrence, and survival information were obtained from medical records and analyzed with the tumor location and morphology to identify prognostic tumor characteristics. Cluster analysis yielded two distinct tumor groups based on centroid location The cluster groups were associated with differences in PFS (p = .044), "central" vs. "lateral" radiological designation (p = .035), and marginally associated with multiple operative interventions (p = .064). Posterior fossa ependymoma can be objectively classified based on quantitative analysis of tumor location, and these classifications are associated with prognostic and treatment factors.

  16. Error Analysis of Determining Airplane Location by Global Positioning System

    OpenAIRE

    Hajiyev, Chingiz; Burat, Alper

    1999-01-01

    This paper studies the error analysis of determining airplane location by global positioning system (GPS) using statistical testing method. The Newton Rhapson method positions the airplane at the intersection point of four spheres. Absolute errors, relative errors and standard deviation have been calculated The results show that the positioning error of the airplane varies with the coordinates of GPS satellite and the airplane.

  17. Centralization vs. Decentralization: A Location Analysis Approach for Librarians

    Science.gov (United States)

    Raffel, Jeffrey; Shishko, Robert

    1972-01-01

    An application of location theory to the question of centralized versus decentralized library facilities for a university, with relevance for special libraries is presented. The analysis provides models for a single library, for two or more libraries, or for decentralized facilities. (6 references) (Author/NH)

  18. Analysis about correlation between the shape and histopathological locations of mammographic microcalcifications

    International Nuclear Information System (INIS)

    Kim, Wha Young; Cho, Young Ah; Choi, Hye Young; Sung, Soon Hee; Bacek, Seung Yeon

    1998-01-01

    To analyze the location of microcalcifications present on pathologic specimens and the relationship between the shape of clustered microcalcifications seen on mammogram and the location of these microcalcifications on pathologic specimen. In 84 female patients aged 25-68, we analysed the location of microcalcifications seen on pathologic speciments. In 65 cases, the shape of these microcalcifications correlated with their location. These shapes, as seen on mammograms, were classified as granular, linear, or branching;the location of microcalcifications was difined as intraductal, stromal, lobular, or a mixture of the three. To determine the difference, if any, between pathologic diagnosis and pathological location and shape as seen on mammograms, statistical analysis using the Chi-square test was performed. Among 84 cases, 51 were benign and 33cases were malignant. In both types of disease, in 45% and 58% of cases, respectively, microcalcifications were located intraductally. There was no statistically significant difference between pathologic diagnosis and pathologic locations (p=3D0.191);analysis of the relationship between shape of microcalcification and pathological location similarly revealed no statistically significant difference(p>0.05). In four of 33 cases of malignant disease(12%), there was microcalcification not only of the tumor itself but also of the adjacent non-tumorous region. Regardless of whether the disease was benign or melignant, microcalcifieations were most commonly intraductal. The relationship between shape and location of microcalcifications seen on pathologic specimens demonstrated no statistical significance.=20

  19. Location analysis of the landfill of waste in Loznica

    Directory of Open Access Journals (Sweden)

    Božović Dejan

    2010-01-01

    Full Text Available The subject of this paper regards the landfill of municipal and industrial waste in Loznica, actually its location and environmental hazards. The research was carried out in order to show the consequences of careless and incomplete evaluation of the conditions for a locating of a landfill in the example of Loznica. Besides the fact that it is located at the floodplain of the Drina River, the landfill is normally located to the direction of predominant wind, which has a significant influence on environmental dispersion processes. The landscape where the landfill is located has been impacted by flooded and groundwater and predominant wind, but on the other side, the environment has also been impacted by pollutants which come from the new system landscape-landfill. The results of the laboratory analysis help to target a gradual process of the soil contamination by heavy metals from the landfill, and to detect the general direction of contaminant migration, from southwest to northeast. Therefore, it is necessary to start working on recultivation and rehabilitation of the landfill and to begin with regional waste disposal. .

  20. Multi-Criteria Analysis for Solar Farm Location Suitability

    Science.gov (United States)

    Mierzwiak, Michal; Calka, Beata

    2017-12-01

    Currently the number of solar farms, as a type of renewable sources of energy, is growing rapidly. Photovoltaic power stations have many advantages, which is an incentive for their building and development. Solar energy is readily available and inexhaustible, and its production is environmentally friendly. In the present study multiple environmental and economic criteria were taken into account to select a potential photovoltaic farm location, with particular emphasis on: protected areas, land cover, solar radiation, slope angle, proximity to roads, built-up areas, and power lines. Advanced data analysis were used because of the multiplicity of criteria and their diverse influence on the choice of a potential location. They included the spatial analysis, the Weighted Linear Combination Technique (WLC), and the Analytic Hierarchy Process (AHP) as a decisionmaking method. The analysis was divided into two stages. In the first one, the areas where the location of solar farms was not possible were excluded. In the second one, the best locations meeting all environmental and economic criteria were selected. The research was conducted for the Legionowo District, using data from national surveying and mapping resources such as: BDOT10k (Database of Topographic Objects), NMT (Numerical Terrain Model), and lands and buildings register. Finally, several areas meeting the criteria were chosen. The research deals with solar farms with up to 40 kW power. The results of the study are presented as thematic maps. The advantage of the method is its versatility. It can be used not only for any area, but with little modification of the criteria, it can also be applied to choose a location for wind farms.

  1. Location of persisting mycobacteria in a Guinea pig model of tuberculosis revealed by r207910.

    Science.gov (United States)

    Lenaerts, Anne J; Hoff, Donald; Aly, Sahar; Ehlers, Stefan; Andries, Koen; Cantarero, Luis; Orme, Ian M; Basaraba, Randall J

    2007-09-01

    The lengthy chemotherapy of tuberculosis reflects the ability of a small subpopulation of Mycobacterium tuberculosis bacteria to persist in infected individuals. To date, the exact location of these persisting bacteria is not known. Lung lesions in guinea pigs infected with M. tuberculosis have striking similarities, such as necrosis, mineralization, and hypoxia, to natural infections in humans. Guinea pigs develop necrotic primary lesions after aerosol infection that differ in their morphology compared to secondary lesions resulting from hematogenous dissemination. In infected guinea pigs conventional therapy for tuberculosis during 6 weeks reduced the bacterial load by 1.7 logs in the lungs and, although this completely reversed lung inflammation associated with secondary lesions, the primary granulomas remained largely unaffected. Treatment of animals with the experimental drug R207910 (TMC207) for 6 weeks was highly effective with almost complete eradication of the bacteria throughout both the primary and the secondary lesions. Most importantly, the few remnants of acid-fast bacilli remaining after R207910 treatment were to be found extracellular, in a microenvironment of residual primary lesion necrosis with incomplete dystrophic calcification. This zone of the primary granuloma is hypoxic and is morphologically similar to what has been described for human lung lesions. These results show that this acellular rim may, therefore, be a primary location of persisting bacilli withstanding drug treatment.

  2. Location of Persisting Mycobacteria in a Guinea Pig Model of Tuberculosis Revealed by R207910▿

    Science.gov (United States)

    Lenaerts, Anne J.; Hoff, Donald; Aly, Sahar; Ehlers, Stefan; Andries, Koen; Cantarero, Luis; Orme, Ian M.; Basaraba, Randall J.

    2007-01-01

    The lengthy chemotherapy of tuberculosis reflects the ability of a small subpopulation of Mycobacterium tuberculosis bacteria to persist in infected individuals. To date, the exact location of these persisting bacteria is not known. Lung lesions in guinea pigs infected with M. tuberculosis have striking similarities, such as necrosis, mineralization, and hypoxia, to natural infections in humans. Guinea pigs develop necrotic primary lesions after aerosol infection that differ in their morphology compared to secondary lesions resulting from hematogenous dissemination. In infected guinea pigs conventional therapy for tuberculosis during 6 weeks reduced the bacterial load by 1.7 logs in the lungs and, although this completely reversed lung inflammation associated with secondary lesions, the primary granulomas remained largely unaffected. Treatment of animals with the experimental drug R207910 (TMC207) for 6 weeks was highly effective with almost complete eradication of the bacteria throughout both the primary and the secondary lesions. Most importantly, the few remnants of acid-fast bacilli remaining after R207910 treatment were to be found extracellular, in a microenvironment of residual primary lesion necrosis with incomplete dystrophic calcification. This zone of the primary granuloma is hypoxic and is morphologically similar to what has been described for human lung lesions. These results show that this acellular rim may, therefore, be a primary location of persisting bacilli withstanding drug treatment. PMID:17517834

  3. Location memory biases reveal the challenges of coordinating visual and kinesthetic reference frames

    Science.gov (United States)

    Simmering, Vanessa R.; Peterson, Clayton; Darling, Warren; Spencer, John P.

    2008-01-01

    Five experiments explored the influence of visual and kinesthetic/proprioceptive reference frames on location memory. Experiments 1 and 2 compared visual and kinesthetic reference frames in a memory task using visually-specified locations and a visually-guided response. When the environment was visible, results replicated previous findings of biases away from the midline symmetry axis of the task space, with stability for targets aligned with this axis. When the environment was not visible, results showed some evidence of bias away from a kinesthetically-specified midline (trunk anterior–posterior [a–p] axis), but there was little evidence of stability when targets were aligned with body midline. This lack of stability may reflect the challenges of coordinating visual and kinesthetic information in the absence of an environmental reference frame. Thus, Experiments 3–5 examined kinesthetic guidance of hand movement to kinesthetically-defined targets. Performance in these experiments was generally accurate with no evidence of consistent biases away from the trunk a–p axis. We discuss these results in the context of the challenges of coordinating reference frames within versus between multiple sensori-motor systems. PMID:17703284

  4. Antibody Competition Reveals Surface Location of HPV L2 Minor Capsid Protein Residues 17–36

    Directory of Open Access Journals (Sweden)

    Stephanie M. Bywaters

    2017-11-01

    Full Text Available The currently available nonavalent human papillomavirus (HPV vaccine exploits the highly antigenic L1 major capsid protein to promote high-titer neutralizing antibodies, but is limited to the HPV types included in the vaccine since the responses are highly type-specific. The limited cross-protection offered by the L1 virus-like particle (VLP vaccine warrants further investigation into cross-protective L2 epitopes. The L2 proteins are yet to be fully characterized as to their precise placement in the virion. Adding to the difficulties in localizing L2, studies have suggested that L2 epitopes are not well exposed on the surface of the mature capsid prior to cellular engagement. Using a series of competition assays between previously mapped anti-L1 monoclonal antibodies (mAbs (H16.V5, H16.U4 and H16.7E and novel anti-L2 mAbs, we probed the capsid surface for the location of an L2 epitope (aa17–36. The previously characterized L1 epitopes together with our competition data is consistent with a proposed L2 epitope within the canyons of pentavalent capsomers.

  5. Antibody Competition Reveals Surface Location of HPV L2 Minor Capsid Protein Residues 17-36.

    Science.gov (United States)

    Bywaters, Stephanie M; Brendle, Sarah A; Tossi, Kerstin P; Biryukov, Jennifer; Meyers, Craig; Christensen, Neil D

    2017-11-10

    The currently available nonavalent human papillomavirus (HPV) vaccine exploits the highly antigenic L1 major capsid protein to promote high-titer neutralizing antibodies, but is limited to the HPV types included in the vaccine since the responses are highly type-specific. The limited cross-protection offered by the L1 virus-like particle (VLP) vaccine warrants further investigation into cross-protective L2 epitopes. The L2 proteins are yet to be fully characterized as to their precise placement in the virion. Adding to the difficulties in localizing L2, studies have suggested that L2 epitopes are not well exposed on the surface of the mature capsid prior to cellular engagement. Using a series of competition assays between previously mapped anti-L1 monoclonal antibodies (mAbs) (H16.V5, H16.U4 and H16.7E) and novel anti-L2 mAbs, we probed the capsid surface for the location of an L2 epitope (aa17-36). The previously characterized L1 epitopes together with our competition data is consistent with a proposed L2 epitope within the canyons of pentavalent capsomers.

  6. Internal Domains of Natural Porous Media Revealed: Critical Locations for Transport, Storage, and Chemical Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Zachara, John M.; Brantley, Susan L.; Chorover, Jon D.; Ewing, Robert P.; Kerisit, Sebastien N.; Liu, Chongxuan; Perfect, E.; Rother, Gernot; Stack, Andrew G.

    2016-03-16

    Internal pore domains exist within rocks, lithic fragments, subsurface sediments and soil aggregates. These domains, which we term internal domains in porous media (IDPM), contain a significant fraction of their porosity as nanopores, dominate the reactive surface area of diverse porous media types, and are important locations for chemical reactivity and hydrocarbon storage. Traditionally difficult to interrogate, advances in instrumentation and imaging methods are providing new insights on the physical structures and chemical attributes of IDPM. In this review we: discuss analytical methods to characterize IDPM, evaluate what has been learned about their size distributions, connectivity, and extended structures; determine whether they exhibit unique chemical reactivity; and assess potential for their inclusion in reactive transport models. Three key findings are noteworthy. 1) A combination of methods now allows complete characterization of the porosity spectrum of natural materials and its connectivity; while imaging microscopies are providing three dimensional representations of the interconnected pore network. 2) Chemical reactivity in pores <10 nm is expected to be different from micro and macropores, yet research performed to date is inconclusive on the nature, direction, and magnitude of effect. 3) Existing continuum reactive transport models treat IDPM as a sub-grid feature with average, empirical, scale-dependent parameters; and are not formulated to include detailed information on pore networks. Overall we find that IDPM are key features controlling hydrocarbon release from shales in hydrofracking systems, organic matter stabilization and recalcitrance in soil, weathering and soil formation, and long term inorganic and organic contaminant behavior in the vadose zone and groundwater. We conclude with an assessment of impactful research opportunities to advance understanding of IDPM, and to incorporate their important effects in reactive transport models

  7. The complex evolution of transient slip revealed by precise tremor locations in western Shikoku, Japan

    Science.gov (United States)

    Shelly, D. R.; Beroza, G. C.; Ide, S.

    2007-12-01

    Transient slow slip events are increasingly being recognized as important components of strain release on faults and may substantially impact the earthquake cycle. Surface-based geodetic instruments provide estimates of the overall slip distribution in larger transients but are unable to capture the detailed evolution of such slip, either in time or space. Accompanying some of these slip transients is a relatively weak, extended duration seismic signal, known as non-volcanic tremor, which has recently been shown to be generated by a sequence of shear failures occurring as part of the slip event. By precisely locating the tremor, we can track some features of slip evolution with unprecedented resolution. Here, we analyze two weeklong episodes of tremor and slow slip in western Shikoku, Japan. We find that these slip transients do not evolve in a smooth and steady fashion but contain numerous sub-events of smaller size and shorter duration. In addition to along-strike migration rates of about 10 km/day observed previously, much faster migration also occurs, usually in the slab dip direction, at rates of 25-150 km/hour over distances of up to 20 km. We observe such migration episodes in both the up-dip and down-dip directions. These episodes may be most common on certain portions of the plate boundary that generate strong tremor in intermittent bursts. The surrounding regions of the fault may slip more continuously, driving these stronger patches to repeated failures. Tremor activity has a strong tidal periodicity, possibly reflecting the modulation of slow slip velocity by tidal stresses.

  8. LOCATION ANALYSIS ON SMART HOUSE USING PROJECTIVE TRANSFORMATION

    Directory of Open Access Journals (Sweden)

    Galih Andi Pradana

    2014-08-01

    Full Text Available In this paper, a method of location analysis for smart house is proposed. The proposed method uses projective transformation to process the input from visual sensor for determining coordinate of resident and also the entire device inside the smart house. With a good calculated coordinate, each device function in the smart house can be optimized for the good of the resident. From the experiment results, the proposed method successfully maps all coordinates of any device in the smart house up to 81% accuracy.

  9. Location analysis of the landfill of waste in Loznica

    OpenAIRE

    Božović Dejan

    2010-01-01

    The subject of this paper regards the landfill of municipal and industrial waste in Loznica, actually its location and environmental hazards. The research was carried out in order to show the consequences of careless and incomplete evaluation of the conditions for a locating of a landfill in the example of Loznica. Besides the fact that it is located at the floodplain of the Drina River, the landfill is normally located to the direction of predominant wind, which has a significant influence o...

  10. Location, location, location

    NARCIS (Netherlands)

    Anderson, S.P.; Goeree, J.K.; Ramer, R.

    1997-01-01

    We analyze the canonical location-then-price duopoly game with general log- concave consumer densities. A unique pure-strategy equilibrium to the two-stage game exists if the density is not "too asymmetric" and not "too concave." These criteria are satisfied by many commonly used densities.

  11. Detection, Source Location, and Analysis of Volcano Infrasound

    Science.gov (United States)

    McKee, Kathleen F.

    The study of volcano infrasound focuses on low frequency sound from volcanoes, how volcanic processes produce it, and the path it travels from the source to our receivers. In this dissertation we focus on detecting, locating, and analyzing infrasound from a number of different volcanoes using a variety of analysis techniques. These works will help inform future volcano monitoring using infrasound with respect to infrasonic source location, signal characterization, volatile flux estimation, and back-azimuth to source determination. Source location is an important component of the study of volcano infrasound and in its application to volcano monitoring. Semblance is a forward grid search technique and common source location method in infrasound studies as well as seismology. We evaluated the effectiveness of semblance in the presence of significant topographic features for explosions of Sakurajima Volcano, Japan, while taking into account temperature and wind variations. We show that topographic obstacles at Sakurajima cause a semblance source location offset of 360-420 m to the northeast of the actual source location. In addition, we found despite the consistent offset in source location semblance can still be a useful tool for determining periods of volcanic activity. Infrasonic signal characterization follows signal detection and source location in volcano monitoring in that it informs us of the type of volcanic activity detected. In large volcanic eruptions the lowermost portion of the eruption column is momentum-driven and termed the volcanic jet or gas-thrust zone. This turbulent fluid-flow perturbs the atmosphere and produces a sound similar to that of jet and rocket engines, known as jet noise. We deployed an array of infrasound sensors near an accessible, less hazardous, fumarolic jet at Aso Volcano, Japan as an analogue to large, violent volcanic eruption jets. We recorded volcanic jet noise at 57.6° from vertical, a recording angle not normally feasible

  12. Centralization Versus Decentralization: A Location Analysis Approach for Librarians.

    Science.gov (United States)

    Shishko, Robert; Raffel, Jeffrey

    One of the questions that seems to perplex many university and special librarians is whether to move in the direction of centralizing or decentralizing the library's collections and facilities. Presented is a theoretical approach, employing location theory, to the library centralization-decentralization question. Location theory allows the analyst…

  13. Location of power stations and measures for local people model analysis concerning location negotiation with local fishery association

    Energy Technology Data Exchange (ETDEWEB)

    Wakatani, Yoshifumi; Yamanaka, Yoshiro (Central Research Inst. of electric Power Industry, Tokyo (Japan))

    1982-05-01

    The recent negotiation of enterprisers and local people concerning the location of power stations tends to extend for long periods because of diversified arguing points and the information exchange of high density, and also to be complicated by the interrelation with other points. It is a large problem to seek the policy of such negotiation for enterprisers to respond to local people. In this study, as the first step, the policy and action appeared in location negotiations and the development of the negotiations were analyzed on the cases of location, and two kinds of the model analysis were carried out, taking fishery compensation negotiation as the object among them. The knowledge was obtained about what response to local fishery associations is effective to promote the location. The classification of location negotiation and the factors affecting the development of negotiation were investigated. It was shown to be effective to divide the process of location negotiation into five stages of advancement. The model analysis was carried out according to game theory and by gaming simulation method. The results are reported.

  14. Location of power stations and measures for local people model analysis concerning location negotiation with local fishery association

    International Nuclear Information System (INIS)

    Wakatani, Yoshifumi; Yamanaka, Yoshiro

    1982-01-01

    The recent negotiation of enterprisers and local people concerning the location of power stations tends to extend for long period because of diversified arguing points and the information exchange of high density, and also to be complicated by the interrelation with other points. It is a large problem to seek the policy of such negotiation for enterprisers to respond to local people. In this study, as the first step, the policy and action appeared in location negotiations and the development of the negotiations were analyzed on the cases of location, and two kinds of the model analysis were carried out, taking fishery compensation negotiation as the object among them. The knowledge was obtained about what response to local fishery associations is effective to promote the location. The classification of location negotiation and the factors affecting the development of negotiation were investigated. It was shown to be effective to divide the process of location negotiation into five stages of advancement. The model analysis was carried out according to game theory and by gaming simulation method. The results are reported. (Kako, I.)

  15. Performance analysis of a self-locating mobile sensor

    DEFF Research Database (Denmark)

    Bøgsted, Martin; Rasmussen, Jakob Gulddahl; Lundbye-Christensen, Søren

    to an autoregressive model. Measurement uncertainty is assumed to follow a Gaussian distribution and the probability for detecting a distance to a given sensor is assumed to fall off exponentially with squared distance. The combined model is formulated as a nonlinear state space model and Bayesian inference......We consider the ability of a mobile sensor to locate its own geographical location, the so-called self-localization problem. The need to locate people and objects has inspired the development of many systems for automatic localization. Most systems are based on location information and measured...... the performance of localization algorithms in mobile and critical situations. This is done by exploring the performance of various filtering techniques for self-localization of a mobile sensor in a field of sensors. More specifically, we model the mobility of the sensor such that the velocity varies according...

  16. Location, Location, Location

    Science.gov (United States)

    Cates, Deborah; Gutiérrez, Eva; Hafer, Sarah; Barrett, Ryan; Corina, David

    2013-01-01

    This article presents an analysis of the relationship between sign structure and iconicity in American Sign Language. Historically, linguists have been pressured to downplay the role of form-meaning relationships (iconicity) in signed languages. However, recent inquiries into the role of traditional phonological parameters of signs (handshape,…

  17. Location of radiotherapy centers: An exploratory geographic analysis for Belgium

    International Nuclear Information System (INIS)

    Cotteels, C.; Peeters, D.; Coucke, P.A.; Thomas, I.

    2012-01-01

    Purpose. - The distance between the patient's home and a radiotherapy department may represent a hurdle for the patient and influence treatment choice. Therefore, it is necessary to check whether the geographical distribution of radiotherapy centers is in accordance with cancer incidence, taking also into account the cost of travelling to the radiotherapy department. The objective of this study is double; first, to map the current locations of radiotherapy centers across the country and second, to evaluate the observed spatial disparities with appropriate tools. Materials and methods. - A model of operational research (P-median) is used to suggest the optimal locations and allocations and to compare them with the current situation. This is an exploratory study with simple inputs. It helps to better understand the current geographical distribution of radiotherapy centers in Belgium as well as its possible limitations. Results-conclusion. - It appears that the current situation is on the average acceptable in terms of accessibility to the service and that the method presents huge potentialities for decision making so as to yield a spatial system that is both efficient and equitable. (authors)

  18. Chemometric Analysis for Pollution Source Assessment of Harbour Sediments in Arctic Locations

    DEFF Research Database (Denmark)

    Pedersen, Kristine B.; Lejon, Tore; Jensen, Pernille Erland

    2015-01-01

    Pollution levels, pollutant distribution and potential source assessments based on multivariate analysis (chemometrics) were made for harbour sediments from two Arctic locations; Hammerfest in Norway and Sisimiut in Greenland. High levels of heavy metals were detected in addition to organic...... pollutants. Preliminary assessments based on principal component analysis (PCA) revealed different sources and pollutant distribution in the sediments of the two harbours. Tributyltin (TBT) was, however, found to originate from point source(s), and the highest concentrations of TBT in both harbours were...... indicated relation primarily to German, Russian and American mixtures in Hammerfest; and American, Russian and Japanese mixtures in Sisimiut. PCA was shown to be an important tool for identifying pollutant sources and differences in pollutant composition in relation to sediment characteristics....

  19. Microhabitat analysis using radiotelemetry locations and polytomous logistic regression

    Science.gov (United States)

    Malcolm P. North; Joel H. Reynolds

    1996-01-01

    Microhabitat analyses often use discriminant function analysis (DFA) to compare vegetation structures or environmental conditions between sites classified by a study animal's presence or absence. These presence/absence studies make questionable assumptions about the habitat value of the comparison sites and the microhabitat data often violate the DFA's...

  20. What does location choice reveal about knowledge-seeking strategies of emerging market multinationals in the EU?

    DEFF Research Database (Denmark)

    Jindra, Bjørn; Hassan, Sohaib Shahzad; Cantner, Uwe

    2016-01-01

    The European Union is one of the largest recipients of outward foreign direct investment from emerging economies. We apply different discrete choice models to analyze the location choice of 4555 emerging market firms in 93 sub-national regions of the European Union. In particular, we test to what...... extent these firms’ location choices are related to agglomeration economies and knowledge externalities, because these have been suggested as potential sources to propel learning and technological catching-up. Our results indicate that emerging market firms’ location choices are positively affected...... by agglomeration economies and knowledge externalities. In addition, we can identify differences in the valuation of various sub-national location factors as well as differences in the substitution pattern between alternative regions for firms originating from emerging markets. The evidence supports the argument...

  1. Characteristics of the tomato chromoplast revealed by proteomic analysis

    OpenAIRE

    Barsan, Cristina; Sanchez-Bel, Paloma; Rombaldi, César Valmor; Egea, Isabel; Rossignol, Michel; Kuntz, Marcel; Zouine, Mohamed; Latché, Alain; Bouzayen, Mondher; Pech, Jean-Claude

    2010-01-01

    Chromoplasts are non-photosynthetic specialized plastids that are important in ripening tomato fruit (Solanum lycopersicum) since, among other functions, they are the site of accumulation of coloured compounds. Analysis of the proteome of red fruit chromoplasts revealed the presence of 988 proteins corresponding to 802 Arabidopsis unigenes, among which 209 had not been listed so far in plastidial databanks. These data revealed several features of the chromoplast. Proteins of lipid metabolism ...

  2. Analysis of co-located MODIS and CALIPSO observations near clouds

    Directory of Open Access Journals (Sweden)

    T. Várnai

    2012-02-01

    Full Text Available This paper aims at helping synergistic studies in combining data from different satellites for gaining new insights into two critical yet poorly understood aspects of anthropogenic climate change, aerosol-cloud interactions and aerosol radiative effects. In particular, the paper examines the way cloud information from the MODIS (MODerate resolution Imaging Spectroradiometer imager can refine our perceptions based on CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization lidar measurements about the systematic aerosol changes that occur near clouds.

    The statistical analysis of a yearlong dataset of co-located global maritime observations from the Aqua and CALIPSO (Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation satellites reveals that MODIS's multispectral imaging ability can greatly help the interpretation of CALIOP observations. The results show that imagers on Aqua and CALIPSO yield very similar pictures, and that the discrepancies – due mainly to wind drift and differences in view angle – do not significantly hinder aerosol measurements near clouds. By detecting clouds outside the CALIOP track, MODIS reveals that clouds are usually closer to clear areas than CALIOP data alone would suggest. The paper finds statistical relationships between the distances to clouds in MODIS and CALIOP data, and proposes a rescaling approach to statistically account for the impact of clouds outside the CALIOP track even when MODIS cannot reliably detect low clouds, for example at night or over sea ice. Finally, the results show that the typical distance to clouds depends on both cloud coverage and cloud type, and accordingly varies with location and season. In maritime areas perceived cloud free, the global median distance to clouds below 3 km altitude is in the 4–5 km range.

  3. The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes

    Directory of Open Access Journals (Sweden)

    Claude Pasquier

    2017-07-01

    Full Text Available Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson–Crick duplex. The “triplex-forming oligonucleotide” (TFO can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored. We identified sequences that are capable of engaging as the “triplex-forming oligonucleotide” in both the pre-lncRNA and pre-mRNA collections of Drosophila melanogaster. These motifs were matched against the Drosophila genome in order to identify putative sequences of triplex formation in intergenic regions, promoters, and introns/exons. Most of the identified TFOs appear to be located in the intronic region of the analyzed genes. Computational prediction of the most targeted genes by TFOs originating from pre-lncRNAs and pre-mRNAs revealed that they are restrictively associated with development- and morphogenesis-related gene networks. The refined analysis by Gene Ontology enrichment demonstrates that some individual TFOs present genome-wide scale matches that are located in numerous genes and regulatory sequences. The triplex DNA:RNA computational mapping at the genome-wide scale suggests broad interference in the regulatory process of the gene networks orchestrated by TFO RNAs acting in association simultaneously at multiple sites.

  4. Chromosomal Locations of 5S and 45S rDNA in Gossypium Genus and Its Phylogenetic Implications Revealed by FISH.

    Science.gov (United States)

    Gan, Yimei; Liu, Fang; Chen, Dan; Wu, Qiong; Qin, Qin; Wang, Chunying; Li, Shaohui; Zhang, Xiangdi; Wang, Yuhong; Wang, Kunbo

    2013-01-01

    We investigated the locations of 5S and 45S rDNA in Gossypium diploid A, B, D, E, F, G genomes and tetraploid genome (AD) using multi-probe fluorescent in situ hybridization (FISH) for evolution analysis in Gossypium genus. The rDNA numbers and sizes, and synteny relationships between 5S and 45S were revealed using 5S and 45S as double-probe for all species, and the rDNA-bearing chromosomes were identified for A, D and AD genomes with one more probe that is single-chromosome-specific BAC clone from G. hirsutum (A1D1). Two to four 45S and one 5S loci were found in diploid-species except two 5S loci in G. incanum (E4), the same as that in tetraploid species. The 45S on the 7th and 9th chromosomes and the 5S on the 9th chromosomes seemed to be conserved in A, D and AD genomes. In the species of B, E, F and G genomes, the rDNA numbers, sizes, and synteny relationships were first reported in this paper. The rDNA pattern agrees with previously reported phylogenetic history with some disagreements. Combined with the whole-genome sequencing data from G. raimondii (D5) and the conserved cotton karyotype, it is suggested that the expansion, decrease and transposition of rDNA other than chromosome rearrangements might occur during the Gossypium evolution.

  5. The structures of cytosolic and plastid-located glutamine synthetases from Medicago truncatula reveal a common and dynamic architecture

    International Nuclear Information System (INIS)

    Torreira, Eva; Seabra, Ana Rita; Marriott, Hazel; Zhou, Min; Llorca, Óscar; Robinson, Carol V.; Carvalho, Helena G.; Fernández-Tornero, Carlos; Pereira, Pedro José Barbosa

    2014-01-01

    The experimental models of dicotyledonous cytoplasmic and plastid-located glutamine synthetases unveil a conserved eukaryotic-type decameric architecture, with subtle structural differences in M. truncatula isoenzymes that account for their distinct herbicide resistance. The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily metabolizable glutamine, which in turn is at the basis of all subsequent biosynthesis of nitrogenous compounds. The essential role performed by glutamine synthetase makes it a prime target for herbicidal compounds, but also a suitable intervention point for the improvement of crop yields. Although the majority of crop plants are dicotyledonous, little is known about the structural organization of glutamine synthetase in these organisms and about the functional differences between the different isoforms. Here, the structural characterization of two glutamine synthetase isoforms from the model legume Medicago truncatula is reported: the crystallographic structure of cytoplasmic GSII-1a and an electron cryomicroscopy reconstruction of plastid-located GSII-2a. Together, these structural models unveil a decameric organization of dicotyledonous glutamine synthetase, with two pentameric rings weakly connected by inter-ring loops. Moreover, rearrangement of these dynamic loops changes the relative orientation of the rings, suggesting a zipper-like mechanism for their assembly into a decameric enzyme. Finally, the atomic structure of M. truncatula GSII-1a provides important insights into the structural determinants of herbicide resistance in this family of enzymes, opening new avenues for the development of herbicide-resistant plants

  6. The structures of cytosolic and plastid-located glutamine synthetases from Medicago truncatula reveal a common and dynamic architecture

    Energy Technology Data Exchange (ETDEWEB)

    Torreira, Eva [Centro de Investigaciones Biológicas – CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain); Seabra, Ana Rita [IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto (Portugal); Marriott, Hazel; Zhou, Min [University of Oxford, South Parks Road, Oxford OX1 3QZ (United Kingdom); Llorca, Óscar [Centro de Investigaciones Biológicas – CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain); Robinson, Carol V. [University of Oxford, South Parks Road, Oxford OX1 3QZ (United Kingdom); Carvalho, Helena G. [IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto (Portugal); Fernández-Tornero, Carlos, E-mail: cftornero@cib.csic.es [Centro de Investigaciones Biológicas – CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain); Pereira, Pedro José Barbosa, E-mail: cftornero@cib.csic.es [IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto (Portugal); Centro de Investigaciones Biológicas – CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)

    2014-04-01

    The experimental models of dicotyledonous cytoplasmic and plastid-located glutamine synthetases unveil a conserved eukaryotic-type decameric architecture, with subtle structural differences in M. truncatula isoenzymes that account for their distinct herbicide resistance. The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily metabolizable glutamine, which in turn is at the basis of all subsequent biosynthesis of nitrogenous compounds. The essential role performed by glutamine synthetase makes it a prime target for herbicidal compounds, but also a suitable intervention point for the improvement of crop yields. Although the majority of crop plants are dicotyledonous, little is known about the structural organization of glutamine synthetase in these organisms and about the functional differences between the different isoforms. Here, the structural characterization of two glutamine synthetase isoforms from the model legume Medicago truncatula is reported: the crystallographic structure of cytoplasmic GSII-1a and an electron cryomicroscopy reconstruction of plastid-located GSII-2a. Together, these structural models unveil a decameric organization of dicotyledonous glutamine synthetase, with two pentameric rings weakly connected by inter-ring loops. Moreover, rearrangement of these dynamic loops changes the relative orientation of the rings, suggesting a zipper-like mechanism for their assembly into a decameric enzyme. Finally, the atomic structure of M. truncatula GSII-1a provides important insights into the structural determinants of herbicide resistance in this family of enzymes, opening new avenues for the development of herbicide-resistant plants.

  7. Saccades to future ball location reveal memory-based prediction in a virtual-reality interception task.

    Science.gov (United States)

    Diaz, Gabriel; Cooper, Joseph; Rothkopf, Constantin; Hayhoe, Mary

    2013-01-16

    Despite general agreement that prediction is a central aspect of perception, there is relatively little evidence concerning the basis on which visual predictions are made. Although both saccadic and pursuit eye-movements reveal knowledge of the future position of a moving visual target, in many of these studies targets move along simple trajectories through a fronto-parallel plane. Here, using a naturalistic and racquet-based interception task in a virtual environment, we demonstrate that subjects make accurate predictions of visual target motion, even when targets follow trajectories determined by the complex dynamics of physical interactions and the head and body are unrestrained. Furthermore, we found that, following a change in ball elasticity, subjects were able to accurately adjust their prebounce predictions of the ball's post-bounce trajectory. This suggests that prediction is guided by experience-based models of how information in the visual image will change over time.

  8. Multi-location wheat stripe rust QTL analysis: genetic background and epistatic interactions.

    Science.gov (United States)

    Vazquez, M Dolores; Zemetra, Robert; Peterson, C James; Chen, Xianming M; Heesacker, Adam; Mundt, Christopher C

    2015-07-01

    Epistasis and genetic background were important influences on expression of stripe rust resistance in two wheat RIL populations, one with resistance conditioned by two major genes and the other conditioned by several minor QTL. Stripe rust is a foliar disease of wheat (Triticum aestivum L.) caused by the air-borne fungus Puccinia striiformis f. sp. tritici and is present in most regions around the world where commercial wheat is grown. Breeding for durable resistance to stripe rust continues to be a priority, but also is a challenge due to the complexity of interactions among resistance genes and to the wide diversity and continuous evolution of the pathogen races. The goal of this study was to detect chromosomal regions for resistance to stripe rust in two winter wheat populations, 'Tubbs'/'NSA-98-0995' (T/N) and 'Einstein'/'Tubbs' (E/T), evaluated across seven environments and mapped with diversity array technology and simple sequence repeat markers covering polymorphic regions of ≈1480 and 1117 cM, respectively. Analysis of variance for phenotypic data revealed significant (P located in chromosomes 2AS and 6AL, with epistatic interaction between them, were responsible for the main phenotypic response. For the T/N population, eight QTL were identified, with those in chromosomes 2AL and 2BL accounting for the largest percentage of the phenotypic variance.

  9. Critical location identification and vulnerability analysis of interdependent infrastructure systems under spatially localized attacks

    International Nuclear Information System (INIS)

    Ouyang, Min

    2016-01-01

    Infrastructure systems are usually spatially distributed in a wide area and are subject to many types of hazards. For each type of hazards, modeling their direct impact on infrastructure components and analyzing their induced system-level vulnerability are important for identifying mitigation strategies. This paper mainly studies spatially localized attacks that a set of infrastructure components located within or crossing a circle shaped spatially localized area is subject to damage while other components do not directly fail. For this type of attacks, taking interdependent power and gas systems in Harris County, Texas, USA as an example, this paper proposes an approach to exactly identify critical locations in interdependent infrastructure systems and make pertinent vulnerability analysis. Results show that (a) infrastructure interdependencies and attack radius largely affect the position of critical locations; (b) spatially localized attacks cause less vulnerability than equivalent random failures; (c) in most values of attack radius critical locations identified by considering only node failures do not change when considering both node and edge failures in the attack area; (d) for many values of attack radius critical locations identified by topology-based model are also critical from the flow-based perspective. - Highlights: • We propose a method to identify critical locations in interdependent infrastructures. • Geographical interdependencies and attack radius largely affect critical locations. • Localized attacks cause less vulnerability than equivalent random failures. • Whether considering both node and edge failures affects critical locations. • Topology-based critical locations are also critical from flow-based perspective.

  10. Design and analysis of the location of an online resale business distribution centre in Japan

    Directory of Open Access Journals (Sweden)

    K. Suzuki

    2016-01-01

    Full Text Available The location of distribution centres for online retailers has become an important issue for many companies. The operation of the distribution centre for e-commerce seems to be different from the traditional concept of distribution centres. This study considers how the location of distribution centres are designed and operated for online retailing using a computer simulation with actual data. This paper analyses current issues in order to propose an effective location for e-commerce distribution centres. An effective location for a multi-distribution system over a wide geographical area is required. This paper clearly points out the importance of locating e-commerce distribution centres over a wide geographical area by performing a computer simulation using actual data on the assumption that online resale business customers live in a metropolitan area. The study created a business model in which a buffer warehouse, which primarily handled commodities with high-frequency shipments, was located near a large consumption area and was used in addition to a large-scale distribution centre. The validity of the created business model was verified by performing a simulation based on actual data. The result revealed that these recommended improvement measures for the location of e-commerce distribution centres can function effectively.

  11. Analysis of Location Ambiguity, GDOP and Station Layout of Threestation in Multilateration

    Directory of Open Access Journals (Sweden)

    Xu Zi Li

    2016-01-01

    Full Text Available In practice, the two-dimensional TDOA source location in the case of three stations would encounter the ambiguity problem of dual solutions. The relationship between distributions of location curve intersections, GDOP and receiving station layout is numerically analyzed, namely the distributions of location curve intersections and GDOP are determined by the receiving station layout, and the areas of two curve intersections are consistent with these of larger GDOP. These analysis results could serve as reference for avoiding or dealing with the ambiguity problem when multilateration is in application.

  12. Location estimation method of steam leak in pipeline using leakage area analysis

    International Nuclear Information System (INIS)

    Kim, Se Oh; Jeon, Hyeong Seop; Son, Ki Sung; Park, Jong Won

    2016-01-01

    It is important to have a pipeline leak-detection system that determines the presence of a leak and quickly identifies its location. Current leak detection methods use a acoustic emission sensors, microphone arrays, and camera images. Recently, many researchers have been focusing on using cameras for detecting leaks. The advantage of this method is that it can survey a wide area and monitor a pipeline over a long distance. However, conventional methods using camera monitoring are unable to target an exact leak location. In this paper, we propose a method of detecting leak locations using leak-detection results combined with multi-frame analysis. The proposed method is verified by experiment

  13. Location estimation method of steam leak in pipeline using leakage area analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Se Oh; Jeon, Hyeong Seop; Son, Ki Sung [Sae An Engineering Corp., Seoul (Korea, Republic of); Park, Jong Won [Dept. of Information Communications Engineering, Chungnam National University, Daejeon (Korea, Republic of)

    2016-10-15

    It is important to have a pipeline leak-detection system that determines the presence of a leak and quickly identifies its location. Current leak detection methods use a acoustic emission sensors, microphone arrays, and camera images. Recently, many researchers have been focusing on using cameras for detecting leaks. The advantage of this method is that it can survey a wide area and monitor a pipeline over a long distance. However, conventional methods using camera monitoring are unable to target an exact leak location. In this paper, we propose a method of detecting leak locations using leak-detection results combined with multi-frame analysis. The proposed method is verified by experiment.

  14. Preliminary spatial analysis of combined BATSE/Ulysses gamma-ray burst locations

    International Nuclear Information System (INIS)

    Kippen, R. Marc; Hurley, Kevin; Pendleton, Geoffrey N.

    1998-01-01

    We present the preliminary spatial analysis of 278 bursts that have been localized by BATSE and the two-spacecraft Compton/Ulysses Interplanetary Network. The large number and superior accuracy of the combined BATSE/Ulysses locations provides improved sensitivity to small-angle source properties. We find that the locations are consistent with large- and small-scale isotropy, with no significant small-angle clustering. We constrain the fraction of sources in clusters and discuss the implications for burst repetition

  15. An Application Of Facility Location Models With Hotspot Analysis For Optimal Location Of Abattoir Bio-Energy Plant In Anambra State Of Nigeria

    Directory of Open Access Journals (Sweden)

    E. C. Chukwuma

    2015-08-01

    Full Text Available Poor waste management strategy in abattoir in the the study area has needs a major attention considering it negative impacts on man land and water. Sitting of centralized biogas plant in a strategic location in the state would be the major means of combating the environmental challenges of increase in abattoir waste generation as result of population explosion in the state. This study investigates optimal location for sitting central abattoir waste treatment facility in Anambra State of Nigeria using facility location models with hotspot analysis in GIS environment. The result of the study shows that Using centre of gravity model the central location was estimated to be at Xc Yc 6.900953016 6.110157865. Based on inadequacy of the model hotspot analysis operation was done the hotspot analysis delineated clusters of abattoirs significantly higher in bio-wastes production than the overall study area. The hotspot analysis shows that the West regions of the study area has many abattoir that is classified as hotspot abattoirs. Using the hotspot abattoirs as proposed sites for load-distance model three abattoirs were identified as proposed sites- Obosi slaugher house Nkpor Private slaughter house and Oye-olise Ogbunike slaugher house. Their load distance values are 17250.40058 16299.24005 and 18210.14631 respectively. The optimal location for construction of central abattoir bio-waste treatment facility based on the application of these location facility models and hotspot analysis is Nkpor private slaughter house or its environs.

  16. Genomic analysis of primordial dwarfism reveals novel disease genes.

    Science.gov (United States)

    Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S

    2014-02-01

    Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.

  17. Data analysis and approximate models model choice, location-scale, analysis of variance, nonparametric regression and image analysis

    CERN Document Server

    Davies, Patrick Laurie

    2014-01-01

    Introduction IntroductionApproximate Models Notation Two Modes of Statistical AnalysisTowards One Mode of Analysis Approximation, Randomness, Chaos, Determinism ApproximationA Concept of Approximation Approximation Approximating a Data Set by a Model Approximation Regions Functionals and EquivarianceRegularization and Optimality Metrics and DiscrepanciesStrong and Weak Topologies On Being (almost) Honest Simulations and Tables Degree of Approximation and p-values ScalesStability of Analysis The Choice of En(α, P) Independence Procedures, Approximation and VaguenessDiscrete Models The Empirical Density Metrics and Discrepancies The Total Variation Metric The Kullback-Leibler and Chi-Squared Discrepancies The Po(λ) ModelThe b(k, p) and nb(k, p) Models The Flying Bomb Data The Student Study Times Data OutliersOutliers, Data Analysis and Models Breakdown Points and Equivariance Identifying Outliers and Breakdown Outliers in Multivariate Data Outliers in Linear Regression Outliers in Structured Data The Location...

  18. Flaw location and characterization in anisotropic materials by ultrasonic spectral analysis

    International Nuclear Information System (INIS)

    Adler, L.; Cook, K.V.; Simpson, W.A.; Lewis, D.K.

    1978-01-01

    A method of quantitatively determining size and location of flaws in anisotropic materials such as stainless steel welds is described. In previous work, it was shown that spectral analysis of a broad band ultrasonic pulse scattered from a defect can be used to determine size and orientation in isotropic materials if the velocity of sound in the material is known. In an anisotropic structural material (stainless steel weld, centrifugal cast pipe), the velocity (both shear and longitudinal) is direction-dependent. When anisotropy is not taken into account, defect location and defect size estimation is misjudged. It will be shown that the effect of this structural variation in materials must be considered to obtain the correct size and location of defects by frequency analysis. A theoretical calculation, including anisotropy, of the scattered field from defects will also be presented

  19. 1999 Baseline Sampling and Analysis Sampling Locations, Geographic NAD83, LOSCO (2004) [BSA_1999_sample_locations_LOSCO_2004

    Data.gov (United States)

    Louisiana Geographic Information Center — The monitor point data set was produced as a part of the Baseline Sampling and Analysis program coordinated by the Louisiana Oil Spill Coordinator's Office. This...

  20. 1997 Baseline Sampling and Analysis Sample Locations, Geographic NAD83, LOSCO (2004) [BSA_1997_sample_locations_LOSCO_2004

    Data.gov (United States)

    Louisiana Geographic Information Center — The monitor point data set was produced as a part of the Baseline Sampling and Analysis (BSA) program coordinated by the Louisiana Oil Spill Coordinator's Office....

  1. 1998 Baseline Sampling and Analysis Sampling Locations, Geographic NAD83, LOSCO (2004) [BSA_1998_sample_locations_LOSCO_2004

    Data.gov (United States)

    Louisiana Geographic Information Center — The monitor point data set was produced as a part of the Baseline Sampling and Analysis program coordinated by the Louisiana Oil Spill Coordinator's Office. This...

  2. Analysis reveals potential rangeland impacts if Williamson Act eliminated

    Directory of Open Access Journals (Sweden)

    William C. Wetzel

    2012-10-01

    Full Text Available California budget cuts have resulted in dramatic reductions in state funding for the Williamson Act, a land protection program that reduces property taxes for the owners of 15 million acres of California farms and rangeland. With state reimbursements to counties eliminated, the decision to continue Williamson Act contracts lies with individual counties. We investigated the consequences of eliminating the Williamson Act, using a geospatial analysis and a mail questionnaire asking ranchers for plans under a hypothetical elimination scenario. The geospatial analysis revealed that 72% of rangeland parcels enrolled in Williamson Act contracts contained habitat important for statewide conservation goals. Presented with the elimination scenario, survey respondents reported an intention to sell 20% of their total 496,889 acres. The tendency of survey participants to respond that they would sell land was highest among full-time ranchers with low household incomes and without off-ranch employment. A majority (76% of the ranchers who reported that they would sell land predicted that the buyers would develop it for nonagricultural uses, suggesting substantial changes to California's landscape in a future without the Williamson Act.

  3. Multilocus analysis reveals three candidate genes for Chinese migraine susceptibility.

    Science.gov (United States)

    An, X-K; Fang, J; Yu, Z-Z; Lin, Q; Lu, C-X; Qu, H-L; Ma, Q-L

    2017-08-01

    Several genome-wide association studies (GWASs) in Caucasian populations have identified 12 loci that are significantly associated with migraine. More evidence suggests that serotonin receptors are also involved in migraine pathophysiology. In the present study, a case-control study was conducted in a cohort of 581 migraine cases and 533 ethnically matched controls among a Chinese population. Eighteen polymorphisms from serotonin receptors and GWASs were selected, and genotyping was performed using a Sequenom MALDI-TOF mass spectrometry iPLEX platform. The genotypic and allelic distributions of MEF2D rs2274316 and ASTN2 rs6478241 were significantly different between migraine patients and controls. Univariate and multivariate analysis revealed significant associations of polymorphisms in the MEF2D and ASTN2 genes with migraine susceptibility. MEF2D, PRDM16 and ASTN2 were also found to be associated with migraine without aura (MO) and migraine with family history. And, MEF2D and ASTN2 also served as genetic risk factors for the migraine without family history. The generalized multifactor dimensionality reduction analysis identified that MEF2D and HTR2E constituted the two-factor interaction model. Our study suggests that the MEF2D, PRDM16 and ASTN2 genes from GWAS are associated with migraine susceptibility, especially MO, among Chinese patients. It appears that there is no association with serotonin receptor related genes. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. Comparative analysis reveals the underlying mechanism of vertebrate seasonal reproduction.

    Science.gov (United States)

    Ikegami, Keisuke; Yoshimura, Takashi

    2016-02-01

    Animals utilize photoperiodic changes as a calendar to regulate seasonal reproduction. Birds have highly sophisticated photoperiodic mechanisms and functional genomics analysis in quail uncovered the signal transduction pathway regulating avian seasonal reproduction. Birds detect light with deep brain photoreceptors. Long day (LD) stimulus induces secretion of thyroid-stimulating hormone (TSH) from the pars tuberalis (PT) of the pituitary gland. PT-derived TSH locally activates thyroid hormone (TH) in the hypothalamus, which induces gonadotropin-releasing hormone (GnRH) and hence gonadotropin secretion. However, during winter, low temperatures increase serum TH for adaptive thermogenesis, which accelerates germ cell apoptosis by activating the genes involved in metamorphosis. Therefore, TH has a dual role in the regulation of seasonal reproduction. Studies using TSH receptor knockout mice confirmed the involvement of PT-derived TSH in mammalian seasonal reproduction. In addition, studies in mice revealed that the tissue-specific glycosylation of TSH diversifies its function in the circulation to avoid crosstalk. In contrast to birds and mammals, one of the molecular machineries necessary for the seasonal reproduction of fish are localized in the saccus vasculosus from the photoreceptor to the neuroendocrine output. Thus, comparative analysis is a powerful tool to uncover the universality and diversity of fundamental properties in various organisms. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Using Geospatial Analysis to Align Little Free Library Locations with Community Literacy Needs

    Science.gov (United States)

    Rebori, Marlene K.; Burge, Peter

    2017-01-01

    We used geospatial analysis tools to develop community maps depicting fourth-grade reading proficiency test scores and locations of facilities offering public access to reading materials (i.e., public libraries, elementary schools, and Little Free Libraries). The maps visually highlighted areas with struggling readers and areas without adequate…

  6. A Preliminary ZEUS Lightning Location Error Analysis Using a Modified Retrieval Theory

    Science.gov (United States)

    Elander, Valjean; Koshak, William; Phanord, Dieudonne

    2004-01-01

    The ZEUS long-range VLF arrival time difference lightning detection network now covers both Europe and Africa, and there are plans for further expansion into the western hemisphere. In order to fully optimize and assess ZEUS lightning location retrieval errors and to determine the best placement of future receivers expected to be added to the network, a software package is being developed jointly between the NASA Marshall Space Flight Center (MSFC) and the University of Nevada Las Vegas (UNLV). The software package, called the ZEUS Error Analysis for Lightning (ZEAL), will be used to obtain global scale lightning location retrieval error maps using both a Monte Carlo approach and chi-squared curvature matrix theory. At the core of ZEAL will be an implementation of an Iterative Oblate (IO) lightning location retrieval method recently developed at MSFC. The IO method will be appropriately modified to account for variable wave propagation speed, and the new retrieval results will be compared with the current ZEUS retrieval algorithm to assess potential improvements. In this preliminary ZEAL work effort, we defined 5000 source locations evenly distributed across the Earth. We then used the existing (as well as potential future ZEUS sites) to simulate arrival time data between source and ZEUS site. A total of 100 sources were considered at each of the 5000 locations, and timing errors were selected from a normal distribution having a mean of 0 seconds and a standard deviation of 20 microseconds. This simulated "noisy" dataset was analyzed using the IO algorithm to estimate source locations. The exact locations were compared with the retrieved locations, and the results are summarized via several color-coded "error maps."

  7. The analysis of the wind potential in selected locations in the southeastern Poland

    Directory of Open Access Journals (Sweden)

    Sornek Krzysztof

    2017-01-01

    Full Text Available This paper shows the results of analysis of the wind potential in selected locations in the southern Poland (placed in the Małopolskie, Świętokrzyskie and Podkarpackie Voivodships. The measurements and analysis of the wind resources in potential locations of the wind turbines are important part of the investment process. The statistical analysis involves the creation of histograms (e.g. histogram of the wind speed and direction and fitting those histograms to theoretical distributions (e.g. Weilbull distributions of wind speed. Such analysis has been described and conducted using measurement data for four selected locations. Basis on the conducted analysis, the economy efficiency and environmental impact of wind turbine operation has been estimated. Three market available wind turbines have been included to calculate NPV, IRR and SPBT indicators. Then, the avoided emissions of CO2, NOx, SO2 and dust have been calculated. There were also conducted some calculation using TRNSYS simulation software. The results of simulations have been compared with measurement data and the level of convergence have been found.

  8. Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.

    Science.gov (United States)

    Ehrmann, Matthias A; Müller, Martin R A; Vogel, Rudi F

    2003-01-01

    Genotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of DL-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G +C content was 37.5 0.2 mol%. The peptidoglycan was of the lysine-D-iso-asparagine (L-Lys-D-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA-DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).

  9. Effect of overlapping on location of peaks in qualitative X-ray fluorescent analysis

    International Nuclear Information System (INIS)

    Jordanov, J.; Stefanov, R.; Tsanov, T.; Jordanov, N.

    1982-01-01

    To determine the location of the maxima in spectra without resorting to the comparatively complex Fourier-analysis apparatus it is proposed to take into account the overlapping of two adjacent peaks. A formula for the correction of the locations of overlapping maxima with an infinitely small step has been obtained and it is recommended when using X-ray apparatus with great resolution. With flat crystal-analyser apparata, which has a comparatively small resolution, a considerable number of maxima are obtained from the overlapping of at least two adjacent peaks. For that case another formula for the estimation of the shift of the maxima's location from their tabular values is proposed. (authors)

  10. Featureous: an Integrated Approach to Location, Analysis and Modularization of Features in Java Applications

    DEFF Research Database (Denmark)

    Olszak, Andrzej

    , it is essential that features are properly modularized within the structural organization of software systems. Nevertheless, in many object-oriented applications, features are not represented explicitly. Consequently, features typically end up scattered and tangled over multiple source code units......, such as architectural layers, packages and classes. This lack of modularization is known to make application features difficult to locate, to comprehend and to modify in isolation from one another. To overcome these problems, this thesis proposes Featureous, a novel approach to location, analysis and modularization...... quantitative and qualitative results suggest that Featureous succeeds at efficiently locating features in unfamiliar codebases, at aiding feature-oriented comprehension and modification, and at improving modularization of features using Java packages....

  11. A methodology for selection of wind energy system locations using multicriterial analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sansevic, M.; Rabadan, Lj. Pilic [Croatia Univ., Faculty of Electrical Engineering, Mechanical Engineering and Naval Architecture, Split (Croatia)

    1996-12-31

    The effectiveness of a wind turbine generator depends not only on its performance but also on the site`s wind resource. Thus the problem of location selection should be approached systematically, by considering a set of relevant parameters particularly those having a significant economical and ecological impact. This paper presents the methodology used in location selection for the operation of wind energy system. It is based on a multicriterial analysis which enables comparison and ranking of locations according to a set of different parameters. Principal objectives (criteria) in location selection are: energy-economical, technical-technological, physical planning and environment and life protection objectives. For the mathematical modeling of this multicriterial problem the PROMETHEE method is chosen which is developed especially for the solution of rather ``poorly`` structured problems, thus justifying its application in the preliminary stage of site selection for the wind energy systems. The developed methodology is applied in selecting the locations in the island of Rhodes using the available database of the Geographic Information System and the wind potential data obtained by means of the AIOLOS program. (Author)

  12. A simulation-based Data Envelopment Analysis (DEA model to evaluate wind plants locations

    Directory of Open Access Journals (Sweden)

    Hossein Sameie

    2015-04-01

    Full Text Available As the world is getting overpopulated and over polluted the human being is seeking to utilize new sources of energy that are cleaner, cheaper, and more accessible. Wind is one of these clean energy sources that is accessible everywhere on the planet earth. This source of energy cannot be stored for later use; therefore, environmental circumstances and geographical location of wind plants are crucial matters. This study proposes a model to decide on the optimum location for a wind farm among the demand area. To tackle the uncertainty related to the geographical position of the nominated location such as wind speed; altitude; mean temperature; and humidity; a simulation method is applied on the problem. Other factors such as the time that a plant is out of service and demand fluctuations also have been considered in the simulation phase. Moreover, a probability distribution function is calculated for the turbine power. Then Data Envelopment Analysis (DEA performs the selection between all the nominated locations for wind farm. The proposed model takes into account several important elements of the problems. Elements such as land cost; average power received from the wind blowing; demand point population etc. are considered at the same time to select the optimum location of wind plants. Finally, the model is applied on a real case in order to demonstrate its reliability and applicability.

  13. Detector location selection based on VIP analysis in near-infrared detection of dural hematoma

    Directory of Open Access Journals (Sweden)

    Qiuming Sun

    2018-03-01

    Full Text Available Detection of dural hematoma based on multi-channel near-infrared differential absorbance has the advantages of rapid and non-invasive detection. The location and number of detectors around the light source are critical for reducing the pathological characteristics of the prediction model on dural hematoma degree. Therefore, rational selection of detector numbers and their distances from the light source is very important. In this paper, a detector position screening method based on Variable Importance in the Projection (VIP analysis is proposed. A preliminary modeling based on Partial Least Squares method (PLS for the prediction of dural position μa was established using light absorbance information from 30 detectors located 2.0–5.0 cm from the light source with a 0.1 cm interval. The mean relative error (MRE of the dural position μa prediction model was 4.08%. After VIP analysis, the number of detectors was reduced from 30 to 4 and the MRE of the dural position μa prediction was reduced from 4.08% to 2.06% after the reduction in detector numbers. The prediction model after VIP detector screening still showed good prediction of the epidural position μa. This study provided a new approach and important reference on the selection of detector location in near-infrared dural hematoma detection. Keywords: Detector location screening, Epidural hematoma detection, Variable importance in the projection

  14. Testing continuous earthquake detection and location in Alentejo (South Portugal) by waveform coherency analysis

    Science.gov (United States)

    Matos, Catarina; Grigoli, Francesco; Cesca, Simone; Custódio, Susana

    2015-04-01

    In the last decade a permanent seismic network of 30 broadband stations, complemented by dense temporary deployments, covered Portugal. This extraordinary network coverage enables now the computation of a high-resolution image of the seismicity of Portugal, which in turn will shed light on the seismotectonics of Portugal. The large data volumes available cannot be analyzed by traditional time-consuming manual location procedures. In this presentation we show first results on the automatic detection and location of earthquakes occurred in a selected region in the south of Portugal Our main goal is to implement an automatic earthquake detection and location routine in order to have a tool to quickly process large data sets, while at the same time detecting low magnitude earthquakes (i.e., lowering the detection threshold). We present a modified version of the automatic seismic event location by waveform coherency analysis developed by Grigoli et al. (2013, 2014), designed to perform earthquake detections and locations in continuous data. The event detection is performed by continuously computing the short-term-average/long-term-average of two different characteristic functions (CFs). For the P phases we used a CF based on the vertical energy trace, while for S phases we used a CF based on the maximum eigenvalue of the instantaneous covariance matrix (Vidale 1991). Seismic event detection and location is obtained by performing waveform coherence analysis scanning different hypocentral coordinates. We apply this technique to earthquakes in the Alentejo region (South Portugal), taking advantage from a small aperture seismic network installed in the south of Portugal for two years (2010 - 2011) during the DOCTAR experiment. In addition to the good network coverage, the Alentejo region was chosen for its simple tectonic setting and also because the relationship between seismicity, tectonics and local lithospheric structure is intriguing and still poorly understood. Inside

  15. Study on Network Error Analysis and Locating based on Integrated Information Decision System

    Science.gov (United States)

    Yang, F.; Dong, Z. H.

    2017-10-01

    Integrated information decision system (IIDS) integrates multiple sub-system developed by many facilities, including almost hundred kinds of software, which provides with various services, such as email, short messages, drawing and sharing. Because the under-layer protocols are different, user standards are not unified, many errors are occurred during the stages of setup, configuration, and operation, which seriously affect the usage. Because the errors are various, which may be happened in different operation phases, stages, TCP/IP communication protocol layers, sub-system software, it is necessary to design a network error analysis and locating tool for IIDS to solve the above problems. This paper studies on network error analysis and locating based on IIDS, which provides strong theory and technology supports for the running and communicating of IIDS.

  16. Isotope analysis reveals foraging area dichotomy for atlantic leatherback turtles.

    Directory of Open Access Journals (Sweden)

    Stéphane Caut

    Full Text Available BACKGROUND: The leatherback turtle (Dermochelys coriacea has undergone a dramatic decline over the last 25 years, and this is believed to be primarily the result of mortality associated with fisheries bycatch followed by egg and nesting female harvest. Atlantic leatherback turtles undertake long migrations across ocean basins from subtropical and tropical nesting beaches to productive frontal areas. Migration between two nesting seasons can last 2 or 3 years, a time period termed the remigration interval (RI. Recent satellite transmitter data revealed that Atlantic leatherbacks follow two major dispersion patterns after nesting season, through the North Gulf Stream area or more eastward across the North Equatorial Current. However, information on the whole RI is lacking, precluding the accurate identification of feeding areas where conservation measures may need to be applied. METHODOLOGY/PRINCIPAL FINDINGS: Using stable isotopes as dietary tracers we determined the characteristics of feeding grounds of leatherback females nesting in French Guiana. During migration, 3-year RI females differed from 2-year RI females in their isotope values, implying differences in their choice of feeding habitats (offshore vs. more coastal and foraging latitude (North Atlantic vs. West African coasts, respectively. Egg-yolk and blood isotope values are correlated in nesting females, indicating that egg analysis is a useful tool for assessing isotope values in these turtles, including adults when not available. CONCLUSIONS/SIGNIFICANCE: Our results complement previous data on turtle movements during the first year following the nesting season, integrating the diet consumed during the year before nesting. We suggest that the French Guiana leatherback population segregates into two distinct isotopic groupings, and highlight the urgent need to determine the feeding habitats of the turtle in the Atlantic in order to protect this species from incidental take by

  17. Quantitative flux analysis reveals folate-dependent NADPH production

    Science.gov (United States)

    Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

    2014-06-01

    ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

  18. How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches

    Directory of Open Access Journals (Sweden)

    Barbara Diana

    2017-08-01

    Full Text Available The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance. This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013—First Leg. The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann–Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.

  19. How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches.

    Science.gov (United States)

    Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M; Jonsson, Gudberg K; Anguera, M Teresa

    2017-01-01

    The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013-First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann-Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.

  20. Integrated analysis tools for trade studies of spacecraft controller and sensor locations

    Science.gov (United States)

    Rowell, L. F.

    1986-01-01

    The present investigation was conducted with the aim to evaluate the practicality and difficulties of modern control design methods for large space structure controls. The evaluation is used as a basis for the identification of useful computer-based analysis tools which would provide insight into control characteristics of a spacecraft concept. A description is presented of the wrap-rib antenna and its packaging concept. Attention is given to active control requirements, a mathematical model of structural dynamics, aspects of sensor and actuator location, the analysis approach, controllability, observability, the concept of balanced realization, transmission zeros, singular value plots, analysis results, model reduction, and an interactive computer program. It is pointed out that the application of selected control analysis tools to the wrap-rib antenna demonstrates several capabilities which can be useful during conceptual design.

  1. Analysis of neurological sequelae from radiosurgery of arteriovenous malformations: how location effects outcome

    International Nuclear Information System (INIS)

    Flickinger, John C.; Kondziolka, Douglas; Maitz, Ann H.; Lunsford, L. Dade

    1997-01-01

    Purpose/Objective: To elucidate how the risks of developing temporary and permanent neurological sequelae from radiosurgery for arteriovenous malformations (AVM) relate to AVM location, the addition of stereotactic magnetic resonance (MR) imaging to angiographic targeting, and prior hemorrhage or neurological deficits. Materials and Methods: We evaluated follow-up imaging and clinical data in 332 AVM patients who received gamma knife radiosurgery at the University of Pittsburgh between 1987 and 1994. All patients had regular clinical or imaging follow up for a minimum of two years (range: 24-96 mo., median=45 mo.). 83 patients had MR. planning, and 187 previously bled. Results: Symptomatic post-radiosurgery sequelae (any neurological problem including headache) developed in 30/332 patients (9.0%). Symptoms resolved in 58% of patients within 24 mo. with a significantly greater proportion (p=0.006) resolving in patients with Dmin <20 vs. ≥20 Gy (89 vs. 36%). The 7 yr. actuarial rate for developing persistent symptomatic sequelae was 3.8%. We first evaluated the relative risks for different locations to construct a post-radiosurgery injury expression (PIE) score for AVM location (see Table 1). Multivariate logistic regression analysis of symptomatic post-radiosurgery injury identified independent significant correlations with PIE location score (p=0.0007) and 12 Gy volume (p=0.008) but none of the other factors tested (p≥0.3) including the addition of MR targeting, average radiation dose in 20 cc, prior bleed or neurological deficit. We used these results to construct risk prediction models for any symptomatic post-radiosurgery sequelae and for symptomatic necrosis. Conclusion: The risks of complications from AVM radiosurgery can be predicted according to location with the PIE score and by the 12 Gy treatment volume (Table 2)

  2. Potential Coastal Pumped Hydroelectric Energy Storage Locations Identified using GIS-based Topographic Analysis

    Science.gov (United States)

    Parsons, R.; Barnhart, C. J.; Benson, S. M.

    2013-12-01

    Large-scale electrical energy storage could accommodate variable, weather dependent energy resources such as wind and solar. Pumped hydroelectric energy storage (PHS) and compressed energy storage area (CAES) have life cycle energy and financial costs that are an order of magnitude lower than conventional electrochemical storage technologies. However PHS and CAES storage technologies require specific geologic conditions. Conventional PHS requires an upper and lower reservoir separated by at least 100 m of head, but no more than 10 km in horizontal distance. Conventional PHS also impacts fresh water supplies, riparian ecosystems, and hydrologic environments. A PHS facility that uses the ocean as the lower reservoir benefits from a smaller footprint, minimal freshwater impact, and the potential to be located near off shore wind resources and population centers. Although technologically nascent, today one coastal PHS facility exists. The storage potential for coastal PHS is unknown. Can coastal PHS play a significant role in augmenting future power grids with a high faction of renewable energy supply? In this study we employ GIS-based topographic analysis to quantify the coastal PHS potential of several geographic locations, including California, Chile and Peru. We developed automated techniques that seek local topographic minima in 90 m spatial resolution shuttle radar topography mission (SRTM) digital elevation models (DEM) that satisfy the following criteria conducive to PHS: within 10 km from the sea; minimum elevation 150 m; maximum elevation 1000 m. Preliminary results suggest the global potential for coastal PHS could be very significant. For example, in northern Chile we have identified over 60 locations that satisfy the above criteria. Two of these locations could store over 10 million cubic meters of water or several GWh of energy. We plan to report a global database of candidate coastal PHS locations and to estimate their energy storage capacity.

  3. Gis Based Analysis For Suitability Location Finding In The Residential Development Areas Of Greater Matara Region

    Directory of Open Access Journals (Sweden)

    H.K.G.M Madurika

    2017-02-01

    Full Text Available Urban Planning and Land utilization for the Residential is one of crucial factors in high density Cities. Many theories in Planning explain the Residential areas are moving to periphery areas in cities by its commercial development. Martara is one of developing city in Southern Sri Lanka and Residential land value are comparative high in city sub urban areas. In this study it is examined that where is the best locations for residential development in Grater Matara Region by using five criteria. GIS based Multi Criteria Method MCE method have been applied to find the suitable locations. The results of analysis have been shown that there are 5378.99 hectares area suitable within study area and however extremely importance areas only 1.40 hectares accordingly given criteria but very strongly importance and importance category have 1560.51 and 2468.22 respectively.

  4. Regression Analysis of Top of Descent Location for Idle-thrust Descents

    Science.gov (United States)

    Stell, Laurel; Bronsvoort, Jesper; McDonald, Greg

    2013-01-01

    In this paper, multiple regression analysis is used to model the top of descent (TOD) location of user-preferred descent trajectories computed by the flight management system (FMS) on over 1000 commercial flights into Melbourne, Australia. The independent variables cruise altitude, final altitude, cruise Mach, descent speed, wind, and engine type were also recorded or computed post-operations. Both first-order and second-order models are considered, where cross-validation, hypothesis testing, and additional analysis are used to compare models. This identifies the models that should give the smallest errors if used to predict TOD location for new data in the future. A model that is linear in TOD altitude, final altitude, descent speed, and wind gives an estimated standard deviation of 3.9 nmi for TOD location given the trajec- tory parameters, which means about 80% of predictions would have error less than 5 nmi in absolute value. This accuracy is better than demonstrated by other ground automation predictions using kinetic models. Furthermore, this approach would enable online learning of the model. Additional data or further knowl- edge of algorithms is necessary to conclude definitively that no second-order terms are appropriate. Possible applications of the linear model are described, including enabling arriving aircraft to fly optimized descents computed by the FMS even in congested airspace. In particular, a model for TOD location that is linear in the independent variables would enable decision support tool human-machine interfaces for which a kinetic approach would be computationally too slow.

  5. RAPD Analysis and Antibiotic Susceptibility for Mycobacterium tuberculosis Strains Isolated from Different Locations in Egypt

    Directory of Open Access Journals (Sweden)

    Ali, A. M.

    2011-01-01

    Full Text Available The routine identification of mycobacterial strains isolated from patients in different locations in Egypt was confirmed by specific DNA fragment amplification. The susceptibilities of 72 Mycobacterium tuberculosis strains against the four antibiotics used in tuberculosis treatment (Isoniazid, INH; Rifampicin, Rif; Streptomycin, St and Ethambutol, E were examined. Our results indicated that, multi drug resistant tuberculosis (MDR-TB represents about 19.5% of the tested strains, whereas sensitive strains represented 26.4%. The genetic polymorphism of the tested strains was examined using RAPD analysis. Six selected strains represent the different antibiotic susceptibility groups were examined using RAPD fingerprinting. No difference between the strains was recorded using the RFLP analysis of amplified specific fragment. The discrimination power of RAPD analysis was inadequate to clarify the genetic correlation between the tested strains. MDR-TB was approximately double time in 2008 compared with the value in 2007. Most of the new MDRTB was correlated with resident dense population regions.

  6. Analysis of potato virus X replicase and TGBp3 subcellular locations

    International Nuclear Information System (INIS)

    Bamunusinghe, Devinka; Hemenway, Cynthia L.; Nelson, Richard S.; Sanderfoot, Anton A.; Ye, Chang M.; Silva, Muniwarage A.T.; Payton, M.; Verchot-Lubicz, Jeanmarie

    2009-01-01

    Potato virus X (PVX) infection leads to certain cytopathological modifications of the host endomembrane system. The subcellular location of the PVX replicase was previously unknown while the PVX TGBp3 protein was previously reported to reside in the ER. Using PVX infectious clones expressing the green fluorescent protein reporter, and antisera detecting the PVX replicase and host membrane markers, we examined the subcellular distribution of the PVX replicase in relation to the TGBp3. Confocal and electron microscopic observations revealed that the replicase localizes in membrane bound structures that derive from the ER. A subset of TGBp3 resides in the ER at the same location as the replicase. Sucrose gradient fractionation showed that the PVX replicase and TGBp3 proteins co-fractionate with ER marker proteins. This localization represents a region where both proteins may be synthesized and/or function. There is no evidence to indicate that either PVX protein moves into the Golgi apparatus. Cerulenin, a drug that inhibits de novo membrane synthesis, also inhibited PVX replication. These combined data indicate that PVX replication relies on ER-derived membrane recruitment and membrane proliferation.

  7. A Visual Analysis Approach for Inferring Personal Job and Housing Locations Based on Public Bicycle Data

    Directory of Open Access Journals (Sweden)

    Xiaoying Shi

    2017-07-01

    Full Text Available Information concerning the home and workplace of residents is the basis of analyzing the urban job-housing spatial relationship. Traditional methods conduct time-consuming user surveys to obtain personal job and housing location information. Some new methods define rules to detect personal places based on human mobility data. However, because the travel patterns of residents are variable, simple rule-based methods are unable to generalize highly changing and complex travel modes. In this paper, we propose a visual analysis approach to assist the analyzer in inferring personal job and housing locations interactively based on public bicycle data. All users are first clustered to find potential commuting users. Then, several visual views are designed to find the key candidate stations for a specific user, and the visited temporal pattern of stations and the user’s hire behavior are analyzed, which helps with the inference of station semantic meanings. Finally, a number of users’ job and housing locations are detected by the analyzer and visualized. Our approach can manage the complex and diverse cycling habits of users. The effectiveness of the approach is shown through case studies based on a real-world public bicycle dataset.

  8. A statistical analysis of the location and width of Saturn's southern auroras

    Directory of Open Access Journals (Sweden)

    S. V. Badman

    2006-12-01

    Full Text Available A selection of twenty-two Hubble Space Telescope images of Saturn's ultraviolet auroras obtained during 1997–2004 has been analysed to determine the median location and width of the auroral oval, and their variability. Limitations of coverage restrict the analysis to the southern hemisphere, and to local times from the post-midnight sector to just past dusk, via dawn and noon. It is found that the overall median location of the poleward and equatorward boundaries of the oval with respect to the southern pole are at ~14° and ~16° co-latitude, respectively, with a median latitudinal width of ~2°. These median values vary only modestly with local time around the oval, though the poleward boundary moves closer to the pole near noon (~12.5° such that the oval is wider in that sector (median width ~3.5° than it is at both dawn and dusk (~1.5°. It is also shown that the position of the auroral boundaries at Saturn are extremely variable, the poleward boundary being located between 2° and 20° co-latitude, and the equatorward boundary between 6° and 23°, this variability contrasting sharply with the essentially fixed location of the main oval at Jupiter. Comparison with Voyager plasma angular velocity data mapped magnetically from the equatorial magnetosphere into the southern ionosphere indicates that the dayside aurora lie poleward of the main upward-directed field-aligned current region associated with corotation enforcement, which maps to ~20°–24° co-latitude, while agreeing reasonably with the position of the open-closed field line boundary based on estimates of the open flux in Saturn's tail, located between ~11° and ~15°. In this case, the variability in location can be understood in terms of changes in the open flux present in the system, the changes implied by the Saturn data then matching those observed at Earth as fractions of the total planetary flux. We infer that the broad (few degrees diffuse auroral emissions

  9. A Time-constrained Network Voronoi Construction and Accessibility Analysis in Location-based Service Technology

    Science.gov (United States)

    Yu, W.; Ai, T.

    2014-11-01

    Accessibility analysis usually requires special models of spatial location analysis based on some geometric constructions, such as Voronoi diagram (abbreviated to VD). There are many achievements in classic Voronoi model research, however suffering from the following limitations for location-based services (LBS) applications. (1) It is difficult to objectively reflect the actual service areas of facilities by using traditional planar VDs, because human activities in LBS are usually constrained only to the network portion of the planar space. (2) Although some researchers have adopted network distance to construct VDs, their approaches are used in a static environment, where unrealistic measures of shortest path distance based on assumptions about constant travel speeds through the network were often used. (3) Due to the computational complexity of the shortest-path distance calculating, previous researches tend to be very time consuming, especially for large datasets and if multiple runs are required. To solve the above problems, a novel algorithm is developed in this paper. We apply network-based quadrat system and 1-D sequential expansion to find the corresponding subnetwork for each focus. The idea is inspired by the natural phenomenon that water flow extends along certain linear channels until meets others or arrives at the end of route. In order to accommodate the changes in traffic conditions, the length of network-quadrat is set upon the traffic condition of the corresponding street. The method has the advantage over Dijkstra's algorithm in that the time cost is avoided, and replaced with a linear time operation.

  10. Built environment analysis for road traffic hotspot locations in Moshi, Tanzania.

    Science.gov (United States)

    Waldon, Meredith; Ibingira, Treasure Joelson; de Andrade, Luciano; Mmbaga, Blandina T; Vissoci, João Ricardo N; Mvungi, Mark; Staton, Catherine A

    2018-02-08

    Road traffic injuries (RTIs) cause significant morbidity and mortality in low- and middle-income countries. Investigation of high risk areas for RTIs is needed to guide improvements. This study provides built environmental analysis of road traffic crash hotspots within Moshi, Tanzania. Spatial analysis of police data identified 36 hotspots. Qualitative comparative analysis revealed 40% of crash sites were on local roads without night lighting and increased motorcycle density. Paved narrow roads represented 26% of hotspots and 13% were unpaved roads with uneven roadsides. Roadside unevenness was more predominate in low risk [n = 19, (90.5%)] than high risk sites [n = 7 (46.7%)]. Both low [n = 6 (28.6%)] and high risk [n = 1 (6.7%)] sites had minimal signage. All sites had informal pedestrian pathways. Little variability between risk sites suggests hazardous conditions are widespread. Findings suggest improvement in municipal infrastructure, signage and enforcement is needed to reduce RTI burden.

  11. VNTR analysis reveals unexpected genetic diversity within Mycoplasma agalactiae, the main causative agent of contagious agalactia

    Directory of Open Access Journals (Sweden)

    Ayling Roger D

    2008-11-01

    Full Text Available Abstract Background Mycoplasma agalactiae is the main cause of contagious agalactia, a serious disease of sheep and goats, which has major clinical and economic impacts. Previous studies of M. agalactiae have shown it to be unusually homogeneous and there are currently no available epidemiological techniques which enable a high degree of strain differentiation. Results We have developed variable number tandem repeat (VNTR analysis using the sequenced genome of the M. agalactiae type strain PG2. The PG2 genome was found to be replete with tandem repeat sequences and 4 were chosen for further analysis. VNTR 5 was located within the hypothetical protein MAG6170 a predicted lipoprotein. VNTR 14 was intergenic between the hypothetical protein MAG3350 and the hypothetical protein MAG3340. VNTR 17 was intergenic between the hypothetical protein MAG4060 and the hypothetical protein MAG4070 and VNTR 19 spanned the 5' end of the pseudogene for a lipoprotein MAG4310 and the 3' end of the hypothetical lipoprotein MAG4320. We have investigated the genetic diversity of 88 M. agalactiae isolates of wide geographic origin using VNTR analysis and compared it with pulsed field gel electrophoresis (PFGE and random amplified polymorphic DNA (RAPD analysis. Simpson's index of diversity was calculated to be 0.324 for PFGE and 0.574 for VNTR analysis. VNTR analysis revealed unexpected diversity within M. agalactiae with 9 different VNTR types discovered. Some correlation was found between geographical origin and the VNTR type of the isolates. Conclusion VNTR analysis represents a useful, rapid first-line test for use in molecular epidemiological analysis of M. agalactiae for outbreak tracing and control.

  12. A genetic analysis of segregation distortion revealed by molecular ...

    Indian Academy of Sciences (India)

    Journal of Genetics, Vol. 90, No. ... Segregation analysis was based on 64 molecular markers, including 26 .... FHB of RIL populations was controlled by quantitative trait ... The authors acknowledge financial support by the National Basic.

  13. Analysis of Geodynamical Conditions of Region of Burning Coal Dumps Location

    Science.gov (United States)

    Batugin, Andrian; Musina, Valeria; Golovko, Irina

    2017-12-01

    Spontaneous combustion of coal dumps and their impact on the environment of mining regions remain important environmental problem, in spite of the measures that are being taken. The paper presents the hypothesis, which states that the location of coal dumps at the boundaries of geodynamically active crust blocks promotes the appearance of conditions for their combustion. At present geodynamically active crust faults that affect the operating conditions of engineering facilities are observed not only in the areas of tectonic activity, but also on platforms. According to the concept of geodynamical zoning, geodynamically dangerous zones for engineering structures can be not only large, well-developed crust faults, but also just formed fractures that appear as boundaries of geodynamically impacting and hierarchically ordered crust blocks. The purpose of the study is to estimate the linkage of burning dumps to boundaries of geodynamically active crust blocks (geodynamically dangerous zones) for subsequent development of recommendations for reducing environmental hazard. The analysis of 27 coal dumps location was made for one of the Eastern Donbass regions (Russia). Nine of sixteen burning dumps are located in geodynamically dangerous zones, which, taking into account relatively small area occupied by all geodynamically dangerous zones, results that there is a concentration (pcs/km2) of burning dumps, which is 14 times higher than the baseline value. While the probability of accidental obtaining of such a result is extremely low, this can be considered as the evidence of the linkage of burning dumps to geodynamically dangerous zones. Taking into account the stressed state of the rock massif in this region, all geodynamically dangerous zones can be divided into compression and tension zones. The statistic is limited, but nevertheless in tension zones the concentration of burning dumps is 2 times higher than in compression zones. Available results of thermal monitoring of

  14. Spatial and Temporal Analysis of Eruption Locations, Compositions, and Styles in Northern Harrat Rahat, Kingdom of Saudi Arabia

    Science.gov (United States)

    Dietterich, H. R.; Stelten, M. E.; Downs, D. T.; Champion, D. E.

    2017-12-01

    Harrat Rahat is a predominantly mafic, 20,000 km2 volcanic field in western Saudi Arabia with an elongate volcanic axis extending 310 km north-south. Prior mapping suggests that the youngest eruptions were concentrated in northernmost Harrat Rahat, where our new geologic mapping and geochronology reveal >300 eruptive vents with ages ranging from 1.2 Ma to a historic eruption in 1256 CE. Eruption compositions and styles vary spatially and temporally within the volcanic field, where extensive alkali basaltic lavas dominate, but more evolved compositions erupted episodically as clusters of trachytic domes and small-volume pyroclastic flows. Analysis of vent locations, compositions, and eruption styles shows the evolution of the volcanic field and allows assessment of the spatio-temporal probabilities of vent opening and eruption styles. We link individual vents and fissures to eruptions and their deposits using field relations, petrography, geochemistry, paleomagnetism, and 40Ar/39Ar and 36Cl geochronology. Eruption volumes and deposit extents are derived from geologic mapping and topographic analysis. Spatial density analysis with kernel density estimation captures vent densities of up to 0.2 %/km2 along the north-south running volcanic axis, decaying quickly away to the east but reaching a second, lower high along a secondary axis to the west. Temporal trends show slight younging of mafic eruption ages to the north in the past 300 ka, as well as clustered eruptions of trachytes over the past 150 ka. Vent locations, timing, and composition are integrated through spatial probability weighted by eruption age for each compositional range to produce spatio-temporal models of vent opening probability. These show that the next mafic eruption is most probable within the north end of the main (eastern) volcanic axis, whereas more evolved compositions are most likely to erupt within the trachytic centers further to the south. These vent opening probabilities, combined with

  15. High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

    Directory of Open Access Journals (Sweden)

    Soichi Inagaki

    Full Text Available Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

  16. High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

    Science.gov (United States)

    Inagaki, Soichi; Henry, Isabelle M; Lieberman, Meric C; Comai, Luca

    2015-01-01

    Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

  17. Network analysis reveals multiscale controls on streamwater chemistry

    Science.gov (United States)

    Kevin J. McGuire; Christian E. Torgersen; Gene E. Likens; Donald C. Buso; Winsor H. Lowe; Scott W. Bailey

    2014-01-01

    By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in...

  18. A GEOGRAPHIC ANALYSIS OF OPTIMAL SIGNAGE LOCATION SELECTION IN SCENIC AREA

    Directory of Open Access Journals (Sweden)

    L. Ruan

    2016-06-01

    Full Text Available As an important part of the scenic area infrastructure services, signage guiding system plays an indispensable role in guiding the way and improving the quality of tourism experience. This paper proposes an optimal method in signage location selection and direction content design in a scenic area based on geographic analysis. The object of the research is to provide a best solution to arrange limited guiding boards in a tourism area to show ways arriving at any scenic spot from any entrance. There are four steps to achieve the research object. First, the spatial distribution of the junction of the scenic road, the passageway and the scenic spots is analyzed. Then, the count of scenic roads intersection on the shortest path between all entrances and all scenic spots is calculated. Next, combing with the grade of the scenic road and scenic spots, the importance of each road intersection is estimated quantitatively. Finally, according to the importance of all road intersections, the most suitable layout locations of signage guiding boards can be provided. In addition, the method is applied in the Ming Tomb scenic area in China and the result is compared with the existing signage guiding space layout.

  19. a Geographic Analysis of Optimal Signage Location Selection in Scenic Area

    Science.gov (United States)

    Ruan, Ling; Long, Ying; Zhang, Ling; Wu, Xiao Ling

    2016-06-01

    As an important part of the scenic area infrastructure services, signage guiding system plays an indispensable role in guiding the way and improving the quality of tourism experience. This paper proposes an optimal method in signage location selection and direction content design in a scenic area based on geographic analysis. The object of the research is to provide a best solution to arrange limited guiding boards in a tourism area to show ways arriving at any scenic spot from any entrance. There are four steps to achieve the research object. First, the spatial distribution of the junction of the scenic road, the passageway and the scenic spots is analyzed. Then, the count of scenic roads intersection on the shortest path between all entrances and all scenic spots is calculated. Next, combing with the grade of the scenic road and scenic spots, the importance of each road intersection is estimated quantitatively. Finally, according to the importance of all road intersections, the most suitable layout locations of signage guiding boards can be provided. In addition, the method is applied in the Ming Tomb scenic area in China and the result is compared with the existing signage guiding space layout.

  20. Newborn screening blood spot analysis in the UK: influence of spot size, punch location and haematocrit.

    Science.gov (United States)

    Lawson, A J; Bernstone, L; Hall, S K

    2016-03-01

    In dried blood spot analysis, punch location and variations in applied sample volume and haematocrit can produce different measured concentrations of analytes. We investigated the magnitude of these effects in newborn screening in the UK. Heparinized blood spiked with thyroid stimulating hormone (TSH), phenylalanine, tyrosine, leucine, methionine, octanoyl carnitine (C8), and immunoreactive trypsinogen (IRT) was spotted onto filter paper: (i) at a constant haematocrit of 50% at various volumes, and (ii) at a range of haematocrits using a constant volume. Subpunches (3.2 mm) of the dried blood spots were then analysed. Compared with a central punch from a 50 µL blood spot with 50% haematocrit, 10 µL spots can have significantly lower measured concentrations of all analytes, with decreases of 15% or more observed for leucine, methionine, phenylalanine, and tyrosine. Punching at the edge of a spot can increase measured concentrations up to 35%. Higher haematocrit decreased measured TSH and C8 yet increased amino acids and IRT by 15% compared with 50% haematocrit. Lower haematocrits had the opposite effect, but only with higher concentrations of some analytes. Differences in blood spot size, haematocrit and punch location substantially affect measured concentrations for analytes used in the UK newborn screening programme, and this could affect false positive and negative rates. To minimize analytical bias, these variables should be controlled or adjusted for where possible. © The Author(s) 2015.

  1. Notch Filter Analysis and Its Application in Passive Coherent Location Radar (in English

    Directory of Open Access Journals (Sweden)

    Li Ji-chuan

    2015-01-01

    Full Text Available The Normalized Least-Mean-Squares (NLMS algorithm is widely used to cancel the direct and multiple path interferences in Passive Coherent Location (PCL radar systems. This study proposes that the interference cancelation using the NLMS algorithm and the calculation of the radar Cross Ambiguity Function (CAF can be modeled as a notch filter, with the notch located at zero Doppler frequency in the surface of the radar CAF. The analysis shows that the notch’s width and depth are closely related to the step size of the NLMS algorithm. Subsequently, the effect of the notch in PCL radar target detection is analyzed. The results suggest that the detection performance of the PCL radar deteriorates because of the wide notch. Furthermore, the Nonuniform NLMS (NNLMS algorithm is proposed for removing the clutter with the Doppler frequency by using notch filtering. A step-size matrix is adopted to mitigate the low Doppler frequency clutter and lower the floor of the radar CAF. With the step-size matrix, can be obtained notches of different depths and widths in different range units of the CAF, which can filter the low Doppler frequency clutter. In addition, the convergence rate of the NNLMS algorithm is better than that of the traditional NLMS algorithm. The validity of the NNLMS algorithm is verified by experimental results.

  2. An Information-Based Approach to Precision Analysis of Indoor WLAN Localization Using Location Fingerprint

    Directory of Open Access Journals (Sweden)

    Mu Zhou

    2015-12-01

    Full Text Available In this paper, we proposed a novel information-based approach to precision analysis of indoor wireless local area network (WLAN localization using location fingerprint. First of all, by using the Fisher information matrix (FIM, we derive the fundamental limit of WLAN fingerprint-based localization precision considering different signal distributions in characterizing the variation of received signal strengths (RSSs in the target environment. After that, we explore the relationship between the localization precision and access point (AP placement, which can provide valuable suggestions for the design of the highly-precise localization system. Second, we adopt the heuristic simulated annealing (SA algorithm to optimize the AP locations for the sake of approaching the fundamental limit of localization precision. Finally, the extensive simulations and experiments are conducted in both regular line-of-sight (LOS and irregular non-line-of-sight (NLOS environments to demonstrate that the proposed approach can not only effectively improve the WLAN fingerprint-based localization precision, but also reduce the time overhead.

  3. Failure location prediction by finite element analysis for an additive manufactured mandible implant.

    Science.gov (United States)

    Huo, Jinxing; Dérand, Per; Rännar, Lars-Erik; Hirsch, Jan-Michaél; Gamstedt, E Kristofer

    2015-09-01

    In order to reconstruct a patient with a bone defect in the mandible, a porous scaffold attached to a plate, both in a titanium alloy, was designed and manufactured using additive manufacturing. Regrettably, the implant fractured in vivo several months after surgery. The aim of this study was to investigate the failure of the implant and show a way of predicting the mechanical properties of the implant before surgery. All computed tomography data of the patient were preprocessed to remove metallic artefacts with metal deletion technique before mandible geometry reconstruction. The three-dimensional geometry of the patient's mandible was also reconstructed, and the implant was fixed to the bone model with screws in Mimics medical imaging software. A finite element model was established from the assembly of the mandible and the implant to study stresses developed during mastication. The stress distribution in the load-bearing plate was computed, and the location of main stress concentration in the plate was determined. Comparison between the fracture region and the location of the stress concentration shows that finite element analysis could serve as a tool for optimizing the design of mandible implants. Copyright © 2015 IPEM. Published by Elsevier Ltd. All rights reserved.

  4. Revealing the underlying drivers of disaster risk: a global analysis

    Science.gov (United States)

    Peduzzi, Pascal

    2017-04-01

    Disasters events are perfect examples of compound events. Disaster risk lies at the intersection of several independent components such as hazard, exposure and vulnerability. Understanding the weight of each component requires extensive standardisation. Here, I show how footprints of past disastrous events were generated using GIS modelling techniques and used for extracting population and economic exposures based on distribution models. Using past event losses, it was possible to identify and quantify a wide range of socio-politico-economic drivers associated with human vulnerability. The analysis was applied to about nine thousand individual past disastrous events covering earthquakes, floods and tropical cyclones. Using a multiple regression analysis on these individual events it was possible to quantify each risk component and assess how vulnerability is influenced by various hazard intensities. The results show that hazard intensity, exposure, poverty, governance as well as other underlying factors (e.g. remoteness) can explain the magnitude of past disasters. Analysis was also performed to highlight the role of future trends in population and climate change and how this may impacts exposure to tropical cyclones in the future. GIS models combined with statistical multiple regression analysis provided a powerful methodology to identify, quantify and model disaster risk taking into account its various components. The same methodology can be applied to various types of risk at local to global scale. This method was applied and developed for the Global Risk Analysis of the Global Assessment Report on Disaster Risk Reduction (GAR). It was first applied on mortality risk in GAR 2009 and GAR 2011. New models ranging from global assets exposure and global flood hazard models were also recently developed to improve the resolution of the risk analysis and applied through CAPRA software to provide probabilistic economic risk assessments such as Average Annual Losses (AAL

  5. Modeling and performance analysis of movement-based group location management using RFID sensing in public transportation systems.

    Science.gov (United States)

    Chung, Yun Won

    2012-11-22

    Location management, which consists of location registration and paging, is essential to provide mobile communication services to mobile stations (MSs). Since MSs riding on a public transportation system (TS) generates significant location registration signaling loads simultaneously when a TS with riding MSs moves between location areas (LAs), group location management was proposed. Under the group location management, an MS performs group registration when it gets on a TS and performs group deregistration when it gets off a TS. Then, only a TS updates its current location when it changes LA, on behalf of all riding MSs. In this paper, movement-based group location management using radio frequency identification (RFID) is proposed, where the MS's getting on and getting off behaviors are detected using RFID and only location update of a TS is carried out if the number of crossed cells from the last updated cell exceeds a predefined movement threshold, on behalf of all riding MSs. Then, we develop an analytical model for the performance analysis of the movement-based group location management and analyze the effects of various parameters on the performance. The results show that the movement-based group location management has reduced signaling cost compared with movement-based individual location management, and optimal performance can be achieved by choosing appropriate movement threshold values.

  6. Sensitization trajectories in childhood revealed by using a cluster analysis

    DEFF Research Database (Denmark)

    Schoos, Ann-Marie M.; Chawes, Bo L.; Melen, Erik

    2017-01-01

    Prospective Studies on Asthma in Childhood 2000 (COPSAC2000) birth cohort with specific IgE against 13 common food and inhalant allergens at the ages of ½, 1½, 4, and 6 years. An unsupervised cluster analysis for 3-dimensional data (nonnegative sparse parallel factor analysis) was used to extract latent......BACKGROUND: Assessment of sensitization at a single time point during childhood provides limited clinical information. We hypothesized that sensitization develops as specific patterns with respect to age at debut, development over time, and involved allergens and that such patterns might be more...... biologically and clinically relevant. OBJECTIVE: We sought to explore latent patterns of sensitization during the first 6 years of life and investigate whether such patterns associate with the development of asthma, rhinitis, and eczema. METHODS: We investigated 398 children from the at-risk Copenhagen...

  7. Fractal analysis reveals reduced complexity of retinal vessels in CADASIL.

    Directory of Open Access Journals (Sweden)

    Michele Cavallari

    2011-04-01

    Full Text Available The Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL affects mainly small cerebral arteries and leads to disability and dementia. The relationship between clinical expression of the disease and progression of the microvessel pathology is, however, uncertain as we lack tools for imaging brain vessels in vivo. Ophthalmoscopy is regarded as a window into the cerebral microcirculation. In this study we carried out an ophthalmoscopic examination in subjects with CADASIL. Specifically, we performed fractal analysis of digital retinal photographs. Data are expressed as mean fractal dimension (mean-D, a parameter that reflects complexity of the retinal vessel branching. Ten subjects with genetically confirmed diagnosis of CADASIL and 10 sex and age-matched control subjects were enrolled. Fractal analysis of retinal digital images was performed by means of a computer-based program, and the data expressed as mean-D. Brain MRI lesion volume in FLAIR and T1-weighted images was assessed using MIPAV software. Paired t-test was used to disclose differences in mean-D between CADASIL and control groups. Spearman rank analysis was performed to evaluate potential associations between mean-D values and both disease duration and disease severity, the latter expressed as brain MRI lesion volumes, in the subjects with CADASIL. The results showed that mean-D value of patients (1.42±0.05; mean±SD was lower than control (1.50±0.04; p = 0.002. Mean-D did not correlate with disease duration nor with MRI lesion volumes of the subjects with CADASIL. The findings suggest that fractal analysis is a sensitive tool to assess changes of retinal vessel branching, likely reflecting early brain microvessel alterations, in CADASIL patients.

  8. Penicillium simile sp. nov. revealed by morphological and phylogenetic analysis.

    Science.gov (United States)

    Davolos, Domenico; Pietrangeli, Biancamaria; Persiani, Anna Maria; Maggi, Oriana

    2012-02-01

    The morphology of three phenetically identical Penicillium isolates, collected from the bioaerosol in a restoration laboratory in Italy, displayed macro- and microscopic characteristics that were similar though not completely ascribable to Penicillium raistrickii. For this reason, a phylogenetic approach based on DNA sequencing analysis was performed to establish both the taxonomic status and the evolutionary relationships of these three peculiar isolates in relation to previously described species of the genus Penicillium. We used four nuclear loci (both rRNA and protein coding genes) that have previously proved useful for the molecular investigation of taxa belonging to the genus Penicillium at various evolutionary levels. The internal transcribed spacer region (ITS1-5.8S-ITS2), domains D1 and D2 of the 28S rDNA, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and sequenced. Analysis of the rRNA genes and of the benA and cmd sequence data indicates the presence of three isogenic isolates belonging to a genetically distinct species of the genus Penicillium, here described and named Penicillium simile sp. nov. (ATCC MYA-4591(T)  = CBS 129191(T)). This novel species is phylogenetically different from P. raistrickii and other related species of the genus Penicillium (e.g. Penicillium scabrosum), from which it can be distinguished on the basis of morphological trait analysis.

  9. Subfield profitability analysis reveals an economic case for cropland diversification

    Science.gov (United States)

    Brandes, E.; McNunn, G. S.; Schulte, L. A.; Bonner, I. J.; Muth, D. J.; Babcock, B. A.; Sharma, B.; Heaton, E. A.

    2016-01-01

    Public agencies and private enterprises increasingly desire to achieve ecosystem service outcomes in agricultural systems, but are limited by perceived conflicts between economic and ecosystem service goals and a lack of tools enabling effective operational management. Here we use Iowa—an agriculturally homogeneous state representative of the Maize Belt—to demonstrate an economic rationale for cropland diversification at the subfield scale. We used a novel computational framework that integrates disparate but publicly available data to map ˜3.3 million unique potential management polygons (9.3 Mha) and reveal subfield opportunities to increase overall field profitability. We analyzed subfield profitability for maize/soybean fields during 2010-2013—four of the most profitable years in recent history—and projected results for 2015. While cropland operating at a loss of US 250 ha-1 or more was negligible between 2010 and 2013 at 18 000-190 000 ha (profitable areas, incorporating conservation management that breaks even (e.g., planting low-input perennials), into low-yielding portions of fields could increase overall cropland profitability by 80%. This approach is applicable to the broader region and differs substantially from the status quo of ‘top-down’ land management for conservation by harnessing private interest to align profitability with the production of ecosystem services.

  10. Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus

    Directory of Open Access Journals (Sweden)

    Ann Ray

    2016-07-01

    Full Text Available Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells.

  11. Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium.

    Science.gov (United States)

    Iskandar, Christelle F; Borges, Frédéric; Taminiau, Bernard; Daube, Georges; Zagorec, Monique; Remenant, Benoît; Leisner, Jørgen J; Hansen, Martin A; Sørensen, Søren J; Mangavel, Cécile; Cailliez-Grimal, Catherine; Revol-Junelles, Anne-Marie

    2017-01-01

    Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium .

  12. Proteomic Analysis of Hylocereus polyrhizus Reveals Metabolic Pathway Changes

    Directory of Open Access Journals (Sweden)

    Qingzhu Hua

    2016-09-01

    Full Text Available Red dragon fruit or red pitaya (Hylocereus polyrhizus is the only edible fruit that contains betalains. The color of betalains ranges from red and violet to yellow in plants. Betalains may also serve as an important component of health-promoting and disease-preventing functional food. Currently, the biosynthetic and regulatory pathways for betalain production remain to be fully deciphered. In this study, isobaric tags for relative and absolute quantitation (iTRAQ-based proteomic analyses were used to reveal the molecular mechanism of betalain biosynthesis in H. polyrhizus fruits at white and red pulp stages, respectively. A total of 1946 proteins were identified as the differentially expressed between the two samples, and 936 of them were significantly highly expressed at the red pulp stage of H. polyrhizus. RNA-seq and iTRAQ analyses showed that some transcripts and proteins were positively correlated; they belonged to “phenylpropanoid biosynthesis”, “tyrosine metabolism”, “flavonoid biosynthesis”, “ascorbate and aldarate metabolism”, “betalains biosynthesis” and “anthocyanin biosynthesis”. In betalains biosynthesis pathway, several proteins/enzymes such as polyphenol oxidase, CYP76AD3 and 4,5-dihydroxy-phenylalanine (DOPA dioxygenase extradiol-like protein were identified. The present study provides a new insight into the molecular mechanism of the betalain biosynthesis at the posttranscriptional level.

  13. Platinum atom location on the internal walls of nanocavities investigated by ion channeling analysis

    International Nuclear Information System (INIS)

    Kinomura, A.; Williams, J.S.; Tsubouchi, N.; Horino, Y.

    2002-01-01

    Atomic locations of Pt trapped at hydrogen-induced cavities in Si have been investigated by ion channeling analysis. A Pt dose of 1x10 14 cm -2 , corresponding to a monolayer coverage of the internal walls of cavities, was implanted into cavity-containing samples. The gettering of Pt to the cavities was induced by annealing at 850 deg. C for 1 h. Clear channeling effects were observed in aligned and random backscattering spectra for the , and axes. Angular yield profiles for three crystalline axes exhibited dips with a narrowing of Pt signal half width compared with the Si matrix. Results suggested that the Pt atoms trapped at the cavities are closely aligned with the Si atomic strings bounding axial channels in Si

  14. Gas Hydrate-Sediment Morphologies Revealed by Pressure Core Analysis

    Science.gov (United States)

    Holland, M.; Schultheiss, P.; Roberts, J.; Druce, M.

    2006-12-01

    Analysis of HYACINTH pressure cores collected on IODP Expedition 311 and NGHP Expedition 1 showed gas hydrate layers, lenses, and veins contained in fine-grained sediments as well as gas hydrate contained in coarse-grained layers. Pressure cores were recovered from sediments on the Cascadia Margin off the North American West Coast and in the Krishna-Godavari Basin in the Western Bay of Bengal in water depths of 800- 1400 meters. Recovered cores were transferred to laboratory chambers without loss of pressure and nondestructive measurements were made at in situ pressures and controlled temperatures. Gamma density, P-wave velocity, and X-ray images showed evidence of grain-displacing and pore-filling gas hydrate in the cores. Data highlights include X-ray images of fine-grained sediment cores showing wispy subvertical veins of gas hydrate and P-wave velocity excursions corresponding to grain-displacing layers and pore-filling layers of gas hydrate. Most cores were subjected to controlled depressurization experiments, where expelled gas was collected, analyzed for composition, and used to calculate gas hydrate saturation within the core. Selected cores were stored under pressure for postcruise analysis and subsampling.

  15. Matching office firms types and location characteristics: an exploratory analysis using Bayesian classifier networks

    NARCIS (Netherlands)

    Manzato, G.G.; Arentze, T.A.; Timmermans, H.J.P.; Ettema, D.F.

    2010-01-01

    While most models of location decisions of firms are based on the principle of utility-maximizing behavior, the present study assumes that location decisions are just part of business cycle models, in which location is considered along other business decisions. The business model results in a series

  16. Gene Locater

    DEFF Research Database (Denmark)

    Anwar, Muhammad Zohaib; Sehar, Anoosha; Rehman, Inayat-Ur

    2012-01-01

    software's for calculating recombination frequency is mostly limited to the range and flexibility of this type of analysis. GENE LOCATER is a fully customizable program for calculating recombination frequency, written in JAVA. Through an easy-to-use interface, GENE LOCATOR allows users a high degree...... of flexibility in calculating genetic linkage and displaying linkage group. Among other features, this software enables user to identify linkage groups with output visualized graphically. The program calculates interference and coefficient of coincidence with elevated accuracy in sample datasets. AVAILABILITY...

  17. Changes in cod muscle proteins during frozen storage revealed by proteome analysis and multivariate data analysis

    DEFF Research Database (Denmark)

    Kjærsgård, Inger Vibeke Holst; Nørrelykke, M.R.; Jessen, Flemming

    2006-01-01

    Multivariate data analysis has been combined with proteomics to enhance the recovery of information from 2-DE of cod muscle proteins during different storage conditions. Proteins were extracted according to 11 different storage conditions and samples were resolved by 2-DE. Data generated by 2-DE...... was subjected to principal component analysis (PCA) and discriminant partial least squares regression (DPLSR). Applying PCA to 2-DE data revealed the samples to form groups according to frozen storage time, whereas differences due to different storage temperatures or chilled storage in modified atmosphere...... light chain 1, 2 and 3, triose-phosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, aldolase A and two ?-actin fragments, and a nuclease diphosphate kinase B fragment to change in concentration, during frozen storage. Application of proteomics, multivariate data analysis and MS/MS to analyse...

  18. Differential network analysis reveals genetic effects on catalepsy modules.

    Directory of Open Access Journals (Sweden)

    Ovidiu D Iancu

    Full Text Available We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS formed by crossing four inbred strains (HS4 and a heterogeneous stock (HS-CC formed from the inbred strain founders of the Collaborative Cross (CC. All three selections were successful, with large differences in haloperidol response emerging within three generations. Using a custom differential network analysis procedure, we found that gene coexpression patterns changed significantly; importantly, a number of these changes were concordant across genetic backgrounds. In contrast, absolute gene-expression changes were modest and not concordant across genetic backgrounds, in spite of the large and similar phenotypic differences. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections.

  19. Network analysis reveals distinct clinical syndromes underlying acute mountain sickness.

    Directory of Open Access Journals (Sweden)

    David P Hall

    Full Text Available Acute mountain sickness (AMS is a common problem among visitors at high altitude, and may progress to life-threatening pulmonary and cerebral oedema in a minority of cases. International consensus defines AMS as a constellation of subjective, non-specific symptoms. Specifically, headache, sleep disturbance, fatigue and dizziness are given equal diagnostic weighting. Different pathophysiological mechanisms are now thought to underlie headache and sleep disturbance during acute exposure to high altitude. Hence, these symptoms may not belong together as a single syndrome. Using a novel visual analogue scale (VAS, we sought to undertake a systematic exploration of the symptomatology of AMS using an unbiased, data-driven approach originally designed for analysis of gene expression. Symptom scores were collected from 292 subjects during 1110 subject-days at altitudes between 3650 m and 5200 m on Apex expeditions to Bolivia and Kilimanjaro. Three distinct patterns of symptoms were consistently identified. Although fatigue is a ubiquitous finding, sleep disturbance and headache are each commonly reported without the other. The commonest pattern of symptoms was sleep disturbance and fatigue, with little or no headache. In subjects reporting severe headache, 40% did not report sleep disturbance. Sleep disturbance correlates poorly with other symptoms of AMS (Mean Spearman correlation 0.25. These results challenge the accepted paradigm that AMS is a single disease process and describe at least two distinct syndromes following acute ascent to high altitude. This approach to analysing symptom patterns has potential utility in other clinical syndromes.

  20. Demographic analysis reveals gradual senescence in the flatworm Macrostomum lignano

    Directory of Open Access Journals (Sweden)

    Braeckman Bart P

    2009-07-01

    Full Text Available Abstract Free-living flatworms ("Turbellaria" are appropriate model organisms to gain better insight into the role of stem cells in ageing and rejuvenation. Ageing research in flatworms is, however, still scarce. This is partly due to culture difficulties and the lack of a complete set of demographic data, including parameters such as median lifespan and age-specific mortality rate. In this paper, we report on the first flatworm survival analysis. We used the species Macrostomum lignano, which is an emerging model for studying the reciprocal influence between stem cells, ageing and rejuvenation. This species has a median lifespan of 205 ± 13 days (average ± standard deviation [SD] and a 90th percentile lifespan of 373 ± 32 days. The maximum lifespan, however, is more than 745 days, and the average survival curve is characterised by a long tail because a small number of individuals lives twice as long as 90% of the population. Similar to earlier observations in a wide range of animals, in M. lignano the age-specific mortality rate increases exponentially, but levels off at the oldest ages. To compare the senescence of M. lignano with that of other ageing models, we determined the mortality rate doubling time, which is 0.20 ± 0.02 years. As a result, we can conclude that M. lignano shows gradual senescence at a rate similar to the vertebrate ageing models Rattus norvegicus and Mus musculus. We argue that M. lignano is a suitable model for ageing and rejuvenation research, and especially for the role of stem cells in these processes, due to its accessible stem cell system and regeneration capacity, and the possibility of combining stem cell studies with demographic analyses.

  1. Network analysis reveals multiscale controls on streamwater chemistry

    Science.gov (United States)

    McGuire, Kevin J.; Torgersen, Christian E.; Likens, Gene E.; Buso, Donald C.; Lowe, Winsor H.; Bailey, Scott W.

    2014-01-01

    By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks.

  2. Network analysis reveals multiscale controls on streamwater chemistry.

    Science.gov (United States)

    McGuire, Kevin J; Torgersen, Christian E; Likens, Gene E; Buso, Donald C; Lowe, Winsor H; Bailey, Scott W

    2014-05-13

    By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks.

  3. Visual quality analysis of femtosecond LASIK and iris location guided mechanical SBK for high myopia

    Directory of Open Access Journals (Sweden)

    Hong-Su Jiang

    2015-07-01

    Full Text Available AIM: To make a analysis of visual quality of iris location guided femtosecond laser assisted in situ keratomi(LASIKand iris location guided mechanical sub-bowman keratomileusis(SBKfor high myopia treatment. METHODS:Femtosecond LASIK(study groupwas performed in 102 eyes of 51 patients with high myopia and 70 eyes of 35 patients were received mechanical SBK(control groupfrom January to October 2013. The spherical refraction of all the patients was from -6.00~-9.50D. Best corrected visual acuity(BCVAof the patients was ≥1.0. Uncorrected visual acuity(UCVA, BCVA, thickness of cornea flap, contrast sensitivity function(CSFand senior ocular aberration were examined in these patients and follow-up was 1a. RESULTS: At 1a after surgery 94.1% UCVA in study group reached ≥1.0 and there was 94.3% in control group. There was no significant difference between two groups(P>0.05. Residual refraction of study group was -0.08±0.10 D and control group was -0.10±0.07 D. There was no significant difference of residual refraction between two groups(P>0.05. C12, C8 of senior ocular aberration and RMSH in study group was less than control group, amplification: 0.1642±0.0519 and 0.2229±0.0382(t=8.077, Pt=0.556, P>0.05. C8 was 0.0950±0.069 and 0.1858±0.095(t=7.261, Pt=12.801, PP>0.05.CONCLUSION: Femtosecond LASIK and mechanical SBK is effective for high myopia. Compared to mechanical SBK, femtosecond LASIK shows more advantages in the senior ocular aberration and visual quality. The cornea flap is more regular from central to peripheral area with femtosecond laser.

  4. Phylogenetic analysis of ferlin genes reveals ancient eukaryotic origins

    Directory of Open Access Journals (Sweden)

    Lek Monkol

    2010-07-01

    Full Text Available Abstract Background The ferlin gene family possesses a rare and identifying feature consisting of multiple tandem C2 domains and a C-terminal transmembrane domain. Much currently remains unknown about the fundamental function of this gene family, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease. The availability of genome sequences from a wide range of species makes it possible to explore the evolution of the ferlin family, providing contextual insight into characteristic features that define the ferlin gene family in its present form in humans. Results Ferlin genes were detected from all species of representative phyla, with two ferlin subgroups partitioned within the ferlin phylogenetic tree based on the presence or absence of a DysF domain. Invertebrates generally possessed two ferlin genes (one with DysF and one without, with six ferlin genes in most vertebrates (three DysF, three non-DysF. Expansion of the ferlin gene family is evident between the divergence of lamprey (jawless vertebrates and shark (cartilaginous fish. Common to almost all ferlins is an N-terminal C2-FerI-C2 sandwich, a FerB motif, and two C-terminal C2 domains (C2E and C2F adjacent to the transmembrane domain. Preservation of these structural elements throughout eukaryotic evolution suggests a fundamental role of these motifs for ferlin function. In contrast, DysF, C2DE, and FerA are optional, giving rise to subtle differences in domain topologies of ferlin genes. Despite conservation of multiple C2 domains in all ferlins, the C-terminal C2 domains (C2E and C2F displayed higher sequence conservation and greater conservation of putative calcium binding residues across paralogs and orthologs. Interestingly, the two most studied non-mammalian ferlins (Fer-1 and Misfire in model organisms C. elegans and D. melanogaster, present as outgroups in the phylogenetic analysis, with results suggesting

  5. CATHENA analysis of CANDU 6 steam generators for steam main break at a remote location

    Energy Technology Data Exchange (ETDEWEB)

    Liu, T. [Atomic Energy of Canada Limited, Chalk River, Ontario (Canada)

    2009-07-01

    CATHENA (Canadian Algorithm for THErmalhydraulic Network Analysis) is a nonequilibrium, two-phase, two fluid network analysis code that has been in use for over two decades by various groups in Canada and around the world. It is the primary Thermalhydraulics network analysis tool used by Atomic Energy Canada Ltd. (AECL) in the design, safety and licensing analysis of power and research reactors as well as test facilities. In the thermalhydraulic model, the liquid and vapor phases may have different pressures, velocities, and temperatures. The objective of the present paper is to present the detailed modeling of a CANDU 6 Steam Generator (SG) using the transient, thermalhydraulics network code CATHENA. The model represents the secondary side, primary side and the main steam system including the main steam line up to the assumed break location. The present model is designed such that the transient pressure drops across Tube Support Plates (TSP) could be extracted. The resistances of degraded/fouled TSPs were modeled by using the increased/reduced flow area of the TSPs. CATHENA then calculates the flow resistance in two-phase flow based on the area contraction/expansion at the TSPs. Three sets of simulations were performed; one with the degraded steam generator data provided by the utility users, and the other two with waterlanced (cleaned with high pressure water jet) TSPs. One run assumed the flow area increased by 25 percent, the other run assumed the flow area increased by 50 percent. on the hot side of the SG. No significant changes in the break discharge rates were observed between the runs. However, the steam generator downcomer flow for the waterlanced case did not reverse during the blowdown as was calculated for the degraded case. As expected, the pressure drop across the TSPs was decreased in the waterlanced cases comparing with degraded cases. The CATHENA simulation provides estimates of the velocity, density, and quality in the tube bundle as well as

  6. GAUSS Market Analysis for Integrated Satellite Communication and Navigation Location Based services

    Science.gov (United States)

    Di Fazio, Antonella; Dricot, Fabienne; Tata, Francesco

    2003-07-01

    The demand for mobile information services coupled with positioning technologies for delivering value- added services that depend on a user's location has rapidly increased during last years. In particular, services and applications related with improved mobility safety and transport efficiency look very attractive.Solutions for location services vary in respect of positioning accuracy and the technical infrastructure required, and the associated investment in terminals and networks. From the analysis of the state-of-the art, it comes that various technologies are currently available on the European market, while mobile industry is gearing up to launch a wide variety of location services like tracking, alarming and locating.Nevertheless, when addressing safety of life as well as security applications, severe hurdles have to be posed in the light of existing technologies. Existing navigation (e.g. GPS) and communication systems are not able to completely satisfy the needs and requirements of safety-of-life-critical applications. As a matter of fact, the GPS system's main weaknesses today is its lack of integrity, which means its inability to warn users of a malfunction in a reasonable time, while the other positioning techniques do not provide satisfactory accuracy as well, and terrestrial communication networks are not capable to cope with stringent requirement in terms of service reliability and coverage.In this context, GAUSS proposes an innovative satellite-based solution using novel technology and effective tools for addressing mobility challenges in a cost efficient manner, improving safety and effectiveness.GAUSS (Galileo And UMTS Synergetic System) is a Research and Technological Development project co- funded by European Commission, within the frame of the 5th IST Programme. The project lasted two years, and it was successfully completed in November 2002. GAUSS key concept is the integration of Satellite Navigation GNSS and UMTS communication technology, to

  7. THE POSSIBILITIES OF PRACTICAL IMPLEMENTATION OF REGRESSION ANALYSIS IN LOCATION CHOICE

    Directory of Open Access Journals (Sweden)

    Marija Andjelković PEŠIĆ

    2008-06-01

    Full Text Available “Location, location, location” is a well worn catch phrase of the real estate industry. Invest in a property in the right location and watch your investment soar in value. The same catch cry may or may not hold true for the restaurant (hotel industry, open a restaurant in the right location and are you on the way to become a winner? The question is: Did the best locations for a restaurant (hotel automatically mean that the restaurant (hotel is profitable? The intention of this paper is to show if there is positive correlation between the best location and restaurant’s (hotel’s profitability.

  8. Gender, space, and the location changes of jobs and people: a spatial simultaneous equations analysis.

    Science.gov (United States)

    Hoogstra, Gerke J

    2012-01-01

    This article summarizes a spatial econometric analysis of local population and employment growth in the Netherlands, with specific reference to impacts of gender and space. The simultaneous equations model used distinguishes between population- and gender-specific employment groups, and includes autoregressive and cross-regressive spatial lags to detect relations both within and among these groups. Spatial weights matrices reflecting different bands of travel times are used to calculate the spatial lags and to gauge the spatial nature of these relations. The empirical results show that although population–employment interaction is more localized for women's employment, no gender difference exists in the direction of interaction. Employment growth for both men and women is more influenced by population growth than vice versa. The interaction within employment groups is even more important than population growth. Women's, and especially men's, local employment growth mostly benefits from the same employment growth in neighboring locations. Finally, interaction between these groups is practically absent, although men's employment growth may have a negative impact on women's employment growth within small geographic areas. In summary, the results confirm the crucial roles of gender and space, and offer important insights into possible relations within and among subgroups of jobs and people.

  9. Magnetic Resonance Imaging (MRI) Analysis of Fibroid Location in Women Achieving Pregnancy After Uterine Artery Embolization

    International Nuclear Information System (INIS)

    Walker, Woodruff J.; Bratby, Mark John

    2007-01-01

    The purpose of this study was to evaluate the fibroid morphology in a cohort of women achieving pregnancy following treatment with uterine artery embolization (UAE) for symptomatic uterine fibroids. A retrospective review of magnetic resonance imaging (MRI) of the uterus was performed to assess pre-embolization fibroid morphology. Data were collected on fibroid size, type, and number and included analysis of follow-up imaging to assess response. There have been 67 pregnancies in 51 women, with 40 live births. Intramural fibroids were seen in 62.7% of the women (32/48). Of these the fibroids were multiple in 16. A further 12 women had submucosal fibroids, with equal numbers of types 1 and 2. Two of these women had coexistent intramural fibroids. In six women the fibroids could not be individually delineated and formed a complex mass. All subtypes of fibroid were represented in those subgroups of women achieving a live birth versus those who did not. These results demonstrate that the location of uterine fibroids did not adversely affect subsequent pregnancy in the patient population investigated. Although this is only a small qualitative study, it does suggest that all types of fibroids treated with UAE have the potential for future fertility

  10. Quantitative analysis of polycomb response elements (PREs at identical genomic locations distinguishes contributions of PRE sequence and genomic environment

    Directory of Open Access Journals (Sweden)

    Okulski Helena

    2011-03-01

    Full Text Available Abstract Background Polycomb/Trithorax response elements (PREs are cis-regulatory elements essential for the regulation of several hundred developmentally important genes. However, the precise sequence requirements for PRE function are not fully understood, and it is also unclear whether these elements all function in a similar manner. Drosophila PRE reporter assays typically rely on random integration by P-element insertion, but PREs are extremely sensitive to genomic position. Results We adapted the ΦC31 site-specific integration tool to enable systematic quantitative comparison of PREs and sequence variants at identical genomic locations. In this adaptation, a miniwhite (mw reporter in combination with eye-pigment analysis gives a quantitative readout of PRE function. We compared the Hox PRE Frontabdominal-7 (Fab-7 with a PRE from the vestigial (vg gene at four landing sites. The analysis revealed that the Fab-7 and vg PREs have fundamentally different properties, both in terms of their interaction with the genomic environment at each site and their inherent silencing abilities. Furthermore, we used the ΦC31 tool to examine the effect of deletions and mutations in the vg PRE, identifying a 106 bp region containing a previously predicted motif (GTGT that is essential for silencing. Conclusions This analysis showed that different PREs have quantifiably different properties, and that changes in as few as four base pairs have profound effects on PRE function, thus illustrating the power and sensitivity of ΦC31 site-specific integration as a tool for the rapid and quantitative dissection of elements of PRE design.

  11. Using multinomial logistic regression analysis to understand anglers willingness to substitute other fishing locations

    Science.gov (United States)

    Woo-Yong Hyun; Robert B. Ditton

    2007-01-01

    The concept of recreation substitutability has been a continuing research topic for outdoor recreation researchers. This study explores the relationships among variables regarding the willingness to substitute one location for another location. The objectives of the study are 1) to ascertain and predict the extent to which saltwater anglers were willing to substitute...

  12. Complete genome sequence analysis of novel human bocavirus reveals genetic recombination between human bocavirus 2 and human bocavirus 4.

    Science.gov (United States)

    Khamrin, Pattara; Okitsu, Shoko; Ushijima, Hiroshi; Maneekarn, Niwat

    2013-07-01

    Epidemiological surveillance of human bocavirus (HBoV) was conducted on fecal specimens collected from hospitalized children with diarrhea in Chiang Mai, Thailand in 2011. By partial sequence analysis of VP1 gene, an unusual strain of HBoV (CMH-S011-11), was initially identified as HBoV4. The complete genome sequence of CMH-S011-11 was performed and analyzed further to clarify whether it was a recombinant strain or a new HBoV variant. Analysis of complete genome sequence revealed that the coding sequence starting from NS1, NP1 to VP1/VP2 was 4795 nucleotides long. Interestingly, the nucleotide sequence of NS1 gene of CMH-S011-11 was most closely related to the HBoV2 reference strains detected in Pakistan, which contradicted to the initial genotyping result of the partial VP1 region in the previous study. In addition, comparison of NP1 nucleotide sequence of CMH-S011-11 with those of other HBoV1-4 reference strains also revealed a high level of sequence identity with HBoV2. On the other hand, nucleotide sequence of VP1/VP2 gene of CMH-S011-11 was most closely related to those of HBoV4 reference strains detected in Nigeria. The overall full-length sequence analysis revealed that this CMH-S011-11 was grouped within HBoV4 species, but located in a separate branch from other HBoV4 prototype strains. Recombination analysis revealed that CMH-S011-11 was the result of recombination between HBoV2 and HBoV4 strains with the break point located near the start codon of VP2. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Three-dimensional Crustal Structure beneath the Tibetan Plateau Revealed by Multi-scale Gravity Analysis

    Science.gov (United States)

    Xu, C.; Luo, Z.; Sun, R.; Li, Q.

    2017-12-01

    The Tibetan Plateau, the largest and highest plateau on Earth, was uplifted, shorten and thicken by the collision and continuous convergence of the Indian and Eurasian plates since 50 million years ago, the Eocene epoch. Fine three-dimensional crustal structure of the Tibetan Plateau is helpful in understanding the tectonic development. At present, the ordinary method used for revealing crustal structure is seismic method, which is inhibited by poor seismic station coverage, especially in the central and western plateau primarily due to the rugged terrain. Fortunately, with the implementation of satellite gravity missions, gravity field models have demonstrated unprecedented global-scale accuracy and spatial resolution, which can subsequently be employed to study the crustal structure of the entire Tibetan Plateau. This study inverts three-dimensional crustal density and Moho topography of the Tibetan Plateau from gravity data using multi-scale gravity analysis. The inverted results are in agreement with those provided by the previous works. Besides, they can reveal rich tectonic development of the Tibetan Plateau: (1) The low-density channel flow can be observed from the inverted crustal density; (2) The Moho depth in the west is deeper than that in the east, and the deepest Moho, which is approximately 77 km, is located beneath the western Qiangtang Block; (3) The Moho fold, the directions of which are in agreement with the results of surface movement velocities estimated from Global Positioning System, exists clearly on the Moho topography.This study is supported by the National Natural Science Foundation of China (Grant No. 41504015), the China Postdoctoral Science Foundation (Grant No. 2015M572146), and the Surveying and Mapping Basic Research Programme of the National Administration of Surveying, Mapping and Geoinformation (Grant No. 15-01-08).

  14. Genome-wide analysis of gene expression in primate taste buds reveals links to diverse processes.

    Directory of Open Access Journals (Sweden)

    Peter Hevezi

    Full Text Available Efforts to unravel the mechanisms underlying taste sensation (gustation have largely focused on rodents. Here we present the first comprehensive characterization of gene expression in primate taste buds. Our findings reveal unique new insights into the biology of taste buds. We generated a taste bud gene expression database using laser capture microdissection (LCM procured fungiform (FG and circumvallate (CV taste buds from primates. We also used LCM to collect the top and bottom portions of CV taste buds. Affymetrix genome wide arrays were used to analyze gene expression in all samples. Known taste receptors are preferentially expressed in the top portion of taste buds. Genes associated with the cell cycle and stem cells are preferentially expressed in the bottom portion of taste buds, suggesting that precursor cells are located there. Several chemokines including CXCL14 and CXCL8 are among the highest expressed genes in taste buds, indicating that immune system related processes are active in taste buds. Several genes expressed specifically in endocrine glands including growth hormone releasing hormone and its receptor are also strongly expressed in taste buds, suggesting a link between metabolism and taste. Cell type-specific expression of transcription factors and signaling molecules involved in cell fate, including KIT, reveals the taste bud as an active site of cell regeneration, differentiation, and development. IKBKAP, a gene mutated in familial dysautonomia, a disease that results in loss of taste buds, is expressed in taste cells that communicate with afferent nerve fibers via synaptic transmission. This database highlights the power of LCM coupled with transcriptional profiling to dissect the molecular composition of normal tissues, represents the most comprehensive molecular analysis of primate taste buds to date, and provides a foundation for further studies in diverse aspects of taste biology.

  15. Stereotactic body radiotherapy for centrally located stage I NSCLC. A multicenter analysis

    Energy Technology Data Exchange (ETDEWEB)

    Schanne, Daniel H.; Nestle, Ursula; Grosu, Anca L. [Universitaetsklinik Freiburg, Klinik fuer Strahlenheilkunde, Freiburg (Germany); Allgaeuer, Michael [Barmherzige Brueder, Klinik fuer Strahlentherapie, Regensburg (Germany); Andratschke, Nicolaus; Molls, Michael [TU Muenchen, Klinik und Poliklinik fuer Strahlentherapie und Radiologische Onkologie, Muenchen (Germany); Appold, Steffen [Universitaetsklinikum Dresden, Klinik und Poliklinik fuer Strahlentherapie und Radioonkologie, Dresden (Germany); Dieckmann, Ute [Allgemeines Krankenhaus Wien, Univ. Klinik fuer Strahlentherapie, Wien (Austria); Ernst, Iris [Universitaetsklinikum Muenster, Klinik fuer Strahlentherapie, Muenster (Germany); Ganswindt, Ute [LMU Muenchen, Klinik und Poliklinik fuer Strahlentherapie und Radioonkologie, Muenchen (Germany); Holy, Richard [Universitaetsklinikum Aachen, Klinik fuer Strahlentherapie, Aachen (Germany); Nevinny-Stickel, Meinhard [Medizinischen Universitaet Innsbruck, Univ. Klinik fuer Strahlentherapie und Radioonkologie, Innsbruck (Austria); Semrau, Sabine [Universitaetsklinikum Erlangen, Strahlenklinik Erlangen, Erlangen (Germany); Sterzing, Florian [Universitaetsklinikum Heidelberg, Klinik fuer Radioonkologie und Strahlentherapie, Heidelberg (Germany); Wittig, Andrea [Philipps-Universitaet Marburg, Klinik fuer Strahlentherapie und Radioonkologie, Marburg (Germany); Guckenberger, Matthias [Universitaet Wuerzburg, Klinik und Poliklinik fuer Strahlentherapie, Wuerzburg (Germany)

    2014-08-27

    The purpose of this work is to analyze patterns of care and outcome after stereotactic body radiotherapy (SBRT) for centrally located, early-stage, non-small cell lung cancer (NSCLC) and to address the question of potential risk for increased toxicity in this entity. A total of 90 patients with centrally located NSCLC were identified among 613 cases in a database of 13 German and Austrian academic radiotherapy centers. The outcome of centrally located NSCLC was compared to that of cases with peripheral tumor location from the same database. Patients with central tumors most commonly presented with UICC stage IB (50 %), while the majority of peripheral lesions were stage IA (56 %). Average tumor diameters were 3.3 cm (central) and 2.8 cm (peripheral). Staging PET/CT was available for 73 and 74 % of peripheral and central tumors, respectively. Biopsy was performed in 84 % (peripheral) and 88 % (central) of cases. Doses varied significantly between central and peripheral lesions with a median BED{sub 10} of 72 Gy and 84 Gy, respectively (p < 0.001). Fractionation differed as well with medians of 5 (central) and 3 (peripheral) fractions (p < 0.001). In the Kaplan-Meier analysis, 3-year actuarial overall survival was 29 % (central) and 51 % (peripheral; p = 0.004) and freedom from local progression was 52 % (central) and 84 % (peripheral; p < 0.001). Toxicity after treatment of central tumors was low with no grade III/IV and one grade V event. Mortality rates were 0 and 1 % after 30 and 60 days, respectively. Local tumor control in patients treated with SBRT for centrally located, early-stage NSCLC was favorable, provided ablative radiation doses were prescribed. This was, however, not the case in the majority of patients, possibly due to concerns about treatment-related toxicity. Reported toxicity was low, but prospective trials are needed to resolve the existing uncertainties and to establish safe high-dose regimens for this cohort of patients. (orig.) [German] Ziel

  16. Error Analysis of Fast Moving Target Geo-location in Wide Area Surveillance Ground Moving Target Indication Mode

    Directory of Open Access Journals (Sweden)

    Zheng Shi-chao

    2013-12-01

    Full Text Available As an important mode in airborne radar systems, Wide Area Surveillance Ground Moving Target Indication (WAS-GMTI mode has the ability of monitoring a large area in a short time, and then the detected moving targets can be located quickly. However, in real environment, many factors introduce considerable errors into the location of moving targets. In this paper, a fast location method based on the characteristics of the moving targets in WAS-GMTI mode is utilized. And in order to improve the location performance, those factors that introduce location errors are analyzed and moving targets are relocated. Finally, the analysis of those factors is proved to be reasonable by simulation and real data experiments.

  17. Application of Multi-Objective Optimization on the Basis of Ratio Analysis (MOORA Method for Bank Branch Location Selection

    Directory of Open Access Journals (Sweden)

    Ali Gorener

    2013-04-01

    Full Text Available Location selection problem in banking is an important issue for the commercial success in competitive environment. There is a strategic fit between the location selection decision and overall performance of a new branch. Providing physical service in requested location as well as alternative distribution channels to meet profitable client needs is the current problematic to achieve the competitive advantage over the rivalry in financial system. In this paper, an integrated model has been developed to support in the decision of branch location selection for a new bank branch. Analytic Hierarchy Process (AHP technique has been conducted to prioritize of evaluation criteria, and multi-objective optimization on the basis of ratio analysis (MOORA method has been applied to rank location alternatives of bank branch.   

  18. Analysis of the location for peak heating in CHP based combined district heating systems

    International Nuclear Information System (INIS)

    Wang, Haichao; Lahdelma, Risto; Wang, Xin; Jiao, Wenling; Zhu, Chuanzhi; Zou, Pinghua

    2015-01-01

    Combined heat and power (CHP) is the main technology for providing the base load of district heating in China. However, CHP is not efficient for providing the peak load; instead, a peak boiler with high efficiency could be used to compensate the peak load. This paper studies how the location of the peak boiler can affect the energy efficiency and economic performance of such CHP based combined district heating system. Firstly, the connection mode and the control strategy for different peak heating locations are analyzed. Then the effect of the peak boiler's location on the initial investment of the network and the cost for distributing heat is studied. The objective is to place the peak boiler in a location where the overall costs are the smallest. Following this rule, the results indicate that the peak boiler should be located at the CHP plant if that allows using cheaper ‘self-use electricity’ in CHP for distributing the heat. However, if the market electricity price is used everywhere, or if energy efficiency is more emphasized, the location of the peak boiler should be closer to the users with dense heat loads. - Highlights: • Location for peak heating in the CHP based combined DH system is studied. • Regulation or control strategies for combined DH are summarized. • The heat load duration curve for combined DH is demonstrated. • Network design for combined DH with peak boiler outside of the CHP is analyzed

  19. Numerical analysis for the optimal location of a thin PCM layer in frame walls

    International Nuclear Information System (INIS)

    Jin, Xing; Medina, Mario A.; Zhang, Xiaosong

    2016-01-01

    Highlights: • The optimal PCM location was estimated by a mathematical model. • The optimal PCM location was affected by the properties of PCM. • The optimal PCM location was affected by the environmental conditions. - Abstract: The thermal performance of building walls can be improved using phase change materials (PCMs). The objective of this study was to estimate the optimal location of a “thin” PCM layer to be incorporated into frame walls, parallel to the frame and insulation, for the purpose of increasing thermal mass and reducing peak heat fluxes through the wall. Based on a mathematical model built in this paper, it was found that an optimal location of this “thin” PCM layer can be estimated, and it was affected by the thermal properties of PCM and the environmental conditions. The optimal locations for the PCM layer were found to be closer to the exterior surface of the wall when the thickness of PCM layer, the heat of fusion of PCM, and the PCM melting temperature were increased, while the optimal location was closer to the interior surface of the wall when the interior surface temperature of the wall was increased.

  20. Relationship between mode choice and the location of supermarkets – empirical analysis in Austria

    Directory of Open Access Journals (Sweden)

    Roman KLEMENTSCHITZ

    2014-03-01

    Full Text Available Main goal of the study work is to gain data about shopping and mobility behaviour at small local supermarkets with sales floor space less than 1.000 m2. Four location types have been defined and discussed; rural  peripheral location, rural  central location, urban – central location and urban – peripheral location. 200 shoppers each location were interviewed at the exit of the supermarket, which means a total of 800 interviews were carried out during all day times and working days of the supermarket. As expected, the mode choice is strongly dependent on the location of the supermarket. In car oriented settlements, which can be found at rural peripheral locations, nearly all shoppers accessed the supermarket with their cars. If weighting the expenditure per visit with the frequency of visits, the average expenditure per month and mode can be derived. The average purchase per month between the modes is more or less balanced. A difference in behaviour lies in the fact that cyclists and pedestrians go shopping more frequently but are spending less per visit. Additionally, the results of this study are indicating the existence of a potential mode shift, especially if there is better land use planning for supermarket locations. Furthermore, considering the given situation and a given threshold of less than 5 kilograms of weight of the goods purchased, more than fifty percent of all shoppers could use non motorised modes with insignificant loss of travel quality. Combined with short travel distances to the next shop (the average distance is 4.9 km, a change to alternative means of transport would be relatively easy for a significant number of shoppers.

  1. Analysis of Taipei Basin Response for Earthquakes of Various Depths and Locations Using Empirical Data

    Directory of Open Access Journals (Sweden)

    Vladimir Sokolov

    2009-01-01

    Full Text Available The response of Taipei basin upon earthquake excitation was studied using records of recent earthquakes. The strong-motion database includes records obtained at 32 stations of the Taipei TSMIP net work from 83 deep and 142 shallow earthquakes (M > 4.0 that occurred in 1992 - 2004. The characteristics of frequency-de pendent site response were obtained as spectral ratios between the actual earthquake records (horizontal components and those modelled for a hypothetical Very Hard Rock (VHR condition. The models for VHR spectra of Taiwan earthquakes had been recently proposed by Sokolov et al. (2005b, 2006. Analysis of site response characteristics and comparison with simple 1D models of the soil column resulted in the following conclusions: (1 The spectral ratios through out the basin obtained from deep earth quakes (depth > 35 km exhibit good agreement with the theoretical ratios calculated using the 1D models constructed using avail able geological and geotechnical data. (2 The spectral ratios obtained from shallow earth quakes show influence of: (a surface waves generated when travelling from distant sources to the basin and (b relatively low-frequency (< 1 - 2 Hz waves generated within the basin. (3 Some shallow earth quakes pro duce extremely high amplification at frequencies 0.3 - 1 Hz within the basin that may be dangerous for high-rise buildings and high way bridges. (4 The obtained results may be used in probabilistic seismic microzonation of the basin when many possible earth quakes located at various distances are considered. 2D and 3D simulation is necessary to model the seismic influence from particularly large earthquakes.

  2. The role of location in headquarters-subsidiaries relationships: An analysis of French multinationals in emerging markets

    OpenAIRE

    Hanane Beddi; Ulrike Mayrhofer

    2010-01-01

    International audience; This paper examines the role of location in the relationships established between headquarters and foreign subsidiaries. The analysis focuses on new challenges faced by MNEs from mature economies, considering the growing importance of subsidiaries located in emerging countries. The empirical study is based on three in-depth case-studies of French multinationals. The authors conducted 31 interviews with managers from both the headquarters and foreign subsidiaries. The f...

  3. Lipase genes in Mucor circinelloides: identification, sub-cellular location, phylogenetic analysis and expression profiling during growth and lipid accumulation.

    Science.gov (United States)

    Zan, Xinyi; Tang, Xin; Chu, Linfang; Zhao, Lina; Chen, Haiqin; Chen, Yong Q; Chen, Wei; Song, Yuanda

    2016-10-01

    Lipases or triacylglycerol hydrolases are widely spread in nature and are particularly common in the microbial world. The filamentous fungus Mucor circinelloides is a potential lipase producer, as it grows well in triacylglycerol-contained culture media. So far only one lipase from M. circinelloides has been characterized, while the majority of lipases remain unknown in this fungus. In the present study, 47 potential lipase genes in M. circinelloides WJ11 and 30 potential lipase genes in M. circinelloides CBS 277.49 were identified by extensive bioinformatics analysis. An overview of these lipases is presented, including several characteristics, sub-cellular location, phylogenetic analysis and expression profiling of the lipase genes during growth and lipid accumulation. All of these proteins contained the consensus sequence for a classical lipase (GXSXG motif) and were divided into four types including α/β-hydrolase_1, α/β-hydrolase_3, class_3 and GDSL lipase (GDSL) based on gene annotations. Phylogenetic analyses revealed that class_3 family and α/β-hydrolase_3 family were the conserved lipase family in M. circinelloides. Additionally, some lipases also contained a typical acyltransferase motif of H-(X) 4-D, and these lipases may play a dual role in lipid metabolism, catalyzing both lipid hydrolysis and transacylation reactions. The differential expression of all lipase genes were confirmed by quantitative real-time PCR, and the expression profiling were analyzed to predict the possible biological roles of these lipase genes in lipid metabolism in M. circinelloides. We preliminarily hypothesized that lipases may be involved in triacylglycerol degradation, phospholipid synthesis and beta-oxidation. Moreover, the results of sub-cellular localization, the presence of signal peptide and transcriptional analyses of lipase genes indicated that four lipase in WJ11 most likely belong to extracellular lipases with a signal peptide. These findings provide a platform

  4. Error Analysis in the Joint Event Location/Seismic Calibration Inverse Problem

    National Research Council Canada - National Science Library

    Rodi, William L

    2006-01-01

    This project is developing new mathematical and computational techniques for analyzing the uncertainty in seismic event locations, as induced by observational errors and errors in travel-time models...

  5. The location-, word-, and arrow-based Simon effects: An ex-Gaussian analysis.

    Science.gov (United States)

    Luo, Chunming; Proctor, Robert W

    2018-04-01

    Task-irrelevant spatial information, conveyed by stimulus location, location word, or arrow direction, can influence the response to task-relevant attributes, generating the location-, word-, and arrow-based Simon effects. We examined whether different mechanisms are involved in the generation of these Simon effects by fitting a mathematical ex-Gaussian function to empirical response time (RT) distributions. Specifically, we tested whether which ex-Gaussian parameters (μ, σ, and τ) show Simon effects and whether the location-, word, and arrow-based effects are on different parameters. Results show that the location-based Simon effect occurred on mean RT and μ but not on τ, and a reverse Simon effect occurred on σ. In contrast, a positive word-based Simon effect was obtained on all these measures (including σ), and a positive arrow-based Simon effect was evident on mean RT, σ, and τ but not μ. The arrow-based Simon effect was not different from the word-based Simon effect on τ or σ but was on μ and mean RT. These distinct results on mean RT and ex-Gaussian parameters provide evidence that spatial information conveyed by the various location modes are different in the time-course of activation.

  6. Sunflower mega-environments in Serbia revealed by GGE biplot analysis

    Directory of Open Access Journals (Sweden)

    Balalić Igor

    2013-01-01

    Full Text Available Sunflower mega-environment analysis was conducted for the grain yield data of 20 hybrids and 19 test locations during 2006, and 20 hybrids and 16 test locations during 2007. Combined data included 15 hybrids and 9 test locations common for both years and it was analyzed as balanced experiment. The analysis of variance components showed that hybrid by location interaction explained 2.74, 5.8, and 3.72 times more variation than hybrid, for grain yield, for 2006, 2007, combined data, respectively, and indicated potential mega-environment existence. Our results showed the existence of two mega-environments in Serbia sunflower growing region: (1 Kula Vitovnica, Aleksa Šantić, Sombor and (2 Rimski Šančevi, Kikinda. It has been concluded that if we want promising sunflower hybrids to be optimally used, they should be cropped differently for the two determined mega-environments.

  7. Isointegral analysis of body surface maps for the assessment of location and size of myocardial infarction

    International Nuclear Information System (INIS)

    Tonooka, I.; Kubota, I.; Watanabe, Y.; Tsuiki, K.; Yasui, S.

    1983-01-01

    To estimate the location and size of myocardial infarction (MI), an isointegral mapping technique was adopted from among various body surface electrocardiographic mapping techniques. QRS isointegral and departure maps were made in 35 patients with MI. These patients were separated into 3 groups, based on the location of MI: anterior, inferior, and anterior plus inferior. The severity and location of MI were estimated by thallium-201 myocardial perfusion imaging and the degree of scintigraphic defect was represented by a defect score. The extent of MI was expected to be reflected on the QRS isointegral maps as a distribution of negative QRS complex time-integral values. However, the extent and the location of MI were hardly detectable by the original maps. A departure mapping technique was then devised to observe the distribution of departure index on the body surface. Particular attention was given to the area where the departure index was less than -2, and this area was expected to reflect the location and size of specific abnormality of isointegral map due to MI. There were strong correlations between departure area and defect score in the anterior and inferior MI cases (r . 0.88 and r . 0.79, respectively). However, patients with anterior MI plus inferior MI showed no such correlation. Q-wave mapping was compared with QRS isointegral mapping, and QRS isointegral mapping was found to be more accurate in the estimation of the location and size of MI than Q wave mapping. Thus, QRS isointegral mapping, especially departure mapping, is more useful and convenient for detecting the location and size of MI than methods such as isopotential and Q wave mapping

  8. Location of gliomas in relation to mobile telephone use: a case-case and case-specular analysis

    DEFF Research Database (Denmark)

    Larjavaara, Suvi; Schüz, Joachim; Swerdlow, Anthony

    2011-01-01

    approaches: In a case-case analysis, tumor locations were compared with varying exposure levels; in a case-specular analysis, a hypothetical reference location was assigned for each glioma, and the distances from the actual and specular locations to the handset were compared. The study included 888 gliomas......The energy absorbed from the radio-frequency fields of mobile telephones depends strongly on distance from the source. The authors' objective in this study was to evaluate whether gliomas occur preferentially in the areas of the brain having the highest radio-frequency exposure. The authors used 2...... from 7 European countries (2000-2004), with tumor midpoints defined on a 3-dimensional grid based on radiologic images. The case-case analyses were carried out using unconditional logistic regression, whereas in the case-specular analysis, conditional logistic regression was used. In the case-case...

  9. Solution study of the Escherichia coli DNA polymerase III clamp loader reveals the location of the dynamic ψχ heterodimer

    Directory of Open Access Journals (Sweden)

    Farzaneh Tondnevis

    2015-09-01

    Full Text Available Several X-ray crystal structures of the E. coli core clamp loader containing the five core (δ′, δ, and three truncated γ subunits have been determined, but they lack the ψ and χ subunits. We report the first solution structure of the complete seven-subunit clamp loader complex using small angle X-ray scattering. This structure not only provides information about the location of the χ and ψ subunits but also provides a model of the dynamic nature of the clamp loader complex.

  10. Analysis of Natural Ventilation in a Passive House Located in Cold Conditions

    DEFF Research Database (Denmark)

    Oropeza-Perez, Ivan; Østergaard, Poul Alberg; Remmen, Arne

    2013-01-01

    in Vejle during cooling season, in the months of June, July and August. The dwelling belongs to a Danish project of passive houses denominated Komfort Husene, where its occupants claim there is no thermal comfort in summer time. The results show that the use of natural ventilation helps to reduce......This article shows the potential of using natural ventilation as a passive method of cooling buildings that are located in cold climate countries using Denmark as a case study. The energy saving potential of natural ventilation is found by performing thermal simulations of a household located...

  11. Design and analysis of a ranking approach to private location-based services

    DEFF Research Database (Denmark)

    Yiu, Ma Lung; Jensen, Christian S.; Møller, Jesper

    2011-01-01

    solution that expresses the server-side functionality in a single SQL statement. In its basic form, SpaceTwist utilizes well-known incremental NN query processing on the server. When augmented with a server-side granular search technique, SpaceTwist is capable of exploiting relaxed query accuracy......Twist, aims to offer location privacy for k nearest neighbor (kNN) queries at low communication cost without requiring a trusted anonymizer. The solution can be used with a conventional DBMS as well as with a server optimized for location-based services. In particular, we believe that this is the first...

  12. Spatiotemporal analysis of single-trial EEG of emotional pictures based on independent component analysis and source location

    Science.gov (United States)

    Liu, Jiangang; Tian, Jie

    2007-03-01

    The present study combined the Independent Component Analysis (ICA) and low-resolution brain electromagnetic tomography (LORETA) algorithms to identify the spatial distribution and time course of single-trial EEG record differences between neural responses to emotional stimuli vs. the neutral. Single-trial multichannel (129-sensor) EEG records were collected from 21 healthy, right-handed subjects viewing the emotion emotional (pleasant/unpleasant) and neutral pictures selected from International Affective Picture System (IAPS). For each subject, the single-trial EEG records of each emotional pictures were concatenated with the neutral, and a three-step analysis was applied to each of them in the same way. First, the ICA was performed to decompose each concatenated single-trial EEG records into temporally independent and spatially fixed components, namely independent components (ICs). The IC associated with artifacts were isolated. Second, the clustering analysis classified, across subjects, the temporally and spatially similar ICs into the same clusters, in which nonparametric permutation test for Global Field Power (GFP) of IC projection scalp maps identified significantly different temporal segments of each emotional condition vs. neutral. Third, the brain regions accounted for those significant segments were localized spatially with LORETA analysis. In each cluster, a voxel-by-voxel randomization test identified significantly different brain regions between each emotional condition vs. the neutral. Compared to the neutral, both emotional pictures elicited activation in the visual, temporal, ventromedial and dorsomedial prefrontal cortex and anterior cingulated gyrus. In addition, the pleasant pictures activated the left middle prefrontal cortex and the posterior precuneus, while the unpleasant pictures activated the right orbitofrontal cortex, posterior cingulated gyrus and somatosensory region. Our results were well consistent with other functional imaging

  13. THE LOCATION OF NON-THERMAL VELOCITY IN THE EARLY PHASES OF LARGE FLARES—REVEALING PRE-ERUPTION FLUX ROPES

    International Nuclear Information System (INIS)

    Harra, Louise K.; Matthews, Sarah; Culhane, J. L.; Cheung, Mark C. M.; Kontar, Eduard P.; Hara, Hirohisa

    2013-01-01

    Non-thermal velocity measurements of the solar atmosphere, particularly from UV and X-ray emission lines have demonstrated over the decades that this parameter is important in understanding the triggering of solar flares. Enhancements have often been observed before intensity enhancements are seen. However, until the launch of Hinode, it has been difficult to determine the spatial location of the enhancements to better understand the source region. The Hinode EUV Imaging Spectrometer has the spectral and spatial resolution to allow us to probe the early stages of flares in detail. We analyze four events, all of which are GOES M- or X-classification flares, and all are located toward the limb for ease of flare geometry interpretation. Three of the flares were eruptive and one was confined. In all events, pre-flare enhancement in non-thermal velocity at the base of the active region and its surroundings has been found. These enhancements seem to be consistent with the footpoints of the dimming regions, and hence may be highlighting the activation of a coronal flux rope for the three eruptive events. In addition, pre-flare enhancements in non-thermal velocity were found above the looptops for the three eruptive events

  14. Ground Motion Analysis of Co-Located DAS and Seismometer Sensors

    Science.gov (United States)

    Wang, H. F.; Fratta, D.; Lord, N. E.; Lancelle, C.; Thurber, C. H.; Zeng, X.; Parker, L.; Chalari, A.; Miller, D.; Feigl, K. L.; Team, P.

    2016-12-01

    The PoroTomo research team deployed 8700-meters of Distributed Acoustic Sensing (DAS) cable in a shallow trench and 400-meters in a borehole at Brady Hot Springs, Nevada in March 2016 together with an array of 246, three-component geophones. The seismic sensors occupied a natural laboratory 1500 x 500 x 400 meters overlying the Brady geothermal field. The DAS cable was laid out in three parallel zig-zag lines with line segments approximately 100-meters in length and geophones were spaced at approximately 50-m intervals. In several line segments, geophones were co-located within one meter of the DAS cable. Both DAS and the conventional geophones recorded continuously over 15 days. A large Vibroseis truck (T-Rex) provided the seismic source at approximately 250 locations outside and within the array. The Vibroseis protocol called for excitation in one vertical and two orthogonal horizontal directions at each location. For each mode, three, 5-to-80-Hz upsweeps were made over 20 seconds. In addition, a moderate-sized earthquake with a local magnitude of 4.3 was recorded on March 21, 2016. Its epicenter was approximately 150-km away. Several DAS line segments with co-located geophone stations were used to test relationships between the strain rate recorded by DAS and ground velocity recorded by the geophones.

  15. GIS-based locational analysis of petrol filling stations in Kaduna ...

    African Journals Online (AJOL)

    Location of environmental sensitive commercial and service activities in densely populated urban areas are guided by planning principles and standards, expressed in either structure plans or land use development plans. There has been an upsurge of filling stations within Kaduna metropolis thereby raising the questions ...

  16. Analysis of age, sex, location, size and multiplicity of colonic diverticulosis in Korean

    International Nuclear Information System (INIS)

    Son, Mi Young; Chang, Jae Chun; Kwoen, Hyuk Po; Jung, Kyung Hwa; Byun, Woo Mok; Kim, Sun Yong; Hwang, Mi Soo; Park, Bok Hwan

    1989-01-01

    Recently, colonic diverticulosis in Korea is one of rapidly increased disease in its incidence but it is different from that of western counties in the incidence or developing pattern. So, authors reviewed 1921 cases of double contrast study performed during 20 months, from Jan 1st , 1987 to Aug 30th, 1988 at the Department of Radiology. Yeungnam University Hospital to analyzed current disease pattern of the colonic diverticulosis. The results were as follows; 1. The incidence were 11.8%(226/1921) and predominant in male. 2. The mean age of patients was 48.41 years and older in female, but their incidence was not increased with advancing age over 6th decade. 3. The mean number of diverticular was 7.6 and higher in cases involving several anatomic location than limited to one location. 4. Diverticulosis more commonly involved several anatomic location than one location. 5. Left sided colonic diverticulosis was found in relatively older age group and more frequently involved descending colon than sigmoid colon most commonly seen in western people. 6. Recently, the incidence of colonic diverticulosis is increasing in both the right and left colon, which is thought to be due to various factors and partly to the routine use of double contrast study of the colon

  17. Analysis of age, sex, location, size and multiplicity of colonic diverticulosis in Korean

    Energy Technology Data Exchange (ETDEWEB)

    Son, Mi Young; Chang, Jae Chun; Kwoen, Hyuk Po; Jung, Kyung Hwa; Byun, Woo Mok; Kim, Sun Yong; Hwang, Mi Soo; Park, Bok Hwan [Yeungnam University College of Medicine, Chinju (Korea, Republic of)

    1989-02-15

    Recently, colonic diverticulosis in Korea is one of rapidly increased disease in its incidence but it is different from that of western counties in the incidence or developing pattern. So, authors reviewed 1921 cases of double contrast study performed during 20 months, from Jan 1st , 1987 to Aug 30th, 1988 at the Department of Radiology. Yeungnam University Hospital to analyzed current disease pattern of the colonic diverticulosis. The results were as follows; 1. The incidence were 11.8%(226/1921) and predominant in male. 2. The mean age of patients was 48.41 years and older in female, but their incidence was not increased with advancing age over 6th decade. 3. The mean number of diverticular was 7.6 and higher in cases involving several anatomic location than limited to one location. 4. Diverticulosis more commonly involved several anatomic location than one location. 5. Left sided colonic diverticulosis was found in relatively older age group and more frequently involved descending colon than sigmoid colon most commonly seen in western people. 6. Recently, the incidence of colonic diverticulosis is increasing in both the right and left colon, which is thought to be due to various factors and partly to the routine use of double contrast study of the colon.

  18. Load flow analysis for determining the location of NPP power distribution in West Kalimantan

    International Nuclear Information System (INIS)

    Citra Candranurani; Rizki Finnansyah Setya Budi; Sahala M Lumbanraja

    2015-01-01

    Electricity crisis condition happened in West Kalimantan (Kalbar) as a result of power plant capacity almost equal to the peak load. The system will experience a shortfall if there are plants that not operating and do not have reserve. The policy of electricity planning until 2022 is replacing diesel power plant with steam power plant. For long-term planning is required the role of new and renewable energy in order to reduce dependency on fossil fuel consumption, such as NPP utilization. The purpose of this study was to determine the optimum location of the NPP power distribution in order to prepare electricity infrastructure. Load flow calculation in this study using ETAP 12.5 software. NPP is planned to supply base load, so the optimum capacity factor is above 80 %. The result show that there are three location where NPP can generate over 80 % of its capacity, namely: Mempawah Substation, Singkawang Substation, and Sambas Substation. The most optimum located in Mempawah Substation with capacity factor 83.5 %. The location of the three Substation are onshore and in line with one requirement for NPP construction, namely: the availability of cooling water. (author)

  19. Leak before break analysis for cracking at multiple weld locations in BWR recirculation piping

    International Nuclear Information System (INIS)

    Zahoor, A.; Gamble, R.

    1984-01-01

    Periodically over the past decade, intergranular stress corrosion cracking (IGSCC) has been found in austenitic stainless steel piping at Boiling Water Reactor facilities. The effect of IGSCC on piping integrity has been evaluated previously in various BWR Owners Group and NRC studies. In these studies, the analyses were performed assuming the presence of a crack at a single weld location in the pipe run. The purpose of this investigation was to compare the leak rate and potential for unstable crack extension associated with a throughwall crack for the following two conditions in a BWR recirculation system: (1) the recirculation piping contains part through cracks at multiple weld locations and a single throughwall crack, and (2) the piping contains only a throughwall crack at one weld location. Two type BWRs were evaluated; namely, the ring header and five individual loop designs. The results from the analyses indicate that the potential for unstable crack extension at large bending loads, and leak rate at normal operation are not affected by the presence of part through cracks at multiple weld locations. The differences in the respective calculated L/sub eff/ and leak rates for the single and multiply cracked conditions are less than 2%

  20. Location and optimization analysis of capillary tube network embedded in active tuning building wall

    International Nuclear Information System (INIS)

    Niu, Fuxin; Yu, Yuebin

    2016-01-01

    In this study, a building wall with a thermal tuning function is further investigated. This design turns the building wall from a passive thermal system to an active system. A capillary tube network is installed inside the wall to manipulate the thermodynamics and realize more flexibility and potentials of the wall. This novel building wall structure performs efficiently in terms of building load reduction and supplementary heating and cooling, and the structure is convenient for applying low grade or natural energy with a wider temperature range. The capillary tube network's location inside the wall greatly impacts the thermal and energy performance of the building wall. The effects of three locations including external, middle and internal side are analyzed. The results indicate that the internal wall surface temperature can be neutralized from the ambient environment when the embedded tubes are fed with thermal water. The wall can work with a wide range of water temperature and the optimal location of the tube network is relatively constant in different modes. Power benefit with the wall changes from 2 W to 39 W when the outdoor air temperature changes, higher in summer than in winter. - Highlights: • A building wall with a tuning function is proposed using a capillary pipe network. • Low-grade thermal water can be used to actively manipulate the thermal mass. • Location of the capillary network is investigated to maximize the performance. • The innovation can potentially lower down the grade of energy use in buildings.

  1. Locations of Racism in Education: A Speech Act Analysis of a Policy Chain

    Science.gov (United States)

    Arneback, Emma; Quennerstedt, Ann

    2016-01-01

    This article explores how racism is located in an educational policy chain and identifies how its interpretation changes throughout the chain. A basic assumption is that the policy formation process can be seen as a chain in which international, national and local policies are "links"--separate entities yet joined. With Sweden as the…

  2. Multidimensional Analysis and Location Intelligence Application for Spatial Data Warehouse Hotspot in Indonesia using SpagoBI

    Science.gov (United States)

    Uswatun Hasanah, Gamma; Trisminingsih, Rina

    2016-01-01

    Spatial data warehouse refers to data warehouse which has a spatial component that represents the geographic location of the position or an object on the Earth's surface. Spatial data warehouse can be visualized in the form of a crosstab tables, graphs, and maps. Spatial data warehouse of hotspot in Indonesia has been constructed by researchers from FIRM NASA 2006-2015. This research develops multidimensional analysis module and location intelligence module using SpagoBI. The multidimensional analysis module is able to visualize online analytical processing (OLAP). The location intelligence module creates dynamic map visualization in map zone and map point. Map zone can display the different colors based on the number of hotspot in each region and map point can display different sizes of the point to represent the number of hotspots in each region. This research is expected to facilitate users in the presentation of hotspot data as needed.

  3. The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4

    International Nuclear Information System (INIS)

    Shen, Peter S.; Enderlein, Dirk; Nelson, Christian D.S.; Carter, Weston S.; Kawano, Masaaki; Xing Li; Swenson, Robert D.; Olson, Norman H.; Baker, Timothy S.; Cheng, R. Holland; Atwood, Walter J.; Johne, Reimar; Belnap, David M.

    2011-01-01

    Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting β-hairpin observed in other polyomaviruses. We postulate that the terminal β-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses.

  4. Multivariate pattern analysis reveals anatomical connectivity differences between the left and right mesial temporal lobe epilepsy

    Directory of Open Access Journals (Sweden)

    Peng Fang

    2015-01-01

    Full Text Available Previous studies have demonstrated differences of clinical signs and functional brain network organizations between the left and right mesial temporal lobe epilepsy (mTLE, but the anatomical connectivity differences underlying functional variance between the left and right mTLE remain uncharacterized. We examined 43 (22 left, 21 right mTLE patients with hippocampal sclerosis and 39 healthy controls using diffusion tensor imaging. After the whole-brain anatomical networks were constructed for each subject, multivariate pattern analysis was applied to classify the left mTLE from the right mTLE and extract the anatomical connectivity differences between the left and right mTLE patients. The classification results reveal 93.0% accuracy for the left mTLE versus the right mTLE, 93.4% accuracy for the left mTLE versus controls and 90.0% accuracy for the right mTLE versus controls. Compared with the right mTLE, the left mTLE exhibited a different connectivity pattern in the cortical-limbic network and cerebellum. The majority of the most discriminating anatomical connections were located within or across the cortical-limbic network and cerebellum, thereby indicating that these disease-related anatomical network alterations may give rise to a portion of the complex of emotional and memory deficit between the left and right mTLE. Moreover, the orbitofrontal gyrus, cingulate cortex, hippocampus and parahippocampal gyrus, which exhibit high discriminative power in classification, may play critical roles in the pathophysiology of mTLE. The current study demonstrated that anatomical connectivity differences between the left mTLE and the right mTLE may have the potential to serve as a neuroimaging biomarker to guide personalized diagnosis of the left and right mTLE.

  5. Multivariate pattern analysis reveals anatomical connectivity differences between the left and right mesial temporal lobe epilepsy.

    Science.gov (United States)

    Fang, Peng; An, Jie; Zeng, Ling-Li; Shen, Hui; Chen, Fanglin; Wang, Wensheng; Qiu, Shijun; Hu, Dewen

    2015-01-01

    Previous studies have demonstrated differences of clinical signs and functional brain network organizations between the left and right mesial temporal lobe epilepsy (mTLE), but the anatomical connectivity differences underlying functional variance between the left and right mTLE remain uncharacterized. We examined 43 (22 left, 21 right) mTLE patients with hippocampal sclerosis and 39 healthy controls using diffusion tensor imaging. After the whole-brain anatomical networks were constructed for each subject, multivariate pattern analysis was applied to classify the left mTLE from the right mTLE and extract the anatomical connectivity differences between the left and right mTLE patients. The classification results reveal 93.0% accuracy for the left mTLE versus the right mTLE, 93.4% accuracy for the left mTLE versus controls and 90.0% accuracy for the right mTLE versus controls. Compared with the right mTLE, the left mTLE exhibited a different connectivity pattern in the cortical-limbic network and cerebellum. The majority of the most discriminating anatomical connections were located within or across the cortical-limbic network and cerebellum, thereby indicating that these disease-related anatomical network alterations may give rise to a portion of the complex of emotional and memory deficit between the left and right mTLE. Moreover, the orbitofrontal gyrus, cingulate cortex, hippocampus and parahippocampal gyrus, which exhibit high discriminative power in classification, may play critical roles in the pathophysiology of mTLE. The current study demonstrated that anatomical connectivity differences between the left mTLE and the right mTLE may have the potential to serve as a neuroimaging biomarker to guide personalized diagnosis of the left and right mTLE.

  6. Effects of prefrontal tDCS on executive function: Methodological considerations revealed by meta-analysis.

    Science.gov (United States)

    Imburgio, Michael J; Orr, Joseph M

    2018-05-01

    A meta-analysis of studies using single-session transcranial direct current stimulation (tDCS) to target the dorsolateral prefrontal cortex (DLPFC) was undertaken to examine the effect of stimulation on executive function (EF) in healthy samples. 27 studies were included in analyses, yielding 71 effect sizes. The most relevant measure for each task was determined a priori and used to calculate Hedge's g. Methodological characteristics of each study were examined individually as potential moderators of effect size. Stimulation effects on three domains of EF (inhibition of prepotent responses, mental set shifting, and information updating and monitoring) were analyzed separately. In line with previous work, the current study found no significant effect of anodal unilateral tDCS, cathodal unilateral tDCS, or bilateral tDCS on EF. Further moderator and subgroup analyses were only carried out for anodal unilateral montages due to the small number of studies using other montages. Subgroup analyses revealed a significant effect of anodal unilateral tDCS on updating tasks, but not on inhibition or set-shifting tasks. Cathode location significantly moderated the effect of anodal unilateral tDCS. Extracranial cathodes yielded a significant effect on EF while cranial cathodes yielded no effect. Anode size also significantly moderated effect of anodal unilateral tDCS, with smaller anodes being more effective than larger anodes. In summary, anodal DLPFC stimulation is more effective at improving updating ability than inhibition and set-shifting ability, but anodal stimulation can significantly improve general executive function when extracranial cathodes or small anodes are used. Future meta-analyses may examine how stimulation's effects on specific behavioral tasks, rather than broader domains, might be affected by methodological moderators. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Silk and Sakoku : a simulation analysis of industrial location in Edo period Japan

    OpenAIRE

    ATSUMI, Toshihiro

    2012-01-01

    Japan closed itself to international trade from the 17^ century to the mid-19^ century during the Edo period, known as the Sakoku. After the closure, industries dispersed from western coastal cities to inland areas in western and eastern Japan. This paper investigates how the Sakoku may have aff ected industrial locations within Japan by applying a footloose entrepreneur type geography model to an economy with agricultural raw materials in a continuous space setting. The simulations based on ...

  8. A Panel data analysis of locational determinants of outward Foreign Direct Investment from China and India

    OpenAIRE

    Duanmu, J; Guney, Y

    2009-01-01

    The upsurge of Chinese and Indian outward foreign direct investment (FDI) raises an unanswered question about locational determinants of direct investment from the two countries. Using an unbalanced bilateral FDI database, we find that Chinese and Indian FDI are attracted to countries with large market size, low GDP growth, high volumes of imports from China or India, and low corporate tax rates. We also find important differences between China and India. While Chinese FDI is drawn to countri...

  9. ANALYSIS OF TERRESTRIAL PLANET FORMATION BY THE GRAND TACK MODEL: SYSTEM ARCHITECTURE AND TACK LOCATION

    Energy Technology Data Exchange (ETDEWEB)

    Brasser, R.; Ida, S. [Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550 (Japan); Matsumura, S. [School of Science and Engineering, Division of Physics, Fulton Building, University of Dundee, Dundee DD1 4HN (United Kingdom); Mojzsis, S. J. [Collaborative for Research in Origins (CRiO), Department of Geological Sciences, University of Colorado, UCB 399, 2200 Colorado Avenue, Boulder, Colorado 80309-0399 (United States); Werner, S. C. [The Centre for Earth Evolution and Dynamics, University of Oslo, Sem Saelandsvei 24, NO-0371 Oslo (Norway)

    2016-04-20

    The Grand Tack model of terrestrial planet formation has emerged in recent years as the premier scenario used to account for several observed features of the inner solar system. It relies on the early migration of the giant planets to gravitationally sculpt and mix the planetesimal disk down to ∼1 au, after which the terrestrial planets accrete from material remaining in a narrow circumsolar annulus. Here, we investigate how the model fares under a range of initial conditions and migration course-change (“tack”) locations. We run a large number of N-body simulations with tack locations of 1.5 and 2 au and test initial conditions using equal-mass planetary embryos and a semi-analytical approach to oligarchic growth. We make use of a recent model of the protosolar disk that takes into account viscous heating, includes the full effect of type 1 migration, and employs a realistic mass–radius relation for the growing terrestrial planets. Our results show that the canonical tack location of Jupiter at 1.5 au is inconsistent with the most massive planet residing at 1 au at greater than 95% confidence. This favors a tack farther out at 2 au for the disk model and parameters employed. Of the different initial conditions, we find that the oligarchic case is capable of statistically reproducing the orbital architecture and mass distribution of the terrestrial planets, while the equal-mass embryo case is not.

  10. An analysis of headquarters location in the Canadian oil and gas sector

    International Nuclear Information System (INIS)

    Hirsch, K.T.

    1993-04-01

    Headquarters location theory identifies several factors which are expected to influence the location of corporate head offices. Some of these factors directly affect the costs of operation and the basic profitability of the company, such as the cost of office space, tax levels, availability of qualified labour, cost of labour, proximity to corporate activities, and agglomeration with other services and companies. Headquarters location theory is applied to Canada's energy sector. During the previous 27 years, concentration of energy company headquarters has shifted from Toronto to Calgary. A regression model tests the extent to which those factors identified in the literature appear to be statistically significant for the headquarters relocation experience in Canada's energy sector. The results of the tests suggest that certain factors do appear to significantly influence relocation decisions. These factors are agglomeration with other oil and gas companies, and relative proximity to oil and gas operations (which unexpectedly displayed a negative coefficient). The agglomeration factor was by far the most significant. 44 refs., 3 figs., 2 tabs

  11. Elemental analysis and radiation hazards parameters of bauxite located in Saudi Arabia

    Science.gov (United States)

    Alashrah, S.; E Taher, A.

    2017-04-01

    Since Bauxite has been widely used in industry and in scientific investigations for producing Aluminum, it is important to measure the radionuclides concentrations to determine the health effect. The Bauxite mine is located in Az Zabirah city in Saudi Arabia. The concentrations of the radionuclides in the bauxite samples were measured using γ-ray spectrometer NaI (Tl). The average and range values of the concentrations of 226Ra, 232Th and 40K were 102.2 (141.1-62.7), 156.3 (202.8-102.8) and 116.8 (191.7- 48.9) Bq/kg respectively. These results were compared with the reported ranges in the literature from other locations around the world. The radiation hazard parameters; radium equivalent activity, annual dose, external hazard were also calculated and compared with the recommended levels by International Commission on Radiological Protection (ICRP-60) and united nations scientific committee on the effects of atomic radiation UNSCEAR reports. There are no studies for the natural radioactivity in the bauxite mine in Az Zabirah city, so these results are a start to establishing a database in this location.

  12. Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

    Directory of Open Access Journals (Sweden)

    Guillermo Nourdin-Galindo

    2017-10-01

    Full Text Available Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these

  13. Comparative analysis of diffused solar radiation models for optimum tilt angle determination for Indian locations

    International Nuclear Information System (INIS)

    Yadav, P.; Chandel, S.S.

    2014-01-01

    Tilt angle and orientation greatly are influenced on the performance of the solar photo voltaic panels. The tilt angle of solar photovoltaic panels is one of the important parameters for the optimum sizing of solar photovoltaic systems. This paper analyses six different isotropic and anisotropic diffused solar radiation models for optimum tilt angle determination. The predicted optimum tilt angles are compared with the experimentally measured values for summer season under outdoor conditions. The Liu and Jordan model is found to exhibit t lowest error as compared to other models for the location. (author)

  14. Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method

    Directory of Open Access Journals (Sweden)

    Yu Xiu-Juan

    2007-10-01

    Full Text Available Abstract Background The nucleotide compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years. It is interesting to mention that almost all bacterial genomes exhibit the same kind of base asymmetry. This work aims to investigate the strand biases in Chlamydia muridarum genome and show the potential of the Z curve method for quantitatively differentiating genes on the leading and lagging strands. Results The occurrence frequencies of bases of protein-coding genes in C. muridarum genome were analyzed by the Z curve method. It was found that genes located on the two strands of replication have distinct base usages in C. muridarum genome. According to their positions in the 9-D space spanned by the variables u1 – u9 of the Z curve method, K-means clustering algorithm can assign about 94% of genes to the correct strands, which is a few percent higher than those correctly classified by K-means based on the RSCU. The base usage and codon usage analyses show that genes on the leading strand have more G than C and more T than A, particularly at the third codon position. For genes on the lagging strand the biases is reverse. The y component of the Z curves for the complete chromosome sequences show that the excess of G over C and T over A are more remarkable in C. muridarum genome than in other bacterial genomes without separating base and/or codon usages. Furthermore, for the genomes of Borrelia burgdorferi, Treponema pallidum, Chlamydia muridarum and Chlamydia trachomatis, in which distinct base and/or codon usages have been observed, closer phylogenetic distance is found compared with other bacterial genomes. Conclusion The nature of the strand biases of base composition in C. muridarum is similar to that in most other bacterial genomes. However, the base composition asymmetry between the leading and lagging strands in C. muridarum is more significant than that in

  15. Analysis of neurological sequelae from radiosurgery of arteriovenous malformations: how location affects outcome

    International Nuclear Information System (INIS)

    Flickinger, John C.; Kondziolka, Douglas; Maitz, Ann H.; Lunsford, L. Dade

    1998-01-01

    Purpose/Objective: To elucidate how the risks of developing temporary and permanent neurological sequelae from radiosurgery for arteriovenous malformations (AVM) are related to AVM location, the addition of stereotactic magnetic resonance (MR) imaging to angiographic targeting, and prior hemorrhage or neurological deficits. Materials and Methods: We evaluated follow-up imaging and clinical data in 332 AVM patients who received gamma knife radiosurgery at the University of Pittsburgh between 1987 and 1994. All patients had regular clinical or imaging follow-up for a minimum of 2 years (range: 24-96 months, median = 45 months). There were 83 patients with MR-assisted planning, 187 with prior hemorrhages, and 143 with prior neurological deficits. Results: Symptomatic postradiosurgery sequelae (any neurological problem including headache) developed in 30 (9%) of 332 patients. Symptoms resolved in 58% of patients within 27 months with a significantly greater proportion (p = 0.006) resolving in patients with Dmin 0.3), including the addition of MR targeting, average radiation dose in 20 cc, prior hemorrhage, or neurological deficit. We used these results to construct a risk prediction model for symptomatic postradiosurgery sequelae. The risk of radiation necrosis was significantly correlated with PIE score (p < 0.048), but not with 12-Gy volume. Conclusion: The risks of developing complications from AVM radiosurgery can be predicted according to location with the PIE score, in conjunction with the 12-Gy treatment volume. Further study of factors affecting persistence of these sequelae (progression to radiation necrosis) is needed

  16. Acoustic emission source location in plates using wavelet analysis and cross time frequency spectrum.

    Science.gov (United States)

    Mostafapour, A; Davoodi, S; Ghareaghaji, M

    2014-12-01

    In this study, the theories of wavelet transform and cross-time frequency spectrum (CTFS) are used to locate AE source with frequency-varying wave velocity in plate-type structures. A rectangular array of four sensors is installed on the plate. When an impact is generated by an artificial AE source such as Hsu-Nielsen method of pencil lead breaking (PLB) at any position of the plate, the AE signals will be detected by four sensors at different times. By wavelet packet decomposition, a packet of signals with frequency range of 0.125-0.25MHz is selected. The CTFS is calculated by the short-time Fourier transform of the cross-correlation between considered packets captured by AE sensors. The time delay is calculated when the CTFS reaches the maximum value and the corresponding frequency is extracted per this maximum value. The resulting frequency is used to calculate the group velocity of wave velocity in combination with dispersive curve. The resulted locating error shows the high precision of proposed algorithm. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Design and Analysis of Photovoltaic (PV) Power Plant at Different Locations in Malaysia

    Science.gov (United States)

    Islam, M. A.; Hasanuzzaman, M.; Rahim, N. A.

    2018-05-01

    Power generation from sun oriented vitality through a photovoltaic (PV) system is ended up prevalent over the world due to clean innovation. Geographical location of Malaysia is very favorable for PV power generation system. The Malaysian government has also taken different steps to increase the use of solar energy especially by emphasizing on building integrated PV (BIPV) system. Comparative study on the feasibility of BIPV installation at the different location of Malaysia is rarely found. On the other hand, solar cell temperature has a negative impact on the electricity generation. So in this study cost effectiveness and initial investment cost of building integrated grid connected solar PV power plant in different regions of Malaysia have been carried. The effect of PV solar cell temperature on the payback period (PBP) is also investigated. Highest PBP is 12.38 years at Selangor and lowest PBP is 9.70 years at Sabah (Kota Kinabalu). Solar cell temperature significantly increases the PBP of PV plant and highest 14.64% and lowest 13.20% raise of PBP are encountered at Penang and Sarawak respectively.

  18. Spatial patterns of serial murder: an analysis of disposal site location choice.

    Science.gov (United States)

    Lundrigan, S; Canter, D

    2001-01-01

    Although the murders committed by serial killers may not be considered rational, there is growing evidence that the locations in which they commit their crimes may be guided by an implicit, if limited rationality. The hypothesized logic of disposal site choice of serial killers led to predictions that (a) their criminal domains would be around their home base and relate to familiar travel distances, (b) they would have a size that was characteristic of each offender, (c) the distribution would be biased towards other non-criminal activities, and (d) the size of the domains would increase over time. Examination of the geographical distribution of the sites at which 126 US and 29 UK serial killers disposed of their victims' bodies supported all four hypotheses. It was found that rational choice and routine activity models of criminal behavior could explain the spatial choices of serial murderers. It was concluded that the locations at which serial killers dispose of their victims' bodies reflect the inherent logic of the choices that underlie their predatory activities. Copyright 2001 John Wiley & Sons, Ltd.

  19. Selection of adequate site location during early stages of construction project management: A multi-criteria decision analysis approach

    Science.gov (United States)

    Marović, Ivan; Hanak, Tomaš

    2017-10-01

    In the management of construction projects special attention should be given to the planning as the most important phase of decision-making process. Quality decision-making based on adequate and comprehensive collaboration of all involved stakeholders is crucial in project’s early stages. Fundamental reasons for existence of this problem arise from: specific conditions of construction industry (final products are inseparable from the location i.e. location has a strong influence of building design and its structural characteristics as well as technology which will be used during construction), investors’ desires and attitudes, and influence of socioeconomic and environment aspects. Considering all mentioned reasons one can conclude that selection of adequate construction site location for future investment is complex, low structured and multi-criteria problem. To take into account all the dimensions, the proposed model for selection of adequate site location is devised. The model is based on AHP (for designing the decision-making hierarchy) and PROMETHEE (for pairwise comparison of investment locations) methods. As a result of mixing basis feature of both methods, operational synergies can be achieved in multi-criteria decision analysis. Such gives the decision-maker a sense of assurance, knowing that if the procedure proposed by the presented model has been followed, it will lead to a rational decision, carefully and systematically thought out.

  20. An analysis of Emergency Medical Services demand: Time of day, day of the week, and location in the city.

    Science.gov (United States)

    Sariyer, Gorkem; Ataman, Mustafa Gokalp; Akay, Serhat; Sofuoglu, Turhan; Sofuoglu, Zeynep

    2017-06-01

    Effective planning of Emergency Medical Services (EMS), which is highly dependent on the analysis of past data trends, is important in reducing response time. Thus, we aimed to analyze demand for these services based on time and location trends to inform planning for an effective EMS. Data for this retrospective study were obtained from the Izmir EMS 112 system. All calls reaching these services during first six months of 2013 were descriptively analyzed, based on time and location trends as a heat-map form. The analyses showed that demand for EMS varied within different time periods of day, and according to day of the week. For the night period, demand was higher at the weekend compared to weekdays, whereas for daytime hours, demand was higher during the week. For weekdays, a statistically significant relation was observed between the call distribution of morning and evening periods. It was also observed that the percentage of demand changed according to location. Among 30 locations, the five most frequent destinations for ambulances, which are also correlated with high population densities, accounted for 55.66% of the total. The results of this study shed valuable light on the areas of call center planning and optimal ambulance locations of Izmir, which can also be served as an archetype for other cities.

  1. Locating new uranium occurrence by integrated weighted analysis in Kaladgi basin, Karnataka

    International Nuclear Information System (INIS)

    Sridhar, M.; Chaturvedi, A.K.; Rai, A.K.

    2014-01-01

    This study aims at identifying uranium potential zones by integrated analysis of thematic layer interpreted and derived from airborne radiometric and magnetic data, satellite data along with available ground geochemical data in western part of Kaladgi basin. Integrated weighted analysis of spatial datasets which included airborne radiometric data (eU, eTh and % K conc.), litho-structural map. hydrogeochemical U conc., and geomorphological data pertaining to study area, was attempted. The weightage analysis was done in GIS environment where different spatial dataset were brought on to a single platform and were analyzed by integration

  2. Does the Location of Bruch's Membrane Opening Change Over Time? Longitudinal Analysis Using San Diego Automated Layer Segmentation Algorithm (SALSA).

    Science.gov (United States)

    Belghith, Akram; Bowd, Christopher; Medeiros, Felipe A; Hammel, Naama; Yang, Zhiyong; Weinreb, Robert N; Zangwill, Linda M

    2016-02-01

    We determined if the Bruch's membrane opening (BMO) location changes over time in healthy eyes and eyes with progressing glaucoma, and validated an automated segmentation algorithm for identifying the BMO in Cirrus high-definition coherence tomography (HD-OCT) images. We followed 95 eyes (35 progressing glaucoma and 60 healthy) for an average of 3.7 ± 1.1 years. A stable group of 50 eyes had repeated tests over a short period. In each B-scan of the stable group, the BMO points were delineated manually and automatically to assess the reproducibility of both segmentation methods. Moreover, the BMO location variation over time was assessed longitudinally on the aligned images in 3D space point by point in x, y, and z directions. Mean visual field mean deviation at baseline of the progressing glaucoma group was -7.7 dB. Mixed-effects models revealed small nonsignificant changes in BMO location over time for all directions in healthy eyes (the smallest P value was 0.39) and in the progressing glaucoma eyes (the smallest P value was 0.30). In the stable group, the overall intervisit-intraclass correlation coefficient (ICC) and coefficient of variation (CV) were 98.4% and 2.1%, respectively, for the manual segmentation and 98.1% and 1.9%, respectively, for the automated algorithm. Bruch's membrane opening location was stable in normal and progressing glaucoma eyes with follow-up between 3 and 4 years indicating that it can be used as reference point in monitoring glaucoma progression. The BMO location estimation with Cirrus HD-OCT using manual and automated segmentation showed excellent reproducibility.

  3. Saccades to remembered target locations: an analysis of systematic and variable errors.

    Science.gov (United States)

    White, J M; Sparks, D L; Stanford, T R

    1994-01-01

    We studied the effects of varying delay interval on the accuracy and velocity of saccades to the remembered locations of visual targets. Remembered saccades were less accurate than control saccades. Both systematic and variable errors contributed to the loss of accuracy. Systematic errors were similar in size for delay intervals ranging from 400 msec to 5.6 sec, but variable errors increased monotonically as delay intervals were lengthened. Compared to control saccades, remembered saccades were slower and the peak velocities were more variable. However, neither peak velocity nor variability in peak velocity was related to the duration of the delay interval. Our findings indicate that a memory-related process is not the major source of the systematic errors observed on memory trials.

  4. Line-to-Line Fault Analysis and Location in a VSC-Based Low-Voltage DC Distribution Network

    Directory of Open Access Journals (Sweden)

    Shi-Min Xue

    2018-03-01

    Full Text Available A DC cable short-circuit fault is the most severe fault type that occurs in DC distribution networks, having a negative impact on transmission equipment and the stability of system operation. When a short-circuit fault occurs in a DC distribution network based on a voltage source converter (VSC, an in-depth analysis and characterization of the fault is of great significance to establish relay protection, devise fault current limiters and realize fault location. However, research on short-circuit faults in VSC-based low-voltage DC (LVDC systems, which are greatly different from high-voltage DC (HVDC systems, is currently stagnant. The existing research in this area is not conclusive, with further study required to explain findings in HVDC systems that do not fit with simulated results or lack thorough theoretical analyses. In this paper, faults are divided into transient- and steady-state faults, and detailed formulas are provided. A more thorough and practical theoretical analysis with fewer errors can be used to develop protection schemes and short-circuit fault locations based on transient- and steady-state analytic formulas. Compared to the classical methods, the fault analyses in this paper provide more accurate computed results of fault current. Thus, the fault location method can rapidly evaluate the distance between the fault and converter. The analyses of error increase and an improved handshaking method coordinating with the proposed location method are presented.

  5. Biomechanical analysis of suture locations of the distal plantar fascia in partial foot.

    Science.gov (United States)

    Guo, Jun-Chao; Wang, Li-Zhen; Mo, Zhong-Jun; Chen, Wei; Fan, Yu-Bo

    2015-12-01

    The aim of this study was to evaluate the rationality of the suture locations of distal plantar fascia (DPF) after foot amputation to avoid the risk factors of re-amputation or plantar fasciitis. The tensile strain of plantar fascia (PF) in the different regions was measured by uni-axial tensile experiment. A three-dimensional (3D) finite element model was also developed to simulate tensile behaviour of PF in weight bearing conditions. The model includes 12 bones, ligaments, PF, cartilage and soft tissues. Four suture location models for the DPF were considered: the fourth and fifth DPF were sutured on the third metatarsal, the cuboid, and both the third metatarsal and the cuboid, and one un-sutured model. The peak tensile strain of the first, second and third PF was 0.134, 0.128 and 0.138 based on the mechanical test, respectively. The fourth and fifth DPF sutured at the cuboid and the third metatarsal could offer more favourable outcomes. The peak strain of 4.859 × 10(-2), 2.347 × 10(-2) and 1.364 × 10(-2) in the first, second and third PF showed the least outcomes in stance phase. Also, peak strain and stress of the residual PF reduced to 4.859 × 10(-2) and 1.834 MPa, respectively. The stress region was redistributed on the mid-shaft of the first and third PF and the peak stress of medial cuneiform bone evidently decreased. The fourth and fifth DPF suture at the third metatarsal and cuboid was appropriate for the partial foot. The findings are expected to suggest optimal surgical plan of the DPF suture and guide further therapeutic planning of partial foot patients.

  6. Power flow analysis and optimal locations of resistive type superconducting fault current limiters.

    Science.gov (United States)

    Zhang, Xiuchang; Ruiz, Harold S; Geng, Jianzhao; Shen, Boyang; Fu, Lin; Zhang, Heng; Coombs, Tim A

    2016-01-01

    Based on conventional approaches for the integration of resistive-type superconducting fault current limiters (SFCLs) on electric distribution networks, SFCL models largely rely on the insertion of a step or exponential resistance that is determined by a predefined quenching time. In this paper, we expand the scope of the aforementioned models by considering the actual behaviour of an SFCL in terms of the temperature dynamic power-law dependence between the electrical field and the current density, characteristic of high temperature superconductors. Our results are compared to the step-resistance models for the sake of discussion and clarity of the conclusions. Both SFCL models were integrated into a power system model built based on the UK power standard, to study the impact of these protection strategies on the performance of the overall electricity network. As a representative renewable energy source, a 90 MVA wind farm was considered for the simulations. Three fault conditions were simulated, and the figures for the fault current reduction predicted by both fault current limiting models have been compared in terms of multiple current measuring points and allocation strategies. Consequently, we have shown that the incorporation of the E - J characteristics and thermal properties of the superconductor at the simulation level of electric power systems, is crucial for estimations of reliability and determining the optimal locations of resistive type SFCLs in distributed power networks. Our results may help decision making by distribution network operators regarding investment and promotion of SFCL technologies, as it is possible to determine the maximum number of SFCLs necessary to protect against different fault conditions at multiple locations.

  7. The Analysis of Sophisticated Direction of Arrival Estimation Methods in Passive Coherent Locators

    National Research Council Canada - National Science Library

    Ozcetin, Ahmet

    2002-01-01

    ...). The goal is to compare the ACMA to the MUSIC, and CBF algorithms for application to PCL. The results and analysis presented here support the use of constant modulus information, where available, as an important addition to DOA estimation...

  8. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

    Directory of Open Access Journals (Sweden)

    Yonglong Yu

    2016-04-01

    Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

  9. Location and Size Planning of Distributed Photovoltaic Generation in Distribution network System Based on K-means Clustering Analysis

    Science.gov (United States)

    Lu, Siqi; Wang, Xiaorong; Wu, Junyong

    2018-01-01

    The paper presents a method to generate the planning scenarios, which is based on K-means clustering analysis algorithm driven by data, for the location and size planning of distributed photovoltaic (PV) units in the network. Taken the power losses of the network, the installation and maintenance costs of distributed PV, the profit of distributed PV and the voltage offset as objectives and the locations and sizes of distributed PV as decision variables, Pareto optimal front is obtained through the self-adaptive genetic algorithm (GA) and solutions are ranked by a method called technique for order preference by similarity to an ideal solution (TOPSIS). Finally, select the planning schemes at the top of the ranking list based on different planning emphasis after the analysis in detail. The proposed method is applied to a 10-kV distribution network in Gansu Province, China and the results are discussed.

  10. Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina

    DEFF Research Database (Denmark)

    Gallo, G.; Renzone, G.; Alduina, R.

    2010-01-01

    A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially...... available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal-proteome-maps). Functional clustering analysis revealed that differentially expressed proteins belong to functional groups involved in central carbon metabolism, amino acid metabolism and protein biosynthesis...... intermediates, were upregulated during antibiotic production. qRT-PCR analysis revealed that 8 out of 14 upregulated genes showed a positive correlation between changes at translational and transcriptional expression level. Furthermore, proteomic analysis of two nonproducing mutants, restricted to a sub...

  11. Locative media

    CERN Document Server

    Wilken, Rowan

    2014-01-01

    Not only is locative media one of the fastest growing areas in digital technology, but questions of location and location-awareness are increasingly central to our contemporary engagements with online and mobile media, and indeed media and culture generally. This volume is a comprehensive account of the various location-based technologies, services, applications, and cultures, as media, with an aim to identify, inventory, explore, and critique their cultural, economic, political, social, and policy dimensions internationally. In particular, the collection is organized around the perception that the growth of locative media gives rise to a number of crucial questions concerning the areas of culture, economy, and policy.

  12. System analysis of industrial waste management: A case study of industrial plants located between Tehran and Karaj

    OpenAIRE

    Mohammad Amin Karami; Mohsen Sadani; Mehdi Farzadkia; Nezam Mirzaei; Anvar Asadi

    2015-01-01

    Aims: In this study, management of industrial waste in industries located between Tehran and Karaj in 2009-2010 was examined. Materials and Methods: This is a cross-sectional study which was done by site survey (Iranian environmental protection organization) questionnaire usage and results analysis. This questionnaire was consisted of 45 questions about industrial waste, quantity, quality, and management. A total number of industries with over 50 employees was 283, and Stratified sampling...

  13. Seismic precursors of vulcanian explosions at Ubinas volcano (Peru) : Statistical analysis and source locations

    Science.gov (United States)

    Métaxian, J.-P.; Macedo, O.; Lengline, O.; Monteiller, V.; Taipe, E.

    2009-04-01

    Ubinas stratovolcano (5672 m), located 60 km east from Arequipa city is historically the most active volcano in Peru. The present eruption began on March 25th 2006. A lava plug has been observed at the bottom of the pit crater situated in the south part of the caldeira. The eruptive activity involves very brought closer exhalations rising a few hundred meters above the crater rim to larger plumes produced by explosions that may reach up to 3 kilometers. The seismic activity is characterized by high rates of long-period (LP) event production accompanying eruptive activity and very long period (VLP) events observed at the same time as vulcanian explosions. The LP and VLP events have a spectral content respectively dominated by frequencies between 2-5 Hz and 0.3-0.9 Hz. The vulcanian explosive activity is characterized by the occurrence of LP swarm preceding most of the VLPs by about 2 hours. In some occasions, the LP swarm merges into tremor about half an hour before the explosion. LPs belonging to the same swarm have similar waveform suggesting a unique source area, which could be the conduit and/or the lava plug surface. The monitoring system includes 4 seismic stations, among which one is equipped with a broadband sensor and 2 tiltmeters. In this work we analyzed a catalogue of data including more than 40000 LP events and 130 VLP events recorded between May 2006 and December 2008. The evolution of the average number of LP events preceding explosions was computed. The variation of the LP rate is clearly diverging from the background rate ~ 0.1 days before explosions. In particular, the most energetic explosions are correlated with the biggest increases of seismicity. However this general behavior is not observed for every single explosion. A direct test is now under study in order to check if the earthquake rate can be used as an alert tool for future explosions. To locate the source of LP events belonging to the swarms, we used a method based on the measurement of

  14. An empirical orthogonal function analysis of ocean shoreline location on the Virginia barrier islands

    Science.gov (United States)

    Haluska, J. D.

    2017-12-01

    Shoreline change along the Eastern Atlantic shore of Virginia has been studied for the individual barrier islands but not as an integrated system. This study combines the Atlantic shoreline locations for eleven barrier islands obtained from LANDSAT 5, 7, and 8 images. Approximately 250 shoreline locations over a 24-year period from Jan 1990 to Dec 2014 were extracted from the digitized shoreline data at 338 transects. The resulting 338 by 250 matrix was analyzed by the empirical orthogonal function (EOF) technique. The first four principal components (PC) explained 86 percent of the sample variance. Since the data was not detrended, the first PC was the overall trend of the data with a discontinuity in 2004-2005. The 2004-2005 interval included storm events and large shoreline changes. PCs 2 to 4 reflect the effects of El Nino events and tropical and non-tropical storms. Eigenvectors 1 to 4 all show the effects of the nine inlets in the island group. Eigenvector (EV) 1 explains 59 percent of the shoreline spatial variance and shows the largest changes at the northern and southern island ends. EVs 2 to 4 reflect the pattern of EV1 but at sequentially smaller percentages of the spatial variance. As a group, the eleven islands are losing ocean side shoreline. The lone exception is Hog Island. Sea level had the strongest correlation with the shoreline loss trend of PC1. The coefficient of determination was 0.41. The NAO and MEI also correlated with PC1 with correlations of determination of 0.05 and 0.12 respectively. These confidence level for the three factors was better than 99 percent. Sea level also correlated with PC3 and PC4. The PCs as a group show that the year intervals 2004-2005 and 2009-2010 had large effects on the shoreline change pattern for the island group. EVs 1 to 4 had the highest range of shoreline change at the island ends indicating the effect the changes of the inlets have on the adjacent islands. The smaller islands as a group had a higher level

  15. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    OpenAIRE

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the exis...

  16. Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal

    OpenAIRE

    Sheng, Yue; Zhao, Wei; Song, Ying; Li, Zhigang; Luo, Majing; Lei, Quan; Cheng, Hanhua; Zhou, Rongjia

    2015-01-01

    A variety of mechanisms are engaged in sex determination in vertebrates. The teleost fish swamp eel undergoes sex reversal naturally and is an ideal model for vertebrate sexual development. However, the importance of proteome-wide scanning for gonad reversal was not previously determined. We report a 2-D electrophoresis analysis of three gonad types of proteomes during sex reversal. MS/MS analysis revealed a group of differentially expressed proteins during ovary to ovotestis to testis transf...

  17. Revealing the equivalence of two clonal survival models by principal component analysis

    International Nuclear Information System (INIS)

    Lachet, Bernard; Dufour, Jacques

    1976-01-01

    The principal component analysis of 21 chlorella cell survival curves, adjusted by one-hit and two-hit target models, lead to quite similar projections on the principal plan: the homologous parameters of these models are linearly correlated; the reason for the statistical equivalence of these two models, in the present state of experimental inaccuracy, is revealed [fr

  18. Analysis of limb function after various reconstruction methods according to tumor location following resection of pediatric malignant bone tumors

    Directory of Open Access Journals (Sweden)

    Tokuhashi Yasuaki

    2010-05-01

    Full Text Available Abstract Background In the reconstruction of the affected limb in pediatric malignant bone tumors, since the loss of joint function affects limb-length discrepancy expected in the future, reconstruction methods that not only maximally preserve the joint function but also maintain good limb function are necessary. We analysis limb function of reconstruction methods by tumor location following resection of pediatric malignant bone tumors. Patients and methods We classified the tumors according to their location into 3 types by preoperative MRI, and evaluated reconstruction methods after wide resection, paying attention to whether the joint function could be preserved. The mean age of the patients was 10.6 years, Osteosarcoma was observed in 26 patients, Ewing's sarcoma in 3, and PNET(primitive neuroectodermal tumor and chondrosarcoma (grade 1 in 1 each. Results Type I were those located in the diaphysis, and reconstruction was performed using a vascularized fibular graft(vascularized fibular graft. Type 2 were those located in contact with the epiphyseal line or within 1 cm from this line, and VFG was performed in 1, and distraction osteogenesis in 1. Type III were those extending from the diaphysis to the epiphysis beyond the epiphyseal line, and a Growing Kotz was mainly used in 10 patients. The mean functional assessment score was the highest for Type I (96%: n = 4 according to the type and for VFG (99% according to the reconstruction method. Conclusion The final functional results were the most satisfactory for Types I and II according to tumor location. Biological reconstruction such as VFG and distraction osteogenesis without a prosthesis are so high score in the MSTS rating system. Therefore, considering the function of the affected limb, a limb reconstruction method allowing the maximal preservation of joint function should be selected after careful evaluation of the effects of chemotherapy and the location of the tumor.

  19. Statistical analysis of PM₁₀ concentrations at different locations in Malaysia.

    Science.gov (United States)

    Sansuddin, Nurulilyana; Ramli, Nor Azam; Yahaya, Ahmad Shukri; Yusof, Noor Faizah Fitri Md; Ghazali, Nurul Adyani; Madhoun, Wesam Ahmed Al

    2011-09-01

    Malaysia has experienced several haze events since the 1980s as a consequence of the transboundary movement of air pollutants emitted from forest fires and open burning activities. Hazy episodes can result from local activities and be categorized as "localized haze". General probability distributions (i.e., gamma and log-normal) were chosen to analyze the PM(10) concentrations data at two different types of locations in Malaysia: industrial (Johor Bahru and Nilai) and residential (Kota Kinabalu and Kuantan). These areas were chosen based on their frequently high PM(10) concentration readings. The best models representing the areas were chosen based on their performance indicator values. The best distributions provided the probability of exceedances and the return period between the actual and predicted concentrations based on the threshold limit given by the Malaysian Ambient Air Quality Guidelines (24-h average of 150 μg/m(3)) for PM(10) concentrations. The short-term prediction for PM(10) exceedances in 14 days was obtained using the autoregressive model.

  20. Analysis of magnetite crystals and inclusion bodies inside magnetotactic bacteria from different environmental locations

    Science.gov (United States)

    Oestreicher, Z.; Lower, B.; Lower, S.; Bazylinski, D. A.

    2011-12-01

    Biomineralization occurs throughout the living world; a few common examples include iron oxide in chiton teeth, calcium carbonate in mollusk shells, calcium phosphate in animal bones and teeth, silica in diatom shells, and magnetite crystals inside the cells of magnetotactic bacteria. Biologically controlled mineralization is characterized by biominerals that have species-specific properties such as: preferential crystallographic orientation, consistent particle size, highly ordered spatial locations, and well-defined composition and structure. It is well known that magnetotactic bacteria synthesize crystals of magnetite inside of their cells, but how they mineralize the magnetite is poorly understood. Magnetosomes have a species-specific morphology that is due to specific proteins involved in the mineralization process. In addition to magnetite crystals, magnetotactic bacteria also produce inclusion bodies or granules that contain different elements, such as phosphorus, calcium, and sulfur. In this study we used the transmission electron microscope to analyze the structure of magnetite crystals and inclusion bodies from different species of magnetotactic bacteria in order to determine the composition of the inclusion bodies and to ascertain whether or not the magnetite crystals contain elements other than iron and oxygen. Using energy dispersive spectroscopy we found that different bacteria from different environments possess inclusion bodies that contain different elements such as phosphorus, calcium, barium, magnesium, and sulfur. These differences may reflect the conditions of the environment in which the bacteria inhabit.

  1. Bus Travel Time Deviation Analysis Using Automatic Vehicle Location Data and Structural Equation Modeling

    Directory of Open Access Journals (Sweden)

    Xiaolin Gong

    2015-01-01

    Full Text Available To investigate the influences of causes of unreliability and bus schedule recovery phenomenon on microscopic segment-level travel time variance, this study adopts Structural Equation Modeling (SEM to specify, estimate, and measure the theoretical proposed models. The SEM model establishes and verifies hypotheses for interrelationships among travel time deviations, departure delays, segment lengths, dwell times, and number of traffic signals and access connections. The finally accepted model demonstrates excellent fitness. Most of the hypotheses are supported by the sample dataset from bus Automatic Vehicle Location system. The SEM model confirms the bus schedule recovery phenomenon. The departure delays at bus terminals and upstream travel time deviations indeed have negative impacts on travel time fluctuation of buses en route. Meanwhile, the segment length directly and negatively impacts travel time variability and inversely positively contributes to the schedule recovery process; this exogenous variable also indirectly and positively influences travel times through the existence of signalized intersections and access connections. This study offers a rational approach to analyzing travel time deviation feature. The SEM model structure and estimation results facilitate the understanding of bus service performance characteristics and provide several implications for bus service planning, management, and operation.

  2. VETRA - offline analysis and monitoring software platform for the LHCb Vertex Locator

    International Nuclear Information System (INIS)

    Szumlak, Tomasz

    2010-01-01

    The LHCb experiment is dedicated to studying CP violation and rare decay phenomena. In order to achieve these physics goals precise tracking and vertexing around the interaction point is crucial. This is provided by the VELO (VErtex LOcator) silicon detector. After digitization, FPGAs are employed to run several algorithms to suppress noise and reconstruct clusters. This is performed by an FPGA based processing board. An off-line software project, VETRA, has been developed which performs a bit perfect emulation of this complex processing in the FPGAs. This is a novel development as this hardware emulation is not standalone but rather is fully integrated into the LHCb software to allow the reconstruction of full data from the detector. This software platform facilitates the development and understanding of the behaviour of the processing algorithms, the optimization of the parameters of the algorithms that will be loaded into the FPGA and monitoring of the detector performance. This framework has also been adopted by the Silicon Tracker detector of LHCb. This processing framework was successfully used with the first 1500 tracks of data in the VELO obtained from the first LHC beam in September 2008. The software architecture and utilisation of the VETRA project will be discussed in detail.

  3. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit.

    Science.gov (United States)

    Ashoori, Maryam; Burns, Catherine M; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamwork and leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams.

  4. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    Science.gov (United States)

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. Practitioner Summary: This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams PMID:24837514

  5. Superposed ruptile deformational events revealed by field and VOM structural analysis

    Science.gov (United States)

    Kumaira, Sissa; Guadagnin, Felipe; Keller Lautert, Maiara

    2017-04-01

    Virtual outcrop models (VOM) is becoming an important application in the analysis of geological structures due to the possibility of obtaining the geometry and in some cases kinematic aspects of analyzed structures in a tridimensional photorealistic space. These data are used to gain quantitative information on the deformational features which coupled with numeric models can assist in understands deformational processes. Old basement units commonly register superposed deformational events either ductile or ruptile along its evolution. The Porongos Belt, located at southern Brazil, have a complex deformational history registering at least five ductile and ruptile deformational events. In this study, we presents a structural analysis of a quarry in the Porongos Belt, coupling field and VOM structural information to understand process involved in the last two deformational events. Field information was acquired using traditional structural methods for analysis of ruptile structures, such as the descriptions, drawings, acquisition of orientation vectors and kinematic analysis. VOM was created from the image-based modeling method through photogrammetric data acquisition and orthorectification. Photogrammetric data acquisition was acquired using Sony a3500 camera and a total of 128 photographs were taken from ca. 10-20 m from the outcrop in different orientations. Thirty two control point coordinates were acquired using a combination of RTK dGPS surveying and total station work, providing a precision of few millimeters for x, y and z. Photographs were imported into the Photo Scan software to create a 3D dense point cloud from structure from-motion algorithm, which were triangulated and textured to generate the VOM. VOM was georreferenced (oriented and scaled) using the ground control points, and later analyzed in OpenPlot software to extract structural information. Data was imported in Wintensor software to obtain tensor orientations, and Move software to process and

  6. Using trajectory sensitivity analysis to find suitable locations of series compensators for improving rotor angle stability

    DEFF Research Database (Denmark)

    Nasri, Amin; Eriksson, Robert; Ghandhar, Mehrdad

    2014-01-01

    This paper proposes an approach based on trajectory sensitivity analysis (TSA) to find most suitable placement of series compensators in the power system. The main objective is to maximize the benefit of these devices in order to enhance the rotor angle stability. This approach is formulated...

  7. Gender, Space, and the Location Changes of Jobs and People : A Spatial Simultaneous Equations Analysis

    NARCIS (Netherlands)

    Hoogstra, Gerke J.

    This article summarizes a spatial econometric analysis of local population and employment growth in the Netherlands, with specific reference to impacts of gender and space. The simultaneous equations model used distinguishes between population- and gender-specific employment groups, and includes

  8. Multi-scale location analysis of vulnerabilities and their link to disturbances within digital ecosystems

    OpenAIRE

    Jackson, Jennifer

    2017-01-01

    As computer networks evolve, so too does the techniques used by attackers to exploit new vulnerabilities. Natural ecosystems already have resistant and resilient properties that help protect them from unwanted disturbances despite the existence of different vulnerabilities. Computer networks and their environments can be considered as digital ecosystems with different vulnerabilities, and security attacks can be considered as unwanted disturbances. Analysis of vulnerabilities and attacks from...

  9. Space diffuses multiobjective analysis: A tool to locate lineal projects with a focus of environmental management

    International Nuclear Information System (INIS)

    Patricia Jaramillo A Liliana Vinasco T

    2005-01-01

    This paper presents a methodological proposal that is developed to identify corridors for lineal projects (highways, transmission lines, pipelines, etc), with environmental management criteria, when there is not complete information about the area of influence of the project, or some of the information is imprecise. Also a computational module is developed that allow the use of the methodological proposal. The proposal is based in the fuzzy multiobjective analysis concept, which takes elements of the diffuse logic and the traditional Multiobjective Analysis; the first one, it conserves its properties with imprecise information and of the second allows, the minimization of multiple objective correspond to the least environmental the physical, biological, cultural, economical and political dimensions of the environment uses the Geographic Information SIG this proposal is being constituted a complete tool for taking decisions in which space attributed is included. The FMA is a recent technique that is in development [S integration to GIS is stiller. The proposal is a contribution to the construction of a conceptual scheme for future applications in this aspects constitute a tool for the environmental planning which decreasing the risks, future cost analysis of natural resources and human group

  10. Vacuum structure revealed by over-improved stout-link smearing compared with the overlap analysis for quenched QCD

    International Nuclear Information System (INIS)

    Ilgenfritz, E.M.; Leinweber, D.; Moran, P.; Koller, K.; Weinberg, V.; Freie Univ. Berlin

    2008-01-01

    A detailed comparison is made between the topological structure of quenched QCD as revealed by the recently proposed over-improved stout-link smearing in conjunction with an improved gluonic definition of the topological density on one hand and a similar analysis made possible by the overlap-fermionic topological charge density both with and without variable ultraviolet cutoff λ cut . The matching is twofold, provided by fitting the density-density two-point functions on one hand and by a point-by-point fitting of the topological densities according to the two methods. We point out the similar cluster structure of the topological density for moderate smearing and 200 MeV cut <600 MeV, respectively. We demonstrate the relation of the gluonic topological density for extensive smearing to the location of the overlap zero modes and the lowest overlap non-zero mode as found for the unsmeared configurations. (orig.)

  11. Vacuum structure revealed by over-improved stout-link smearing compared with the overlap analysis for quenched QCD

    Energy Technology Data Exchange (ETDEWEB)

    Ilgenfritz, E.M.; Leinweber, D.; Moran, P. [Adelaide Univ., SA (AU). Special Research Centre for the Subatomic Structure of Matter (CSSM); Koller, K. [Muenchen Univ. (Germany). Sektion Physik; Schierholz, G. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Weinberg, V. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Freie Univ. Berlin (Germany). Inst. fuer Theoretische Physik

    2008-01-11

    A detailed comparison is made between the topological structure of quenched QCD as revealed by the recently proposed over-improved stout-link smearing in conjunction with an improved gluonic definition of the topological density on one hand and a similar analysis made possible by the overlap-fermionic topological charge density both with and without variable ultraviolet cutoff {lambda}{sub cut}. The matching is twofold, provided by fitting the density-density two-point functions on one hand and by a point-by-point fitting of the topological densities according to the two methods. We point out the similar cluster structure of the topological density for moderate smearing and 200 MeV<{lambda}{sub cut}<600 MeV, respectively. We demonstrate the relation of the gluonic topological density for extensive smearing to the location of the overlap zero modes and the lowest overlap non-zero mode as found for the unsmeared configurations. (orig.)

  12. Location, location, location: Extracting location value from house prices

    OpenAIRE

    Kolbe, Jens; Schulz, Rainer; Wersing, Martin; Werwatz, Axel

    2012-01-01

    The price for a single-family house depends both on the characteristics of the building and on its location. We propose a novel semiparametric method to extract location values from house prices. After splitting house prices into building and land components, location values are estimated with adaptive weight smoothing. The adaptive estimator requires neither strong smoothness assumptions nor local symmetry. We apply the method to house transactions from Berlin, Germany. The estimated surface...

  13. Analysis of Co-Located MODIS and CALIPSO Observations Near Clouds

    Science.gov (United States)

    Varnai, Tamas; Marshak, Alexander

    2011-01-01

    The purpose of this paper is to help researchers combine data from different satellites and thus gain new insights into two critical yet poorly understood aspects of anthropogenic climate change, aerosol-cloud interactions and aerosol radiative effects, For this, the paper explores whether cloud information from the Aqua satellite's MODIS instrument can help characterize systematic aerosol changes near clouds by refining earlier perceptions of these changes that were based on the CALIPSO satellite's CALIOP instrument. Similar to a radar but using visible and ncar-infrared light, CALIOP sends out laser pulses and provides aerosol and cloud information along a single line that tracks the satellite orbit by measuring the reflection of its pulses. In contrast, MODIS takes images of reflected sunlight and emitted infrared radiation at several wavelengths, and covers wide areas around the satellite track. This paper analyzes a year-long global dataset covering all ice-free oceans, and finds that MODIS can greatly help the interpretation of CALIOP observations, especially by detecting clouds that lie outside the line observed by CALlPSO. The paper also finds that complications such as differences in view direction or clouds drifting in the 72 seconds that elapse between MODIS and CALIOP observations have only a minor impact. The study also finds that MODIS data helps refine but does not qualitatively alter perceptions of the systematic aerosol changes that were detected in earlier studies using only CALIOP data. It then proposes a statistical approach to account for clouds lying outside the CALIOP track even when MODIS cannot as reliably detect low clouds, for example at night or over ice. Finally, the paper finds that, because of variations in cloud amount and type, the typical distance to clouds in maritime clear areas varies with season and location. The overall median distance to clouds in maritime clear areas around 4-5 km. The fact that half of all clear areas is

  14. Rail transportation corridor analysis report: Deaf Smith County location in the Palo Duro Basin, Texas

    International Nuclear Information System (INIS)

    1986-10-01

    An environmental data base was developed for the purpose of preliminary siting of potential rail access corridors between existing rail lines and the potential repository site in Deaf Smith County, Texas. The categories of the data base were environmental conditions considered significant in rail line construction and operation. These included land cover, population areas, slope, surface hydrology, cultivated prime agricultural lands, cultural features, and utility rights-of-way. The categories were divided into avoidance, constraint, and opportunity features, and the constraint features were then weighted for environmental impact potential. An environmental screening analysis using the computerized Geographical Information System (GIS) was then performed. The analysis involved applying the GIS overlay process to the various constraint data categories to produce a composite constraint map of the study area. The composite constraint map, color coded for various levels of constraint to corridor siting, was subsequently used as a guide for the selection of a series of alternative corridors. By means of a further application of GIS procedures, the corridor alternatives were statistically analyzed for adherence to corridor selection guidelines. In addition, a supplementary analysis was performed to compare the alternatives in terms of four impact categories: road crossings, construction costs, degree of land disruption, and population impact. The statistical and supplementary impact analyses led to a preliminary selection of a preferred corridor. The corridor assessment process indicated the importance of analyzing alternative trade-offs, as well as the need for more detailed investigation of certain conditions and a detailed comparison of alternatives prior to final corridor siting

  15. A comparative analysis of constitutive promoters located in adeno-associated viral vectors.

    Directory of Open Access Journals (Sweden)

    Lkhagvasuren Damdindorj

    Full Text Available The properties of constitutive promoters within adeno-associated viral (AAV vectors have not yet been fully characterized. In this study, AAV vectors, in which enhanced GFP expression was directed by one of the six constitutive promoters (human β-actin, human elongation factor-1α, chicken β-actin combined with cytomegalovirus early enhancer, cytomegalovirus (CMV, simian virus 40, and herpes simplex virus thymidine kinase, were constructed and introduced into the HCT116, DLD-1, HT-1080, and MCF-10A cell lines. Quantification of GFP signals in infected cells demonstrated that the CMV promoter produced the highest GFP expression in the six promoters and maintained relatively high GFP expression for up to eight weeks after infection of HCT116, DLD-1, and HT-1080. Exogenous human CDKN2A gene expression was also introduced into DLD-1 and MCF-10A in a similar pattern by using AAV vectors bearing the human β-actin and the CMV promoters. The six constitutive promoters were subsequently placed upstream of the neomycin resistance gene within AAV vectors, and HCT116, DLD-1, and HT-1080 were infected with the resulting vectors. Of the six promoters, the CMV promoter produced the largest number of G418-resistant colonies in all three cell lines. Because AAV vectors have been frequently used as a platform to construct targeting vectors that permit gene editing in human cell lines, we lastly infected the three cell lines with AAV-based targeting vectors against the human PIGA gene in which one of the six promoters regulate the neomycin resistance gene. This assay revealed that the CMV promoter led to the lowest PIGA gene targeting efficiency in the investigated promoters. These results provide a clue to the identification of constitutive promoters suitable to express exogenous genes with AAV vectors, as well as those helpful to conduct efficient gene targeting using AAV-based targeting vectors in human cell lines.

  16. Source location in plates based on the multiple sensors array method and wavelet analysis

    International Nuclear Information System (INIS)

    Yang, Hong Jun; Shin, Tae Jin; Lee, Sang Kwon

    2014-01-01

    A new method for impact source localization in a plate is proposed based on the multiple signal classification (MUSIC) and wavelet analysis. For source localization, the direction of arrival of the wave caused by an impact on a plate and the distance between impact position and sensor should be estimated. The direction of arrival can be estimated accurately using MUSIC method. The distance can be obtained by using the time delay of arrival and the group velocity of the Lamb wave in a plate. Time delay is experimentally estimated using the continuous wavelet transform for the wave. The elasto dynamic theory is used for the group velocity estimation.

  17. Source location in plates based on the multiple sensors array method and wavelet analysis

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hong Jun; Shin, Tae Jin; Lee, Sang Kwon [Inha University, Incheon (Korea, Republic of)

    2014-01-15

    A new method for impact source localization in a plate is proposed based on the multiple signal classification (MUSIC) and wavelet analysis. For source localization, the direction of arrival of the wave caused by an impact on a plate and the distance between impact position and sensor should be estimated. The direction of arrival can be estimated accurately using MUSIC method. The distance can be obtained by using the time delay of arrival and the group velocity of the Lamb wave in a plate. Time delay is experimentally estimated using the continuous wavelet transform for the wave. The elasto dynamic theory is used for the group velocity estimation.

  18. Analysis of Location Quotient index of poplar wood processing value chain in Iran

    OpenAIRE

    omid hosseinzadeh; Marzieh Hajjarian; Samira Porbar

    2016-01-01

    Value added in the poplar wood value chain has great economic effects for poplar farmers and have a fundamental role in sustainable supplying of required cellulosic materials of industries in long-term. The purpose of this study was to analyze the value chain of poplar and use the results to improve it. In order to determine the poplar value chain, Porter's value chain analysis framework was used. The statistical society consists of 76 experts to identify poplar wood value who were active in ...

  19. Visual Iconicity Across Sign Languages: Large-Scale Automated Video Analysis of Iconic Articulators and Locations

    Science.gov (United States)

    Östling, Robert; Börstell, Carl; Courtaux, Servane

    2018-01-01

    We use automatic processing of 120,000 sign videos in 31 different sign languages to show a cross-linguistic pattern for two types of iconic form–meaning relationships in the visual modality. First, we demonstrate that the degree of inherent plurality of concepts, based on individual ratings by non-signers, strongly correlates with the number of hands used in the sign forms encoding the same concepts across sign languages. Second, we show that certain concepts are iconically articulated around specific parts of the body, as predicted by the associational intuitions by non-signers. The implications of our results are both theoretical and methodological. With regard to theoretical implications, we corroborate previous research by demonstrating and quantifying, using a much larger material than previously available, the iconic nature of languages in the visual modality. As for the methodological implications, we show how automatic methods are, in fact, useful for performing large-scale analysis of sign language data, to a high level of accuracy, as indicated by our manual error analysis.

  20. RNA2 of grapevine fanleaf virus: sequence analysis and coat protein cistron location.

    Science.gov (United States)

    Serghini, M A; Fuchs, M; Pinck, M; Reinbolt, J; Walter, B; Pinck, L

    1990-07-01

    The nucleotide sequence of the genomic RNA2 (3774 nucleotides) of grapevine fanleaf virus strain F13 was determined from overlapping cDNA clones and its genetic organization was deduced. Two rapid and efficient methods were used for cDNA cloning of the 5' region of RNA2. The complete sequence contained only one long open reading frame of 3555 nucleotides (1184 codons, 131K product). The analysis of the N-terminal sequence of purified coat protein (CP) and identification of its C-terminal residue have allowed the CP cistron to be precisely positioned within the polyprotein. The CP produced by proteolytic cleavage at the Arg/Gly site between residues 680 and 681 contains 504 amino acids (Mr 56019) and has hydrophobic properties. The Arg/Gly cleavage site deduced by N-terminal amino acid sequence analysis is the first for a nepovirus coat protein and for plant viruses expressing their genomic RNAs by polyprotein synthesis. Comparison of GFLV RNA2 with M RNA of cowpea mosaic comovirus and with RNA2 of two closely related nepoviruses, tomato black ring virus and Hungarian grapevine chrome mosaic virus, showed strong similarities among the 3' non-coding regions but less similarity among the 5' end non-coding sequences than reported among other nepovirus RNAs.

  1. Content analysis to locate assistive technology in Queensland's motor injury insurance rehabilitation legislation and guidelines.

    Science.gov (United States)

    Steel, Emily J

    2018-06-08

    Reforms to Australia's disability and rehabilitation sectors have espoused the potential of assistive technology as an enabler. As new insurance systems are being developed it is timely to examine the structure of existing systems. This exploratory study examined the policies guiding assistive technology provision in the motor accident insurance sector of one Australian state. Policy documents were analyzed iteratively with set of qualitative questions to understand the intent and interpretation of policies guiding assistive technology provision. Content analysis identified relevant sections and meaningful terminology, and context analysis explored the dominant perspectives informing policy. The concepts and language of assistive technology are not part of the policy frameworks guiding rehabilitation practice in Queensland's motor accident insurance sector. The definition of rehabilitation in the legislation is consistent contemporary international interpretations that focus on optimizing functioning in interaction with the environment. However, the supporting documents are focused on recovery from injuries where decisions are guided by clinical need and affordability. The policies frame rehabilitation in a medical model that assistive technology provision from the rehabilitation plan. The legislative framework provides opportunities to develop and improve assistive technology provision as part of an integrated approach to rehabilitation.

  2. EXPLORATORY DATA ANALYSIS AND MULTIVARIATE STRATEGIES FOR REVEALING MULTIVARIATE STRUCTURES IN CLIMATE DATA

    Directory of Open Access Journals (Sweden)

    2016-12-01

    Full Text Available This paper is on data analysis strategy in a complex, multidimensional, and dynamic domain. The focus is on the use of data mining techniques to explore the importance of multivariate structures; using climate variables which influences climate change. Techniques involved in data mining exercise vary according to the data structures. The multivariate analysis strategy considered here involved choosing an appropriate tool to analyze a process. Factor analysis is introduced into data mining technique in order to reveal the influencing impacts of factors involved as well as solving for multicolinearity effect among the variables. The temporal nature and multidimensionality of the target variables is revealed in the model using multidimensional regression estimates. The strategy of integrating the method of several statistical techniques, using climate variables in Nigeria was employed. R2 of 0.518 was obtained from the ordinary least square regression analysis carried out and the test was not significant at 5% level of significance. However, factor analysis regression strategy gave a good fit with R2 of 0.811 and the test was significant at 5% level of significance. Based on this study, model building should go beyond the usual confirmatory data analysis (CDA, rather it should be complemented with exploratory data analysis (EDA in order to achieve a desired result.

  3. A study and analysis of recommendation systems for location-based social network (LBSN with big data

    Directory of Open Access Journals (Sweden)

    Murale Narayanan

    2016-03-01

    Full Text Available Recommender systems play an important role in our day-to-day life. A recommender system automatically suggests an item to a user that he/she might be interested in. Small-scale datasets are used to provide recommendations based on location, but in real time, the volume of data is large. We have selected Foursquare dataset to study the need for big data in recommendation systems for location-based social network (LBSN. A few quality parameters like parallel processing and multimodal interface have been selected to study the need for big data in recommender systems. This paper provides a study and analysis of quality parameters of recommendation systems for LBSN with big data.

  4. The Smartphone-Based Offline Indoor Location Competition at IPIN 2016: Analysis and Future Work

    Directory of Open Access Journals (Sweden)

    Joaquín Torres-Sospedra

    2017-03-01

    Full Text Available This paper presents the analysis and discussion of the off-site localization competition track, which took place during the Seventh International Conference on Indoor Positioning and Indoor Navigation (IPIN 2016. Five international teams proposed different strategies for smartphone-based indoor positioning using the same reference data. The competitors were provided with several smartphone-collected signal datasets, some of which were used for training (known trajectories, and others for evaluating (unknown trajectories. The competition permits a coherent evaluation method of the competitors’ estimations, where inside information to fine-tune their systems is not offered, and thus provides, in our opinion, a good starting point to introduce a fair comparison between the smartphone-based systems found in the literature. The methodology, experience, feedback from competitors and future working lines are described.

  5. Analysis of peptide uptake and location of root hair-promoting peptide accumulation in plant roots.

    Science.gov (United States)

    Matsumiya, Yoshiki; Taniguchi, Rikiya; Kubo, Motoki

    2012-03-01

    Peptide uptake by plant roots from degraded soybean-meal products was analyzed in Brassica rapa and Solanum lycopersicum. B. rapa absorbed about 40% of the initial water volume, whereas peptide concentration was decreased by 75% after 24 h. Analysis by reversed-phase HPLC showed that number of peptides was absorbed by the roots during soaking in degraded soybean-meal products for 24 h. Carboxyfluorescein-labeled root hair-promoting peptide was synthesized, and its localization, movement, and accumulation in roots were investigated. The peptide appeared to be absorbed by root hairs and then moved to trichoblasts. Furthermore, the peptide was moved from trichoblasts to atrichoblasts after 24 h. The peptide was accumulated in epidermal cells, suggesting that the peptide may have a function in both trichoblasts and atrichoblasts. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.

  6. Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

    Science.gov (United States)

    Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

    2012-01-01

    Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

  7. Stability of GNSS Monumentation: Analysis of Co-Located Monuments in the UNAVCO Plate Boundary Observatory

    Science.gov (United States)

    Blume, F.; Herring, T.; Mattioli, G. S.; Feaux, K.; Walls, C. P.; Austin, K. E.; Dittmann, S. T.

    2017-12-01

    Geodetic-quality permanent GNSS stations have used a number of different monument styles for the purpose of ensuring that the motions of the GNSS antenna reflect those of the Earth's crust while minimizing non-tectonic motions near the surface. Monuments range from simple masts mounted on buildings or drilled into bedrock, costing a few hundred dollars to machine-drilled-braced monuments in soil costing tens of thousands. The stability of an individual monument will depend on its design, the construction techniques used to install it, and the local surface geology where it is installed. Previous studies have separately investigated pairs of identical monuments at a single site, monument type performance using global statistical analysis, and multiple monument styles at a single site, yet the stability of different monument types in similar geologic conditions has not been adequately determined. To better characterize the stability of various monument styles in diverse geologic conditions UNAVCO constructed two additional monuments at five existing PBO stations in 2013. Deep drilled-braced, short drilled-braced, and single mast type monuments were installed at sites with bedrock at the surface; deep drilled-braced, short driven-braced and pillar type monuments were installed at sites with alluvium or soil at the surface. The sites include a variety of geographic, hydrologic, and geologic conditions. Data collected from the PBO Multi-Monument Experiment have been analyzed using a variety of methods. Each site is characterized using quality-control parameters such as multipath, signal-to-noise and previously determined seasonal variations. High-precision processing by PBO Analysis Centers with GAMIT and GIPSY use regional and global schemes and yield time-series with millimeter-level that determine noise content, overall site stability relative to other PBO sites and differential motions between the individual monuments. Sub-millimeter results from single

  8. Quality analysis of effluents from biodigesters in lodges located in the Cuyabeno Wildlife Reserve

    Directory of Open Access Journals (Sweden)

    Isidro Gutiérrez Cruz

    2016-09-01

    Full Text Available In the Cuyabeno Wildlife Reserve near Laguna Grande and Cuyabeno river, several ecological hotels have been built to meet the touristic demand; therefore these eco-lodges generate wastewaters. The Ministry of Environment, responsible for biodiversity conservation, has ordered the implementation of biodigesters for the treatment of these waters. After three years of implementing the system, it is proposed to check the quality of these waters, through the analysis of physical-chemical parameters: temperature, conductivity, pH, sulfates, nitrates and nitrites, detergents, COD, BOD5, oils and fats; and microbiological such as faecal coliforms. These results were compared with the current environmental legislation: TULSMA "Limits discharged to a body of fresh water." Sampling was subject to the provisions of standard Regulation INEN 2 169: 2013 and sampled at the time of high and low rainfall. The results determined that biodigesters only meet the standard regulations in three parameters: nitrates and nitrites; sulfates and temperature; and violate the following regulations: BOD5, COD and pH; while in the remaining four parameters, there is a variation among the results. In conclusion all digesters violate the regulations, at least on one of the parameters.

  9. GPR image analysis to locate water leaks from buried pipes by applying variance filters

    Science.gov (United States)

    Ocaña-Levario, Silvia J.; Carreño-Alvarado, Elizabeth P.; Ayala-Cabrera, David; Izquierdo, Joaquín

    2018-05-01

    Nowadays, there is growing interest in controlling and reducing the amount of water lost through leakage in water supply systems (WSSs). Leakage is, in fact, one of the biggest problems faced by the managers of these utilities. This work addresses the problem of leakage in WSSs by using GPR (Ground Penetrating Radar) as a non-destructive method. The main objective is to identify and extract features from GPR images such as leaks and components in a controlled laboratory condition by a methodology based on second order statistical parameters and, using the obtained features, to create 3D models that allows quick visualization of components and leaks in WSSs from GPR image analysis and subsequent interpretation. This methodology has been used before in other fields and provided promising results. The results obtained with the proposed methodology are presented, analyzed, interpreted and compared with the results obtained by using a well-established multi-agent based methodology. These results show that the variance filter is capable of highlighting the characteristics of components and anomalies, in an intuitive manner, which can be identified by non-highly qualified personnel, using the 3D models we develop. This research intends to pave the way towards future intelligent detection systems that enable the automatic detection of leaks in WSSs.

  10. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2013-01-01

    Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

  11. Ferricyanide-based analysis of aqueous lignin suspension revealed sequestration of water-soluble lignin moieties

    OpenAIRE

    Joshua, CJ; Simmons, BA; Singer, SW

    2016-01-01

    © 2016 The Royal Society of Chemistry. This study describes the application of a ferricyanide-based assay as a simple and inexpensive assay for rapid analysis of aqueous lignin samples. The assay measures the formation of Prussian blue from the redox reaction between a mixture of potassium ferricyanide and ferric chloride, and phenolic hydroxyl groups of lignin or lignin-derived phenolic moieties. This study revealed that soluble lignin moieties exhibited stronger ferricyanide reactivity than...

  12. Effect of spark plug and fuel injector location on mixture stratification in a GDI engine - A CFD analysis

    Science.gov (United States)

    Saw, O. P.; Mallikarjuna, J. M.

    2017-09-01

    The mixture preparation in gasoline direct injection (GDI) engines operating at stratified condition plays an important role in deciding the combustion, performance and emission characteristics of the engine. In a wall-guided GDI engine, with a late fuel injection strategy, piston top surface is designed in such a way that the injected fuel is directed towards the spark plug to form a combustible mixture at the time of ignition. In addition, in these engines, location of spark-plug and fuel injector, fuel injection pressure and timing are also important to create a combustible mixture near the spark plug. Therefore, understanding the mixture formation under the influence of the location of spark plug and fuel injector is very essential for the optimization of the engine parameters. In this study, an attempt is made to understand the effect of spark plug and fuel injector location on the mixture preparation in a four-stroke, four-valve and wall-guided GDI engine operating under a stratified condition by using computational fluid dynamics (CFD) analysis. All the CFD simulations are carried out at an engine speed of 2000 rev/min., and compression ratio of 10.6, at an overall equivalence ratio (ER) of about 0.65. The fuel injection and spark timings are maintained at 605 and 710 CADs respectively. Finally, it is concluded that, combination of central spark plug and side fuel injector results in better combustion and performance.

  13. Numerical analysis of flow in a centrifugal compressor with circumferential grooves: influence of groove location and number on flow instability

    Science.gov (United States)

    Chen, X.; Qin, G.; Ai, Z.; Ji, Y.

    2017-08-01

    As an effective and economic method for flow range enhancement, circumferential groove casing treatment (CGCT) is widely used to increase the stall margin of compressors. Different from traditional grooved casing treatments, in which the grooves are always located over the rotor in both axial and radial compressors, one or several circumferential grooves are located along the shroud side of the diffuser passage in this paper. Numerical investigations were conducted to predict the performance of a low flow rate centrifugal compressor with CGCT in diffuser. Computational fluid dynamics (CFD) analysis is performed under stage environment in order to find the optimum location of the circumferential casing groove in consideration of stall margin enhancement and efficiency gain at design point, and the impact of groove number to the effect of this grooved casing treatment configuration in enhancing the stall margin of the compressor stage is studied. The results indicate that the centrifugal compressor with circumferential groove in vaned diffuser can obtain obvious improvement in the stall margin with sacrificing design efficiency a little. Efforts were made to study blade level flow mechanisms to determine how the CGCT impacts the compressor’s stall margin (SM) and performance. The flow structures in the passage, the tip gap, and the grooves as well as their mutual interactions were plotted and analysed.

  14. Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.

    Directory of Open Access Journals (Sweden)

    Oleg M Ganichkin

    Full Text Available Selenocysteine tRNAs (tRNA(Sec exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec-interacting factors are incompletely understood.We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec. tRNA(Sec lacking the single-stranded 3'-acceptor end ((ΔGCCARNA(Sec yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCARNA(Sec resembles the structure of human tRNA(Sec determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Secin vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec.We provide the most highly resolved structure of a tRNA(Sec molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec support its interaction with proteins.

  15. Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

    Science.gov (United States)

    Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

    2018-05-01

    The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

  16. Library Locations

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Carnegie Library of Pittsburgh locations including address, coordinates, phone number, square footage, and standard operating hours. The map below does not display...

  17. Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding

    Directory of Open Access Journals (Sweden)

    Brewster Aaron S

    2010-08-01

    Full Text Available Abstract Background The mini-chromosome maintenance protein (MCM complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. While the eukaryotic complex consists of six homologous proteins (MCM2-7, the archaeon Sulfolobus solfataricus has only one MCM protein (ssoMCM, six subunits of which form a homohexamer. We have recently reported a 4.35Å crystal structure of the near full-length ssoMCM. The structure reveals a total of four β-hairpins per subunit, three of which are located within the main channel or side channels of the ssoMCM hexamer model generated based on the symmetry of the N-terminal Methanothermobacter thermautotrophicus (mtMCM structure. The fourth β-hairpin, however, is located on the exterior of the hexamer, near the exit of the putative side channels and next to the ATP binding pocket. Results In order to better understand this hairpin's role in DNA binding and helicase activity, we performed a detailed mutational and biochemical analysis of nine residues on this exterior β-hairpin (EXT-hp. We examined the activities of the mutants related to their helicase function, including hexamerization, ATPase, DNA binding and helicase activities. The assays showed that some of the residues on this EXT-hp play a role for DNA binding as well as for helicase activity. Conclusions These results implicate several current theories regarding helicase activity by this critical hexameric enzyme. As the data suggest that EXT-hp is involved in DNA binding, the results reported here imply that the EXT-hp located near the exterior exit of the side channels may play a role in contacting DNA substrate in a manner that affects DNA unwinding.

  18. Analysis of lightning fault detection, location and protection on short and long transmission lines using Real Time Digital Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Andre Luiz Pereira de [Siemens Ltda., Sao Paulo, SP (Brazil)], E-mail: andreluiz.oliveira@siemens.com

    2007-07-01

    The purpose of this paper is to present an analysis of lightning fault detection, location and protection using numeric distance relays applied in high voltage transmission lines, more specifically in the 500 kV transmission lines of CEMIG (Brazilian Energy Utility) between the Vespasiano 2 - Neves 1 (short line - 23.9 km) and Vespasiano 2 - Mesquita (long line - 148.6 km) substations. The analysis was based on the simulations results of numeric distance protective relays on power transmission lines, realized in September 02 to 06, 2002, at Siemens AG's facilities (Erlangen - Germany), using Real Time Digital Simulator (RTDS{sup TM}). Several lightning faults simulations were accomplished, in several conditions of the electrical power system where the protective relays would be installed. The results are presented not only with the times of lightning faults elimination, but also all the functionality of a protection system, including the correct detection, location and other advantages that these modern protection devices make possible to the power system. (author)

  19. Location Study of Solar Thermal Power Plant in the State of Pernambuco Using Geoprocessing Technologies and Multiple-Criteria Analysis

    Directory of Open Access Journals (Sweden)

    Verônica Wilma B. Azevêdo

    2017-07-01

    Full Text Available Solar Thermal Technology for the generation of electricity in large scale has been a reality in the world since the 1980s, when the first large-sized solar plants in the United States were introduced. Brazil presents great potential for the development of large-scale projects, although it is noted that the main barriers for the insertion of this technology in Brazilian market are the lack of incentives and goals and associated costs. In a way to contribute to the insertion of solar thermal technology in Brazil, this paper presents a macro-spatial approach, based on the use of Multiple-Criteria Decision Analysis and Geoprocessing, for the location of solar thermal power plants. The applied methodology for Pernambuco, located in the Northeast Region of Brazil, considered the implantation of parabolic trough solar power plant of 80 MW, operating only in solar mode, without heat storage. Based on performed analysis, it was confirmed that Pernambuco presents great potential for the installation of solar power plants, especially in the backlands of Pernambuco. Performed validations in the model demonstrate that the methodology attended the objective once the consistence between the assigned weights to the thematic layers, individually, and the final Map of site suitability were evidenced.

  20. Data-Independent Acquisition-Based Quantitative Proteomic Analysis Reveals Potential Biomarkers of Kidney Cancer.

    Science.gov (United States)

    Song, Yimeng; Zhong, Lijun; Zhou, Juntuo; Lu, Min; Xing, Tianying; Ma, Lulin; Shen, Jing

    2017-12-01

    Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition. In this study, a DIA workflow is constructed on a quadrupole-Orbitrap LC-MS platform to reveal dysregulated proteins between ccRCC and adjacent normal tissues. More than 4000 proteins are identified, 436 of these proteins are dysregulated in ccRCC tissues. Bioinformatic analysis reveals that multiple pathways and Gene Ontology items are strongly associated with ccRCC. The expression levels of L-lactate dehydrogenase A chain, annexin A4, nicotinamide N-methyltransferase, and perilipin-2 examined through RT-qPCR, Western blot, and immunohistochemistry confirm the validity of the proteomic analysis results. The proposed DIA workflow yields optimum time efficiency and data reliability and provides a good choice for proteomic analysis in biological and clinical studies, and these dysregulated proteins might be potential biomarkers for ccRCC diagnosis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Recent adaptive events in human brain revealed by meta-analysis of positively selected genes.

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    Yue Huang

    Full Text Available BACKGROUND AND OBJECTIVES: Analysis of positively-selected genes can help us understand how human evolved, especially the evolution of highly developed cognitive functions. However, previous works have reached conflicting conclusions regarding whether human neuronal genes are over-represented among genes under positive selection. METHODS AND RESULTS: We divided positively-selected genes into four groups according to the identification approaches, compiling a comprehensive list from 27 previous studies. We showed that genes that are highly expressed in the central nervous system are enriched in recent positive selection events in human history identified by intra-species genomic scan, especially in brain regions related to cognitive functions. This pattern holds when different datasets, parameters and analysis pipelines were used. Functional category enrichment analysis supported these findings, showing that synapse-related functions are enriched in genes under recent positive selection. In contrast, immune-related functions, for instance, are enriched in genes under ancient positive selection revealed by inter-species coding region comparison. We further demonstrated that most of these patterns still hold even after controlling for genomic characteristics that might bias genome-wide identification of positively-selected genes including gene length, gene density, GC composition, and intensity of negative selection. CONCLUSION: Our rigorous analysis resolved previous conflicting conclusions and revealed recent adaptation of human brain functions.

  2. Transcriptomic analysis of human retinal detachment reveals both inflammatory response and photoreceptor death.

    Directory of Open Access Journals (Sweden)

    Marie-Noëlle Delyfer

    Full Text Available BACKGROUND: Retinal detachment often leads to a severe and permanent loss of vision and its therapeutic management remains to this day exclusively surgical. We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment in order to identify new potential pharmacological targets that could be used in combination with surgery to further improve final outcome. METHODOLOGY/PRINCIPAL FINDINGS: Statistical analysis reveals major involvement of the immune response in the disease. Interestingly, using a novel approach relying on coordinated expression, the interindividual variation was monitored to unravel a second crucial aspect of the pathological process: the death of photoreceptor cells. Within the genes identified, the expression of the major histocompatibility complex I gene HLA-C enables diagnosis of the disease, while PKD2L1 and SLCO4A1 -which are both down-regulated- act synergistically to provide an estimate of the duration of the retinal detachment process. Our analysis thus reveals the two complementary cellular and molecular aspects linked to retinal detachment: an immune response and the degeneration of photoreceptor cells. We also reveal that the human specimens have a higher clinical value as compared to artificial models that point to IL6 and oxidative stress, not implicated in the surgical specimens studied here. CONCLUSIONS/SIGNIFICANCE: This systematic analysis confirmed the occurrence of both neurodegeneration and inflammation during retinal detachment, and further identifies precisely the modification of expression of the different genes implicated in these two phenomena. Our data henceforth give a new insight into the disease process and provide a rationale for therapeutic strategies aimed at limiting inflammation and photoreceptor damage associated with retinal detachment and, in turn, improving visual prognosis after retinal surgery.

  3. Spatial analysis related to the location characteristics of park supply. Case study: Music Park and Pendawa Park, Bandung City, Indonesia

    Science.gov (United States)

    Malik, A.; Akbar, R.; Maryati, S.; Natalivan, P.

    2018-05-01

    will use a descriptive methodology, by first explaining the policy of public space provision, the existence of the reality of public space, its function and role, the park as public space, the time of visiting the park by the community, and the various problems that occur in it. This research will look at the characteristics of neighborhood parks based on the aspect of the location of park supply and the spatial policies of Bandung City. The analysis comprised ArcGIS (Geographic Information System) and direct observations to evaluate the locational characteristics of the area around the park by using the case study of Music Park and Pendawa Park.

  4. 3D MRI for Quantitative Analysis of Quadrant Percent Breast Density: Correlation with Quadrant Location of Breast Cancer.

    Science.gov (United States)

    Chen, Jeon-Hor; Liao, Fuyi; Zhang, Yang; Li, Yifan; Chang, Chia-Ju; Chou, Chen-Pin; Yang, Tsung-Lung; Su, Min-Ying

    2017-07-01

    Breast cancer occurs more frequently in the upper outer (UO) quadrant, but whether this higher cancer incidence is related to the greater amount of dense tissue is not known. Magnetic resonance imaging acquires three-dimensional volumetric images and is the most suitable among all breast imaging modalities for regional quantification of density. This study applied a magnetic resonance imaging-based method to measure quadrant percent density (QPD), and evaluated its association with the quadrant location of the developed breast cancer. A total of 126 cases with pathologically confirmed breast cancer were reviewed. Only women who had unilateral breast cancer located in a clear quadrant were selected for analysis. A total of 84 women, including 47 Asian women and 37 western women, were included. An established computer-aided method was used to segment the diseased breast and the contralateral normal breast, and to separate the dense and fatty tissues. Then, a breast was further separated into four quadrants using the nipple and the centroid as anatomic landmarks. The tumor was segmented using a computer-aided method to determine its quadrant location. The distribution of cancer quadrant location, the quadrant with the highest QPD, and the proportion of cancers occurring in the highest QPD were analyzed. The highest incidence of cancer occurred in the UO quadrant (36 out of 84, 42.9%). The highest QPD was also noted most frequently in the UO quadrant (31 out of 84, 36.9%). When correlating the highest QPD with the quadrant location of breast cancer, only 17 women out of 84 (20.2%) had breast cancer occurring in the quadrant with the highest QPD. The results showed that the development of breast cancer in a specific quadrant could not be explained by the density in that quadrant, and further studies are needed to find the biological reasons accounting for the higher breast cancer incidence in the UO quadrant. Copyright © 2017 The Association of University Radiologists

  5. Integrated network analysis reveals potentially novel molecular mechanisms and therapeutic targets of refractory epilepsies.

    Directory of Open Access Journals (Sweden)

    Hongwei Chu

    Full Text Available Epilepsy is a complex neurological disorder and a significant health problem. The pathogenesis of epilepsy remains obscure in a significant number of patients and the current treatment options are not adequate in about a third of individuals which were known as refractory epilepsies (RE. Network medicine provides an effective approach for studying the molecular mechanisms underlying complex diseases. Here we integrated 1876 disease-gene associations of RE and located those genes to human protein-protein interaction (PPI network to obtain 42 significant RE-associated disease modules. The functional analysis of these disease modules showed novel molecular pathological mechanisms of RE, such as the novel enriched pathways (e.g., "presynaptic nicotinic acetylcholine receptors", "signaling by insulin receptor". Further analysis on the relationships between current drug targets and the RE-related disease genes showed the rational mechanisms of most antiepileptic drugs. In addition, we detected ten potential novel drug targets (e.g., KCNA1, KCNA4-6, KCNC3, KCND2, KCNMA1, CAMK2G, CACNB4 and GRM1 located in three RE related disease modules, which might provide novel insights into the new drug discovery for RE therapy.

  6. Network analysis of oyster transcriptome revealed a cascade of cellular responses during recovery after heat shock.

    Directory of Open Access Journals (Sweden)

    Lingling Zhang

    Full Text Available Oysters, as a major group of marine bivalves, can tolerate a wide range of natural and anthropogenic stressors including heat stress. Recent studies have shown that oysters pretreated with heat shock can result in induced heat tolerance. A systematic study of cellular recovery from heat shock may provide insights into the mechanism of acquired thermal tolerance. In this study, we performed the first network analysis of oyster transcriptome by reanalyzing microarray data from a previous study. Network analysis revealed a cascade of cellular responses during oyster recovery after heat shock and identified responsive gene modules and key genes. Our study demonstrates the power of network analysis in a non-model organism with poor gene annotations, which can lead to new discoveries that go beyond the focus on individual genes.

  7. The Revealed Competitiveness of Major Ports in the East Asian Region: An Additive Market Share Analysis

    Directory of Open Access Journals (Sweden)

    Tae Seung Kim

    2015-12-01

    Full Text Available In the single cargo market, the ordinary market share analysis method has been the representative tool for revealed competitiveness analysis. This paper develops and employs an applied market share index called the additive market share (AMS. Data are collected from 15 major container ports for the 1998-2013 period. In comparison to the results of an ordinary market share analysis, the highest AMS is observed for the Bohai Rim port cluster from 2008, not for the Yangtze River cluster or the Pearl River cluster. There are substitutable relationships between Yangtze River and non-Chinese ports and between Pearl River and Bohai Rim ports from 2001. Finally, there is an internal competition at Pearl River and Yangtze River ports, whereas Bohai Rim and non-Chinese ports show internally complementary relationships.

  8. Revealed preferences towards the appraisal of orphan drugs in Poland - multi criteria decision analysis.

    Science.gov (United States)

    Kolasa, Katarzyna; Zwolinski, Krzysztof Miroslaw; Zah, Vladimir; Kaló, Zoltán; Lewandowski, Tadeusz

    2018-04-27

    A Multi Criteria Decision Analysis (MCDA) technique was adopted to reveal the preferences of the Appraisal Body of the Polish HTA agency towards orphan drugs (OMPs). There were 34 positive and 23 negative HTA recommendations out of 54 distinctive drug-indication pairs. The MCDA matrix consisted of 13 criteria, seven of which made the most impact on the HTA process. Appraisal of clinical evidence, cost of therapy, and safety considerations were the main contributors to the HTA guidance, whilst advancement of technology and manufacturing costs made the least impact. MCDA can be regarded as a valuable tool for revealing decision makers' preferences in the healthcare sector. Given that only roughly half of all criteria included in the MCDA matrix were deemed to make an impact on the HTA process, there is certainly some room for improvement with respect to the adaptation of a new approach towards the value assessment of OMPs in Poland.

  9. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells

    DEFF Research Database (Denmark)

    Larsen, Sara C; Sylvestersen, Kathrine B; Mund, Andreas

    2016-01-01

    to the frequency of somatic mutations at arginine methylation sites throughout the proteome, we observed that somatic mutations were common at arginine methylation sites in proteins involved in mRNA splicing. Furthermore, in HeLa and U2OS cells, we found that distinct arginine methyltransferases differentially...... kidney 293 cells, indicating that the occurrence of this modification is comparable to phosphorylation and ubiquitylation. A site-level conservation analysis revealed that arginine methylation sites are less evolutionarily conserved compared to arginines that were not identified as modified...... as coactivator-associated arginine methyltransferase 1 (CARM1)] or PRMT1 increased the RNA binding function of HNRNPUL1. High-content single-cell imaging additionally revealed that knocking down CARM1 promoted the nuclear accumulation of SRSF2, independent of cell cycle phase. Collectively, the presented human...

  10. Computerized analysis of mammographic parenchymal patterns for assessing breast cancer risk: Effect of ROI size and location

    International Nuclear Information System (INIS)

    Li Hui; Giger, Maryellen L.; Huo Zhimin; Olopade, Olufunmilayo I.; Lan Li; Weber, Barbara L.; Bonta, Ioana

    2004-01-01

    The long-term goal of our research is to develop computerized radiographic markers for assessing breast density and parenchymal patterns that may be used together with clinical measures for determining the risk of breast cancer and assessing the response to preventive treatment. In our earlier studies, we found that women at high risk tended to have dense breasts with mammographic patterns that were coarse and low in contrast. With our method, computerized texture analysis is performed on a region of interest (ROI) within the mammographic image. In our current study, we investigate the effect of ROI size and ROI location on the computerized texture features obtained from 90 subjects (30 BRCA1/BRCA2 gene-mutation carriers and 60 age-matched women deemed to be at low risk for breast cancer). Mammograms were digitized at 0.1 mm pixel size and various ROI sizes were extracted from different breast regions in the craniocaudal (CC) view. Seventeen features, which characterize the density and texture of the parenchymal patterns, were extracted from the ROIs on these digitized mammograms. Stepwise feature selection and linear discriminant analysis were applied to identify features that differentiate between the low-risk women and the BRCA1/BRCA2 gene-mutation carriers. ROC analysis was used to assess the performance of the features in the task of distinguishing between these two groups. Our results show that there was a statistically significant decrease in the performance of the computerized texture features, as the ROI location was varied from the central region behind the nipple. However, we failed to show a statistically significant decrease in the performance of the computerized texture features with decreasing ROI size for the range studied

  11. Analysis of foundation type alternative and deep-excavation on candidate site location of Panjang Island, Serang

    International Nuclear Information System (INIS)

    Heri Syaeful; June Mellawati

    2013-01-01

    Panjang Island is one of the alternatives location which is being studied as NPP site candidate. Its soil surface dominated by sand and eggshell deposit to the depth of tens of meter, beside that also the interlayer of sand and clay to the depth of 120 m. Purpose of the research is to analyze the alternative of foundation type and simulation of deep-excavation during foundation construction especially related to the slope stability aspect. The methods includes data collection of the analysis result of soil/rock mechanical laboratory, measurement of shear wave velocity by PS logging method, and analysis of alternative foundation type and deep-excavation. The analysis result of foundation type that can be applied on Panjang Island candidate site is combination of raft and pile foundation. Rock with Vs > 400 m/s in depth of 44 meter could be made as base of raft foundation construction. In the bottom it connected to pile foundation which is constructed to base rock in the depth of 120 m in Vs > 900 m/s. The result of slope stability analysis on deep-excavation with slope height of 44 m, vertical angle, on normal condition yield safety factor of 0,184 and on the condition of seismic load 0,138. Simulation of anchor installation with spacing 1.25 m as much as 15 pieces yield safety factor higher than 1.0 m. (author)

  12. Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

    Science.gov (United States)

    Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I

    2014-02-01

    While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  13. Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

    Science.gov (United States)

    Alvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

  14. Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

    Science.gov (United States)

    Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

  15. High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Yu, E-mail: yuzhang@xmu.edu.c [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Shao Jun [Shanghai EENT Hospital of Fudan University, Shanghai (China); Krausert, Christopher R. [Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States); Zhang Sai [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Jiang, Jack J. [Shanghai EENT Hospital of Fudan University, Shanghai (China); Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States)

    2011-01-15

    Research highlights: Low-dimensional human glottal area data. Evidence of chaos in human laryngeal activity from high-speed digital imaging. Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic analysis is capable of

  16. High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

    International Nuclear Information System (INIS)

    Zhang Yu; Shao Jun; Krausert, Christopher R.; Zhang Sai; Jiang, Jack J.

    2011-01-01

    Research highlights: → Low-dimensional human glottal area data. → Evidence of chaos in human laryngeal activity from high-speed digital imaging. → Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. → Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic

  17. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2014-01-01

    Abstract The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused. Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed

  18. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

    DEFF Research Database (Denmark)

    Hoadley, Katherine A; Yau, Christina; Wolf, Denise M

    2014-01-01

    Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform...... on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset...

  19. Re-Analysis of Metagenomic Sequences from Acute Flaccidmyelitis Patients Reveals Alternatives to Enterovirus D68 Infection

    Science.gov (United States)

    2015-07-13

    caused in some cases by infection with enterovirus D68. We found that among the patients whose symptoms were previously attributed to enterovirus D68...distribution is unlimited. Re-analysis of metagenomic sequences from acute flaccidmyelitis patients reveals alternatives to enterovirus D68...Street Baltimore, MD 21218 -2685 ABSTRACT Re-analysis of metagenomic sequences from acute flaccidmyelitis patients reveals alternatives to enterovirus

  20. Genetic architecture and temporal patterns of biomass accumulation in spring barley revealed by image analysis.

    Science.gov (United States)

    Neumann, Kerstin; Zhao, Yusheng; Chu, Jianting; Keilwagen, Jens; Reif, Jochen C; Kilian, Benjamin; Graner, Andreas

    2017-08-10

    Genetic mapping of phenotypic traits generally focuses on a single time point, but biomass accumulates continuously during plant development. Resolution of the temporal dynamics that affect biomass recently became feasible using non-destructive imaging. With the aim to identify key genetic factors for vegetative biomass formation from the seedling stage to flowering, we explored growth over time in a diverse collection of two-rowed spring barley accessions. High heritabilities facilitated the temporal analysis of trait relationships and identification of quantitative trait loci (QTL). Biomass QTL tended to persist only a short period during early growth. More persistent QTL were detected around the booting stage. We identified seven major biomass QTL, which together explain 55% of the genetic variance at the seedling stage, and 43% at the booting stage. Three biomass QTL co-located with genes or QTL involved in phenology. The most important locus for biomass was independent from phenology and is located on chromosome 7HL at 141 cM. This locus explained ~20% of the genetic variance, was significant over a long period of time and co-located with HvDIM, a gene involved in brassinosteroid synthesis. Biomass is a dynamic trait and is therefore orchestrated by different QTL during early and late growth stages. Marker-assisted selection for high biomass at booting stage is most effective by also including favorable alleles from seedling biomass QTL. Selection for dynamic QTL may enhance genetic gain for complex traits such as biomass or, in the future, even grain yield.

  1. Postural and ergonomic analysis: study of productive activities on a Dairy Cooperative located in the city of Itaperuna - RJ

    Directory of Open Access Journals (Sweden)

    Jéssyca Barrozo de Souza Castilho

    2016-09-01

    Full Text Available This Final Paper proposes an ergonomic and postural analysis of a dairy cooperative located in the city of Itaperuna. Within this scope, the main goal of this study was to analyze the existing ergonomic situation at the cooperative under study. The research method consisted, firstly, of data collection at the company via questionnaires, interviews, photographic records and videos. Later, taking into consideration the data obtained, the OWAS and RULA methods were applied in order to generate a correlation between the movements and positions taken during working hours and the symptoms reported by workers in the proposed questionnaires. Analyzing the questionnaire responses, it was found that 82.1% of employees can be classified as suffering severe fatigue. The tools used for postural assessment, OWAS and RULA, reported the need for corrections in performing some tasks. Thus, measures are proposed in order to reduce the incidence of employee health disorders and, consequently, to increase the organization’s profitability.

  2. Iron site location in Fe-diffused lithium niobate crystals by combined RBS-PIXE-NRA analysis

    Energy Technology Data Exchange (ETDEWEB)

    Zaltron, A. [University of Padova and CNISM, Via Marzolo 8, 35131 Padova (Italy); Argiolas, N., E-mail: nicola.argiolas@unipd.it [University of Padova and CNISM, Via Marzolo 8, 35131 Padova (Italy); Laboratori Nazionali di Legnaro, Istituto Nazionale Fisica Nucleare, Viale dell' Universita 2, 35020 Legnaro (Padova) (Italy); De Salvador, D.; Bazzan, M. [University of Padova and CNISM, Via Marzolo 8, 35131 Padova (Italy); Laboratori Nazionali di Legnaro, Istituto Nazionale Fisica Nucleare, Viale dell' Universita 2, 35020 Legnaro (Padova) (Italy); Ciampolillo, M.V.; Bacci, L.; Sada, C. [University of Padova and CNISM, Via Marzolo 8, 35131 Padova (Italy)

    2012-03-15

    Iron diffused x-cut lithium niobate samples have been studied from a structural point of view by ion beam analysis techniques in channeling conditions. The aim of this work is to determine the most probable position of iron atoms after high temperature diffusion treatment in pure oxygen atmosphere and to verify their location after an additional full reducing annealing at low temperature. The results are compared with the bulk doping case that can be considered the final equilibrium state of the diffusion process. By comparing the iron signal with niobium and lithium counterparts in angular scans along proper crystallographic directions, we demonstrate that iron occupies in any case the lithium site or a very close position regardless of the reduction degree, just as in the case of bulk doped samples.

  3. Stable carbon isotope analysis reveals widespread drought stress in boreal black spruce forests.

    Science.gov (United States)

    Walker, Xanthe J; Mack, Michelle C; Johnstone, Jill F

    2015-08-01

    Unprecedented rates of climate warming over the past century have resulted in increased forest stress and mortality worldwide. Decreased tree growth in association with increasing temperatures is generally accepted as a signal of temperature-induced drought stress. However, variations in tree growth alone do not reveal the physiological mechanisms behind recent changes in tree growth. Examining stable carbon isotope composition of tree rings in addition to tree growth can provide a secondary line of evidence for physiological drought stress. In this study, we examined patterns of black spruce growth and carbon isotopic composition in tree rings in response to climate warming and drying in the boreal forest of interior Alaska. We examined trees at three nested scales: landscape, toposequence, and a subsample of trees within the toposequence. At each scale, we studied the potential effects of differences in microclimate and moisture availability by sampling on northern and southern aspects. We found that black spruce radial growth responded negatively to monthly metrics of temperature at all examined scales, and we examined ∆(13)C responses on a subsample of trees as representative of the wider region. The negative ∆(13)C responses to temperature reveal that black spruce trees are experiencing moisture stress on both northern and southern aspects. Contrary to our expectations, ∆(13)C from trees on the northern aspect exhibited the strongest drought signal. Our results highlight the prominence of drought stress in the boreal forest of interior Alaska. We conclude that if temperatures continue to warm, we can expect drought-induced productivity declines across large regions of the boreal forest, even for trees located in cool and moist landscape positions. © 2015 John Wiley & Sons Ltd.

  4. Dissemination of regional rainfall analysis in design and analysis of urban drainage at un-gauged locations

    DEFF Research Database (Denmark)

    Arnbjerg-Nielsen, K.; Harremoes, Poul; Mikkelsen, Peter Steen

    2002-01-01

    regional variation of extreme rainfalls throughout the country. This has implications for design and analysis of all practical problems related to urban drainage, since the rainfall data so far recommended as input to engineering analyses underestimates the problems. Consequently, the Danish Water......A research program in Denmark on statistical modelling of rainfall has resulted in a model for regional distribution of rainfall extremes. The results show that extreme rainfalls critical to the hydraulic function of urban drainage systems and the pollution discharge are subject to a significant...... Pollution Control Committee has issued a statement recommending a new engineering practice. The dissemination of the research results proved to be difficult due to lack of understanding of the concepts of the new paradigm by practitioners. The traditional means of communication was supplemented by user...

  5. Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal.

    Science.gov (United States)

    Sheng, Yue; Zhao, Wei; Song, Ying; Li, Zhigang; Luo, Majing; Lei, Quan; Cheng, Hanhua; Zhou, Rongjia

    2015-05-18

    A variety of mechanisms are engaged in sex determination in vertebrates. The teleost fish swamp eel undergoes sex reversal naturally and is an ideal model for vertebrate sexual development. However, the importance of proteome-wide scanning for gonad reversal was not previously determined. We report a 2-D electrophoresis analysis of three gonad types of proteomes during sex reversal. MS/MS analysis revealed a group of differentially expressed proteins during ovary to ovotestis to testis transformation. Cbx3 is up-regulated during gonad reversal and is likely to have a role in spermatogenesis. Rab37 is down-regulated during the reversal and is mainly associated with oogenesis. Both Cbx3 and Rab37 are linked up in a protein network. These datasets in gonadal proteomes provide a new resource for further studies in gonadal development.

  6. Proteomic analysis of MG132-treated germinating pollen reveals expression signatures associated with proteasome inhibition.

    Directory of Open Access Journals (Sweden)

    Candida Vannini

    Full Text Available Chemical inhibition of the proteasome has been previously found to effectively impair pollen germination and tube growth in vitro. However, the mediators of these effects at the molecular level are unknown. By performing 2DE proteomic analysis, 24 differentially expressed protein spots, representing 14 unique candidate proteins, were identified in the pollen of kiwifruit (Actinidia deliciosa germinated in the presence of the MG132 proteasome inhibitor. qPCR analysis revealed that 11 of these proteins are not up-regulated at the mRNA level, but are most likely stabilized by proteasome inhibition. These differentially expressed proteins are predicted to function in various pathways including energy and lipid metabolism, cell wall synthesis, protein synthesis/degradation and stress responses. In line with this evidence, the MG132-induced changes in the proteome were accompanied by an increase in ATP and ROS content and by an alteration in fatty acid composition.

  7. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.

    Science.gov (United States)

    Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W; Grubert, Fabian; Candille, Sophie I; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L; Tang, Hua; Ricci, Emiliano; Snyder, Michael P

    2015-11-01

    Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy--many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. © 2015 Cenik et al.; Published by Cold Spring Harbor Laboratory Press.

  8. Reducing travel by design: a micro analysis of new household location and the commute to work in Surrey

    Science.gov (United States)

    Hickman, Robin

    Traffic volumes (and hence energy consumption) from the transport sector continue to rise, yet the potential fundamental role of urban planning in helping to reduce transport energy consumption remains to be poorly understood and hugely underplayed. Current urban planning practice, particularly in suburban areas, tends to increase traffic volumes by dispersing activities and hence facilitates private car travel rather than travel by public transport, walking or cycling. Public transport orientated development as an evolving practice tends to be focused very much on urban areas. This thesis seeks to understand the logic behind travel and suggests that urban planning can be applied more fully, at the strategic and local levels, to reduce energy consumption in car use (at least in the journey to work). The detailed analysis assesses the extent to which the design of the urban environment affects travel behaviour. The research hypothesis is that: "Journey to work travel behaviour generated by new residential development is dependent on a number of land use and socio-economic variables. The strength, significance and range of interaction vary spatially and over time." Within the analysis, the journey to work is used as the dependent variable, and is measured in terms of journey length and time, mode share and composite energy consumption. The independent variables considered include: Land use: resident population density, resident employment density, workplace population density, workplace employment density, resident population size, workplace population size, distance from urban centres and strategic transport networks, jobs-housing balance, resident classification (relative to the urban area), type of journey to work, neighbourhood streetscape design, public transport accessibility, and resident location (relative to the green belt). Socio-economic: household tenure, house type, house size, number of children, car availability, company car ownership, household income

  9. Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.

    Directory of Open Access Journals (Sweden)

    Yong Guo

    Full Text Available The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max. In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.

  10. Co-occurrence correlations of heavy metals in sediments revealed using network analysis.

    Science.gov (United States)

    Liu, Lili; Wang, Zhiping; Ju, Feng; Zhang, Tong

    2015-01-01

    In this study, the correlation-based study was used to identify the co-occurrence correlations among metals in marine sediment of Hong Kong, based on the long-term (from 1991 to 2011) temporal and spatial monitoring data. 14 stations out of the total 45 marine sediment monitoring stations were selected from three representative areas, including Deep Bay, Victoria Harbour and Mirs Bay. Firstly, Spearman's rank correlation-based network analysis was conducted as the first step to identify the co-occurrence correlations of metals from raw metadata, and then for further analysis using the normalized metadata. The correlations patterns obtained by network were consistent with those obtained by the other statistic normalization methods, including annual ratios, R-squared coefficient and Pearson correlation coefficient. Both Deep Bay and Victoria Harbour have been polluted by heavy metals, especially for Pb and Cu, which showed strong co-occurrence with other heavy metals (e.g. Cr, Ni, Zn and etc.) and little correlations with the reference parameters (Fe or Al). For Mirs Bay, which has better marine sediment quality compared with Deep Bay and Victoria Harbour, the co-occurrence patterns revealed by network analysis indicated that the metals in sediment dominantly followed the natural geography process. Besides the wide applications in biology, sociology and informatics, it is the first time to apply network analysis in the researches of environment pollutions. This study demonstrated its powerful application for revealing the co-occurrence correlations among heavy metals in marine sediments, which could be further applied for other pollutants in various environment systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

    Science.gov (United States)

    Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

    2015-01-01

    Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

  12. Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

    Science.gov (United States)

    Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

    2012-01-01

    Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

  13. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

    Science.gov (United States)

    2013-01-01

    Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data. PMID:24059747

  14. Global meta-analysis reveals low consistency of biodiversity congruence relationships.

    Science.gov (United States)

    Westgate, Martin J; Barton, Philip S; Lane, Peter W; Lindenmayer, David B

    2014-05-21

    Knowledge of the number and distribution of species is fundamental to biodiversity conservation efforts, but this information is lacking for the majority of species on earth. Consequently, subsets of taxa are often used as proxies for biodiversity; but this assumes that different taxa display congruent distribution patterns. Here we use a global meta-analysis to show that studies of cross-taxon congruence rarely give consistent results. Instead, species richness congruence is highest at extreme spatial scales and close to the equator, while congruence in species composition is highest at large extents and grain sizes. Studies display highest variance in cross-taxon congruence when conducted in areas with dissimilar areal extents (for species richness) or latitudes (for species composition). These results undermine the assumption that a subset of taxa can be representative of biodiversity. Therefore, researchers whose goal is to prioritize locations or actions for conservation should use data from a range of taxa.

  15. Chromosome 2 short arm translocations revealed by M-FISH analysis of neuroblastoma cell lines.

    Science.gov (United States)

    Van Roy, N; Van Limbergen, H; Vandesompele, J; Van Gele, M; Poppe, B; Laureys, G; De Paepe, A; Speleman, F

    2000-12-01

    M-FISH analysis was performed on 18 neuroblastoma cell lines, which were previously studied with cytogenetic, standard FISH and CGH data. One of the most striking findings of this study was the detection of chromosome 2 short arm rearrangements in 61% of the investigated cell lines. These rearrangements resulted from translocations with various partner chromosomes. All translocations, except one were unbalanced, leading to the consistent gain of chromosome segment 2pter-p22. A cryptic balanced translocation t(2;4) was observed with a breakpoint located in the vicinity of MYCN in cell line NBL-S. Combination of M-FISH results together with cytogenetic, standard FISH and CGH data yielded the most comprehensive description of chromosome 2 short arm rearrangements, leading to a consistent gain of chromosome 2 short arm material. Copyright 2000 Wiley-Liss, Inc.

  16. Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken.

    Science.gov (United States)

    Wragg, David; Mason, Andrew S; Yu, Le; Kuo, Richard; Lawal, Raman A; Desta, Takele Taye; Mwacharo, Joram M; Cho, Chang-Yeon; Kemp, Steve; Burt, David W; Hanotte, Olivier

    2015-10-14

    EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data. An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05). Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.

  17. Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family

    Directory of Open Access Journals (Sweden)

    Nordlund Henri R

    2005-03-01

    Full Text Available Abstract Background A chicken egg contains several biotin-binding proteins (BBPs, whose complete DNA and amino acid sequences are not known. In order to identify and characterise these genes and proteins we studied chicken cDNAs and genes available in the NCBI database and chicken genome database using the reported N-terminal amino acid sequences of chicken egg-yolk BBPs as search strings. Results Two separate hits showing significant homology for these N-terminal sequences were discovered. For one of these hits, the chromosomal location in the immediate proximity of the avidin gene family was found. Both of these hits encode proteins having high sequence similarity with avidin suggesting that chicken BBPs are paralogous to avidin family. In particular, almost all residues corresponding to biotin binding in avidin are conserved in these putative BBP proteins. One of the found DNA sequences, however, seems to encode a carboxy-terminal extension not present in avidin. Conclusion We describe here the predicted properties of the putative BBP genes and proteins. Our present observations link BBP genes together with avidin gene family and shed more light on the genetic arrangement and variability of this family. In addition, comparative modelling revealed the potential structural elements important for the functional and structural properties of the putative BBP proteins.

  18. Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

    Directory of Open Access Journals (Sweden)

    Rebecca A. Weingarten

    2018-02-01

    Full Text Available The hospital environment is a potential reservoir of bacteria with plasmids conferring carbapenem resistance. Our Hospital Epidemiology Service routinely performs extensive sampling of high-touch surfaces, sinks, and other locations in the hospital. Over a 2-year period, additional sampling was conducted at a broader range of locations, including housekeeping closets, wastewater from hospital internal pipes, and external manholes. We compared these data with previously collected information from 5 years of patient clinical and surveillance isolates. Whole-genome sequencing and analysis of 108 isolates provided comprehensive characterization of blaKPC/blaNDM-positive isolates, enabling an in-depth genetic comparison. Strikingly, despite a very low prevalence of patient infections with blaKPC-positive organisms, all samples from the intensive care unit pipe wastewater and external manholes contained carbapenemase-producing organisms (CPOs, suggesting a vast, resilient reservoir. We observed a diverse set of species and plasmids, and we noted species and susceptibility profile differences between environmental and patient populations of CPOs. However, there were plasmid backbones common to both populations, highlighting a potential environmental reservoir of mobile elements that may contribute to the spread of resistance genes. Clear associations between patient and environmental isolates were uncommon based on sequence analysis and epidemiology, suggesting reasonable infection control compliance at our institution. Nonetheless, a probable nosocomial transmission of Leclercia sp. from the housekeeping environment to a patient was detected by this extensive surveillance. These data and analyses further our understanding of CPOs in the hospital environment and are broadly relevant to the design of infection control strategies in many infrastructure settings.

  19. An overview on preseismic anomalies in LF radio signals revealed in Italy by wavelet analysis

    Directory of Open Access Journals (Sweden)

    A. Ermini

    2008-06-01

    Full Text Available Since 1996, the electric field strength of the two broadcasting stations MCO (f=216 kHz, southeast France and CZE (f=270 kHz, Czech Republic has been sampled every ten minutes by a receiver (AS located in central Italy. Here, we review the results obtained by a detailed analysis applied to the data recorded from February 1996 up to December 2004. At first, the daytime and nighttime data were extracted and then, in the daytime data, the data collected in winter were separated from those collected in summer. On the second step the wavelet transform was applied. The results of this analysis are radio anomalies detected as earthquake precursors both for MCO and CZE data. In particular, regarding the MCO data, the main result was the appearance of a very clear anomaly during May-August 1998, at daytime and at nighttime. Such an anomaly can be considered as a precursor of a seismic sequence started on August 15, 1998 with 17 earthquakes (M=2.2-4.6 on the Reatini mountains, a seismogenic zone located 30 km far from the AS receiver along the path MCO-AS. As concerns with the CZE data, the first result was obtained from the summer daytime data and it was the appearance of a very clear anomaly during August-September 1997, that can be considered a precursor of the two earthquakes with magnitude M=5.6 and M=5.9 that occurred on September 26 in the Umbria-Marche region (Central Italy. The second result was the appearance of an anomaly during February-March 1998, at daytime and at nighttime, that can be related to the preparatory phase of the strong (M=5.1-6.0 Slovenia seismic sequence that occurred in a zone lying in the middle of the CZE-AS path.

  20. RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize

    Science.gov (United States)

    Ren, Wen; Yang, Fengling; He, Hang; Zhao, Jiuran

    2015-01-01

    The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize. PMID:26599013

  1. Molecular approaches for blood meal analysis and species identification of mosquitoes (Insecta: Diptera: Culicidae) in rural locations in southern England, United Kingdom.

    Science.gov (United States)

    Hernández-Triana, Luis Miguel; Brugman, Victor Albert; Prosser, Sean Williams John; Weland, Chris; Nikolova, Nadya; Thorne, Leigh; Marco, Mar Fernández DE; Fooks, Anthony Richard; Johnson, Nicholas

    2017-04-03

    Thirty-four species of Culicidae are present in the UK, of which 15 have been implicated as potential vectors of arthropod-borne viruses such as West Nile virus. Identification of mosquito feeding preferences is paramount to the understanding of vector-host-pathogen interactions which, in turn, would assist in the control of disease outbreaks. Results are presented on the application of DNA barcoding for vertebrate species identification in blood-fed female mosquitoes in rural locations. Blood-fed females (n = 134) were collected in southern England from rural sites and identified based on morphological criteria. Blood meals from 59 specimens (44%) were identified as feeding on eight hosts: European rabbit, cow, human, barn swallow, dog, great tit, magpie and blackbird. Analysis of the cytochrome c oxidase subunit I mtDNA barcoding region and the internal transcribed spacer 2 rDNA region of the specimens morphologically identified as Anopheles maculipennis s.l. revealed the presence of An. atroparvus and An. messeae. A similar analysis of specimens morphologically identified as Culex pipiens/Cx. torrentium showed all specimens to be Cx. pipiens (typical form). This study demonstrates the importance of using molecular techniques to support species-level identification in blood-fed mosquitoes to maximize the information obtained in studies investigating host feeding patterns.

  2. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

    Science.gov (United States)

    Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

    2016-01-12

    Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

  3. Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis.

    Science.gov (United States)

    Xie, Jianbo; Tian, Jiaxing; Du, Qingzhang; Chen, Jinhui; Li, Ying; Yang, Xiaohui; Li, Bailian; Zhang, Deqiang

    2016-05-01

    Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

  4. FINANCIAL PERFORMANCE ANALYSIS BASED ON THE FINANCIAL STATEMENTS FOR THE COMPANIES LOCATED IN THE BIHOR - HAJDU BIHAR EUROREGION

    Directory of Open Access Journals (Sweden)

    Droj Laurentiu

    2012-12-01

    Full Text Available This paper will be later used within the Doctoral thesis: “The Mechanism of Financing Investment Projects by Usage of European Structural Funds”, which is currently under development at the University Babeș Bolyai Cluj Napoca, Faculty of Economics and Business Management, under the coordination of the prof. univ. dr. Ioan Trenca. This paper comes also as a result of the European Funded project PERINPRO “Cross-Border Research Programme - Performance Indicators of the Economic Entities from Bihor-Hajdu Bihar Euroregion”. The goal of the project was to identify of a set of common indicators that characterizes companies in the Bihor-Hajdu Bihar Euroregion and which will be used to analyze the financial health of the economic entities in the Euroregion of Hajdu-Bihar- Bihor. The first chapter of the paper will introduce the research and also will present the literature review and the methodological framework: by establishing a common set of indicators for the financial analysis of the companies located in the Bihor-Hajdu Bihar Euroregion. Seven of these indicators considered to be highly important will also briefly described and defined. Some of these indicators are used for the first time in a trans-national analysis over companies located in the Romanian-Hungarian cross border area. In the second chapter the research will be focused over establishing a common ground for usage of the financial reporting documents as basis for the analysis. Several characteristics which differentiate the financial reporting documents from Romania and Hungary will be identified and measures for correction of the values of the indicators will be proposed. This comparative study can be considered an innovation, as well, in the cross-border area since in the past no other studies of this types were performed between Romania and Hungary. The third chapter will be focused over the application of seven identified common indicators to companies based

  5. Supplement analysis for a container system for the management of DOE spent nuclear fuel located at the INEEL

    International Nuclear Information System (INIS)

    1999-01-01

    The Council on Environmental Quality (CEQ) regulations for implementing the NEPA, 40 CFR 1502.9 (c), directs federal agencies to prepare a supplement to an environmental impact statement when an agency makes substantial changes in the Proposed Action that are relevant to environmental concerns, or there are significant new circumstances or information relevant to environmental concerns and bearing on the Proposed Action or impacts. When it is unclear whether a supplemental environmental impact statement is required, DOE regulations (10 CFR 1021.314) direct the preparation of a supplement analysis to assist in making that determination. This supplement analysis evaluates the impacts of employing dual-purpose canisters (DPCs) to prepare DOE SNF located at the INEEL for interim onsite storage and transport outside the State of Idaho. Impacts associated with DPC manufacturing, loading and storage of DOE-ID SNF into DPCs, transport of loaded DPCs outside Idaho, and the cumulative impacts are compared with the impacts previously analyzed in the SNF and INEL EIS and the Navy Container System EIS. This SA provides information to determine whether: (1) an existing EIS should be supplemented; (2) a new EIS should be prepared; or (3) no further NEPA documentation is required

  6. Supplement analysis for a container system for the management of DOE spent nuclear fuel located at the INEEL

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-03-12

    The Council on Environmental Quality (CEQ) regulations for implementing the NEPA, 40 CFR 1502.9 (c), directs federal agencies to prepare a supplement to an environmental impact statement when an agency makes substantial changes in the Proposed Action that are relevant to environmental concerns, or there are significant new circumstances or information relevant to environmental concerns and bearing on the Proposed Action or impacts. When it is unclear whether a supplemental environmental impact statement is required, DOE regulations (10 CFR 1021.314) direct the preparation of a supplement analysis to assist in making that determination. This supplement analysis evaluates the impacts of employing dual-purpose canisters (DPCs) to prepare DOE SNF located at the INEEL for interim onsite storage and transport outside the State of Idaho. Impacts associated with DPC manufacturing, loading and storage of DOE-ID SNF into DPCs, transport of loaded DPCs outside Idaho, and the cumulative impacts are compared with the impacts previously analyzed in the SNF and INEL EIS and the Navy Container System EIS. This SA provides information to determine whether: (1) an existing EIS should be supplemented; (2) a new EIS should be prepared; or (3) no further NEPA documentation is required.

  7. Preliminary safety analysis of a PBMR supplying process heat to a co-located ethylene production plant

    International Nuclear Information System (INIS)

    Scarlat, Raluca O.; Cisneros, Anselmo T.; Koutchesfahani, Tawni; Hong, Rada; Peterson, Per F.

    2012-01-01

    This paper considers the safety analysis and licensing approach for co-locating a pebble bed modular reactor (PBMR) to provide process heat to an ethylene production unit. The PBMR is an advanced nuclear reactor design that provides 400 MW of thermal energy. Ethylene production is an energy intensive process that utilizes large gas furnaces to provide the heat for the process. Coupling a PBMR with an ethylene production plant would open a new market for nuclear power, and would provide the chemical industry with a cleaner power source, helping to achieve the Clean Air Act standards, and eliminating the 0.5 ton of CO 2 emissions per ton of produced ethylene. Our analysis uses the Chevron Phillips chemical plant in Sweeney, TX as a prototypical site. The plant has four ethylene production trains, with a total power consumption of 2.4 GW, for an ethylene output of 3.7 million tons per year, 4% of the global ethylene production capacity. This paper proposes replacement of the gas furnaces by low-emission PBMR modules, and presents the safety concerns and risk mitigation and management options for this coupled system. Two coupling design options are proposed, and the necessary changes to the design basis events and severe accidents for the PBMR licensing application are discussed. A joint effort between the chemical and the nuclear entities to optimize the coupling design, establish preventive maintenance procedures, and develop emergency response plans for both of the units is recommended.

  8. Preliminary safety analysis of a PBMR supplying process heat to a co-located ethylene production plant

    Energy Technology Data Exchange (ETDEWEB)

    Scarlat, Raluca O., E-mail: rscarlat@nuc.berkeley.edu [University of California Berkeley, Nuclear Engineering, 4118 Etcheverry Hall, Berkeley, CA 94720 (United States); Cisneros, Anselmo T. [University of California Berkeley, Nuclear Engineering, 4118 Etcheverry Hall, Berkeley, CA 94720 (United States); Koutchesfahani, Tawni [University of California, Chemical and Biomolecular Engineering, 201 Gilman Hall, Berkeley, CA 94720 (United States); Hong, Rada; Peterson, Per F. [University of California Berkeley, Nuclear Engineering, 4118 Etcheverry Hall, Berkeley, CA 94720 (United States)

    2012-10-15

    This paper considers the safety analysis and licensing approach for co-locating a pebble bed modular reactor (PBMR) to provide process heat to an ethylene production unit. The PBMR is an advanced nuclear reactor design that provides 400 MW of thermal energy. Ethylene production is an energy intensive process that utilizes large gas furnaces to provide the heat for the process. Coupling a PBMR with an ethylene production plant would open a new market for nuclear power, and would provide the chemical industry with a cleaner power source, helping to achieve the Clean Air Act standards, and eliminating the 0.5 ton of CO{sub 2} emissions per ton of produced ethylene. Our analysis uses the Chevron Phillips chemical plant in Sweeney, TX as a prototypical site. The plant has four ethylene production trains, with a total power consumption of 2.4 GW, for an ethylene output of 3.7 million tons per year, 4% of the global ethylene production capacity. This paper proposes replacement of the gas furnaces by low-emission PBMR modules, and presents the safety concerns and risk mitigation and management options for this coupled system. Two coupling design options are proposed, and the necessary changes to the design basis events and severe accidents for the PBMR licensing application are discussed. A joint effort between the chemical and the nuclear entities to optimize the coupling design, establish preventive maintenance procedures, and develop emergency response plans for both of the units is recommended.

  9. Implementation and Analysis of a Wireless Sensor Network-Based Pet Location Monitoring System for Domestic Scenarios.

    Science.gov (United States)

    Aguirre, Erik; Lopez-Iturri, Peio; Azpilicueta, Leyre; Astrain, José Javier; Villadangos, Jesús; Santesteban, Daniel; Falcone, Francisco

    2016-08-30

    The flexibility of new age wireless networks and the variety of sensors to measure a high number of variables, lead to new scenarios where anything can be monitored by small electronic devices, thereby implementing Wireless Sensor Networks (WSN). Thanks to ZigBee, RFID or WiFi networks the precise location of humans or animals as well as some biological parameters can be known in real-time. However, since wireless sensors must be attached to biological tissues and they are highly dispersive, propagation of electromagnetic waves must be studied to deploy an efficient and well-working network. The main goal of this work is to study the influence of wireless channel limitations in the operation of a specific pet monitoring system, validated at physical channel as well as at functional level. In this sense, radio wave propagation produced by ZigBee devices operating at the ISM 2.4 GHz band is studied through an in-house developed 3D Ray Launching simulation tool, in order to analyze coverage/capacity relations for the optimal system selection as well as deployment strategy in terms of number of transceivers and location. Furthermore, a simplified dog model is developed for simulation code, considering not only its morphology but also its dielectric properties. Relevant wireless channel information such as power distribution, power delay profile and delay spread graphs are obtained providing an extensive wireless channel analysis. A functional dog monitoring system is presented, operating over the implemented ZigBee network and providing real time information to Android based devices. The proposed system can be scaled in order to consider different types of domestic pets as well as new user based functionalities.

  10. Analysis of aneuploid lines of bread wheat to map chromosomal locations of genes controlling root hair length.

    Science.gov (United States)

    Liu, Miao; Rathjen, Tina; Weligama, Kumara; Forrest, Kerrie; Hayden, Matthew; Delhaize, Emmanuel

    2017-06-01

    Long root hairs enable the efficient uptake of poorly mobile nutrients such as phosphorus. Mapping the chromosomal locations of genes that control root hair length can help exploit the natural variation within crops to develop improved cultivars. Genetic stocks of the wheat cultivar 'Chinese Spring' were used to map genes that control root hair length. Aneuploid stocks of 'Chinese Spring' were screened using a rapid method based on rhizosheath size and then selected lines were assayed for root hair length to identify chromosomes harbouring genes controlling root hair length. A series of lines with various fractional deletions of candidate chromosomes were then screened to map the root hair loci more accurately. A line with a deletion in chromosome 5A was analysed with a 90 000 single nucleotide polymorphism (SNP) array. The phosphorus acquisition efficiency (PAE) of one deletion line was compared with that of euploid 'Chinese Spring' by growing the seedlings in pots at low and luxury phosphorus supplies. Chromosomes 1A, 1D and 5A were found to harbour genes controlling root hair length. The 90 000 SNP array identified two candidate genes controlling root hair length located on chromosome 5A. The line with a deletion in chromosome 5A had root hairs that were approx. 20 % shorter than euploid 'Chinese Spring', but this was insufficient to reduce its PAE. A rapid screen for rhizosheath size enabled chromosomal regions controlling root hair length to be mapped in the wheat cultivar 'Chinese Spring' and subsequent analysis with an SNP array identified candidate genes controlling root hair length. The difference in root hair length between euploid 'Chinese Spring' and a deletion line identified in the rapid screen was still apparent, albeit attenuated, when the seedlings were grown on a fully fertilized soil. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  11. Implementation and Analysis of a Wireless Sensor Network-Based Pet Location Monitoring System for Domestic Scenarios

    Directory of Open Access Journals (Sweden)

    Erik Aguirre

    2016-08-01

    Full Text Available The flexibility of new age wireless networks and the variety of sensors to measure a high number of variables, lead to new scenarios where anything can be monitored by small electronic devices, thereby implementing Wireless Sensor Networks (WSN. Thanks to ZigBee, RFID or WiFi networks the precise location of humans or animals as well as some biological parameters can be known in real-time. However, since wireless sensors must be attached to biological tissues and they are highly dispersive, propagation of electromagnetic waves must be studied to deploy an efficient and well-working network. The main goal of this work is to study the influence of wireless channel limitations in the operation of a specific pet monitoring system, validated at physical channel as well as at functional level. In this sense, radio wave propagation produced by ZigBee devices operating at the ISM 2.4 GHz band is studied through an in-house developed 3D Ray Launching simulation tool, in order to analyze coverage/capacity relations for the optimal system selection as well as deployment strategy in terms of number of transceivers and location. Furthermore, a simplified dog model is developed for simulation code, considering not only its morphology but also its dielectric properties. Relevant wireless channel information such as power distribution, power delay profile and delay spread graphs are obtained providing an extensive wireless channel analysis. A functional dog monitoring system is presented, operating over the implemented ZigBee network and providing real time information to Android based devices. The proposed system can be scaled in order to consider different types of domestic pets as well as new user based functionalities.

  12. Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia

    Directory of Open Access Journals (Sweden)

    E. Damaraju

    2014-01-01

    Full Text Available Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length, and a dynamic sense, computed using sliding windows (44 s in length and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual, as well as reduced connectivity (hypoconnectivity between sensory networks from all modalities. Dynamic analysis suggests that (1, on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2, that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical–subcortical antagonism (anti-correlations and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity

  13. Study and interpretation of chemical composition of rainwater in selected urban and rural locations in India using multivariate analysis

    Science.gov (United States)

    Chakraborty, Bidisha; Gupta, Abhik

    2018-04-01

    Rainwater is an important untapped resource for all water managers and can be collected and used personally for all uses and simultaneously diverted to ground for recharge of depleting aquifers. Rain water is the most purest form of water until it is contaminated by the atmospheric pollution. Evaluation of rainwater quality analysis is also essential for non-potable applications and to match quality to specific uses. Rainwater quality analysis is, therefore, carried out to understand the problems of rainwater contamination with various pollutants. Rainwater samples were collected from the pre-monsoon season of March 2010 to post-monsoon of October 2013, from seven sampling sites namely Irongmara, Badarpur, Bongaigaon, Dolaigaon, BGR Township, Kolkata and Kharagpur, which characterised typical suburban, urban and industrialised locations respectively. A total of 943 samples were collected during this period from the sampling sites, taking utmost care in sampling and storage were analysed for heavy metals determination. Results for pH, EC, Pb, Cd, Ni, Zn, Cr and Co were reported in this study. The samples were collected using PVC bottles. The highest concentration of elements was observed at the beginning of the rainfall season when large amounts of dust accumulated in the atmosphere scavenged by rain. The values of pH in rainwater samples were relatively within the World Health Organization (WHO) standard for drinking water. Multivariate statistical analysis especially varimax rotation was applied to bring to focus the hidden yet important variables which influence the rainwater quality. It is also observed that rainwater contamination may not be restricted to industrial areas alone but vehicular emission may also contribute significantly in certain areas.

  14. Comprehensive analysis of ultrasonic vocalizations in a mouse model of fragile X syndrome reveals limited, call type specific deficits.

    Directory of Open Access Journals (Sweden)

    Snigdha Roy

    Full Text Available Fragile X syndrome (FXS is a well-recognized form of inherited mental retardation, caused by a mutation in the fragile X mental retardation 1 (Fmr1 gene. The gene is located on the long arm of the X chromosome and encodes fragile X mental retardation protein (FMRP. Absence of FMRP in fragile X patients as well as in Fmr1 knockout (KO mice results, among other changes, in abnormal dendritic spine formation and altered synaptic plasticity in the neocortex and hippocampus. Clinical features of FXS include cognitive impairment, anxiety, abnormal social interaction, mental retardation, motor coordination and speech articulation deficits. Mouse pups generate ultrasonic vocalizations (USVs when isolated from their mothers. Whether those social ultrasonic vocalizations are deficient in mouse models of FXS is unknown. Here we compared isolation-induced USVs generated by pups of Fmr1-KO mice with those of their wild type (WT littermates. Though the total number of calls was not significantly different between genotypes, a detailed analysis of 10 different categories of calls revealed that loss of Fmr1 expression in mice causes limited and call-type specific deficits in ultrasonic vocalization: the carrier frequency of flat calls was higher, the percentage of downward calls was lower and that the frequency range of complex calls was wider in Fmr1-KO mice compared to their WT littermates.

  15. Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population.

    Directory of Open Access Journals (Sweden)

    Kejun Wang

    Full Text Available In this study, 796 male Duroc pigs were used to identify genomic regions controlling growth traits. Three production traits were studied: food conversion ratio, days to 100 KG, and average daily gain, using a panel of 39,436 single nucleotide polymorphisms. In total, we detected 11 genome-wide and 162 chromosome-wide single nucleotide polymorphism trait associations. The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1, seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3, and one for average daily gain (COL27A1. Gene ontology analysis indicated that most of the candidate genes are involved in muscle, fat, bone or nervous system development, nutrient absorption, and metabolism, which are all either directly or indirectly related to growth traits in pigs. Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb. Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.

  16. Differential network analysis reveals evolutionary complexity in secondary metabolism of Rauvolfia serpentina over Catharanthus roseus

    Directory of Open Access Journals (Sweden)

    Shivalika Pathania

    2016-08-01

    Full Text Available Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Towards these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These mechanisms may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of Rauvolfia serpentina, and key genes that contribute towards diversification of specific metabolites.

  17. Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus.

    Science.gov (United States)

    Pathania, Shivalika; Bagler, Ganesh; Ahuja, Paramvir S

    2016-01-01

    Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites.

  18. Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis

    Science.gov (United States)

    Li, Yue; Zhang, Zhaolei

    2014-11-01

    Carcinogenesis consists of oncogenesis and metastasis, and intriguingly microRNAs (miRNAs) are involved in both processes. Although aberrant miRNA activities are prevalent in diverse tumor types, the exact mechanisms for how they regulate cancerous processes are not always clear. To this end, we performed a large-scale pan-cancer analysis via a novel probabilistic approach to infer recurrent miRNA-target interactions implicated in 12 cancer types using data from The Cancer Genome Atlas. We discovered ~20,000 recurrent miRNA regulations, which are enriched for cancer-related miRNAs/genes. Notably, miRNA 200 family (miR-200/141/429) is among the most prominent miRNA regulators, which is known to be involved in metastasis. Importantly, the recurrent miRNA regulatory network is not only enriched for cancer pathways but also for extracellular matrix (ECM) organization and ECM-receptor interactions. The results suggest an intriguing cancer mechanism involving miRNA-mediated cell-to-cell communication, which possibly involves delivery of tumorigenic miRNA messengers to adjacent cells via exosomes. Finally, survival analysis revealed 414 recurrent-prognostic associations, where both gene and miRNA involved in each interaction conferred significant prognostic power in one or more cancer types. Together, our comprehensive pan-cancer analysis provided not only biological insights into metastasis but also brought to bear the clinical relevance of the proposed recurrent miRNA-gene associations.

  19. Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters.

    Science.gov (United States)

    de Menezes, Alexandre B; Prendergast-Miller, Miranda T; Richardson, Alan E; Toscas, Peter; Farrell, Mark; Macdonald, Lynne M; Baker, Geoff; Wark, Tim; Thrall, Peter H

    2015-08-01

    Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal : bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  20. REVEAL - A tool for rule driven analysis of safety critical software

    International Nuclear Information System (INIS)

    Miedl, H.; Kersken, M.

    1998-01-01

    As the determination of ultrahigh reliability figures for safety critical software is hardly possible, national and international guidelines and standards give mainly requirements for the qualitative evaluation of software. An analysis whether all these requirements are fulfilled is time and effort consuming and prone to errors, if performed manually by analysts, and should instead be dedicated to tools as far as possible. There are many ''general-purpose'' software analysis tools, both static and dynamic, which help analyzing the source code. However, they are not designed to assess the adherence to specific requirements of guidelines and standards in the nuclear field. Against the background of the development of I and C systems in the nuclear field which are based on digital techniques and implemented in high level language, it is essential that the assessor or licenser has a tool with which he can automatically and uniformly qualify as many aspects as possible of the high level language software. For this purpose the software analysis tool REVEAL has been developed at ISTec and the Halden Reactor Project. (author)

  1. Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids.

    Science.gov (United States)

    Schmitz, Alexander; Fischer, Sabine C; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H K

    2017-03-03

    Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid's size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 10 5 to 1 × 10 6  cells/mm 3 . Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.

  2. Comparative Analysis of 35 Basidiomycete Genomes Reveals Diversity and Uniqueness of the Phylum

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Otillar, Robert; Fagnan, Kirsten; Boussau, Bastien; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Held, Benjamin; Nagy, Laszlo; Floudas, Dimitris; Morin, Emmanuelle; Manning, Gerard; Baker, Scott; Martin, Francis; Blanchette, Robert; Hibbett, David; Grigoriev, Igor V.

    2013-03-11

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCA analysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth assays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.

  3. Molecular evolution and diversification of snake toxin genes, revealed by analysis of intron sequences.

    Science.gov (United States)

    Fujimi, T J; Nakajyo, T; Nishimura, E; Ogura, E; Tsuchiya, T; Tamiya, T

    2003-08-14

    The genes encoding erabutoxin (short chain neurotoxin) isoforms (Ea, Eb, and Ec), LsIII (long chain neurotoxin) and a novel long chain neurotoxin pseudogene were cloned from a Laticauda semifasciata genomic library. Short and long chain neurotoxin genes were also cloned from the genome of Laticauda laticaudata, a closely related species of L. semifasciata, by PCR. A putative matrix attached region (MAR) sequence was found in the intron I of the LsIII gene. Comparative analysis of 11 structurally relevant snake toxin genes (three-finger-structure toxins) revealed the molecular evolution of these toxins. Three-finger-structure toxin genes diverged from a common ancestor through two types of evolutionary pathways (long and short types), early in the course of evolution. At a later stage of evolution in each gene, the accumulation of mutations in the exons, especially exon II, by accelerated evolution may have caused the increased diversification in their functions. It was also revealed that the putative MAR sequence found in the LsIII gene was integrated into the gene after the species-level divergence.

  4. Sensitivity of human auditory cortex to rapid frequency modulation revealed by multivariate representational similarity analysis.

    Science.gov (United States)

    Joanisse, Marc F; DeSouza, Diedre D

    2014-01-01

    Functional Magnetic Resonance Imaging (fMRI) was used to investigate the extent, magnitude, and pattern of brain activity in response to rapid frequency-modulated sounds. We examined this by manipulating the direction (rise vs. fall) and the rate (fast vs. slow) of the apparent pitch of iterated rippled noise (IRN) bursts. Acoustic parameters were selected to capture features used in phoneme contrasts, however the stimuli themselves were not perceived as speech per se. Participants were scanned as they passively listened to sounds in an event-related paradigm. Univariate analyses revealed a greater level and extent of activation in bilateral auditory cortex in response to frequency-modulated sweeps compared to steady-state sounds. This effect was stronger in the left hemisphere. However, no regions showed selectivity for either rate or direction of frequency modulation. In contrast, multivoxel pattern analysis (MVPA) revealed feature-specific encoding for direction of modulation in auditory cortex bilaterally. Moreover, this effect was strongest when analyses were restricted to anatomical regions lying outside Heschl's gyrus. We found no support for feature-specific encoding of frequency modulation rate. Differential findings of modulation rate and direction of modulation are discussed with respect to their relevance to phonetic discrimination.

  5. Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins

    Science.gov (United States)

    Dallas, David C.; Citerne, Florine; Tian, Tian; Silva, Vitor L. M.; Kalanetra, Karen M.; Frese, Steven A.; Robinson, Randall C.; Mills, David A.; Barile, Daniela

    2015-01-01

    Scope The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Methods and results Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1,500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. Conclusion The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. PMID:26616950

  6. Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins.

    Science.gov (United States)

    Dallas, David C; Citerne, Florine; Tian, Tian; Silva, Vitor L M; Kalanetra, Karen M; Frese, Steven A; Robinson, Randall C; Mills, David A; Barile, Daniela

    2016-04-15

    The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Zebrafish Embryonic Lipidomic Analysis Reveals that the Yolk Cell Is Metabolically Active in Processing Lipid

    Directory of Open Access Journals (Sweden)

    Daniel Fraher

    2016-02-01

    Full Text Available The role of lipids in providing energy and structural cellular components during vertebrate development is poorly understood. To elucidate these roles further, we visualized lipid deposition and examined expression of key lipid-regulating genes during zebrafish embryogenesis. We also conducted a semiquantitative analysis of lipidomic composition using liquid chromatography (LC-mass spectrometry. Finally, we analyzed processing of boron-dipyrromethene (BODIPY lipid analogs injected into the yolk using thin layer chromatography. Our data reveal that the most abundant lipids in the embryo are cholesterol, phosphatidylcholine, and triglyceride. Moreover, we demonstrate that lipids are processed within the yolk prior to mobilization to the embryonic body. Our data identify a metabolically active yolk and body resulting in a dynamic lipid composition. This provides a foundation for studying lipid biology during normal or pharmacologically compromised embryogenesis.

  8. Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

    KAUST Repository

    Feng, Yitao

    2016-10-13

    The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

  9. Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

    KAUST Repository

    Feng, Yitao; Zhang, Lu; Wu, Shaowen; Liu, Zhijun; Gao, Xin; Zhang, Xu; Liu, Maili; Liu, Jianwei; Huang, Xuhui; Wang, Wenning

    2016-01-01

    The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

  10. Distribution patterns of firearm discharge residues as revealed by neutron activation analysis

    International Nuclear Information System (INIS)

    Pillay, K.K.S.; Driscoll, D.C.; Jester, W.A.

    1975-01-01

    A systematic investigation using a variety of handguns has revealed the existence of distinguisable distribution patterns of firearm discharge residues on surfaces below the flight path of a bullet. The residues are identificable even at distances of 12 meters from the gun using nondestructive neutron activation analysis. The results of these investigations show that the distribution pattern for a gun is reproducible using similar ammunition and that there exist two distinct regions to the patterns developed between the firearm and the target-one with respect to the position of the gun and the other in the vicinity of the target. The judicious applications of these findings could be of significant value in criminal investigations. (T.G.)

  11. Genetically based location from triploid populations and gene ontology of a 3.3-mb genome region linked to Alternaria brown spot resistance in citrus reveal clusters of resistance genes.

    Directory of Open Access Journals (Sweden)

    José Cuenca

    Full Text Available Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR to map a genome region linked to Alternaria brown spot (ABS resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids.

  12. Genetically based location from triploid populations and gene ontology of a 3.3-mb genome region linked to Alternaria brown spot resistance in citrus reveal clusters of resistance genes.

    Science.gov (United States)

    Cuenca, José; Aleza, Pablo; Vicent, Antonio; Brunel, Dominique; Ollitrault, Patrick; Navarro, Luis

    2013-01-01

    Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids.

  13. Phenotypic analysis of prostate-infiltrating lymphocytes reveals TH17 and Treg skewing.

    Science.gov (United States)

    Sfanos, Karen Sandell; Bruno, Tullia C; Maris, Charles H; Xu, Lauren; Thoburn, Christopher J; DeMarzo, Angelo M; Meeker, Alan K; Isaacs, William B; Drake, Charles G

    2008-06-01

    Pathologic examination of prostate glands removed from patients with prostate cancer commonly reveals infiltrating CD4+ and CD8+ T cells. Little is known about the phenotype of these cells, despite accumulating evidence suggesting a potential role for chronic inflammation in the etiology of prostate cancer. We developed a technique that samples the majority of the peripheral prostate through serial needle aspirates. CD4+ prostate-infiltrating lymphocytes (PIL) were isolated using magnetic beads and analyzed for subset skewing using both flow cytometry and quantitative reverse transcription-PCR. The transcriptional profile of fluorescence-activated cell sorted prostate-infiltrating regulatory T cells (CD4+, CD25+, GITR+) was compared with naïve, peripheral blood T cells using microarray analysis. CD4+ PIL showed a paucity of TH2 (interleukin-4-secreting) cells, a surprising finding given the generally accepted association of these cells with chronic, smoldering inflammation. Instead, CD4+ PIL seemed to be skewed towards a regulatory Treg phenotype (FoxP3+) as well as towards the TH17 phenotype (interleukin-17+). We also found that a preponderance of TH17-mediated inflammation was associated with a lower pathologic Gleason score. These protein level data were reflected at the message level, as analyzed by quantitative reverse transcription-PCR. Microarray analysis of pooled prostate-infiltrating T(reg) revealed expected Treg-associated transcripts (FoxP3, CTLA-4, GITR, LAG-3) as well as a number of unique cell surface markers that may serve as additional Treg markers. Taken together, these data suggest that TH17 and/or Treg CD4+ T cells (rather than TH2 T cells) may be involved in the development or progression of prostate cancer.

  14. Fine Mapping and Transcriptome Analysis Reveal Candidate Genes Associated with Hybrid Lethality in Cabbage (Brassica Oleracea).

    Science.gov (United States)

    Xiao, Zhiliang; Hu, Yang; Zhang, Xiaoli; Xue, Yuqian; Fang, Zhiyuan; Yang, Limei; Zhang, Yangyong; Liu, Yumei; Li, Zhansheng; Liu, Xing; Liu, Zezhou; Lv, Honghao; Zhuang, Mu

    2017-06-05

    Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage ( Brassica oleracea ) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that BoHL1 was located on chromosome C1 between BoHLTO124 and BoHLTO130, with an interval of 101 kb. BoHL2 was confirmed to be between insertion-deletion (InDels) markers HL234 and HL235 on C4, with a marker interval of 70 kb. Twenty-eight and nine annotated genes were found within the two intervals of BoHL1 and BoHL2 , respectively. We also applied RNA-Seq to analyze hybrid lethality in cabbage. In the region of BoHL1 , seven differentially expressed genes (DEGs) and five resistance (R)-related genes (two in common, i.e., Bo1g153320 and Bo1g153380 ) were found, whereas in the region of BoHL2 , two DEGs and four R-related genes (two in common, i.e., Bo4g173780 and Bo4g173810 ) were found. Along with studies in which R genes were frequently involved in hybrid lethality in other plants, these interesting R-DEGs may be good candidates associated with hybrid lethality. We also used SNP/InDel analyses and quantitative real-time PCR to confirm the results. This work provides new insight into the mechanisms of hybrid lethality in cabbage.

  15. Voronoi-based spatial analysis reveals selective interneuron changes in the cortex of FALS mice.

    Science.gov (United States)

    Minciacchi, Diego; Kassa, Roman M; Del Tongo, Claudia; Mariotti, Raffaella; Bentivoglio, Marina

    2009-01-01

    The neurodegenerative disease amyotrophic lateral sclerosis affects lower motoneurons and corticospinal cells. Mice expressing human mutant superoxide dismutase (SOD)1 provide widely investigated models of the familial form of disease, but information on cortical changes in these mice is still limited. We here analyzed the spatial organization of interneurons characterized by parvalbumin immunoreactivity in the motor, somatosensory, and visual cortical areas of SOD1(G93A) mice. Cell number and sociological spatial behavior were assessed by digital charts of cell location in cortical samples, cell counts, and generation of two-dimensional Voronoi diagrams. In end-stage SOD1-mutant mice, an increase of parvalbumin-containing cortical interneurons was found in the motor and somatosensory areas (about 35% and 20%, respectively) with respect to wild-type littermates. Changes in cell spatial distribution, as documented by Voronoi-derived coefficients of variation, indicated increased tendency of parvalbumin cells to aggregate into clusters in the same areas of the SOD1-mutant cortex. Counts and coefficients of variation of parvalbumin cells in the visual cortex gave instead similar results in SOD1-mutant and wild-type mice. Analyses of motor and somatosensory areas in presymptomatic SOD1-mutant mice provided findings very similar to those obtained at end-stage, indicating early changes of interneurons in these cortical areas during the pathology. Altogether the data reveal in the SOD1-mutant mouse cortex an altered architectonic pattern of interneurons, which selectively affects areas involved in motor control. The findings, which can be interpreted as pathogenic factors or early disease-related adaptations, point to changes in the cortical regulation and modulation of the motor circuit during motoneuron disease.

  16. Lost in Location

    DEFF Research Database (Denmark)

    Hansen, Lone Koefoed

    2009-01-01

    traversed. While becoming destination aware, the individual loses her location awareness. The article proposes that the reason people get lost when using sat-nav is due to a wrong location-performative paradigm. As an alternative, the article introduces and analyzes two performance-related examples...... that illustrate an alternative location-performative paradigm: Meredith Warner's Lost/Found knitting series and Etter and Schecht's Melodious Walkabout. In both examples, the artist's hand becomes the intermediary between alien and location. Thus, by exploring how wayfinding can be a poetically situated...... performance, the article examines how the growing locative media industry can learn from the location-aware performative strategies employed by artists who create situated and urban performances for the curious participant. The academic frames employed in the analysis draw on psychogeography, site...

  17. Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability.

    Directory of Open Access Journals (Sweden)

    Catarina Barbosa

    Full Text Available Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23, under low (67 mg/L and high nitrogen (670 mg/L regimes, at three time points during fermentation (12 h, 24 h and 96 h. Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12 h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this

  18. Comparative Transcriptomic Analysis Reveals Similarities and Dissimilarities in Saccharomyces cerevisiae Wine Strains Response to Nitrogen Availability

    Science.gov (United States)

    Barbosa, Catarina; García-Martínez, José; Pérez-Ortín, José E.; Mendes-Ferreira, Ana

    2015-01-01

    Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12h, 24h and 96h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape

  19. An integrative genomic and transcriptomic analysis reveals potential targets associated with cell proliferation in uterine leiomyomas.

    Directory of Open Access Journals (Sweden)

    Priscila Daniele Ramos Cirilo

    Full Text Available Uterine Leiomyomas (ULs are the most common benign tumours affecting women of reproductive age. ULs represent a major problem in public health, as they are the main indication for hysterectomy. Approximately 40-50% of ULs have non-random cytogenetic abnormalities, and half of ULs may have copy number alterations (CNAs. Gene expression microarrays studies have demonstrated that cell proliferation genes act in response to growth factors and steroids. However, only a few genes mapping to CNAs regions were found to be associated with ULs.We applied an integrative analysis using genomic and transcriptomic data to identify the pathways and molecular markers associated with ULs. Fifty-one fresh frozen specimens were evaluated by array CGH (JISTIC and gene expression microarrays (SAM. The CONEXIC algorithm was applied to integrate the data.The integrated analysis identified the top 30 significant genes (P<0.01, which comprised genes associated with cancer, whereas the protein-protein interaction analysis indicated a strong association between FANCA and BRCA1. Functional in silico analysis revealed target molecules for drugs involved in cell proliferation, including FGFR1 and IGFBP5. Transcriptional and protein analyses showed that FGFR1 (P = 0.006 and P<0.01, respectively and IGFBP5 (P = 0.0002 and P = 0.006, respectively were up-regulated in the tumours when compared with the adjacent normal myometrium.The integrative genomic and transcriptomic approach indicated that FGFR1 and IGFBP5 amplification, as well as the consequent up-regulation of the protein products, plays an important role in the aetiology of ULs and thus provides data for potential drug therapies development to target genes associated with cellular proliferation in ULs.

  20. Modeling and performance analysis of an improved movement-based location management scheme for packet-switched mobile communication systems.

    Science.gov (United States)

    Chung, Yun Won; Kwon, Jae Kyun; Park, Suwon

    2014-01-01

    One of the key technologies to support mobility of mobile station (MS) in mobile communication systems is location management which consists of location update and paging. In this paper, an improved movement-based location management scheme with two movement thresholds is proposed, considering bursty data traffic characteristics of packet-switched (PS) services. The analytical modeling for location update and paging signaling loads of the proposed scheme is developed thoroughly and the performance of the proposed scheme is compared with that of the conventional scheme. We show that the proposed scheme outperforms the conventional scheme in terms of total signaling load with an appropriate selection of movement thresholds.

  1. System analysis of industrial waste management: A case study of industrial plants located between Tehran and Karaj

    Directory of Open Access Journals (Sweden)

    Mohammad Amin Karami

    2015-01-01

    Full Text Available Aims: In this study, management of industrial waste in industries located between Tehran and Karaj in 2009-2010 was examined. Materials and Methods: This is a cross-sectional study which was done by site survey (Iranian environmental protection organization questionnaire usage and results analysis. This questionnaire was consisted of 45 questions about industrial waste, quantity, quality, and management. A total number of industries with over 50 employees was 283, and Stratified sampling method was used. Sample of size 50 was selected from 283cases. Results: The major hazardous waste-generating industries include chemical and plastic. Private sectors disposed 45% of generated waste. Majority of wastes were buried (62%, and only 17% of industrial waste was recycled. Conclusion: For hazardous waste reduction in this zone and health and economic attractions, the opportunity for reuse and recovery for these wastes must maximize in short-term and burial of industrial waste must be minimized. Industries such as chemical-plastic and electronics which have higher hazardous waste, in long-term, must be replaced with other industries such as wood cellulose and paper that have lower hazardous waste production rate.

  2. Systematic identification of fragile sites via genome-wide location analysis of γ-H2AX

    Science.gov (United States)

    Szilard, Rachel K.; Jacques, Pierre-Étienne; Laramée, Louise; Cheng, Benjamin; Galicia, Sarah; Bataille, Alain R.; Yeung, ManTek; Mendez, Megan; Bergeron, Maxime; Robert, François; Durocher, Daniel

    2011-01-01

    Phosphorylation of histone H2AX is an early response to DNA damage in eukaryotes. In Saccharomyces cerevisiae, DNA damage or replication fork stalling results in histone H2A phosphorylation to yield γ-H2A (yeast γ-H2AX) in a Mec1 (ATR)- and Tel1 (ATM)- dependent manner. Here, we describe the genome-wide location analysis of γ-H2A as a strategy to identify loci prone to engage the Mec1 and Tel1 pathways. Remarkably, γ-H2A enrichment overlaps with loci prone to replication fork stalling and is caused by the action of Mec1 and Tel1, indicating that these loci are prone to breakage. Moreover, about half the sites enriched for γ-H2A map to repressed protein-coding genes, and histone deacetylases are necessary for formation of γ-H2A at these loci. Finally, our work indicates that high resolution mapping of γ-H2AX is a fruitful route to map fragile sites in eukaryotic genomes. PMID:20139982

  3. Cost analysis of teg-powered and solar-powered cathodic protection system for a-50 km long buried natural gas pipeline located in Sindh, Pakistan

    International Nuclear Information System (INIS)

    Shahid, M.; Inam, F.; Farooq, M.; Khan, F.N.

    2005-01-01

    Corrosion leaks are of significant concern to oil and gas industry and is considered to be the largest controllable factor in pipeline safety. Cathodic Protection (CP) is a well-established method for preventing corrosion of metallic materials. Electrical power is required and it is usually difficult and expensive to install conventional power lines in remote areas for readily available power supply. Oil/gas organizations make use of thermo-electric generators (TEG), which is relatively expensive in terms of running expenditures. Utilization of renewable energies is now being widely explored due to potential danger of running out of natural resources and dates back mid of 20th century [I]. However, use of solar powered CP system for oil/gas pipelines hasn't been encouraged much in Pakistan, probably due to lack of understanding. A project was undertaken for designing a solar powered CP system for a 52.4 km buried gas pipeline located at Sui/Sara gas fields (Latitude 27.5) of Tullow Pakistan (Dev.) Ltd. in Dharki, Sindh, Pakistan. After detailed analysis of soil condition, electrochemical testing, local climatic variation and cost analysis, it has been revealed that use of solar power is quite feasible for the above-mentioned pipeline section. Cost analysis and comparison have also favored this system since the maintenance cost of the solar-powered system is much less compared to TEG system. Installation cost of the solar system is about 1.57 times the cost of TEG; however, the maintenance cost is only -20% of that for TEG system. The higher installation cost has been estimated to be recoverable in less than one year of service. (author)

  4. Sweet Potato Value Chain Analysis Reveals Opportunities for Increased Income and Food Security in Northern Ghana

    Directory of Open Access Journals (Sweden)

    Issah Sugri

    2017-01-01

    Full Text Available Sweet potato has gained prominence due to its ability to adapt to wide production ecologies and yield response to minimal external inputs. Orange-fleshed cultivars in particular have immense potential to improve household income and nutrition in sub-Saharan Africa. However, the sweet potato value chain (SPVC is not well-developed in many producing countries. The study was conducted in two regions to characterize the production operations as well as identify opportunities to propel the SPVC in Northern Ghana. Data were collected using mixed methods including structured questionnaires via face-to-face interviews. Analysis of strengths, weaknesses, opportunities, and threats (SWOT was conducted at multistakeholder platforms with different actors. Gross margin profit and benefit-cost ratios were determined by using six cost variables. Overall, the industry was largely a fresh produce market, targeting food vendors, processors, and direct selling to wholesalers, retailers, and household consumers. The SWOT analysis revealed wide-ranging opportunities including favourable production ecologies, processing options, and insatiable local and international markets. The institutional actors need to network the primary actors to synergistically operate with a collective profit motive. The most prioritized production constraints such as access to seed, cost of chemical fertilizer, short shelf-life, field pests and diseases, and declining soil fertility should be addressed.

  5. Pre-2014 mudslides at Oso revealed by InSAR and multi-source DEM analysis

    Science.gov (United States)

    Kim, J. W.; Lu, Z.; QU, F.

    2014-12-01

    The landslide is a process that results in the downward and outward movement of slope-reshaping materials including rocks and soils and annually causes the loss of approximately $3.5 billion and tens of casualties in the United States. The 2014 Oso mudslide was an extreme event costing nearly 40 deaths and damaging civilian properties. Landslides are often unpredictable, but in many cases, catastrophic events are repetitive. Historic record in the Oso mudslide site indicates that there have been serial events in decades, though the extent of sliding events varied from time to time. In our study, the combination of multi-source DEMs, InSAR, and time-series InSAR analysis has enabled to characterize the Oso mudslide. InSAR results from ALOS PALSAR show that there was no significant deformation between mid-2006 and 2011. The combination of time-series InSAR analysis and old-dated DEM indicated revealed topographic changes associated the 2006 sliding event, which is confirmed by the difference of multiple LiDAR DEMs. Precipitation and discharge measurements before the 2006 and 2014 landslide events did not exhibit extremely anomalous records, suggesting the precipitation is not the controlling factor in determining the sliding events at Oso. The lack of surface deformation during 2006-2011 and weak correlation between the precipitation and the sliding event, suggest other factors (such as porosity) might play a critical role on the run-away events at this Oso and other similar landslides.

  6. Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

    Science.gov (United States)

    Naboulsi, Wael; Megger, Dominik A; Bracht, Thilo; Kohl, Michael; Turewicz, Michael; Eisenacher, Martin; Voss, Don Marvin; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

    2016-01-04

    Hepatocellular carcinoma (HCC) is one of the most aggressive tumors, and the treatment outcome of this disease is improved when the cancer is diagnosed at an early stage. This requires biomarkers allowing an accurate and early tumor diagnosis. To identify potential markers for such applications, we analyzed a patient cohort consisting of 50 patients (50 HCC and 50 adjacent nontumorous tissue samples as controls) using two independent proteomics approaches. We performed label-free discovery analysis on 19 HCC and corresponding tissue samples. The data were analyzed considering events known to take place in early events of HCC development, such as abnormal regulation of Wnt/b-catenin and activation of receptor tyrosine kinases (RTKs). 31 proteins were selected for verification experiments. For this analysis, the second set of the patient cohort (31 HCC and corresponding tissue samples) was analyzed using selected (multiple) reaction monitoring (SRM/MRM). We present the overexpression of ATP-dependent RNA helicase (DDX39), Fibulin-5 (FBLN5), myristoylated alanine-rich C-kinase substrate (MARCKS), and Serpin H1 (SERPINH1) in HCC for the first time. We demonstrate Versican core protein (VCAN) to be significantly associated with well differentiated and low-stage HCC. We revealed for the first time the evidence of VCAN as a potential biomarker for early-HCC diagnosis.

  7. Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species.

    Science.gov (United States)

    Ronkin, Dana; Seroussi, Eyal; Nitzan, Tali; Doron-Faigenboim, Adi; Cnaani, Avner

    2015-03-01

    Tilapias are a group of freshwater species, which vary in their ability to adapt to high salinity water. Osmotic regulation in fish is conducted mainly in the gills, kidney, and gastrointestinal tract (GIT). The mechanisms involved in ion and water transport through the GIT is not well-characterized, with only a few described complexes. Comparing the transcriptome of the anterior and posterior intestinal sections of a freshwater and saltwater adapted fish by deep-sequencing, we examined the salinity adaptation of two tilapia species: the high salinity-tolerant Oreochromis mossambicus (Mozambique tilapia), and the less salinity-tolerant Oreochromis niloticus (Nile tilapia). This comparative analysis revealed high similarity in gene expression response to salinity change between species in the posterior intestine and large differences in the anterior intestine. Furthermore, in the anterior intestine 68 genes were saltwater up-regulated in one species and down-regulated in the other species (47 genes up-regulated in O. niloticus and down-regulated in O. mossambicus, with 21 genes showing the reverse pattern). Gene ontology (GO) analysis showed a high proportion of transporter and ion channel function among these genes. The results of this study point to a group of genes that differed in their salinity-dependent regulation pattern in the anterior intestine as potentially having a role in the differential salinity tolerance of these two closely related species. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action

    Directory of Open Access Journals (Sweden)

    Faure Claudine

    2007-10-01

    Full Text Available Abstract Background: The v-erbA oncogene, carried by the Avian Erythroblastosis Virus, derives from the c-erbAα proto-oncogene that encodes the nuclear receptor for triiodothyronine (T3R. v-ErbA transforms erythroid progenitors in vitro by blocking their differentiation, supposedly by interference with T3R and RAR (Retinoic Acid Receptor. However, v-ErbA target genes involved in its transforming activity still remain to be identified. Results: By using Serial Analysis of Gene Expression (SAGE, we identified 110 genes deregulated by v-ErbA and potentially implicated in the transformation process. Bioinformatic analysis of promoter sequence and transcriptional assays point out a potential role of c-Myb in the v-ErbA effect. Furthermore, grouping of newly identified target genes by function revealed both expected (chromatin/transcription and unexpected (protein metabolism functions potentially deregulated by v-ErbA. We then focused our study on 15 of the new v-ErbA target genes and demonstrated by real time PCR that in majority their expression was activated neither by T3, nor RA, nor during differentiation. This was unexpected based upon the previously known role of v-ErbA. Conclusion: This paper suggests the involvement of a wealth of new unanticipated mechanisms of v-ErbA action.

  9. Bach Is the Father of Harmony: Revealed by a 1/f Fluctuation Analysis across Musical Genres.

    Science.gov (United States)

    Wu, Dan; Kendrick, Keith M; Levitin, Daniel J; Li, Chaoyi; Yao, Dezhong

    2015-01-01

    Harmony is a fundamental attribute of music. Close connections exist between music and mathematics since both pursue harmony and unity. In music, the consonance of notes played simultaneously partly determines our perception of harmony; associates with aesthetic responses; and influences the emotion expression. The consonance could be considered as a window to understand and analyze harmony. Here for the first time we used a 1/f fluctuation analysis to investigate whether the consonance fluctuation structure in music with a wide range of composers and genres followed the scale free pattern that has been found for pitch, melody, rhythm, human body movements, brain activity, natural images and geographical features. We then used a network graph approach to investigate which composers were the most influential both within and across genres. Our results showed that patterns of consonance in music did follow scale-free characteristics, suggesting that this feature is a universally evolved one in both music and the living world. Furthermore, our network analysis revealed that Bach's harmony patterns were having the most influence on those used by other composers, followed closely by Mozart.

  10. Genetic analysis of Aedes albopictus (Diptera, Culicidae) reveals a deep divergence in the original regions.

    Science.gov (United States)

    Ruiling, Zhang; Tongkai, Liu; Zhendong, Huang; Guifen, Zhuang; Dezhen, Ma; Zhong, Zhang

    2018-05-02

    Aedes albopictus has been described as one of the 100 worst invasive species in the world. This mosquito originated from southeastern Asia and currently has a widespread presence in every continent except Antarctica. The rapid global expansion of Ae. albopictus has increased public health concerns about arbovirus-related disease threats. Adaptation, adaption to novel areas is a biological challenge for invasive species, and the underlying processes can be studied at the molecular level. In this study, genetic analysis was performed using mitochondrial gene NADH dehydrogenase subunit 5 (ND5), based on both native and invasive populations. Altogether, 38 haplotypes were detected with H1 being the dominant and widely distributed in 21 countries. Both phylogenetic and network analyses supported the existence of five clades, with only clade I being involved in the subsequent global spread of Asian tiger mosquito. The other four clades (II, III, IV and V) were restricted to their original regions, which could be ancestral populations that had diverged from clade I in the early stages of evolution. Neutrality tests suggested that most of the populations had experienced recent expansion. Analysis of molecular variance and the population-pair statistic F ST revealed that most populations lacked genetic structure, while high variability was detected within populations. Multiple and independent human-mediated introductions may explain the present results. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Comparative proteomic analysis reveals heart toxicity induced by chronic arsenic exposure in rats

    International Nuclear Information System (INIS)

    Huang, Qingyu; Xi, Guochen; Alamdar, Ambreen; Zhang, Jie; Shen, Heqing

    2017-01-01

    Arsenic is a widespread metalloid in the environment, which poses a broad spectrum of adverse effects on human health. However, a global view of arsenic-induced heart toxicity is still lacking, and the underlying molecular mechanisms remain unclear. By performing a comparative quantitative proteomic analysis, the present study aims to investigate the alterations of proteome profile in rat heart after long-term exposure to arsenic. As a result, we found that the abundance of 81 proteins were significantly altered by arsenic treatment (35 up-regulated and 46 down-regulated). Among these, 33 proteins were specifically associated with cardiovascular system development and function, including heart development, heart morphology, cardiac contraction and dilation, and other cardiovascular functions. It is further proposed that the aberrant regulation of 14 proteins induced by arsenic would disturb cardiac contraction and relaxation, impair heart morphogenesis and development, and induce thrombosis in rats, which is mediated by the Akt/p38 MAPK signaling pathway. Overall, these findings will augment our knowledge of the involved mechanisms and develop useful biomarkers for cardiotoxicity induced by environmental arsenic exposure. - Highlights: • Arsenic exposure has been associated with a number of adverse health effects. • The molecular mechanisms involved in arsenic-induced cardiotoxicity remain unclear. • Differential proteins were identified in arsenic-exposed rat heart by proteomics. • Arsenic induces heart toxicity through the Akt/p38 MAPK signaling pathway. - Label-free quantitative proteomic analysis of rat heart reveals putative mechanisms and biomarkers for arsenic-induced cardiotoxicity.

  12. Social phenotype extended to communities: expanded multilevel social selection analysis reveals fitness consequences of interspecific interactions.

    Science.gov (United States)

    Campobello, Daniela; Hare, James F; Sarà, Maurizio

    2015-04-01

    In social species, fitness consequences are associated with both individual and social phenotypes. Social selection analysis has quantified the contribution of conspecific social traits to individual fitness. There has been no attempt, however, to apply a social selection approach to quantify the fitness implications of heterospecific social phenotypes. Here, we propose a novel social selection based approach integrating the role of all social interactions at the community level. We extended multilevel selection analysis by including a term accounting for the group phenotype of heterospecifics. We analyzed nest activity as a model social trait common to two species, the lesser kestrel (Falco naumanni) and jackdaw (Corvus monedula), nesting in either single- or mixed-species colonies. By recording reproductive outcome as a measure of relative fitness, our results reveal an asymmetric system wherein only jackdaw breeding performance was affected by the activity phenotypes of both conspecific and heterospecific neighbors. Our model incorporating heterospecific social phenotypes is applicable to animal communities where interacting species share a common social trait, thus allowing an assessment of the selection pressure imposed by interspecific interactions in nature. Finally, we discuss the potential role of ecological limitations accounting for random or preferential assortments among interspecific social phenotypes, and the implications of such processes to community evolution. © 2015 The Author(s).

  13. Comparative Transcriptome Analysis Reveals Different Silk Yields of Two Silkworm Strains.

    Directory of Open Access Journals (Sweden)

    Juan Li

    Full Text Available Cocoon and silk yields are the most important characteristics of sericulture. However, few studies have examined the genes that modulate these features. Further studies of these genes will be useful for improving the products of sericulture. JingSong (JS and Lan10 (L10 are two strains having significantly different cocoon and silk yields. In the current study, RNA-Seq and quantitative polymerase chain reaction (qPCR were performed on both strains in order to determine divergence of the silk gland, which controls silk biosynthesis in silkworms. Compared with L10, JS had 1375 differentially expressed genes (DEGs; 738 up-regulated genes and 673 down-regulated genes. Nine enriched gene ontology (GO terms were identified by GO enrichment analysis based on these DEGs. KEGG enrichment analysis results showed that the DEGs were enriched in three pathways, which were mainly associated with the processing and biosynthesis of proteins. The representative genes in the enrichment pathways and ten significant DEGs were further verified by qPCR, the results of which were consistent with the RNA-Seq data. Our study has revealed differences in silk glands between the two silkworm strains and provides a perspective for understanding the molecular mechanisms determining silk yield.

  14. Proteome analysis of schizophrenia patients Wernicke's area reveals an energy metabolism dysregulation

    Directory of Open Access Journals (Sweden)

    Marangoni Sérgio

    2009-04-01

    Full Text Available Abstract Background Schizophrenia is likely to be a consequence of DNA alterations that, together with environmental factors, will lead to protein expression differences and the ultimate establishment of the illness. The superior temporal gyrus is implicated in schizophrenia and executes functions such as the processing of speech, language skills and sound processing. Methods We performed an individual comparative proteome analysis using two-dimensional gel electrophoresis of 9 schizophrenia and 6 healthy control patients' left posterior superior temporal gyrus (Wernicke's area – BA22p identifying by mass spectrometry several protein expression alterations that could be related to the disease. Results Our analysis revealed 11 downregulated and 14 upregulated proteins, most of them related to energy metabolism. Whereas many of the identified proteins have been previously implicated in schizophrenia, such as fructose-bisphosphate aldolase C, creatine kinase and neuron-specific enolase, new putative disease markers were also identified such as dihydrolipoyl dehydrogenase, tropomyosin 3, breast cancer metastasis-suppressor 1, heterogeneous nuclear ribonucleoproteins C1/C2 and phosphate carrier protein, mitochondrial precursor. Besides, the differential expression of peroxiredoxin 6 (PRDX6 and glial fibrillary acidic protein (GFAP were confirmed by western blot in schizophrenia prefrontal cortex. Conclusion Our data supports a dysregulation of energy metabolism in schizophrenia as well as suggests new markers that may contribute to a better understanding of this complex disease.

  15. Metagenomic analysis reveals symbiotic relationship among bacteria in Microcystis-dominated community

    Directory of Open Access Journals (Sweden)

    Meili eXie

    2016-02-01

    Full Text Available Microcystis bloom, a cyanobacterial mass occurrence often found in eutrophicated water bodies, is one of the most serious threats to freshwater ecosystems worldwide. In nature, Microcystis forms aggregates or colonies that contain heterotrophic bacteria. The Microcystis-bacteria colonies were persistent even when they were maintained in lab culture for a long period. The relationship between Microcystis and the associated bacteria was investigated by a metagenomic approach in this study. We developed a visualization-guided method of binning for genome assembly after total colony DNA sequencing. We found that the method was effective in grouping sequences and it did not require reference genome sequence. Individual genomes of the colony bacteria were obtained and they provided valuable insights into microbial community structures. Analysis of metabolic pathways based on these genomes revealed that while all heterotrophic bacteria were dependent upon Microcystis for carbon and energy, Vitamin B12 biosynthesis, which is required for growth by Microcystis, was accomplished in a cooperative fashion among the bacteria. Our analysis also suggests that individual bacteria in the colony community contributed a complete pathway for degradation of benzoate, which is inhibitory to the cyanobacterial growth, and its ecological implication for Microcystis bloom is discussed.

  16. Bach Is the Father of Harmony: Revealed by a 1/f Fluctuation Analysis across Musical Genres.

    Directory of Open Access Journals (Sweden)

    Dan Wu

    Full Text Available Harmony is a fundamental attribute of music. Close connections exist between music and mathematics since both pursue harmony and unity. In music, the consonance of notes played simultaneously partly determines our perception of harmony; associates with aesthetic responses; and influences the emotion expression. The consonance could be considered as a window to understand and analyze harmony. Here for the first time we used a 1/f fluctuation analysis to investigate whether the consonance fluctuation structure in music with a wide range of composers and genres followed the scale free pattern that has been found for pitch, melody, rhythm, human body movements, brain activity, natural images and geographical features. We then used a network graph approach to investigate which composers were the most influential both within and across genres. Our results showed that patterns of consonance in music did follow scale-free characteristics, suggesting that this feature is a universally evolved one in both music and the living world. Furthermore, our network analysis revealed that Bach's harmony patterns were having the most influence on those used by other composers, followed closely by Mozart.

  17. Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Jaiswal Dinesh Kumar

    2012-10-01

    Full Text Available Abstract Background Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. Results To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the identified proteins are putative integral membrane proteins, possessing transmembrane domains. Conclusions The proteomic analysis revealed many resident integral membrane proteins as well as membrane-associated proteins including those not reported earlier. To our knowledge, this is the first report of membrane proteome from aerial tissues of a crop plant. The findings may provide a better understanding of the biochemical machinery of the plant membranes at the molecular level that might help in functional genomics studies of different developmental pathways and stress-responses.

  18. Comparative proteomics and codon substitution analysis reveal mechanisms of differential resistance to hypoxia in congeneric snails

    KAUST Repository

    Mu, Huawei; Sun, Jin; Cheung, Siu Gin; Fang, Ling; Zhou, Haiyun; Luan, Tiangang; Zhang, Huoming; Wong, Chris K.C.; Qiu, Jian-Wen

    2017-01-01

    Although high-throughput proteomics has been widely applied to study mechanisms of environmental adaptation, the conclusions from studies that are based on one species can be confounded by phylogeny. We compare the freshwater snail Pomacea canaliculata (a notorious invasive species) and its congener Pomacea diffusa (a non-invasive species) to understand the molecular mechanisms of their differential resistance to hypoxia. A 72-h acute exposure experiment showed that P. canaliculata is more tolerant to hypoxia than P. diffusa. The two species were then exposed to three levels of dissolved oxygen (6.7, 2.0 and 1.0mgL−1) for 8h, and their gill proteins were analyzed using iTRAQ-coupled LC-MS/MS. The two species showed striking differences in protein expression profiles, with the more hypoxia tolerant P. canaliculata having more up-regulated proteins in signal transduction and down-regulated proteins in glycolysis and the tricarboxylic acid cycle. Evolutionary analysis revealed five orthologous genes encoding differentially expressed proteins having clear signal of positive selection, indicating selection has acted on some of the hypoxia responsive genes. Our case study has highlighted the potential of integrated proteomics and comparative evolutionary analysis for understanding the genetic basis of adaptation to global environmental change in non-model species. SignificanceRapid globalization in recent decades has greatly facilitated species introduction around the world. Successfully established introduced species, so-called invasive species, have threatened the invaded ecosystems. There has been substantial interest in studying how invasive species respond to extreme environmental conditions because the results can help not only predict their range of expansion and manage their impact, but also may reveal the adaptive mechanisms underlying their invasiveness. Our study has adopted a comparative approach to study the differential physiological and proteomic

  19. Comparative proteomics and codon substitution analysis reveal mechanisms of differential resistance to hypoxia in congeneric snails

    KAUST Repository

    Mu, Huawei

    2017-11-06

    Although high-throughput proteomics has been widely applied to study mechanisms of environmental adaptation, the conclusions from studies that are based on one species can be confounded by phylogeny. We compare the freshwater snail Pomacea canaliculata (a notorious invasive species) and its congener Pomacea diffusa (a non-invasive species) to understand the molecular mechanisms of their differential resistance to hypoxia. A 72-h acute exposure experiment showed that P. canaliculata is more tolerant to hypoxia than P. diffusa. The two species were then exposed to three levels of dissolved oxygen (6.7, 2.0 and 1.0mgL−1) for 8h, and their gill proteins were analyzed using iTRAQ-coupled LC-MS/MS. The two species showed striking differences in protein expression profiles, with the more hypoxia tolerant P. canaliculata having more up-regulated proteins in signal transduction and down-regulated proteins in glycolysis and the tricarboxylic acid cycle. Evolutionary analysis revealed five orthologous genes encoding differentially expressed proteins having clear signal of positive selection, indicating selection has acted on some of the hypoxia responsive genes. Our case study has highlighted the potential of integrated proteomics and comparative evolutionary analysis for understanding the genetic basis of adaptation to global environmental change in non-model species. SignificanceRapid globalization in recent decades has greatly facilitated species introduction around the world. Successfully established introduced species, so-called invasive species, have threatened the invaded ecosystems. There has been substantial interest in studying how invasive species respond to extreme environmental conditions because the results can help not only predict their range of expansion and manage their impact, but also may reveal the adaptive mechanisms underlying their invasiveness. Our study has adopted a comparative approach to study the differential physiological and proteomic

  20. Heterogeneity revealed through meta-analysis might link geographical differences with nasopharyngeal carcinoma incidence in Han Chinese populations

    International Nuclear Information System (INIS)

    Su, Wen-Hui; Chiu, Chi-Cking; Yao Shugart, Yin

    2015-01-01

    Nasopharyngeal carcinoma (NPC) is an epithelial malignancy highly prevalent in southern China, and incidence rates among Han Chinese people vary according to geographic region. Recently, three independent genome-wide association studies (GWASs) confirmed that HLA-A is the main risk gene for NPC. However, the results of studies conducted in regions with dissimilar incidence rates contradicted the claims that HLA-A is the sole risk gene and that the association of rs29232 is independent of the HLA-A effect in the chromosome 6p21.3 region. We performed a meta-analysis, selecting five single-nucleotide polymorphisms (SNPs) in chromosome 6p21.3 mapped in three published GWASs and four case–control studies. The studies involved 8994 patients with NPC and 11,157 healthy controls, all of whom were Han Chinese. The rs2517713 SNP located downstream of HLA-A was significantly associated with NPC (P = 1.08 × 10 −91 , odds ratio [OR] = 0.58, 95 % confidence interval [CI] = 0.55–0.61). The rs29232 SNP exhibited a moderate level of heterogeneity (I 2 = 47 %) that disappeared (I 2 = 0 %) after stratification by moderate- and high-incidence NPC regions. Our results suggested that the HLA-A gene is strongly associated with NPC risk. In addition, the heterogeneity revealed by the meta-analysis of rs29232 might be associated with regional differences in NPC incidence among Han Chinese people. The higher OR of rs29232 and the fact that rs29232 was independent of the HLA-A effect in the moderate-incidence population suggested that rs29232 might have greater relevance to NPC incidence in a moderate-incidence population than in a high-incidence population. The online version of this article (doi:10.1186/s12885-015-1607-0) contains supplementary material, which is available to authorized users

  1. Identification of minute damage in composite bridge structures equipped with fiber optic sensors using the location of neutral axis and finite element analysis

    Science.gov (United States)

    Li, Xi; Glisic, Branko

    2016-04-01

    By definition, the neutral axis of a loaded composite beam structure is the curve along which the section experiences zero bending strain. When no axial loading is present, the location of the neutral axis passes through the centroid of stiffness of the beam cross-section. In the presence of damage, the centroid of stiffness, as well as the neutral axis, shift from the healthy position. The concept of neutral axis can be widely applied to all beam-like structures. According to literature, a change in location of the neutral axis can be associated with damage in the corresponding cross-section. In this paper, the movement of neutral axis near locations of minute damage in a composite bridge structure was studied using finite element analysis and experimental results. The finite element model was developed based on a physical scale model of a composite simply-supported structure with controlled minute damage in the reinforced concrete deck. The structure was equipped with long-gauge fiber optic strain and temperature sensors at a healthy reference location as well as two locations of damage. A total of 12 strain sensors were installed during construction and used to monitor the structure during various loading events. This paper aims to explain previous experimental results which showed that the observed positions of neutral axis near damage locations were higher than the predicted healthy locations in some loading events. Analysis has shown that finite element analysis has potential to simulate and explain the physical behavior of the test structure.

  2. Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis.

    Science.gov (United States)

    González, Carolina; Yanquepe, María; Cardenas, Juan Pablo; Valdes, Jorge; Quatrini, Raquel; Holmes, David S; Dopson, Mark

    2014-11-01

    Acidophilic microorganisms inhabit low pH environments such as acid mine drainage that is generated when sulfide minerals are exposed to air. The genome sequence of the psychrotolerant Acidithiobacillus ferrivorans SS3 was compared to a metagenome from a low temperature acidic stream dominated by an A. ferrivorans-like strain. Stretches of genomic DNA characterized by few matches to the metagenome, termed 'metagenomic islands', encoded genes associated with metal efflux and pH homeostasis. The metagenomic islands were enriched in mobile elements such as phage proteins, transposases, integrases and in one case, predicted to be flanked by truncated tRNAs. Cus gene clusters predicted to be involved in copper efflux and further Cus-like RND systems were predicted to be located in metagenomic islands and therefore, constitute part of the flexible gene complement of the species. Phylogenetic analysis of Cus clusters showed both lineage specificity within the Acidithiobacillus genus as well as niche specificity associated with an acidic environment. The metagenomic islands also contained a predicted copper efflux P-type ATPase system and a polyphosphate kinase potentially involved in polyphosphate mediated copper resistance. This study identifies genetic variability of low temperature acidophiles that likely reflects metal resistance selective pressures in the copper rich environment. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  3. Secondary analysis of a marketing research database reveals patterns in dairy product purchases over time.

    Science.gov (United States)

    Van Wave, Timothy W; Decker, Michael

    2003-04-01

    Development of a method using marketing research data to assess food purchase behavior and consequent nutrient availability for purposes of nutrition surveillance, evaluation of intervention effects, and epidemiologic studies of diet-health relationships. Data collected on household food purchases accrued over a 13-week period were selected by using Universal Product Code numbers and household characteristics from a marketing research database. Universal Product Code numbers for 39,408 dairy product purchases were linked to a standard reference for food composition to estimate the nutrient content of foods purchased over time. Two thousand one hundred sixty-one households located in Victoria, Texas, and surrounding communities who were active members of a frequent shopper program. Demographic characteristics of sample households and the nutrient content of their dairy product purchases were analyzed using frequency distribution, cross tabulation, analysis of variance, and t test procedures. A method for using marketing research data was successfully used to estimate household purchases of specific foods and their nutrient content from a marketing database containing hundreds of thousands of records. Distribution of dairy product purchases and their concomitant nutrients between Hispanic and non-Hispanic households were significant (P<.01, P<.001, respectively) and sustained over time. Purchase records from large, nationally representative panels of shoppers, such as those maintained by major market research companies, might be used to accomplish detailed longitudinal epidemiologic studies or surveillance of national food- and nutrient-purchasing patterns within and between countries and segments of their respective populations.

  4. QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance.

    Science.gov (United States)

    Santos, Jansen Rodrigo Pereira; Ndeve, Arsenio Daniel; Huynh, Bao-Lam; Matthews, William Charles; Roberts, Philip Alan

    2018-01-01

    Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN). Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL) population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL) were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.

  5. Integrated bioinformatics analysis reveals key candidate genes and pathways in breast cancer.

    Science.gov (United States)

    Wang, Yuzhi; Zhang, Yi; Huang, Qian; Li, Chengwen

    2018-04-19

    Breast cancer (BC) is the leading malignancy in women worldwide, yet relatively little is known about the genes and signaling pathways involved in BC tumorigenesis and progression. The present study aimed to elucidate potential key candidate genes and pathways in BC. Five gene expression profile data sets (GSE22035, GSE3744, GSE5764, GSE21422 and GSE26910) were downloaded from the Gene Expression Omnibus (GEO) database, which included data from 113 tumorous and 38 adjacent non‑tumorous tissue samples. Differentially expressed genes (DEGs) were identified using t‑tests in the limma R package. These DEGs were subsequently investigated by pathway enrichment analysis and a protein‑protein interaction (PPI) network was constructed. The most significant module from the PPI network was selected for pathway enrichment analysis. In total, 227 DEGs were identified, of which 82 were upregulated and 145 were downregulated. Pathway enrichment analysis results revealed that the upregulated DEGs were mainly enriched in 'cell division', the 'proteinaceous extracellular matrix (ECM)', 'ECM structural constituents' and 'ECM‑receptor interaction', whereas downregulated genes were mainly enriched in 'response to drugs', 'extracellular space', 'transcriptional activator activity' and the 'peroxisome proliferator‑activated receptor signaling pathway'. The PPI network contained 174 nodes and 1,257 edges. DNA topoisomerase 2‑a, baculoviral inhibitor of apoptosis repeat‑containing protein 5, cyclin‑dependent kinase 1, G2/mitotic‑specific cyclin‑B1 and kinetochore protein NDC80 homolog were identified as the top 5 hub genes. Furthermore, the genes in the most significant module were predominantly involved in 'mitotic nuclear division', 'mid‑body', 'protein binding' and 'cell cycle'. In conclusion, the DEGs, relative pathways and hub genes identified in the present study may aid in understanding of the molecular mechanisms underlying BC progression and provide

  6. Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis.

    Directory of Open Access Journals (Sweden)

    Hong Hao

    Full Text Available A stringent control of homeostasis is critical for functional maintenance and survival of neurons. In the mammalian retina, the basic motif leucine zipper transcription factor NRL determines rod versus cone photoreceptor cell fate and activates the expression of many rod-specific genes. Here, we report an integrated analysis of NRL-centered gene regulatory network by coupling chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq data from Illumina and ABI platforms with global expression profiling and in vivo knockdown studies. We identified approximately 300 direct NRL target genes. Of these, 22 NRL targets are associated with human retinal dystrophies, whereas 95 mapped to regions of as yet uncloned retinal disease loci. In silico analysis of NRL ChIP-Seq peak sequences revealed an enrichment of distinct sets of transcription factor binding sites. Specifically, we discovered that genes involved in photoreceptor function include binding sites for both NRL and homeodomain protein CRX. Evaluation of 26 ChIP-Seq regions validated their enhancer functions in reporter assays. In vivo knockdown of 16 NRL target genes resulted in death or abnormal morphology of rod photoreceptors, suggesting their importance in maintaining retinal function. We also identified histone demethylase Kdm5b as a novel secondary node in NRL transcriptional hierarchy. Exon array analysis of flow-sorted photoreceptors in which Kdm5b was knocked down by shRNA indicated its role in regulating rod-expressed genes. Our studies identify candidate genes for retinal dystrophies, define cis-regulatory module(s for photoreceptor-expressed genes and provide a framework for decoding transcriptional regulatory networks that dictate rod homeostasis.

  7. QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance.

    Directory of Open Access Journals (Sweden)

    Jansen Rodrigo Pereira Santos

    Full Text Available Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN. Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.

  8. Bioinformatics analysis of RNA-seq data revealed critical genes in colon adenocarcinoma.

    Science.gov (United States)

    Xi, W-D; Liu, Y-J; Sun, X-B; Shan, J; Yi, L; Zhang, T-T

    2017-07-01

    RNA-seq data of colon adenocarcinoma (COAD) were analyzed with bioinformatics tools to discover critical genes in the disease. Relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. RNA-seq data of COAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. False positive discovery (FDR) 1 were set as the cut-offs to screen out differentially expressed genes (DEGs). Gene coexpression network was constructed with package Ebcoexpress. GO enrichment analysis was performed for the DEGs in the gene coexpression network with DAVID. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was also performed for the genes with KOBASS 2.0. Modules were identified with MCODE of Cytoscape. Relevant small molecules drugs were predicted by Connectivity map. Relevant miRNAs and TFs were searched by WebGestalt. A total of 457 DEGs, including 255 up-regulated and 202 down-regulated genes, were identified from 437 COAD and 39 control samples. A gene coexpression network was constructed containing 40 DEGs and 101 edges. The genes were mainly associated with collagen fibril organization, extracellular matrix organization and translation. Two modules were identified from the gene coexpression network, which were implicated in muscle contraction and extracellular matrix organization, respectively. Several critical genes were disclosed, such as MYH11, COL5A2 and ribosomal proteins. Nine relevant small molecule drugs were identified, such as scriptaid and STOCK1N-35874. Accordingly, a total of 17 TFs and 10 miRNAs related to COAD were acquired, such as ETS2, NFAT, AP4, miR-124A, MiR-9, miR-96 and let-7. Several critical genes and relevant drugs, TFs and miRNAs were revealed in COAD. These findings could advance the understanding of the disease and benefit therapy development.

  9. Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

    Directory of Open Access Journals (Sweden)

    Chamovitz Daniel A

    2009-09-01

    Full Text Available Abstract Background Analyses of gene expression data from microarray experiments has become a central tool for identifying co-regulated, functional gene modules. A crucial aspect of such analysis is the integration of data from different experiments and different laboratories. How to weigh the contribution of different experiments is an important point influencing the final outcomes. We have developed a novel method for this integration, and applied it to genome-wide data from multiple Arabidopsis microarray experiments performed under a variety of experimental conditions. The goal of this study is to identify functional globally co-regulated gene modules in the Arabidopsis genome. Results Following the analysis of 21,000 Arabidopsis genes in 43 datasets and about 2 × 108 gene pairs, we identified a globally co-expressed gene network. We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations. Two types of modules were identified in the regulatory network that differed in their sensitivity to the node-scoring parameter; we further showed these two pertain to general and specialized modules. Some of these modules were further investigated using the Genevestigator compendium of microarray experiments. Analyses of smaller subsets of data lead to the identification of condition-specific modules. Conclusion Our method for identification of gene clusters allows the integration of diverse microarray experiments from many sources. The analysis reveals that part of the Arabidopsis transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules. Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.

  10. Data-driven analysis of simultaneous EEG/fMRI reveals neurophysiological phenotypes of impulse control.

    Science.gov (United States)

    Schmüser, Lena; Sebastian, Alexandra; Mobascher, Arian; Lieb, Klaus; Feige, Bernd; Tüscher, Oliver

    2016-09-01

    Response inhibition is the ability to suppress inadequate but prepotent or ongoing response tendencies. A fronto-striatal network is involved in these processes. Between-subject differences in the intra-individual variability have been suggested to constitute a key to pathological processes underlying impulse control disorders. Single-trial EEG/fMRI analysis allows to increase sensitivity for inter-individual differences by incorporating intra-individual variability. Thirty-eight healthy subjects performed a visual Go/Nogo task during simultaneous EEG/fMRI. Of 38 healthy subjects, 21 subjects reliably showed Nogo-related ICs (Nogo-IC-positive) while 17 subjects (Nogo-IC-negative) did not. Comparing both groups revealed differences on various levels: On trait level, Nogo-IC-negative subjects scored higher on questionnaires regarding attention deficit/hyperactivity disorder; on a behavioral level, they displayed slower response times (RT) and higher intra-individual RT variability while both groups did not differ in their inhibitory performance. On the neurophysiological level, Nogo-IC-negative subjects showed a hyperactivation of left inferior frontal cortex/insula and left putamen as well as significantly reduced P3 amplitudes. Thus, a data-driven approach for IC classification and the resulting presence or absence of early Nogo-specific ICs as criterion for group selection revealed group differences at behavioral and neurophysiological levels. This may indicate electrophysiological phenotypes characterized by inter-individual variations of neural and behavioral correlates of impulse control. We demonstrated that the inter-individual difference in an electrophysiological correlate of response inhibition is correlated with distinct, potentially compensatory neural activity. This may suggest the existence of electrophysiologically dissociable phenotypes of behavioral and neural motor response inhibition with the Nogo-IC-positive phenotype possibly providing

  11. Genome sequencing and analysis reveals possible determinants of Staphylococcus aureus nasal carriage

    Directory of Open Access Journals (Sweden)

    Cole Alexander M

    2008-09-01

    Full Text Available Abstract Background Nasal carriage of Staphylococcus aureus is a major risk factor in clinical and community settings due to the range of etiologies caused by the organism. We have identified unique immunological and ultrastructural properties associated with nasal carriage isolates denoting a role for bacterial factors in nasal carriage. However, despite extensive molecular level characterizations by several groups suggesting factors necessary for colonization on nasal epithelium, genetic determinants of nasal carriage are unknown. Herein, we have set a genomic foundation for unraveling the bacterial determinants of nasal carriage in S. aureus. Results MLST analysis revealed no lineage specific differences between carrier and non-carrier strains suggesting a role for mobile genetic elements. We completely sequenced a model carrier isolate (D30 and a model non-carrier strain (930918-3 to identify differential gene content. Comparison revealed the presence of 84 genes unique to the carrier strain and strongly suggests a role for Type VII secretion systems in nasal carriage. These genes, along with a putative pathogenicity island (SaPIBov present uniquely in the carrier strains are likely important in affecting carriage. Further, PCR-based genotyping of other clinical isolates for a specific subset of these 84 genes raise the possibility of nasal carriage being caused by multiple gene sets. Conclusion Our data suggest that carriage is likely a heterogeneic phenotypic trait and implies a role for nucleotide level polymorphism in carriage. Complete genome level analyses of multiple carriage strains of S. aureus will be important in clarifying molecular determinants of S. aureus nasal carriage.

  12. Dysconnection topography in schizophrenia revealed with state-space analysis of EEG.

    Science.gov (United States)

    Jalili, Mahdi; Lavoie, Suzie; Deppen, Patricia; Meuli, Reto; Do, Kim Q; Cuénod, Michel; Hasler, Martin; De Feo, Oscar; Knyazeva, Maria G

    2007-10-24

    The dysconnection hypothesis has been proposed to account for pathophysiological mechanisms underlying schizophrenia. Widespread structural changes suggesting abnormal connectivity in schizophrenia have been imaged. A functional counterpart of the structural maps would be the EEG synchronization maps. However, due to the limits of currently used bivariate methods, functional correlates of dysconnection are limited to the isolated measurements of synchronization between preselected pairs of EEG signals. To reveal a whole-head synchronization topography in schizophrenia, we applied a new method of multivariate synchronization analysis called S-estimator to the resting dense-array (128 channels) EEG obtained from 14 patients and 14 controls. This method determines synchronization from the embedding dimension in a state-space domain based on the theoretical consequence of the cooperative behavior of simultaneous time series-the shrinking of the state-space embedding dimension. The S-estimator imaging revealed a specific synchronization landscape in schizophrenia patients. Its main features included bilaterally increased synchronization over temporal brain regions and decreased synchronization over the postcentral/parietal region neighboring the midline. The synchronization topography was stable over the course of several months and correlated with the severity of schizophrenia symptoms. In particular, direct correlations linked positive, negative, and general psychopathological symptoms to the hyper-synchronized temporal clusters over both hemispheres. Along with these correlations, general psychopathological symptoms inversely correlated within the hypo-synchronized postcentral midline region. While being similar to the structural maps of cortical changes in schizophrenia, the S-maps go beyond the topography limits, demonstrating a novel aspect of the abnormalities of functional cooperation: namely, regionally reduced or enhanced connectivity. The new method of

  13. Dysconnection topography in schizophrenia revealed with state-space analysis of EEG.

    Directory of Open Access Journals (Sweden)

    Mahdi Jalili

    2007-10-01

    Full Text Available The dysconnection hypothesis has been proposed to account for pathophysiological mechanisms underlying schizophrenia. Widespread structural changes suggesting abnormal connectivity in schizophrenia have been imaged. A functional counterpart of the structural maps would be the EEG synchronization maps. However, due to the limits of currently used bivariate methods, functional correlates of dysconnection are limited to the isolated measurements of synchronization between preselected pairs of EEG signals.To reveal a whole-head synchronization topography in schizophrenia, we applied a new method of multivariate synchronization analysis called S-estimator to the resting dense-array (128 channels EEG obtained from 14 patients and 14 controls. This method determines synchronization from the embedding dimension in a state-space domain based on the theoretical consequence of the cooperative behavior of simultaneous time series-the shrinking of the state-space embedding dimension. The S-estimator imaging revealed a specific synchronization landscape in schizophrenia patients. Its main features included bilaterally increased synchronization over temporal brain regions and decreased synchronization over the postcentral/parietal region neighboring the midline. The synchronization topography was stable over the course of several months and correlated with the severity of schizophrenia symptoms. In particular, direct correlations linked positive, negative, and general psychopathological symptoms to the hyper-synchronized temporal clusters over both hemispheres. Along with these correlations, general psychopathological symptoms inversely correlated within the hypo-synchronized postcentral midline region. While being similar to the structural maps of cortical changes in schizophrenia, the S-maps go beyond the topography limits, demonstrating a novel aspect of the abnormalities of functional cooperation: namely, regionally reduced or enhanced connectivity.The new

  14. Systematic Prioritization and Integrative Analysis of Copy Number Variations in Schizophrenia Reveal Key Schizophrenia Susceptibility Genes

    Science.gov (United States)

    Luo, Xiongjian; Huang, Liang; Han, Leng; Luo, Zhenwu; Hu, Fang; Tieu, Roger; Gan, Lin

    2014-01-01

    Schizophrenia is a common mental disorder with high heritability and strong genetic heterogeneity. Common disease-common variants hypothesis predicts that schizophrenia is attributable in part to common genetic variants. However, recent studies have clearly demonstrated that copy number variations (CNVs) also play pivotal roles in schizophrenia susceptibility and explain a proportion of missing heritability. Though numerous CNVs have been identified, many of the regions affected by CNVs show poor overlapping among different studies, and it is not known whether the genes disrupted by CNVs contribute to the risk of schizophrenia. By using cumulative scoring, we systematically prioritized the genes affected by CNVs in schizophrenia. We identified 8 top genes that are frequently disrupted by CNVs, including NRXN1, CHRNA7, BCL9, CYFIP1, GJA8, NDE1, SNAP29, and GJA5. Integration of genes affected by CNVs with known schizophrenia susceptibility genes (from previous genetic linkage and association studies) reveals that many genes disrupted by CNVs are also associated with schizophrenia. Further protein-protein interaction (PPI) analysis indicates that protein products of genes affected by CNVs frequently interact with known schizophrenia-associated proteins. Finally, systematic integration of CNVs prioritization data with genetic association and PPI data identifies key schizophrenia candidate genes. Our results provide a global overview of genes impacted by CNVs in schizophrenia and reveal a densely interconnected molecular network of de novo CNVs in schizophrenia. Though the prioritized top genes represent promising schizophrenia risk genes, further work with different prioritization methods and independent samples is needed to confirm these findings. Nevertheless, the identified key candidate genes may have important roles in the pathogenesis of schizophrenia, and further functional characterization of these genes may provide pivotal targets for future therapeutics and

  15. Systems-level analysis of risk genes reveals the modular nature of schizophrenia.

    Science.gov (United States)

    Liu, Jiewei; Li, Ming; Luo, Xiong-Jian; Su, Bing

    2018-05-19

    Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10 -31 ). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10 -11 ), closeness centrality (P = 7.56 × 10 -11 ), betweeness centrality (P = 1.29 × 10 -11 ), clustering coefficient (P = 2.22 × 10 -2 ), and shorter average shortest path length (P = 7.56 × 10 -11 ). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Where Do Freestanding Emergency Departments Choose to Locate? A National Inventory and Geographic Analysis in Three States.

    Science.gov (United States)

    Schuur, Jeremiah D; Baker, Olesya; Freshman, Jaclyn; Wilson, Michael; Cutler, David M

    2017-04-01

    We determine the number and location of freestanding emergency departments (EDs) across the United States and determine the population characteristics of areas where freestanding EDs are located. We conducted a systematic inventory of US freestanding EDs. For the 3 states with the highest number of freestanding EDs, we linked demographic, insurance, and health services data, using the 5-digit ZIP code corresponding to the freestanding ED's location. To create a comparison nonfreestanding ED group, we matched 187 freestanding EDs to 1,048 nonfreestanding ED ZIP codes on land and population within state. We compared differences in demographic, insurance, and health services factors between matched ZIP codes with and without freestanding EDs, using univariate regressions with weights. We identified 360 freestanding EDs located in 30 states; 54.2% of freestanding EDs were hospital satellites, 36.6% were independent, and 9.2% were not classifiable. The 3 states with the highest number of freestanding EDs accounted for 66% of all freestanding EDs: Texas (181), Ohio (34), and Colorado (24). Across all 3 states, freestanding EDs were located in ZIP codes that had higher incomes and a lower proportion of the population with Medicaid. In Texas and Ohio, freestanding EDs were located in ZIP codes with a higher proportion of the population with private insurance. In Texas, freestanding EDs were located in ZIP codes that had fewer Hispanics, had a greater number of hospital-based EDs and physician offices, and had more physician visits and medical spending per year than ZIP codes without a freestanding ED. In Ohio, freestanding EDs were located in ZIP codes with fewer hospital-based EDs. In Texas, Ohio, and Colorado, freestanding EDs were located in areas with a better payer mix. The location of freestanding EDs in relation to other health care facilities and use and spending on health care varied between states. Copyright © 2016 American College of Emergency Physicians

  17. Proteomic and comparative genomic analysis reveals adaptability of Brassica napus to phosphorus-deficient stress.

    Science.gov (United States)

    Chen, Shuisen; Ding, Guangda; Wang, Zhenhua; Cai, Hongmei; Xu, Fangsen

    2015-03-18

    Given low solubility and immobility in many soils of the world, phosphorus (P) may be the most widely studied macronutrient for plants. In an attempt to gain an insight into the adaptability of Brassica napus to P deficiency, proteome alterations of roots and leaves in two B. napus contrasting genotypes, P-efficient 'Eyou Changjia' and P-inefficient 'B104-2', under long-term low P stress and short-term P-free starvation conditions were investigated, and proteomic combined with comparative genomic analyses were conducted to interpret the interrelation of differential abundance protein species (DAPs) responding to P deficiency with quantitative trait loci (QTLs) for P deficiency tolerance. P-efficient 'Eyou Changjia' had higher dry weight and P content, and showed high tolerance to low P stress compared with P-inefficient 'B104-2'. A total of 146 DAPs were successfully identified by MALDI TOF/TOF MS, which were categorized into several groups including defense and stress response, carbohydrate and energy metabolism, signaling and regulation, amino acid and fatty acid metabolism, protein process, biogenesis and cellular component, and function unknown. 94 of 146 DAPs were mapped to a linkage map constructed by a B. napus population derived from a cross between the two genotypes, and 72 DAPs were located in the confidence intervals of QTLs for P efficiency related traits. We conclude that the identification of these DAPs and the co-location of DAPs with QTLs in the B. napus linkage genetic map provide us novel information in understanding the adaptability of B. napus to P deficiency, and helpful to isolate P-efficient genes in B. napus. Low P seriously limits the production and quality of B. napus. Proteomics and genetic linkage map were widely used to study the adaptive strategies of B. napus response to P deficiency, proteomic combined with comparative genetic analysis to investigate the correlations between DAPs and QTLs are scarce. Thus, we herein investigated

  18. Changes in transport behavior during the financial crisis. An analysis of urban form, location and transport behavior in the greater Copenhagen area 2006-2011

    DEFF Research Database (Denmark)

    Nielsen, Thomas Alexander Sick

    2015-01-01

    A multitude of studies have focussed on the connections between urban form, location and transport behavior to inform sustainable and resilient urban planning. However, few have studied the stability of urban form and location effects under changing economic conditions. This paper presents...... an analysis of the changes in urban form and location correlates of travel distances in the Danish Zealand/Copenhagen region from before the financial crisis (2006/07) to some years after the financial downturn (2010/11). Significant changes are found in the socio-economic as well as urban form and location....../destinations. It follows that the location pattern, the geographical configuration of the urban region, is a factor in households' adaptive strategies which partly determine the possibilities for reducing travel and the possibilities for adaption and regional resilience....

  19. Biophysical analysis of HTLV-1 particles reveals novel insights into particle morphology and Gag stochiometry

    Directory of Open Access Journals (Sweden)

    Fogarty Keir H

    2010-09-01

    Full Text Available Abstract Background Human T-lymphotropic virus type 1 (HTLV-1 is an important human retrovirus that is a cause of adult T-cell leukemia/lymphoma. While an important human pathogen, the details regarding virus replication cycle, including the nature of HTLV-1 particles, remain largely unknown due to the difficulties in propagating the virus in tissue culture. In this study, we created a codon-optimized HTLV-1 Gag fused to an EYFP reporter as a model system to quantitatively analyze HTLV-1 particles released from producer cells. Results The codon-optimized Gag led to a dramatic and highly robust level of Gag expression as well as virus-like particle (VLP production. The robust level of particle production overcomes previous technical difficulties with authentic particles and allowed for detailed analysis of particle architecture using two novel methodologies. We quantitatively measured the diameter and morphology of HTLV-1 VLPs in their native, hydrated state using cryo-transmission electron microscopy (cryo-TEM. Furthermore, we were able to determine HTLV-1 Gag stoichiometry as well as particle size with the novel biophysical technique of fluorescence fluctuation spectroscopy (FFS. The average HTLV-1 particle diameter determined by cryo-TEM and FFS was 71 ± 20 nm and 75 ± 4 nm, respectively. These values are significantly smaller than previous estimates made of HTLV-1 particles by negative staining TEM. Furthermore, cryo-TEM reveals that the majority of HTLV-1 VLPs lacks an ordered structure of the Gag lattice, suggesting that the HTLV-1 Gag shell is very likely to be organized differently compared to that observed with HIV-1 Gag in immature particles. This conclusion is supported by our observation that the average copy number of HTLV-1 Gag per particle is estimated to be 510 based on FFS, which is significantly lower than that found for HIV-1 immature virions. Conclusions In summary, our studies represent the first quantitative biophysical

  20. Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds.

    Science.gov (United States)

    Xie, Shanshan; Yang, Xukai; Wang, Dehe; Zhu, Feng; Yang, Ning; Hou, Zhuocheng; Ning, Zhonghua

    2018-01-01

    Selection for cold tolerance in chickens is important for improving production performance and animal welfare. The identification of chicken breeds with higher cold tolerance and production performance will help to target candidates for the selection. The thyroid gland plays important roles in thermal adaptation, and its function is influenced by breed differences and transcriptional plasticity, both of which remain largely unknown in the chicken thyroid transcriptome. In this study, we subjected Bashang Long-tail (BS) and Rhode Island Red (RIR) chickens to either cold or warm environments for 21 weeks and investigated egg production performance, body weight changes, serum thyroid hormone concentrations, and thyroid gland transcriptome profiles. RIR chickens had higher egg production than BS chickens under warm conditions, but BS chickens produced more eggs than RIRs under cold conditions. Furthermore, BS chickens showed stable body weight gain under cold conditions while RIRs did not. These results suggested that BS breed is a preferable candidate for cold-tolerance selection and that the cold adaptability of RIRs should be improved in the future. BS chickens had higher serum thyroid hormone concentrations than RIRs under both environments. RNA-Seq generated 344.3 million paired-end reads from 16 sequencing libraries, and about 90% of the processed reads were concordantly mapped to the chicken reference genome. Differential expression analysis identified 46-1,211 genes in the respective comparisons. With regard to breed differences in the thyroid transcriptome, BS chickens showed higher cell replication and development, and immune response-related activity, while RIR chickens showed higher carbohydrate and protein metabolism activity. The cold environment reduced breed differences in the thyroid transcriptome compared with the warm environment. Transcriptional plasticity analysis revealed different adaptive responses in BS and RIR chickens to cope with the cold

  1. Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family.

    Science.gov (United States)

    Pearce, Stephen; Huttly, Alison K; Prosser, Ian M; Li, Yi-dan; Vaughan, Simon P; Gallova, Barbora; Patil, Archana; Coghill, Jane A; Dubcovsky, Jorge; Hedden, Peter; Phillips, Andrew L

    2015-06-05

    The gibberellin (GA) pathway plays a central role in the regulation of plant development, with the 2-oxoglutarate-dependent dioxygenases (2-ODDs: GA20ox, GA3ox, GA2ox) that catalyse the later steps in the biosynthetic pathway of particularly importance in regulating bioactive GA levels. Although GA has important impacts on crop yield and quality, our understanding of the regulation of GA biosynthesis during wheat and barley development remains limited. In this study we identified or assembled genes encoding the GA 2-ODDs of wheat, barley and Brachypodium distachyon and characterised the wheat genes by heterologous expression and transcript analysis. The wheat, barley and Brachypodium genomes each contain orthologous copies of the GA20ox, GA3ox and GA2ox genes identified in rice, with the exception of OsGA3ox1 and OsGA2ox5 which are absent in these species. Some additional paralogs of 2-ODD genes were identified: notably, a novel gene in the wheat B genome related to GA3ox2 was shown to encode a GA 1-oxidase, named as TaGA1ox-B1. This enzyme is likely to be responsible for the abundant 1β-hydroxylated GAs present in developing wheat grains. We also identified a related gene in barley, located in a syntenic position to TaGA1ox-B1, that encodes a GA 3,18-dihydroxylase which similarly accounts for the accumulation of unusual GAs in barley grains. Transcript analysis showed that some paralogs of the different classes of 2-ODD were expressed mainly in a single tissue or at specific developmental stages. In particular, TaGA20ox3, TaGA1ox1, TaGA3ox3 and TaGA2ox7 were predominantly expressed in developing grain. More detailed analysis of grain-specific gene expression showed that while the transcripts of biosynthetic genes were most abundant in the endosperm, genes encoding inactivation and signalling components were more highly expressed in the seed coat and pericarp. The comprehensive expression and functional characterisation of the multigene families encoding the 2-ODD

  2. Multichannel detrended fluctuation analysis reveals synchronized patterns of spontaneous spinal activity in anesthetized cats.

    Directory of Open Access Journals (Sweden)

    Erika E Rodríguez

    Full Text Available The analysis of the interaction and synchronization of relatively large ensembles of neurons is fundamental for the understanding of complex functions of the nervous system. It is known that the temporal synchronization of neural ensembles is involved in the generation of specific motor, sensory or cognitive processes. Also, the intersegmental coherence of spinal spontaneous activity may indicate the existence of synaptic neural pathways between different pairs of lumbar segments. In this study we present a multichannel version of the detrended fluctuation analysis method (mDFA to analyze the correlation dynamics of spontaneous spinal activity (SSA from time series analysis. This method together with the classical detrended fluctuation analysis (DFA were used to find out whether the SSA recorded in one or several segments in the spinal cord of the anesthetized cat occurs either in a random or in an organized manner. Our results are consistent with a non-random organization of the sets of neurons involved in the generation of spontaneous cord dorsum potentials (CDPs recorded either from one lumbar segment (DFA-α mean = 1.04[Formula: see text]0.09 or simultaneously from several lumbar segments (mDFA-α mean = 1.01[Formula: see text]0.06, where α = 0.5 indicates randomness while α = 0.5 indicates long-term correlations. To test the sensitivity of the mDFA method we also examined the effects of small spinal lesions aimed to partially interrupt connectivity between neighboring lumbosacral segments. We found that the synchronization and correlation between the CDPs recorded from the L5 and L6 segments in both sides of the spinal cord were reduced when a lesion comprising the left dorsal quadrant was performed between the segments L5 and L6 (mDFA-[Formula: see text] = 0.992 as compared to initial conditions mDFA-α = 1.186. The synchronization and correlation were reduced even further after a similar additional right spinal lesion (mDFA-α = 0

  3. Estimation of electrode location in a rat motor cortex by laminar analysis of electrophysiology and intracortical electrical stimulation

    Science.gov (United States)

    Yazdan-Shahmorad, A.; Lehmkuhle, M. J.; Gage, G. J.; Marzullo, T. C.; Parikh, H.; Miriani, R. M.; Kipke, D. R.

    2011-08-01

    While the development of microelectrode arrays has enabled access to disparate regions of a cortex for neurorehabilitation, neuroprosthetic and basic neuroscience research, accurate interpretation of the signals and manipulation of the cortical neurons depend upon the anatomical placement of the electrode arrays in a layered cortex. Toward this end, this report compares two in vivo methods for identifying the placement of electrodes in a linear array spaced 100 µm apart based on in situ laminar analysis of (1) ketamine-xylazine-induced field potential oscillations in a rat motor cortex and (2) an intracortical electrical stimulation-induced movement threshold. The first method is based on finding the polarity reversal in laminar oscillations which is reported to appear at the transition between layers IV and V in laminar 'high voltage spindles' of the rat cortical column. Analysis of histological images in our dataset indicates that polarity reversal is detected 150.1 ± 104.2 µm below the start of layer V. The second method compares the intracortical microstimulation currents that elicit a physical movement for anodic versus cathodic stimulation. It is based on the hypothesis that neural elements perpendicular to the electrode surface are preferentially excited by anodic stimulation while cathodic stimulation excites those with a direction component parallel to its surface. With this method, we expect to see a change in the stimulation currents that elicits a movement at the beginning of layer V when comparing anodic versus cathodic stimulation as the upper cortical layers contain neuronal structures that are primarily parallel to the cortical surface and lower layers contain structures that are primarily perpendicular. Using this method, there was a 78.7 ± 68 µm offset in the estimate of the depth of the start of layer V. The polarity reversal method estimates the beginning of layer V within ±90 µm with 95% confidence and the intracortical stimulation

  4. Network Analysis Reveals Putative Genes Affecting Meat Quality in Angus Cattle.

    Science.gov (United States)

    Mateescu, Raluca G; Garrick, Dorian J; Reecy, James M

    2017-01-01

    Improvements in eating satisfaction will benefit consumers and should increase beef demand which is of interest to the beef industry. Tenderness, juiciness, and flavor are major determinants of the palatability of beef and are often used to reflect eating satisfaction. Carcass qualities are used as indicator traits for meat quality, with higher quality grade carcasses expected to relate to more tender and palatable meat. However, meat quality is a complex concept determined by many component traits making interpretation of genome-wide association studies (GWAS) on any one component challenging to interpret. Recent approaches combining traditional GWAS with gene network interactions theory could be more efficient in dissecting the genetic architecture of complex traits. Phenotypic measures of 23 traits reflecting carcass characteristics, components of meat quality, along with mineral and peptide concentrations were used along with Illumina 54k bovine SNP genotypes to derive an annotated gene network associated with meat quality in 2,110 Angus beef cattle. The efficient mixed model association (EMMAX) approach in combination with a genomic relationship matrix was used to directly estimate the associations between 54k SNP genotypes and each of the 23 component traits. Genomic correlated regions were identified by partial correlations which were further used along with an information theory algorithm to derive gene network clusters. Correlated SNP across 23 component traits were subjected to network scoring and visualization software to identify significant SNP. Significant pathways implicated in the meat quality complex through GO term enrichment analysis included angiogenesis, inflammation, transmembrane transporter activity, and receptor activity. These results suggest that network analysis using partial correlations and annotation of significant SNP can reveal the genetic architecture of complex traits and provide novel information regarding biological mechanisms

  5. Gene array analysis of PD-1H overexpressing monocytes reveals a pro-inflammatory profile

    Directory of Open Access Journals (Sweden)

    Preeti Bharaj

    2018-02-01

    Full Text Available We have previously reported that overexpression of Programmed Death -1 Homolog (PD-1H in human monocytes leads to activation and spontaneous secretion of multiple pro inflammatory cytokines. Here we evaluate changes in monocytes gene expression after enforced PD-1H expression by gene array. The results show that there are significant alterations in 51 potential candidate genes that relate to immune response, cell adhesion and metabolism. Genes corresponding to pro-inflammatory cytokines showed the highest upregulation, 7, 3.2, 3.0, 5.8, 4.4 and 3.1 fold upregulation of TNF-α, IL-1 β, IFN-α, γ, λ and IL-27 relative to vector control. The data are in agreement with cytometric bead array analysis showing induction of proinflammatory cytokines, IL-6, IL-1β and TNF-α by PD-1H. Other genes related to inflammation, include transglutaminase 2 (TG2, NF-κB (p65 and p50 and toll like receptors (TLR 3 and 4 were upregulated 5, 4.5 and 2.5 fold, respectively. Gene set enrichment analysis (GSEA also revealed that signaling pathways related to inflammatory response, such as NFκB, AT1R, PYK2, MAPK, RELA, TNFR1, MTOR and proteasomal degradation, were significantly upregulated in response to PD-1H overexpression. We validated the results utilizing a standard inflammatory sepsis model in humanized BLT mice, finding that PD-1H expression was highly correlated with proinflammatory cytokine production. We therefore conclude that PD-1H functions to enhance monocyte activation and the induction of a pro-inflammatory gene expression profile.

  6. Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps.

    Science.gov (United States)

    Huang, Xing; Xu, Jing; Chen, Lin; Wang, Yu; Gu, Xiaobin; Peng, Xuerong; Yang, Guangyou

    2017-04-20

    Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. Analysis of a total of 8,620 annotated mRNA sequences from T. multiceps indicated only a weak codon bias, with mean GC and GC3 content values of 49.29% and 51.43%, respectively. Our analysis indicated that nucleotide composition, mutational pressure, natural selection, gene expression level, amino acids with grand average of hydropathicity (GRAVY) and aromaticity (Aromo) and the effective selection of amino-acids all contributed to the codon usage in T. multiceps. Among these factors, natural selection was implicated as the major factor affecting the codon usage variation in T. multiceps. The codon usage of ribosome genes was affected mainly by mutations, while the essential genes were affected mainly by selection. In addition, 21codons were identified as "optimal codons". Overall, the optimal codons were GC-rich (GC:AU, 41:22), and ended with G or C (except CGU). Furthermore, different degrees of variation in codon usage were found between T. multiceps and Escherichia coli, yeast, Homo sapiens. However, little difference was found between T. multiceps and Taenia pisiformis. In this study, the codon usage pattern of T. multiceps was analyzed systematically and factors affected CUB were also identified. This is the first study of codon biology in T. multiceps. Understanding the codon usage pattern in T. multiceps can be helpful for the discovery of new genes, molecular genetic engineering and evolutionary studies.

  7. Secretome analysis of Aspergillus fumigatus reveals Asp-hemolysin as a major secreted protein.

    Science.gov (United States)

    Wartenberg, Dirk; Lapp, Katrin; Jacobsen, Ilse D; Dahse, Hans-Martin; Kniemeyer, Olaf; Heinekamp, Thorsten; Brakhage, Axel A

    2011-11-01

    Surface-associated and secreted proteins represent primarily exposed components of Aspergillus fumigatus during host infection. Several secreted proteins are known to be involved in defense mechanisms or immune evasion, thus, probably contributing to pathogenicity. Furthermore, several secreted antigens were identified as possible biomarkers for the verification of diseases caused by Aspergillus species. Nevertheless, there is only limited knowledge about the composition of the secretome and about molecular functions of particular proteins. To identify secreted proteins potentially essential for virulence, the core secretome of A. fumigatus grown in minimal medium was determined. Two-dimensional gel electrophoretic separation and subsequent MALDI-TOF-MS/MS analyses resulted in the identification of 64 different proteins. Additionally, secretome analyses of A. fumigatus utilizing elastin, collagen or keratin as main carbon and nitrogen source were performed. Thereby, the alkaline serine protease Alp1 was identified as the most abundant protein and hence presumably represents an important protease during host infection. Interestingly, the Asp-hemolysin (Asp-HS), which belongs to the protein family of aegerolysins and which was often suggested to be involved in fungal virulence, was present in the secretome under all growth conditions tested. In addition, a second, non-secreted protein with an aegerolysin domain annotated as Asp-hemolysin-like (HS-like) protein can be found to be encoded in the genome of A. fumigatus. Generation and analysis of Asp-HS and HS-like deletion strains revealed no differences in phenotype compared to the corresponding wild-type strain. Furthermore, hemolysis and cytotoxicity was not altered in both single-deletion and double-deletion mutants lacking both aegerolysin genes. All mutant strains showed no attenuation in virulence in a mouse infection model for invasive pulmonary aspergillosis. Overall, this study provides a comprehensive

  8. Comparative transcriptome analysis reveals differentially expressed genes associated with sex expression in garden asparagus (Asparagus officinalis).

    Science.gov (United States)

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gao, Wu-Jun

    2017-08-22

    Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation in plants. However, the sex expression mechanisms in asparagus remain poorly understood. De novo transcriptome sequencing via Illumina paired-end sequencing revealed more than 26 billion bases of high-quality sequence data from male and female asparagus flower buds. A total of 72,626 unigenes with an average length of 979 bp were assembled. In comparative transcriptome analysis, 4876 differentially expressed genes (DEGs) were identified in the possible sex-determining stage of female and male/supermale flower buds. Of these DEGs, 433, including 285 male/supermale-biased and 149 female-biased genes, were annotated as flower related. Of the male/supermale-biased flower-related genes, 102 were probably involved in anther development. In addition, 43 DEGs implicated in hormone response and biosynthesis putatively associated with sex expression and reproduction were discovered. Moreover, 128 transcription factor (TF)-related genes belonging to various families were found to be differentially expressed, and this finding implied the essential roles of TF in sex determination or differentiation in asparagus. Correlation analysis indicated that miRNA-DEG pairs were also implicated in asparagus sexual development. Our study identified a large number of DEGs involved in the sex expression and reproduction of asparagus, including known genes participating in plant reproduction, plant hormone signaling, TF encoding, and genes with unclear functions. We also found that miRNAs might be involved in the sex differentiation process. Our study could provide a valuable basis for further investigations on the regulatory networks of sex determination and differentiation in asparagus and facilitate further genetic and genomic studies on this dioecious species.

  9. Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

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    Yanliang Jiang

    Full Text Available The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

  10. Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

    Science.gov (United States)

    Jiang, Yanliang; Zhang, Songhao; Xu, Jian; Feng, Jianxin; Mahboob, Shahid; Al-Ghanim, Khalid A; Sun, Xiaowen; Xu, Peng

    2014-01-01

    The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied. In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains. In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

  11. Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development.

    Science.gov (United States)

    Wang, Yong-Qiang; Yang, Yong; Fei, Zhangjun; Yuan, Hui; Fish, Tara; Thannhauser, Theodore W; Mazourek, Michael; Kochian, Leon V; Wang, Xiaowu; Li, Li

    2013-02-01

    Chromoplasts are unique plastids that accumulate massive amounts of carotenoids. To gain a general and comparative characterization of chromoplast proteins, this study performed proteomic analysis of chromoplasts from six carotenoid-rich crops: watermelon, tomato, carrot, orange cauliflower, red papaya, and red bell pepper. Stromal and membrane proteins of chromoplasts were separated by 1D gel electrophoresis and analysed using nLC-MS/MS. A total of 953-2262 proteins from chromoplasts of different crop species were identified. Approximately 60% of the identified proteins were predicted to be plastid localized. Functional classification using MapMan bins revealed large numbers of proteins involved in protein metabolism, transport, amino acid metabolism, lipid metabolism, and redox in chromoplasts from all six species. Seventeen core carotenoid metabolic enzymes were identified. Phytoene synthase, phytoene desaturase, ζ-carotene desaturase, 9-cis-epoxycarotenoid dioxygenase, and carotenoid cleavage dioxygenase 1 were found in almost all crops, suggesting relative abundance of them among the carotenoid pathway enzymes. Chromoplasts from different crops contained abundant amounts of ATP synthase and adenine nucleotide translocator, which indicates an important role of ATP production and transport in chromoplast development. Distinctive abundant proteins were observed in chromoplast from different crops, including capsanthin/capsorubin synthase and fibrillins in pepper, superoxide dismutase in watermelon, carrot, and cauliflower, and glutathione-S-transferease in papaya. The comparative analysis of chromoplast proteins among six crop species offers new insights into the general metabolism and function of chromoplasts as well as the uniqueness of chromoplasts in specific crop species. This work provides reference datasets for future experimental study of chromoplast biogenesis, development, and regulation in plants.

  12. Comparative Genomic Analysis of Clinical and Environmental Vibrio Vulnificus Isolates Revealed Biotype 3 Evolutionary Relationships

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    Yael eKotton

    2015-01-01

    Full Text Available In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59% and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 kbp to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C and environmental (E, all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins were present in all human pathogenic strains (both biotype 3 and non-biotype 3 and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and

  13. Human processing of short temporal intervals as revealed by an ERP waveform analysis

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    Yoshitaka eNakajima

    2011-12-01

    Full Text Available To clarify the time course over which the human brain processes information about durations up to ~300 ms, we reanalyzed the data that were previously reported by Mitsudo et al. (2009 using a multivariate analysis method. Event-related potentials were recorded from 19 scalp electrodes on 11 (9 original and 2 additional participants while they judged whether two neighboring empty time intervals—called t1 and t2 and marked by three tone bursts—had equal durations. There was also a control condition in which the participants were presented the same temporal patterns but without a judgment task. In the present reanalysis, we sought to visualize how the temporal patterns were represented in the brain over time. A correlation matrix across channels was calculated for each temporal pattern. Geometric separations between the correlation matrices were calculated, and subjected to multidimensional scaling. We performed such analyses for a moving 100-ms time window after the t1 presentations. In the windows centered at < 100 ms after the t2 presentation, the analyses revealed the local maxima of categorical separation between temporal patterns of perceptually equal durations versus perceptually unequal durations, both in the judgment condition and in the control condition. Such categorization of the temporal patterns was prominent only in narrow temporal regions. The analysis indicated that the participants determined whether the two neighboring time intervals were of equal duration mostly within 100 ms after the presentation of the temporal patterns. A very fast brain activity was related to the perception of elementary temporal patterns without explicit judgments. This is consistent with the findings of Mitsudo et al., and it is in line with the processing time hypothesis proposed by Nakajima et al. (2004. The validity of the correlation matrix analyses turned out to be an effective tool to grasp the overall responses of the brain to temporal

  14. Network analysis of ChIP-Seq data reveals key genes in prostate cancer.

    Science.gov (United States)

    Zhang, Yu; Huang, Zhen; Zhu, Zhiqiang; Liu, Jianwei; Zheng, Xin; Zhang, Yuhai

    2014-09-03

    Prostate cancer (PC) is the second most common cancer among men in the United States, and it imposes a considerable threat to human health. A deep understanding of its underlying molecular mechanisms is the premise for developing effective targeted therapies. Recently, deep transcriptional sequencing has been used as an effective genomic assay to obtain insights into diseases and may be helpful in the study of PC. In present study, ChIP-Seq data for PC and normal samples were compared, and differential peaks identified, based upon fold changes (with P-values calculated with t-tests). Annotations of these peaks were performed. Protein-protein interaction (PPI) network analysis was performed with BioGRID and constructed with Cytoscape, following which the highly connected genes were screened. We obtained a total of 5,570 differential peaks, including 3,726 differentially enriched peaks in tumor samples and 1,844 differentially enriched peaks in normal samples. There were eight significant regions of the peaks. The intergenic region possessed the highest score (51%), followed by intronic (31%) and exonic (11%) regions. The analysis revealed the top 35 highly connected genes, which comprised 33 differential genes (such as YWHAQ, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein and θ polypeptide) from ChIP-Seq data and 2 differential genes retrieved from the PPI network: UBA52 (ubiquitin A-52 residue ribosomal protein fusion product (1) and SUMO2 (SMT3 suppressor of mif two 3 homolog (2) . Our findings regarding potential PC-related genes increase the understanding of PC and provides direction for future research.

  15. Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle.

    Science.gov (United States)

    Załuga, Joanna; Stragier, Pieter; Baeyen, Steve; Haegeman, Annelies; Van Vaerenbergh, Johan; Maes, Martine; De Vos, Paul

    2014-05-22

    The genus Clavibacter harbors economically important plant pathogens infecting agricultural crops such as potato and tomato. Although the vast majority of Clavibacter strains are pathogenic, there is an increasing number of non-pathogenic isolates reported. Non-pathogenic Clavibacter strains isolated from tomato seeds are particularly problematic because they affect the current detection and identification tests for Clavibacter michiganensis subsp. michiganensis (Cmm), which is regulated with a zero tolerance in tomato seed. Their misidentification as pathogenic Cmm hampers a clear judgment on the seed quality and health. To get more insight in the genetic features linked to the lifestyle of these bacteria, a whole-genome sequence of the tomato seed-borne non-pathogenic Clavibacter LMG 26808 was determined. To gain a better understanding of the molecular determinants of pathogenicity, the genome sequence of LMG 26808 was compared with that of the pathogenic Cmm strain (NCPPB 382). The comparative analysis revealed that LMG 26808 does not contain plasmids pCM1 and pCM2 and also lacks the majority of important virulence factors described so far for pathogenic Cmm. This explains its apparent non-pathogenic nature in tomato plants. Moreover, the genome analysis of LMG 26808 detected sequences from a plasmid originating from a member of Enterobacteriaceae/Klebsiella relative. Genes received that way and coding for antibiotic resistance may provide a competitive advantage for survival of LMG 26808 in its ecological niche. Genetically, LMG 26808 was the most similar to the pathogenic Cmm NCPPB 382 but contained more mobile genetic elements. The genome of this non-pathogenic Clavibacter strain contained also a high number of transporters and regulatory genes. The genome sequence of the non-pathogenic Clavibacter strain LMG 26808 and the comparative analyses with other pathogenic Clavibacter strains provided a better understanding of the genetic bases of virulence and

  16. Comparative Analysis of Membrane Vesicles from Three Piscirickettsia salmonis Isolates Reveals Differences in Vesicle Characteristics.

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    Julia I Tandberg

    Full Text Available Membrane vesicles (MVs are spherical particles naturally released from the membrane of Gram-negative bacteria. Bacterial MV production is associated with a range of phenotypes including biofilm formation, horizontal gene transfer, toxin delivery, modulation of host immune responses and virulence. This study reports comparative profiling of MVs from bacterial strains isolated from three widely disperse geographical areas. Mass spectrometry identified 119, 159 and 142 proteins in MVs from three different strains of Piscirickettsia salmonis isolated from salmonids in Chile (LF-89, Norway (NVI 5692 and Canada (NVI 5892, respectively. MV comparison revealed several strain-specific differences related to higher virulence capability for LF-89 MVs, both in vivo and in vitro, and stronger similarities between the NVI 5692 and NVI 5892 MV proteome. The MVs were similar in size and appearance as analyzed by electron microscopy and dynamic light scattering. The MVs from all three strains were internalized by both commercial and primary immune cell cultures, which suggest a potential role of the MVs in the bacterium's utilization of leukocytes. When MVs were injected into an adult zebrafish infection model, an upregulation of several pro-inflammatory genes were observed in spleen and kidney, indicating a modulating effect on the immune system. The present study is the first comparative analysis of P. salmonis derived MVs, highlighting strain-specific vesicle characteristics. The results further illustrate that the MV proteome from one bacterial strain is not representative of all bacterial strains within one species.

  17. Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs.

    Science.gov (United States)

    Chao, Tianle; Ji, Zhibin; Hou, Lei; Wang, Jin; Zhang, Chunlan; Wang, Guizhi; Wang, Jianmin

    2018-01-01

    As widely distributed domestic animals, sheep are an important species and the source of mutton. In this study, we aimed to evaluate the regulatory lncRNAs associated with muscle growth and development between high production mutton sheep (Dorper sheep and Qianhua Mutton Merino sheep) and low production mutton sheep (Small-tailed Han sheep). In total, 39 lncRNAs were found to be differentially expressed. Using co-expression analysis and functional annotation, 1,206 co-expression interactions were found between 32 lncRNAs and 369 genes, and 29 of these lncRNAs were found to be associated with muscle development, metabolism, cell proliferation and apoptosis. lncRNA-mRNA interactions revealed 6 lncRNAs as hub lncRNAs. Moreover, three lncRNAs and their associated co-expressed genes were demonstrated by cis-regulatory gene analyses, and we also found a potential regulatory relationship between the pseudogene lncRNA LOC101121401 and its parent gene FTH1. This study provides a genome-wide resolution of lncRNA and mRNA regulation in muscles from mutton sheep.

  18. A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways

    Science.gov (United States)

    Yang, Yunlai; Arouri, Khaled

    2016-03-01

    A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations.

  19. Metabolomics analysis reveals the metabolic and functional roles of flavonoids in light-sensitive tea leaves.

    Science.gov (United States)

    Zhang, Qunfeng; Liu, Meiya; Ruan, Jianyun

    2017-03-20

    As the predominant secondary metabolic pathway in tea plants, flavonoid biosynthesis increases with increasing temperature and illumination. However, the concentration of most flavonoids decreases greatly in light-sensitive tea leaves when they are exposed to light, which further improves tea quality. To reveal the metabolism and potential functions of flavonoids in tea leaves, a natural light-sensitive tea mutant (Huangjinya) cultivated under different light conditions was subjected to metabolomics analysis. The results showed that chlorotic tea leaves accumulated large amounts of flavonoids with ortho-dihydroxylated B-rings (e.g., catechin gallate, quercetin and its glycosides etc.), whereas total flavonoids (e.g., myricetrin glycoside, epigallocatechin gallate etc.) were considerably reduced, suggesting that the flavonoid components generated from different metabolic branches played different roles in tea leaves. Furthermore, the intracellular localization of flavonoids and the expression pattern of genes involved in secondary metabolic pathways indicate a potential photoprotective function of dihydroxylated flavonoids in light-sensitive tea leaves. Our results suggest that reactive oxygen species (ROS) scavenging and the antioxidation effects of flavonoids help chlorotic tea plants survive under high light stress, providing new evidence to clarify the functional roles of flavonoids, which accumulate to high levels in tea plants. Moreover, flavonoids with ortho-dihydroxylated B-rings played a greater role in photo-protection to improve the acclimatization of tea plants.

  20. A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer.

    Science.gov (United States)

    El-Athman, Rukeia; Fuhr, Luise; Relógio, Angela

    2018-06-20

    Accumulating evidence points to a significant role of the circadian clock in the regulation of splicing in various organisms, including mammals. Both dysregulated circadian rhythms and aberrant pre-mRNA splicing are frequently implicated in human disease, in particular in cancer. To investigate the role of the circadian clock in the regulation of splicing in a cancer progression context at the systems-level, we conducted a genome-wide analysis and compared the rhythmic transcriptional profiles of colon carcinoma cell lines SW480 and SW620, derived from primary and metastatic sites of the same patient, respectively. We identified spliceosome components and splicing factors with cell-specific circadian expression patterns including SRSF1, HNRNPLL, ESRP1, and RBM 8A, as well as altered alternative splicing events and circadian alternative splicing patterns of output genes (e.g., VEGFA, NCAM1, FGFR2, CD44) in our cellular model. Our data reveals a remarkable interplay between the circadian clock and pre-mRNA splicing with putative consequences in tumor progression and metastasis. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  1. Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles.

    Science.gov (United States)

    Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-Yu; Zhang, Xiao-Mei; Song, Da-Feng; Zhang, Chen

    2016-08-01

    In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.

  2. Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles* #

    Science.gov (United States)

    Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-yu; Zhang, Xiao-mei; Song, Da-feng; Zhang, Chen

    2016-01-01

    Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate. PMID:27487802

  3. Transcriptome analysis of Phytophthora litchii reveals pathogenicity arsenals and confirms taxonomic status.

    Science.gov (United States)

    Sun, Jinhua; Gao, Zhaoyin; Zhang, Xinchun; Zou, Xiaoxiao; Cao, Lulu; Wang, Jiabao

    2017-01-01

    Litchi downy blight, caused by Peronophythora litchii, is one of the major diseases of litchi and has caused severe economic losses. P. litchii has the unique ability to produce downy mildew like sporangiophores under artificial culture. The pathogen had been placed in a new family Peronophytophthoraceae by some authors. In this study, the whole transcriptome of P. litchii from mycelia, sporangia, and zoospores was sequenced for the first time. A set of 23637 transcripts with an average length of 1284 bp was assembled. Using six open reading frame (ORF) predictors, 19267 representative ORFs were identified and were annotated by searching against several public databases. There were 4666 conserved gene families and various sets of lineage-specific genes among P. litchii and other four closely related oomycetes. In silico analyses revealed 490 pathogen-related proteins including 128 RXLR and 22 CRN effector candidates. Based on the phylogenetic analysis of 164 single copy orthologs from 22 species, it is validated that P. litchii is in the genus Phytophthora. Our work provides valuable data to elucidate the pathogenicity basis and ascertain the taxonomic status of P. litchii.

  4. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    Science.gov (United States)

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

  5. Stochasticity in the enterococcal sex pheromone response revealed by quantitative analysis of transcription in single cells.

    Science.gov (United States)

    Breuer, Rebecca J; Bandyopadhyay, Arpan; O'Brien, Sofie A; Barnes, Aaron M T; Hunter, Ryan C; Hu, Wei-Shou; Dunny, Gary M

    2017-07-01

    In Enterococcus faecalis, sex pheromone-mediated transfer of antibiotic resistance plasmids can occur under unfavorable conditions, for example, when inducing pheromone concentrations are low and inhibiting pheromone concentrations are high. To better understand this paradox, we adapted fluorescence in situ hybridization chain reaction (HCR) methodology for simultaneous quantification of multiple E. faecalis transcripts at the single cell level. We present direct evidence for variability in the minimum period, maximum response level, and duration of response of individual cells to a specific inducing condition. Tracking of induction patterns of single cells temporally using a fluorescent reporter supported HCR findings. It also revealed subpopulations of rapid responders, even under low inducing pheromone concentrations where the overall response of the entire population was slow. The strong, rapid induction of small numbers of cells in cultures exposed to low pheromone concentrations is in agreement with predictions of a stochastic model of the enterococcal pheromone response. The previously documented complex regulatory circuitry controlling the pheromone response likely contributes to stochastic variation in this system. In addition to increasing our basic understanding of the biology of a horizontal gene transfer system regulated by cell-cell signaling, demonstration of the stochastic nature of the pheromone response also impacts any future efforts to develop therapeutic agents targeting the system. Quantitative single cell analysis using HCR also has great potential to elucidate important bacterial regulatory mechanisms not previously amenable to study at the single cell level, and to accelerate the pace of functional genomic studies.

  6. Phenotypic factor analysis of psychopathology reveals a new body-related transdiagnostic factor.

    Science.gov (United States)

    Pezzoli, Patrizia; Antfolk, Jan; Santtila, Pekka

    2017-01-01

    Comorbidity challenges the notion of mental disorders as discrete categories. An increasing body of literature shows that symptoms cut across traditional diagnostic boundaries and interact in shaping the latent structure of psychopathology. Using exploratory and confirmatory factor analysis, we reveal the latent sources of covariation among nine measures of psychopathological functioning in a population-based sample of 13024 Finnish twins and their siblings. By implementing unidimensional, multidimensional, second-order, and bifactor models, we illustrate the relationships between observed variables, specific, and general latent factors. We also provide the first investigation to date of measurement invariance of the bifactor model of psychopathology across gender and age groups. Our main result is the identification of a distinct "Body" factor, alongside the previously identified Internalizing and Externalizing factors. We also report relevant cross-disorder associations, especially between body-related psychopathology and trait anger, as well as substantial sex and age differences in observed and latent means. The findings expand the meta-structure of psychopathology, with implications for empirical and clinical practice, and demonstrate shared mechanisms underlying attitudes towards nutrition, self-image, sexuality and anger, with gender- and age-specific features.

  7. Alanine Enhances Aminoglycosides-Induced ROS Production as Revealed by Proteomic Analysis

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    Jin-zhou Ye

    2018-01-01

    Full Text Available Metabolite-enabled killing of antibiotic-resistant pathogens by antibiotics is an attractive strategy to manage antibiotic resistance. Our previous study demonstrated that alanine or/and glucose increased the killing efficacy of kanamycin on antibiotic-resistant bacteria, whose action is through up-regulating TCA cycle, increasing proton motive force and enhancing antibiotic uptake. Despite the fact that alanine altered several metabolic pathways, other mechanisms could be potentially involved in alanine-mediated kanamycin killing of bacteria which remains to be explored. In the present study, we adopted proteomic approach to analyze the proteome changes induced by exogenous alanine. Our results revealed that the expression of three outer membrane proteins was altered and the deletion of nagE and fadL decreased the intracellular kanamycin concentration, implying their possible roles in mediating kanamycin transport. More importantly, the integrated analysis of proteomic and metabolomic data pointed out that alanine metabolism could connect to riboflavin metabolism that provides the source for reactive oxygen species (ROS production. Functional studies confirmed that alanine treatment together with kanamycin could promote ROS production that in turn potentiates the killing of antibiotic-resistant bacteria. Further investigation showed that alanine repressed the transcription of antioxidant-encoding genes, and alanine metabolism to riboflavin metabolism connected with riboflavin metabolism through TCA cycle, glucogenesis pathway and pentose phosphate pathway. Our results suggest a novel mechanism by which alanine facilitates kanamycin killing of antibiotic-resistant bacteria via promoting ROS production.

  8. Integrated Analysis of Alzheimer's Disease and Schizophrenia Dataset Revealed Different Expression Pattern in Learning and Memory.

    Science.gov (United States)

    Li, Wen-Xing; Dai, Shao-Xing; Liu, Jia-Qian; Wang, Qian; Li, Gong-Hua; Huang, Jing-Fei

    2016-01-01

    Alzheimer's disease (AD) and schizophrenia (SZ) are both accompanied by impaired learning and memory functions. This study aims to explore the expression profiles of learning or memory genes between AD and SZ. We downloaded 10 AD and 10 SZ datasets from GEO-NCBI for integrated analysis. These datasets were processed using RMA algorithm and a global renormalization for all studies. Then Empirical Bayes algorithm was used to find the differentially expressed genes between patients and controls. The results showed that most of the differentially expressed genes were related to AD whereas the gene expression profile was little affected in the SZ. Furthermore, in the aspects of the number of differentially expressed genes, the fold change and the brain region, there was a great difference in the expression of learning or memory related genes between AD and SZ. In AD, the CALB1, GABRA5, and TAC1 were significantly downregulated in whole brain, frontal lobe, temporal lobe, and hippocampus. However, in SZ, only two genes CRHBP and CX3CR1 were downregulated in hippocampus, and other brain regions were not affected. The effect of these genes on learning or memory impairment has been widely studied. It was suggested that these genes may play a crucial role in AD or SZ pathogenesis. The different gene expression patterns between AD and SZ on learning and memory functions in different brain regions revealed in our study may help to understand the different mechanism between two diseases.

  9. MRI Texture Analysis Reveals Deep Gray Nuclei Damage in Amyotrophic Lateral Sclerosis.

    Science.gov (United States)

    de Albuquerque, Milena; Anjos, Lara G V; Maia Tavares de Andrade, Helen; de Oliveira, Márcia S; Castellano, Gabriela; Junqueira Ribeiro de Rezende, Thiago; Nucci, Anamarli; França Junior, Marcondes Cavalcante

    2016-01-01

    Amyotrophic Lateral Sclerosis (ALS) is characterized by extensive corticospinal damage, but extrapyramidal involvement is suggested in pathological studies. Texture analysis (TA) is an image processing technique that evaluates the distribution of gray levels between pixels in a given region of interest (ROI). It provides quantitative data and has been employed in several neurodegenerative disorders. Here, we used TA to investigate possible deep gray nuclei (DGN) abnormalities in a cohort of ALS patients. Thirty-two ALS patients and 32 healthy controls underwent MRI in a 3T scanner. The T1 volumetric sequence was used for DGN segmentation and extraction of 11 texture parameters using the MaZda software. Statistical analyses were performed using the Mann-Whitney non-parametric test, with a significance level set at α = 0.025 (FDR-corrected) for TA. Patients had significantly higher values for the parameter correlation (CO) in both thalami and in the right caudate nucleus compared to healthy controls. Also, the parameter Inverse Difference Moment or Homogeneity (IDM) presented significantly smaller values in the ALS group in both thalami. TA of T1 weighted images revealed DGN alterations in patients with ALS, namely in the thalami and caudate nuclei. Copyright © 2015 by the American Society of Neuroimaging.

  10. Genomic analysis reveals the molecular basis for capsule loss in the group B Streptococcus population.

    Directory of Open Access Journals (Sweden)

    Roberto Rosini

    Full Text Available The human and bovine bacterial pathogen Streptococcus agalactiae (Group B Streptococcus, GBS expresses a thick polysaccharide capsule that constitutes a major virulence factor and vaccine target. GBS can be classified into ten distinct serotypes differing in the chemical composition of their capsular polysaccharide. However, non-typeable strains that do not react with anti-capsular sera are frequently isolated from colonized and infected humans and cattle. To gain a comprehensive insight into the molecular basis for the loss of capsule expression in GBS, a collection of well-characterized non-typeable strains was investigated by genome sequencing. Genome based phylogenetic analysis extended to a wide population of sequenced strains confirmed the recently observed high clonality among GBS lineages mainly containing human strains, and revealed a much higher degree of diversity in the bovine population. Remarkably, non-typeable strains were equally distributed in all lineages. A number of distinct mutations in the cps operon were identified that were apparently responsible for inactivation of capsule synthesis. The most frequent genetic alterations were point mutations leading to stop codons in the cps genes, and the main target was found to be cpsE encoding the portal glycosyl transferase of capsule biosynthesis. Complementation of strains carrying missense mutations in cpsE with a wild-type gene restored capsule expression allowing the identification of amino acid residues essential for enzyme activity.

  11. Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis.

    Science.gov (United States)

    Zheng, Wenning; Tan, Mui Fern; Old, Lesley A; Paterson, Ian C; Jakubovics, Nicholas S; Choo, Siew Woh

    2017-06-07

    Streptococcus gordonii and Streptococcus sanguinis are pioneer colonizers of dental plaque and important agents of bacterial infective endocarditis (IE). To gain a greater understanding of these two closely related species, we performed comparative analyses on 14 new S. gordonii and 5 S. sanguinis strains using various bioinformatics approaches. We revealed S. gordonii and S. sanguinis harbor open pan-genomes and share generally high sequence homology and number of core genes including virulence genes. However, we observed subtle differences in genomic islands and prophages between the species. Comparative pathogenomics analysis identified S. sanguinis strains have genes encoding IgA proteases, mitogenic factor deoxyribonucleases, nickel/cobalt uptake and cobalamin biosynthesis. On the contrary, genomic islands of S. gordonii strains contain additional copies of comCDE quorum-sensing system components involved in genetic competence. Two distinct polysaccharide locus architectures were identified, one of which was exclusively present in S. gordonii strains. The first evidence of genes encoding the CylA and CylB system by the α-haemolytic S. gordonii is presented. This study provides new insights into the genetic distinctions between S. gordonii and S. sanguinis, which yields understanding of tooth surfaces colonization and contributions to dental plaque formation, as well as their potential roles in the pathogenesis of IE.

  12. Deep Sequence Analysis of AgoshRNA Processing Reveals 3' A Addition and Trimming.

    Science.gov (United States)

    Harwig, Alex; Herrera-Carrillo, Elena; Jongejan, Aldo; van Kampen, Antonius Hubertus; Berkhout, Ben

    2015-07-14

    The RNA interference (RNAi) pathway, in which microprocessor and Dicer collaborate to process microRNAs (miRNA), was recently expanded by the description of alternative processing routes. In one of these noncanonical pathways, Dicer action is replaced by the Argonaute2 (Ago2) slicer function. It was recently shown that the stem-length of precursor-miRNA or short hairpin RNA (shRNA) molecules is a major determinant for Dicer versus Ago2 processing. Here we present the results of a deep sequence study on the processing of shRNAs with different stem length and a top G·U wobble base pair (bp). This analysis revealed some unexpected properties of these so-called AgoshRNA molecules that are processed by Ago2 instead of Dicer. First, we confirmed the gradual shift from Dicer to Ago2 processing upon shortening of the hairpin length. Second, hairpins with a stem larger than 19 base pair are inefficiently cleaved by Ago2 and we noticed a shift in the cleavage site. Third, the introduction of a top G·U bp in a regular shRNA can promote Ago2-cleavage, which coincides with a loss of Ago2-loading of the Dicer-cleaved 3' strand. Fourth, the Ago2-processed AgoshRNAs acquire a short 3' tail of 1-3 A-nucleotides (nt) and we present evidence that this product is subsequently trimmed by the poly(A)-specific ribonuclease (PARN).

  13. Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum.

    Science.gov (United States)

    Kenyon, Amy; Gavriouchkina, Daria; Zorman, Jernej; Napolitani, Giorgio; Cerundolo, Vincenzo; Sauka-Spengler, Tatjana

    2017-07-26

    The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β. Crispr/Cas9-mediated knockout of caspase b, which acts by proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterial infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial neutrophil response to mycobacterial infection. Further perturbation of the IEGs exposes egr3 as a key transcriptional regulator controlling il1β transcription.

  14. Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays

    Directory of Open Access Journals (Sweden)

    Chen David P

    2010-10-01

    Full Text Available Abstract Background Diagnosis and treatment of patients in the clinical setting is often driven by known symptomatic factors that distinguish one particular condition from another. Treatment based on noticeable symptoms, however, is limited to the types of clinical biomarkers collected, and is prone to overlooking dysfunctions in physiological factors not easily evident to medical practitioners. We used a vector-based representation of patient clinical biomarkers, or clinarrays, to search for latent physiological factors that underlie human diseases directly from clinical laboratory data. Knowledge of these factors could be used to improve assessment of disease severity and help to refine strategies for diagnosis and monitoring disease progression. Results Applying Independent Component Analysis on clinarrays built from patient laboratory measurements revealed both known and novel concomitant physiological factors for asthma, types 1 and 2 diabetes, cystic fibrosis, and Duchenne muscular dystrophy. Serum sodium was found to be the most significant factor for both type 1 and type 2 diabetes, and was also significant in asthma. TSH3, a measure of thyroid function, and blood urea nitrogen, indicative of kidney function, were factors unique to type 1 diabetes respective to type 2 diabetes. Platelet count was significant across all the diseases analyzed. Conclusions The results demonstrate that large-scale analyses of clinical biomarkers using unsupervised methods can offer novel insights into the pathophysiological basis of human disease, and suggest novel clinical utility of established laboratory measurements.

  15. A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways.

    Science.gov (United States)

    Yang, Yunlai; Arouri, Khaled

    2016-03-11

    A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations.

  16. Comparative genomic analysis of isoproturon-mineralizing sphingomonads reveals the isoproturon catabolic mechanism.

    Science.gov (United States)

    Yan, Xin; Gu, Tao; Yi, Zhongquan; Huang, Junwei; Liu, Xiaowei; Zhang, Ji; Xu, Xihui; Xin, Zhihong; Hong, Qing; He, Jian; Spain, Jim C; Li, Shunpeng; Jiang, Jiandong

    2016-12-01

    The worldwide use of the phenylurea herbicide, isoproturon (IPU), has resulted in considerable concern about its environmental fate. Although many microbial metabolites of IPU are known and IPU-mineralizing bacteria have been isolated, the molecular mechanism of IPU catabolism has not been elucidated yet. In this study, complete genes that encode the conserved IPU catabolic pathway were revealed, based on comparative analysis of the genomes of three IPU-mineralizing sphingomonads and subsequent experimental validation. The complete genes included a novel hydrolase gene ddhA, which is responsible for the cleavage of the urea side chain of the IPU demethylated products; a distinct aniline dioxygenase gene cluster adoQTA1A2BR, which has a broad substrate range; and an inducible catechol meta-cleavage pathway gene cluster adoXEGKLIJC. Furthermore, the initial mono-N-demethylation genes pdmAB were further confirmed to be involved in the successive N-demethylation of the IPU mono-N-demethylated product. These IPU-catabolic genes were organized into four transcription units and distributed on three plasmids. They were flanked by multiple mobile genetic elements and highly conserved among IPU-mineralizing sphingomonads. The elucidation of the molecular mechanism of IPU catabolism will enhance our understanding of the microbial mineralization of IPU and provide insights into the evolutionary scenario of the conserved IPU-catabolic pathway. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. Revealing spatio-spectral electroencephalographic dynamics of musical mode and tempo perception by independent component analysis.

    Science.gov (United States)

    Lin, Yuan-Pin; Duann, Jeng-Ren; Feng, Wenfeng; Chen, Jyh-Horng; Jung, Tzyy-Ping

    2014-02-28

    Music conveys emotion by manipulating musical structures, particularly musical mode- and tempo-impact. The neural correlates of musical mode and tempo perception revealed by electroencephalography (EEG) have not been adequately addressed in the literature. This study used independent component analysis (ICA) to systematically assess spatio-spectral EEG dynamics associated with the changes of musical mode and tempo. Empirical results showed that music with major mode augmented delta-band activity over the right sensorimotor cortex, suppressed theta activity over the superior parietal cortex, and moderately suppressed beta activity over the medial frontal cortex, compared to minor-mode music, whereas fast-tempo music engaged significant alpha suppression over the right sensorimotor cortex. The resultant EEG brain sources were comparable with previous studies obtained by other neuroimaging modalities, such as functional magnetic resonance imaging (fMRI) and positron emission tomography (PET). In conjunction with advanced dry and mobile EEG technology, the EEG results might facilitate the translation from laboratory-oriented research to real-life applications for music therapy, training and entertainment in naturalistic environments.

  18. Analysis of Location of Laminar-Turbulent Transition on the FX 66-S-196 V1 Airfoil

    Directory of Open Access Journals (Sweden)

    Laurynas Naujokaitis

    2011-04-01

    Full Text Available The transition location on the FX 66‑S‑196 V1 wing section was analyzed with the using interactive program XFOIL of Mark Drela, MIT. Calculated results of transition location were compared with published measurement data from a wind tunnel at Delft University of Technology (Netherlands. The airfoil was analyzed at the Reynolds number Re = 0,5·106 and Re = 1,5·106. Article in Lithuanian

  19. Risk Analysis Reveals Global Hotspots for Marine Debris Ingestion by Sea Turtles

    Science.gov (United States)

    Schuyler, Q. A.; Wilcox, C.; Townsend, K.; Wedemeyer-Strombel, K.; Balazs, G.; van Sebille, E.; Hardesty, B. D.

    2016-02-01

    Plastic marine debris pollution is rapidly becoming one of the critical environmental concerns facing wildlife in the 21st century. Here we present a risk analysis for plastic ingestion by sea turtles on a global scale. We combined global marine plastic distributions based on ocean drifter data with sea turtle habitat maps to predict exposure levels to plastic pollution. Empirical data from necropsies of deceased animals were then utilised to assess the consequence of exposure to plastics. We modelled the risk (probability of debris ingestion) by incorporating exposure to debris and consequence of exposure, and included life history stage, species of sea turtle, and date of stranding observation as possible additional explanatory factors. Life history stage is the best predictor of debris ingestion, but the best-fit model also incorporates encounter rates within a limited distance from stranding location, marine debris predictions specific to the date of the stranding study, and turtle species. There was no difference in ingestion rates between stranded turtles vs. those caught as bycatch from fishing activity, suggesting that stranded animals are not a biased representation of debris ingestion rates in the background population. Oceanic life-stage sea turtles are at the highest risk of debris ingestion, and olive ridley turtles are the most at-risk species. The regions of highest risk to global sea turtle populations are off of the east coasts of the USA, Australia, and South Africa; the east Indian Ocean, and Southeast Asia. Model results can be used to predict the number of sea turtles globally at risk of debris ingestion. Based on currently available data, initial calculations indicate that up to 52% of sea turtles may have ingested debris.

  20. Risk analysis reveals global hotspots for marine debris ingestion by sea turtles.

    Science.gov (United States)

    Schuyler, Qamar A; Wilcox, Chris; Townsend, Kathy A; Wedemeyer-Strombel, Kathryn R; Balazs, George; van Sebille, Erik; Hardesty, Britta Denise

    2016-02-01

    Plastic marine debris pollution is rapidly becoming one of the critical environmental concerns facing wildlife in the 21st century. Here we present a risk analysis for plastic ingestion by sea turtles on a global scale. We combined global marine plastic distributions based on ocean drifter data with sea turtle habitat maps to predict exposure levels to plastic pollution. Empirical data from necropsies of deceased animals were then utilised to assess the consequence of exposure to plastics. We modelled the risk (probability of debris ingestion) by incorporating exposure to debris and consequence of exposure, and included life history stage, species of sea turtle and date of stranding observation as possible additional explanatory factors. Life history stage is the best predictor of debris ingestion, but the best-fit model also incorporates encounter rates within a limited distance from stranding location, marine debris predictions specific to the date of the stranding study and turtle species. There is no difference in ingestion rates between stranded turtles vs. those caught as bycatch from fishing activity, suggesting that stranded animals are not a biased representation of debris ingestion rates in the background population. Oceanic life-stage sea turtles are at the highest risk of debris ingestion, and olive ridley turtles are the most at-risk species. The regions of highest risk to global sea turtle populations are off of the east coasts of the USA, Australia and South Africa; the east Indian Ocean, and Southeast Asia. Model results can be used to predict the number of sea turtles globally at risk of debris ingestion. Based on currently available data, initial calculations indicate that up to 52% of sea turtles may have ingested debris. © 2015 John Wiley & Sons Ltd.

  1. Integrated Experimental and Model-based Analysis Reveals the Spatial Aspects of EGFR Activation Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Shankaran, Harish; Zhang, Yi; Chrisler, William B.; Ewald, Jonathan A.; Wiley, H. S.; Resat, Haluk

    2012-10-02

    The epidermal growth factor receptor (EGFR) belongs to the ErbB family of receptor tyrosine kinases, and controls a diverse set of cellular responses relevant to development and tumorigenesis. ErbB activation is a complex process involving receptor-ligand binding, receptor dimerization, phosphorylation, and trafficking (internalization, recycling and degradation), which together dictate the spatio-temporal distribution of active receptors within the cell. The ability to predict this distribution, and elucidation of the factors regulating it, would help to establish a mechanistic link between ErbB expression levels and the cellular response. Towards this end, we constructed mathematical models for deconvolving the contributions of receptor dimerization and phosphorylation to EGFR activation, and to examine the dependence of these processes on sub-cellular location. We collected experimental datasets for EGFR activation dynamics in human mammary epithelial cells, with the specific goal of model parameterization, and used the data to estimate parameters for several alternate models. Model-based analysis indicated that: 1) signal termination via receptor dephosphorylation in late endosomes, prior to degradation, is an important component of the response, 2) less than 40% of the receptors in the cell are phosphorylated at any given time, even at saturating ligand doses, and 3) receptor dephosphorylation rates at the cell surface and early endosomes are comparable. We validated the last finding by measuring EGFR dephosphorylation rates at various times following ligand addition both in whole cells, and in endosomes using ELISAs and fluorescent imaging. Overall, our results provide important information on how EGFR phosphorylation levels are regulated within cells. Further, the mathematical model described here can be extended to determine receptor dimer abundances in cells co-expressing various levels of ErbB receptors. This study demonstrates that an iterative cycle of

  2. DNA methylation analysis reveals distinct methylation signatures in pediatric germ cell tumors

    International Nuclear Information System (INIS)

    Amatruda, James F; Frazier, A Lindsay; Poynter, Jenny N; Ross, Julie A; Christensen, Brock; Fustino, Nicholas J; Chen, Kenneth S; Hooten, Anthony J; Nelson, Heather; Kuriger, Jacquelyn K; Rakheja, Dinesh

    2013-01-01

    Aberrant DNA methylation is a prominent feature of many cancers, and may be especially relevant in germ cell tumors (GCTs) due to the extensive epigenetic reprogramming that occurs in the germ line during normal development. We used the Illumina GoldenGate Cancer Methylation Panel to compare DNA methylation in the three main histologic subtypes of pediatric GCTs (germinoma, teratoma and yolk sac tumor (YST); N = 51) and used recursively partitioned mixture models (RPMM) to test associations between methylation pattern and tumor and demographic characteristics. We identified genes and pathways that were differentially methylated using generalized linear models and Ingenuity Pathway Analysis. We also measured global DNA methylation at LINE1 elements and evaluated methylation at selected imprinted loci using pyrosequencing. Methylation patterns differed by tumor histology, with 18/19 YSTs forming a distinct methylation class. Four pathways showed significant enrichment for YSTs, including a human embryonic stem cell pluripotency pathway. We identified 190 CpG loci with significant methylation differences in mature and immature teratomas (q < 0.05), including a number of CpGs in stem cell and pluripotency-related pathways. Both YST and germinoma showed significantly lower methylation at LINE1 elements compared with normal adjacent tissue while there was no difference between teratoma (mature and immature) and normal tissue. DNA methylation at imprinted loci differed significantly by tumor histology and location. Understanding methylation patterns may identify the developmental stage at which the GCT arose and the at-risk period when environmental exposures could be most harmful. Further, identification of relevant genetic pathways could lead to the development of new targets for therapy

  3. Transcriptome analysis reveals molecular anthelmintic effects of procyanidins in C. elegans.

    Directory of Open Access Journals (Sweden)

    Verena Spiegler

    Full Text Available Worldwide, more than 1 billion people are affected by infestations with soil-transmitted helminths and also in veterinary medicine helminthiases are a severe threat to livestock due to emerging resistances against the common anthelmintics. Proanthocyanidins have been increasingly investigated for their anthelmintic properties, however, except for an interaction with certain proteins of the nematodes, not much is known about their mode of action. To investigate the anthelmintic activity on a molecular level, a transcriptome analysis was performed in Caenorhabditis elegans after treatment with purified and fully characterized oligomeric procyanidins (OPC. The OPCs had previously been obtained from a hydro-ethanolic (1:1 extract from the leaves of Combretum mucronatum, a plant which is traditionally used in West Africa for the treatment of helminthiasis, therefore, also the crude extract was included in the study. Significant changes in differential gene expression were observed mainly for proteins related to the intestine, many of which were located extracellularly or within cellular membranes. Among the up-regulated genes, several hitherto undescribed orthologues of structural proteins in humans were identified, but also genes that are potentially involved in the worms' defense against tannins. For example, T22D1.2, an orthologue of human basic salivary proline-rich protein (PRB 2, and numr-1 (nuclear localized metal responsive were found to be strongly up-regulated. Down-regulated genes were mainly associated with lysosomal activity, glycoside hydrolysis or the worms' innate immune response. No major differences were found between the groups treated with purified OPCs versus the crude extract. Investigations using GFP reporter gene constructs of T22D1.2 and numr-1 corroborated the intestine as the predominant site of the anthelmintic activity. The current findings support previous hypotheses of OPCs interacting with intestinal surface proteins

  4. Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments

    Science.gov (United States)

    Saxena, Rituja; Dhakan, Darshan B.; Mittal, Parul; Waiker, Prashant; Chowdhury, Anirban; Ghatak, Arundhuti; Sharma, Vineet K.

    2017-01-01

    Extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. India harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. The aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central India namely, Badi Anhoni, Chhoti Anhoni, and Tattapani at two geographically distinct regions (Anhoni and Tattapani), to uncover the resident microbial community and their metabolic traits. Samples were collected from seven distinct sites of the three hot spring locations with temperature ranging from 43.5 to 98°C. The 16S rRNA gene amplicon sequencing of V3 hypervariable region and shotgun metagenome sequencing uncovered a unique taxonomic and metabolic diversity of the resident thermophilic microbial community in these hot springs. Genes associated with hydrocarbon degradation pathways, such as benzoate, xylene, toluene, and benzene were observed to be abundant in the Anhoni hot springs (43.5–55°C), dominated by Pseudomonas stutzeri and Acidovorax sp., suggesting the presence of chemoorganotrophic thermophilic community with the ability to utilize complex hydrocarbons as a source of energy. A high abundance of genes belonging to methane metabolism pathway was observed at Chhoti Anhoni hot spring, where methane is reported to constitute >80% of all the emitted gases, which was marked by the high abundance of Methylococcus capsulatus. The Tattapani hot spring, with a high-temperature range (61.5–98°C), displayed a lower microbial diversity and was primarily dominated by a nitrate-reducing archaeal species Pyrobaculum aerophilum. A higher abundance of cell metabolism pathways essential for the microbial survival in extreme conditions was observed at Tattapani. Taken together

  5. Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

    Science.gov (United States)

    Denas, Olgert; Sandstrom, Richard; Cheng, Yong; Beal, Kathryn; Herrero, Javier; Hardison, Ross C; Taylor, James

    2015-02-14

    Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidate how differences among species arise. Despite active experimental and computational research, relationships among sequence, conservation, and function are still poorly understood. We compared transcription factor occupied segments (TFos) for 116 human and 35 mouse TFs in 546 human and 125 mouse cell types and tissues from the Human and the Mouse ENCODE projects. We based the map between human and mouse TFos on a one-to-one nucleotide cross-species mapper, bnMapper, that utilizes whole genome alignments (WGA). Our analysis shows that TFos are under evolutionary constraint, but a substantial portion (25.1% of mouse and 25.85% of human on average) of the TFos does not have a homologous sequence on the other species; this portion varies among cell types and TFs. Furthermore, 47.67% and 57.01% of the homologous TFos sequence shows binding activity on the other species for human and mouse respectively. However, 79.87% and 69.22% is repurposed such that it binds the same TF in different cells or different TFs in the same cells. Remarkably, within the set of repurposed TFos, the corresponding genome regions in the other species are preferred locations of novel TFos. These events suggest exaptation of some functional regulatory sequences into new function. Despite TFos repurposing, we did not find substantial changes in their predicted target genes, suggesting that CRMs buffer evolutionary events allowing little or no change in the TFos - target gene associations. Thus, the small portion of TFos with strictly conserved occupancy underestimates the degree of conservation of regulatory interactions. We mapped regulatory sequences from an extensive number of TFs and cell types between human and mouse using WGA. A comparative analysis of this correspondence unveiled the

  6. Proteomic analysis reveals changes in carbohydrate and protein metabolism associated with broiler breast myopathy.

    Science.gov (United States)

    Kuttappan, Vivek A; Bottje, Walter; Ramnathan, Ranjith; Hartson, Steven D; Coon, Craig N; Kong, Byung-Whi; Owens, Casey M; Vazquez-Añon, Mercedes; Hargis, Billy M

    2017-08-01

    White Striping (WS) and Woody Breast (WB) are 2 conditions that adversely affect consumer acceptance as well as quality of poultry meat and meat products. Both WS and WB are characterized with degenerative myopathic changes. Previous studies showed that WS and WB in broiler fillets could result in higher ultimate pH, increased drip loss, and decreased marinade uptake. The main objective of the present study was to compare the proteomic profiles of muscle tissue (n = 5 per group) with either NORM (no or few minor myopathic lesions) or SEV (with severe myopathic changes). Proteins were extracted from these samples and analyzed using a hybrid LTQ-OrbitrapXL mass spectrometer (LC-MS/MS). Over 800 proteins were identified in the muscle samples, among which 141 demonstrated differential (P < 0.05) expression between NORM and SEV. The set of differentially (P < 0.05) expressed proteins was uploaded to Ingenuity Pathway Analysis® (IPA) software to determine the associated biological networks and pathways. The IPA analysis showed that eukaryotic initiation factor-2 (eIF-2) signaling, mechanistic target of rapamycin (mTOR) signaling, as well as regulation of eIF4 and p70S6K signaling were the major canonical pathways up-regulated (P < 0.05) in SEV muscle compared to NORM. The up-regulation of these pathways indicate an increase in protein synthesis which could be part of the rapid growth as well as cellular stress associated with ongoing muscle degeneration and the attempt to repair tissue damage in SEV birds. Furthermore, IPA analysis revealed that glycolysis and gluconeogenesis were the major down-regulated (P < 0.05) canonical pathways in SEV with respect to NORM muscle. Down-regulation of these pathways could be the reason for higher ultimate pH seen in SEV muscle samples indicating reduced glycolytic potential. In conclusion, comparison of proteomic profiles of NORM and SEV muscle samples showed differences in protein profile which explains some of the observed

  7. A synbiotic improves the immunity of white shrimp, Litopenaeus vannamei: Metabolomic analysis reveal compelling evidence.

    Science.gov (United States)

    Huynh, Truong-Giang; Cheng, Ann-Chang; Chi, Chia-Chun; Chiu, Kuo-Hsun; Liu, Chun-Hung

    2018-05-18

    In this study, we examined the synergistic effects of a diet-administered synbiotic comprising galactooligosaccharide (GOS) and the probiotic Lactobacillus plantarum 7-40 on immune responses, immune-related gene expressions, and disease resistance to Vibrio alginolyticus in white shrimp Litopenaeus vannamei. To unravel the regulatory role of the synbiotic in activating the immune system of shrimp, 1 H nuclear magnetic resonance (NMR)-based metabolomic analysis were used to investigate hepatopancreas metabolites, then significantly altered metabolites were confirmed in both the hepatopancreas and plasma by reverse-phase high-performance liquid chromatography (RP-HPLC) and spectrophotometric analysis. Shrimp were fed four experimental diets for 60 days, including a basal diet with no GOS or probiotic (control), 0.4% GOS (PRE), probiotic (PRO), and 0.4% GOS in combination with the probiotic (SYN). Results showed that the SYN diet significantly increased survival of L. vannamei 24 h after a V. alginolyticus injection. Immune parameters such as phenoloxidase activity, respiratory bursts, phagocytic activity and gene expressions, including prophenoloxidase I, serine proteinase, and peroxinectin, of shrimp fed the SYN diet significantly increased, compared to the other treatments and control. In addition, results from the 1 H NMR analysis revealed that 22 hepatopancreas metabolites were matched and identified between the SYN and control groups, among which three metabolites, i.e., inosine monophosphate (IMP), valine, and betaine, significantly increased in the SYN group. Confirmation using RP-HPLC and spectrophotometric methods showed that IMP presented high amounts in the hepatopancreas, but not in the plasma of shrimp; in contrast, valine and betaine metabolites were in high concentrations in both the hepatopancreas and plasma. Our results suggested that GOS and the probiotic had a synergistic effect on enhancing immunity and disease resistance of L. vannamei against

  8. The Immersive Virtual Reality Experience: A Typology of Users Revealed Through Multiple Correspondence Analysis Combined with Cluster Analysis Technique.

    Science.gov (United States)

    Rosa, Pedro J; Morais, Diogo; Gamito, Pedro; Oliveira, Jorge; Saraiva, Tomaz

    2016-03-01

    Immersive virtual reality is thought to be advantageous by leading to higher levels of presence. However, and despite users getting actively involved in immersive three-dimensional virtual environments that incorporate sound and motion, there are individual factors, such as age, video game knowledge, and the predisposition to immersion, that may be associated with the quality of virtual reality experience. Moreover, one particular concern for users engaged in immersive virtual reality environments (VREs) is the possibility of side effects, such as cybersickness. The literature suggests that at least 60% of virtual reality users report having felt symptoms of cybersickness, which reduces the quality of the virtual reality experience. The aim of this study was thus to profile the right user to be involved in a VRE through head-mounted display. To examine which user characteristics are associated with the most effective virtual reality experience (lower cybersickness), a multiple correspondence analysis combined with cluster analysis technique was performed. Results revealed three distinct profiles, showing that the PC gamer profile is more associated with higher levels of virtual reality effectiveness, that is, higher predisposition to be immersed and reduced cybersickness symptoms in the VRE than console gamer and nongamer. These findings can be a useful orientation in clinical practice and future research as they help identify which users are more predisposed to benefit from immersive VREs.

  9. Functional proteomic analysis reveals the involvement of KIAA1199 in breast cancer growth, motility and invasiveness

    International Nuclear Information System (INIS)

    Jami, Mohammad-Saeid; Huang, Xin; Peng, Hong; Fu, Kai; Li, Yan; Singh, Rakesh K; Ding, Shi-Jian; Hou, Jinxuan; Liu, Miao; Varney, Michelle L; Hassan, Hesham; Dong, Jixin; Geng, Liying; Wang, Jing; Yu, Fang

    2014-01-01

    KIAA1199 is a recently identified novel gene that is up-regulated in human cancer with poor survival. Our proteomic study on signaling polarity in chemotactic cells revealed KIAA1199 as a novel protein target that may be involved in cellular chemotaxis and motility. In the present study, we examined the functional significance of KIAA1199 expression in breast cancer growth, motility and invasiveness. We validated the previous microarray observation by tissue microarray immunohistochemistry using a TMA slide containing 12 breast tumor tissue cores and 12 corresponding normal tissues. We performed the shRNA-mediated knockdown of KIAA1199 in MDA-MB-231 and HS578T cells to study the role of this protein in cell proliferation, migration and apoptosis in vitro. We studied the effects of KIAA1199 knockdown in vivo in two groups of mice (n = 5). We carried out the SILAC LC-MS/MS based proteomic studies on the involvement of KIAA1199 in breast cancer. KIAA1199 mRNA and protein was significantly overexpressed in breast tumor specimens and cell lines as compared with non-neoplastic breast tissues from large-scale microarray and studies of breast cancer cell lines and tumors. To gain deeper insights into the novel role of KIAA1199 in breast cancer, we modulated KIAA1199 expression using shRNA-mediated knockdown in two breast cancer cell lines (MDA-MB-231 and HS578T), expressing higher levels of KIAA1199. The KIAA1199 knockdown cells showed reduced motility and cell proliferation in vitro. Moreover, when the knockdown cells were injected into the mammary fat pads of female athymic nude mice, there was a significant decrease in tumor incidence and growth. In addition, quantitative proteomic analysis revealed that knockdown of KIAA1199 in breast cancer (MDA-MB-231) cells affected a broad range of cellular functions including apoptosis, metabolism and cell motility. Our findings indicate that KIAA1199 may play an important role in breast tumor growth and invasiveness, and that it

  10. Transcriptional Analysis and Subcellular Protein Localization Reveal Specific Features of the Essential WalKR System in Staphylococcus aureus.

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    Olivier Poupel

    Full Text Available The WalKR two-component system, controlling cell wall metabolism, is highly conserved among Bacilli and essential for cell viability. In Staphylococcus aureus, walR and walK are followed by three genes of unknown function: walH, walI and walJ. Sequence analysis and transcript mapping revealed a unique genetic structure for this locus in S. aureus: the last gene of the locus, walJ, is transcribed independently, whereas transcription of the tetra-cistronic walRKHI operon occurred from two independent promoters located upstream from walR. Protein topology analysis and protein-protein interactions in E. coli as well as subcellular localization in S. aureus allowed us to show that WalH and WalI are membrane-bound proteins, which associate with WalK to form a complex at the cell division septum. While these interactions suggest that WalH and WalI play a role in activity of the WalKR regulatory pathway, deletion of walH and/or walI did not have a major effect on genes whose expression is strongly dependent on WalKR or on associated phenotypes. No effect of WalH or WalI was seen on tightly controlled WalKR regulon genes such as sle1 or saouhsc_00773, which encodes a CHAP-domain amidase. Of the genes encoding the two major S. aureus autolysins, AtlA and Sle1, only transcription of atlA was increased in the ΔwalH or ΔwalI mutants. Likewise, bacterial autolysis was not increased in the absence of WalH and/or WalI and biofilm formation was lowered rather than increased. Our results suggest that contrary to their major role as WalK inhibitors in B. subtilis, the WalH and WalI proteins have evolved a different function in S. aureus, where they are more accessory. A phylogenomic analysis shows a striking conservation of the 5 gene wal cluster along the evolutionary history of Bacilli, supporting the key importance of this signal transduction system, and indicating that the walH and walI genes were lost in the ancestor of Streptococcaceae, leading to their

  11. Transcriptional Analysis and Subcellular Protein Localization Reveal Specific Features of the Essential WalKR System in Staphylococcus aureus.

    Science.gov (United States)

    Poupel, Olivier; Moyat, Mati; Groizeleau, Julie; Antunes, Luísa C S; Gribaldo, Simonetta; Msadek, Tarek; Dubrac, Sarah

    2016-01-01

    The WalKR two-component system, controlling cell wall metabolism, is highly conserved among Bacilli and essential for cell viability. In Staphylococcus aureus, walR and walK are followed by three genes of unknown function: walH, walI and walJ. Sequence analysis and transcript mapping revealed a unique genetic structure for this locus in S. aureus: the last gene of the locus, walJ, is transcribed independently, whereas transcription of the tetra-cistronic walRKHI operon occurred from two independent promoters located upstream from walR. Protein topology analysis and protein-protein interactions in E. coli as well as subcellular localization in S. aureus allowed us to show that WalH and WalI are membrane-bound proteins, which associate with WalK to form a complex at the cell division septum. While these interactions suggest that WalH and WalI play a role in activity of the WalKR regulatory pathway, deletion of walH and/or walI did not have a major effect on genes whose expression is strongly dependent on WalKR or on associated phenotypes. No effect of WalH or WalI was seen on tightly controlled WalKR regulon genes such as sle1 or saouhsc_00773, which encodes a CHAP-domain amidase. Of the genes encoding the two major S. aureus autolysins, AtlA and Sle1, only transcription of atlA was increased in the ΔwalH or ΔwalI mutants. Likewise, bacterial autolysis was not increased in the absence of WalH and/or WalI and biofilm formation was lowered rather than increased. Our results suggest that contrary to their major role as WalK inhibitors in B. subtilis, the WalH and WalI proteins have evolved a different function in S. aureus, where they are more accessory. A phylogenomic analysis shows a striking conservation of the 5 gene wal cluster along the evolutionary history of Bacilli, supporting the key importance of this signal transduction system, and indicating that the walH and walI genes were lost in the ancestor of Streptococcaceae, leading to their atypical 3 wal gene

  12. Trophic structure of cold-water coral communities revealed from the analysis of tissue isotopes and fatty acid composition

    NARCIS (Netherlands)

    Van Oevelen, D.; Duineveld, G.; Lavaleye, M.S.S.; Kutti, T.; Soetaert, K.

    2018-01-01

    The trophic structure of cold-water coral reef communities at two contrasting locations, the 800-m deep Belgica Mounds (Irish margin) and the 300-m deep Træna reefs (Norwegian Shelf), was investigated using stable isotope (δ13C and δ15N) and fatty-acid composition analysis. A broad range of

  13. Metabolite analysis of Mycobacterium species under aerobic and hypoxic conditions reveals common metabolic traits.

    Science.gov (United States)

    Drapal, Margit; Wheeler, Paul R; Fraser, Paul D

    2016-08-01

    A metabolite profiling approach has been implemented to elucidate metabolic adaptation at set culture conditions in five Mycobacterium species (two fast- and three slow-growing) with the potential to act as model organisms for Mycobacterium tuberculosis (Mtb). Analysis has been performed over designated growth phases and under representative environments (nutrient and oxygen depletion) experienced by Mtb during infection. The procedure was useful in determining a range of metabolites (60-120 compounds) covering nucleotides, amino acids, organic acids, saccharides, fatty acids, glycerols, -esters, -phosphates and isoprenoids. Among these classes of compounds, key biomarker metabolites, which can act as indicators of pathway/process activity, were identified. In numerous cases, common metabolite traits were observed for all five species across the experimental conditions (e.g. uracil indicating DNA repair). Amino acid content, especially glutamic acid, highlighted the different properties between the fast- and slow-growing mycobacteria studied (e.g. nitrogen assimilation). The greatest similarities in metabolite composition between fast- and slow-growing mycobacteria were apparent under hypoxic conditions. A comparison to previously reported transcriptomic data revealed a strong correlation between changes in transcription and metabolite content. Collectively, these data validate the changes in the transcription at the metabolite level, suggesting transcription exists as one of the predominant modes of cellular regulation in Mycobacterium. Sectors with restricted correlation between metabolites and transcription (e.g. hypoxic cultivation) warrant further study to elucidate and exploit post-transcriptional modes of regulation. The strong correlation between the laboratory conditions used and data derived from in vivo conditions, indicate that the approach applied is a valuable addition to our understanding of cell regulation in these Mycobacterium species.

  14. Proteomic analysis reveals metabolic and regulatory systems involved the syntrophic and axenic lifestyle of Syntrophomonas wolfei.

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    Jessica Rhea Sieber

    2015-02-01

    Full Text Available Microbial syntrophy is a vital metabolic interaction necessary for the complete oxidation of organic biomass to methane in all-anaerobic ecosystems. However, this process is thermodynamically constrained and represents an ecosystem-level metabolic bottleneck. To gain insight into the physiology of this process, a shotgun proteomic approach was used to quantify the protein landscape of the model syntrophic metabolizer, Syntrophomonas wolfei, grown axenically and syntrophically with Methanospirillum hungatei. Remarkably, the abundance of most proteins as represented by normalized spectral abundance factor (NSAF value changed very little between the pure and coculture growth conditions. Among the most abundant proteins detected were GroEL and GroES chaperonins, a small heat shock protein, and proteins involved in electron transfer, beta-oxidation, and ATP synthesis. Several putative energy conservation enzyme systems that utilize NADH and ferredoxin were present. The abundance of an EtfAB2 and the membrane-bound iron-sulfur oxidoreductase (Swol_0698 gene product delineated a potential conduit for electron transfer between acyl-CoA dehydrogenases and membrane redox carriers. Proteins detected only when S. wolfei was grown with M. hungatei included a zinc-dependent dehydrogenase with a GroES domain, whose gene is present in genomes in many organisms capable of syntrophy, and transcriptional regulators responsive to environmental stimuli or the physiological status of the cell. The proteomic analysis revealed an emphasis macromolecular stability and energy metabolism to S. wolfei and presence of regulatory mechanisms responsive to external stimuli and cellular physiological status.

  15. Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces

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    Jones Huw

    2011-11-01

    Full Text Available Abstract Background Understanding the evolution of cultivated barley is important for two reasons. First, the evolutionary relationships between different landraces might provide information on the spread and subsequent development of barley cultivation, including the adaptation of the crop to new environments and its response to human selection. Second, evolutionary information would enable landraces with similar traits but different genetic backgrounds to be identified, providing alternative strategies for the introduction of these traits into modern germplasm. Results The evolutionary relationships between 651 barley landraces were inferred from the genotypes for 24 microsatellites. The landraces could be divided into nine populations, each with a different geographical distribution. Comparisons with ear row number, caryopsis structure, seasonal growth habit and flowering time revealed a degree of association between population structure and phenotype, and analysis of climate variables indicated that the landraces are adapted, at least to some extent, to their environment. Human selection and/or environmental adaptation may therefore have played a role in the origin and/or maintenance of one or more of the barley landrace populations. There was also evidence that at least some of the population structure derived from geographical partitioning set up during the initial spread of barley cultivation into Europe, or reflected the later introduction of novel varieties. In particular, three closely-related populations were made up almost entirely of plants with the daylength nonresponsive version of the photoperiod response gene PPD-H1, conferring adaptation to the long annual growth season of northern Europe. These three populations probably originated in the eastern Fertile Crescent and entered Europe after the initial spread of agriculture. Conclusions The discovery of population structure, combined with knowledge of associated phenotypes and

  16. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.

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    Michelle Davison

    Full Text Available The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2-13, Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838 domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics.

  17. Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

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    Weis Patrick

    2010-01-01

    Full Text Available Abstract Background The newt Notophthalmus viridescens possesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur during the course of regeneration. To begin to decipher the molecular processes, that underlie restoration of functional cardiac tissue, we generated an EST database from regenerating newt hearts and compared the transcriptional profile of selected candidates with genes deregulated during zebrafish heart regeneration. Results A cDNA library of 100,000 cDNA clones was generated from newt hearts 14 days after ventricular injury. Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs. BLAST searches revealed 1695 sequences with potential homology to sequences from the NCBI database. BLAST searches to TrEMBL and Swiss-Prot databases assigned 1116 proteins to Gene Ontology terms. We also identified a relatively large set of 174 ORFs, which are likely to be unique for urodele amphibians. Expression analysis of newt-zebrafish homologues confirmed the deregulation of selected genes during heart regeneration. Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms. Comparison of data from regenerating zebrafish hearts identified biological processes, which were uniformly overrepresented during cardiac regeneration in newt and zebrafish. Conclusion We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles. The design of the newly established newt EST database allows identification of molecular pathways important for heart regeneration.

  18. Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation

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    Rismani-Yazdi Hamid

    2012-09-01

    Full Text Available Abstract Background The lack of sequenced genomes for oleaginous microalgae limits our understanding of the mechanisms these organisms utilize to become enriched in triglycerides. Here we report the de novo transcriptome assembly and quantitative gene expression analysis of the oleaginous microalga Neochloris oleoabundans, with a focus on the complex interaction of pathways associated with the production of the triacylglycerol (TAG biofuel precursor. Results After growth under nitrogen replete and nitrogen limiting conditions, we quantified the cellular content of major biomolecules including total lipids, triacylglycerides, starch, protein, and chlorophyll. Transcribed genes were sequenced, the transcriptome was assembled de novo, and the expression of major functional categories, relevant pathways, and important genes was quantified through the mapping of reads to the transcriptome. Over 87 million, 77 base pair high quality reads were produced on the Illumina HiSeq sequencing platform. Metabolite measurements supported by genes and pathway expression results indicated that under the nitrogen-limiting condition, carbon is partitioned toward triglyceride production, which increased fivefold over the nitrogen-replete control. In addition to the observed overexpression of the fatty acid synthesis pathway, TAG production during nitrogen limitation was bolstered by repression of the β-oxidation pathway, up-regulation of genes encoding for the pyruvate dehydrogenase complex which funnels acetyl-CoA to lipid biosynthesis, activation of the pentose phosphate pathway to supply reducing equivalents to inorganic nitrogen assimilation and fatty acid biosynthesis, and the up-regulation of lipases—presumably to reconstruct cell membranes in order to supply additional fatty acids for TAG biosynthesis. Conclusions Our quantitative transcriptome study reveals a broad overview of how nitrogen stress results in excess TAG production in N. oleoabundans, and

  19. Impact of enrofloxacin on the human intestinal microbiota revealed by comparative molecular analysis.

    Science.gov (United States)

    Kim, Bong-Soo; Kim, Jong Nam; Yoon, Seok-Hwan; Chun, Jongsik; Cerniglia, Carl E

    2012-06-01

    The indigenous human intestinal microbiota could be disrupted by residues of antibiotics in foods as well as therapeutically administered antibiotics to humans. These disruptions may lead to adverse health outcomes. To observe the possible impact of residues of antibiotics at concentrations below therapeutic levels on human intestinal microbiota, we performed studies using in vitro cultures of fecal suspensions from three individuals with 10 different concentrations (0, 0.1, 0.5, 1, 5, 10, 15, 25, 50 and 150 μg/ml) of the fluoroquinolone, enrofloxacin. The bacterial communities of the control and enrofloxacin dosed fecal samples were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. In addition, changes of functional gene expression were analyzed by a pyrosequencing-based random whole-community mRNA sequencing method. Although each individual had a unique microbial composition, the communities of all individuals were affected by enrofloxacin. The proportions of two phyla, namely, Bacteroidetes and Proteobacteria, were significantly reduced with increasing concentrations of enrofloxacin exposure, while the proportion of Firmicutes increased. Principal Coordinate Analysis (PCoA) using the Fast UniFrac indicated that the community structures of intestinal microbiota were shifted by enrofloxacin. Most of the mRNA transcripts and the anti-microbial drug resistance genes increased with increasing concentrations of enrofloxacin. 16S rRNA gene pyrosequencing of control and enrofloxacin treated fecal suspensions provided valuable information of affected bacterial taxa down to the species level, and the community transcriptomic analyses using mRNA revealed the functional gene expression responses of the changed bacterial communities by enrofloxacin. Published by Elsevier Ltd.

  20. fMRI Analysis-by-Synthesis Reveals a Dorsal Hierarchy That Extracts Surface Slant.

    Science.gov (United States)

    Ban, Hiroshi; Welchman, Andrew E

    2015-07-08

    The brain's skill in estimating the 3-D orientation of viewed surfaces supports a range of behaviors, from placing an object on a nearby table, to planning the best route when hill walking. This ability relies on integrating depth signals across extensive regions of space that exceed the receptive fields of early sensory neurons. Although hierarchical selection and pooling is central to understanding of the ventral visual pathway, the successive operations in the dorsal stream are poorly understood. Here we use computational modeling of human fMRI signals to probe the computations that extract 3-D surface orientation from binocular disparity. To understand how representations evolve across the hierarchy, we developed an inference approach using a series of generative models to explain the empirical fMRI data in different cortical areas. Specifically, we simulated the responses of candidate visual processing algorithms and tested how well they explained fMRI responses. Thereby we demonstrate a hierarchical refinement of visual representations moving from the representation of edges and figure-ground segmentation (V1, V2) to spatially extensive disparity gradients in V3A. We show that responses in V3A are little affected by low-level image covariates, and have a partial tolerance to the overall depth position. Finally, we show that responses in V3A parallel perceptual judgments of slant. This reveals a relatively short computational hierarchy that captures key information about the 3-D structure of nearby surfaces, and more generally demonstrates an analysis approach that may be of merit in a diverse range of brain imaging domains. Copyright © 2015 Ban and Welchman.

  1. Image Restoration and Analysis of Influenza Virions Binding to Membrane Receptors Reveal Adhesion-Strengthening Kinetics.

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    Donald W Lee

    Full Text Available With the development of single-particle tracking (SPT microscopy and host membrane mimics called supported lipid bilayers (SLBs, stochastic virus-membrane binding interactions can be studied in depth while maintaining control over host receptor type and concentration. However, several experimental design challenges and quantitative image analysis limitations prevent the widespread use of this approach. One main challenge of SPT studies is the low signal-to-noise ratio of SPT videos, which is sometimes inevitable due to small particle sizes, low quantum yield of fluorescent dyes, and photobleaching. These situations could render current particle tracking software to yield biased binding kinetic data caused by intermittent tracking error. Hence, we developed an effective image restoration algorithm for SPT applications called STAWASP that reveals particles with a signal-to-noise ratio of 2.2 while preserving particle features. We tested our improvements to the SPT binding assay experiment and imaging procedures by monitoring X31 influenza virus binding to α2,3 sialic acid glycolipids. Our interests lie in how slight changes to the peripheral oligosaccharide structures can affect the binding rate and residence times of viruses. We were able to detect viruses binding weakly to a glycolipid called GM3, which was undetected via assays such as surface plasmon resonance. The binding rate was around 28 folds higher when the virus bound to a different glycolipid called GD1a, which has a sialic acid group extending further away from the bilayer surface than GM3. The improved imaging allowed us to obtain binding residence time distributions that reflect an adhesion-strengthening mechanism via multivalent bonds. We empirically fitted these distributions using a time-dependent unbinding rate parameter, koff, which diverges from standard treatment of koff as a constant. We further explain how to convert these models to fit ensemble-averaged binding data

  2. Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma

    International Nuclear Information System (INIS)

    Dai, Wei; Cheung, Arthur Kwok Leung; Ko, Josephine Mun Yee; Cheng, Yue; Zheng, Hong; Ngan, Roger Kai Cheong; Ng, Wai Tong; Lee, Anne Wing Mui; Yau, Chun Chung; Lee, Victor Ho Fu; Lung, Maria Li

    2015-01-01

    Altered patterns of DNA methylation are key features of cancer. Nasopharyngeal carcinoma (NPC) has the highest incidence in Southern China. Aberrant methylation at the promoter region of tumor suppressors is frequently reported in NPC; however, genome-wide methylation changes have not been comprehensively investigated. Therefore, we systematically analyzed methylome data in 25 primary NPC tumors and nontumor counterparts using a high-throughput approach with the Illumina HumanMethylation450 BeadChip. Comparatively, we examined the methylome data of 11 types of solid tumors collected by The Cancer Genome Atlas (TCGA). In NPC, the hypermethylation pattern was more dominant than hypomethylation and the majority of de novo methylated loci were within or close to CpG islands in tumors. The comparative methylome analysis reveals hypermethylation at chromosome 6p21.3 frequently occurred in NPC (false discovery rate; FDR=1.33 × 10 −9 ), but was less obvious in other types of solid tumors except for prostate and Epstein–Barr virus (EBV)-positive gastric cancer (FDR<10 −3 ). Bisulfite pyrosequencing results further confirmed the aberrant methylation at 6p in an additional patient cohort. Evident enrichment of the repressive mark H3K27me3 and active mark H3K4me3 derived from human embryonic stem cells were found at these regions, indicating both DNA methylation and histone modification function together, leading to epigenetic deregulation in NPC. Our study highlights the importance of epigenetic deregulation in NPC. Polycomb Complex 2 (PRC2), responsible for H3K27 trimethylation, is a promising therapeutic target. A key genomic region on 6p with aberrant methylation was identified. This region contains several important genes having potential use as biomarkers for NPC detection

  3. Comparative proteomic and metabolomic analysis reveal the antiosteoporotic molecular mechanism of icariin from Epimedium brevicornu maxim.

    Science.gov (United States)

    Xue, Liming; Jiang, Yiping; Han, Ting; Zhang, Naidan; Qin, Luping; Xin, Hailiang; Zhang, Qiaoyan

    2016-11-04

    Icariin, a principal flavonoid glycoside of Epimedium brevicornu Maxim, has been widely proved to possess antiosteoporotic activity with promoting bone formation and decreasing bone resorption. However, the involving mechanisms remain unclear. To clear a global insight of signal pathways involved in anti-osteoporotic mechanism of icariin at proteins and metabolites level by integrating the proteomics and NMR metabonomics, in a systems biology approach. Mice were divided into sham, OVX model and icariin-treated OVX group, after 90 days treatment, difference gel electrophoresis combined with MALDI-TOF/TOF proteomics analysis on bone femur and serum metabolomics were carried out for monitor intracellular processes and elucidate anti-osteoporotic mechanism of icariin. Osteoblast and osteoclast were applied to evaluate the potential signal pathways. Twenty three proteins in bone femur, and 8 metabolites in serum, were significantly altered and identified, involving in bone remodeling, energy metabolism, cytoskeleton, lipid metabolism, MAPK signaling, Ca 2+ signaling et, al. Furthermore, animal experiment show icariin could enhance the BMD and BMC, decrease CTX-I level in ovariectomized mice. The mitochondrial membrane potential and the intracellular ATP levels were increased significantly, and the cytoskeleton were improved in icariin-treatment osteoblast and osteoclast. Icariin also increased mRNA expression of Runx2 and osterix of OB, decreased CTR and CAII mRNA expression and protein expression of P38 and JNK. However, icariin did not reveal any inhibition of the collagenolytic activity of cathepsin K, mRNA expression of MMP-9 and protein expression of ERK in osteoclast. we consider icariin as multi-targeting compounds for treating with osteoporosis, involve initiating osteoblastogenesis, inhibiting adipogenesis, and preventing osteoclast differentiation. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  4. Altered spontaneous brain activity in adolescent boys with pure conduct disorder revealed by regional homogeneity analysis.

    Science.gov (United States)

    Wu, Qiong; Zhang, Xiaocui; Dong, Daifeng; Wang, Xiang; Yao, Shuqiao

    2017-07-01

    Functional magnetic resonance imaging (fMRI) studies have revealed abnormal neural activity in several brain regions of adolescents with conduct disorder (CD) performing various tasks. However, little is known about the spontaneous neural activity in people with CD in a resting state. The aims of this study were to investigate CD-associated regional activity abnormalities and to explore the relationship between behavioral impulsivity and regional activity abnormalities. Resting-state fMRI (rs-fMRI) scans were administered to 28 adolescents with CD and 28 age-, gender-, and IQ-matched healthy controls (HCs). The rs-fMRI data were subjected to regional homogeneity (ReHo) analysis. ReHo can demonstrate the temporal synchrony of regional blood oxygen level-dependent signals and reflect the coordination of local neuronal activity facilitating similar goals or representations. Compared to HCs, the CD group showed increased ReHo bilaterally in the insula as well as decreased ReHo in the right inferior parietal lobule, right middle temporal gyrus and right fusiform gyrus, left anterior cerebellum anterior, and right posterior cerebellum. In the CD group, mean ReHo values in the left and the right insula correlated positively with Barratt Impulsivity Scale (BIS) total scores. The results suggest that CD is associated with abnormal intrinsic brain activity, mainly in the cerebellum and temporal-parietal-limbic cortices, regions that are related to emotional and cognitive processing. BIS scores in adolescents with CD may reflect severity of abnormal neuronal synchronization in the insula.

  5. Deep Sequence Analysis of AgoshRNA Processing Reveals 3’ A Addition and Trimming

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    Alex Harwig

    2015-01-01

    Full Text Available The RNA interference (RNAi pathway, in which microprocessor and Dicer collaborate to process microRNAs (miRNA, was recently expanded by the description of alternative processing routes. In one of these noncanonical pathways, Dicer action is replaced by the Argonaute2 (Ago2 slicer function. It was recently shown that the stem-length of precursor-miRNA or short hairpin RNA (shRNA molecules is a major determinant for Dicer versus Ago2 processing. Here we present the results of a deep sequence study on the processing of shRNAs with different stem length and a top G·U wobble base pair (bp. This analysis revealed some unexpected properties of these so-called AgoshRNA molecules that are processed by Ago2 instead of Dicer. First, we confirmed the gradual shift from Dicer to Ago2 processing upon shortening of the hairpin length. Second, hairpins with a stem larger than 19 base pair are inefficiently cleaved by Ago2 and we noticed a shift in the cleavage site. Third, the introduction of a top G·U bp in a regular shRNA can promote Ago2-cleavage, which coincides with a loss of Ago2-loading of the Dicer-cleaved 3’ strand. Fourth, the Ago2-processed AgoshRNAs acquire a short 3’ tail of 1–3 A-nucleotides (nt and we present evidence that this product is subsequently trimmed by the poly(A-specific ribonuclease (PARN.

  6. Bcl2-associated Athanogene 3 Interactome Analysis Reveals a New Role in Modulating Proteasome Activity*

    Science.gov (United States)

    Chen, Ying; Yang, Li-Na; Cheng, Li; Tu, Shun; Guo, Shu-Juan; Le, Huang-Ying; Xiong, Qian; Mo, Ran; Li, Chong-Yang; Jeong, Jun-Seop; Jiang, Lizhi; Blackshaw, Seth; Bi, Li-Jun; Zhu, Heng; Tao, Sheng-Ce; Ge, Feng

    2013-01-01

    Bcl2-associated athanogene 3 (BAG3), a member of the BAG family of co-chaperones, plays a critical role in regulating apoptosis, development, cell motility, autophagy, and tumor metastasis and in mediating cell adaptive responses to stressful stimuli. BAG3 carries a BAG domain, a WW domain, and a proline-rich repeat (PXXP), all of which mediate binding to different partners. To elucidate BAG3's interaction network at the molecular level, we employed quantitative immunoprecipitation combined with knockdown and human proteome microarrays to comprehensively profile the BAG3 interactome in humans. We identified a total of 382 BAG3-interacting proteins with diverse functions, including transferase activity, nucleic acid binding, transcription factors, proteases, and chaperones, suggesting that BAG3 is a critical regulator of diverse cellular functions. In addition, we characterized interactions between BAG3 and some of its newly identified partners in greater detail. In particular, bioinformatic analysis revealed that the BAG3 interactome is strongly enriched in proteins functioning within the proteasome-ubiquitination process and that compose the proteasome complex itself, suggesting that a critical biological function of BAG3 is associated with the proteasome. Functional studies demonstrated that BAG3 indeed interacts with the proteasome and modulates its activity, sustaining cell survival and underlying resistance to therapy through the down-modulation of apoptosis. Taken as a whole, this study expands our knowledge of the BAG3 interactome, provides a valuable resource for understanding how BAG3 affects different cellular functions, and demonstrates that biologically relevant data can be harvested using this kind of integrated approach. PMID:23824909

  7. Molecular determinants of juvenile hormone action as revealed by 3D QSAR analysis in Drosophila.

    Directory of Open Access Journals (Sweden)

    Denisa Liszeková

    Full Text Available BACKGROUND: Postembryonic development, including metamorphosis, of many animals is under control of hormones. In Drosophila and other insects these developmental transitions are regulated by the coordinate action of two principal hormones, the steroid ecdysone and the sesquiterpenoid juvenile hormone (JH. While the mode of ecdysone action is relatively well understood, the molecular mode of JH action remains elusive. METHODOLOGY/PRINCIPAL FINDINGS: To gain more insights into the molecular mechanism of JH action, we have tested the biological activity of 86 structurally diverse JH agonists in Drosophila melanogaster. The results were evaluated using 3D QSAR analyses involving CoMFA and CoMSIA procedures. Using this approach we have generated both computer-aided and species-specific pharmacophore fingerprints of JH and its agonists, which revealed that the most active compounds must possess an electronegative atom (oxygen or nitrogen at both ends of the molecule. When either of these electronegative atoms are replaced by carbon or the distance between them is shorter than 11.5 A or longer than 13.5 A, their biological activity is dramatically decreased. The presence of an electron-deficient moiety in the middle of the JH agonist is also essential for high activity. CONCLUSIONS/SIGNIFICANCE: The information from 3D QSAR provides guidelines and mechanistic scope for identification of steric and electrostatic properties as well as donor and acceptor hydrogen-bonding that are important features of the ligand-binding cavity of a JH target protein. In order to refine the pharmacophore analysis and evaluate the outcomes of the CoMFA and CoMSIA study we used pseudoreceptor modeling software PrGen to generate a putative binding site surrogate that is composed of eight amino acid residues corresponding to the defined molecular interactions.

  8. [Consideration of algorithms to presume the lesion location by using X-ray images of the stomach--geometric analysis of four direction radiography for the U region].

    Science.gov (United States)

    Henmi, Shuichi

    2013-01-01

    The author considered algorithms to presume the lesion location from a series of X-ray images obtained by four direction radiography without blind area for the U region of the stomach. The objects of analysis were six cases that protruding lesions were noticed in the U region. Firstly, from the length of short axis and measure of the lateral width of U region projected on the film, we presumed the length of longitudinal axis and angle between short axis and the film. Secondly, we calculated the rate of length to stomach walls from right side and left side of every image to the lateral width at the height passing through the center of the lesion. Using the lesion location calculated from these values, we presumed that the values that almost agreed between two images to be the lesion location. As the result of analysis, there were some cases that the lesion location could be presumed certainly or un-certainly, on the other hand, there were some cases that the lesion location could not be presumed. Since the form of the U region can be distorted by a change of position, or the angle between longitudinal axis and sagittal plane was changed, the error might have been made in calculation, and so it was considered that the lesion location could not be presumed.

  9. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses.

    Science.gov (United States)

    Zai, Xiaodong; Yang, Qiaoling; Yin, Ying; Li, Ruihua; Qian, Mengying; Zhao, Taoran; Li, Yaohui; Zhang, Jun; Fu, Ling; Xu, Junjie; Chen, Wei

    2017-01-01

    Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS) via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs) that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular homeostasis and metabolic

  10. Deep sequencing analysis of the developing mouse brain reveals a novel microRNA

    Directory of Open Access Journals (Sweden)

    Piltz Sandra

    2011-04-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are small non-coding RNAs that can exert multilevel inhibition/repression at a post-transcriptional or protein synthesis level during disease or development. Characterisation of miRNAs in adult mammalian brains by deep sequencing has been reported previously. However, to date, no small RNA profiling of the developing brain has been undertaken using this method. We have performed deep sequencing and small RNA analysis of a developing (E15.5 mouse brain. Results We identified the expression of 294 known miRNAs in the E15.5 developing mouse brain, which were mostly represented by let-7 family and other brain-specific miRNAs such as miR-9 and miR-124. We also discovered 4 putative 22-23 nt miRNAs: mm_br_e15_1181, mm_br_e15_279920, mm_br_e15_96719 and mm_br_e15_294354 each with a 70-76 nt predicted pre-miRNA. We validated the 4 putative miRNAs and further characterised one of them, mm_br_e15_1181, throughout embryogenesis. Mm_br_e15_1181 biogenesis was Dicer1-dependent and was expressed in E3.5 blastocysts and E7 whole embryos. Embryo-wide expression patterns were observed at E9.5 and E11.5 followed by a near complete loss of expression by E13.5, with expression restricted to a specialised layer of cells within the developing and early postnatal brain. Mm_br_e15_1181 was upregulated during neurodifferentiation of P19 teratocarcinoma cells. This novel miRNA has been identified as miR-3099. Conclusions We have generated and analysed the first deep sequencing dataset of small RNA sequences of the developing mouse brain. The analysis revealed a novel miRNA, miR-3099, with potential regulatory effects on early embryogenesis, and involvement in neuronal cell differentiation/function in the brain during late embryonic and early neonatal development.

  11. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses

    Directory of Open Access Journals (Sweden)

    Xiaodong Zai

    2017-11-01

    Full Text Available Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular

  12. The Effect of Fast-Food Availability on Obesity: An Analysis by Gender, Race, and Residential Location

    OpenAIRE

    Richard A. Dunn

    2010-01-01

    This paper employs an identification strategy based on county-level variation in the number of fast-food restaurants to investigate the effect of fast-food availability on weight outcomes by geographic location, gender, and race/ethnicity. The number of interstate exits in the county of residence is employed as an instrument for restaurant location. Using the 2004--2006 Behavioral Risk Factor Surveillance System and self-collected data on the number of fast-food restaurants, I find that avail...

  13. Expression analysis revealing destabilizing mutations in phosphomannomutase 2 deficiency (PMM2-CDG): expression analysis of PMM2-CDG mutations.

    Science.gov (United States)

    Vega, Ana Isabel; Pérez-Cerdá, Celia; Abia, David; Gámez, Alejandra; Briones, Paz; Artuch, Rafael; Desviat, Lourdes R; Ugarte, Magdalena; Pérez, Belén

    2011-08-01

    Deficiency of phosphomannomutase (PMM2, MIM#601785) is the most common congenital disorder of glycosylation. Herein we report the genetic analysis of 22 Spanish PMM2 deficient patients and the functional analysis of 14 nucleotide changes in a prokaryotic expression system in order to elucidate their molecular pathogenesis. PMM2 activity assay revealed the presence of six protein changes with no enzymatic activities (p.R123Q, p.R141H, p.F157S, p.P184T, p.F207S and p.D209G) and seven mild protein changes with residual activities ranging from 16 to 54% (p.L32R, p.V44A p.D65Y, p.P113L p.T118S, p.T237M and p.C241S) and also one variant change with normal activity (p.E197A). The results obtained from Western blot analysis, degradation time courses of 11 protein changes and structural analysis of the PMM2 protein, suggest that the loss-of-function of most mutant proteins is based on their increased susceptibility to degradation or aggregation compared to the wild type protein, considering PMM2 deficiency as a conformational disease. We have identified exclusively catalytic protein change (p.D209G), catalytic protein changes affecting protein stability (p.R123Q and p.R141H), two protein changes disrupting the dimer interface (p.P113L and p.T118S) and several misfolding changes (p.L32R, p.V44A, p.D65Y, p.F157S, p.P184T, p.F207S, p.T237M and p.C241S). Our current work opens a promising therapeutic option using pharmacological chaperones to revert the effect of the characterized misfolding mutations identified in a wide range of PMM2 deficient patients.

  14. How Much is Location Information Worth? A Competitive Analysis of the Online Traveling Salesman Problem with Two Disclosure Dates

    NARCIS (Netherlands)

    F.J. Srour (Jordan); R.A. Zuidwijk (Rob)

    2008-01-01

    textabstractIn this paper we derive the worst-case ratio of an online algorithm for the Traveling Salesman Problem (TSP) with two disclosure dates. This problem, a variant of the online TSP with release dates, is characterized by the disclosure of a job’s location at one point in time followed by

  15. Transcriptome Analysis Reveals Regulation of Gene Expression for Lipid Catabolism in Young Broilers by Butyrate Glycerides

    Science.gov (United States)

    Yin, Fugui; Yu, Hai; Lepp, Dion; Shi, Xuejiang; Yang, Xiaojian; Hu, Jielun; Leeson, Steve; Yang, Chengbo; Nie, Shaoping; Hou, Yongqing; Gong, Joshua

    2016-01-01

    indicated that dietary BG intervention induced 79 and 205 characterized DEGs in the jejunum and liver, respectively. In addition, 255 and 165 TSEGs were detected in the liver and jejunum of BG-fed group, while 162 and 211 TSEGs genes were observed in the liver and jejunum of BD-fed birds, respectively. Bioinformatic analysis with both IPA and DAVID-BR further revealed a significant enrichment of DEGs and TSEGs in the biological processes for reducing the synthesis, storage, transportation and secretion of lipids in the jejunum, while those in the liver were for enhancing the oxidation of ingested lipids and fatty acids. In particular, transcriptional regulators of THRSP and EGR-1 as well as several DEGs involved in the PPAR-α signaling pathway were significantly induced by dietary BG intervention for lipid catabolism. Conclusions Our results demonstrate that BG reduces body fat deposition via regulation of gene expression, which is involved in the biological events relating to the reduction of synthesis, storage, transportation and secretion, and improvement of oxidation of lipids and fatty acids. PMID:27508934

  16. Non-destructive Analysis Reveals Effect of Installation Details on Plywood Siding Performance

    Science.gov (United States)

    Christopher G. Hunt; Gregory T. Schueneman; Steven Lacher; Xiping Wang; R. Sam Williams

    2015-01-01

    This study evaluated the influence of a variety of construction techniques on the performance of plywood siding and the applied paint, using both ultrasound and conventional visual inspection techniques. The impact of bottom edge contact, flashing vs. caulking board ends, priming the bottom edge, location (Wisconsin vs. Mississippi) and a gap behind the siding to...

  17. Sequence analysis reveals how G protein-coupled receptors transduce the signal to the G protein.

    NARCIS (Netherlands)

    Oliveira, L.; Paiva, P.B.; Paiva, A.C.; Vriend, G.

    2003-01-01

    Sequence entropy-variability plots based on alignments of very large numbers of sequences-can indicate the location in proteins of the main active site and modulator sites. In the previous article in this issue, we applied this observation to a series of well-studied proteins and concluded that it

  18. Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera.

    Science.gov (United States)

    Whittington, Emma; Forsythe, Desiree; Borziak, Kirill; Karr, Timothy L; Walters, James R; Dorus, Steve

    2017-12-02

    Rapid evolution is a hallmark of reproductive genetic systems and arises through the combined processes of sequence divergence, gene gain and loss, and changes in gene and protein expression. While studies aiming to disentangle the molecular ramifications of these processes are progressing, we still know little about the genetic basis of evolutionary transitions in reproductive systems. Here we conduct the first comparative analysis of sperm proteomes in Lepidoptera, a group that exhibits dichotomous spermatogenesis, in which males produce a functional fertilization-competent sperm (eupyrene) and an incompetent sperm morph lacking nuclear DNA (apyrene). Through the integrated application of evolutionary proteomics and genomics, we characterize the genomic patterns potentially associated with the origination and evolution of this unique spermatogenic process and assess the importance of genetic novelty in Lepidopteran sperm biology. Comparison of the newly characterized Monarch butterfly (Danaus plexippus) sperm proteome to those of the Carolina sphinx moth (Manduca sexta) and the fruit fly (Drosophila melanogaster) demonstrated conservation at the level of protein abundance and post-translational modification within Lepidoptera. In contrast, comparative genomic analyses across insects reveals significant divergence at two levels that differentiate the genetic architecture of sperm in Lepidoptera from other insects. First, a significant reduction in orthology among Monarch sperm genes relative to the remainder of the genome in non-Lepidopteran insect species was observed. Second, a substantial number of sperm proteins were found to be specific to Lepidoptera, in that they lack detectable homology to the genomes of more distantly related insects. Lastly, the functional importance of Lepidoptera specific sperm proteins is broadly supported by their increased abundance relative to proteins conserved across insects. Our results identify a burst of genetic novelty

  19. Comparative analysis of alfalfa (Medicago sativa L.) leaf transcriptomes reveals genotype-specific salt tolerance mechanisms.

    Science.gov (United States)

    Lei, Yunting; Xu, Yuxing; Hettenhausen, Christian; Lu, Chengkai; Shen, Guojing; Zhang, Cuiping; Li, Jing; Song, Juan; Lin, Honghui; Wu, Jianqiang

    2018-02-15

    Soil salinity is an important factor affecting growth, development, and productivity of almost all land plants, including the forage crop alfalfa (Medicago sativa). However, little is known about how alfalfa responds and adapts to salt stress, particularly among different salt-tolerant cultivars. Among seven alfalfa cultivars, we found that Zhongmu-1 (ZM) is relatively salt-tolerant and Xingjiang Daye (XJ) is salt-sensitive. Compared to XJ, ZM showed slower growth under low-salt conditions, but exhibited stronger tolerance to salt stress. RNA-seq analysis revealed 2237 and 1125 differentially expressed genes (DEGs) between ZM and XJ in the presence and absence of salt stress, among which many genes are involved in stress-related pathways. After salt treatment, compared with the controls, the number of DEGs in XJ (19373) was about four times of that in ZM (4833). We also detected specific differential gene expression patterns: In response to salt stress, compared with XJ, ZM maintained relatively more stable expression levels of genes related to the ROS and Ca 2+ pathways, phytohormone biosynthesis, and Na + /K + transport. Notably, several salt resistance-associated genes always showed greater levels of expression in ZM than in XJ, including a transcription factor. Consistent with the suppression of plant growth resulting from salt stress, the expression of numerous photosynthesis- and growth hormone-related genes decreased more dramatically in XJ than in ZM. By contrast, the expression levels of photosynthetic genes were lower in ZM under low-salt conditions. Compared with XJ, ZM is a salt-tolerant alfalfa cultivar possessing specific regulatory mechanisms conferring exceptional salt tolerance, likely by maintaining high transcript levels of abiotic and biotic stress resistance-related genes. Our results suggest that maintaining this specific physiological status and/or plant adaptation to salt stress most likely arises by inhibition of plant growth in ZM through

  20. An Analysis of the Effects of Wing Aspect Ratio and Tail Location on Static Longitudinal Stability Below the Mach Number of Lift Divergence

    Science.gov (United States)

    Axelson, John A.; Crown, J. Conrad

    1948-01-01

    An analysis is presented of the influence of wing aspect ratio and tail location on the effects of compressibility upon static longitudinal stability. The investigation showed that the use of reduced wing aspect ratios or short tail lengths leads to serious reductions in high-speed stability and the possibility of high-speed instability.

  1. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

    Directory of Open Access Journals (Sweden)

    Henry D Priest

    Full Text Available Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  2. A sedimentological analysis of sediments corresponding to the San Gregorio Formation )Lower Permian), located in the eastern border of the North Uruguayan Basin, Sierra Guazunambi

    International Nuclear Information System (INIS)

    Goso Aguilar, C.; Gama, E.

    1998-01-01

    A sedimentological analysis of sediments corresponding to the San Gregorio Formation (Lower Permian), located in the eastern border of the Norte Uruguayan Basin, Sierra Guazunambi, Cerro Largo Departament was made. Facies analysis of about 100 otucrops fand more than 1.300 meters, in an area of 45 square kilometers showed diamictites rhytmites and massive sandstones, formed by gravitational sedimentary flows. Also present are prodelta mudrocks and deltaic front sandstones.(author)

  3. Identifying location and severity of multiple cracks in reinforced concrete cantilever beams using modal and wavelet analysis

    Directory of Open Access Journals (Sweden)

    Tahere Arefzade

    2016-06-01

    Full Text Available In this paper, a method of multiple cracks detection in a cantilever reinforced concrete beam based on wavelet transform is presented. For this purpose, different damage scenarios in concrete beam were considered. Then, the four first mode shapes of undamaged and damaged beam using ABAQUS software were extracted. The estimated mode shapes of the beam are analyzed by the continuous and discrete wavelet transform (CWT & DWT to detect the damage scenarios. It was found that DWT is more sensitive to damage location than CWT in the concrete beam which introduced in this paper. Also, the influence of the mode order and the effect of damage distance from support on the effectiveness of damage detection was evaluated. It was observed that the distance of cracks to each other have no effect on identifying their location.

  4. An Analysis on Sensor Locations of the Human Body for Wearable Fall Detection Devices: Principles and Practice

    Directory of Open Access Journals (Sweden)

    Ahmet Turan Özdemir

    2016-07-01

    Full Text Available Wearable devices for fall detection have received attention in academia and industry, because falls are very dangerous, especially for elderly people, and if immediate aid is not provided, it may result in death. However, some predictive devices are not easily worn by elderly people. In this work, a huge dataset, including 2520 tests, is employed to determine the best sensor placement location on the body and to reduce the number of sensor nodes for device ergonomics. During the tests, the volunteer’s movements are recorded with six groups of sensors each with a triaxial (accelerometer, gyroscope and magnetometer sensor, which is placed tightly on different parts of the body with special straps: head, chest, waist, right-wrist, right-thigh and right-ankle. The accuracy of individual sensor groups with their location is investigated with six machine learning techniques, namely the k-nearest neighbor (k-NN classifier, Bayesian decision making (BDM, support vector machines (SVM, least squares method (LSM, dynamic time warping (DTW and artificial neural networks (ANNs. Each technique is applied to single, double, triple, quadruple, quintuple and sextuple sensor configurations. These configurations create 63 different combinations, and for six machine learning techniques, a total of 63 × 6 = 378 combinations is investigated. As a result, the waist region is found to be the most suitable location for sensor placement on the body with 99.96% fall detection sensitivity by using the k-NN classifier, whereas the best sensitivity achieved by the wrist sensor is 97.37%, despite this location being highly preferred for today’s wearable applications.

  5. An Analysis on Sensor Locations of the Human Body for Wearable Fall Detection Devices: Principles and Practice.

    Science.gov (United States)

    Özdemir, Ahmet Turan

    2016-07-25

    Wearable devices for fall detection have received attention in academia and industry, because falls are very dangerous, especially for elderly people, and if immediate aid is not provided, it may result in death. However, some predictive devices are not easily worn by elderly people. In this work, a huge dataset, including 2520 tests, is employed to determine the best sensor placement location on the body and to reduce the number of sensor nodes for device ergonomics. During the tests, the volunteer's movements are recorded with six groups of sensors each with a triaxial (accelerometer, gyroscope and magnetometer) sensor, which is placed tightly on different parts of the body with special straps: head, chest, waist, right-wrist, right-thigh and right-ankle. The accuracy of individual sensor groups with their location is investigated with six machine learning techniques, namely the k-nearest neighbor (k-NN) classifier, Bayesian decision making (BDM), support vector machines (SVM), least squares method (LSM), dynamic time warping (DTW) and artificial neural networks (ANNs). Each technique is applied to single, double, triple, quadruple, quintuple and sextuple sensor configurations. These configurations create 63 different combinations, and for six machine learning techniques, a total of 63 × 6 = 378 combinations is investigated. As a result, the waist region is found to be the most suitable location for sensor placement on the body with 99.96% fall detection sensitivity by using the k-NN classifier, whereas the best sensitivity achieved by the wrist sensor is 97.37%, despite this location being highly preferred for today's wearable applications.

  6. Lattice Boltzmann analysis of effect of heating location and Rayleigh number on natural convection in partially heated open ended cavity

    Energy Technology Data Exchange (ETDEWEB)

    Gangawane, Krunal Madhukar; Bharti, Ram Prakash; Kumar, Surendra [Indian Institute of Technology Roorkee, Uttarakhand (India)

    2015-08-15

    Natural convection characteristics of a partially heated open ended square cavity have been investigated numerically by using an in-house computational flow solver based on the passive scalar thermal lattice Boltzmann method (PS-TLBM) with D2Q9 (two-dimensional and nine-velocity link) lattice model. The partial part of left wall of the cavity is heated isothermally at either of the three different (bottom, middle and top) locations for the fixed heating length as half of characteristic length (H/2) while the right wall is open to the ambient conditions. The other parts of the cavity are thermally isolated. In particular, the influences of partial heating locations and Rayleigh number (103≤ Ra≤106) in the laminar zone on the local and global natural convection characteristics (such as streamline, vorticity and isotherm contours; centerline variations of velocity and temperature; and local and average Nusselt numbers) have been presented and discussed for the fixed value of the Prandtl number (Pr=0.71). The streamline patterns show qualitatively similar nature for all the three heating cases and Rayleigh numbers, except the change in the recirculation zone which is found to be largest for middle heating case. Isotherm patterns are shifted towards a partially heated wall on increasing Rayleigh number and/or shifting of heating location from bottom to top. Both the local and average Nusselt numbers, as anticipated, shown proportional increase with Rayleigh number. The cavity with middle heating location shown higher heat transfer rate than that for the top and bottom heating cases. Finally, the functional dependence of the average Nusselt number on flow governing parameters is also presented as a closure relationship for the best possible utilization in engineering practices and design.

  7. Quantitative analysis of Curcuminoid collected from different location in Indonesia by TLC-Densitometry and its antioxidant capacity

    Science.gov (United States)

    Wahyuni, D. S. C.; Artanti, A. N.; Rinanto, Y.

    2018-04-01

    Curcuminoid, consisting of curcumin, demethoxycurcumin and bis demethoxycurcumin, is the active compound in Curcuma longa L. rhizome. It yielded vary depend on the environment and varieties. Curcumin has been known to have a potent antioxidants activity. The present work was conducted to assess the curcuminoid content and antioxidant capacity in the crude extracts of C. longa L. collected from eight different locations in Indonesia. Samples were collected from eight locations including Java island, Sumatera island and Nusa Tenggara island. All samples were extracted using 96% ethanol and analyzed quantitatively using TLC-Densitometry. Antioxidant activity was assessed using diphenylpicrylhydrazyl (DPPH) radical scavenging assay and analyzed at 517 nm using a spectrophotometer. Curcuminoid content in C. longa varied among eight different locations (0.53±0.05 - 5.33±0.12 % w/w). The highest curcumin, demethoxycurcumin and bisdemethoxycurcumin yield were found in the samples from Magetan (5.33±0.12%, 1.54±0.05%, 0.46±0.02% w/w, respectively). In contrast, the lowest curcumin, demethoxycurcumin and bisdemethoxycurcumin yield were found in the sample from Demak (0.53±0.05%, 0.17±0.05%, 0.17±0.05% w/w, respectively). Antioxidant capacity showed similar for all places unless sample from Magetan which exhibited two times lower than other locations. It is apparently curcuminoid content and antioxidant activity varied among places. These results are useful information for curcuminoid standardization method in pharmaceutical products.

  8. Location Planning Problem of Service Centers for Sustainable Home Healthcare: Evidence from the Empirical Analysis of Shanghai

    Directory of Open Access Journals (Sweden)

    Gang Du

    2015-11-01

    Full Text Available It is of theoretical and practical significance to understand what factors influence the sustainable development of home healthcare services in China. Based on a face-to-face survey, we find that the location planning, which is decisive for the improvement of patient satisfaction, can effectively reduce the risks, as well as the costs of redundant construction and re-construction of service centers for home healthcare and, thus, helps ensure the sustainability of health and the environment. The purposes of this paper are to investigate the existing problem of home healthcare in Shanghai and to find the optimum location planning scheme under several realistic constraints. By considering differentiated services provided by the medical staff at different levels and the degrees of patient satisfaction, a mixed integer programming model is built to minimize the total medical cost. The IBM ILOGCPLEX is used to solve the above model. Finally, a case study of Putuo district in Shanghai is conducted to validate the proposed model and methodology. Results indicate that the model used in this paper can effectively reduce the total medical cost and enhance the medical sustainability, and therefore, the results of the model can be used as a reference for decision makers on the location planning problem of home healthcare services in China.

  9. The application of a multi-parameter analysis in choosing the location of a new solid waste landfill in Serbia.

    Science.gov (United States)

    Milosevic, Igor; Naunovic, Zorana

    2013-10-01

    This article presents a process of evaluation and selection of the most favourable location for a sanitary landfill facility from three alternative locations, by applying a multi-criteria decision-making (MCDM) method. An incorrect choice of location for a landfill facility can have a significant negative economic and environmental impact, such as the pollution of air, ground and surface waters. The aim of this article is to present several improvements in the practical process of landfill site selection using the VIKOR MCDM compromise ranking method integrated with a fuzzy analytic hierarchy process approach for determining the evaluation criteria weighing coefficients. The VIKOR method focuses on ranking and selecting from a set of alternatives in the presence of conflicting and non-commensurable (different units) criteria, and on proposing a compromise solution that is closest to the ideal solution. The work shows that valuable site ranking lists can be obtained using the VIKOR method, which is a suitable choice when there is a large number of relevant input parameters.

  10. What influences national and foreign physicians' geographic distribution? An analysis of medical doctors' residence location in Portugal.

    Science.gov (United States)

    Russo, Giuliano; Ferrinho, Paulo; de Sousa, Bruno; Conceição, Cláudia

    2012-07-02

    The debate over physicians' geographical distribution has attracted the attention of the economic and public health literature over the last forty years. Nonetheless, it is still to date unclear what influences physicians' location, and whether foreign physicians contribute to fill the geographical gaps left by national doctors in any given country. The present research sets out to investigate the current distribution of national and international physicians in Portugal, with the objective to understand its determinants and provide an evidence base for policy-makers to identify policies to influence it. A cross-sectional study of physicians currently registered in Portugal was conducted to describe the population and explore the association of physician residence patterns with relevant personal and municipality characteristics. Data from the Portuguese Medical Council on physicians' residence and characteristics were analysed, as well as data from the National Institute of Statistics on municipalities' population, living standards and health care network. Descriptive statistics, chi-square tests, negative binomial and logistic regression modelling were applied to determine: (a) municipality characteristics predicting Portuguese and International physicians' geographical distribution, and; (b) doctors' characteristics that could increase the odds of residing outside the country's metropolitan areas. There were 39,473 physicians in Portugal in 2008, 51.1% of whom male, and 40.2% between 41 and 55 years of age. They were predominantly Portuguese (90.5%), with Spanish, Brazilian and African nationalities also represented. Population, Population's Purchasing Power, Nurses per capita and Municipality Development Index (MDI) were the municipality characteristics displaying the strongest association with national physicians' location. For foreign physicians, the MDI was not statistically significant, while municipalities' foreign population applying for residence

  11. What influences national and foreign physicians’ geographic distribution? An analysis of medical doctors’ residence location in Portugal

    Directory of Open Access Journals (Sweden)

    Russo Giuliano

    2012-07-01

    Full Text Available Abstract Background The debate over physicians’ geographical distribution has attracted the attention of the economic and public health literature over the last forty years. Nonetheless, it is still to date unclear what influences physicians’ location, and whether foreign physicians contribute to fill the geographical gaps left by national doctors in any given country. The present research sets out to investigate the current distribution of national and international physicians in Portugal, with the objective to understand its determinants and provide an evidence base for policy-makers to identify policies to influence it. Methods A cross-sectional study of physicians currently registered in Portugal was conducted to describe the population and explore the association of physician residence patterns with relevant personal and municipality characteristics. Data from the Portuguese Medical Council on physicians’ residence and characteristics were analysed, as well as data from the National Institute of Statistics on municipalities’ population, living standards and health care network. Descriptive statistics, chi-square tests, negative binomial and logistic regression modelling were applied to determine: (a municipality characteristics predicting Portuguese and International physicians’ geographical distribution, and; (b doctors’ characteristics that could increase the odds of residing outside the country’s metropolitan areas. Results There were 39,473 physicians in Portugal in 2008, 51.1% of whom male, and 40.2% between 41 and 55 years of age. They were predominantly Portuguese (90.5%, with Spanish, Brazilian and African nationalities also represented. Population, Population’s Purchasing Power, Nurses per capita and Municipality Development Index (MDI were the municipality characteristics displaying the strongest association with national physicians’ location. For foreign physicians, the MDI was not statistically significant

  12. Microarray analysis reveals transcriptional plasticity in the reef building coral Acropora millepora

    DEFF Research Database (Denmark)

    Bay, L. K.; Ulstrup, K. E.; Nielsen, H. B.

    2009-01-01

    ) following translocation to a lower light and turbidity environment. Such metabolic downregulation may indicate nonoxidative stress, hibernation or caloric restriction associated with the changed environmental conditions. Green fluorescent protein-related genes were the most differentially expressed and were...... exclusively downregulated; however, green fluorescent protein levels remained unchanged following translocation. Photophysiological responses of corals from both locations were characterized by a decline when introduced to the common laboratory environment but remained healthy (F-v/F-m > 0.6). Declines...

  13. On English Locative Subjects

    Directory of Open Access Journals (Sweden)

    Gabriela Brůhová

    2017-07-01

    Full Text Available The paper analyses English sentences with thematic locative subjects. These subjects were detected as translation counterparts of Czech sentenceinitial locative adverbials realized by prepositional phrases with the prepositions do (into, na (on, v/ve (in, z/ze (from complemented by a noun. In the corresponding English structure, the initial scene-setting adverbial is reflected in the thematic subject, which results in the locative semantics of the subject. The sentences are analysed from syntactic, semantic and FSP aspects. From the syntactic point of view, we found five syntactic patterns of the English sentences with a locative subject (SV, SVA, SVO, SVpassA and SVCs that correspond to Czech sentences with initial locative adverbials. On the FSP level the paper studies the potential of the sentences to implement the Presentation or Quality Scale. Since it is the “semantic content of the verb that actuates the presentation semantics of the sentence” (Duškova, 2015a: 260, major attention is paid to the syntactic-semantic structure of the verb. The analysis of the semantics of the English sentences results in the identification of two semantic classes of verbs which co-occur with the English locative subject.

  14. Association analysis of the chromosome 4p-located G protein-coupled receptor 78 (GPR78) gene in bipolar affective disorder and schizophrenia.

    Science.gov (United States)

    Underwood, S L; Christoforou, A; Thomson, P A; Wray, N R; Tenesa, A; Whittaker, J; Adams, R A; Le Hellard, S; Morris, S W; Blackwood, D H R; Muir, W J; Porteous, D J; Evans, K L

    2006-04-01

    The orphan G protein-coupled receptor 78 (GPR78) gene lies within a region of chromosome 4p where we have previously shown linkage to bipolar affective disorder (BPAD) in a large Scottish family. GPR78 was screened for single-nucleotide polymorphisms (SNPs) and a linkage disequilibrium map was constructed. Six tagging SNPs were selected and tested for association on a sample of 377 BPAD, 392 schizophrenia (SCZ) and 470 control individuals. Using standard chi(2) statistics and a backwards logistic regression approach to adjust for the effect of sex, SNP rs1282, located approximately 3 kb upstream of the coding region, was identified as a potentially important variant in SCZ (chi(2) P=0.044; LRT P=0.065). When the analysis was restricted to females, the strength of association increased to an uncorrected allele P-value of 0.015 (odds ratios (OR)=1.688, 95% confidence intervals (CI): 1.104-2.581) and uncorrected genotype P-value of 0.015 (OR=5.991, 95% CI: 1.545-23.232). Under the recessive model, the genotype P-value improved further to 0.005 (OR=5.618, 95% CI: 1.460-21.617) and remained significant after correcting for multiple testing (P=0.017). No single-marker association was detected in the SCZ males, in the BPAD individuals or with any other SNP. Haplotype analysis of the case-control samples revealed several global and individual haplotypes, with P-values <0.05, all but one of which contained SNP rs1282. After correcting for multiple testing, two haplotypes remained significant in both the female BPAD individuals (P=0.038 and 0.032) and in the full sample of affected female individuals (P=0.044 and 0.033). Our results provide preliminary evidence for the involvement of GPR78 in susceptibility to BPAD and SCZ in the Scottish population. Molecular Psychiatry (2006) 11, 384-394. doi:10.1038/sj.mp.4001786; published online 3 January 2006.

  15. CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits

    NARCIS (Netherlands)

    Macé, Aurélien; Tuke, Marcus A; Deelen, Patrick; Kristiansson, Kati; Mattsson, Hannele; Nõukas, Margit; Sapkota, Yadav; Schick, Ursula; Porcu, Eleonora; Rüeger, Sina; McDaid, Aaron F; Porteous, David; Winkler, Thomas W; Salvi, Erika; Shrine, Nick; Liu, Xueping; Ang, Wei Q; Zhang, Weihua; Feitosa, Mary F; Venturini, Cristina; van der Most, Peter J; Rosengren, Anders; Wood, Andrew R; Beaumont, Robin N; Jones, Samuel E; Ruth, Katherine S; Yaghootkar, Hanieh; Tyrrell, Jessica; Havulinna, Aki S; Boers, Harmen; Mägi, Reedik; Kriebel, Jennifer; Müller-Nurasyid, Martina; Perola, Markus; Nieminen, Markku; Lokki, Marja-Liisa; Kähönen, Mika; Viikari, Jorma S; Geller, Frank; Lahti, Jari; Palotie, Aarno; Koponen, Päivikki; Lundqvist, Annamari; Rissanen, Harri; Bottinger, Erwin P; Afaq, Saima; Wojczynski, Mary K; Lenzini, Petra; Nolte, Ilja M; Sparsø, Thomas; Schupf, Nicole; Christensen, Kaare; Perls, Thomas T; Newman, Anne B; Werge, Thomas; Snieder, Harold; Spector, Timothy D; Chambers, John C; Koskinen, Seppo; Melbye, Mads; Raitakari, Olli T; Lehtimäki, Terho; Tobin, Martin D; Wain, Louise V; Sinisalo, Juha; Peters, Annette; Meitinger, Thomas; Martin, Nicholas G; Wray, Naomi R; Montgomery, Grant W; Medland, Sarah E; Swertz, Morris A; Vartiainen, Erkki; Borodulin, Katja; Männistö, Satu; Murray, Anna; Bochud, Murielle; Jacquemont, Sébastien; Rivadeneira, Fernando; Hansen, Thomas F; Oldehinkel, Albertine J; Mangino, Massimo; Province, Michael A; Deloukas, Panos; Kooner, Jaspal S; Freathy, Rachel M; Pennell, Craig; Feenstra, Bjarke; Strachan, David P; Lettre, Guillaume; Hirschhorn, Joel; Cusi, Daniele; Heid, Iris M; Hayward, Caroline; Männik, Katrin; Beckmann, Jacques S; Loos, Ruth J F; Nyholt, Dale R; Metspalu, Andres; Eriksson, Johan G; Weedon, Michael N; Salomaa, Veikko; Franke, Lude; Reymond, Alexandre; Frayling, Timothy M; Kutalik, Zoltán

    2017-01-01

    There are few examples of robust associations between rare copy number variants (CNVs) and complex continuous human traits. Here we present a large-scale CNV association meta-analysis on anthropometric traits in up to 191,161 adult samples from 26 cohorts. The study reveals five CNV associations at

  16. Phylogenetic analysis reveals two genotypes of the emerging fungus Mucor indicus, an opportunistic human pathogen in immunocompromised patients

    NARCIS (Netherlands)

    Taj-Aldeen, Saad J.; Almaslamani, Muna; Theelen, B.J.F.; Boekhout, Teun

    2017-01-01

    Mucormycosis is a rare fungal infection caused by Mucor indicus. Phylogenetic analysis of many M. indicus isolates, mainly sampled from different clinical and environmental specimens collected worldwide, revealed two genotypes, I and II, based on ITS and D1/D2 LSU rDNA sequences. A retrospective

  17. Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria

    NARCIS (Netherlands)

    Salzman, NH; de Jong, H; Paterson, Y; Harmsen, HJM; Welling, GW; Bos, NA

    2002-01-01

    Total genomic DNA from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for PCR amplification of 16S rRNA gene sequences with conserved bacterial primers. Phylogenetic analysis of the amplification products revealed 40 unique 16S rDNA sequences. Of

  18. Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns

    DEFF Research Database (Denmark)

    Lundby, Alicia; Hansen, Kasper Lage; Weinert, Brian Tate

    2012-01-01

    ,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals...

  19. Degrees of Cooperation in Household Consumption Models : A Revealed Preference Analysis

    NARCIS (Netherlands)

    Cherchye, L.J.H.; Demuynck, T.; de Rock, B.

    2009-01-01

    We develop a revealed preference approach to analyze non-unitary con- sumption models with intrahousehold allocations deviating from the cooper- ative (or Pareto e¢ cient) solution. At a theoretical level, we establish re- vealed preference conditions of household consumption models with varying

  20. Phylogeographic analysis reveals significant spatial genetic structure of Incarvillea sinensis as a produc